The Community for Technology Leaders
7th IEEE International Conference on Bioinformatics and Bioengineering (2007)
Boston, MA
Oct. 14, 2007 to Oct. 17, 2007
ISBN: 1-4244-1509-8
TABLE OF CONTENTS

IEEE 7th BIBE Invited Plenary Keynote: Intrinsically Disordered Proteins: Predictions and Applications (PDF)

A. Keith Dunker , Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202. kedunker@iupui.edu
Christopher J. Oldfield , Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202
Jingwei Meng , Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
Pedro Romero , Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202
Jack Y. Yang , Department of Radiation Oncology, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts 02114
Zoran Obradovic , Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
Vladimir N. Uversky , Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Puschino, Moscow Region, Russia. vuversky@iupui.edu
pp. 1

IEEE 7th BIBE Invited Plenary Keynote: Stochasticity and Networks in Genomic Data (PDF)

John Quackenbush , Dana-Farber Cancer Institute and the Harvard School of Public Health, Harvard University, Boston, MA 02115. johnq@jimmy.harvard.edu
pp. 2

IEEE 7th BIBE Research Tutorial Lecture: Decoding Novel Genomes: From Microbiomes to the Eukaryota (PDF)

Mark Borodovsky , Department of Biomedical Engineering and Division of Computational Science, Georgia Institute of Technology, Atlanta, Georgia, USA
pp. 3

IEEE 7th BIBE Keynote: Promoter studies in the human genome: one perspective on an unfinished story (PDF)

Mary Qu Yang , National Human Genome Research Institute, National Institutes Health (NIH), And Oak Ridge, DOE. yangma@mail.nih.gov
Laura L. Elnitski , Head of Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes Health (NIH), Rockville MD, 20852 USA. elnitski@mail.nih.gov
pp. 4-6

Protein Structure Prediction and Its Understanding Based on Machine Learning Methods (PDF)

Yi Pan , Chair and Professor, Computer Science Department, Georgia State University, Atlanta, GA 30303, USA. Email: pan@cs.gsu.edu
pp. 7

IEEE 7th BIBE Invited Plenary Keynote: Statistial Analysis of nucleosome occupancy and histone modification data (PDF)

Guocheng Yuan , Harvard University, Boston, MA 02115. gcyuan@jimmy.harvard.edu
Jun S Liu , Harvard University, Cambridge, MA 02493. jliu@stat.harvard.edu
pp. 8

An Investigation into the Feasibility of Detecting Microscopic Disease Using Machine Learning (PDF)

Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20852, Amd also Oak Ridge, DOE yangma@mail.NIH.gov
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140-0888 USA. yang@hadron.mgh.Harvard.edu
pp. 9-10

IEEE 7th BIBE Invited Workshop Keynote: Nanobioinformatics: The Enabling Technology of Personalized Medicine (PDF)

Linda K. Molnar , National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. molnarl@mail.nih.gov
pp. 11

IEEE 7th BIBE Invited Tutorial Lecture: Intrinsically Disordered Proteins in Human Diseases (PDF)

Vladimir N. Uversky , Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia. vuversky@iupui.edu
Christopher J. Oldfield , Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202
A. Keith Dunker , Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202. kedunker@iupui.edu
pp. 12

IEEE 7th BIBE Invited Keynote Lecture: Metallobiochemistry of Alzheimer's Disease and Its Theranostic Agent Development (PDF)

Xudong Huang , Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02120, U.S.A.
pp. 13

Identification of Conserved Domain Combinations in S.cerevisiae Proteins (PDF)

Suk Hoon Jung , School of Engineering, Information and Communications University, P.O.Box 77, Yusong, Daejeon 305-600, Korea. Email: jsh@icu.ac.kr
Hee-Young Hur , School of Engineering, Information and Communications University, P.O.Box 77, Yusong, Daejeon 305-600, Korea. Email: hyerue@icu.ac.kr
Desok Kim , School of Engineering, Information and Communications University, P.O.Box 77, Yusong, Daejeon 305-600, Korea. Email: kimdesok@icu.ac.kr
Dong-Soo Han , School of Engineering, Information and Communications University, P.O.Box 77, Yusong, Daejeon 305-600, Korea. Email: dshan@icu.ac.kr, telephone: +82-042-866-6290
pp. 14-20

Multiclass Fuzzy Clustering Support Vector Machines for Protein Local Structure Prediction (PDF)

Wei Zhong , Division of Math and Computer Science, USC Upstate, Spartanburg, SC 29303, USA. wzhong@uscupstate.edu
Jieyue He , Department of Computer Science and Engineering, Southeast University, Nanjing, 210096, China
Yi Pan , Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
pp. 21-26

A New Alignment-Independent Algorithm for Clustering Protein Sequences (PDF)

Abdellali Kelil , Department of Computer Sciences, Sherbrooke University, Sherbrooke, QC, Canada. Abdellali.Kelil@USherbrooke.ca
Shengrui Wang , Department of Computer Sciences, Sherbrooke University, Sherbrooke, QC, Canada. Shengrui.Wang@USherbrooke.ca
Ryszard Brzezinski , Department of Biology, Sherbrooke University, Sherbrooke, QC, Canada. Ryszard.Brzezinski@USherbrooke.ca
pp. 27-34

Metropolis-Hastings Algorithm and Continuous Regression for finding Next-State Models of Protein Modification using Information Scores (PDF)

David J. John , Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109-7311. djj@wfu.edu
Jacquelyn S. Fetrow , Departments of Computer Science and Physics, Wake Forest University, Winston-Salem, NC 27109-7311. fetrowjs@wfu.edu
James L. Norris , Department of Mathematics, Wake Forest University, Winston-Salem, NC 27109-7388. norris@wfu.edu
pp. 35-41

Protein function prediction from interaction networks using a random walk ranking algorithm (PDF)

Valerio Freschi , University of Urbino, Information Science and Technology Institute (ISTI), Piazza della Repubblica, 13-61029 Urbino, Italy. Email: freschi@sti.uniurb.it
pp. 42-48

Intrinsically Disordered Proteins: An Update (PDF)

A. Keith Dunker , Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202. kedunker@iupui.edu
Christopher J. Oldfield , Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202
Jingwei Meng , Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
Pedro Romero , Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202
Jack Y. Yang , Department of Radiation Oncology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
Zoran Obradovic , Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
Vladimir N. Uversky , Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Puschino, Moscow Region, Russia. vuversky@iupui.edu
pp. 49-58

Linking Protein Mass with Function via Organismal Massome Networks (PDF)

Gil Alterovitz , Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA; Children's Hospital Informatics Program at Health Sciences and Technology, Harvard Medical School, Boston, MA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA; Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA. gil@mit.edu
Eugenia Lyashenko , Department of Biomedical Informatics, Columbia University, New York, NY.
Michael Xiang , Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA.
Marco F. Ramoni , Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA; Children's Hospital Informatics Program at Health Sciences and Technology, Harvard Medical School, Boston, MA; Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA. marco_ramoni@harvard.edu
pp. 59-65

Ensemble of Probabilistic Neural Networks for Protein Fold Recognition (PDF)

Yuehui Chen , School of Information Science and Engineering, University of Jinan, Jiwei road 106, Jinan 250022, P.R.China. Email: yhchen@ujn.edu.cn
Xueqin Zhang , School of Information Science and Engineering, University of Jinan, Jiwei road 106, Jinan 250022, P.R.China
Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health (NIH), U.S. Department of Health and Human Services Bethesda, MD 20852 USA. Email: yangma@mail.NIH.gov
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140-0888 USA. Email: yang@hadron.mgh.Harvard.edu
pp. 66-70

HICCUP: Hierarchical Clustering Based Value Imputation using Heterogeneous Gene Expression Microarray Datasets (PDF)

Qiankun Zhao , AOL Labs China. qiankun.zhao@corp.aol.com
Prasenjit Mitra , Penn State University, USA. pmitra@ist.psu.edu
Dongwon Lee , Penn State University, USA. dongwon@psu.edu
Jaewoo Kang , Korea University, Korea. kangj@korea.ac.kr
pp. 71-78

On the Effectiveness of Constraints Sets in Clustering Genes (PDF)

Erliang Zeng , Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, Florida, 33199, USA. E-mail: ezeng001@cs.fiu.edu
Chengyong Yang , Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, Florida, 33199, USA; Applied Biosystems Inc., Foster City, CA. E-mail: cyang01@cs.fiu.edu, chengyong_yang@appliedbiosystems.com
Tao Li , Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, Florida, 33199, USA. E-mail: taoli@cs.fiu.edu
Giri Narasimhan , Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, Florida, 33199, USA. E-mail: giri@cs.fiu.edu
pp. 79-86

Integrate Qualitative Biological Knowledge to Build Gene Networks by Parallel Dynamic Bayesian Network Structure Learning (PDF)

Song Li , Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011, USA
pp. 87-92

Finding Clusters of Positive and Negative Coregulated Genes in Gene Expression Data (PDF)

Kerstin Koch , Hasselt University & Transnational University of Limburg, Theoretical Computer Science, kerstin.koch@uhasselt.be
Stefan Schonauer , University of Helsinki, Helsinki Institute for Information Technology, stefan.schoenauer@cs.helsinki.fi
Ivy Jansen , Hasselt University, Center for Statistics, ivy.jansen@uhasselt.be
Jan van den Bussche , Hasselt University & Transnational University of Limburg, Theoretical Computer Science, jan.vandenbussche@uhasselt.be
Tomasz Burzykowski , Hasselt University, Center for Statistics, tomasz.burzykowski@uhasselt.be
pp. 93-99

Pattern Cores And Connectedness in Cancer Gene Expression (PDF)

Noha A. Yousri , Student, IEEE, PAMI lab, Electrical and Computer Engineering, University of Waterloo, Ontario, Canada; Computers and System Engineering, University of Alexandria, Egypt. nyousri@pami.uwaterloo.ca, nyousri@alexeng.edu.eg
Mohamed S. Kamel , Fellow IEEE, PAMI lab, Electrical and Computer Engineering, University of Waterloo, Ontario, Canada. mkamel@pami.uwaterloo.ca
Mohamed A. Ismail , Computers and System Engineering, University of Alexandria, Egypt. m.a.ismail@pua.edu.eg
pp. 100-107

PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays (PDF)

Peter Warren , Systems Biology Group, EMD Serono, Rockland, Massachusetts. peter.warren@verizon.net
Deanne Taylor , Systems Biology Group, EMD Serono, Rockland, Massachusetts. dtaylor@hsph.harvard.edu
Paolo G. V. Martini , Systems Biology Group, EMD Serono, Rockland, Massachusetts
Jennifer Jackson , Systems Biology Group, EMD Serono, Rockland, Massachusetts
Jadwiga Bienkowska , Systems Biology Group, EMD Serono, Rockland, Massachusetts
pp. 108-115

Cooperative Partitional-Divisive Clustering and Its Application in Gene Expression Analysis (PDF)

R. Kashef , Student Member, IEEE, Electrical and Computer Engineering Department, University of Waterloo, Waterloo, Canada. rkashef@pami.uwaterloo.ca
M.S. Kamel , Fellow Member, IEEE, Electrical and Computer Engineering Department, University of Waterloo, Waterloo, Canada. mkamel@pami.uwaterloo.ca
pp. 116-122

On the Design of Oligos for Gene Synthesis (PDF)

Chris Thachuk , School of Computing Science, Simon Fraser University, Burnaby BC, Canada. cthachuk@cs.sfu.ca
Anne Condon , Department of Computer Science, University of British Columbia, Vancouver BC, Canada. condon@cs.ubc.ca
pp. 123-130

Evidence for Proximal to Distal Appendage Amputation Site Effects from Global Gene Expression Correlations Found in Newt Microarrays (PDF)

Kenneth A. Marx , Departments of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854. Kenneth_Marx@uml.edu
John Sharko , Computer Science, University of Massachusetts Lowell, Lowell, MA 01854. jsharko@cs.uml.edu
Georges G. Grinstein , Computer Science, University of Massachusetts Lowell, Lowell, MA 01854. grinstein@cs.uml.edu
Shannon Odelberg , Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
Hans-Georg Simon , Children's Memorial Research Center, Feinberg School of Medicine, Northwestern University, Chicago, IL. 60614
pp. 131-136

Denoising of Array-Based DNA Copy Number Data Using The Dual-tree Complex Wavelet Transform (PDF)

Nha Nguyen , Department of Electrical Engineering, University of Texas at Arlington. Email: nhn3175@exchange.uta.edu
Heng Huang , Department of Computer Science and Engineering, University of Texas at Arlington. Email: heng@uta.edu
Soontorn Oraintara , Department of Electrical Engineering, University of Texas at Arlington. Email: oraintar@uta.edu
Yuhang Wang , Department of Computer Science and Engineering, Southern Methodist University, Email: yuhangw@engr.smu.edu
pp. 137-144

Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier (PDF)

Brian E. Howard , Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina. itsbehoward@hotmail.com
Beate Sick , Institute of Data Analysis and Process Design, Zurich University of Applied Science Winterthur, Winterthur, Switzerland. sib@zhwin.ch
Imara Perera , Department of Plant Biology, North Carolina State University, Raleigh, North Carolina. iperera@unity.ncsu.edu
Yang Ju Im , Department of Plant Biology, North Carolina State University, Raleigh, North Carolina. yangju_im@unity.ncsu.edu
Heike Winter-Sederoff , Department of Plant Biology, North Carolina State University, Raleigh, North Carolina. heike_winter@unity.ncsu.edu
Steffen Heber , Department of Computer Science, North Carolina State University, Raleigh, North Carolina. sheber@ncsu.edu
pp. 145-150

Comparing Cancer and Normal Gene Regulatory Networks Based on Microarray Data and Transcription Factor Analysis (PDF)

Yu-Chun Lin , Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan. g9565505@oz.nthu.edu.tw, d926708@oz.nthu.edu.tw g946708@oz.nthu.edu.tw
Hsiang-Yuan Yeh , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan. g9565505@oz.nthu.edu.tw, d926708@oz.nthu.edu.tw g946708@oz.nthu.edu.tw
Shih-Wu Cheng , Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan. g9565505@oz.nthu.edu.tw, d926708@oz.nthu.edu.tw g946708@oz.nthu.edu.tw
Von-Wun Soo , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan; Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan; Department of Computer Science and Information Engineering, National University of Kaohsiung, Kaohsiung 811, Taiwan. soo@cs.nthu.edu.tw, g9565505@oz.nthu.edu.tw, d926708@oz.nthu.edu.tw g946708@oz.nthu.edu.tw
pp. 151-157

Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm (PDF)

Chan-Hoon Park , School of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea. chpark@bi.snu.ac.kr
Soo-Jin Kim , Graduate Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea. sjkim@bi.snu.ac.kr
Sun Kim , School of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea. skim@bi.snu.ac.kr
Dong-Yeon Cho , School of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea. dycho@bi.snu.ac.kr
Byoung-Tak Zhang , School of Computer Science and Engineering, Graduate Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea. btzhang@bi.snu.ac.kr
pp. 158-163

A Two-Stage Gene Selection Algorithm by Combining ReliefF and mRMR (PDF)

Yi Zhang , School of Computing and Information Sciences, Florida International University, Miami, Florida 33199. Email: yzhan004@cs.fiu.edu
Chris Ding , Department of Computer Science and Engineering, University of Texas, Arlington, TX 76019. Email: chqding@uta.edu
Tao Li , School of Computing and Information Sciences, Florida International University, Miami, Florida 33199. Email: taoli@cs.fiu.edu
pp. 164-171

Estimating Classification Error to Identify Biomarkers in Time Series Expression Data (PDF)

John H. Phan , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. jhphan@gatech.edu
May D. Wang , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. maywang@bme.gatech.edu
pp. 172-179

Detection and Prediction of Alternative Splicing within Acceptor/Donor Sites in pre-mRNA of Arabidopsis thaliana (PDF)

Minseo Park , Department of Computer Science, University of Massachusetts, Lowell, MA 01854. Email: mpark@cs.uml.edu
Deane L. Falcone , Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854. Email: Deane_Falcone@uml.edu
Kil-Young Yun , Department of Biological Sciences, University of Maine, Orono, ME 04469. Email: kil-young.yun@umit.maine.edu
Karen M. Daniels , Department of Computer Science, University of Massachusetts, Lowell, MA 01854. Email: kdaniels@cs.uml.edu
pp. 180-186

An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments (PDF)

Mehdi Pirooznia , Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
Arun Rawat , Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
Jack Y. Yang , Harvard University, Harvard Medical School, Cambridge, Massachusetts 02140-0888 U.S.A
Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20852 USA
Ping Gong , SpecPro Inc., Vicksburg, MS, 39180, USA
Edward J. Perkins , Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA
Youping Deng , Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
pp. 187-191

SNPMiner: A Domain-Specific Deep Web Mining Tool (PDF)

Fan Wang , Department of Computer Science and Engineering, Ohio State University, Columbus OH 43210. wangfa@cse.ohio-state.edu
Gagan Agrawal , Department of Computer Science and Engineering, Ohio State University, Columbus OH 43210. agrawal@cse.ohio-state.edu
Ruoming Jin , Department of Computer Science, Kent State University, Kent OH 44242. jin@cs.kent.edu
Helen Piontkivska , Department of Biological Sciences, Kent State University, Kent OH 44242. opiontki@kent.edu
pp. 192-199

Fast and Robust Detection of Epilepsy in Noisy EEG Signals Using Permutation Entropy (PDF)

Iman Veisi , Department of Electrical Engineering, Ferdowsi University, Mashhad, Iran. iveisi@gmail.com
Naser Pariz , Department of Electrical Engineering, Ferdowsi University, Mashhad, Iran. n-pariz@um.ac.ir
Ali Karimpour , Department of Electrical Engineering, Ferdowsi University, Mashhad, Iran. karimpor@um.ac.ir
pp. 200-203

A Robotic System for Real-time Tumor Manipulation During Image guided Breast Biopsy (PDF)

Vishnu Mallapragada , Robotics and Autonomous Systems Laboratory, Vanderbilt University, Nashville, TN, USA. vishnu.mallapragada
Nilanjan Sarkar , Robotics and Autonomous Systems Laboratory, Vanderbilt University, Nashville, TN, USA. nilanajan.sarkar@vanderbilt.edu
Tarun K. Podder , Department of Radiation Oncology, Thomas Jefferson University Hospital, Philadelphia, PA, USA. Tarun.Podder@jeffersonhospital.org
pp. 204-210

Morphometric Analysis of Hippocampal Shape in Mild Cognitive Impairment: An Imaging Genetics Study (PDF)

Li Shen , Center for Neuroimaging, Dept. of Radiology, Center for Computational Biology & Bioinformatics, Indiana University School of Medicine, 950 W Walnut St, R2 E124, Indianapolis, IN 46202. Email: shenli@iupui.edu
Andrew J. Saykin , Center for Neuroimaging, Dept. of Radiology, Center for Computational Biology & Bioinformatics, Indiana University School of Medicine, 950 W Walnut St, R2 E124, Indianapolis, IN 46202. Email: asaykin@iupui.edu
Moo K. Chung , Biostatistics & Medical Informatics, Univ. of Wisconsin Madison, 1300 University Ave., Madison, WI 53706. Email: mkchung@wisc.edu
Heng Huang , Computer Science & Engineering, Univ. of Texas at Arlington, Box 19015, 416 Yates St., Arlington, TX 76019. Email: heng@uta.edu
pp. 211-217

A Compartmentalized Approach to the Assembly of Physical Maps (PDF)

Serdar Bozdag , Department of Computer Science and Engineering, University of California, Riverside, CA 92521. sbozdag@cs.ucr.edu
Timothy J Close , Department of Botany and Plant Sciences, University of California, Riverside, CA 92521. timothy.close@ucr.edu
Stefano Lonardi , Department of Computer Science and Engineering, University of California, Riverside, CA 92521. stelo@cs.ucr.edu
pp. 218-225

Graph Theory Application in Cell Nuleus Segmentation, Tracking and Identification (PDF)

Lelin Zhang , Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China. zhanglelin.sjtu@gmail.com
Hongkai Xiong , Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China. xionghongkai@sjtu.edu.cn
Kai Zhang , Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China. zhangkai0619@sjtu.edu.cn
Xiaobo Zhou , HCNR-BWH Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School and Functional and Molecular, Imaging Center, Brigham and Women's Hospital, zhou@crystal.harvard.edu
pp. 226-232

An End-to-End Process for Cancer Identification from Images of Lung Tissue (PDF)

Walker H. Land , Department of Bioengineering, Binghamton University, Binghamton, USA
Dan Mckee , Dept. of Math. and Comp. Science, Mansfield University, Mansfield, USA
Tatyana Zhukov , H. Lee Moffitt Cancer Center, University of South Florida, Tampa, USA
Dansheng Song , H. Lee Moffitt Cancer Center, University of South Florida, Tampa, USA
Wei Qian , H. Lee Moffitt Cancer Center, University of South Florida, Tampa, USA
pp. 233-239

Rat Mammary Fat Pad Segmentation and Growth Rate Evaluation in T1 Weighted MR Images (PDF)

Bin Wang , Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA. Email: binwang@vt.edu
Jianhua Xuan , Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA. Email: xuan@vt.edu
Matthew T. Freedman , Department of Oncology and the Lombardi Cancer Center, Georgetown University, Washington, DC 20057, USA. Email: freedmmt@georgetown.edu
Peter G. Shields , Department of Oncology and the Lombardi Cancer Center, Georgetown University, Washington, DC 20057, USA. Email: pgs2@georgetown.edu
Yue Wang , Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA. Email: yuewang@vt.edu
pp. 240-245

A Simulation-Based 3D Axon Axis Extraction in Confocal Fluorescence Microscopy Images (PDF)

Kai Zhang , Dept. Electronic Engineering, Shanghai Jiao Tong University, Shanghai, China. zhangkai0619@sjtu.edu.cn
Hongkai Xiong , Dept. Electronic Engineering, Shanghai Jiao Tong University, Shanghai, China. xionghongkai@sjtu.edu.cn
Xiaobo Zhou , Bioinformatics core and the Department of Radiology, The Methodist Hospital Research Institute & Cornell University, Houston, TX 77030, US. zhou@crystal.harvard.edu
pp. 246-250

Advancements in Automated Diagnostic Mammography (Abstract)

Walker H. Land , Department of Bioengineering, Binghamton University, Binghamton, USA
Alda Mizaku , Department of Bioengineering, Binghamton University, Binghamton, USA
Thomas Raway , Department of Bioengineering, Binghamton University, Binghamton, USA
John Heine , H. Lee Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, USA
Claudia Berman , H. Lee Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, USA
Nataliya Kovalchuk , H. Lee Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, USA
pp. 251-256

Calcium De-blooming in Coronary CT Image (PDF)

Zhuangli Liang , Department of Biomedical Engineering, Boston University, Boston, MA. sliang@bu.edu
W. Clem Karl , Department of Biomedical Engineering, Boston University, Boston, MA. wckarl@bu.edu
Synho Do , Department of Radiology, Massachusetts General Hospital Boston, MA. sdo@partners.org
Udo Hoffmann , Department of Radiology, Massachusetts General Hospital Boston, MA. uhoffmann@partners.org
Thomas Brady , Department of Radiology, Massachusetts General Hospital Boston, MA. tom@nmr.mgh.harvard.edu
Homer Pien , Department of Radiology, Massachusetts General Hospital Boston, MA. hpien@nmr.mgh.harvard.edu
pp. 257-262

Distance Preserving Dimension Reduction Using the QR Factorization or the Cholesky Factorization (PDF)

Hyunsoo Kim , College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. E-mail: hskim@cc.gatech.edu
Haesun Park , College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. E-mail: hpark@cc.gatech.edu
Hongyuan Zha , College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. E-mail: zha@cc.gatech.edu
pp. 263-269

Discrete Methods for Association Search and Status Prediction in Genotype Case-Control Studies (PDF)

Dumitru Brinza , Dep. Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093. Email: dima@cs.ucsd.edu
Alexander Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, GA 30303. Email: alexz@cs.gsu.edu
pp. 270-277

A Multi-Objective Genetic Algorithm that Employs a Hybrid Approach for Isolating Codon Usage Bias Indicative of Translational Efficiency (PDF)

Douglas W. Raiford , Department of Computer Science and Engineering, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, United States
Dan E. Krane , Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, United States
Travis E. Doom , Department of Computer Science and Engineering, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, United States
Michael L. Raymer , Department of Computer Science and Engineering, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, United States. michael.raymer@wright.edu
pp. 278-285

Rapid Detection and Classification of Bacterial Contamination Using Grid Computing (PDF)

Wamiq M. Ahmed , School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907
Bulent Bayraktar , School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907
Arun K. Bhunia , Molecular Food Microbiology Laboratory, Purdue University, West Lafayette, IN 47907
E. Dan Hirleman , School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
J. Paul Robinson , Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907; Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
Bartek Rajwa , Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
pp. 286-293

Sensitivity Analysis of Biomolecular Simulations using Symbolic Models (PDF)

Sadaf R. Alam , Oak Ridge National Laboratory, Oak Ridge, USA. alamsr@ornl.gov
Nikhil Bhatia , Oak Ridge National Laboratory, Oak Ridge, USA. bhatia@ornl.gov
Jeffrey S. Vetter , Oak Ridge National Laboratory, Oak Ridge, USA. vetter@ornl.gov
pp. 294-300

Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences (PDF)

Xiaoyong Fang , School of Computer Science, National University of Defense Technology, Changsha, China. xyfang@nudt.edu.cn
Zhigang Luo , School of Computer Science, National University of Defense Technology, Changsha, China. zgluo@nudt.edu.cn
Bo Yuan , Department of Biomedical Informatics, Ohio State University, Columbus Ohio, USA
Zhenghua Wang , School of Computer Science, National University of Defense Technology, Changsha, China
pp. 301-306

The RNA String Kernel for siRNA Efficacy Prediction (PDF)

Shibin Qiu , Pathwork Diagnostics, Inc., 1196 Borregas Ave, Sunnyvale, CA, 94089, USA. sqiu@pathworkdx.com
Terran Lane , Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA. terran@cs.unm.edu
pp. 307-314

A Machine Learning Approach for Prediction of Lipid-Interacting Residues in Amino Acid Sequences (PDF)

Stephanie Jimenez Irausquin , Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
Liangjiang Wang , Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; Greenwood Genetic Center, Greenwood, SC 29646, USA. liangjw@clemson.edu
pp. 315-319

Assessing the Performance of Macromolecular Sequence Classifiers (PDF)

Cornelia Caragea , Computer Science Department, Iowa State University, Ames, Iowa, USA. Email: cornelia@cs.iastate.edu
Jivko Sinapov , Computer Science Department, Iowa State University, Ames, Iowa, USA. Email: jsinapov@cs.iastate.edu
Vasant Honavar , Computer Science Department, Iowa State University, Ames, Iowa, USA. Email: honavar@cs.iastate.edu
Drena Dobbs , Department of Genetics and Cell Biology, Iowa State University, Ames, Iowa, USA. Email: ddobbs@iastate.edu
pp. 320-326

Shortest Path Approaches for the Longest Common Subsequence of a Set of Strings (PDF)

Marina Barsky , Department of Computer Science, University of Victoria, Canada. Email: mgbarsky@cs.uvic.ca
Ulrike Stege , Department of Computer Science, University of Victoria, Canada. Email: stege@cs.uvic.ca
Alex Thomo , Department of Computer Science, University of Victoria, Canada. Email: thomo@cs.uvic.ca
Chris Upton , Department of Biochemistry & Microbiology, University of Victoria, Canada. Email: cupton@uvic.ca
pp. 327-333

Constrained RNA Structural Alignment: Algorithms and Application to Motif Detection in the Untranslated Regions of Trypanosoma brucei mRNAs (PDF)

Mugdha Khaladkar , Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102.
Vivian Bellofatto , Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, International Center for Public Health, 225Warren Street, Newark, NJ 07103.
Jason T. L. Wang , Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, NJ 07102. wangj@njit.edu
Vandanaben Patel , Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102.
Marvin K. Nakayama , Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102.
pp. 334-341

Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks (PDF)

Young-Rae Cho , Department of Computer Science and Engineering, State University of New York at Buffalo. ycho8@cse.buffalo.edu
Woochang Hwang , Department of Computer Science and Engineering, State University of New York at Buffalo. whwang2@cse.buffalo.edu
Aidong Zhang , Department of Computer Science and Engineering, State University of New York at Buffalo. azhang@cse.buffalo.edu
pp. 342-349

Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways (PDF)

Qiong Cheng , Department of Computer Science, Georgia State University, Atlanta, Georgia 30303. Email: cscqxcx@cs.gsu.edu
Robert Harrison , Department of Computer Science, Georgia State University, Atlanta, Georgia 30303. Email: rharrison@cs.gsu.edu
Alexander Zelikovsky , Department of Computer Science, Georgia State University, Atlanta, Georgia 30303. Email: alexz@cs.gsu.edu
pp. 350-357

Review of Systems Biology Simulation Tools for Translational Research (PDF)

M. Freedenberg , Georgia Inst. of Technol. & Emory Univ., Atlanta
C. Kaddi , Georgia Inst. of Technol. & Emory Univ., Atlanta
C.F. Quo , Georgia Inst. of Technol. & Emory Univ., Atlanta
M.D. Wang , Georgia Inst. of Technol. & Emory Univ., Atlanta
W.H. Coulter , Georgia Inst. of Technol. & Emory Univ., Atlanta
pp. 358-365

Combined expression data with missing values and gene interaction network analysis: a Markovian integrated approach (PDF)

Juliette Blanchet , INRIA Rhône-Alpes, 655, av. de l'Europe, 38330 Saint Ismier Cedex, France. Email: juliette.blanchet@inrialpes.fr
Matthieu Vignes , BioSS at Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK. Email: matthieu@bioss.ac.uk
pp. 366-373

A Systematic Approach to Quantifying Evolutionary Functional Trends Across the Universal Tree of Life (PDF)

Gil Alterovitz , Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA; Children's Hospital Informatics Program, Boston, MA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA; Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA. gil@mit.edu
Taro Muso , Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA. muso@mit.edu
Paresh Malalur , Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA. pareshmg@mit.edu
Marco F. Ramoni , Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA; Children's Hospital Informatics Program, Boston, MA; Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA. marco_ramoni@harvard.edu
pp. 374-378

Super Granular Shrink-SVM Feature Elimination (Super GS-SVM-FE) Model for Protein Sequence Motif Information Extraction (PDF)

Bernard Chen , Georgia State University, Computer Science department, 34 Peachtree Street Suit 1450 Atlanta, GA, 30303. bchen3@cs.gsu.edu
Stephen Pellicer , Georgia State University, Computer Science department, 34 Peachtree Street Suit 1450 Atlanta, GA, 30303
Phang C. Tai , Georgia State University, Biology department, 34 Peachtree Street Suit 1450 Atlanta, GA, 30303
Robert Harrison , Georgia State University, Computer Science and Biology department, 34 Peachtree Street Suit 1450 Atlanta, GA, 30303
Yi Pan , Georgia State University, Computer Science department, 34 Peachtree Street Suit 1450 Atlanta, GA, 30303
pp. 379-386

False Discovery Rates in Identifying Functional DNA Motifs (PDF)

Osman Abul , Department of Computer Engineering, TOBB University of Economics and Technology, Ankara, Turkey. Email: osmanabul@etu.edu.tr
Geir Kjetil Sandve , Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway. Email: sandve@idi.ntnu.no
Finn Drablos , Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway. Email: finn.drablos@ntnu.no
pp. 387-394

A Geometrical Model for the SNP Motif Identification Problem (PDF)

Gaofeng Huang , Computing Laboratory, Oxford University, Gaofeng.Huang@comlab.ox.ac.uk
Peter Jeavons , Computing Laboratory, Oxford University, Peter.Jeavons@comlab.ox.ac.uk
pp. 395-402

A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure (PDF)

Fei Xiong , Department of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
Chris Bailey-Kellogg , Department of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA. Email: cbk@cs.dartmouth.edu
pp. 403-410

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots (PDF)

Xiang Chen , Key Lab of Intelligent Information Processing, Chinese Academy of Sciences, Beijing 100080, China; Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China; Graduate University of Chinese Academy of Sciences, Beijing 100039, China. xchen@jdl.ac.cn
Si-Min He , Key Lab of Intelligent Information Processing, Chinese Academy of Sciences, Beijing 100080, China; Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
Dong-Bo Bu , Key Lab of Intelligent Information Processing, Chinese Academy of Sciences, Beijing 100080, China; Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
Run-Sheng Chen , Insitute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Wen Gao , Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
pp. 411-417

Mining Conserved Structures of Enzymes from Functional Hierarchical Classification (PDF)

Yu-Feng Huang , Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, R.O.C. yfhuang@csie.ntu.edu.tw, r93103@csie.ntu.edu.tw
Yu-Shin Lin , Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, R.O.C. r93103@csie.ntu.edu.tw
Tian-Wei Hsu , Department of Engineering Science and Ocean Engineering, National Taiwan University, Taipei, Taiwan, R.O.C. r93525052@ntu.edu.tw
Chien-Kang Huang , Department of Engineering Science and Ocean Engineering, National Taiwan University, Taipei, Taiwan, R.O.C. ckhuang@ntu.edu.tw, r93525052@ntu.edu.tw
pp. 418-424

Database Approaches and Data Representation in Structural Bioinformatics (PDF)

Kreshna Gopal , Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A.
James C. Sacchettini , Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, U.S.A.
Thomas R. Ioerger , Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A.
pp. 425-432

Identifying Genomic Regulators of Set-Wise Co-Expression (PDF)

Jung Hoon Woo , Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea; Macrogen Inc., Seoul, Korea.
Tian Zheng , Department of Statistics, Columbia University, New York, NY, USA.
Ju Han Kim , Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea; Human Genome Research Institute, Seoul National University College of Medicine, Seoul 110-799, Korea. Email: juhan@snu.ac.kr
pp. 433-439

Tracing Lineage in Multi-version Scientific Databases (PDF)

Mingwu Zhang , Department of Computer Science, Purdue University, West Lafayette, IN 47907-1398, USA. mzhang2@cs.purdue.edu
Daisuke Kihara , Department of Computer Science, Purdue University, West Lafayette, IN 47907-1398, USA. dkihara@cs.purdue.edu
Sunil Prabhakar , Department of Computer Science, Purdue University, West Lafayette, IN 47907-1398, USA. sunil@cs.purdue.edu
pp. 440-447

Resolving Scientific Service Interoperability With Schema Mapping (PDF)

Nadia Yacoubi Ayadi , Scientific Data Management Lab, Arizona State University, Tempe AZ 85287-5706, USA. nadia.yacoubi@asu.edu
Zoe Lacroix , Scientific Data Management Lab, Arizona State University, Tempe AZ 85287-5706, USA. zoe.lacroix@asu.edu
pp. 448-455

A Machine Learning Approach to Pharmacological Profiling of the Quinone Scaffold in the NCI Database: A Compound Class Enriched in Those Effective Against Melanoma and Leukemia Cell Lines (PDF)

ML Ujwal , Discovery Informatics, Eli Lilly & Co, Indianapolis, IN 46285
Patrick Hoffman , InforSense, Cambridge, MA 02141
Kenneth A. Marx , Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854. E-mail: Kenneth_marx@uml.edu
pp. 456-463

Biomarker Selection for Predicting Alzheimer Disease Using High-Resolution MALDI-TOF Data (PDF)

Jung Hun Oh , Department of Computer Science and Engineering, The University of Texas, Arlington, TX 76019, USA. Email: jung.oh@uta.edu
Young Bun Kim , Department of Computer Science and Engineering, The University of Texas, Arlington, TX 76019, USA. Email: ybkim@uta.edu
Prem Gurnani , Department of Pathology, Division of Translational Pathology, University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
Kevin P. Rosenblatt , Department of Pathology, Division of Translational Pathology, University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
Jean Gao , Department of Computer Science and Engineering, The University of Texas, Arlington, TX 76019, USA. Email: gao@uta.edu
pp. 464-471

Multivariate Analysis of Imaging Mass Spectrometry Data (PDF)

E. R. Muir , Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, USA.
I. J. Ndiour , Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
N. A. LeGoasduff , Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
R. A. Moffitt , Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, USA.
Y. Liu , School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
M.C. Sullards , School of Biology, Department of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
A.H. Merrill , School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
Y. Chen , Department of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
M. D. Wang , Department of Biomedical Engineering, Georgia Institute of Technology, Emory University; Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
pp. 472-479

Phagocyte Transmigration Modeling Using System Dynamic Controls (PDF)

Jiaxing Xue , Department of Computer Science, University of Texas at Arlington, Arlington, Texas, 76019, USA. Email: joshjx@yahoo.com
Jean Gao , Department of Computer Science, University of Texas at Arlington, Arlington, Texas, 76019, USA. Email: gao@uta.edu
Liping Tang , Department of Bioengineering, University of Texas at Arlington, Arlington, Texas, 76019, USA. Email: ltang@uta.edu
pp. 480-485

A Novel Approach for Signal Transduction Networks Simulation at a Mesoscopic Level (PDF)

Chenxi Shao , MOE-Microsoft Key Laboratory of Multimedia Computing and Communication, University of Science and Technology of China, Hefei, Anhui, 230027, China; Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, 230027, China; Anhui Province Key Laboratory of Software in Computing and Communication, Hefei, Anhui, 230027, China. cxshao@ustc.edu.cn, lynnyang@mail.ustc.edu.cn
Hongli Deng , MOE-Microsoft Key Laboratory of Multimedia Computing and Communication, University of Science and Technology of China, Hefei, Anhui, 230027, China; Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, 230027, China. lynnyang@mail.ustc.edu.cn
pp. 487-494

Microtubule Dynamics Classification Using a Statistical Model of the Movement of Outer Tips (PDF)

Christopher Alberti , School of Electrical and Computer Engineering, Georgia Institute of Technology, calberti3@gatech.edu
Jean-Philippe Villareal , School of Electrical and Computer Engineering, Georgia Institute of Technology, jvillareal3@gatech.edu
Delano Billingsley , School of Electrical and Computer Engineering, Georgia Institute of Technology, delano@gatech.edu
Koon Yin Kong , School of Electrical and Computer Engineering, Georgia Institute of Technology, kykong@gatech.edu
Adam I. Marcus , Winship Cancer Institute, Emory University, adam.marcus@emory.org
Paraskevi Giannakakou , Wallace H. Coulter Department of Biomedical Engineering, Weill Cornell Medical College of Cornell University, pag2015@med.cornell.edu
May D. Wang , School of Electrical and Computer Engineering, Georgia Institute of Technology; Winship Cancer Institute, Emory University; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, maywang@gatech.edu
pp. 495-502

Computer Aided Histopathological Classification of Cancer Subtypes (PDF)

S. Waheed , Electrical and Computer Engineering, Georgia Institute of Technology
R. A. Moffitt , Biomedical Engineering, Georgia Institute of Technology and Emory University
Q. Chaudry , Electrical and Computer Engineering, Georgia Institute of Technology
A. N. Young , Pathology & Laboratory Medicine, Emory University
M.D. Wang , Electrical and Computer Engineering, Georgia Institute of Technology; Biomedical Engineering, Georgia Institute of Technology and Emory University, maywang@bme.gatech.edu
pp. 503-508

Evolving Biological Behavior in Gene-Based Cellular Simulations (PDF)

John H. Phan , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. jhphan@gatech.edu
Richard A. Moffitt , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. r.moffitt@gatech.edu
Todd H. Stokes , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. todd.stokes@bme.gatech.edu
May D. Wang , The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. maywang@bme.gatech.edu
pp. 509-516

Engineering Multifunctional Biologically-Amenable Nanomaterials for Interfacial Therapeutic Delivery and Substrate-Based Cellular Interrogation (PDF)

Mark Chen , Departments of Biomedical and Mechanical Engineering, Northwestern University
Brian Huang , Departments of Biomedical and Mechanical Engineering, Northwestern University
Eric Shin , Departments of Biomedical and Mechanical Engineering, Northwestern University
Erik Robinson , Departments of Biomedical and Mechanical Engineering, Northwestern University
Erik Pierstorff , Departments of Biomedical and Mechanical Engineering, Northwestern University
Houjin Huang , Departments of Biomedical and Mechanical Engineering, Northwestern University
Dean Ho , Departments of Biomedical and Mechanical Engineering, Northwestern University, d-ho@northwestern.edu
pp. 517-523

Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling (PDF)

Jack Y. Yang , Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114 USA. yang@hadron.mgh.Harvard.edu
Andrzej Niemierko , Division of Biomathematics and Biostatistics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20852 U.S.A. yangma@mail.NIH.gov
Youping Deng , Department of Biological Sciences, Bioinformatics and Cancer Biology Laboratory, University of Southern Mississippi, Hattiesburg, MS 39406 USA
pp. 524-531

Novel Materials for the Direct Removal of Water and Ions from the Body for Patients with Dialysis Needs (PDF)

Lisa Furby , Department of Mechanical Engineering and Energy Processes
Ravinder Gupta , Department of Mechanical Engineering and Energy Processes
Ajay Mahajan , Department of Mechanical Engineering and Energy Processes
Jarlen Don , Department of Mechanical Engineering and Energy Processes
Tsuchin Chu , Department of Mechanical Engineering and Energy Processes
Bakul Dave , Department of Chemistry and Biochemistry, Southern Illinois University Carbondale
Brad Schwartz , Department of Urology, School of Medicine, Southern Illinois University Springfield
pp. 532-537

A Robust Method for Generating Discriminative Gene Clusters (PDF)

Min Xu , Molecular and Computational Biology, University of Southern California, Los Angeles, USA. mxu@usc.edu
Louxin Zhang , Department of Mathematics, National University of Singapore, Singapore. matzlx@nus.edu.sg
Pei Li Joe Zhou , Mobile Commerce Centre, Monash Univeristy, Victoria, Australia. joe.zhou@infotech.monash.edu.au
pp. 538-545

Biological Mechanism on a Chip: Modeling and Realization of Growth Hormone Secretion Mechanism (PDF)

John R. Shell , Electrical Engineering, Southern Illinois University, Carbondale, IL 62901-6603. jshell@siu.edu
Yonglian Wang , Electrical Engineering, Southern Illinois University, Carbondale, IL 62901-6603. yonglianwang@yahoo.com
Nazeih M. Botros , Electrical Engineering, Southern Illinois University, Carbondale, IL 62901-6603. botrosn@siu.edu
pp. 546-552

Retrieval Analysis of a Cementless Modular Total Hip Arthroplasty Prosthesis (PDF)

Manish Paliwal , School of Engineering, The College of New Jersey, Ewing, NJ 08618
D. Gordon Allan , Division of Orthopaedic Surgery, SIU School of Medicine, Springfield, IL 62794
Peter Filip , Center for Advanced Friction Studies, SIU at Carbondale, Carbondale, IL 62901
pp. 553-558

Trabecular Metal Patella Implanted into Soft-Tissue in a Post-Patellectomized Knee A Case Report (PDF)

D. Gordon Allan , Division of Orthopaedic Surgery, SIU School of Medicine, Springfield, IL 62794
Manish Paliwal , School of Engineering, The College of New Jersey, Ewing, NJ 08618
Peter Filip , Center for Advanced Friction Studies, SIU at Carbondale, Carbondale, IL 62901
pp. 559-562

A comparison between traditional shift-and-add (SAA) and point-by-point back projection (BP) -- relevance to morphology of microcalcifications for isocentric motion in Digital Breast tomosynthesis (DBT) (PDF)

Ying Chen , Department of Electrical and Computer Engineering, Southern Illinois University Carbondale, Carbondale, IL 62901; Department of Biomedical Engineering, Duke University and Duke University Medical Center, Durham, North Carolina 27710; Duke Advanced Imaging Laboratories, Duke University and Duke University Medical Center, Durham, North Carolina 27710. ada_yingchen@yahoo.com
Joseph Y. Lo , Department of Biomedical Engineering, Duke University and Duke University Medical Center, Durham, North Carolina 27710; Duke Advanced Imaging Laboratories, Duke University and Duke University Medical Center, Durham, North Carolina 27710; Medical Physics Graduate Program, Duke University and Duke University Medical Center, Durham, North Carolina 27710
James T. Dobbins , Department of Biomedical Engineering, Duke University and Duke University Medical Center, Durham, North Carolina 27710; Duke Advanced Imaging Laboratories, Duke University and Duke University Medical Center, Durham, North Carolina 27710; Medical Physics Graduate Program, Duke University and Duke University Medical Center, Durham, North Carolina 27710
pp. 563-569

Methodology for Evaluating DNA Pattern Searching Algorithms on Multiprocessor (PDF)

Benfano Soewito , Dept. of Electrical and Computer Engineering, Southern Illinois University, Carbondale, IL 62901. soewito@engr.siu.edu
Ning Weng , Dept. of Electrical and Computer Engineering, Southern Illinois University, Carbondale, IL 62901. weng@engr.siu.edu
pp. 570-577

An Efficient Compression Method for Multiplanar Reformulated Biomedical Images (PDF)

Qiang Cheng , Computer Science Department, Southern Illinois University, Carbondale, IL 62901; Siemens Medical, Princeton, NJ 08536. Email: qcheng@cs.siu.edu
Mehdi Zargham , Computer Science Department, Southern Illinois University, Carbondale, IL 62901. Email: mehdi@cs.siu.edu
pp. 578-584

A Computational Approach to Understand Arabidopsis thaliana and Soybean Resistance to Fusarium solani (Fsg) (PDF)

Jiazheng Yuan , Department Plant, Soil Sciences, and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901; Department of Plant Biology, Southern Illinois University at Carbondale, IL 62901. jyuan@siu.edu, ga4082@siu.edu
Mengxia Zhu , Department of Computer Science, Southern Illinois University at Carbondale, IL 62901. ga4082@siu.edu
M. Javed Iqbal , Department Plant, Soil Sciences, and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901. ga4082@siu.edu
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, MA 02140. ga4082@siu.edu
David A. Lightfoot , Department Plant, Soil Sciences, and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901; Department of Plant Biology, Southern Illinois University at Carbondale, IL 62901. ga4082@siu.edu
pp. 585-592

Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays (Abstract)

Yunfeng Yang , Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA, 37831. Email: yangy@ornl.gov
Michelle M. Zhu , Computer Science Department, Southern Illinois University, Carbondale, IL, USA, 62901. Email: mengxia@cs.siu.edu
Liyou Wu , Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA, 73019. Email: lwu@rccc.ou.edu
Jizhong Zhou , Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA, 73019. Email: jzhou@rccc.ou.edu
pp. 593-600

Dynamic Load Balancing for Mining of Molecular Structures using Genetic Algorithm (PDF)

Salahuddin Mohammad Masum , Department of Electrical and Computer Engineering, The University of Memphis, Memphis, TN 38152, USA. smmasum@memphis.edu
Mohammed Yeasin , Department of Electrical and Computer Engineering, The University of Memphis, Memphis, TN 38152, USA. myeasin@memphis.edu
pp. 601-608

I/O Induced Scalability Limits of Bioinformatics Applications (PDF)

Robert Henschel , Technische Universität Dresden, Center for Information Services and High Performance Computing (ZIH), 01062 Dresden, Germany. Robert.Henschel@tu-dresden.de
Matthias S. Muller , Technische Universität Dresden, Center for Information Services and High Performance Computing (ZIH), 01062 Dresden, Germany. Matthias.Mueller@tu-dresden.de
pp. 609-613

Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations (PDF)

Marek Freindorf , Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260. mfrein@buffalo.edu
Matthew D. Jones , Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260
Yihan Shao , Q-Chem Inc. 5001 Baum Blvd, Suite 690, Pittsburgh, PA 15213
Jing Kong , Q-Chem Inc. 5001 Baum Blvd, Suite 690, Pittsburgh, PA 15213
Thomas R. Furlani , Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260
pp. 614-619

MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation (PDF)

Jeffrey L. Tilson , Renaissance Computing Institute, University of Illinois, Urbana-Champaign
Gloria Rendon , National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign
Mao-Feng Ger , Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign
Eric Jakobsson , National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign; Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign
pp. 620-627

Toward Petascale Simulation of Cellular Microphysiology (PDF)

Scott B. Baden , Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, 92093-0404. Email: baden@cs.ucsd.edu
Terrence J. Sejnowski , The Salk Institute, San Diego, California, 92186-5800. Email: terry@salk.edu
Thomas M. Bartol , The Salk Institute, San Diego, California, 92186-5800. Email: bartol@salk.edu
Joel Stiles , Pittsburgh Supercomputing Center and Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213. Email: stiles@psc.edu
pp. 628-634

Silent Killing: an Object-Oriented View of Hypertension and Kidney Failures Part I (PDF)

Jacqueline Signorini , Artificial Intelligence Laboratory of Saint-Denis, University Paris 8
Patrick Greussay , Artificial Intelligence Laboratory of Saint-Denis, University Paris 8
pp. 635-640

Medical Image Retrieval Based on Bidimensional Empirical Mode Decomposition (PDF)

Wei Liu , Institute for Biomedical Engineering and Instrumentation, School of Automation, Hangzhou Dianzi University, Hangzhou, China. bme.liuwei@gmail.com
Weidong Xu , Institute for Biomedical Engineering and Instrumentation, School of Automation, Hangzhou Dianzi University, Hangzhou, China
Lihua Li , Institute for Biomedical Engineering and Instrumentation, School of Automation, Hangzhou Dianzi University, Hangzhou, China
pp. 641-646

A Modified Fuzzy Kohonen's Competitive Learning Algorithms Incorporating Local Information for MR Image Segmentation (PDF)

Jun Kong , Computer School, Northeast Normal University, Changchun, Jilin Province, China; Key Laboratory for Applied Statistics of MOE, China. kongjun@nenu.edu.cn
Wenjing Lu , Computer School, Northeast Normal University, Changchun, Jilin Province, China; Key Laboratory for Applied Statistics of MOE, China. luwj116@nenu.edu.cn
Jianzhong Wang , Computer School, Northeast Normal University, Changchun, Jilin Province, China; Key Laboratory for Applied Statistics of MOE, China. wangjz019@nenu.edu.cn
Na Che , Computer School, Northeast Normal University, Changchun, Jilin Province, China; Key Laboratory for Applied Statistics of MOE, China. chen286@nenu.edu.cn
Yinghua Lu , Computer School, Northeast Normal University, Changchun, Jilin Province, China; Key Laboratory for Applied Statistics of MOE, China. luyh@nenu.edu.cn
pp. 647-653

An Efficient Modeling and Simulation System on the Kidney Matching, Distribution and Exchange Problems (PDF)

Liu Siyuan , Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. liusiyuan@ict.ac.cn
Liu Chao , Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. liuchao.beijing@yahoo.com.cn
Liu Yu , College of Mathematics and System Science, Shandong University, Jinan, China
Zhao Chunzhe , Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing, China
pp. 654-661

SiteSeeker - A Motif Discovery Tool (PDF)

Klaus Ecker , Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, Ohio 45701, USA. ecker@ohio.edu
Lonnie Welch , Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, Ohio 45701, USA. welch@Ohio.edu
Dazhang Gu , Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, Ohio 45701, USA. gud@ohio.edu
pp. 662-664

Modeling protein interaction network and mechanisms in exocytosis (PDF)

Wen Zhou , Department of Mathematics, Iowa State University, Ames, IA 50010, e-mail: riczw@iastate.edu
Tian Xia , Program of Bioinformatics and computational biology, Iowa State University, Ames, IA 50010, e-mail: netscape@iastate.edu
Jiansong Tong , Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50010, e-mail: tjs100@iastate.edu
Julie Dickerson , Program of Bioinformatics and computational biology, Iowa State University, Ames, IA 50010, e-mail: netscape@iastate.edu, julied@iastate.edu
Bo Su , Department of Mathematics, Iowa State University, Ames, IA 50010, e-mail: riczw@iastate.edu, bosu@iastate.edu
Xun Gu , Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50010, e-mail: xgu@iastate.edu
pp. 665-672

Toward a Realistic Model for Gene Network Evolution (PDF)

Wenhai Chen , National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Science Beijing 100080, PR China
Tianzi Jiang , National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences Beijing 100080, PR China. jiangtz@nlpr.ia.ac.cn
Tian Xia , Center for Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011
Xun Gu , Center for Bioinformatics and Biological Statistics, Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011. xgu@iastate.edu
pp. 673-679

Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing (PDF)

Pan Du , Robert H. Lurie Comprehensive Cancer Center Northwestern University, Chicago, IL, 60611, USA. dupan@northwestern.edu
Simon M. Lin , Robert H. Lurie Comprehensive Cancer Center Northwestern University, Chicago, IL, 60611, USA. s-lin2@northwestern.edu
Warren A. Kibbe , Robert H. Lurie Comprehensive Cancer Center Northwestern University, Chicago, IL, 60611, USA. wakibbe@northwestern.edu
Haihui Wang , LMIB, Department of Mathematics, Beihang University, Beijing, 100083, CHINA. whhmath@buaa.edu.cn
pp. 680-686

Pathway Complements of Four Yersinia (PDF)

Jennifer L. Neary , Department of Biology, The University of Texas, San Antonio, San Antonio TX, USA
Maribel Sanchez , Department of Biology, The University of Texas, San Antonio, San Antonio TX, USA
Yufeng Wang , Department of Biology, The University of Texas, San Antonio, San Antonio TX, USA. Yufeng.Wang@utsa.edu
Timothy G. Lilburn , Department of Bacteriology, American Type Culture Collection, Manassas VA, USA. tlilburn@atcc.org
pp. 687-692

An Improved Ant Colony Optimization Algorithm Based on Route Optimization and Its Applications in Travelling Salesman Problem (PDF)

Yi Zhang , College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education; Department of Computer Science, Jilin Business and Technology College. E-mail: whdzy2000@vip.sina.com
Zhi-li Pei , College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education; College of Mathematics and Computer Science, Inner Mongolia, University for Nationalities
Jin-hui Yang , College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education
Yan-chun Liang , College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education. E-mail: ycliang@jlu.edu.cn
pp. 693-698

Characterization of MYC expression in gefitinib versus Acute Myeloid Leukemia reveals novel therapeutic targets (PDF)

James F. Courage , The Cancer Therapy and Research Center Institute for Drug Development, San Antonio, TX 78245; Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249. jcourage@ctrc.net
Saurabh Gupta , The Cancer Therapy and Research Center Institute for Drug Development, San Antonio, TX 78245
Yufeng Wang , Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249. yufeng.wang@utsa.edu
pp. 699-706

Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates (PDF)

M. L. Rajaram , Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA 50011. mishar@iastate.edu
V. N. Minin , Department of Statistics, University of Washington, Seattle, WA 98195. vminin@stat.washington.edu
M. A. Suchard , Departments of Biomathematics, Human Genetics, and Biostatistics, University of California, Los Angeles, Los Angeles, CA 90095. msuchard@ucla.edu
K. S. Dorman , Departments of Statistics and Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011. kdorman@iastate.edu
pp. 707-714

Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles (PDF)

Ryo Yoshida , Institute of Statistical Mathematics, Research Organization of Information and Systems 4-6-7 Minami-Azabu, Minato-ku, Tokyo, 103-8569, Japan, Email: yoshidar@ism.ac.jp
Kazuyuki Numata , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Seiya Imoto , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Masao Nagasaki , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Atsushi Doi , Gene Network International, 4-2-12 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
Kazuko Ueno , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Satoru Miyano , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
pp. 715-722

Mining Frequent Contiguous Sequence Patterns in Biological Sequences (PDF)

Tae Ho Kang , Department of Computer and Communication Engineering, Chungbuk National University, Cheongju, South Korea. thkang@chungbuk.ac.kr
Jae Soo Yoo , Department of Computer and Communication Engineering, Chungbuk National University, Cheongju, South Korea. yjs@chungbuk.ac.kr
Hak Yong Kim , Department of Biochemistry, Chungbuk National University, Cheongju, South Korea. hykim@chungbuk.ac.kr
pp. 723-728

Efficient Methods for Biomedical Named Entity Recognition (PDF)

Shing-Kit Chan , Department of Systems Engineering and Engineering Management, The Chinese University of Hong Kong, Shatin, Hong Kong. skchan@se.cuhk.edu.hk
Wai Lam , Department of Systems Engineering and Engineering Management, The Chinese University of Hong Kong, Shatin, Hong Kong. wlam@se.cuhk.edu.hk
pp. 729-735

Stochastic Simulation Model for Patterned Neural Multi-Electrode Arrays (PDF)

Dong-Soo Kahng , Dept. of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea. dskahng@biosoft.kaist.ac.kr
Yoonkey Nam , Dept. of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea. ynam@kaist.ac.kr
Doheon Lee , Dept. of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea. dhlee@kaist.ac.kr
pp. 736-740

Classification of Enzyme Function from Protein Sequence based on Feature Representation (PDF)

Bum Ju Lee , Database/Bioinformatics laboratory, Chungbuk National University, Chungju, South Korea. bjlee@dblab.chungbuk.ac.r
Heon Gu Lee , Database/Bioinformatics laboratory, Chungbuk National University, Chungju, South Korea. hglee@dblab.chungbuk.ac.kr
Jong Yun Lee , Department of Computer Education, Chungbuk National University, Chungju, South Korea. jongyun@chungbuk.ac.kr
Keun Ho Ryu , Database/Bioinformatics laboratory, Chungbuk National University, Chungju, South Korea. khryu@dblab.chungbuk.ac.kr
pp. 741-747

Inferring Behavioral-level Circuits of Caenorhabditis elegans from the Topology of its Wiring Diagram (PDF)

Yunkyu Sohn , Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea. ysohn@kaist.ac.kr
Jaeseung Jeong , Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea; Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY USA. jsjeong@kaist.ac.kr
pp. 748-752

HAMMER Algorithm: Hashing with Arithmetic Modulo-4 for Motif Extraction of Regulatory Elements (PDF)

Huitao Sheng , Department of Electrical Engineering & Computer Science, Syracuse University, Syracuse, NY 13244, USA
Kishan Mehrotra , Department of Electrical Engineering & Computer Science, Syracuse University, Syracuse, NY 13244, USA
Chilukuri Mohan , Department of Electrical Engineering & Computer Science, Syracuse University, Syracuse, NY 13244, USA
Ramesh Raina , Department of Biology, Syracuse University, Syracuse, NY 13244, USA
pp. 753-758

A Tale of Intronless Genes in Eukaryotic Genomes (PDF)

Meena Kishore Sakharkar , School of MAE, Nanyang Technological University, Singapore. mmeena@ntu.edu.sg
Kishore R. Sakharkar , NUMI, YLL School of Medicine, National University of Singapore, Singapore. Email: nmikrs@nus.edu.sg
pp. 759-765

To fuse or not to fuse (PDF)

Kishore R. Sakharkar , NUMI, YLL School of Medicine, National University of Singapore, Singapore. Email: nmikrs@nus.edu.sg
Meena Kishore Sakharkar , School of MAE, Nanyang Technological University, Singapore. mmeena@ntu.edu.sg
pp. 766-773

Using Parsimony to Guide Maximum Likelihood Searches (PDF)

Kenneth Sundberg , Computer Science Department, Brigham Young University, Provo, Utah 84606. Email: kasundberg@gmail.com
Timothy O'Connor , Integrative Biology Department, Brigham Young University, Provo, Utah 84606. Email: timothydoconnor@gmail.com
Hyrum Carroll , Computer Science Department, Brigham Young University, Provo, Utah 84606. Email: hdc@cs.byu.edu
Mark Clement , Computer Science Department, Brigham Young University, Provo, Utah 84606. Email: clement@cs.byu.edu
Quinn Snell , Computer Science Department, Brigham Young University, Provo, Utah 84606. Email: snell@cs.byu.edu
pp. 774-779

QOMA2: Optimizing the alignment of many sequences (PDF)

Xu Zhang , Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32611. xuzhang@cise.ufl.edu
Tamer Kahveci , Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32611. tamer@cise.ufl.edu
pp. 780-787

A Reliable Metric for Quantifying Multiple Sequence Alignment (PDF)

Ken D. Nguyen , Department of Computer Science, Georgia State University, PO Box 3994, Atlanta, Georgia 30303. Email: knguyen@cs.gsu.edu
Yi Pan , Department of Computer Science, Georgia State University, PO Box 3994, Atlanta, Georgia 30303. Email: pan@cs.gsu.edu
pp. 788-795

Amino Acid Substitution Matrices Based on 4-Body Delaunay Contact Profiles (PDF)

Ahmet Sacan , Computer Engineering Department, Middle East Technical University Ankara, TURKEY. Email: ahmet@ceng.metu.edu.tr
I. Hakki Toroslu , Computer Engineering Department, Middle East Technical University Ankara, TURKEY. Email: toroslu@ceng.metu.edu.tr
pp. 796-801

A Heuristic for Phylogenetic Reconstruction Using Transposition (PDF)

Feng Yue , Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA. Email: yue2@cse.sc.edu
Meng Zhang , College of Computer Science and Technology, Jilin University, Changchun 130012, China. Email: zm@mail.edu.cn
Jijun Tang , Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA. Email: jtang@cse.sc.edu
pp. 802-808

Phylogeny By Top Down Clustering Using a Given Multiple Alignment (PDF)

Abdullah N. Arslan , Department of Computer Science, The University of Vermont, Burlington, VT 05405, USA. Email: aarslan@cs.uvm.edu
Peyman Bizargity , College of Medicine, The University of Vermont, Burlington, VT 05405, USA. Email: Peyman.Bizargity@uvm.edu
pp. 809-814

Reconstructing Mutational Pathways from Serial Evolutionary Trees (PDF)

Patricia Buendia , Miami Center for Computational Sciences, University of Miami, Department of Biology, University of Miami, Coral Gables, FL 33146, USA. pbuendia@bio.miami.edu
pp. 815-820

Towards Construction of Optimal Strip-Exchanging Moves (PDF)

Swapnoneel Roy , IBM India Pvt. Ltd., swapnoneel.roy@in.ibm.com
Ashok Kumar Thakur , IBM India Pvt. Ltd., ashok.thakur@in.ibm.com
pp. 821-827

Rough Overlapping Biclustering of Gene Expression Data (PDF)

Ruizhi Wang , Department of Computer Science and Technology, Tongji University, Shanghai, P.R.China
Duoqian Miao , Department of Computer Science and Technology, Tongji University, Shanghai, P.R.China
Gang Li , Department of Computer Science and Technology, Tongji University, Shanghai, P.R.China
Hongyun Zhang , Department of Computer Science and Technology, Tongji University, Shanghai, P.R.China
pp. 828-834

Using Domain-Based Structural Ensemble to Improve Structure Modeling (PDF)

Fa Zhang , Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. zf@ncic.ac.cn
Zhaoyun Ma , Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. mazhaoyun@ncic.ac.cn
Zhiyong Liu , Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. zyliu@ict.ac.cn
Bo Yuan , Department of Computer, Shanghai Jiao Tong University, Shanghai, China. yuanbo@cs.sjtu.edu.cn
pp. 835-841

Support Vector Regression with Feature Selection for the Multivariate Calibration of Spectrofluorimetric Determination of Aromatic Amino Acids (PDF)

Guo-Zheng Li , State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, China; School of Computer Science & Engineering, Shanghai University, Shanghai 200072, China. Email: gzli@shu.edu.cn
Hao-Hua Meng , State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, China; School of Computer Science & Engineering, Shanghai University, Shanghai 200072, China
Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health (NIH), U.S. Department of Health and Human Services, Bethesda, MD 20852 USA. Email: yangma@mail.NIH.GOV
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140 USA. Email: jyang@hadron.mgh.Harvard.edu
pp. 842-848

Bottom-Up Multiple Row Addition Algorithms for the Biclustering-Problem (PDF)

Hyung-Won Koh , ISAS - Institute for Analytical Sciences, 44139 Dortmund, Germany. Email: koh@isas.de
Lars Hildebrand , University of Dortmund, 44221 Dortmund, Germany. Email: lars.hildebrand@udo.edu
pp. 849-856

Fast Computation of Human Genetic Linkage (PDF)

Hongling Wang , Center for Quantitative and Computational Biology, Columbus Children's Research Institute, Columbus, Ohio 43205. Email: wangh@ccri.net
Alberto Maria Segre , Department of Computer Science, University of Iowa, Iowa City, IA 52242. Email: segre@cs.uiowa.edu
Yungui Huang , Center for Quantitative and Computational Biology, Columbus Children's Research Institute, Columbus, Ohio 43205. Email: huangy@ccri.net
Jeffrey R. O'Connell , Department of Medicine, University of Maryland, Baltimore, Maryland 21201. Email: joconnel@medicine.umaryland.edu
Veronica J. Vieland , Center for Quantitative and Computational Biology, Columbus Children's Research Institute, Columbus, Ohio 43205; Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205. Email: vielandv@ccri.net
pp. 857-863

3D Spectrum Analysis of DNA Sequence: Application to Caenorhabditis elegans Genome (PDF)

Afef Elloumi Oueslati , Unité Signal, Image et Reconnaissance de Formes, Département de Génie Electrique, ENIT, BP 37, Campus Universitaire, Le Belvédère, 1002, Tunis, Tunisie. afefelloumi@gmail.com
Noureddine Ellouze , Unité Signal, Image et Reconnaissance de Formes, Département de Génie Electrique, ENIT, BP 37, Campus Universitaire, Le Belvédère, 1002, Tunis, Tunisie. n.ellouze@enit.rnu.tn
Zied Lachiri , Département de Génie Physique et Instrumentation, INSAT, BP 676, Centre Urbain Cedex, 1080, Tunis, Tunisie. zied.lachiri@enit.rnu.tn
pp. 864-871

MotifNetwork: Genome-Wide Domain Analysis using Grid-enabled Workflows (PDF)

Jeffrey L. Tilson , Renaissance Computing Institute, Chapel Hill, U.S.A. jtilson@renci.org
Alan Blatecky , Renaissance Computing Institute, Chapel Hill, U.S.A. alan@renci.org
Gloria Rendon , National Center for Supercomputing Applications, Urbana-Champaign, U.S.A. grendon@uiuc.edu
Mao-Feng Ger , Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, U.S.A.
Eric Jakobsson , Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, U.S.A.
pp. 872-879

Profilins, Formins and Katanins as Flagellar Proteins of Leishmania spp.: a Genome-based, Multi-step Bioinformatics-driven Description (PDF)

Michel T. Kamimura , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Elton J.R. Vasconcelos , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Joao J.S. Gouveia , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Fabiana F. Araujo , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Michely C. Diniz , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Ana C.L. Pacheco , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Marcilia P. Costa , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Rodrigo Maggioni , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Raimundo Araujo-Filho , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Raimundo B. Costa , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil
Diana Magalhaes de Oliveira , Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformática - NUGEN, Universidade Estadual do Ceará - UECE, Fortaleza, Ceará - Brazil. Corresponding author: diana.magalhaes@uece.br
pp. 880-887

FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data (PDF)

Jason D. Bakos , Dept. of Computer Science and Engineering, University of South Carolina, Columbia, SC USA. jbakos@cse.sc.edu
Panormitis E. Elenis , Dept. of Computer Science and Engineering, University of South Carolina, Columbia, SC USA. elenis@cse.sc.edu
Jijun Tang , Dept. of Computer Science and Engineering, University of South Carolina, Columbia, SC USA. jtang@cse.sc.edu
pp. 888-895

A Preliminary Study of Correlation between Depth and Path Length of GO Nodes with Gene Sequence Similarity (PDF)

Elham Khabiri , School of Science and Computer Engineering, University of Houston-Clear Lake, Houston, TX, USA. khabirie8390@uhcl.edu
pp. 896-899

Mathematical Models and Optimization Discussion on EA System on AIDS/HIV Spread Estimating and Countermeasures Evaluating (PDF)

Liu Siyuan , Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. liusiyuan@ict.ac.cn
Liu Chao , Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. liuchao.beijing@yahoo.com.cn
Zhao Chunzhe , Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing, China
Liu Yu , College of Mathematics and System Science, Shandong University, Jinan, China
pp. 900-907

Fractal Dimension of Mie Scattering Spectra for the Appraisal of Infected HeLa Cells in Cultures (PDF)

Radu Dobrescu , Faculty of Control and Computers, Politehnica University of Bucharest, 313 Splaiul Independentei, Romania. E-mail: radud@isis.pub.ro
Loretta Ichim , Faculty of Control and Computers, Politehnica University of Bucharest, 313 Splaiul Independentei, Romania; "Stefan S. Nicolau" Institute of Virology, Romanian Academy, 285 Mihai Bravu, Bucharest, Romania. E-mail: iloretta@yahoo.com
pp. 908-913

Complexity-theoretic Modeling of Biological Cyanide Poisoning as Security Attack in Self-organizing Networks (PDF)

Jiejun Kong , Dept. of Electric & Computer Eng., University of Florida, Gainesville, FL 32611. jiejunkong@yahoo.com
Xiaoyan Hong , Dept. of Computer Science, University of Alabama, Tuscaloosa, AL 35487. hxy@cs.ua.edu
Dapeng Wu , Dept. of Electric & Computer Eng., University of Florida, Gainesville, FL 32611. wu@ece.ufl.edu
Mario Gerla , Dept. of Computer Science, University of California, Los Angeles, CA 90095. gerla@cs.ucla.edu
pp. 914-921

Quantitative and Probabilistic Modeling in Pathway Logic (PDF)

Alessandro Abate , EECS Department, UC Berkeley, aabate@eecs.berkeley.edu
Yu Bai , Biophysics Program, Stanford University, yubai@stanford.edu
Nathalie Sznajder , École Normale Superiéure, sznajder@lsv.ens-cachan.fr
Carolyn Talcott , CS Lab, SRI International, clt@csl.sri.com
Ashish Tiwari , CS Lab, SRI International, tiwari@csl.sri.com
pp. 922-929

A 2D Vibration Array as an Assistive Device for Visually Impaired (PDF)

D. Dakopoulos , College of Engineering and Computer Science, Assistive Technologies Research Center, Wright State University, Dayton, OH, USA. dakopoulos.2@wright.edu
S. K. Boddhu , College of Engineering and Computer Science, Computational Autonomy Research Lab, Wright State University, Dayton, OH, USA
N. Bourbakis , College of Engineering and Computer Science, Assistive Technologies Research Center, Wright State University, Dayton, OH, USA. nikolaos.bourbakis@wright.edu
pp. 930-937

Characterizing and Predicting Catalytic Residues in Enzyme Active Sites Based on Local Properties: A Machine Learning Approach (PDF)

Leonardo Bobadilla , Department of Statistics, National University of Colombia, jlbobadillam@unal.edu.co
Fernando Nino , Department of Statistics, National University of Colombia, lfninov@unal.edu.co
Edilberto Cepeda , Department of Statistics, National University of Colombia, ecepedac@unal.edu.co
Manuel A. Patarroyo , Fundación Instituto de Inmunología, FIDIC, mapatarr@fidic.org.co
pp. 938-945

Predicting Protein-Protein Interaction Based on Fisher Scores Extracted from Domain Profiles (PDF)

Tapan Patel , Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA
Li Liao , Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA. lliao@cis.udel.edu
pp. 946-951

A Novel Sequence-Structure Approach for Accurate Prediction of Resistance to HIV-1 Protease Inhibitors (PDF)

Majid Masso , Laboratory for Structural Bioinformatics, George Mason University, Manassas, Virginia. mmasso@gmu.edu
Iosif I. Vaisman , Laboratory for Structural Bioinformatics, George Mason University, Manassas, Virginia. ivaisman@gmu.edu
pp. 952-958

Prediction of Histone Modifications in DNA sequences (PDF)

Tho Hoan Pham , Hanoi National University of Education, 136 Xuan-Thuy, CauGiay, Hanoi, Vietnam. h-pham@jaist.ac.jp
Tu Bao Ho , Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Japan. bao@jaist.ac.jp
Dang Hung Tran , Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Japan. hungtd@jaist.ac.jp
Kenji Satou , Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Japan. ken@jaist.ac.jp
pp. 959-966

Feature Selection and Partial Least Squares Based Dimension Reduction for Tumor Classification (PDF)

Hua-Long Bu , School of Computer Engineering & Science, Shanghai University, Shanghai 200072, China; State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, China
Guo-Zheng Li , School of Computer Engineering & Science, Shanghai University, Shanghai 200072, China; State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, China
Xue-Qiang Zeng , School of Computer Engineering & Science, Shanghai University, Shanghai 200072, China; State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, China
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, Massachusetts, 02140 USA
Mary Qu Yang , National Human Genome, Research Institute National Institutes of Health (NIH), U.S. Department of Health and Human Services Bethesda, MD, 20852 USA
pp. 967-973

αCORR: a novel algorithm for clustering gene expression data (PDF)

Hossam S. Sharara , Department of Computers and Systems Engineering, Faculty of Engineering, Alexandria University, Egypt. Email: Hossam.Sharara@alex.edu.eg
Mohamed A. Ismail , Department of Computers and Systems Engineering, Faculty of Engineering, Alexandria University, Egypt
pp. 974-981

An Intelligent System for Searching Genomic Sequences (PDF)

Vandana Gummuluru , Department of Computer Information Science & Engineering (CISE), University of Floirda, Gainesville, FL 32611, USA. vgummulue@cise.ufl.edu
Su-Shing Chen , CISE, Genetics Institute, University of Florida, Gainesville, FL 32611, USA; CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China. suchen@cise.ufl.edu
pp. 982-986

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes (PDF)

Michael L. Blinov , Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA. blinov@uchc.edu
Ion I. Moraru , Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA. moraru@panda.uchc.edu
pp. 987-994

BALBOA: Extending Bicluster Analysis to Classify ORFs using Expression Data (PDF)

Kenneth Bryan , Department of Computer Science and Informatics, University College Dublin, kenneth.bryan@ucd.ie
Padraig Cunningham , Complex and Adaptive Systems Laboratory, University College Dublin, padraig.cunningham@ucd.ie
pp. 995-1002

A Comprehensive Fuzzy-Based Framework for Cancer Microarray Data Gene Expression Analysis (PDF)

Zhenyu Wang , Computing Laboratory, Oxford University, Oxford, OX1 3QD, UK. Email: Zhen.Yu.Wang@comlab.ox.ac.uk
Vasile Palade , Computing Laboratory, Oxford University, Oxford, OX1 3QD, UK. Email: Vasile.Palade@comlab.ox.ac.uk
pp. 1003-1010

Ensemble of Kernel Based Classifiers to Improve the Human Cancer Prediction using DNA Microarrays (PDF)

Angela Blanco , Universidad Pontificia de Salamanca (UPSA), C/Compañía 5, 37002, Salamanca, Spain. ablancogo@upsa.es
Manuel Martin-Merino , Universidad Pontificia de Salamanca (UPSA), C/Compañía 5, 37002, Salamanca, Spain. mmartinmac@upsa.es
Javier De Las Rivas , Cancer Research Center (CIC-IBMCC, CSIC/USAL), Salamanca, Spain. jrivas@usal.es
pp. 1011-1018

Mining Order Preserving Patterns in Microarray Data by Finding Frequent Orders (PDF)

Li Teng , Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
Laiwan Chan , Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
pp. 1019-1026

A New Smoothing Model for Analyzing Array CGH Data (PDF)

Nha Nguyen , Department of Electrical Engineering, University of Texas at Arlington. Email: nhn3175@exchange.uta.edu
Heng Huang , Department of Computer Science and Engineering, University of Texas at Arlington. Email: heng@uta.edu
Soontorn Oraintara , Department of Electrical Engineering, University of Texas at Arlington. Email: oraintar@uta.edu
An Vo , Department of Electrical Engineering, University of Texas at Arlington. Email: vpnan@gauss.uta.edu
pp. 1027-1034

Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles (PDF)

Sheehyun Kim , Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea. kimsheehyun@kaist.ac.kr
Dongsup Kim , Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea. kds@kaist.ac.kr
pp. 1035-1040

Multivariate Feature Selection using Random Subspace Classifiers for Gene Expression Data (PDF)

Vidya P. Kamath , Biomedical Engineering Program, University of South Florida and H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. Vidya.Kamath@moffitt.org
Lawrence O. Hall , Dept. of Computer Science and Engineering, University of South Florida, Tampa, Florida, USA. hall@cse.usf.edu
Timothy J. Yeatman , Dept. Interdisciplinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. Tim.Yeatman@moffitt.org
Steven. A Eschrich , Dept. Interdisciplinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. Steven.Eschrich@moffitt.org
pp. 1041-1045

Gene Selection via Matrix Factorization (PDF)

Fei Wang , State Key Lab of Intelligent Technologies and Systems, Department of Automation, Tsinghua University, feiwang03@mails.thu.edu.cn
Tao Li , School of Computer Science, Florida International University, Miami, FL 33199, U.S.A. taoli@cs.fiu.edu
pp. 1046-1050

Mutual Information based Minimum Spanning Trees Model for Selecting Discriminative Genes (PDF)

Fang Zhou , School of Computer Science and Engineering, Southeast University, Jiangsu, China, baiding_0_0@163.com
Jieyue He , School of Computer Science and Engineering, Southeast University, Jiangsu, China, jieyuehe@seu.edu.cn
Wei Zhong , Division of Math and Computer Science, University of South Carolina Upstate, Spartanburg, USA. wzhong@uscupstate.edu
pp. 1051-1055

Gene-Markers Representation for Microarray Data Integration (PDF)

Elena Baralis , Politecnico di Torino, Torino - Italy. Email: elena.baralis@polito.it
Elisa Ficarra , Politecnico di Torino, Torino - Italy. Email: elisa.ficarra@polito.it
Alessandro Fiori , Politecnico di Torino, Torino - Italy. Email: alessandro.fiori@polito.it
Enrico Macii , Politecnico di Torino, Torino - Italy. Email: enrico.macii@polito.it
pp. 1056-1060

Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis (PDF)

Yinyin Yuan , Department of Computer Science, University of Warwick, Coventry, United Kingdom. Email: yina@dcs.warwick.ac.uk
Chang-Tsun Li , Department of Computer Science, University of Warwick, Coventry, United Kingdom. Email: ctli@dcs.warwick.ac.uk
pp. 1061-1065

rSWTi: A Robust Stationary Wavelet Denoising Method for Array CGH Data (PDF)

Yuhang Wang , Department of Computer Science and Engineering, Southern Methodist University, Dallas, TX 75205. Email: yuhangw@engr.smu.edu
Siling Wang , Department of Computer Science and Engineering, Southern Methodist University, Dallas, TX 75205. Email: swang@engr.smu.edu
Andrew R. Zinn , Department of Internal Medicine and McDermott Center for Human Growth and Development UT Southwestern Medical Center at Dallas, Dallas, TX 75390. Email: andrew.zinn@utsouthwestern.edu
pp. 1066-1070

An Empirical CDF Approach to Estimate the Significance of Gene Ranking for Finding Differentially Expressed Genes (PDF)

J. Shaik , Electrical and Computer Engineering, University of Memphis, Memphis, TN- 38152. jshaik@memphis.edu
E.O. George , Department of Mathematics, University of Memphis, Memphis, TN- 38152. eogeorge@memphis.edu
M. Yeasin , Electrical and Computer Engineering, University of Memphis, Memphis, TN- 38152. myeasin@memphis.edu
pp. 1071-1075

Gene expression profiling and machine learning to understand and predict primary graft dysfunction (PDF)

Monika Ray , Computer Science and Engineering, Washington University, St. Louis, Missouri 63130
Sekhar Dharmarajan , Dept. of Surgery, Washington University, School of Medicine, St. Louis, Missouri 63110
Johannes Freudenberg , Biomedical Informatics, Cincinnati Children's Hospital Medical Centre, Cincinnati OH 45229
G. Alexander Patterson , Dept. of Surgery, Washington University, School of Medicine, St. Louis, Missouri 63110
Weixiong Zhang , Computer Science and Engineering, Washington University, St. Louis, Missouri 63130. Email: zhang@cse.wustl.edu, Tel: 3149358788, Fax: 3149357302
pp. 1076-1080

Sensitivity and Consistency of Affymetrix GeneChip Normalization Methods (PDF)

Jared Fox , Computer Science Department, University of California Los Angeles, jaredfox@ucla.edu
Nik Brown , Computer Science Department, University of California Los Angeles, nik@ucla.edu
pp. 1081-1086

Statistical Shape Analysis of the Corpus Callosum in Subtypes of Autism (PDF)

Qing He , Department of Computer Science, University of Missouri-Columbia, Columbia, MO, USA. qhgb2@mizzou.edu
Ye Duan , Department of Computer Science, University of Missouri-Columbia, Columbia, MO, USA. duanye@missouri.edu
Judith Miles , Thompson Center for Autism, University of Missouri-Columbia, Columbia, MO, USA
Nicole Takahashi , Thompson Center for Autism, University of Missouri-Columbia, Columbia, MO, USA
pp. 1087-1091

Simulation and Visualization of Menisci-Femur Contact Using Patient-Specific Deformable Models (PDF)

Ying Zhu , Department of Computer Science, Georgia State University, yzhu@cs.gsu.edu
pp. 1092-1096

Improved edge map of geometrical active contour model based on coupling to anisotropic diffusion filtering (PDF)

Foued Derraz , Valenciennes and Hainaut Cambresis University, LAMIH UMR CNRS 8530, Valenciennes, France. Foued.Derraz@meletu.univ-valenciennes.fr
Abdelmalik Taleb-Ahmed , Valenciennes and Hainaut Cambresis University, LAMIH UMR CNRS 8530, Valenciennes, France. Abdelmalik.taleb-ahmed@univ-valenciennes.fr
Azzeddine Chikh , Engineer college, Abou Bekr Belkaid University, Genie Biomedical Laboratory, Tlemcen, Algeria. az_chikh@mail.univ-tlemcen.dz
Fethi Bereksi-Reguig , Engineer college, Abou Bekr Belkaid University, Genie Biomedical Laboratory, Tlemcen, Algeria. f_bereksi@mail.univ-tlemcen.dz
pp. 1097-1101

Analysis of cardiac wall motion estimation methods (PDF)

Soroor behbahani , Biomedical Engineering Department, Science and Research Branch, Islamic Azad University, Tehran, Iran; member of researcher club of -Biomedical Engineering Department, Science and Research Branch, Islamic Azad University, Tehran, Iran. Soroor_behbahani@yahoo.com
Keivan magholi , Biomedical Engineering Department, Science and Research Branch, Islamic Azad University, Tehran, Iran.
pp. 1102-1107

Partial transmission high-speed continuous tracking multi-leaf collimator for 4D adaptive radiation therapy (PDF)

Tarun K. Podder , Member, IEEE, Department of Radiation Oncology, Kimmel Cancer Center (NCI-designated), Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA. Email: tarun.podder@jeffersonhospital.org
Ivan Buzurovic , Department of Radiation Oncology, Kimmel Cancer Center (NCI-designated), Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
Yida Hu , Department of Radiation Oncology, Kimmel Cancer Center (NCI-designated), Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
James M. Galvin , Department of Radiation Oncology, Kimmel Cancer Center (NCI-designated), Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
Yan Yu , Department of Radiation Oncology, Kimmel Cancer Center (NCI-designated), Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
pp. 1108-1112

Quantitative Analysis of Inter-object Spatial Relationships in Biological Images (PDF)

Wamiq M. Ahmed , School of Electrical and Computer Engineering, 465 Northwestern Avenue, Purdue University, West Lafayette, IN 47907
Magdalena Jonczyk , Bindley Bioscience Center, 1203 West State Street, Purdue University, West Lafayette, IN 47907
Ali Shamsaie , Bindley Bioscience Center, 1203 West State Street, Purdue University, West Lafayette, IN 47907
Arif Ghafoor , School of Electrical and Computer Engineering, 465 Northwestern Avenue, Purdue University, West Lafayette, IN 47907
J. Paul Robinson , Weldon School of Biomedical Engineering, 206 South Intramural Drive, Purdue University, West Lafayette, IN 47907; Bindley Bioscience Center, 1203 West State Street, Purdue University, West Lafayette, IN 47907
pp. 1113-1117

Histogram Transformation for Inter-Modality Image Registration (PDF)

Joerg Meyer , University of California at Irvine; Biomedical Engineering Department, 644E Engineering Tower, Irvine, CA 92697-2625. Email: jmeyer@uci.edu
pp. 1118-1123

The GPU on biomedical image processing for color and phenotype analysis (PDF)

Antonio Ruiz , Computer Architecture Dept., University of Malaga, ETSI Informática. Campus Teatinos, Malaga 29071, Spain
Manuel Ujaldon , Computer Architecture Dept., University of Malaga, ETSI Informática. Campus Teatinos, Malaga 29071, Spain
Jose Antonio Andrades , Cell Biology, Genetics and Phisiology Dept. University of Malaga, Faculty of Sciences. Campus Teatinos, Malaga 29071, Spain
Jose Becerra , Cell Biology, Genetics and Phisiology Dept. University of Malaga, Faculty of Sciences. Campus Teatinos, Malaga 29071, Spain
Kun Huang , Biomedical Informatics Dept., Ohio State University, 3197 Graves Hall. 333 W. 10th Ave., Columbus, Ohio 43210. U.S.A.
Tony Pan , Biomedical Informatics Dept., Ohio State University, 3197 Graves Hall. 333 W. 10th Ave., Columbus, Ohio 43210. U.S.A.
Joel Saltz , Biomedical Informatics Dept., Ohio State University, 3197 Graves Hall. 333 W. 10th Ave., Columbus, Ohio 43210. U.S.A.
pp. 1124-1128

Tissue Identification in Ultrasound Images using Rayleigh Local Parameter Estimation (Abstract)

Santiago Aja-Fernandez , LPI, ETSI Telecomunicación, Universidad de Valladolid, SPAIN. sanaja@tel.uva.es
Marcos Martin-Fernandez , LPI, ETSI Telecomunicación, Universidad de Valladolid, SPAIN. marcma@tel.uva.es
Carlos Alberola-Lopez , LPI, ETSI Telecomunicación, Universidad de Valladolid, SPAIN. caralb@tel.uva.es
pp. 1129-1133

Exploring Cardioneural Signals from Noninvasive ECG Measurement (PDF)

Amirali Shayan Arani , Computer Science and Engineering Department, University of California San Diego, La Jolla, CA, USA. amirali@ucsd.edu
Yi Zhu , Computer Science and Engineering Department, University of California San Diego, La Jolla, CA, USA. y2zhu@ucsd.edu
Yi-Ning Cheng , Computer Science and Engineering Department, University of California San Diego, La Jolla, CA, USA
Chung-Kuan Cheng , Computer Science and Engineering Department, University of California San Diego, La Jolla, CA, USA. ckcheng@ucsd.edu
Shien-Fong Lin , Krannert Institute of Cardiology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. linsf@iupui.edu
Peng-Sheng Chen , Krannert Institute of Cardiology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. chenpp@iupui.edu
pp. 1134-1138

MS Lesions Detection in MRI Using Grouping Artificial Immune Networks (PDF)

Akmal A. Younis , Department of Electrical and Computer Engineering, University of Miami, Miami, FL, USA. ayounis@miami.edu
Ahmed T. Soliman , Department of Electrical and Computer Engineering, University of Miami, Miami, FL, USA. a.soliman@umiami.edu
Mansur R. Kabuka , Department of Electrical and Computer Engineering, University of Miami, Miami, FL, USA. m.kabuka@miami.edu
Nigel M. John , Department of Electrical and Computer Engineering, University of Miami, Miami, FL, USA. nigel.john@miami.edu
pp. 1139-1146

Non-negative Tensor Factorization Based on Alternating Large-scale Non-negativity-constrained Least Squares (PDF)

Hyunsoo Kim , College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. E-mail: hskim@cc.gatech.edu
Haesun Park , College of Computing, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA. E-mail: hpark@cc.gatech.edu
Lars Elden , Department of Mathematics, Linköping University, SE-581, 83 Linköping, Sweden. E-mail: laeld@math.liu.se
pp. 1147-1151

A Computer Aided Tool for the Assessment of Human Sperm Morphology (PDF)

Henry Carrillo , IEEE Student Member, Department of Electrical and Electronic Engineering, Universidad del Norte., Barranquilla, Colombia. henrydcl@gmail.com, mandi6co@gmail.com
Jorge Villarreal , IEEE Student Member, Department of Electrical and Electronic Engineering, Universidad del Norte., Barranquilla, Colombia. mandi6co@gmail.com
Miguel Sotaquira , Department of Electrical and Electronic Engineering, Universidad del Norte., Barranquilla, Colombia. msotaquira@uninorte.edu.co, mandi6co@gmail.com
Alvaro Goelkel , Department of Chemistry and Biology, Universidad del Norte., Barranquilla, Colombia. agoelkel@uninorte.edu.co, mandi6co@gmail.com
Ricardo Gutierrez , Department of Chemistry and Biology, Universidad del Norte., Barranquilla, Colombia. rgutierr@uninorte.edu.co, mandi6co@gmail.com
pp. 1152-1157

Feature Estimation for Vocal Fold Edema Detection Using Short-Term Cepstral Analysis (PDF)

Benedito G. Aguiar Neto , IEEE Member, Federal University of Campina Grande, Brazil; Institute of Technology, University of Washington, Tacoma, USA. bganeto@u.washington.edu
Joseana M. Fechine , Federal University of Campina Grande, Paraíba, Brazil. joseana@dsc.ufcg.edu.br
Silvana Cunha Costa , Federal Center of Technological Education, CEFET-PB, Federal University of Campina Grande, Brazil. silvana@cefetpb.edu.br
Menaka Muppa , Institute of Technology, University of Washington, Tacoma, USA. mmuppa@u.washington.edu
pp. 1158-1162

A New Hybrid Technique for Dermatological Image Registration (PDF)

Heng Huang , Computer Science and Engineering, Univ. of Texas at Arlington. Email: heng@uta.edu
Paul Bergstresser , Department of Dermatology, Univ. of Texas Southwestern Medical Center, Email: bergstre@utsw.swmed.edu
pp. 1163-1167

PID Control based on BP Neural Network for the Regulation of Blood Glucose Level in Diabetes (PDF)

Chengwei Li , School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin, China. chengweili@hit.edu.cn
Ruiqiang Hu , Institute of Biomedical Engineering, Yan Shan University, Qinhuangdao, China. huruiqiang163@163.com
pp. 1168-1172

Spatiotemporal Analysis of an Agent-Based Model of a Colony of Keratinocytes: A First Approach for the Development of Validation Methods (PDF)

Cesar Pichardo-Almarza , Department of Computer Science, University of Sheffield, Sheffield, U.K. c.pichardo@sheffield.ac.uk
Rod Smallwood , Department of Computer Science, University of Sheffield, Sheffield, U.K. r.smallwood@sheffield.ac.uk
S. A. Billings , Department of Automatic Control and System Engineering, University of Sheffield, Sheffield, U.K. s.billings@sheffield.ac.uk
pp. 1173-1177

A Suffix Tree Construction Algorithm for DNA Sequences (PDF)

Hongwei Huo , School of Computer Science and Technology, Xidian University, Xi'an 710071, China. hwhuo@mail.xidian.edu.cn
Vojislav Stojkovic , Computer Science Department, Morgan State University, Baltimore, MD 21251, USA. stojkovi@jewel.morgan.edu
pp. 1178-1182

Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder (PDF)

Viktor Martyanov , Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire USA 03755
Larkin Elderon , Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire USA 03755
Amy Gladfelter , Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire USA 03755
Dhanalakshmi R. Nair , Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire USA 03755
Robert H. Gross , Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire USA 03755. robert.h.gross@dartmouth.edu
pp. 1183-1187

Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers (Abstract)

Tieming Ji , Department of Computer Science, New Mexico State University, Las Cruces, NM, 88003, USA
Desh Ranjan , Department of Computer Science, New Mexico State University, Las Cruces, NM, 88003, USA
Jeanne Curry , Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
Mary O'Connell , Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
pp. 1188-1192

Speeding Up Pairwise Sequence Alignments: A Scoring Scheme Reweighting Based Approach (PDF)

Yong Gao , Department of Computer Science, Irving K. Barber School of Arts and Sciences, University of British Columbia Okanagan, Kelowna, Canada V1V 1V7. Email: yong.gao@ubc.ca
Michael Henderson , Department of Computer Science, Irving K. Barber School of Arts and Sciences, University of British Columbia Okanagan, Kelowna, Canada V1V 1V7
pp. 1194-1198

Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching (PDF)

Dan He , Department of Computer Science, The University of Vermont, Burlington, VT 05405, USA. Email: hedanxkhc@hotmail.com
Abdullah N. Arslan , Department of Computer Science, The University of Vermont, Burlington, VT 05405, USA. Email: aarslan@cs.uvm.edu
Yu He , Department of Computer Science, The University of Vermont, Burlington, VT 05405, USA. Email: heyv2002@gmail.com
Xindong Wu , Department of Computer Science, The University of Vermont, Burlington, VT 05405, USA. Email: xwu@cs.uvm.edu
pp. 1199-1203

Determining Domain Similarity and Domain-Protein Similarity Using Functional Similarity Measurements of Gene Ontology Terms (PDF)

Lisa M. Guntly , Department of Computer Science, University of Missouri-Rolla, Rolla, MO 65409, USA
Jennifer L. Leopold , Department of Computer Science, University of Missouri-Rolla, Rolla, MO 65409, USA
Anne M. Maglia , Department of Biological Sciences, University of Missouri-Rolla, Rolla, MO 65409, USA
pp. 1209-1213

Signal Representation and Processing of Nucleotide Sequences (PDF)

Paul Cristea , Bio-Medical Engineering Center, University "Politehnica" of Bucharest, Bucharest, Romania. pcristea@dsp.pub.ro
Rodica Tuduce , Bio-Medical Engineering Center, University "Politehnica" of Bucharest, Bucharest, Romania
Iulian Nastac , Bio-Medical Engineering Center, University "Politehnica" of Bucharest, Bucharest, Romania
Jan Cornelis , ETRO Department, Vrije Universiteit Brussel, Brussels, Belgium
Rudi Deklerck , ETRO Department, Vrije Universiteit Brussel, Brussels, Belgium
Marius Andrei , Google Inc, Mountain View, CA, USA
pp. 1214-1219

Cluster Analysis of Regulatory Sequences with a Log Likelihood Ratio Statistics-based Similarity Measure (PDF)

Huiru Zheng , School of Computing and Mathematics, University of Ulster, N. Ireland, UK. h.zheng@ulster.ac.uk
Haiying Wang , School of Computing and Mathematics, University of Ulster, N. Ireland, UK. hy.wang@ulster.ac.uk
Jinglu Hu , Waseda University, Japan. jinglu@waseda.jp
pp. 1220-1224

A PQRM-based PACS System for Advanced Medical Services under Grid Environment (PDF)

Yong-Jie Ni , School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, Daejeon, 305-732, Korea. yjni@icu.ac.kr
Chan-Hyun Youn , School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, Daejeon, 305-732, Korea. chyoun@icu.ac.kr
Byoung-Jin Kim , School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, Daejeon, 305-732, Korea. bjkim@icu.ac.kr
Young-Joo Han , School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, Daejeon, 305-732, Korea. yjhan@icu.ac.kr
Peng Liu , School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, Daejeon, 305-732, Korea. liu@icu.ac.kr
pp. 1225-1229

Middleware based Inpatient Healthcare Information System (PDF)

M. Y. Jan , Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan
S. H. Hsieh , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan
Y. C. Weng , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan
T. H. Yang , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Department of Information Management, National Taiwan University, Taipei, Taiwan
Feipei Lai , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan; Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University, Taiwan
P. H. Cheng , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan
X.O. Ping , Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan
S. L. Hsieh , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Network and Computer Centre, National Chiao Tung University, Hsin Chu, Taiwan
J.C. Lin , Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
C.H. Peng , Department of Computer Science and Information Engineering National Taiwan University, Taipei, Taiwan
K.H. Huang , Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
L. F. Ko , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan; Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
C. H. Chen , Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
K. P. Hsu , Information Systems Office, National Taiwan University Hospital, Taipei, Taiwan
pp. 1230-1234

Generating social networks of intimate contacts for the study of public health intervention strategies (PDF)

Courtney D. Corley , University of North Texas, Department of Computer Science and Engineering, Denton, TX. corley@unt.edu
Lindsey Brown , University of North Texas, Department of Computer Science and Engineering, Denton, TX. lmb0105@unt.edu
Armin R. Mikler , University of North Texas, Department of Computer Science and Engineering, Denton, TX. mikler@cse.unt.edu
Diane J. Cook , Washington State University, School of Electrical Engineering and Computer Science, Pullman, WA. cook@eecs.wsu.edu
Karan Singh , UNT Health Science Center, Department of Biostatistics, Ft. Worth, TX. ksingh@hsc.unt.edu
pp. 1235-1239

Yin Yang Mental Squares - An Equilibrium-Based System For Bipolar Neurobiological Pattern Classification and Analysis (PDF)

Wen-Ran Zhang , Member, IEEE, Dept. of Computer Science, College of Information Technology, Georgia Southern University, Statesboro, GA USA. wrzhang@georgiasouthern.edu
Karl E. Peace , Georgia Cancer Coalition and The Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA USA. kepeace@georgiasouthern.edu
pp. 1240-1244

Automatically Extracting Acronyms from Biomedical Text (PDF)

Jared Fox , Computer Science Department, University of California Los Angeles, jaredfox@ucla.edu
Nik Brown , Computer Science Department, University of California Los Angeles, nik@ucla.edu
pp. 1245-1248

Feature Extraction and Parameters Selection of Classification Model on Brain-Computer Interface (Abstract)

Mingyuan Zhao , School of Computer Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. zmgyn@mail.sc.cninfo.net
Mingtian Zhou , School of Computer Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. zmgyn@mail.sc.cninfo.net
Qingxin Zhu , School of Computer Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. zmgyn@mail.sc.cninfo.net
Ping Yang , School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. tianqingli@yahoo.com
pp. 1249-1253

Consistent Modeling, Integration and Simulation of Molecular Interaction Networks in Space-Time Dimension (PDF)

Rui Chang , Department of Computer Science, Technical University of Munich, Germany. Email: chang.rui@hotmail.com
pp. 1254-1259

Feature Reduction for Gene Regulatory Network Control (PDF)

Mehmet Tan , Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, mtan@ceng.metu.edu.tr; scholar, Dept. of Computer Science, University of Calgary, Calgary, Alberta, Canada; mtan@cpsc.ucalgary.ca
Faruk Polat , Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, polat@ceng.metu.edu.tr
Reda Alhajj , Department of Computer Science, University of Calgary, Calgary, Alberta, Canada; mtan@cpsc.ucalgary.ca, alhajj@cpsc.ucalgary.ca; Dept. of Computer Science, Global University, Beirut, Lebanon
pp. 1260-1264

Graph Mining of Networks from Genome Biology (PDF)

George Chin , Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA. george.chin@pnl.gov
Grant C. Nakamura , Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA. grant.nakamura@pnl.gov
Daniel G. Chavarria , Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA. daniel.chavarria@pnl.gov
Heidi J. Sofia , Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA. heidi.sofia@pnl.gov
pp. 1265-1269

Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae (PDF)

Martin S.R. Paradesi , Department of Computing and Information Sciences, Kansas State University, Manhattan, KS 66506 USA. pmsr@cis.ksu.edu
Doina Caragea , Department of Computing and Information Sciences, Kansas State University, Manhattan, KS 66506 USA. dcaragea@cis.ksu.edu
William H. Hsu , Department of Computing and Information Sciences, Kansas State University, Manhattan, KS 66506 USA. bhsu@cis.ksu.edu
pp. 1270-1274

Complete Backtranslation of Oligopeptides for Metabolic Pathways Exploration of Complex Environments using Functional Microarrays (PDF)

Mohieddine Missaoui , Laboratoire d'informatique et de modélisation et optimization des systèmes (LIMOS), 63170 Aubière, France. missaoui@isima.fr
David R.C. Hill , Laboratoire d'informatique et de modélisation et optimization des systèmes (LIMOS), 63170 Aubière, France. drch@isima.fr
Cecile Militon , Laboratoire de Biologie des Protistes (LBP), 63000 Aubière, France. cemilito@univ-bpclermont.fr
Pierre Peyret , Laboratoire de Biologie des Protistes (LBP), 63000 Aubière, France. pierre.peyret@univ-bpclermont.fr
pp. 1275-1279

A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks (PDF)

Kazuyuki Numata , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Email: numata@ims.u-tokyo.ac.jp
Seiya Imoto , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Email: imoto@ims.u-tokyo.ac.jp
Satoru Miyano , Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Email: miyano@ims.u-tokyo.ac.jp
pp. 1280-1284

Toward The Recognition Code Of Protein-DNA Recognition (PDF)

Juan Shan , Department of Computer Science, Utah State University, Logan, UT. juans@cc.usu.edu
Yuxuan Wang , Department of Computer Science, Utah State University, Logan, UT. yuxuanwang@cc.usu.edu
Changhui Yan , Department of Computer Science, Utah State University, Logan, UT. cyan@cc.usu.edu
pp. 1290-1293

Self-Optimizing Parallel Algorithms for Haplotype Reconstruction and Their Evaluation on the JPT and CHB Genotype Data (PDF)

Dragos Trinca , Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA. dtrinca@engr.uconn.edu
Sanguthevar Rajasekaran , Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA. rajasek@engr.uconn.edu
pp. 1294-1298

Reducing Folding Scenario Candidates in Pseudoknots Detection Using PLMM_DPSS Algorithm Integrated With Energy Filters (PDF)

Xiaolu Huang , Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182. xhuang@unmc.edu
Hesham Ali , Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182. hesham@unomaha.edu
pp. 1299-1303

Exploring Topological Properties of NMR Graphs (PDF)

Paulius Micikevicius , School of Computing, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, GA 31419. paulius@cs.armstrong.edu
Narsingh Deo , School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362. deo@cs.ucf.edu
pp. 1304-1307

Probability Analysis on Associations of Adverse Drug Events with Drug-Drug Interactions (PDF)

Yu-Ting Huang , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan. nightfelidae@gamil.com, g9565537@oz.nthu.edu.tw, redjava@gmail.com, d926708@oz.nthu.edu.tw
Shih-Fang Lin , Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan. nightfelidae@gamil.com, g9565537@oz.nthu.edu.tw, redjava@gmail.com, d926708@oz.nthu.edu.tw
Chung-Cheng Chiu , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan. nightfelidae@gamil.com, g9565537@oz.nthu.edu.tw, redjava@gmail.com, d926708@oz.nthu.edu.tw
Hsiang-Yuan Yeh , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan. nightfelidae@gamil.com, g9565537@oz.nthu.edu.tw, redjava@gmail.com, d926708@oz.nthu.edu.tw
Von-Wun Soo , Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan; Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan; Department of Computer Science and Information Engineering, National University of Kaohsiung, Kaohsiung, 811, Taiwan. soo@cs.nthu.edu.tw, nightfelidae@gamil.com, g9565537@oz.nthu.edu.tw, redjava@gmail.com, d926708@oz.nthu.edu.tw
pp. 1308-1312

Combining Semantics, Context, and Statistical Evidence in Genomics Literature Search (PDF)

Jay Urbain , Information Retrieval Laboratory, Illinois Institute of Technology, Chicago, IL. urbajay@iit.edu
Nazli Goharian , Information Retrieval Laboratory, Illinois Institute of Technology, Chicago, IL. goharian@iit.edu
Ophir Frieder , Computer Science Department, Georgetown University, Washington, DC. ophir@cs.georgetown.edu
pp. 1313-1317

Graph and Topological Structure Mining on Scientific Articles (PDF)

Fan Wang , Department of Computer Science and Engineering, Ohio State University, Columbus OH 43210. wangfa@cse.ohio-state.edu
Ruoming Jin , Department of Computer Science, Kent State University, Kent OH 44242. jin@cs.kent.edu
Gagan Agrawal , Department of Computer Science and Engineering, Ohio State University, Columbus OH 43210. agrawal@cse.ohio-state.edu
Helen Piontkivska , Department of Biological Sciences, Kent State University, Kent OH 44242. opiontki@kent.edu
pp. 1318-1322

Supervised HITS Algorithm for MEDLINE Citation Ranking (PDF)

Ying Liu , Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083-0688. ying.liu@utdallas.edu
Yongjing Lin , Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083-0688
pp. 1323-1327

Storing Efficiently Bioinformatics Workflows (PDF)

Michel Kinsy , Arizona State University, PO Box 875706 Tempe AZ 85287-5706, USA
Zoe Lacroix , Arizona State University, PO Box 875706 Tempe AZ 85287-5706, USA
pp. 1328-1332

Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases (PDF)

Chen Lin , Computer Science Department, Brandeis University, Waltham, USA. clin@brandeis.edu
Wayne Mak , Computer Science Department, Brandeis University, Waltham, USA
Pengyu Hong , Computer Science Department, Brandeis University, Waltham, USA. hongpeng@brandeis.edu
Katharine Sepp , Department of Genetics, Harvard Medical School, Boston, USA
Norbert Perrimon , Department of Genetics, Harvard Medical School, Boston, USA; Howard Hughes Medical Institute, Boston, USA
pp. 1333-1337

GPX: A Tool for the Exploration and Visualization of Genome Evolution (PDF)

Neha Nahar , Department of Computer Science and Statistics, University of Rhode Island, Kingston, USA. nnahar@cs.uri.edu
Lutz Hamel , Department of Computer Science and Statistics, University of Rhode Island, Kingston, USA. hamel@cs.uri.edu
Maria S. Poptsova , Department of Molecular and Cell Biology, University of Connecticut, Storrs, USA. maria.poptsova@uconn.edu
J. Peter Gogarten , Department of Molecular and Cell Biology, University of Connecticut, Storrs, USA. gogarten@uconn.edu
pp. 1338-1342

SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing (Abstract)

Tom Milledge , BioRG, School of Computing and Information Science, Florida International University, tmille01@cs.fiu.edu
Gaolin Zheng , Department of Mathematics and Computer Science, North Carolina Central University, gzheng@nccu.edu
Tim Mullins , IBM Systems and Technology Group, Rochester, MN 55901. mullinst@us.ibm.com
Giri Narasimhan , BioRG, School of Computing and Information Science, Florida International University, giri@cs.fiu.edu
pp. 1343-1347

G-protein Coupled Receptor Subfamilies Prediction Based on Nearest Neighbor Approach (PDF)

Mudassir Fayyaz , Faculty of Computer Science & Engineering, Ghulam Ishaq Khan Institute of Engineering Science & Technology, Swabi, Pakistan. mudassir.fayyaz@gmail.com
Adnan Mujahid , Faculty of Computer Science & Engineering, Ghulam Ishaq Khan Institute of Engineering Science & Technology, Swabi, Pakistan
Asifullah Khan , Department of Mechatronics, Gwangju Institute of Science and technology, 1 Oryong-Dong, Buk-Gu, Gwangju, 500-712, Republic of Korea. asifullah@gist.ac.kr
Tae-Sun Choi , Department of Mechatronics, Gwangju Institute of Science and technology, 1 Oryong-Dong, Buk-Gu, Gwangju, 500-712, Republic of Korea. tschoi@gist.ac.kr
Nadeem Iqbal , Department of Bio & Brain Engineering, Korea Advanced Institute of Science and Technology KAIST 373-1, Yuesong-gu, Daejeon 305-701 Republic of Korea. nadeem@neuron.kaist.ac.kr
pp. 1348-1354

Protein Secondary Structure Prediction Using Genetic Neural Support Vector Machines (PDF)

Anjum Reyaz-Ahmed , Department Of Computer Science, Georgia State University, Atlanta, USA. anjumrahmed@gmail.com
Yan-Qing Zhang , Department Of Computer Science, Georgia State University, Atlanta, USA. yzhang@cs.gsu.edu
pp. 1355-1359

An HV-SVM Classifier to Infer TF-TF Interactions Using Protein Domains and GO Annotations (PDF)

Xiao-Li Li , Data Mining Department, Institute for Infocomm Research, Singapore, 119613. xlli@i2r.a-star.edu.sg
Jun-Xiang Lee , Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576. j.l@nus.edu.sg
Bharadwaj Veeravalli , Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576. elebv@nus.edu.sg
See-Kiong Ng , Data Mining Department, Institute for Infocomm Research, Singapore, 119613. skng@i2r.a-star.edu.sg
pp. 1360-1364

Supervised Statistical and Machine Learning Approaches to Inferring Pairwise and Module-Based Protein Interaction Networks (PDF)

Fiona Browne , School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK
Haiying Wang , School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK
Huiru Zheng , School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK
Francisco Azuaje , School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK. fj.azuaje@ulster.ac.uk
pp. 1365-1369

Predicting Protein Subcelluar Localizations Using Weighted Euclidian Distance (PDF)

Jing Hu , Department of Computer Science, Utah State University, Logan, UT 84322. Jinghu@cc.usu.edu
Changhui Yan , Department of Computer Science, Utah State University, Logan, UT 84322. cyan@cc.usu.edu
pp. 1370-1373

An efficient data structure for applying multiple seeds in homology search (PDF)

Alireza Hadj Khodabakhshi , School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. alireza@cs.sfu.ca
Mehdi Mirzazadeh , School of Computing Science, University of Waterloo, Waterloo, ON, Canada. mmirzaza@cs.uwaterloo.ca
Arvind Gupta , School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. arvind@cs.sfu.ca
pp. 1374-1378

A Mixture of Experts Method for Predicting Domain Boundaries in Proteins (PDF)

Ian MacDonald , Department of Computer Science, College of Saint Rose, Albany, NY, USA. ianmacdonald@strose.edu
George Berg , Department of Computer Science, University at Albany, SUNY, Albany, NY, USA. berg@cs.albany.edu
pp. 1379-1383

SIGN: reliable protein interaction identification by integrating the Similarity In GO and the similarity in protein interaction Networks (PDF)

Woochang Hwang , Department of Computer Science and Engineering, State University of New York at Buffalo, USA. Email: whwang2@cse.buffalo.edu
Taehyong Kim , Department of Computer Science and Engineering, State University of New York at Buffalo, USA. Email: thkim7@cse.buffalo.edu
Young-Rae Cho , Department of Computer Science and Engineering, State University of New York at Buffalo, USA. Email: ycho8@cse.buffalo.edu
Aidong Zhang , Department of Computer Science and Engineering, State University of New York at Buffalo, USA. Email: azhang@cse.buffalo.edu
Murali Ramanathan , Department of Pharmaceutical Sciences, State University of New York at Buffalo, USA. Email: murali@acsu.buffalo.edu
pp. 1384-1388

Identification of Differential Flow Cytometry Expression (PDF)

Elizabeth Rossin , Broad Institute of MIT and Harvard, Cambridge, United States. rossin@broad.mit.edu
Saumyadipta Pyne , Broad Institute of MIT and Harvard, Cambridge, United States. spyne@broad.mit.edu
Florian Hahne , German Cancer Research Center, Heidelberg, Germany. f.hahne@dkfz-heidelberg.de
Philip L. De Jager , Brigham & Women's Hospital, Boston, United States. pdejager@rics.bwh.harvard.edu
pp. 1389-1393

Performance Characterization of BLAST for the Grid (PDF)

Enis Afgan , Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294-1170, USA. afgane@uab.edu
Purushotham Bangalore , Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294-1170, USA. puri@uab.edu
pp. 1394-1398

Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing (PDF)

Sihui Zhao , Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. szhao3@ncsu.edu
Jihye Kim , Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. jkim4@ncsu.edu
Steffen Heber , Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. sheber@ncsu.edu
pp. 1399-1403

Semiparametric RMA Background-Correction for Oligonucleotide Arrays (PDF)

Ionut Bebu , Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Suite 180, Building D 4000 Reservoir Rd, NW Washington, DC 20057-1484. Email: ib62@georgetown.edu
Francoise Seillier-Moiseiwitsch , Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Suite 180, Building D 4000 Reservoir Rd, NW Washington, DC 20057-1484. Email: seillier@georgetown.edu
Hongfang Liu , Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Suite 180, Building D 4000 Reservoir Rd, NW Washington, DC 20057-1484. Email: hl224@georgetown.edu
pp. 1404-1408

Alternative Splicing: Associating Frequency with Isoforms (PDF)

Anuradha Roy , Department of Computer Science, University of Missouri-Rolla, Rolla, MO 65409, USA
Jennifer L. Leopold , Department of Computer Science, University of Missouri-Rolla, Rolla, MO 65409, USA
Anne M. Maglia , Department of Biological Sciences, University of Missouri-Rolla, Rolla, MO 65409, USA
pp. 1409-1413

A Proposed Statistical Protocol for the Analysis of Metabolic Toxicological Data Derived from NMR Spectroscopy (PDF)

Benjamin J. Kelly , Wright State University, Dept. of Computer Science and Engineering, Dayton, OH 45435
Paul E. Anderson , Wright State University, Dept. of Computer Science and Engineering, Dayton, OH 45435
Nicholas V. Reo , Wright State University, Dept. of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Kettering, OH 45429
Nicholas J. DelRaso , Air Force Research Laboratory, Human Effectiveness Directorate, Wright-Patterson AFB, OH 45433
Travis E. Doom , Wright State University, Dept. of Computer Science and Engineering, Dayton, OH 45435
Michael L. Raymer , Wright State University, Dept. of Computer Science and Engineering, Dayton, OH 45435. michael.raymer@wright.edu
pp. 1414-1418

A Framework for Mass Spectral Quality Assessment without Prior Information (PDF)

Fang-Xiang Wu , Department of Mechanical Engineering, Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr., Saskatoon, SK Canada, S7N 5A9. Email: faw341@mail.usask.ca
Jiarui Ding , Department of Mechanical Engineering, Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr., Saskatoon, SK Canada, S7N 5A9
Guy G. Poirier , Health and Environment Unit, Eastern Quebec Proteomics Center, Laval University Medical Research Center (CHUL), Faculty of Medicine, 2705 Blvd. Laurier, Ste-Foy, Quebec, Canada, G1V 4G2
pp. 1419-1423

Using long fragments to reconstruct RNA backbones (PDF)

Tapani Utriainen , Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden. tapani@cs.chalmers.se
Graham J.L. Kemp , Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden. kemp@cs.chalmers.se
pp. 1424-1428

A Modified Uniformization Method for the Chemical Master Equation (PDF)

Jingwei Zhang , Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106. jwzhang@vt.edu
Layne T. Watson , Department of Computer Science and Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106. ltw@cs.vt.edu
pp. 1429-1433

Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women (PDF)

Jonathan L. Jesneck , Department of Biomedical Engineering; Department of Statistical Science; Computational Biology and Bioinformatics Program; Duke Advanced Imaging Labs
Sayan Mukherjee , Department of Statistical Science; Institute for Genome Sciences and Policy; Department of Computer Science, Duke University
Loren W. Nolte , Department of Biomedical Engineering; Department of Electrical and Computer Engineering
Anna E. Lokshin , Division of Hematology/Oncology; University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213
Jeffrey R. Marks , Institute for Genome Sciences and Policy; Department of Experimental Surgery, Duke University Medical Center
Joseph Lo , Department of Biomedical Engineering; Duke Advanced Imaging Labs; Medical Physics Graduate Program, Duke University, Durham NC 27708, USA. Joseph.Lo@duke.edu
pp. 1434-1438

Partial Least Squares Based Dimension Reduction with Gene Selection for Tumor Classification (PDF)

Guo-Zheng Li , School of Computer Science & Engineering, Shanghai University, Shanghai 200072, China. Email: stamina_gzli@shu.edu.cn
Xue-Qiang Zeng , School of Computer Science & Engineering, Shanghai University, Shanghai 200072, China. Email: zeng@shu.edu.cn
Jack Y. Yang , Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140 USA. Email: jyang@hadron.mgh.Harvard.edu
Mary Qu Yang , National Human Genome Research Institute, National Institutes of Health (NIH), U.S. Department of Health and Human Services, Bethesda, MD 20852 USA. Email: yangma@mail.NIH.GOV
pp. 1439-1444

Functional and Molecular Imaging: Key Components of Personalized Healthcare (PDF)

Steven Seltzer , Philip H. Cook Professor of Medicine, Harvard Medical School, Chief of Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA. sseltzer@partners.org
pp. 1445

Biomedical Literature Mining (PDF)

Xiaohua Hu , Drexel University, College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. thu@ischool.drexel.edu
pp. 1446

An Overview of Bidirectional Promoters (PDF)

Mary Qu Yang , National Human Genome Research Institute, National Institutes Health (NIH), U.S. Department of Health and Human Services, Rockville, MD 20852 U.S.A.; Oak Ridge, DOE. yangma@mail.nih.gov
Laura L. Elnitski , Head of Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes Health (NIH), U.S. Department of Health and Human Services, Rockville, MD 20852 U.S.A. elnitski@mail.nih.gov
pp. 1447

Distributed Wireless Sensors on the Human Body (PDF)

Ruzena Bajcsy , University of California, Berkeley, CA, USA
pp. 1448

Transforming Medicine: Genomics, Bioinformatics, and Human Health (PDF)

Andreas D. Baxevanis , National Human Genome Research Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD USA
pp. 1449

Integrative Biomedical Informatics (PDF)

Brian D. Athey , University of Michigan, and National Center for Integrative Biomedical Informatics
pp. 1450

Bio-Nano-Info Integration for Personalized Medicine (PDF)

Eric Jakobsson , National Center for Biomimetic Nanoconductors, Beckman Institute for Advanced Science and Technology, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign
May D. Wang , Emory-GT Center of Cancer Nanotechnology Excellence, Georgia Tech and Emory University
Linda Molnar , National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, USA
pp. 1452

Using The Soybean Genome Database (SoyGD) To Display and Analyze a 1 Gbp Genome Sequence (PDF)

David Lightfoot , Biotechnology and Genomics, Southern Illinois University at Carbondale
Mengxia Michelle Zhu , Computer Science, Southern Illinois University at Carbondale; Oak Ridge National Laboratory, U.S. Department of Energy
pp. 1453

Biometrics Intelligence Information Systems and Applications (PDF)

Patrick S. P. Wang , College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA. ptawang@MIT.edu
pp. 1454

Knowledge Modeling for High Content Screening of Multimedia Biological Data (PDF)

Arif Ghafoor , School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 USA
J. Paul Robinson , Department of Basic Medical Science, Purdue University, West Lafayette, Indiana 47907 USA
pp. 1455

Reconstructing Signal Transduction from Raw Genomic Data (PDF)

Igor B. Zhulin , Oak Ridge National Laboratory, U.S. Department of Energy
pp. 1456

Lecture on Progress toward Petascale Applications in Bioinformatics and Computational Biology (PDF)

Craig A. Stewart , Indiana University
Malinda Lingwall , Indiana University
David Bader , Georgia Institute of Technology
pp. 1458

Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System (PDF)

Sadaf R. Alam , Oak Ridge National Laboratory, Oak Ridge, USA. alamsr@ornl.gov
Pratul K. Agarwal , Oak Ridge National Laboratory, Oak Ridge, USA. agarwalpk@ornl.gov
Jeffery A. Kuehn , Oak Ridge National Laboratory, Oak Ridge, USA. kuehn@ornl.gov
pp. 1459-1466
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