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 (Abstract)

Mary Qu Yang , National Human Genome Research Institute, National Institutes Health (NIH), U.S. Department of Health and Human Services, Rockville, MD, U.S.A.;
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, U.S.A.
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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