The Community for Technology Leaders
2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (2009)
Washington, DC USA
Nov. 1, 2009 to Nov. 4, 2009
ISBN: 978-1-4244-5121-0
TABLE OF CONTENTS
Papers

[Front cover] (PDF)

pp. c1

Title page (PDF)

pp. 1

Clustering microarray time-series data using expectation maximization and multiple profile alignment (Abstract)

C.J. Burden , Centre for Bioinformation Sci., Australian Nat. Univ., Canberra, ACT, Australia
N. Subhani , Sch. of Comput. Sci., Univ. of Windsor, Windsor, ON, Canada
A. Ngom , Sch. of Comput. Sci., Univ. of Windsor, Windsor, ON, Canada
L. Rueda , Sch. of Comput. Sci., Univ. of Windsor, Windsor, ON, Canada
pp. 2-7

A comparison of data mining approaches in the categorization of oral anticoagulation patients (Abstract)

I. Giordani , Disco, Univ. of Milano-Bicocca, Milan, Italy
F. Archetti , Disco, Univ. of Milano-Bicocca, Milan, Italy
E. Messina , Disco, Univ. of Milano-Bicocca, Milan, Italy
G. Ogliari , IRCCS Ist. Auxologico Italiano, Univ. of Milano, Milano, Italy
D. Mari , IRCCS Ist. Auxologico Italiano, Univ. of Milano, Milano, Italy
pp. 8-13

Evaluation of Weight Matrix Models in the splice junction recognition problem (Abstract)

C.R.E. Lima , Bioinf. Lab., Fed. Univ. of Technol. Parana, Curitiba, Brazil
L.G. Tavares , Dept. of Electr. Eng., Positivo Univ., Curitiba, Brazil
H.S. Lopes , Bioinf. Lab., Fed. Univ. of Technol. Parana, Curitiba, Brazil
pp. 14-19

Relational clustering and Bayesian networks for linking gene expression profiles and drug activity patterns (Abstract)

I. Giordani , Dept. of Inf. Syst.&Commun., Univ. of Milano Bicocca, Milan, Italy
E. Messina , Dept. of Inf. Syst.&Commun., Univ. of Milano Bicocca, Milan, Italy
F. Archetti , Dept. of Inf. Syst.&Commun., Univ. of Milano Bicocca, Milan, Italy
E. Fersini , Dept. of Inf. Syst.&Commun., Univ. of Milano Bicocca, Milan, Italy
pp. 20-25

A ground truth based comparative study on detecting epistatic SNPs (Abstract)

Lei Song , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
Yue Wang , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
Yongmei Liu , Div. of Public Health Sci., Wake Forest Univ., Wake Forest, NC, USA
C. Langefeld , Div. of Public Health Sci., Wake Forest Univ., Wake Forest, NC, USA
D. Herrington , Dept. of Internal Med., Wake Forest Univ., Wake Forest, NC, USA
Guoqiang Yu , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
D.J. Miller , Dept. of Electr. Eng., Pennsylvania State Univ., State College, PA, USA
Li Chen , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
pp. 26-31

A new distance distribution paradigm to detect the variability of the influenza-A virus in high dimensional spaces (Abstract)

S.C. Kremer , Dept. of Comput.&Inf. Sci., Univ. of Guelph, Guelph, ON, Canada
M. Daoud , Dept. of Comput.&Inf. Sci., Univ. of Guelph, Guelph, ON, Canada
pp. 32-37

CGM: A biomedical text categorization approach using concept graph mining (Abstract)

G. Lushington , Dept. of Electr. Eng.&Comput. Sci., Univ. of Kansas, KS, USA
A. Smalter , Dept. of Electr. Eng.&Comput. Sci., Univ. of Kansas, KS, USA
Min Song , Dept. of Inf. Syst., New Jersey Inst. of Technol., Newark, NJ, USA
Jun Huan , Dept. of Electr. Eng.&Comput. Sci., Univ. of Kansas, KS, USA
S. Bleik , Dept. of Inf. Syst., New Jersey Inst. of Technol., Newark, NJ, USA
pp. 38-43

On a general method for matrix factorisation applied to supervised classification (Abstract)

V. Nikulin , Dept. of Math., Univ. of Queensland, Brisbane, QLD, Australia
G.J. McLachlan , Dept. of Math., Univ. of Queensland, Brisbane, QLD, Australia
pp. 44-49

Domain content based protein function prediction using incomplete GO annotation information (Abstract)

Lirong Tan , Dept. of Comput. Sci., City Univ. of Hong Kong, Hong Kong, China
Hau-San Wong , Dept. of Comput. Sci., City Univ. of Hong Kong, Hong Kong, China
Zhiwen Yu , Sch. of Comput. Sci.&Eng., South China Univ. of Technol., Guangzhou, China
pp. 50-55

Selection of negative examples in learning gene regulatory networks (Abstract)

L. Cerulo , Bioinf. CORE-Lab., Biogem s.c.ar.l., Ariano Irpino, Italy
M. Ceccarelli , Dept. of Biol.&Environ. Studies, Univ. of Sannio, Benevento, Italy
pp. 56-61

A novel Graph-based Selection Wrapper for learning enhancement in a semi-supervised manner (Abstract)

Yi Pan , Dept. of Comput. Sci., Georgia State Univ., Atlanta, GA, USA
Jieyue He , Sch. of Comput. Sci.&Eng., Southeast Univ., Nanjing, China
Zhenggang Chang , Sch. of Comput. Sci.&Eng., Southeast Univ., Nanjing, China
Wei Zhong , Div. of Math&Comput. Sci., Univ. of South Carolina Upstate, Spartanburg, SC, USA
pp. 62-67

A graph algorithm for extracting features from transcription factor binding sites (Abstract)

Junfeng Qu , Dept. of Inf. Technol., Clayton State Univ., Clayton, GA, USA
Chunmei Liu , Dept. of Syst.&Comput. Sci., Howard Univ., Washington, DC, USA
Yinglei Song , Dept. of Math.&Comput. Sci., Univ. of MD Eastern Shore, Princess Anne, MD, USA
A.U. Andy , Dept. of Syst.&Comput. Sci., Howard Univ., Washington, DC, USA
pp. 68-72

Learning parameters for non-coding RNA sequence-structure alignment (Abstract)

Chunmei Liu , Dept. of Syst.&Comput. Sci., Howard Univ., Washington, DC, USA
Yinglei Song , Dept. of Math.&Comput. Sci., Univ. of MD Eastern Shore, Princess Anne, MD, USA
Junfeng Qu , Dept. of Inf. Technol., Clayton State Univ., Morrow, GA, USA
pp. 73-77

Polynomial-time disulfide bond determination using mass spectrometry data (Abstract)

W. Murad , Dept. of Comput. Sci., San Francisco State Univ., San Francisco, CA, USA
R. Singh , Dept. of Comput. Sci., San Francisco State Univ., San Francisco, CA, USA
pp. 79-86

Density-based classification of protein structures using iterative TM-score (Abstract)

J. Galgonek , Dept. of Software Eng., Charles Univ. in Prague, Prague, Czech Republic
D. Hoksza , Dept. of Software Eng., Charles Univ. in Prague, Prague, Czech Republic
pp. 87-92

A global optimization algorithm for protein surface alignment (Abstract)

C. Guerra , Dipt. di Ing. Inf., Univ. di Padova, Padova, Italy
G. Liuzzi , Ist. di Analisi dei Sist. ed Inf., Consiglio Naz. delle Ric., Rome, Italy
P. Bertolazzi , Ist. di Analisi dei Sist. ed Inf., Consiglio Naz. delle Ric., Rome, Italy
pp. 93-100

Upper bounds for foldings in the FCC-HP protein model (Abstract)

A.D. Ullah , Dept. of Comput. Sci., King's Coll. London, London, UK
K. Steinhofel , Dept. of Comput. Sci., King's Coll. London, London, UK
pp. 101-106

Node degree distribution in amino acid interaction networks (Abstract)

S. Balev , LITIS Lab., Le Havre Univ., Le Havre, France
O. Gaci , LITIS Lab., Le Havre Univ., Le Havre, France
pp. 107-112

Matching observed alpha helix lengths to predicted secondary structure (Abstract)

B. Cloteaux , Nat. Inst. of Stand.&Technol., Gaithersburg, MD, USA
N. Serova , Univ. of Maryland, Baltimore, MD, USA
pp. 113-119

Prediction of protein long-range contacts using GaMC approach with sequence profile centers (Abstract)

Jinyan Li , Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
Peng Chen , Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
pp. 128-135

Generalized spring tensor models for protein fluctuation dynamics and conformation changes (Abstract)

Tu-Liang Lin , Comput. Sci. Dept., Iowa State Univ., Ames, IA, USA
Guang Song , Comput. Sci. Dept., Iowa State Univ., Ames, IA, USA
pp. 136-143

Computational testing of protein-protein interactions (Abstract)

A. Kloczkowski , L.H. Baker Center for Bioinf.&Biol. Stat., Iowa State Univ., Ames, IA, USA
R.L. Jeringan , L.H. Baker Center for Bioinf.&Biol. Stat., Iowa State Univ., Ames, IA, USA
A.R. Katebi , L.H. Baker Center for Bioinf.&Biol. Stat., Iowa State Univ., Ames, IA, USA
pp. 144-151

An artificial backbone of hydrogens for finding the conformation of protein molecules (Abstract)

N. Maculan , COPPE, Fed. Univ. of Rio de Janeiro, Rio de Janeiro, Brazil
C. Lavor , Dept. of Appl. Math. (IMECC-UNICAMP), State Univ. of Campinas, Campinas, Brazil
A. Mucherino , COPPE, Fed. Univ. of Rio de Janeiro, Rio de Janeiro, Brazil
L. Liberti , COPPE, Fed. Univ. of Rio de Janeiro, Rio de Janeiro, Brazil
pp. 152-155

Discrimination of thermophilic and mesophilic proteins (Abstract)

T.J. Taylor , Nat. Inst. of Stand.&Technol., Gaithersburg, MD, USA
pp. 156-164

Sequence-based B-cell epitope prediction by using associations in antibody-antigen structural complexes (Abstract)

Liang Zhao , Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
Jinyan Li , Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
pp. 165-172

An efficient geometric build-up algorithm, for protein structure determination with, sparse exact distance data (Abstract)

C. Ernst , Dept. of Math.&Comput. Sci., Western Kentucky Univ., Bowling Green, KY, USA
R.T. Davis , Dept. of Math.&Comput. Sci., Western Kentucky Univ., Bowling Green, KY, USA
Di Wu , Dept. of Math.&Comput. Sci., Western Kentucky Univ., Bowling Green, KY, USA
pp. 173-180

Effect of sidechain anisotropy on residue contact determination (Abstract)

Jing He , Dept. of Comput. Sci., Old Dominion Univ., Norfolk, VA, USA
Weitao Sun , Zhou Pei-Yuan Center for Appl. Math., Tsinghua Univ., Beijing, China
pp. 181-188

How does the periodicity associated with nucleosomal DNA reflect on its intrinsic curvature? (Abstract)

T.M. Nair , Dept. of Biol. Sci.&Comput. Sci./Inf., Indiana Univ. South Bend, South Bend, IN, USA
pp. 189-193

Data mining for biomarker discovery: The time is ripe (Abstract)

Vincent S. Tseng , Dept. Computer Science and Information, Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C.
Hui-Huang Hsu , Dept. Computer Science and Information, Engineering, Tamkang University, Tamsui, Taipei, Taiwan, R.O.C.
Jake Y. Chen , School of Informatics Indiana University - Purdue University, Indianapolis, IN 46202 USA
pp. 195-196

A cooperative feature gene extraction algorithm that combines classification and clustering (Abstract)

Hailong Zhu , Hong Kong Polytech. Univ., Hung Hom, China
M.W. Lingen , Depts. of Pathology, Univ. of Chicago, Chicago, IL, USA
W.P. Kuo , Med. Sch., Lab. for Innovative Translational Technol., Harvard Univ., Boston, MA, USA
J. Lacy , Med. Sch., Lab. for Innovative Translational Technol., Harvard Univ., Boston, MA, USA
Chi Kin Chow , Hong Kong Polytech. Univ., Hung Hom, China
K. Chan , Hong Kong Polytech. Univ., Hung Hom, China
pp. 197-202

Lasso based gene selection for linear classifiers (Abstract)

Weixiang Liu , Biomed. Eng. Lab., Shenzhen Univ., Shenzhen, China
Songfeng Zheng , Dept. of Math., Missouri State Univ., Springfield, MO, USA
pp. 203-208

Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms (Abstract)

Chia-Sheng Chuang , Dept. of Comput. Sci.&Eng., Nat. Taiwan Ocean Univ., Keelung, Taiwan
Zhen-Li Huang , Dept. of Comput. Sci.&Eng., Nat. Taiwan Ocean Univ., Keelung, Taiwan
Tun-Wen Pai , Dept. of Comput. Sci.&Eng., Nat. Taiwan Ocean Univ., Keelung, Taiwan
Chien-Ming Chen , Dept. of Comput. Sci.&Eng., Nat. Taiwan Ocean Univ., Keelung, Taiwan
pp. 209-213

Meta-analysis of cancer microarray data reveals signaling pathway hotspots (Abstract)

Jaewoo Kang , Dept. of Comput. Sci.&Eng., Korea Univ., Seoul, South Korea
P. Chopra , Dept. of Electr. Eng., Columbia Univ., New York, NY, USA
Seung-Mo Hong , Med. Instns., Dept. of Pathology, Johns Hopkins Univ., Baltimore, MD, USA
pp. 214-219

Seed-weighted random walks ranking method and its application to leukemia cancer biomarker prioritizations (Abstract)

Tianxiao Huan , Life Sci. Sch., Shandong Univ., Jinan, China
Xiaogang Wu , Sch. of Inf., Indiana Univ., Indianapolis, IN, USA
J.Y. Chen , Sch. of Inf., Indiana Univ., Indianapolis, IN, USA
Zengliang Bai , Life Sci. Sch., Shandong Univ., Jinan, China
pp. 220-225

A two-phase clustering approach for peak alignment in mining mass spectrometry data (Abstract)

V.S. Tseng , Dept. of Comput. Sci.&Inf. Eng., Nat. Cheng-Kung Univ., Tainan, Taiwan
Lien-Chin Chen , Dept. of Comput. Sci.&Inf. Eng., Nat. Cheng-Kung Univ., Tainan, Taiwan
Chi-Wei Liu , Dept. of Comput. Sci.&Inf. Eng., Nat. Cheng-Kung Univ., Tainan, Taiwan
Yu-Cheng Liu , Dept. of Comput. Sci.&Inf. Eng., Nat. Cheng-Kung Univ., Tainan, Taiwan
pp. 226-230

Mapping short reads to a genome without using hash look-up table algorithm and Burrows Wheeler Transformation (Abstract)

Chia-Han Chu , Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
Chun Yuan Lin , Dept. of Comput. Sci.&Inf. Eng., Chang Gung Univ., Taoyuan, Taiwan
Ming-Yuan Huang , Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
P. Tang , Bioinf. Center, Chang Gung Univ., Taoyuan, Taiwan
Chuan Yi Tang , Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
pp. 232-237

Cluster validation: An integrative method for cluster analysis (Abstract)

H.L. Gerald , Bioinf. Core Facility, Univ. of Kansas, Lawrence, KS, USA
P. Smith , Univ. of Kansas Med. Center, KS, USA
B.S. Adagarla , Bioinf. Core Facility, Univ. of Kansas, Lawrence, KS, USA
M. Visvanathan , Bioinf. Core Facility, Univ. of Kansas, Lawrence, KS, USA
pp. 238-242

A topology-sharing based method for protein function prediction via analysis of protein functional association networks (Abstract)

Hui Jiang , Dept of Comp Sc&Engg, York Univ., Toronto, ON, Canada
A. Emili , Centre for Cellular&Biomol. Res., Univ. of Toronto, Toronto, ON, Canada
Pingzhao Hu , Dept of Comp. Sc&Eng., Univ. of Toronto, Toronto, ON, Canada
pp. 243-248

Identification of structured motifs (Abstract)

Huitao Sheng , Dept. of Electr. Eng.&Comput. Sci., Syracuse Univ., Syracuse, NY, USA
C. Mohan , Dept. of Electr. Eng.&Comput. Sci., Syracuse Univ., Syracuse, NY, USA
K. Mehrotra , Dept. of Electr. Eng.&Comput. Sci., Syracuse Univ., Syracuse, NY, USA
R. Raina , Dept. of Biol., Syracuse Univ., Syracuse, NY, USA
pp. 249-253

Mining association rules among gene functions in clusters of similar gene expression maps (Abstract)

V. Megalooikonomou , Dept. of Comput.&Inf. Sci., Temple Univ., Philadelphia, PA, USA
O. Bodenreider , Lister Hill Nat. Center for Biomed. Commun., U.S. Nat. Libr. of Med., Washington, DC, USA
D. Smith , Dept. of Mol.&Med. Pharmacology, UCLA, CA, USA
Z. Obradovic , Center for Inf. Sci.&Technol., Temple Univ., Philadelphia, PA, USA
Li An , Dept. of Comput.&Inf. Sci., Temple Univ., Philadelphia, PA, USA
pp. 254-259

EpICS: A system for genome-wide epistasis and genetic variation analysis using protein-protein interactions (Abstract)

A. Bhattacharjee , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
H. Jamil , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
K.Z. Sultana , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
pp. 261-266

PathMapper-an integrative approach for oncogene pathway identification (Abstract)

M. Visvanathan , Bioinf. Core Facility, Univ. of Kansas, Lawrence, KS, USA
A. Vijayan , Sch. of Biotechnol., Amrita Vishwa Vidyapeetham, Kollam, India
G.H. Lushington , Bioinf. Core Facility, Univ. of Kansas, Lawrence, KS, USA
S. Subramaniam , Sch. of Biotechnol., Amrita Vishwa Vidyapeetham, Kollam, India
B.G. Nair , Sch. of Biotechnol., Amrita Vishwa Vidyapeetham, Kollam, India
B.E. Skariah , Sch. of Biotechnol., Amrita Vishwa Vidyapeetham, Kollam, India
pp. 267-271

Gene prioritization using a probabilistic knowledge model (Abstract)

Shuguang Wang , Intell. Syst. Program, Univ. of Pittsburgh, Pittsburgh, PA, USA
S. Visweswaran , Dept. of Biomed. Inf., Univ. of Pittsburgh, Pittsburgh, PA, USA
M. Hauskrecht , Dept. of Comput. Sci., Univ. of Pittsburgh, Pittsburgh, PA, USA
pp. 272-278

Towards automatic extraction of social networks of organizations in PubMed abstracts (Abstract)

G. Gonzalez , Dept. of Biomed. Inf., Arizona State Univ., Phoenix, AZ, USA
S. Jonnalagadda , Lnx Res. LLC, Orange, CA, USA
P. Topham , Lnx Res. LLC, Orange, CA, USA
pp. 279-286

MetNetGE: Visualizing biological networks in hierarchical views and 3D tiered layouts (Abstract)

Ming Jia , Dept. of Electr.&Comput. Eng., Iowa State Univ., Ames, IA, USA
S. Swaminathan , Dept. of Genetics Dev.&Cell Biol., Iowa State Univ., Ames, IA, USA
J. Dickerson , Dept. of Electr.&Comput. Eng., Iowa State Univ., Ames, IA, USA
E.S. Wurtele , Dept. of Genetics Dev.&Cell Biol., Iowa State Univ., Ames, IA, USA
pp. 287-294

NLP-NG -- A new NLP system for biomedical text analysis (Abstract)

J. Satterley , Biol. Knowledge Lab., Northeastern Univ., Boston, MA, USA
R.P. Futrelle , Biol. Knowledge Lab., Northeastern Univ., Boston, MA, USA
T. McCormack , Biol. Knowledge Lab., Northeastern Univ., Boston, MA, USA
pp. 296-301

Speech recognition in a dialog system for patient health monitoring (Abstract)

J. Quinn , Univ. of Rochester, Rochester, NY, USA
G. Ferguson , Univ. of Rochester, Rochester, NY, USA
J. Allen , Univ. of Rochester, Rochester, NY, USA
M. Swift , Univ. of Rochester, Rochester, NY, USA
L. Galescu , Inst. for Human&Machine Cognition, Pensacola, FL, USA
pp. 302-307

Investigating and annotating the role of citation in biomedical full-text articles (Abstract)

N. Frid , Univ. of Wisconsin-Milwaukee, Milwaukee, WI, USA
Hong Yu , Univ. of Wisconsin-Milwaukee, Milwaukee, WI, USA
S. Agarwal , Univ. of Wisconsin-Milwaukee, Milwaukee, WI, USA
pp. 308-313

Automated classification of radiology reports for acute lung injury: Comparison of keyword and machine learning based natural language processing approaches (Abstract)

I. Solti , Dept. of Med. Educ.&Biomed. Inf., Univ. of Washington, Seattle, WA, USA
M.M. Wurfel , Div. of Pulmonary&Critical Care, Univ. of Washington, Seattle, WA, USA
C.R. Cooke , Div. of Pulmonary&Critical care, Univ. of Michigan, Ann Arbor, MI, USA
Fei Xia , Dept. of Linguistics, Univ. of Washington, Seattle, WA, USA
pp. 314-319

Information flow in intensive care narratives (Abstract)

H. Lundgren-Laine , Dept. of Nursing Sci., Univ. of Turku, Turku, Finland
H. Suominen , Dept. of Inf. Technol., Univ. of Turku, Turku, Finland
T. Salakoski , Dept. of Inf. Technol., Univ. of Turku, Turku, Finland
S. Salantera , Dept. of Nursing Sci., Univ. of Turku, Turku, Finland
H. Karsten , Dept. of Inf. Technol., Abo Akad. Univ., Abo, Finland
pp. 325-340

Evaluating the weighted-keyword model to improve clinical question answering (Abstract)

J. Ely , Univ. of Iowa, Iowa City, IA, USA
Hong Yu , Univ. of Wisconsin-Milwaukee, Milwaukee, WI, USA
Yong-Gang Cao , Univ. of Wisconsin-Milwaukee, Milwaukee, WI, USA
pp. 331-335

Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models (Abstract)

B. Anchang , Inst. of Functional Genomics&Bioinf., Univ. of Regensburg, Regensburg, Germany
M. Sadeh , Inst. of Functional Genomics&Bioinf., Univ. of Regensburg, Regensburg, Germany
A. Tresch , Dept. of Chem.&Biochem., Ludwig-Maximilians-Univ. Muenchen, Munich, Germany
R. Spang , Inst. of Functional Genomics&Bioinf., Univ. of Regensburg, Regensburg, Germany
M.O. Vlad , Dept. of Chem., Stanford Univ., Stanford, CA, USA
P.J. Oefner , Inst. of Functional Genomics&Bioinf., Univ. of Regensburg, Regensburg, Germany
J. Jacob , Inst. of Functional Genomics&Bioinf., Univ. of Regensburg, Regensburg, Germany
pp. 337

Constructing gene-expression based survival prediction model for Non-Small Cell Lung Cancer (NSCLC) in all stages and early stages (Abstract)

Ying-Wooi Wan , Lane Dept. of CSEE, West Virginia Univ., Morgantown, WV, USA
N.L. Guo , Lane Dept. of CSEE, West Virginia Univ., Morgantown, WV, USA
pp. 338

The mutation at H254 of organophosphorus hydrolase increases the substrate specificity of profenofos (Abstract)

Chu-His Fan , Dept. of Microbiol., Dev. Center for Biotechnol., Taipei, Taiwan
Chia-Chi Lin , Dept. of Microbiol., Dev. Center for Biotechnol., Taipei, Taiwan
Shih-Chong Tsai , Dept. of Microbiol., Dev. Center for Biotechnol., Taipei, Taiwan
Kuen-Jou Wei , Dept. of Microbiol., Dev. Center for Biotechnol., Taipei, Taiwan
pp. 339

Information- and graph-theoretic analysis of bacterial two component system (Abstract)

Kwangmin Choi , Sch. of Inf.&Comput., Indiana Univ., Bloomington, IN, USA
Sun Kim , Sch. of Inf.&Comput., Indiana Univ., Bloomington, IN, USA
pp. 340

Knowledge management for systems biology and translational medicine. Experiences from the EU BioBridge project (Abstract)

P. Krubasik , Biomax Inf. AG, Martinsried, Germany
J. Villa i Freixa , Res. Unit on Biomed. Inf., Univ. Pompeu Fabra, Barcelona, Spain
D. Maier , Biomax Inf. AG, Martinsried, Germany
M. Hernandez , Res. Unit on Biomed. Inf., Univ. Pompeu Fabra, Barcelona, Spain
S. Losko , Biomax Inf. AG, Martinsried, Germany
pp. 341

Mining gene-related information from biomedical literature (Abstract)

C.O. Tudor , Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
K. Vijay-Shanker , Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
C.J. Schmidt , Animal&Food Sci., Univ. of Delaware, Newark, DE, USA
pp. 342

Computational analysis using CisFind of the 3'UTR of cytosolic Glutamine synthetase genes involved in posttranscriptional regulation (Abstract)

C. Sengupta-Gopalan , Dept. of Plant&Environ. Sci., New Mexico State Univ., Las Cruces, NM, USA
D. Ranjan , Dept. of Comput. Sci., Old Dominion Univ., Norfolk, VA, USA
B. Vasudevan-Simon , Grad. Program in Mol. Biol., New Mexico State Univ., Las Cruces, NM, USA
P.K. Yelavarthi , Dept. of Comput. Sci., New Mexico State Univ., Las Cruces, NM, USA
pp. 343

iMOWSE, a scoring scheme bridging in silico and in vitro digestion in peptide mass fingerprints (Abstract)

S.K.-W. Tsui , Sch. of Biomed. Sci., Chinese Univ. of Hong Kong, Hong Kong, China
Ka-Kit Leung , Hong Kong Bioinf. Centre, Chinese Univ. of Hong Kong, Hong Kong, China
pp. 344

The classification of a protein from its primary sequence using functional and structural-specific PSSMs in quantitative measurement (Abstract)

Kyung Dae Ko , Dept. of Biol., Penn State Univ., University park, PA, USA
D.B. van Rossum , Dept. of Biol., Penn State Univ., University park, PA, USA
R.L. Patterson , Dept. of Biol., Penn State Univ., University park, PA, USA
Yoo Jin Hong , Dept. of CSE, Penn State Univ., University park, PA, USA
pp. 345

Development of dbOGAP: A bioinformatics resource of O-GlcNAcylated proteins and site prediction (Abstract)

G.W. Hart , Sch. of Med., Johns Hopkins Univ., Baltimore, MD, USA
Hongfang Liu , Dept. of Biostat., Bioinf.&Biomath., Georgetown Univ. Med. Center, Washington, DC, USA
Zhang-Zhi Hu , Dept. of Oncology, Georgetown Univ. Med. Center, Washington, DC, USA
M. Torii , ISIS Center, Georgetown Univ. Med. Center, Washington, DC, USA
Jinlian Wang , Dept. of Oncology, Georgetown Univ. Med. Center, Washington, DC, USA
pp. 346

Predicting functional sites in biological sequences using canonical correlation analysis (Abstract)

C.H. Wu , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
A.J. Gonzalez , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
Li Liao , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
pp. 347

Prediction of biological pathways with integrated information (Abstract)

C.J. Schmidt , Dept. of Animal&Food Sci., Univ. of Delaware, Newark, DE, USA
K.S. Decker , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
A.J. Stachnik , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
Li Jin , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
pp. 348

Gene-set Cohesion Analysis Tool (GCAT): A literature based web tool for calculating functional cohesiveness of gene groups (Abstract)

M.W. Berry , Dept. of Comput. Sci., Univ. of Tennessee, Knoxville, TN, USA
Lijing Xu , Bioinf. Program, Univ. of Memphis, Memphis, TN, USA
E.O. George , Dept. of Math., Univ. of Memphis, Memphis, TN, USA
R. Homayouni , Bioinf. Program, Univ. of Memphis, Memphis, TN, USA
K.E. Heinrich , Computable Genomix LLC, Memphis, TN, USA
N.A. Furlotte , Comput. Sci. Dept., Univ. of California, Los Angeles, CA, USA
pp. 349

Mining impact of protein modifications on protein-protein interactions from literature (Abstract)

J. Nchoutmboube , Delaware Biotechnol. Inst., Univ. of Delaware, Newark, DE, USA
K. Vijay-Shanker , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
C.H. Wu , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
C. Arighi , Delaware Biotechnol. Inst., Univ. of Delaware, Newark, DE, USA
C.O. Tudor , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
A. Siu , Dept. of Comput.&Inf. Sci., Univ. of Delaware, Newark, DE, USA
pp. 350

Discovery of cancer-related new drug target proteins from re-constructed human disease network based on protein-protein interaction netowk (Abstract)

Yoon Kyeong Lee , Dept. of Bio&Inf. Technol., Chungbuk Nat. Univ., Cheongju, South Korea
Hak Yong Kim , Dept. of Biochem., Chungbuk Nat. Univ., Cheongju, South Korea
pp. 351

Microbial dynamics of human obesity (Abstract)

M. Pop , Dept. of Comput. Sci., Univ. of Maryland - Coll. Park, College Park, MD, USA
J.R. White , Appl. Math.&Sci. Comput. Program, Univ. of Maryland - Coll. Park, College Park, MD, USA
pp. 352

SAMON: Sleep apnea monitoring (Abstract)

A. Goni , Fac. de Inf., Univ. of the Basque Country, Donostia, Spain
A. Illarramendi , Fac. de Inf., Univ. of the Basque Country, Donostia, Spain
J. Bermudez , Fac. de Inf., Univ. of the Basque Country, Donostia, Spain
A. Burgos , Fac. de Inf., Univ. of the Basque Country, Donostia, Spain
pp. 353

Inhibition study of the SOD-Cu/Zn of Taenia solium by computational methods (Abstract)

P. Garcia-Gutierrez , Dept. de Quim., Univ. Autonoma Metropolitana-Iztapalapa, Mexico City, Mexico
A. Landa , Dept. de Microbiologia y Parasitologia, Univ. Nac. Autonoma de Mexico, Mexico City, Mexico
A. Rojo-Dominguez , Dept. de Quim., Univ. Autonoma Metropolitana-Iztapalapa, Mexico City, Mexico
pp. 354

Learning a highly resolved tree of phenotypes using genomic data clustering (Abstract)

R. Clarke , Dept. of Oncology, Georgetown Univ. Med. Center, Georgetown, WA, USA
Yue Wang , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
Yuanjian Feng , Dept. of Electr.&Comput. Eng., Virginia Polytech. Inst.&State Univ., Blacksburg, VA, USA
D.J. Miller , Dept. of Electr. Eng., Pennsylvania State Univ., State College, PA, USA
pp. 355

Physical Markov model for protein structure prediction (Abstract)

C.M. Fortmann , Mater. Sci. Dept., Stony Brook Univ., Stony Book, NY, USA
Yeona Kang , Mater. Sci. Dept., Stony Brook Univ., Stony Book, NY, USA
pp. 356

Integration of mutual information and text mining methods for extracting gene-gene interactions from gene expression data (Abstract)

L.K. Matukumalli , Dept. of Bioinf.&Comput. Biol., George Mason Univ., Manassas, VA, USA
J.L. Solka , Dept. of Bioinf.&Comput. Biol., George Mason Univ., Manassas, VA, USA
D.H. Millis , Dept. of Bioinf.&Comput. Biol., George Mason Univ., Manassas, VA, USA
pp. 357

Correlation between computed equilibrium secondary structure free energy and siRNA efficiency (Abstract)

P. Bhattacharjee , Dept. of Comput. Sci.&Applic., Virginia Tech, Blacksburg, VA, USA
L.S. Heath , Dept. of Comput. Sci.&Applic., Virginia Tech, Blacksburg, VA, USA
N. Ramakrishnan , Dept. of Comput. Sci.&Applic., Virginia Tech, Blacksburg, VA, USA
A.V. Onufriev , Dept. of Comput. Sci.&Phys., Virginia Tech, Blacksburg, VA, USA
pp. 358

Toward real time image to mesh conversion for non rigid registration (Abstract)

N. Chrisochoides , Dept. of Comput. Sci., Coll. of William&Mary, Williamsburg, VA, USA
P. Foteinos , Dept. of Comput. Sci., Coll. of William&Mary, Williamsburg, VA, USA
A. Chernikov , Dept. of Comput. Sci., Coll. of William&Mary, Williamsburg, VA, USA
pp. 359

Author index (PDF)

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