RECOMB 2007

Poster Presenters

RECOMB 2007 POSTER PRESENTERS

Session A
Sunday, April 22: 5:30 pm – 7:30 pm
Monday, April 23: 7:30 am – 5:00pm

Sahar Abubucker, Makedonka Mitreva

Gene Identification and Functional Classification of the Hookworm Genome

Gulsah Altun, Hae-Jin Hu, Stefan Gremalschi, Yi Pan, Robert W Harrison

Support Vector machine and Clique based Approach for Feature Selection in Protein Profiles

Trever Blackstone, Yuanan Diao, Javier Arsuaga

Linking of Chromosomes During Interphase

Xuefei Wang, Bai-Lian Li, Cheryl L. Willman, Susan R. Atlas

Identification, combination and implementation of linguistic fuzzy rules in acute leukemia using gene expression and covariate data

Markus Bauer, Gunnar W. Klaau, Knut Reinert

Accurate Sequence-Structure Alignment of Multiple RNA Sequences

Andrew Bordner, Andrey A. Gorin

Structural information greatly improves the accuracy of protein interactions inferred from homology

Robert Bradley, Ian Holmes

RNA Structure Evolution and Transducer Composition

Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant Honavar

Glycosylation Site Prediction Using Machine Learning Approaches

Sheng-Da Hsu, Paul Wei-Che Hsu, Hsien-Da Huang

miRTar: a fast and efficient microRNA target prediction web server

Tzong Yi Lee, Yung-Hao Wong, Hsien-Da Huang

PTM-X: an Integrated Platform for Identifying Protein Post-Translational Modification Sites

Tzu-Hao Chang, Hsien-Da Huang, Jorng-Tzong Horng, Li-Ching Wu

RNASMotif: A Web Server for Discovering RNA Structural Motif in Unaligned Sequences

Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert

A statistical approach using network structure in the prediction of protein characteristics

Allen Chen, Jack Chen, Lynn Hlatky, Caoan Wang, Dan Levy, Mariel Vazquez, Rainer Sachs

Human X chromosome reveals pronounced early population subdivisions and recent bottlenecks

Ting-Ying Chien, Chien-Yu Chen, Darby Tein-Hao Chang, Chen-Ming Hsu

Deriving Functional Signatures from Protein Sequences by Iterative Pattern Mining

Eunjung Cho, Anu G. Bourgeois

Efficient Molecular Dynamics (MD) simulation on Field Programmable Gate Array (FPGA)s with MultiGrid method

Hideo Imamura, Jason H. Persampieri, Jeffrey Chuang

Sequences Conserved by Selection across Mouse and Human Malaria Species

Adriana Climescu-Haulica, Michelle Quirk

A Fuzzy Games Approach of RNA-based Gene Regulation

Ofir Davidovich, Gad Kimmel, Eran Halperin, Ron Shamir

Maximizing SNP Prediction Accuracy Increases the Power in Association Studies

Michael Terribilini, Jeffry Sander, Jae-Hyung Lee, Robert L. Jernigan, Vasant Honavar, Drena Dobbs

Comparing Sequence vs Structure-based Predictions of RNA Binding Sites in Proteins

Henrik Bengtsson

Anonymous in-house and public reference sets for copy-number analysis of a small number of Affymetrix SNP arrays

Sherief El-Shazly, S. Ahman, A.S. Mustafa, R. Al-Attiya, D. Krajci

In vitro and in vivo expression, immunological characterization and invasin-like role of mammalian cell entry (Mce) proteins encoded by mce3 operon of Mycobacterium tuberculosis

Xiaodan Fan, Jun Zhu, Eric E. Schadt, Jun S. Liu

On Criterions of Multiple Alignment Quality

Vanathi Gopalakrishnan

Prior Knowledge for Discovery Proteomics Data Interpretation

B A Gowri Shankar, Michael Charleston, Michael Murray, David Hibbs

Cytochrome P450 Structures _ Structural and Phylogenetic analysis

Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander Hartemink

Informative Positional Priors Improve De Novo Motif Discovery

Gregory J. Hather, Terence P. Speed, Mary C. Wildermuth

A semiparametric mixture model for identifying cis-acting regulatory elements

Andrew Uzilov, Mitchell Skinner, Chris Mungall, Ian Holmes

Enhancements to the GBrowse Genome Browser

Minmei Hou, Robert Harris, Webb Miller

A new seeding strategy for DNA alignment

Jia-Ming Chang, Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu

PSLDoc:Protein Subcellular Localization prediction based on Document classification

Kuan-Hua Jen, Hsi-Yuan Huang, Chia-Hung Chien, Hsien-Da Huang,Tsu-Hao Wang

Heart Aged-Match between Human Fetus and Mouse Fetus Based on Microarray Gene Expression Profiles

Wolfgang Lehrach, Dirk Husmeier

Inference in Phylogenetic Factorial Hidden Markov Models

Rene Hussong, Andreas Hildebrandt

The Isotope Wavelet: A Signal Theoretic Framework for Analyzing Mass Spectrometry Data

Hyunmin Kim,
Katherina J. Kechris, Lawrence Hunter

Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP enriched Regions

Ivy Jansen, Kerstin Koch, Natalia Kwasnikowska, Tomasz Burzykowski

An Algorithm to Find Co-Regulated Gene Clusters: Adjustment for Random Variability of Gene Expression Data.

Boris Kiryutin, Alexandre Souvorov, Tatiana Tatusova

ProSplign-Protein to Genomic Alignment Tool

Segun Fatumo, Kitiporn Plaimas, Jan-Phllip Stier, Ezekiel Adebiyi, Marcus Oswald, Roland Eils, Rainer Konig

Computational Identification of Essential Reactions in Plasmodium falciparum to yield Potential Drug Targets

Itamar Landau, Nathan Shayefar, Xia Hua, Juliet Portillo, Janella Slaga, Mariel Vazquez

Modeling DNA unknotting by type II topoisomerases

Kwang Hee Lee, Sunghoon Lee, Pan-Gyu Kim, Kiejung Park

BioCell : A Visualization System for Protein Interactions and Comparmentations

Christina Chaivorapol, Marica Grskovic, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos

Systematic Identification Of Cis-Acting Sequences Reveals NF-Y As A Regulator Of Embryonic Stem Cells

Galih Kunarso, Kee-Yew Wong, Lawrence W. Stanton, Leonard Lipovich

Experimental validation of computationally identified novel transcriptional units in mouse embryonic stem cells

James Long, Tom Marr, Shawn Houston

A Simple Genbank Search Engine

Nitin Bhardwaj, Hui Lu

Membrane-Binding Mechanism of Peripheral Proteins Elucidated by Integration of Bioinformatics Prediction and Molecular Dynamics Simulations

Valentina A. Boeva, Mireille Regnier, Mikhail A. Roytberg, Vsevolod J. Makeev

Statistics of multiple PWM occurrences in biopolymer sequences

Jochen Maydt, Thomas Lengauer

Handling Gaps in Recombination Analysis Using RECCO

Ali Navid, Eivind Almaas

Analysis of systems properties of the Yersinia pestis biovars using a genome-scale constraint based model

Elon Portugaly, Steve Johnson, Matan Ninio, Sean R. Eddy

Improved HMMERHEAD for Better Sensitivity

Martin Paluszewski, Pawel Winter

Branch and Bound Algorithm for Protein Structure Prediction Using Efficient Bounding: Poster Abstract

Hongseok Tae, Hyeweon Nam, Jaekyang Song, Kiejung Park

A Web Based Polyketide Analysis System for Modular Polyketide Synthases

Thomas Kelder, Alexander R. Pico, Martijn van Iersel, Bruce Conklin, Chris Evelo

WikiPathways: Pathway Editing for the People

Katherine S. Pollard, Sofie R. Salama, Jakob S. Pedersen, Sol Katzman, Bryan King, Adam Siepel, David Williamson, Haller Igel, Manuel Ares Jr., Pierre Vanderhaeghen, David Haussler

The Fastest Evolving Regions in the Human Genome

Iosifina Pournara, Lorenz Wernisch

Time-series factor analysis for reconstructing transcription factor activities

Melissa Freedenberg, Chanchala Kaddi, Chang F. Quo, May D. Wang

Review and Comparison of Systems Biology Simulation Tools for Translational Research

Nini Rao, Xu Lei, Zhenglong Ren

A Novel Sliding Window Strategy for Accurate Location of Coding Regions Based on Power Spectrum Analysis

Rohit Reja, Gaurav Kumar Maheshwari

Homology modeling of human protein cathepsin A

Shuchi Nagar, Sanchita Mullick, Subhendu Mukherjee, Arup Mukherjee, Achintya Saha

Pharmacophore Mapping for MCF Cell Inhibition of Arylbenzothiopene Derivatives

Konrad Scheffler, Cathal Seoighe

PARRIS: a PARtitioning approach for Robust Inference of Selection

Dina Schneidman-Duhovny, Yuval Inbar Ruth Nussinov, Haim J. Wolfson

Prediction of symmetric assemblies by docking

Xinwei She, Jason Johnson, Ronghua Chen

Identification of Mammalian Housekeeping Genes

Jing Shi, Michael G. Walker, Stanley N. Cohen

Improving gene correlation estimation by applying filters for low-variability genes

Mingzhou (Joe) Song, Eric R. Lance, Chris K. Lewis, Elissa J. Chesler, Roumyana Kirova, Susan E. Bergeson

Maximum Likelihood Quantization and Logical Networks for Modeling Biological Interactions

Kevin Sullivan, Micah Hamady, Rob Knight, William S. Marshall, Anastasia Khvorova, Amanda Birmingham

Fast-FIND Sequence Similarity Search: An Improved Approach for siRNA Design

Shuying Sun, Shili Lin

Classifying differentially methylated genes in breast cancer cell lines using the reversible jump Markov Chain Monte Carlo method

Y-h. Taguchi, Michael Gromiha

Recognition of protein folds using amino acid occurrence

Hisamitsu Akiba, Y-h. Taguchi

Nonmetric distances for Barcode of Life

Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato

Tools for Simulating and Analyzing RNA Folding Kinetics

Sophie Tanny

Nonrandom dispersal of functionally related genes in eukaryotic genomes: Arabidopsis and mouse

Yuanyuan Tian, Richard C. McEachin, Carlos Santos, David J. States, Jignesh M. Patel

SAGA: Subgraph Matching Tool for Biological Graphs

Kentaro Tomii

Statistical Features of the Residue Environment in Proteins

Tamir Tuller, Sagi Snir

The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks

Igor Ulitsky, Ron Shamir

Joint analysis of genetic and physical interactions in yeast reveals pathway redundancy and protein essentiality

Thiago M. Venancio, Ricardo DeMarco, Katia C. Oliveira, Giulliana T. Almeida, Sergio Verjovski-Almeida

Gene expression analyses in the parasite Schistosoma mansoni using oligonucleotide microarrays

Iain Wallace, Desmond Higgins

Supervised multivariate analysis of sequence groups to identify specificity determining residues

Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev

A Genome-Wide Study of Gene Duplication and Loss Histories

Bartek Wilczynski, Jerzy Tiuryn

Reconstructing Regulatory Networks from Expression Data using Stochastic Logical Networks

Lin Xu, Fa Zhang, Dongbo Bu, Bo Yuan

A novel query-profile alignment algorithm for homology modeling

Chenggang Yu, Valmik Desai, Nela Zavaljevski, Seth Johnson, Fred Stevens, Jaques Reifman

PIPA: A Pipeline for High-Throughput Protein Function Annotation

Zheng Zhang, Jon Sorenson, Joel Malek

Finding indels in resequencing

Xin Zhou, David P. Tuck

Gene Selection Using a New Error Bound for Support Vector Machines

Andrey Kalinin, Nikolai Daraselia

Reconstruction of pathways for instracellular receptor signaling

Paul Yoo, Bing Bing Zhou, Albert Y. Zomaya

The Role of Long-Range Interaction in Protein Secondary Structure
Prediction

Session B
Tuesday, April 24: 3:30 pm – 5:30 pm
Wednesday, April 25: 7:30 am – 3:00pm

Anna Larsson, Satoshi Okawa, Dag Ahren	Metabolic Network and Gene Duplications in Neurospora Crassa
Iris Antes, Thomas Lengauer	Prediction of Bound MHC-peptide Conformations
Perit Bezek, O. Sinan Sarac, Volkan Atalay, Rengul Cetin-Atalay	Spectral Clustering based Subsequence Feature Map for Protein Classification
Nuno Bandeira, Karl Clauser, Pavel Pevzner	Modification-tolerant Shotgun Protein Sequencing of a Snake Venom Proteome
Gurkan Bebek, Keiji Takaomoto	Accurate Elimination of False Protein-Protein Interactions
Guillaume Bourque, Vinsensius B. Vega, Yijun Ruan, Chia-Lin Wei, Edison T. Liu	Genome-wide Binding Site Map of Mammalian Transcription Factors Reveals Rapid Turnover
Yu Lin, Yantao Qiao, Chungong Yu, Shiwei Sun, Dongbo Bu	Peptide Identification Through The Distribution of Fragmentation Events During Mass Spectrometry
Liad Carmel-Ulitsky, Igor Ulitsky, Rachel Kupiec, Miguel Weil	Meta-Analysis of Gene Expression during Neural Progenitor Cell Differentiation
Anu Chakicherla, Ying Chen	A Method to Detect Differential Gene Expression in Cross-species Hybridization Experiments
Anu Chakicherla, Martha Ligon Dang, Virginia Rodriguez, J. Norman Hansen, Adam Zemla	Function prediction of an interacting protein pair using domain fusion analysis: SpaR and SpaK
Gal Chechik, Aviv Regev, Daphne Koller	Combining Heterogeneous Data and Network Motifs for Filling Missing Enzymes in Yeast Metabolic Pathways
Liang Chen, Tiejun Tong, Hongyu Zhao	False Discovery Control for Genetic Dissection of Transcriptional Regulation
Chien-Yu Chen, Chen-Ming Hsu, Chung-Tsai Su, Ai-Mi Chen, Yung-Chia Chen, Baw-Jhiune Liu	Prediction of DNA-binding Regions by Detecting Intra-molecular Interactions with Pattern Mining
Soo-Young Cho, Hye-Myeong Seo, Young-Seek Lee	Prediction for Tissue Specific Gene and Gene Regulatory Network in Mouse Embryonic Stem Cell
Rezaul Alam Chowdhury, Hai-Son Le, Vijaya Ramachandran	Cache-oblivious String Algorithms for Bioinformatics
Myungguen Chung, Minho Kim, Hoyoul Jung, Pora Kim, Seonhee Park, Soojun Park	The Combination Pattern Extraction of Regulatory Motif by Using the Longest Common Prefix
The MouseFunc Consortium, Murat Tasan	MouseFunc: A Competition for Mouse Gene Function Prediction
Malarmathy Ramachandran, Zakaria A Almsherqi, Yuru Deng	A novel mitochondrial inner membrane protein `Miticulon` controls cristae morphology.
Peter Zaback, Jeffry D. Sander, J. Keith Joung, Daniel F. Voytas, Drena Dobbs	Designing C2H2 Zinc Finger Proteins to Target Specific Sites in Genomic DNA
Matthew D. Dyer, T.M. Murali, Bruno W. Sobral	Computational Prediction of Host-Pathogen Protein Interactions
Frank Emmert-Streib, Lin Chen, John D. Storey	FDR Controlled Topological Core of the Transcriptional Regulatory Network of Saccharomyces cerevisiae
Yifat Felder, Tamir Tuller, Nana Ginzbourg, Udi Rubinstein, Michael Gurevich, Anat Achiron	A new approach for inferring regulatory networks from literature and gene expression measurements
Menachem Fromer, Chen Yanover, Julia Shiman, Yair Weiss	A Probabilistic Approach to the Design of Structural Selectivity of Proteins
Cheol-Min Ghim, Eivind Almaas	Combinatorial Principles of Feedback Control in Biochemical Networks
B A Gowri Shankar, B. Vasundhar, K. Sekar	Ion-Pair in Non-Redundant Protein Structures
Allister Bernard, David Vaughn, Alexander J. Hartemink	PROCTOR: An algorithm for reconstructing the internal interaction topology of protein complexes
Ting Wang, David Haussler	Systematic Study of the Evolution and Function of Human Regulatory Non-coding Sequences
Natalia Poluliakh, Harada Hajime, Wataru Fujibuchi, Paul Horton	SHOE: A Promoter Analysis Tool
Shawn Houston, Dan Cardin, Jim Long	The Compute Portal Project
Zehra Cataltepe, Ugur Ayan, Eser Aygun	Protein Function Prediction Using Motifs, Sequence Features, Alignment Scores
Adriano V. Werhli, Dirk Husmeier	Reverse engineering gene regulatory networks with Bayesian networks from expression data combined with multiple sources of biological prior knowledge
Daniel H. Huson, Tobias Dezulian, Markus Franz, Christian Rausch, Daniel C. Richter, Regula Rupp	Dendroscope: An interactive viewer for large phylogenetic trees
Chris Hyland, Glenn McConkey, David R. Westhead	Comparative Analysis of Metabolic Networks using Gene Expression Data
Shin Lin, Benilton S. Carvalho, Dan Arking, Aravinda Chakravarti, Rafael A. Irizarry	Validation of a Novel Empirical Bayes Method for SNP Calling on Arrays
Ho-Youl Jung, Minho Kim, Myungguen Chung, Pora Kim, Seo-hee Park, Soo-Jun Park	XpressVista: Expression Analysis and Visualization Tool
Minho Kim, Ho-Youl Jung, Myungguen Chung, Pora Kim, Seo-Hee Park, Soo-Jun Park	Regression-based Clustering of Short-Time Course Gene Expression Datasets
Pan-Gyu Kim, Daesang Lee, Chang-Hyuk Kwon, Young-Lyeol Yang, Kiejung Park	PAMES: Pathway Mapping and Editing System
Dennis Kostka, Martin Vingron	Reconstructing phenotypical hierarchies: a linear programming approach
Harri Lahdesmaki, Antti Larjo, Olli Yli-Harja, Ilya Shmulevich	Inferring Dynamic Signalling Networks from Steady State Measurements
Katherina Kechris, Hao Li	Incorporating Phylogenetic Conservation to Detect Motifs that Correlate with Expression
Jia Zheng, Hon Wai Leong, Haixu Tang	An Improved Algorithm for Error Correction of Reads in DNA Fragment Assembly
Brad Sickler, Ripan S. Malhi, Jessica Satkoski, Debbie George, Sree Kanthaswamy, David Smith, Dawei Lin	MAMUPipe: A Computational Pipeline for Identifying Novel SNP/SIDP in Rhesus Macaques Based on 454 Pyrosequencing Technology
Yaniv Loewenstein, Michal Linial	Structural alignment from sequence alone by integration of predicted secondary structure
Robert Langlois, Hui Lu	Boosting the Prediction and Understanding of DNA-Binding Proteins
Gil Alterovitz, Eugenia Lyashenko, Michael Xiang, Marco F. Ramoni	Functional Enrichment Across Organism Massomes
Florian Martin, Irfan Gunduz	Kernel filtering by Orthogonal-PLS and application to the general core promoter recognition problem
Kevin S. McLoughlin, Shea N. Gardner, Peter L. Williams, Thomas R. Slezak	Classifying Families of Multi-Protein Systems Using Phylogenomic Profiling and Hidden Markov Models
Serban Nacu, Rebecca Critchley-Thorne, Peter Lee, Susan Holmes	Gene Expression Network Analysis, and Applications to Immunology
Frank Neven, Dieter Van de Craen	Efficient algorithms to monitor bioinformatics data
Andrija Tomovic, Edward J. Oakeley	Modeling position dependencies in transcription factor binding site prediction
Yue Pan, Timothy Durfee, Joseph Bockhorst, Mark Craven	Connecting Quantitative Regulatory-Network Models to the Genome
Alexander Pico, NathanSalomonis, Kristina Hanspers, Karen Vranizan, Steven Lawlor, Martijn van Iersel, Thomas Kelder, Chris Evelo, Allan Kuchinsky, Bruce Conklin	GenMAPP for Pathway Analysis: Current and Future Development
John W. Pinney, Magnus Rattary, David L. Robertson	Inferring ancestral states of a protein interaction network
Elon Portugaly, Nathan Linial, Michal Linial	Assessment of Protein Domain Classifications: SCOP, CATH, Dali and EVEREST
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant	Refining Multiple Sequence Alignments with Conserved Core Regions.
Melissa Freedenberg, Chang F. Quo, May D. Wang	Systematic Study of Numerical Solvers for Complex Oscillatory Biochemical System Models
Sergei V. Rahmanov, Vsevolod J. Makeev	Knowledge-based atomic solvation potentials for analysis of protein structure stability and protein interaction
Christian Rausch, Ilka Hoof, Tilmann Weber, Wolfgang Wohlleben, Daniel H. Huson	Towards predicting composition and order of non-ribosomal peptides
Sheila M. Reynolds, Jeff A. Bilmes, William S. Noble	A Hybrid SVM / DBN Approach to Detecting SNPs in Diploid DNA Samples
Peter Rogen, Per W. Karlsson	Quantifying the Relative Positions of Proteins Secondary Structure Elements
Zhiyan Fu, Roberto Sanchez	Structure-based Prediction of Clinical Phenotypes in Lysosomal Storage Diseases
Rahul Satija, Lior Pachter, Jotun Hein	Combining Statistical Alignment and Phylogenetic Footprinting to Detect Conserved Regulatory Elements
Gabriele Scheler	Antagonistic regulation allows controlled access to multistability in neuroadaptivity
Alexandra M. Schnoes, Igor Dodevski, Patricia C. Babbitt	Leveraging Sequence and Structure to Evaluate Misannotation
Maxim Shatsky, Richard Hall, Robert Glaeser, Steven E. Brenner	Image Alignment of Heterogeneous Macromolecules from Electron Microscopy
Saad I. Sheikh, Tanya Y. Berger-Wolf, Wanpracha A. Chaovalitwongse, Mary V. Ashley, Bhaskar Dasgupta, Isabelle Caballero	A combinatorial approach to kinship analysis using microsatellite data
Jing Shi, Michael G. Walker, Peter D. Karp, Stanley N. Cohen	A Bayesian Approach for Evaluating the Metabolic Pathways Predicted by PathoLogic
Marco D. Sorani, Kathleen M. Giacomini	Benign SNPs are over-represented near oligomeric interfaces in human aquaporins
Oranit Dror, Yuval Inbar, Dina Schneidman-Duhovny, Ruth Nussinov, Haim J. Wolfson	Pharmacophore Detection by Multiple Flexible Alignment of Drug-Like Molecules Pharmacophore Detection by Multiple Flexible Alignment of Drug-Like Molecules
Gergely J. Szollosi, Imre Derenyi, Tibor Vellai	The maintenance of sex in bacteria is ensured by its potential to reload genes
Tokitaka Oyama, Hiroshi Ito, Takao Kondo, Y-h. Taguchi	Gene expression profile analysis for circadian promoter activities of cyanobacterial bioluminescent reporter strains using non-metric multidimensional scaling
Kazuhisa Makabe, Y-h. Taguchi	Gene arrangement for cell division cycle microarray experiments without sinusoidal fittings
Wenzhe Ma, Luhua Lai, Qi Ouyang, Chao Tang	Robustness and modular design of the Drosophila segment polarity network
Lydia Tapia, Xinyu Tang, Shawna Thomas, Nancy M. Amato	Kinetics Analysis Methods For Approximate Folding Landscapes
Shawna Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato	Distinguishing Folding Behavior using Rigidity
Jared Toettcher, Eric Batchelor, Galit Lahav, Bruce Tidor	Decoding Multiple Feedback Loops in Biological Networks
Ala Trusina, Feroz Papa, Chao Tang	The role of the Translation Attenuation pathway in Unfolded Protein Response
Igor Ulitsky, Ron Shamir	Identification of Functional Modules using Network Topology and High-throughput Data
Dirk Valkenborg, Tomasz Burzykowski	A new method for monoisotopic mass determination
Ulrich Wagner, Attila Gyenesei, Etzard Stolte, Ralph Schlapbach	Detection of functional associations in gene expression data by mining co-regulated gene profiles
Wenyi Wang, Benilton Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizzary	Estimating Genome-wide Copy Number using Allele Specific Mixture Models
Zhi Wei, Hongzhe Li	PMRF: a Pathway-based Markov Random Field Model for Analysis of Genomic Data
Roy Wollman, Gul Civelekoglu-Scholey, Jonathan Scholey, Alex Mogilner	Search for the `right` model for mitosis
Hossein Zare, Mostafa Kaveh, Arkady Khodursky	Modeling and Identification of Transcription Factor Binding Sites Using Higher Order Position Weight Matrices
Kangyu Zhang, Xiaotu Ma, Siddharth Adelkar, Hideki Innan, X. Jasmine Zhou	Comparative Genomic Study of the Evolution of Cis-regulatory Elements in Recent Duplicated Genes from S. Cerevisiae
Yuping Zhang, Minping Qian, Qi Ouyang, Minghua Deng, Fangting Li, Chao Tang	Stochastic Modeling of Yeast Cell Cycle Network using Markov Chains
Ying Zhang, Boguslaw Stee, Adam Godzik	Between order and disorder in protein structures - analysis of "dual personality" fragments
Degui Zhi, Maxim Shatsky, Steven E. Brenner	Ultra-Fast Local Structural Comparison with Writhe Decomposition
Dongxiao Zhu, Hua Li, Alfred O. Hero	Reconstructing Condition-Specific Signal Transduction Hierarchy using Bayesian Networks
Gerard R. Lazo, Debbie Laudencia-Chingcuanco, Yong Q. Gu, Olin D. Anderson	Gene mining for conserved cis elements in model genomes using gene expression patterns