RECOMB 2007

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

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