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Poster categories

A Biomedicine, epidemiology & agriculture
B Computational genomics
C Computer-aided drug design
D Databases & database integration
E Evolution & phylogenetics
F Metabolomics
G Ontologies
H Pathways, networks & systems
J Proteomics
K Sequence analysis
L Simulation & system dynamics
M Structural bioinformatics
N Text mining
P Transcriptomics
Q Other


A: Biomedicine, epidemiology & agriculture

A02 Moran Elishmereni, Antonio Cappuccio, Zvia Agur: Cancer Immunotherapy by Interleukin-21: Theoretical Evaluation of Potential Treatment Strategies
A04 Ravit Saada, Moran Weinberger, Ramit Mehr: Models for Antigen Receptor Gene Rearrangement: CDR3 Length
A06 Soliman Khatib, Jacob Vaya: New Derivatives of DPPacid as Tyrosinase Inhibitors: Structure-Activity Relationships
A07 Itai Kela, Alon Harmelin, Judith Chermesh, Tami Danon, Tova Waks, Avi Orr-Urtreger, Eytan Domany, Zelig Eshhar: Developing a Predictive Tool for Prostate Cancer Metastases using the TRAMP Model

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B: Computational genomics

B01 O. Reva: Microbial Genome Signatures and their Application in Metagenomics to Monitor the Environment and to Control Infection Outbreaks
B02 Elena D. Stavrovskaya, Vsevolod J. Makeev, Igor V. Merkeev, Andrey A. Mironov: Tool for Automatic Detection of Co-regulated Genes
B03 Lukas Chavez, Silvia Fluch: Comparative Genomics: Testing the Limit of Cross-Species Hybridization
B04 Georgios S Vernikos, Julian Parkhill: IVOMs for Identification of Horizontally Acquired DNA: Revisiting the Salmonella Pathogenicity Islands
B05 Tal Shay, Wanyu L. Lambiv, Anastasia Murat, Eugenia Migliavacca, Anjan Misra, Burt Feuerstein, Mauro Delorenzi, Roger Stupp, Monika E. Hegi, Eytan Domany: Effects of DNA Copy Number on Gene Expression in Glioblastoma Multiforme (GBM)
B06 Galina Kovaleva, Mikhail Gelfand: Evolution of the Methionine Biosynthesis Regulation in Streptococci
B07 A. Molares, E. Carrillo, G. Gomez, G. Munoz Molina, I. Muguruza, I. Sanchez, R. Moreno, V. Leiro, F. Carrillo , E. Caso: cRNA Microarrays and Bioinformatics Application in Lung Adenocarcinoma Samples
B08 Anat Kats, Sagi Shporer, Benny Chor, Hanne Volpin: Organ-Specific Linear Order of Gene Transcript Abundance in Arabidopsis
B10 Simon Furney, Stephen Madden, Des Higgins, Nuria Lopez-Bigas: Computational Study of Human Cancer: Properties of Proto-Oncogenes and Tumour Suppressor Genes
B11 Alex Mira, Ravindra Pushker, Francisco Rodriguez-Valera: Genomic Location and the Evolution of Paralogous Genes
B12 Yonit Halperin, Chaim Linhart, Gidi Weber, Ron Shamir: The AMADEUS Motif Discovery Tool
B13 Ofir Davidovich, Gad Kimmel, Ron Shamir: GEVALT - An Integrated Software Tool for Genotype Analysis
B14 Hadas Ner-Gaon: Whole Genome Microarray in Arabidopsis Facilitates Global Analysis of Retained Introns
B15 Elizabeth Permina, Mikhail Gelfand: Microarray and Comparative Genomic Analysis of sigB Regulon in Bacillus Group: An Estimation of Correspondence
B16 Yaki Setty, David Harel, Irun Cohen: Towards a Comprehensive, Realistic and Interactive 4-Dimensional Model of Pancreatic Development
B17 Eilon Sharon, Tali Sadka, Eran Segal: A Probabilistic Model for Identifying the Key Features of Protein-DNA Interactions
B18 Tirza Doniger, Yair Horesh, Inna Myslyuk, Shulamit Michaeli, Ron Unger: A Genome-wide Computational Scan for Novel Single-stem H/ACA-like snoRNA
B19 Anna V. Gerasimova, Dmitriy A. Ravcheev, Mikhail S. Gelfand: Multiple Regulation of Respiration in Gamma-Proteobacteria: FNR, ArcA, NarP and ModE Regulons
B21 Ido Sher, Sarit Edelheit, Ronen Shemesh, Dvir Dahary: Regulation of Alternative Splicing by Natural Antisense Transcripts is a Common Mechanism in the Human Genome
B23 Orna Man, Yitzhak Pilpel: Phenotypic Divergence among Diverse Yeast Species is Affected by Translational Control Signals in Protein Coding Sequence
B25 Martin Akerman, Yael Mandel-Gutfreund: Choosing the End: Regulation of Alternative 3' Splice Sites
B29 Lilach Soreq, Adi Gilboa-Geffen, Paul Lacoste, Hagai Bergman, Sonia Berrih-Aknin, Hermona Soreq: Approaching Alternative Splicing Patterns in Exon Microarray Data from Thymoma Tumors
B31 Igor Ulitsky, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon, Ron Shamir: EXPANDER - A One-Stop Shop for Microarray Data Analysis
B32 Yefim Ronin, Irine Ronin: A Mix of Bernoulli Distributions for Identification of Differentially Expressed Genes Detected by Replicated Microarray
B34 Eduardo Eyras, Mireya Plass: Differentiated Evolutionary Rates in Alternative Exons and the Implications for Splicing Regulation
B36 J. Hicks, A. Krasnitz, B. Lakshmi, X. Zhao, L. Norton, T. Sorlie, A.-L. Borresen-Dale, A. Zetterberg, P. Lundin, M. Wigler: Computational Analysis of ROMA-derived Copy Number Variations in Cancer
B38 Nicolas Delhomme, Natalia Becker, Felix Engel, Frederic Blond, Peter Lichter, Grischa Toedt: CrossChip: A Tool for Correlating Gene Expression Data with Genomic Imbalances
B43 Sonya Liberman, Nir Friedman, Hanah Margalit: Predicting Novel Transcription Factor Binding Sites in Human Using a Machine Learning Approach  Late-Breaking Results

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C: Computer-aided drug design

C02 Dilimulati Yusufujiangaili: An Alternative Method for the Evaluation of Docking Performance: Real Space R Value (RSR) vs. RMSD
C03 Menachem Fromer, Chen Yanover, Julia Shifman, Yair Weiss: A Probabilistic Approach to the Design of Structural Selectivity of Proteins
C04 Hilda David, Yael Mandel-Gutfreund: Analysis of Antibiotic Binding Pockets on the Ribosome Large Subunit using Structure-Based Networks
C05 Assaf Avihoo, Danny Barash: Computational Design of RNA Structural Switches from Building Blocks
C07 Itay Mayrose, Tomer Shlomi, Nimrod D. Rubinstein, Jonathan M. Gershoni, Eytan Ruppin, Roded Sharan, Tal Pupko: Mapping Protein-Protein Interfaces using Combinatorial Libraries
C08 Hadar Benyamini, Chen Katz, Shahar Rotem, Assaf Friedler: Revealing the Interaction Network of the Pro-apoptotic Protein ASPP2: Combination of Docking and Experiment  Late-Breaking Results

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D: Databases & database integration

D01 Asaf Madi, Alexandra Sirota, Tzvika Keilin, Tzvika Kushnirski, Keren Alfasi, Elad Balmor, Anat Katz, Eytan Shvimmer, Hanne Volpin: GreenExpress: A Web-Based Bioinformatics Infrastructure for Plant Genomic Information
D02 Alexandra Sirota, Hanne Volpin, Asaf Madi, Rivka Hadas: The Israeli Gene Bank Documentation Center: A Novel Infrastructure for Knowledge Discovery
D03 Carlos Prieto, Javier De Las Rivas: APID, an Integrated Web Platform to Explore and Evaluate Protein-Protein Interaction Networks
D04 Alexander Gout, Neilson Martin, David Ravine: A Locus Specific Gene Variant Database for Autosomal Dominant Polycystic Kidney Disease: PKDB
D05 Denis Shestakov, Tapio Salakoski: XML Format for Codon Usage Data
D07 S. Ron, L. Strichman-Almashanu, M. Shmoish, O. Greenshpan, A. Sirota, A. Madi, T. Iny-Stein, N. Rosen, I. Dalah, O. Shmueli, M. Safran, Y. Aumann, D. Lancet: GeneDecks: Gene-Set Analyses of GeneCards Annotations
D08 Tim Harder, Iddo Friedberg, Adam Godzik: JAFA: A Protein Function Prediction Meta-Server
D10 Stefan Goetz, Ana Conesa, Juan Miguel Garcia-Gomez, Manuel Talon, Montserrat Robles: Functional Annotation with Blast2GO v.2: A Comprehensive Gene Ontology Based Framework for Function Analysis
D11 Jan Baumbach, Sven Rahmen, Andreas Tauch: CoryneRegNet: An Integrative Bioinformatics Platform for the Analysis of Transcription Factors and Regulatory Networks
D13 Michael Han, Todd Harris, William Spooner, Lincoln Stein, Richard Durbin, The WormBase Consortium: WormBase - A Comprehensive Resource for C. elegans
D14 Florian Odronitz, Martin Kollmar: Two Web Applications: A Tool for Protein Family Analysis and a Resource for Genomic Research
D15 Jae-Hun Choi, Jong-Min Park, Soo-Jun Park: Predicting Homologous Complexes in Large Protein-Protein Interaction Networks
D17 Myungeun Lim, Myung-Guen Chung, Yong-Ho Lee, Soo-Jun Park: Implementation of a Dynamic Query Processing Model to Support Biological Data Integration
D19 Olga Krebs, Andreas Weidemann, Ulrike Wittig, Renate Kania, Martin Golebiewski, Saqib Mir, Isabel Rojas: SABIO-RK: Integrating Reaction Kinetics Data for Systems Biology
D20 Darren Otgaar, Junaid Gamieldien, Fernando Martinez, Dan Jacobson: DigraBase - A Multigraph-based Data Store for Integrating Biological Data
D21 Amnon Shabo, Dolev Dotan, Ohad Greenshpan: The Seventh Layer of Clinical Genomics - An Infrastructure for Using Genomic Data in Healthcare  Late-Breaking Results
D22 Ilya Venger, Sergey Gerzon, Ilana Rogachev, Sergey Malitsky, Asaph Aharoni: MetaboBase: A Computational Platform for Metabolomics Data Integration, Storage and Interpretation

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E: Evolution & phylogenetics

E01 Joanna Elson, Robert Lightowlers, Neil Howell: Keeping a Watchful Eye for Mammalian mtDNA Recombination
E02 Tsviya Olender, Ester Feldmesser, Ronny Aloni, Doron Lancet: Molecular Recognition and Evolution in the Olfactory Receptor Gene Family
E03 Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora: Genomic Coevolution of Syntenic Genes in Rhizobiales
E04 Juris Viksna, David Gilbert: Analysis of Probabilities of Evolutionary Changes in Protein Structures
E05 Neta S. Zuckerman, Katy McCann, Christian H. Ottensmeier, Freda S. Stevenson, Ramit Mehr: Lineage Tree Analysis and the Dynamics of FL and DLBCL
E06 Ilan Wapinski, Nir Friedman, Avi Pfeffer, Aviv Regev: Trees and Forests: A Genome-Wide Reconstruction of Orthologous Groups and their Evolution
E08 Julie Baussand, Alessandra Carbone: Periodic Distribution of Hydrophobic Amino-Acids Use for Distantly Related Proteins Alignment and Homology Search
E09 Osnat Penn, Tal Pupko: A Covarion-like Evolutionary Model for the Detection of Rate Shifts
E10 Philipp W. Messer, Peter F. Arndt: The Evolution of the Human Genome: Prevalence of Tandem Duplications on Small Scales
E11 Adi Doron-Faigenboim, Tal Pupko: Converting Empirical Amino-Acid Replacement Matrices into Codon-Based Substitution Matrices

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F: Metabolomics

F01 Karsten Hiller, Beatrice Benkert, Andreas Grote, Bernhard Thielen, Richard Munch, Dietmar Schomburg, Dieter Jahn: The Metabolomic Landscape: Emergent Self Organizing Maps for Metabolome Analysis
F02 Ilya Venger*, Ilana Rogachev*, Tali Mandel, Yitzhak Pilpel, Asaph Aharoni: Metabolomics in Plants and Yeast: Gene Function and Metabolic Pathway Discovery via Analytical Chemistry, Chemometrics and Computational Biology

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G: Ontologies

G01 Myung-Guen Chung, Myung-Eun Lim, Myung-Nam Bae, Yong-Ho Lee, Soo-Jun Park: Design Principles of Ontology-based Query and Development of Ontology Wrapper

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H: Pathways, networks & systems

H01 Einat Zalckvar, Adi Kimchi: System Level Analysis of the Cell Death Network via RNAi Knock-Down Experiments
H02 Shay Stern, Tali Dror, Elad Stolovicki, Naama Brenner, Erez Braun: Genome-Wide Adaptive Reprogramming of Gene Regulation in Yeast
H03 Andrew Capaldi, Tommy Kaplan, Ying Liu, Kristen Cook, Naomi Habib, Yoseph Barash, Nir Friedman, Aviv Regev, Erin K O'Shea: Structure and Function of Transcriptional Networks: Rewiring and Crosstalk in the Yeast Osmolarity Pathway
H04 Axel von Kamp, Stefan Schuster: Decomposition of Metabolic Networks for Distributed Computation of Elementary Modes
H05 Gali Niv, Hanah Margalit: Understanding the Integrated Network of Signal Transduction and Protein-Protein Interaction using Network Analysis Tools
H06 Israel Steinfeld, Ron Shamir, Martin Kupiec: A Systematic Analysis of Chromatin Modifiers that Act as Transcriptional Co-Factors in the Yeast Genome
H07 Tali Goren, Ohad Manor, Tommy Kaplan, Nir Friedman: ENRICH: A Computational Aid Tool for Finding Enrichment in Various Data Sets
H08 Naomi Habib, Tommy Kaplan, Hanah Margalit, Nir Friedman: A Novel Bayesian Probabilistic Method for Comparing Transcription Factor Binding Site Profiles
H09 Joan Planas-Iglesias, Daniel Aguilar, Baldomero Oliva: On the Construction of a Hypothetical Metabolic Network: Analysis of the Intersection with the Interactome
H10 Moran Yassour, Tommy Kaplan, Ariel Jaimovich, Chih Long Liu, Guocheng Yuan, Oliver J Rando, Nir Friedman: Genome-Scale Identification of Nucleosome Positions during Cell Cycle Reveals Insights on Transcriptional Regulation
H11 Ana Conesa, Jose Manuel Prats-Montalban, Maria Jose Nueda, Manuel Talon, Alberto Ferrer: A Multi-way Strategy for the Integrative Analysis of High Dimensionality
H12 Todd A. Gibson, Debra S. Goldberg: Modeling Evolution of Gene and Protein Interactions
H15 Philippa Melamed, Stefan Lim, Min Luo, Mingshi Koh: Derepression of the follicle stimulating hormone beta subunit gene by GnRH involves CaMKI, calcineurin and Nur77
H17 Ying Wang, Natasa Przulj: Biological Implications of Anti-motifs in Transcriptional Regulation Networks
H18 Alexandra Shulman-Peleg, Oranit Dror, Dina Schneidman, Roded Sharan, Ruth Nussinov, Haim Wolfson: Structural Similarity is a Prominent Feature of Genetic Interactions
H21 Ho-Youl Jung, Myung-Guen Chung, Minho Kim, Pora Kim, Seon-Hee Park, Soo-Jun Park: preCLUE: PREdiction system for CLUstering and regulatory rElation
H24 Felix Engel, Nicolas Delhomme, Natalia Becker, Frederic Blond, Peter Lichter, Grischa Toedt: Comprehensive Gene Pathway Analysis - A Tool for Pathway Analysis of CGH and Microarray Data
H27 Joan Valls, Monica Grau, Xavier Sole, Pilar Hernandez, David Montaner, Joaquin Dopazo, Miguel A Peinado, Gabriel Capella, Miguel Angel Pujana, Victor Moreno: Combining Inference from Differential Expression and Variability in Microarray Data Analysis
H28 Hilah Gal, Ninette Amariglio, Luba Trakhtenbrot, Jasmine Jacob-Hirsh, Ofer Margalit, Abraham Avigdor, Arnon Nagler, Sigal Tavor, Liat Ein-Dor, Tsvee Lapidot, Eytan Domany, Gideon Rechavi, David Givol: Gene Expression Profiles of AML Derived Stem Cells; Similarity to Hematopoietic Stem Cells
H29 Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Mali Weisz, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir: SPIKE - A Database, Visualization and Analysis Tool for Signaling Pathways
H31 Pablo Minguez, Fatima Al-Shahrour, David Montaner, Joaquin Dopazo: Functional Profiling of Microarray Experiments Using Text-Mining Derived Bioentities

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J: Proteomics

J01 M. Portnoi, A. Adawi, D. Kafka, N. Porat, R. Dagan, Y. Mizrachi-Nebenzahl: Comparative Proteomics of Different Morphological Types of Streptococcus pneumoniae
J02 Witold Dyrka, Jean-Christophe Nebel: A Pseudo Probabilistic Context-Free Grammar for the Detection of Binding Sites from a Protein Sequence
J03 Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit: Evolutionary Conservation of Domain-Domain Interactions
J04 Matthias E. Futschik, Gautam Chaurasia, Erich Wanker, Hanspeter Herzel: Comparative Assessment of Large-Scale Maps of the Human Protein Interactome
J06 Thorsten Schmidt, Dmitrij Frishman: PROMPT: A Protein Mapping and Comparison Tool
J07 Bareket Dassa, Shmuel Pietrokovski: Sequence to Function Analysis of New Protein-Splicing Domains
J08 Iris Bahir, Michal Linial: Functional Identification of Protein Signatures
J09 Alexey Dolgov, Elena Bogacheva, Alexey Chulichkov, Alexander Shishkov, Ekaterina Vedeniapina: Computer Simulation in Tritium Planigraphy
J13 Daniel K Shenfeld, Itamar Kass, Joshua Manor, Isaiah T Arkin: A Geometric Approach to Integration of Site-Directed FTIR Data on Transmembrane Proteins as a Base for Modeling
J14 Ole Schulz-Trieglaff, Clemens Gropl, Joachim Thiemann, Knut Reinert, Hartmut Schlueter: Peptide Biomarker Discovery for the Diagnosis of Renal Allograft Rejection
J15 Karin Noy, Anne-Katrin Emde, Daniel Fasulo: A Novel Method for Model-Based Feature Extraction in Mass Spectra
J16 Jonathan A. Epstein, Matthew T. Olson, Alfred L. Yergey: De Novo Peptide Sequencing Using Exhaustive Enumeration of Peptide Composition and MALDI TOF/TOF
J17 Lawrence Okoror, Bayo Momodu, Ibiwumi Oloye: Protein Function Prediction of a Lassa Virus Glycoprotein from a Newly Extracted Lassa Virus Gene  Late-Breaking Results
J18 Andrey Alexeyenko, Erik Sonnhammer: Networks of Functional Coupling in Eukaryotes  Late-Breaking Results

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K: Sequence analysis

K02 Marjanca Starcic Erjavec, Marko Erjavec, Darja Zgur-Bertok: A Computer Program to Predict Gene Position and Reveal Inconsistent Designation of Similar Genes in Different Organisms
K03 Orly Noivirt, Miriam Eisenstein, Amnon Horovitz: Detection and Reduction of Evolutionary Noise in Correlated Mutation Analysis
K06 Ying Sheng, Par G. Engstrom, Boris Lenhard: Mammalian microRNA Prediction using a Support Vector Machine Model of Sequence and Structure
K08 Noam Kaplan, Michal Linial: Classifying High-Level Protein Functionality: Toxins and Toxin-Like Proteins
K12 Eyal Akiva, Hanah Margalit: Built-in Switches Allow Versatility in Domain-Domain Interactions
K13 Yaniv Loewenstein, Elon Portugaly, Michal Linial: Augmenting Protein Sequence Alignment of Remote Homologues using Secondary Structure Confidence Scores
K14 Holger Klein, Martin Vingron: Using Co-occurrence of Transcription Factor Binding Sites for the Assessment of Regulatory Potential
K15 Assaf Gottlieb, Tsviya Olender, Doron Lancet , David Horn: Olfactory Receptors in Peptide Space
K17 Oliver Keller, Katharina Surovcik, Thomas Brodag, Rainer Merkl, Roman Asper, Carsten Damm, Stephan Waack: SIGI-HMM: Score-Based Prediction of Genomic Islands in Prokaryotic Genomes using HMMs
K18 Mindaugas Margelevicius, Ceslovas Venclovas: A New Approach for Estimation of Statistical Significance in Sequence Profile-Profile Comparisons
K20 Jaina Mistry, Alex Bateman, Rob Finn: An Algorithm for the Identification of Active Site Residues Using Pfam Alignments
K23 Alexander Bolshoy: Information Content and Sequence Periodicity
K24 Steinar Thorvaldsen, Tor Fla, Nils P. Willassen: DeltaProt: Toolbox for Molecular Comparison of Proteins based on Sequence Alignments
K25 Elon Portugaly, Nathan Linial, Michal Linial: Assessment of Protein Domain Classifications: Automatic Sequence-Based Method and Methods based on 3D Structures
K27 Costas Tsirigos, Pantelis Bagos , Vasilis Promponas, Stavros Hamodrakas: Enhancing Transmembrane Beta-Barrel Topology Prediction by Information Encoded in Multiple Sequence Alignments
K28 Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, Jakob C. Mueller: On the Kinetics of Prokaryotic Transcription Initiation
K29 Avihay Apatoff, Eddo Kim, Yossef Kliger: Towards Alignment Independent Quantitative Assessment of Homology Detection Methods  Late-Breaking Results

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L: Simulation & system dynamics

L04 Gil Hornung, Brian Berkowitz, Naama Barkai: Morphogen Gradient Formation in a Complex Environment: An Anomalous Diffusion Model
L05 Sivan Pearl, Chana Gabay, Amos Oppenheim, Nathalie Q. Balaban: Non Genetic Individuality in Host-Phage Interaction
L06 Matej Butala, Milan Hodoscek, Darja Zgur-Bertok: LexA Repressor - DNA Model, Binding Characteristics
L07 Tal El-Hay, Nir Friedman, Daphne Koller, Raz Kupferman: Continuous Time Markov Networks
L08 Yossi Tsfadia, Jonathan Kadmon, Anna Seltzer, Ran Friedman, Esther Nachliel, Menachem Gutman: Molecular Dynamics Simulation for the Complete Entry of Fatty Acid-Ligand of Toad Liver FABP through the Portal Region
L09 Yuri Porozov, Raluca Andrei, Monica Zoppe': Visualization and Modelling of Moving Biomolecules: A New Approach Based on Professional 3D Animation Software
L10 Anna Feldman-Salit, Domantas Motiejunas, Razif Gabdoulline, Markus Wirtz, Rudiger Hell, Rebecca Wade: Protein Recognition Processes: The "Cysteine Synthase" Complex
L11 Mali Salmon-Divon, Sofia Johansson, Maria Johansson, Marjet Elemans, Petter Hoglund, Ramit Mehr: Modeling Natural Killer Cell Development and Repertoire Formation
L14 Dan Fishelovitch, Haim J. Wolfson, Ruth Nussinov: Structural Dynamics of the Cooperative Binding of the Human Cytochrome P450 (Cyp450) 3A4
L15 Vladimir Vainstein, Yuval Ginosar, Meir Shoham, Anton Ianovski, Alexander Rabinovich, Yuri Kogan, Vera Selitser, Zvia Agur: Improving Cancer Therapy by Doxorubicin and GCSF: Insights from a Computerized Mathematical Model of Granulopoiesis
L17 Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli: A Gene Network Simulator Integrating Boolean Regulation in a Continuous Dynamic Model
L18 Dace Ruklisa, Alvis Brazma, Karlis Cerans, Juris Viksna: Analysis of Dynamics of Gene Regulatory Networks under Finite State Linear Model

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M: Structural bioinformatics

M03 Angelo Favia, Janet Thornton, Rafael Najmanovich, Fabian Glaser, Irene Nobeli: A Computational Study of Substrate Specificity in the Family of Short-Chain Dehydrogenases
M05 Masha Y. Niv, Lucy Skrabanek, Richard J. Roberts, Harold Scheraga, Harel Weinstein: Scan2S: Regular Expression Scan Algorithm for Detection of Type II Restriction Endonucleases
M06 Ofer Rahat, Gideon Schreiber: Evolutionary Cluster Conservation of Proteins
M08 Marcin Krol, Paul A. Bates: Scoring Protein-Protein Complexes using MD-Generated Ensembles
M09 Daniel Barthel, Jonathan D. Hirst, Natalio Krasnogor: The ProCKSi-Server: A Server for Similarity Comparisons of Protein Structures
M10 Mickey Kosloff, Barry Honig: Computational Investigations of the Reversible Interactions of G-proteins with Membranes Surfaces
M11 Mickey Kosloff, Rachel Kolodny, Barry Honig: Sequence-Similar, Structure-Dissimilar Protein Pairs in the PDB
M12 Leon Peshkin, Virginia Savova: Hierarchical Structure Induction by Compression in Graphs
M13 Mati Cohen, Dana Reichmann, Gideon Schreiber: Protein-Protein Interactions: De-Novo Rational Protein-Interface Design
M15 Michal Rabani, Michael Kertesz: Systematic Discovery of Functional RNA Structural Motifs
M16 Milana Frenkel-Morgenstern, Shmuel Pietrokovski: Refining Intra-Protein Contact Predictions using Graph Analysis
M17 Chen Yanover, Tomer Hertz, Ora Schueler-Furman: "Learning to Learn" HLA-Peptide Binding Specificity using Supertypes
M18 Hani Neuvirth, David Birnbaum, Uri Heinemann, Naftali Tishby, Gideon Schreiber: ProMateus: An Open Research Approach to Protein Binding Sites Analysis
M19 Javier Garcia-Garcia, Baldomero Oliva: A WebServer Integrative Approach for the Combination and Validation of Inter-residue Contacts
M20 Inna Myslyuk, Avihay Apatoff, Avraham Hury, Ron Unger, Shulamit Michaeli: Analysis of Sequence and Structure Features of H/ACA Like Box SnoRNA in Trypanosomatids
M21 Hector Romero, Martin Grana, Pablo Dans, Hugo Naya: Scaling in Biology: Exploring Surface-to-Volume Ratios and other Properties within Thousands of X-ray Structures
M22 Nir London, Ora Furman Schueler: Funnel Hunting in a Rough Terrain: Learning and Discriminating Energy Funnels
M23 Einat Sitbon, Shmuel Pietrokovski: Effects of Protein Sequence Conservation on Protein Secondary Structure Patterns
M25 Vladimir Potapov, Dana Reichmann, Vladimir Sobolev, Marvin Edelman, Gideon Schreiber: High Affinity and Binding Specificity of Computationally Redesigned Protein Interfaces
M26 Alexander Churkin, Ofer Peleg, Danny Barash: Predictions of Single Point Mutations that Substantially Alter the RNA Secondary Structure
M27 Shula Shazman, Yael Mandel-Gutfreund: A Machine Learning Approach for Predicting RNA-Binding Proteins from Three Dimensional Structure
M28 Idan Gabdank, Assaf Avihoo, Danny Barash, Michal Shapira: In Search of Short RNA Thermoswitches Using Computational and Experimental Analyses
M29 Marian Novotny, Henrik Hansson, Helena Strombergsson, Gerard J. Kleywegt: Detection of Out-Of-Register Errors in Protein Crystal Structures
M30 Benjamin Schuster-Boeckler, Robert D. Finn, Alex Bateman: Are There More Structural Interaction Types than Previously Thought?
M32 Mariana Babor, Sergey Gerzon, Barak Raveh, Vladimir Sobolev, Marvin Edelman: Efficient Prediction of Metal Binding Sites in Apo-Protein Structures
M33 Chan-Yong Park, Sung-Hee Park, Dae-Hee Kim, Soo-Jun Park, Man-Kyu Sung, Hongro-Lee, Chi-Jung Hwang: Fast Protein Structure Alignment by Joining Similar Substructure Pair
M34 Noga Kowalsman, Miriam Eisenstein: Inherent Limitations in Protein-Protein Docking Procedures
M35 Dina Schneidman, Yuval Inbar, Ruth Nussinov, Haim Wolfson: Prediction of Symmetric Assemblies by Docking
M36 Oranit Dror, Yuval Inbar, Dina Schneidman, Ruth Nussinov, Haim Wolfson: Pharmacophore Detection: Multiple Flexible Alignment of Drug-Like Molecules
M38 Michal J. Gajda, Marta Kaczor, Alan M. Friedman, Chris Bailey-Kellogg, Janusz M. Bujnicki: FILTREST3D: A Simple Method for Discrimination of Multiple Structural Models against Spatial Restraints
M39 Yuval Inbar, Ruth Nussinov, Haim J. Wolfson: 3D Segmentation of Low and Intermediate Resolution EM Density Maps
M40 Jan E. Gewehr, Fabian Birzele, Ralf Zimmer: Optimizing Scoring Matrices for Alignment Ranking
M43 Michal J. Gajda, Janusz M. Bujnicki, Chris Bailey-Kellogg: Contact Prediction using Secondary Structure Pairings
M44 Majid Masso, Iosif I. Vaisman: Accurate Prediction of Enzyme Mutant Activity based on a Multibody Statistical Potential
M45 Gregory M. Reck, Iosif I. Vaisman: A Novel Approach to Protein-Water Interaction Characteristics Using Computational Geometry
M46 Todd Taylor, Iosif I. Vaisman: Protein Structural Domain Assignment Using a Delaunay-Tessellation Derived Lattice
M47 Dietlind Gerloff, Shakir Ali, Xueping Quan, Rupert Koenig: A Simplified Representation of Electrostatic Model Surfaces for Addressing Protein-Protein Interaction Problems
M48 Ami Levy-Moonshine, Tatiana Maximova, Chen Keasar: A Cooperative Energy Term for Hydrogen Bonds

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N: Text mining

N01 Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman: Association Rule Mining and Protein Databases: Exceptions Point to Annotation Errors
N02 David Alarcon Gallego, Baldomero Oliva: Finding Optimal Microarray Platform to Analyze High-Risk Pathologies
N04 Evangelos Pafilis: Cross-Discipline Knowledge Integration

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P: Transcriptomics

P01 Itay Tirosh, Adina Weinberger, Naama Barkai: A Conserved Genetic Signature of Gene Expression Divergence
P02 Carmiya Bar-Or, Eugene Novikov, Anat Reiner, Henryk Czosnek, Hinanit Koltai: Derivation of Valid Biological Data from Cross-Species Hybridizations (CSHs) to cDNA Microarrays
P03 Bruno Zeitouni, Bruno Monier, Michel Semeriva, Laurent Perrin: Expression Profiling of Drosophila Heart Remodelling during Metamorphosis
P04 Paz Polak, Eytan Domany: Regulating Signals on Alu Play a Significant Role in Development
P07 Roi Gilat, Dorit Shweiki: Embryonic Genes are Reactivated in Human Cancers
P09 Levent Carkacioglu, Ozlen Konu, Tolga Can, Volkan Atalay, Rengul Cetin-Atalay: Expression Pattern Analysis of Housekeeping Genes Across Large Number of Microarray Experiments
P10 V Strumba, T Blackwell, E Sliwerska, R Bernard, J Li, AJ Schatzberg, EG Jones, WE Bunney, RM Myers, H Akil, SJ Watson, M Burmeister: Effect of Functional Variants on Gene Expression in Human Brain
P11 Hadar Less, Gad Galili: Elucidating Factors Influencing Probes Sensitivity and Specificity in High Density Micro Arrays Using Affymetrix Setup
P12 Yuval Tabach, Anat Reiner, Ran Brosh, Assif Yitzhaky, Varda Rotter, Eytan Domany: Over Represented and Functional Human Transcription Factor Binding Motifs Appear Mainly Within 200bp from the TSS
P13 Tali Sadka, Ulrike Gaul, Eran Segal: A Thermodynamic Model for Understanding Spatio-Temporal Control of Gene Expression
P14 Ananyo Choudhury, Ansuman Lahiri: Analysis of Regulatory Element and Functional Class Associations: Comparison in Arabidopsis and Other Plants
P16 Merja Oja, Jaakko Peltonen, Samuel Kaski: A Hidden Markov Model Mixture for Estimating Human Endogenous Retrovirus Activities from Expressed Sequence Databases
P17 Or Zuk, Liat Ein-Dor, Eytan Domany: Thousands of Samples are Needed to Generate a Robust Gene List for Predicting Outcome in Cancer
P18 Roy Varshavsky, David Horn, Michal Linial: Clustering Algorithms Optimizer - A Framework for Large Datasets
P19 Ophir Shalem, Yitzhak Pilpel, Eran Segal: Genome-Wide mRNA Decay Profiles Modeled by First-Principles Kinetics
P20 Henning Redestig, Dirk Repsilber, Florian Sohler, Joachim Selbig: Integrating Functional Knowledge during Sample Clustering for Microarray Data using Unsupervised Decision Trees
P22 Dikla Dotan Cohen, Avraham A. Melkman, Simon Kasif: Seeing the Forest for Hierarchical Subtrees: Improving Cluster Coherence and Functional Prediction by Tree Snipping
P23 Guy Horev, Greg I. Elmer, Ilan Golani, Neri Kafkafi, Norman H. Lee, Anat Reiner, Daniel Yekutieli, Yoav Benjamini: Wall-Guidance and Attraction in Mice Correlate With Gene-Expression Patterns in Specific Brain Areas

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Q: Other

Q01 Andreas Grote, Alex Dalpiaz, Guido Melzer, Ursula Rinas, Bernd Northemann, Petra Dersch, Dietmar C. Hempel, Dieter Jahn: Investigations on the Systems Biology of Aspergillus niger
Q02 Hugo Ceulemans, Lijs Beke, Mathieu Bollen: The Stability of the Ancestral Eukaryotic Protein Complexome in Extant Eukaryotes and its Implications
Q03 Tanya Y. Berger-Wolf, Ilya R. Fischhoff, Daniel I. Rubenstein, Jared Saia, Siva R. Sundaresan: A Computational Framework for Analysis of Dynamic Social Structures
Q04 Avital Sadot, Jasmin Fisher, Dan Barak, Yishai Admanit, Michael J. Stern, E. Jane Albert Hubbard, David Harel: Towards Verified Biological Models
Q05 Tessa E. Pronk , Simon Polstra, Andy D. Pimentel, Marco Roos, Timo M. Breit: Evaluating the Design of Biological Cells Using a Computer Workbench
Q08 Fernando Martinez, Junaid Gamieldien, Darren Otgaar, Dan Jacobson: BioFrame: A Java-based Software Development framework for Bioinformatics
Q09 Michael Levitt, Peter S. Stern: Sequence Dependence of DNA Conformation and Deformation Calculated by Normal Mode Dynamics
Q11 Dan Jacobson, Nicky Mulder, Trushar Shah: Building Bioinformatics across Africa
Q18 Michael J. Moorhouse, Bert Eussen, Tobias A. Knoch, Michael Lesnussa, Albert D. M. E. Osterhaus, Frank Grosveld, Annelies deKlein: G3DV: A New 3D Genome Browser and Experimental Data Viewer  Late-Breaking Results

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