Biology by other means
Posters
Poster Session Information
Posters are required to be displayed throughout the conference. Please place your poster on the board bearing the code associated with it and reported below. Poster authors are required to be available for presentation during the scheduled sessions:
| Monday,22 September 2008 | |
14:00.17:30 |
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All posters set up (poster must be set by 17:30). | |
| Tuesday,23 September 2008 |
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16:10.18:00 | |
Poster Session 1 (Odd numbered (A-1, A-3, ..) posters presented. | |
| Thursday,25 September 2008 |
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16:10.18:00 | |
Poster Session 2 (Even numbered (A-2, A-4, ..) posters presented. |
Presenting authors are kindly asked to remove their posters on Friday, 26 September 2008 from 13:00 to 16:30. After that no responsibility in case of loss or damage will be accepted.
Poster Categories
A: Algorithms and phylogeny
| A01 | MaxAlign: maximizing usable data in an alignment Gouveia-Oliveira R., Sackett P.W., Pedersen A.G. |
| A02 | Detection and correction of outliers in high-throughput experiments data Anton, MA, Rubio, A |
| A03 | Investigating einkorn domestication using phylogenetic networks Ayling S.C., Bunning S.L., Brown T.A. |
| A04 | Microarray Design using the Hilbert-Schmidt Independence Criterion Bedo J |
| A05 | Day-to-day variability in microarray experiment: a new algorithm to summarize probe levels and minimize this effect Roberta Bosotti, Paolo Magni, Angela Simeoni |
| A06 | Classification of HIV-1 Using Coalescent Theory Ingo Bulla, Anne-Kathrin Schulz, Ming Zhang, Thomas Leitner, Bette Korber, Burkhard Morgenstern, Mario Stanke |
| A07 | A novel high-throughput profile-based sequence identification method Hekkelman M.L., Vroling B., Vriend G. |
| A08 | Haplotype Block Partitioning and TagSNP Selection using Mutual Information Katanforoush A., Sadeghi M., Pezeshk H. |
| A09 | A novel protein homology detection method based on the analytical theory of profile comparisons Margelevicius M., Venclovas C. |
| A10 | Wavelet based sequence alignment. Menozzi G., Cereda M., Fumagalli M, Sironi M., Comi G. P., Bresolin N., Pozzoli U. |
| A11 | MAD-DPD: designing highly degenerate primers with maximum amplification specificity Hamed Shateri Najafabadi, Amir Saberi, Noorossadat Torabi, Mariam Okhovat Ghahfarokhi, Mahmood Chamankhah |
| A12 | Evaluation of existing motif detection tools on their ability to retrieve regulatory motifs in sequence data Storms V., Sanchez A., Claeys M., Marchal K., De Moor B. |
B: Databases
| B01 | Genomic and proteomic information integration and query Nardelli M., Masseroli M. |
| B02 | Unified access to bioinformatic resources: SRS, Biomart and EB-Eye Alberto Labarga, Evangelos Pafilis |
| B03 | Alternative splicing and protein structure: integration and analysis of available information D’Antonio M., Masseroli M. |
| B04 | Visual Exploration of Biological Data Alberto Labarga |
| B05 | The African Plasmodium falciparum database (afriPFdb) Ewejobi, I., Adebiyi, E., Ekenna, C, Rebai, A., Koenig, R., Brors, B., Doumbia, S. , Oyelade, J., Osamor, V., Fatumo, S., Eils, R., Lanzer, M. |
| B06 | MouseBook - Online integrated mouse information system Blake A, Mallon A, Greenaway S, Beck T, Hancock J |
| B07 | The Protein Model Portal Lorenza Bordoli, Konstantin Arnold, Jürgen Kopp, James Battey, Florian Kiefer, Michael Podvinec, John Westbrook, Helen Berman, Torsten Schwede |
| B08 | NORINE : database and efficient algorithms dedicated to nonribosomal peptides Caboche S., Pupin M., Leclere V., Jacques P., Kucherov G. |
| B09 | EUROCARBDB: A DATABASE RESOURCE FOR THE AUTOMATIC ANNOTATION AND STORAGE OF HPLC PROFILES Campbell M.P, Royle L, Rudd P.M |
| B10 | EuroCarbDB-MS: bioinformatics resources for interpretation, annotation and storage of mass spectrometric data of glycans Alessio Ceroni, Kai Maass, René Ranzinger, Matt J. Harrison, Kim Henrick, Hildegard Geyer, Rudolf Geyer, Anne Dell, Stuart M. Haslam |
| B11 | GRIP: a genome research informatics pipeline with open and closed integration of biological databases Chan Hee Park, Mingoo Kim, Hee-Joon Chung, Young-Ji Na, Ju Han Kim |
| B12 | TollML: an XML database of Toll-like receptors Jing Gong, Tiandi Wei, Ferdinand Jamtzky, Wolfgang M. Heckl, Shaila C. Rössle |
| B13 | ChEBI - Chemical Entities of Biological Interest Janna Hastings, Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Alan McNaught, Kristian Axelsen, Christoph Steinbeck |
| B14 | Standardizing and Annotating Kinetic Data: The SABIO-RK Database Renate Kania, Ulrike Wittig, Martin Golebiewski, Olga Krebs, Andreas Weidemann, Saqib Mir, Henriette Engelken, Isabel Rojas |
| B15 | Establishment of Clinical Omics Database System by in-tegrating clinical and molecular biological information. Hiroshi Tanaka, Yasen Mahmut, Jun Nakaya, Masahiro Nishibori, Kazuo Shimokawa, Kaoru Mogushi, Wataru Ohashi, Ken Miyaguchi, Masaya Itoda, Ayumi Kondo, Eiichi Araki, Ayako Fujisaki, Toshiaki Ishikawa, Narikazu Uzawa, Masahiko Miura, Shinji Tanaka, Hitoshi Shibuya, Mitsuo Amagasa, Kenichi Sugihara, Shigeki Arii, Joji Inazawa, Yoshio Miki, Hiroshi Mizushima |
| B16 | Symbiosis: the novel “one-design-fits-all” database for heterogeneous systems biology data Fady Mohareb, Conrad Bessant |
| B17 | GePh-CARD: Genotype-Phenotype Correlation, Analysis and Research Database Mordenti M., D'Ascia S., Pedrini E., Frangiamone G., Sangiorgi L. |
| B18 | EuroPhenome: A Mouse Phenotyping Resource Morgan, H., Beck, T., Blake, A., Mallon, A-M., Hancock, J.M. |
| B19 | ASPICdb: a database resource for alternative splicing analysis Castrignanò T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio De Meo P, D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Bonizzoni P, Pesole G |
| B20 | An XML format for peptide datasets Jelena Repar, Nives Škunca, Fran Supek, Tomislav Šmuc |
| B21 | PRODORIC - a platform for the elucidation of gene regulatory networks in prokaryotes Johannes Klein, Ida Retter, Stefan Leupold, Richard Münch |
| B22 | GabiPD: The Gabi Primary Database - a plant integrative ‘omics’ database Diego Mauricio Riaño-Pachón, Axel Nagel, Robert Wagner, Jost Neigenfind, Elke Weber, Svenja Diehl, Birgit Kersten |
| B23 | Reporting Standards and Public Infrastructure for Omics Data @ EBI Philippe Rocca-Serra, Marco Brandizi, Nataliya Sklyar, Chris Taylor, Eamonn Maguire, Daniel Schober, and Susanna-Assunta Sansone |
| B24 | FunSimMat: a comprehensive functional similarity database and its application to phenotype similarity Schlicker A., Blankenburg H., Lengauer T., Albrecht M. |
| B25 | NPIDB, a database of structures of nucleic acid – protein complexes Spirin S.A., Alexeevski A.V., Karyagina A.S., Titov M.L. |
| B26 | Analysing Experimental Data in the context of Integrated Biological Networks Taubert J., Weile J., Hindle M., Lysenko A., Hassani-Pak K., Canevet C., Rawlings C.J. |
| B27 | LRRML: a conformational LRR database Tiandi Wei, Jing Gong, Ferdinand Jamtzky, Wolfgang M. Heckl, Shaila C. Rössle |
| B28 | Large Scale Prediction of Computational Hot Spots in Protein Interfaces Guney E., Tuncbag N., Gursoy A., Keskin O. |
| B29 | SIMBIOMS: – an integrated software system for managing information in biomedical studies Alvis Brazma, Sudeshna Guha Neogi, Maria Krestyaninova, Natalja Kurbatova, Karlis Podnieks, Ugis Sarkans, Juris Viksna, Andris Zarins |
| B30 | GPCRDB: an information system for G protein-coupled receptors Vroling B., Oliveira L., Hekkelman M.L., Vriend G. |
| B31 | PROTOPOLO: PROtein complex TOPOLOgy database Isakh Weheliye, Jeyaram Deivachandran, Jean-Christophe Nebel |
C: Text mining
| C01 | Adaptive integration of text mining data sources for gene clustering Shi Yu, Leon-Charles Tranchevent, Bart De Moor, Yves Moreau |
| C02 | An integrated approach to extract functional gene information from literature Keywan Hassani-Pak, Jan Taubert, Matthew Hindle, Artem Lysenko, Chris Rawlings |
| C03 | CRAB – Cancer Risk Assessment and Biomedical Text Mining Anna Korhonen, Ian Lewin, Ilona Silins, Johan Hogberg, Ulla Stenius |
| C04 | Literature-aided gene annotation enhances meta-analysis of microarray studies 't Hoen, P.A.C., Jelier, R., Sterrenburg, E., van Ommen, G.J.B., den Dunnen, J.T., Kors, J.A., Mons, B. |
| C05 | Prediction of protein-protein interactions based on literature evidence using concept profile methodology H.H.H.B.M. van Haagen, A. Botelho Bovo, B. Mons, P.A.C. ’t Hoen, J.A. Kors, C. Chichester, M.J. Schuemie |
D: Genomes and protein analysis
| D01 | IMPROVEMENTS IN ENSEMBL HUMAN GENOME ANNOTATION Aken B.L., Ballester B., Beal K., Birney E., Chen Y., Clarke L., Cunningham F., Curwen V., Fairley S., Fernandez-Banet J., Fernandez-Suarez X., Fitzgerald S., Flicek P., Gräf S., Hammond M., Herrero J., Howe K., Johnson N., Kähäri A., Kulesha E., Lawson D., Longden I., Megy K., Meidl P., Overduin B., Parker A., Proctor G., Rios D., Schuster M., Searle S., Smedley D., Smith J., Spudich G., Trevanion S., Vilella A., Vogel J., White S., Zadissa A., Hubbard T. |
| D02 | SODIUM: Small ORF Detection in Intergenic and Unannotated DNA Alaguraj Veluchamy, Stéphane Avner, Sankaran Krishnaswamy, Frédérique Barloy-Hubler |
| D03 | Characteristics and evolution of unique genes in plants David Armisen, Alain Lecharny, Sebastien Aubourg |
| D04 | Prokaryotic immunity systems of the CRISPR type in metagenomes. Sorokin Valery A. , Gelfand Mikhail S. , Artamonova Irena I. |
| D05 | Chromosomal gene enrichment analysis Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, Yves Moreau |
| D06 | A benchmark of methods for horizontal transfer detection Jennifer Becq, Cecile Churlaud, Patrick Deschavanne |
| D07 | Transmembrane helix recognition by the ER translocon Andreas Bernsel |
| D08 | Identification of core promoters in the P. falciparum genome using DNA physiochemical properties. Kevin Brick, Elisabetta Pizzi |
| D09 | Fine mapping of the recombination in S. Cerevisiae: High density tiling arrays and semi-supervised clustering Mancera Eugenio, Bourgon Richard, Brozzi Alessandro, Wolfgang Huber, Lars M. Steinmetz |
| D10 | Evolution of proteins through gains and losses of domains Buljan M., Bateman A. |
| D11 | Sequence and structure analysis of P. falciparum RIFIN protein family Bultrini E., Brick K., Pizzi E. |
| D12 | CAZY: An Expert Annotation Resource for Complex Carbohydrate Metabolism. Cantarel, BL, Rancurel, C, Coutinho PM, Henrissat B |
| D13 | Subcellular localisation and GPI anchor prediction in Eukaryotes Bartoli L., Fariselli P., Fronza R., Martelli P.L., Montanucci L., Pierleoni A., Rossi I., Tasco G., Casadio R. |
| D14 | Splice site position specific conservation between human and chimpanzee Cereda M., Fumagalli M., Menozzi G., Sironi M., Comi G.P., Bresolin N., Pozzoli U. |
| D15 | CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data Cesaroni M., Cittaro D., Brozzi A., Pelicci P.G., Luzi L |
| D16 | Prediction of DNA-binding Regions from Sequence Conservation and Composition Ai-Mi Chen, Chien-Yu Chen |
| D17 | Assemblies of uncommon DNA patterns at the transcription start sites of genes in Human and Mouse genomes Miklós Cserző, Gábor Turu, Péter Várnai, László Hunyady |
| D18 | Massively overrepresented 8-14bp oligonucleotides as markers for whole bacterial genomes Colin F Davenport, Jens Neugebauer, Oleg N. Reva, Burkhard Tümmler |
| D19 | Optimal Spliced Alignments of Short Sequence Reads Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Rätsch |
| D20 | genePI: Improved prediction of promoter regions by using a feature-based classification strategy Petra Catalina Schwalie, Finn Drabløs |
| D21 | Comparative plasmidomics: insights into microbial evolution Marco Fondi, Matteo Brilli, Bacci G., Emiliani G., Maida I., Papaleo M. C., Fani R. |
| D22 | Identification of evolutionary hotspots in Mycobacteria based on gene-gene comparison & oligonucleotide usage parameters Hamilton Ganesan, Oleg Reva |
| D23 | Prediction of functional residues and clustering for protein families using mixtures Benjamin Georgi, Joerg Schultz , Alexander Schliep |
| D24 | Shaving the bacterial surface: the SLEP server Giombini E., Orsini M., Tramontano A. |
| D25 | Novel peptides shed light on evolution of Olfactory Receptors Gottlieb Assaf, Olender Tsviya, Lancet Doron, Horn David |
| D26 | Transcriptional and Post-Transcriptional Plasticity After the Whole-Genome Duplication event in Yeast Luigi Grassi, Davide Corà, Diana Fusco, Marco Cosentino Lagomarsino, Bruno Bassetti, Michele Caselle |
| D27 | Exalign: a new method for comparative analysis of exon-intron gene structures Zambelli F, Pavesi G, Pesole G |
| D28 | Characterization of ERalpha Binding Regions Detected in Responsive Cells by Massively Parallel Sequencing (ChIP-Seq). Grober O.M.V., Mutarelli M., Cicatiello L., Paris O., Ravo M., Weisz A. |
| D29 | Bioinformatics analyses of chemotaxis proteins Hamer R., Chen P-Y., Dean C., Reinert G., Armitage J. |
| D30 | A functional genomics sequence workbench and relationship visualization system Hefer CA, Joubert F |
| D31 | Searching a best pseudocount of PSSM in comparing 2 profiles to predict functional sites. Hiroyuki Oda, Tetsuya Sato, Motonori Ota, Hiroyuki Toh |
| D32 | Predicting genes on metagenomic DNA fragments with high specificity using machine learning techniques Katharina J. Hoff, Maike Tech, Peter Meinicke |
| D33 | Analyses of conditions for KMSKS loop in Tyrosyl-tRNA synthetase by building a randomized mutant library Shunsuke Kamijo, Akihiko Fujii, Kenji Onodera, Kenichi Wakabayashi, Takatsugu Kobayashi, Kensaku Sakamoto |
| D34 | Evaluating chromosome instability in cancer using gene expression data and location information Do Kyoon Kim, Ji Hun Kim, Sung Bum Cho, Young Ji Na, Hee Joon Chung, Ju Han Kim |
| D35 | Comparison between tandem repeats in coding and non-coding regions of the human genome Mularoni L., Ledda A., Alba M. |
| D36 | Scott: genome-wide palindrome exploration and annotation capable of hardware acceleration Kotrs J., Lexa M., Martinek T., Brazdova M., Fucik O. |
| D37 | Connect the dots: Exposing hidden protein family connections from the entire sequence tree Yaniv Loewenstein, Michal Linial |
| D38 | Strategies for computational Transcription Factor Binding Site discovery in humans Geoff Macintyre, Adam Kowalczyk, James Bailey, Izhak Haviv |
| D39 | Optimal combination of homology information using dynamic programming Malde, K. |
| D40 | Improved alignment of spliced DNA sequences to genomic data using Graphics Processor Units Svetlin A. Manavski, Alessandro Albiero, Claudio Forcato, Nicola Vitulo, Giorgio Valle |
| D41 | Intron Evolution in Drosophila Eshwar Meduri, Ashley Farlow, Christian Schloetterer |
| D42 | Evidence for transcriptional regulation by non-5’ CpG islands in the human genome Medvedeva Y.M., Fridman M.V., Oparina N.J., Malko D.B., Ermakova E.O., Kulakovskiy I.A., Makeev V.J. |
| D43 | Integrated Analysis of Estrogen-Responsive Transcriptome and ERalpha Binding Regions by ChIP-SEQ in Breast Cancer Cells Mutarelli M., Grober O.M.V, Cicatiello L., Paris O., Ferraro L., Weisz A. |
| D44 | A novel index to select appropriate sequences for multiple sequence alignment to predict functional regions of a protein Nemoto W, Toh H |
| D45 | Analyzing copy number variation: the human olfactory receptor subgenome as a model Olender T., Hasin Y., Khen M., Reed D., Wysocki C., Gerstein M., Kim P., Korbel J., Lancet D. |
| D46 | A novel approach to guide contig assembly in de novo sequencing of bacterial genomes by high-throughput methods Petrillo M., Cozzuto L., Paolella G. |
| D47 | Mining complex cancer patterns of chromosome aberration measured by Illumina 300K SNP bead array. Popova T., Manié E., Stoppa-Lyonnet D., Barillot E., Stern M.-H. |
| D48 | Codon Usage Bias and Protein Function in Multi-cellular Organisms Prat Y., Linial M. |
| D49 | A new hybrid, structure and artificial intelligence-based method for prediction of class II T-cell epitopes Pupo A, Moreno E |
| D50 | String Kernel Based Prediction of N-Terminal Acetylation of Proteins Ermir Qeli, Erich Brunner, Konrad Basler, Christian Ahrens |
| D51 | CISPPY : A Tool For Identifying Cis-regulatory Binding Sites with New Approach Faisal Ibne Rezwan, Mark Robinson, Yi Sun, Neil Davey, Rod Adams |
| D52 | From aCGH log-ratios to high-density DNA replication timing maps. Daniel Rico, Eduardo Andres, Luis R. Borlado, Javier Suela, Juan C. Cigudosa, Juan Mendez, David G. Pisano |
| D53 | Meta-analysis prediction of binding sites in the mouse genome Mark Robinson, Yi Sun, Rod Adams, Neil Davey, Alistair G. Rust |
| D54 | Intronic functional motifs network Gabriele Sales, Ivan Molineris, Concetta Miccio, Michele Caselle |
| D55 | Predicting gene function in S. cerevisiae and A. thaliana using hierarchical multi-label decision trees Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel, Dragi Kocev, Saso Dzeroski |
| D56 | JpHMM: A jumping profile HMM to detect recombinations in HIV-1 Schultz A.-K., Zhang M., Bulla I., Leitner T., Kuiken C., Korber B., Morgenstern B., Stanke M. |
| D57 | Fast Learning of Variable Order Markov Chains Marcel H. Schulz, David Weese, Hugues Richard, Tobias Rausch, Andreas Doering, Knut Reinert, Martin Vingron |
| D58 | Bioinformatic evidence for horizontal gene transfer in fungal genomes Shelest E., Guthke R., Brakhage A. |
| D59 | Evolution of amino acid repeats and disordered regions in developmental protein families and signalling pathways. Simon M., Mularoni L., Alba M., Hancock J. |
| D60 | Evaluation of intergene distances across bacterial species Skunca N., Supek F., Repar J., Smuc T. |
| D61 | Predicting Binding Sites in the Mouse Genome Using Meta Classification Methods Sun Y., Robinson M., Adams R., Rust A., Davey N. |
| D62 | On the assembly of short DNA fragments Swiercz A., Blazewicz J., Gawron P., Kasprzak M., Platt D., Szajkowski L. |
| D63 | Computational analysis of putative Type I and III restriction-modification systems in bacterial genomes Timinskas A., Venclovas Č. |
| D64 | Evaluating the influence of the choice of a background model in matrix-based pattern matching approaches Turatsinze J-V., Thomas-Chollier M., van Helden J. |
| D65 | Statistical Significance of Above Neutral Conservation in Local Alignments Kimmo Palin, Jussi Taipale, Esko Ukkonen |
| D66 | Predicting sub-Golgi localization of type II transmembrane proteins van Dijk A.D.J., Bosch D., ter Braak C.J.F., van der Krol S., van Ham R.C.H.J. |
| D67 | Gene prediction platform improved with second generation sequencers Nicola Vitulo, Alessandro Albiero, Claudio Forcato, Elisa Caniato, Alessandra Bilardi, Svetlin A.Manavski, Davide Campagna, Giorgio Valle |
| D68 | ANALYSIS OF THE HORSE GENOME IN ENSEMBL USING COMPARATIVE GENOMICS J.-H. Vogel, B. Aken, B. Ballester, K. Beal, E. Birney, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, V. Curwen, R. Durbin , T. Eyre, J. Fernandez-Banet, X.M. Fernandez-Suarez, S. Fitzgerald, S. Graef, M. Hammond, J. Herrero, K. Howe, N. Johnson, A. Kaehaeri, D. Keefe, E. Kulesha, D. Lawson, I. Longden, K. Megy, B. Overduin, A. Parker, G. Proctor, S. Rice, D. Rios, M. Schuster, S. Searle, G. Slater, D. Smedley, J. Smith, G. Spudich, S. Trevanion, A. Viella, S. White, T. Hubbard |
| D69 | Co-expression and Protein Interactions in Important Cellular Complexes Webb E.C., Westhead D.R. |
| D70 | Inference of spatial details in bacterial protein interaction from multi-species sequence data Martin Weigt, Robert A. White, Hendrik Szurmant, James A. Hoch, Terence Hwa |
| D71 | A Method for the Determination of Conservation of Exonic Structure
Wesselink, J.J., Rodriguez, J.M, Tress, M.L., Guigo, R., Valencia, A. |
| D72 | Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn |
E: Structural Bioinformatics
| E01 | Increasing precision of PROSITE motifs using secondary structure constraints Lucy Skrabanek, Masha Y. Niv |
| E02 | InterMap3D: predicting and visualizing co-evolving protein residues Gouveia-Oliveira R., Roque F. S., Wernersson R., Sicheritz-Pontén T., Sackett P.W., Mølgaard A., Pedersen A.G. |
| E03 | A Trusty Knowledge-Based Potential Energy Based on Pairwise Residue Contact Area S. Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk |
| E04 | Insilico study of lead compounds against RNA viruses S. Asthana, S. Shukla, G. Giliberti, M. Pezzullo, M. Ceccarelli, P. Ruggerone, P. La Colla |
| E05 | A biased model for the apo form of cyclic AMP receptor protein in E. coli Aykac Fas B., Tutar Y., Haliloglu T |
| E06 | Homology Protein Modelling of 5-HT3 Receptor: computational study of antagonists in receptor binding Barbosa A., De Rienzo F., Menziani M.C. |
| E07 | DETERMINANTS FOR SELECTIVITY IN MAP KINASE INHIBITORS BY COMPUTATIONAL SIMULATIONS Basant Nikita, Menziani Christina Maria |
| E08 | Improved scoring functions for the quality assessment of single protein structure models and ensembles Pascal Benkert, Silvio C.E. Tosatto, Torsten Schwede |
| E09 | The structure of the arsenate reductase LmACR2 highlights the substrate plasticity of the rhodanese fold. Bordo D., Mukhopadhyay R. |
| E10 | Role of model quality in the assessment of ligand-protein docking Bordogna A., Pandini A., Bonati L. |
| E11 | IMPROVED Local Protein Structure Prediction Assessed by Local Structure Networks. Bornot A., Etchebest C., de Brevern A.G. |
| E12 | Structural determinants of the interaction between the human cytomegalovirus UL18 protein and the CD85j immune receptor Marzia Occhino, Fabio Ghiotto, Simonetta Soro, Mimosa Mortarino, Stefania Bosi, Massimo Maffei, Silvia Bruno, Marco Nardini, Mariangela Figini, Anna Tramontano, Ermanno Ciccone |
| E13 | DYNAMIC ANALYSIS of Beta-LACTAMASE LIGAND RECOGNITION NILAY BUDEYRI, PINAR KANLIKILICER, BERNA SARIYAR AKBULUT, AMABLE HORTACSU, ELIF OZKIRIMLI OLMEZ |
| E14 | A repository of 3D models of human VDACs Bartoli L., Fariselli P., Fronza R., Martelli P.L., Montanucci L., Pierleoni A., Rossi I., Tasco G., Casadio R. |
| E15 | From Discoidal to Spheroidal HDL particles through Coarse Grained and All Atom Molecular Dynamics Simulations Catte A., Vuorela T., Niemelä P., Murtola T., Segrest J.P., Marrink S.J., Karttunen M., Vattulainen I. |
| E16 | Distortions induced by proline in alpha-helices REY Julien, DEVILLE Julie, CHABBERT Marie |
| E17 | A molecular approach to ligand-receptor interaction model Collu Francesca, Ceccarelli Matteo, Ruggerone Paolo |
| E18 | Molecular dynamics study of the structural changes induced by ATP hydrolysis in the NBD dimer of ABC transporter HlyB Damas J.M., Oliveira A.S.F., Baptista A.M., Soares C.M. |
| E19 | Using diverse interaction data to develop semi-atomic structural models of large multimeric complexes Davis C.A., Devos D., Betts M.J., Russell R.B. |
| E20 | A composite model for DNA torsion dynamics Cadoni, M., De Leo, R., Demelio, S., Gaeta, G. |
| E21 | Discrete optimization techniques for optimal bond order assignment Dehof A.K., Rurainski A., Mueller S., Lenhof H.P., Hildebrandt A. |
| E22 | CING: Validation Tools for Biomolecular NMR Structures Jurgen F. Doreleijers, Alan W.S. da Silva , Chris A. Spronk, Sander B. Nabuurs, Gert Vriend, Geerten W. Vuister |
| E23 | Structure prediction of a protein channel based on probabilistic formal grammars and the continuous ion flow model Dyrka W., Kotulska M., Nebel J.-C. |
| E24 | Identification of sequence patterns associated with proline cis/trans isomerization Exarchos K.P., Exarchos T.P., Papaloukas C., Troganis A.N., Fotiadis D.I. |
| E25 | Modelling and analysis of the structures of hyperthermophilic nucleoside hydrolases from S. solfataricus Anna Marabotti, Marina Porcelli, Iolanda Peluso, Giovanna Cacciapuoti, Angelo Facchiano |
| E26 | Protein Alignment based on Collective vibrational dynamics Sanjurjo L., Rocha C., Maguid S., Parisi G., Fernandez-Alberti S. |
| E27 | Optimized Null Model for Protein Structure Networks Filippis I., Milenkovic T., Lappe M., Przulj N. |
| E28 | Comparison of protein flexibilities: a study case on wild type and mutants of the SH3 domain. Fraccalvieri D., Pandini A., Bonati L. |
| E29 | REVELING TRNA-BINDING AND RECOGNITION SITES OF AMINO-ACYL TRNA SYNTHETASES BY MEANS OF CORRELATED MUTATIONS ANALYSIS Milana Frenkel-Morgenstern, Dmitry Tworowski, Mark G Safro |
| E30 | RAS-OMICS: an integrative approach Fuentes G., Valencia A. |
| E31 | Drug discovery at the protein-protein interface: a view from the binding site Fuller J.C., Burgoyne N.J., Jackson R.M. |
| E32 | A novel method for the detection of protein structural motifs binding specific ligand fragments Pier Federico Gherardini, Gabriele Ausiello, Elena Gatti, Manuela Helmer-Citterich |
| E33 | Structural and functional implications of cancer-related mutations of the KPNA5 gene. Travaglione A., Giorgetti A., Raimondo D., Tramontano A. |
| E34 | Applications of the BioShell package Dominik Gront |
| E35 | SCOTCHing protein complexes from the robust detection of coevolution events at their interfaces. Madaoui M., Faure G., Guerois R. |
| E36 | Structural and functional analysis of NMDA receptor complex and modelling interactions in NMDAR-PSD95-SynGAP complex Kamran Haider, James D Watson, Janet M Thornton |
| E37 | Structural determinants of antibiotic transport through bacterial outer membrane proteins eric hajjar, amit kumar, Francesca Collu, Enrico Spiga, Attilio Vargiu, Paolo Ruggerone , Matteo Ceccarelli |
| E38 | Re-refinement of macromolecular X-ray structures Joosten R.P., Vriend G. |
| E39 | RNA StructVis - RNA secondary structure visualization Daniel Jurczak, Andreas Heinzel, Martina Kutmon, Stefan Luger, Susanne Schaller, Andreas Schoenegger, Verena Hoenninger, Regina Kofler, Christian Siehs |
| E40 | Predicting drug-target promiscuity via ligand/protein superimpositions: phosphodiesterases as an illustrative example Kalinina O.V., Russell R.B. |
| E41 | A high throughput approach for structural peptide/MHC binding prediction Knapp, B., Omasits, U., Schreiner, W. |
| E42 | Binding-sites prediction assisting protein-protein docking Konc J., Janežič D. |
| E43 | Structural model of human MutLalpha protein and its experimental validation Kosinski J., Plotz G., Guarne A., Bujnicki J.M., Friedhoff P. |
| E44 | FireDB, firestar and SQUARE – a suite for the prediction of functionally important residues Gonzalo López, Alfonso Valencia, Michael L. Tress |
| E45 | Interaction Of Host Factor Protein With RNA Under Different Ionic Strengths - A Molecular Dynamics Simulation Approach Prettina Lazar, Keun Woo Lee |
| E46 | A global optimization algorithm for protein surface alignment Paola Bertolazzi, Concettina Guerra, Giampaolo Liuzzi |
| E47 | A molecular perspective of enzyme enantioselectivity in nonaqueous media Lousa D.A, Vidinha P., Cabral J. M. S, Barreiros S., Soares C. M. |
| E48 | Different molecular strategies for protein stabilization: effect of pH and temperature evaluated by MD simulations. Anna Marabotti, Angelo Facchiano, Andrea Scirè, Vincenzo Aurilia, Maria Staiano, Paola Ringhieri, Luisa Iozzino, Roberta Crescenzo, Fabio Tanfani, Sabato D'Auria |
| E49 | PIGS: Automatic prediction of immunoglobulin structures Marcatili P., Tramontano A. |
| E50 | A New Approach for Modeling Backbone Flexibility in Docking Mashiach Efrat, Nussinov Ruth, Wolfson Haim J. |
| E51 | A new web resource to retrieve and compare ubiquitin E2-E3 structural models Melquiond A.S.J., de Vries S.J., van Dijk M., van Wijk S.J.L., Timmers H.T.M., Boelens R., Bonvin A.M.J.J. |
| E52 | Refining Homology Built Models of Protein Structures by a Replica Exchange Monte Carlo Procedure Mendez-Giraldez R., Han R., Bastolla U., Ortiz A. R. |
| E53 | Impact of residue accessible surface area on the prediction of protein secondary structures Amir Momen-Roknabadi , Mehdi Sadeghi , Hamid Pezeshk , Sayed-Amir Marashi |
| E54 | Automated prediction of protein backbone structural motifs by recursive neural networks and remote homology information Mooney C., Pollastri G. |
| E55 | Do rotamer libraries reproduce the side chain conformations of peptidic ligands from the PDB? Pupo A., Moreno E. |
| E56 | A highthroughput tool for pitting proteins Andrea Bernini, Ottavia Spiga, Marco Dioguardi, Elisa Vannuccini, Erika Severini, Silvia Bottini, Neri Niccolai |
| E57 | Analysing the origin of long-range interactions in proteins using lattice models Noivirt-Brik O., Horovitz A., Unger R. |
| E58 | Estimation of effective length of chemical cross-linkers using computer simulations Obarska-Kosinska A., Kosinski J., Friedhoff P., Bujnicki J.M. |
| E59 | ASSESSING Alzheimer’s Protein-Protein Interaction Network Alarcon D., Kosmopoulou A., Bonet J., Panjkovich A., Aloy P., Oliva B. |
| E60 | Insights into functional diversity of aquaporins by comparative analysis of their sequences and structures Oliva R., Maiwald T., Calamita G., Thornton J. M., Pellegrini-Calace M. |
| E61 | INSIGHTS INTO THE ATP-HYDRLYSIS MECHANISM OF AN ABC-transporter: Conformational changes in the NBD dimer of MJ0796 Oliveira ASF, Baptista, AM, Soares, CM |
| E62 | MHC presentation of myelin basic protein in EAE - a molecular dynamics simulation study Ulrich Omasits, Bernhard Knapp, Wolfgang Schreiner, Michelle Epstein |
| E63 | Analysis of Protein Tyrosine Phosphatase 1B Dynamics using Biased Molecular Dynamics Simulations and Time Series Models Elif Ozkirimli, Burak Alakent |
| E64 | MinSet: automatic derivation of maximally representative subsets of protein structural domains Pandini A., Bonati L., Fraternali F., Kleinjung J. |
| E65 | PoreWalker: a novel tool to identify and characterize transmembrane protein channels from their 3D structure Marialuisa Pellegrini-Calace , Tim Maiwald , Janet M Thornton |
| E66 | Pepsite: A structural method to predict peptide/protein binding Petsalaki E., Stark A., Urdiales E.G., Russell R.B. |
| E67 | MAISTAS: Automatic Structural Evaluation of Alternative Splicing Products Floris M., Raimondo D., Orsini M., Camilli F., Giorgetti A., Tramontano A. |
| E68 | Extraction of important structural motifs from protein loops using statistical method and structural alphabet approach Regad L., Martin J., Nuel G., Camproux A.C. |
| E69 | Classical and quantum mechanical calculations of copper-1,10-phenanthroline complexes binding the DNA Robertazzi A., Vargiu A.V., Magistrato A., de Hoog P., Ruggerone P., Carloni P. , Reedijk J. |
| E70 | Inclusion of solvent into the concept of correlated mutations Samsonov S., Teyra J., Anders G. , Pisabarro M.T. |
| E71 | Sequential protein folding - implications for secondary structure Rhodri Saunders, Dr Charlotte M. Deane |
| E72 | Molecular Dynamics simulations of ligand binding in Myoglobins Mariano Andrea Scorciapino, Mariano Casu, Enrico Spiga, Paolo Ruggerone, Matteo Ceccarelli |
| E73 | Molecular dynamics simulations of two-domain constructs from copper-transporting ATPases Sharma S., Rosato A. |
| E74 | Prediction of Protein Flexible/Rigid Regions Based on Sequence Armita Sheari, S. Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi |
| E75 | Structure-based functional annotation of uncharacterized proteins with striking phenotypes in RNAi screenings Sontheimer J., Theis M., Buchholz F., Pisabarro M.T. |
| E76 | Reaching its target: the translocation of the moxifloxacin through OmpF Spiga Enrico, Ruggerone Paolo, Ceccarelli Matteo |
| E77 | Automated sequential assignment in 3D NMR spectra of RNAs Marta Szachniuk |
| E78 | Computer modeling studies on binding of curare-like Aconitum and Delphinium alkaloids to acetylcholine-binding protein Turabekova M.A., Rasulev B.F., Dzhakhangirov F.N. |
| E79 | Structural analysis of chromatin fiber architecture Giulia Turchetti, Anita Scipioni, Stefano Morosetti, Pasquale De Santis |
| E80 | Elastic network modeling of type II restriction endonucleases complexed with cognate and non-cognate DNA Arzu Uyar, Ozge Kurkcuoglu, Lennart Nilsson, Pemra Doruker |
| E81 | Characterization of site-specific interactions of the MTGase enzyme with G-CSF: why is Q134 PEGylated and Q131 is not? Valentini M., Giorgetti A., Raimondo D., Maullu C., Sergi M., Caboi F. |
| E82 | Mechanisms and kinetics of drug/DNA unbinding investigated by metadynamics Vargiu A.V., Ruggerone P., Magistrato A., Carloni P. |
| E83 | Simultaneous fitting of protein assembly components into cryoEM density maps Daven Vasishtan, Maya Topf |
| E84 | The Eukaryotic Linear Motif structural filter Via A., Gould C.M., Gemünd C., Gibson T.J., Helmer-Citterich M., and the ELM Consortium |
| E85 | Dioxygen and Nitric Oxide affinity and pathways to the catalytic site of Rubredoxin:Oxygen Oxidoreductase from D. gigas Victor B.L., Baptista A.M., Soares C.M. |
| E86 | MHC Binding Prediction Based on Pocket Specificity Library Hao Zhang, Morten Nielson, Ole Lund |
F: Transcriptomics
| F01 | Design and Implementation of a MicroRNAs-mRNAs cancer warehouse Reinier Frederic, Orsini Massimiliano, Enrico Capobianco |
| F02 | Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages Calura E., Cagnin S., Raffaello A. , Lanfranchi G., Romualdi C. |
| F03 | Combinatorial regulation across species: co-regulatory associations, hierarchy of regulation and evolutionary dynamics Nitin Bhardwaj, Mark Gerstein |
| F04 | A comparison on effects of normalizations in the detection of differentially expressed genes Risso D., Chiogna M., Massa MS., Romualdi C. |
| F05 | waviCGH: Web Analysis Visualization and Integration of CGH data. Angel Carro, Daniel Rico, Eduardo Andres, Francesco Acquadro, Cristina I. Gomez, Gonzalo Gomez-Lopez, David G. Pisano |
| F06 | Multi-Class Kernel-Imbedded Gaussian Processes for Microarray Data Analysis Cheung L.W.K., Zhao X. |
| F07 | SSHscreen and SSHdb, a software pipeline for microarray based screening and sequence management of cDNA libraries. Coetzer N. , Berger D.K., Gazendam I. |
| F08 | Dissecting an alternative splicing analysis pipe-line for Exon 1.0 ST Affymetrix arrays. Cristina Della Beffa, Francesca Cordero, Raffaele A. Calogero |
| F09 | Creation of expression compendia from cross-platform microarray data Engelen K, Qiang F, Lemmens K, Desmet R, Carolina F, Thijs I, Marchal K |
| F10 | Accounting for the presence of paralogs in microarray gene-set analyses using Indygene Andre J. Faure, Cathal Seoighe, Nicola Mulder |
| F11 | Bayesian population models to learn gene networks from multiple expression experiments Ferrazzi F. , Rinaldi S. , Parikh A., Shaulsky G., Zupan B., Bellazzi R. |
| F12 | Comparative analysis of gene expression across species Ana Carolina Fierro, Peyman Zarrineh, Kristof Engelen, Mieke Verstuyf, Guy Eelen, Lieve Verlinden, Kathleen Marchal |
| F13 | Systematic detection errors of alternative splicing caused by variable probe response characteristics in exon arrays Gaidatzis D., Oakeley E., Stadler M.B. |
| F14 | Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. Greco D, Somervuo P, Di Lieto A, Raitila T, Nitsch L, Castrén E, Auvinen P |
| F15 | Sequence and structure requirements for miRNA-dependent RISC binding and mRNA degradation Hausser J., Landthaler M., Gaidatzis D., Tuschl T., Zavolan M. |
| F16 | Transcriptome Analysis by High-Throughput Sequencing of cDNA using the Illumina® Genome Analyzer Khrebtukova I., Luo S., Yan J., Vermaas E., Quijano V., Schroth G.P. |
| F17 | Gene Ontology Assisted Clustering of Microarrays Geoff Macintyre, James Bailey, Daniel Gustafsson, Alex Boussioutas, Izhak Haviv, Adam Kowalczyk |
| F18 | Modeling gene expression in biological networks Lahti, L., Knuuttila, J.E.A., Kaski, S. |
| F19 | A model based approach to probe design for high-performance microarrays German Gaston Leparc, Thomas Tüchler, Gerald Striedner, Karl Bayer, Peter Sykacek, Ivo Hofacker |
| F20 | Sequencing the transcriptome in prostate cancer Nacu S., Kan Z., Seshagiri S., Wu T. |
| F21 | Segmentation of gene expression helps to discover parts of the genome correlated with Copy Number alterations Ortiz M., Rubio A. |
| F22 | Semiparametric models with many smoothers for the analysis of microarray data Marcin Przystalski, Pawel Krajewski |
| F23 | KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences Schultheiss S.J., Busch W., Lohmann J.U., Kohlbacher O., Raetsch G. |
| F24 | Comparison of exon array analysis methods for detecting splice variants Axel Rasche, Ralf Herwig |
| F25 | Genomic and transcriptomic mapping of microarray probes at locus and exon level to achieve accurate expression profiles Risueno A., Fontanillo C., De Las Rivas J. |
| F26 | Finding temporal patterns of GO processes in DNA microarray experiments Sacchi L., Nuzzo A., Decontardi F., Bellazzi R. |
| F27 | The prediction of differential expression in transcriptomic data from co-expression in A. Thaliana Shanahan, H |
| F28 | Correcting for sequence dependencies in whole genome methylation measurements in mammals Sylvia Tippmann, Michael Stadler, Dimosthenis Gaidatzis, Fabio Mohn, Michael Weber, Dirk Schuebeler |
| F29 | Indentification of stress responsive protein subnetworks Dr Frances Turner |
| F30 | COMPARATIVE expression analysis of human and canine breast tumors Uva P., Palombo F., Aurisicchio L., Mesiti G., Lahm A., La Monica N., De Rinaldis, E. |
G: Proteomics
| G01 | A procedure for the analysis of MALDI imaging data Nicola Barbarini, Christian Fuchsberger, Wolfgang Wieder, Georg Bartsch, Günther Bonn, Helmut Klocker, Riccardo Bellazzi |
| G02 | Backing up 2DE Depletion with Wavelet Detection Methods Soggiu A. , Marullo O. , Roncada P. , Capobianco E. |
| G03 | Novel visualization tools for proteomics data Luca Bianco, Eleonora Grosso, Jennifer A. Mead, Conrad Bessant |
| G04 | Processing Enhancement In Image Proteomics Allow To Derive Protein Differential Fingerprint Via Machine Learning Cannistraci C.V., Montevecchi F. M., Alessio M. |
| G05 | A Comparison of Time Warping Algorithms based on High Quality Mass Traces Christin Christin, Age Smilde, Huub Hoefsloot, Frank Suits, Rainer Bischoff, Peter Horvatovich |
| G06 | KINASE- specific phosphorylation site prediction based on a Conditional Random Fields model Dang H.T., Leemput K.V., Verschoren A., Laukens K. |
| G07 | Machine learning based membrane protein identification from tandem mass spectra Tejas Gandhi, Hjalmar Permentier, Bert Poolman, Rainer Breitling |
| G08 | Fuzzy Clustering of Likelihood Curves to Reveal Protein Modifications Claudia Hundertmark, Frank Klawonn, Lothar Jänsch |
| G09 | Applying community standard MS/MS datasets to evaluate proteomic data analysis pipeline performance Mead J.A., Bianco L., Bessant C. |
| G10 | MsPI: a tool for the analysis of peptide mass fingerprinting data Tiengo A., Barbarini N., Troiani S., Rusconi L., Magni P. |
| G11 | A model-based method for the analysis of enzymatic stable-isotope labeled peptides in MALDI-TOF mass-spectra. Valkenborg D., Burzykowski T. |
| G12 | Applying statistical feature selection to Proteomics and Metabolomic data for Prostate Cancer biomarkers identification Yue Fan, Brendan Murphy, Jennifer Byrne, Lorraine Brennan, John Fitzpatrick, William Watson |
H: Pathways and interactions
| H01 | Photoperception in Halobacterium salinarum: a systems biology approach. Cangelosi D., Cercignani G., Chiarugi D., Felicioli C., Freschi L., Fulgentini L., Marangoni R. |
| H02 | FUNCTIONAL Module Identification through Protein Interaction Network Alignment Ali W, Deane CM |
| H03 | Discovering Geometric Structure in Protein-Protein Interaction Networks: The Embedding Algorithm Desmond J. Higham, Marija Rasajski, Natasa Przulj |
| H04 | An Efficient Method for Identifying Statistical Interactors in Graphical Models Alina Andrei, Christina Kendziorski |
| H05 | GraphCrunch: a tool for large network analyses Milenkovic, T., Lai, J., Przulj, N. |
| H06 | Random generation of metabolic networks with biochemical constraints Georg Basler, Zoran Nikoloski, Oliver Ebenhöh |
| H07 | Pathway analysis improves comparability of different data sets: an application to the study of renal carcinoma Luca Beltrame, Ingrid Cifola, Roberta Spinelli, Clelia Peano, Duccio Cavalieri, Cristina Battaglia |
| H08 | Integrative Analysis of the Oct-4 Regulatory Network in hESCs Chavez L., Adjaye J., Lehrach H., Herwig R. |
| H09 | CENTRALITY of immunolgy proteins in the human interactome Clancy T, Hovig E |
| H10 | The identification of similarities between biological networks Cootes A.P., Sternberg M.J.E., Muggleton S.H., Ranganathan S. |
| H11 | Pathway Alignment: A Comparative Approach in Understanding Metabolic Evolution Dutta A., Paul S., Bag S.K., Dutta C. |
| H12 | Constructing and Investigating mouse gene and phenotype networks Octavio Espinosa, John M. Hancock |
| H13 | Insights into protein-protein interface patterns. Iakes Ezkurdia, Michael Tress, Alfonso Valencia, Lisa Bartoli, Rita Casadio, Piero Fariselli |
| H14 | Extracting Sub-Networks of Knowledge (SNK) from Protein-Protein Interaction data. Luis Fernandes, Franca Fraternali |
| H15 | TAG_TSEMA: Enhancing the prediction of protein pairings between interacting families using “a-priori” information Izarzugaza JM G. , Juan D., Valencia A., Pazos F. |
| H16 | The gene expression networks of Clostridium perfringens strain 13 from gene expression profiles Hirakawa H., Ohno M., Furuichi E., Ohtani K., Shimizu T., Kuhara S. |
| H17 | Characterization of Protein Interfaces in the Human Cancer Protein-Protein Interaction Network Kar G., Gursoy A., Keskin O. |
| H18 | Differential equations method for clustering gene expression time-courses. Krawczyk M.J., Dziedzicka-Wasylewska M., Kulakowski K. |
| H19 | Panel Screening & Network Analysis: Better understanding of compound profiling Gonzalez Couto, E. , Felciano, R. , Kremer, A. |
| H20 | Combining Molecular Dynamics Simulations with Experiment to design Antibiotics with Improved Permeation Properties Amit Kumar, Eric Hajjar, Enrico Spiga, Paolo Ruggerone, Matteo Ceccarelli |
| H21 | BIOGRANAT - Molecular Biology Graph Visualisation and Analysis Tool Lehne B., Bente I., Hellmann B., Kammeyer H., Kirstein S., Mendig A., Schulz A., Steinmetz M., Vieweg J., Zimmer B., Sprengel F., Ahlers V., Schlitt T. |
| H22 | Uncovering Biological Network Function via Graphlet Degree Signatures Milenkovic, T., Przulj, N. |
| H23 | Human metabolic pathways in the small molecule chemical space Macchiarulo A., Thornton J. M., Nobeli I. |
| H24 | Discovering new apoptosis proteins from protein interaction networks: determination of the best cadidates Joan Planas-Iglesias, Kevin A. Robertson, Sobia Raza, Tom C. Freeman, Peter Ghazal, Baldo Oliva |
| H25 | Comparison and assessment of structural domain-domain intercations to improve protein-protein interaction data Carlos Prieto, Javier De Las Rivas |
| H26 | Enabling a Remote Collaboration Environment for Integration of Quantitative Molecular Pathways Eva Sciacca, V A Shiva Ayyadurai, C Forbes Dewey |
I: Systems biology
| I01 | An Iterative, Analysis-driven Experimentation (ADE) Feedback Loop to Enable Complete Proteome Coverage Projects Christian H. Ahrens,, Ermir Qeli,, Sandra Götze,, Eva Niederer,, Ralph Schlapbach,, Ruedi Aebersold,, Erich Brunner,, Konrad Basler |
| I02 | Common problems in simulating biological systems Cangelosi D., Cercignani G., Chiarugi D., Felicioli C., Freschi L., Fulgentini L., van Klinken J.B., Marangoni R. |
| I03 | Inferring Modularity Aspects from Human Protein Interactome Classes Chaurasia G., Marras E. , Futschik M.E., Capobianco E. |
| I04 | THE M-FUNC PROJECT: NEW BOINFORMATIC METHODS FOR THE PREDICTION OF MULTIFUNCTIONAL PROTEINS Emmanuelle Becker, Jean-Baptiste Angelleli, Alain Guenoche, Carl Herrmann, Christine Brun |
| I05 | The human interactome: inference of a comprehensive gene network in human cells. Belcastro V., Cutillo L., di Bernardo D. |
| I06 | Protein-protein interaction networks and tissue-specificity Souiai O., Becker E., Brun C. |
| I07 | The role of promoter similarity and gene clustering in establishing co-expression networks in myeloid cells. Coppe A., Ferrari F., Bisognin A., Bicciato S., Ferrari S., Danieli GA., Bortoluzzi S. |
| I08 | Reverse engineering: role of system complexity and multi-experiment design on networks reconstruction and hub detection Corradin A., Di Camillo B., Toffolo G.M., Cobelli C. |
| I09 | PIN-AP: an epigenetic synthetic toggle switch Cuccato G., Polynikis A., di Bernardo M., di Bernardo D. |
| I10 | A new opensource software for the 3D realistic modelling and visualization of supramolecular assemblies Lariviere D., Fourmentin E. |
| I11 | Investigation of the Effects of Medium Composition and Relating Biomass Composition on Metabolic Modelling of Yeast Dikicioglu D., Kirdar B., Oliver S. G. |
| I12 | Tracing the evolution of protein interaction networks Janusz Dutkowski, Jerzy Tiuryn |
| I13 | A systematic approach of osteoclastogenesis Elefsinioti A., Simeone A., Michaelson J.J., Beyer A. |
| I14 | An integrative approach to infer the transcriptional regulatory network of Bacillus subtilis Fadda A., Joshi A., Engelen K., Lemmens K., Fierro A. C., Van de Peer Y., Marchal K. |
| I15 | Logical Modelling of the Budding Yeast Cell Cycle: a Modular Approach Adrien Fauré, Aurélien Naldi, Fabrice Lopez, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry |
| I16 | Correlation structure of co-expression networks - visualisation and feature detection Feher K.M. |
| I17 | SCOPE - A metabolite reference library building tool Godin N., Gordon M., Rubin E. |
| I18 | Comparison of Algorithms for Reverse Engineering from RNAi experiment data Hendrik Hache, Hans Lehrach, Ralf Herwig |
| I19 | Optimizing graph alignments Michal Kolář, Michael Lässig, Johannes Berg |
| I20 | Results of the combination of multiple partitions for the analysis of short time series microarray data G. Kırçiçeği Y. KORKMAZ, Rengül ÇETİN-ATALAY, Volkan ATALAY |
| I21 | The role of elastic stresses on leaf venation morphogenesis Maria Fabiana Laguna, Steffen Bohn, Eduardo Jagla |
| I22 | NIRest: a tool for simultaneous gene network and mode of action inference Lauria M., Iorio F. , di Bernardo D. |
| I23 | Computer system for modeling and analysis of plant tissue development Lavrekha V.V, Penenko A.V., Nikolaev S.V, Kolchanov N.A. |
| I24 | Modelling metabolic processes in insulin-secreting pancreatic beta-cells Lee D. Hazelwood, John M. Hancock |
| I25 | Exploring the interplay between topology and dynamical properties of directed biological networks: a case-study Mancosu G, Pieroni E, Fotia G, Maggio F, de la Fuente A |
| I26 | Computational systems biology approach to investigate microRNAs role in Ewing system. Martignetti L., Zinovyev A., Stoll G., Tirode F., Laud-Duval K., Delattre O., Barillot E. |
| I27 | How to model a synthetic network. Lucia Marucci, Irene Cantone, Stefania Santini, Mario di Bernardo, Maria Pia Cosma, Diego di Bernardo. |
| I28 | Identifying cancer specific differentially expressed modules in Protein Interaction Networks Mentzen W.I., Corno D., Pala M., Bulfone A., Galli R., de la Fuente A. |
| I29 | PRECISION AND SCALING IN DROSOPHILA EMBRYO PATTERNING Aitana Morton de Lachapelle, Sven Bergmann |
| I30 | Mean-shift clustering approach to the analysis of phenotypic data of an image-based genome-wide siRNA screen. Nikolay Samusik, Yannis Kalaidzidis, Marino Zerial |
| I31 | Ab initio gene prioritization Nitsch D., Moreau Y. |
| I32 | Genome wide survey of MicroRNA - Transcription Factors regulatory circuits in human Re Angela, Cora Davide, Caselle Michele |
| I33 | A systems biology approach to link gene regulation and fermentation phenotypes in wine yeast Rossouw D, Bauer FF |
| I34 | How to synchronize a genetic network Russo G., di Bernardo M. |
| I35 | Role of network structure and experimental design on the performance of two Reverse Engineering methods. Sambo F., Di Camillo B., Toffolo G. |
| I36 | Towards the construction of a biological clock in a mammalian system Velia Siciliano, Diego di Bernardo |
| I37 | Towards genetic regulatory networks of neurogenesis in the fruitfly, Drosophila melanogaster. Simpson, T. I., Townshend, H. C., Jarman, A. P. |
| I38 | ModuleVisualization: visualize gene module network Hong Sun, Jan Bollen, Tim Van den Bulckel, Karen Lemmen, Bart De Moor, Kathleen Marchal |
| I39 | Facilitating ChIP-chip-based reconstruction of regulatory networks by combining omics data Thijs I.M., De Smet R., Engelen K., De Keersmaecker S.C.J., Vanderleyden J., Marchal K. |
| I40 | Characterising interactions between human and bacteria using transcriptomics and proteomics: a systems biology approach van Baarlen P., Groenen M.A.M., Aslam W.M.L., Everest P., Wells J.M. |
| I41 | Studying the organization and evolution of transcriptional control in Arabidopsis through coexpression networks Klaas Vandepoele, Yves Van de Peer |
| I42 | Metabolic network structure analysis: a case study on glycolysis in Lactococcus lactis Susana Vinga, Karl Thomaseth, João M. Lemos, Ana Rute Neves, Helena Santos, Ana T. Freitas |
| I43 | Stochasticity in the EGFR-stimulated activation of ras Russ Harmer, Joshua Havumaki, Isha Antani, Gordon Webster |
| I44 | Predictive models in the face of uncertainty: a Monte Carlo strategy to develop a systems biology of cancer Wierling C., Daskalaki A., Maschke-Dutz E., Herwig R., Lehrach H. |
| I45 | A new method for modeling binding reaction kinetics in immunoassays Ylander P.Y., Hänninen P., Koskinen J.O. |
| I46 | Identification of overlapping biclusters using probabilistic relational models, applied to gene expression data. Tim Van den Bulcke, Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal |
J: Bioinformatics for diseases
| J01 | Modeling the Protein-Protein Interactions of the Pro-Apoptotic Protein ASPP2 Benyamini H., Katz C., Rotem S., Friedler A. |
| J02 | Computational redesign of binding of the cytosolic NEP peptide to merlin and moesin proteins Masha Y. Niv, Katsuyuki Iida, Rong Zheng, Akio Horiguchi, David M. Nanus |
| J03 | Bag of Peaks: interpretation of NMR spectroscopy Manuele Bicego, Gavin Brelstaff, Nicola Culeddu, Matilde Chessa |
| J04 | Kernel ENDEAVOUR: a web platform for kernel based gene prioritization by data fusion Shi Yu, Leon-Charles Tranchevent, Roland Barriot, Daniela Nitsch, Tijl De Bie, Bart De Moor, Yves Moreau |
| J05 | Dealing with bias in clinical data sets: Distribution matching and transfer learning for HIV therapy selection Bogojeska J., Bickel S., Scheffer T., Lengauer T. |
| J06 | IDENTIFICATION OF SIGNIFICANT OVERLAP OF DIFFERENTIALLY EXPRESSED AND GENOMIC IMBALANCED REGIONS IN CANCER DATASETS Ferrari F., Spinelli R., Mangano E., Beltrame L., Zampieri M., Cifola I., Peano C., Bicciato S., Battaglia C. |
| J07 | Robust multiclass predictor based on redefined genes: study on leukemias to reveal gene signatures associated Fontanillo C., Risueño A., Prieto C., De Las Rivas J. |
| J08 | Functional symbiont-host relationship between Epstein-Barr virus and Homo sapiens Aymeric Fouquier d'Herouel, Maria Werner |
| J09 | Extensive analysis of human blood group antigen genes suggest non neutral evolution at multiple loci Fumagalli M., Pozzoli U., Menozzi G., Cereda M., Cagliani R., Comi G.P., Bresolin N., Sironi M. |
| J10 | Comparative QSAR Modeling of Anti-tubercular Activity of Nitrofuranyl Amide Derivatives Payel Ghosh, Dr. Manish C. Bagchi |
| J11 | Understanding drug Mode-of-Action: Mining the cMap dataset Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo |
| J12 | Predicting response of HIV patients using SNP-drug interactions Marek D., Tarr P., Telenti A., Beckmann J., Bergmann S. |
| J13 | GenSense: An "end to end" genome wide association study platform Kalaitzopoulos D., Van der Hall P., Pescatori M., Van den Hout M., Munro R., Verkerk A., Van der Spek, Stubbs A. |
| J14 | Gene-Environment iNteraction Simulator (GENS) for assessing the power of feature selection methods in complex diseases Amato R., D'Andrea D., Miele G., Nicodemi M., Pinelli M., Raiconi G., Tagliaferri R., Cocozza S. |
| J15 | A proper machine learning approach to validate the HME Classification Mordenti M., Ferrari E., Locatelli M., Pedrini E., Muselli M., Sangiorgi L. |
| J16 | Optimization of BRC peptide for the inhibition of the human Rad51 protein filament formation Nomme J., Renodon-Corniere A., Tran V., Takahashi M. |
| J17 | Lung cancer DSA: A platform for discovery of biomarkers in Lung cancer Gavin R. Oliver, Austin Tanney, Vadim Farztdinov, Richard D. Kennedy, Jude M. Mulligan, Ciaran E. Fulton, Susan M. Farragher, John K. Field, Patrick G. Johnston, D. Paul Harkin, Vitali Proutski, Karl A. Mulligan |
| J18 | Multiple instance learning allows MHC class II epitope predictions for alleles without experimental data Nico Pfeifer, Oliver Kohlbacher |
| J19 | Expression profiling of medulloblastoma Cancer Stem Cells (CSCs) in comparison with normal neural stem cells (NSCs) Pillai R., Pala M., Scintu F., Caria S., Corno D., Galli R., Bulfone A. |
| J20 | Prediction of Human Disease Genes by Analysis of Conserved Coexpression Ugo Ala, Rosario M. Piro, Elena Grassi, Christian Damasco, Lorenzo Silengo, Martin Oti, Paolo Provero, Ferdinando Di Cunto |
| J21 | The Italian Network for Oncology Bioinformatics Romano P., Crescenzi M. |
| J22 | Microarray Meta-Analysis Highlights Neuro-Immune Signaling in Parkinson's Disease Patients Lilach Soreq, Zvi Israel, Hagai Bergman, Hermona Soreq |
| J23 | Computational analysis of in vitro screening data highlights an atypical cytostatic mechanism of a cytosine derivative Fran Supek, Marijeta Kralj, Biserka Zinic, Tomislav Smuc |
| J24 | In Silico Study of wild-type and Raltegravir-selected Mutants of HIV-1: Structural and DNA Recognition Properties Tchertanov L., Mouscadet J.-F. |
| J25 | Gene prioritization through genomic data fusion: algorithm and applications. Leon-Charles Tranchevent, Stein Aerts, Bernard Thienpont, Peter Van Loo, Shi Yu, Bert Coessens, Roland Barriot, Steven Van Vooren, Bassem Hassam, Yves Moreau |
| J26 | INNOVATION in bioinformatics education: tailor-made course material from high school to PhD Van Gelder C., Joosten R., Guillard M., Venselaar H., Vriend G. |
| J27 | Consensus Filtering of Narrow DNA Aberrations in SNP Array Data: Proof of Principle Gerard Wong, Christopher Leckie, Ian Campbell, Kylie Gorringe, Izhak Haviv, Adam Kowalczyk |