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 
   
All posters set up (poster must be set by 17:30).  
Tuesday,23 September 2008
  
16:10.18:00   
Poster Session 1 (Odd numbered (A-1, A-3, ..) posters presented.  
Thursday,25 September 2008
  
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 Guidelines
 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.
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 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
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 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
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 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
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 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
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 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.
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 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
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 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
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 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
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 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
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