Bioinformatics

ECCB 2008 CONFERENCE PROCEEDINGS 22-26 SEPTEMBER 2008, CAGLIARI, ITALY

EDITORIALS

Anna Tramontano On behalf of the ECCB’08 steering committee

Editorial
Bioinformatics 2008 24: i1; doi:10.1093/bioinformatics/btn377 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ECCB 2008 Organization
Bioinformatics 2008 24: i3-i5; doi:10.1093/bioinformatics/btn369 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS

DATABASES

Get checked abstract Daniel Dalevi, Natalia N. Ivanova, Konstantinos Mavromatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C. Kyrpides, and Victor M. Markowitz

Annotation of metagenome short reads using proxygenes
Bioinformatics 2008 24: i7-i13; doi:10.1093/bioinformatics/btn276 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, and Chi-Ying F. Huang

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
Bioinformatics 2008 24: i14-i20; doi:10.1093/bioinformatics/btn297 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract A.M. Willemsen, G.A. Jansen, J.C. Komen, S. van Hooff, H.R. Waterham, P.M.T. Brites, R.J.A. Wanders, and A.H.C. van Kampen

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
Bioinformatics 2008 24: i21-i27; doi:10.1093/bioinformatics/btn274 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PATHWAYS/INTERACTIONS/PROTEOMICS

Get checked abstract Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, and Ananth Grama

Functional coherence in domain interaction networks
Bioinformatics 2008 24: i28-i34; doi:10.1093/bioinformatics/btn296 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sven-Eric Schelhorn, Thomas Lengauer, and Mario Albrecht

An integrative approach for predicting interactions of protein regions
Bioinformatics 2008 24: i35-i41; doi:10.1093/bioinformatics/btn290 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Lukas Käll, John D. Storey, and William Stafford Noble

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
Bioinformatics 2008 24: i42-i48; doi:10.1093/bioinformatics/btn294 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sebastian Böcker and Florian Rasche

Towards de novo identification of metabolites by analyzing tandem mass spectra
Bioinformatics 2008 24: i49-i55; doi:10.1093/bioinformatics/btn270 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Gabi Kastenmüller, Johann Gasteiger, and Hans-Werner Mewes

An environmental perspective on large-scale genome clustering based on metabolic capabilities
Bioinformatics 2008 24: i56-i62; doi:10.1093/bioinformatics/btn302 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

TRANSCRIPTOMICS

Get checked abstract Elena Tsiporkova and Veselka Boeva

Fusing time series expression data through hybrid aggregation and hierarchical merge
Bioinformatics 2008 24: i63-i69; doi:10.1093/bioinformatics/btn264 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pei Gao, Antti Honkela, Magnus Rattray, and Neil D. Lawrence

Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities
Bioinformatics 2008 24: i70-i75; doi:10.1093/bioinformatics/btn278 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fantine Mordelet and Jean-Philippe Vert

SIRENE: supervised inference of regulatory networks
Bioinformatics 2008 24: i76-i82; doi:10.1093/bioinformatics/btn273 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hubert Rehrauer, Susan Schönmann, Leo Eberl, and Ralph Schlapbach

PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays
Bioinformatics 2008 24: i83-i89; doi:10.1093/bioinformatics/btn269 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Israel Steinfeld, Roy Navon, Diego Ardigò, Ivana Zavaroni, and Zohar Yakhini

Clinically driven semi-supervised class discovery in gene expression data
Bioinformatics 2008 24: i90-i97; doi:10.1093/bioinformatics/btn279 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Gergely Csaba, Fabian Birzele, and Ralf Zimmer

Protein structure alignment considering phenotypic plasticity
Bioinformatics 2008 24: i98-i104; doi:10.1093/bioinformatics/btn271 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rafael Najmanovich, Natalja Kurbatova, and Janet Thornton

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
Bioinformatics 2008 24: i105-i111; doi:10.1093/bioinformatics/btn263 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Emidio Capriotti and Marc A. Marti-Renom

RNA structure alignment by a unit-vector approach
Bioinformatics 2008 24: i112-i118; doi:10.1093/bioinformatics/btn288 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

TEXT MINING

Get checked abstract Shi Yu, Steven Van Vooren, Leon-Charles Tranchevent, Bart De Moor, and Yves Moreau

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining
Bioinformatics 2008 24: i119-i125; doi:10.1093/bioinformatics/btn291 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, and Graciela Gonzalez

Inter-species normalization of gene mentions with GNAT
Bioinformatics 2008 24: i126-i132; doi:10.1093/bioinformatics/btn299 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Crystal L. Kahn and Benjamin J. Raphael

Analysis of segmental duplications via duplication distance
Bioinformatics 2008 24: i133-i138; doi:10.1093/bioinformatics/btn292 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ALGORITHMS AND PHYLOGENY

Get checked abstract Erez Ben-Yaacov and Yonina C. Eldar

A fast and flexible method for the segmentation of aCGH data
Bioinformatics 2008 24: i139-i145; doi:10.1093/bioinformatics/btn272 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Wei Xu, Benoît Alain, and David Sankoff

Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases
Bioinformatics 2008 24: i146-i152; doi:10.1093/bioinformatics/btn295 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Vikas Bansal and Vineet Bafna

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
Bioinformatics 2008 24: i153-i159; doi:10.1093/bioinformatics/btn298 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Paulo G. S. da Fonseca, Katia S. Guimarães, and Marie-France Sagot

Efficient representation and P-value computation for high-order Markov motifs
Bioinformatics 2008 24: i160-i166; doi:10.1093/bioinformatics/btn282 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, and Hiroshi Mamitsuka

Mining significant tree patterns in carbohydrate sugar chains
Bioinformatics 2008 24: i167-i173; doi:10.1093/bioinformatics/btn293 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENOMES AND PROTEIN ANALYSIS

Get checked abstract Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar Rätsch

Optimal spliced alignments of short sequence reads
Bioinformatics 2008 24: i174-i180; doi:10.1093/bioinformatics/btn300 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Marie-Laure Martin-Magniette, Tristan Mary-Huard, Caroline Bérard, and Stéphane Robin

ChIPmix: mixture model of regressions for two-color ChIP–chip analysis
Bioinformatics 2008 24: i181-i186; doi:10.1093/bioinformatics/btn280 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cedric Notredame, and Knut Reinert

Segment-based multiple sequence alignment
Bioinformatics 2008 24: i187-i192; doi:10.1093/bioinformatics/btn281 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yaniv Loewenstein and Michal Linial

Connect the dots: exposing hidden protein family connections from the entire sequence tree
Bioinformatics 2008 24: i193-i199; doi:10.1093/bioinformatics/btn301 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nir Yosef, Roded Sharan, and William Stafford Noble

Improved network-based identification of protein orthologs
Bioinformatics 2008 24: i200-i206; doi:10.1093/bioinformatics/btn277 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yana Bromberg and Burkhard Rost

Comprehensive in silico mutagenesis highlights functionally important residues in proteins
Bioinformatics 2008 24: i207-i212; doi:10.1093/bioinformatics/btn268 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Julio Saez-Rodriguez, Stefan Gayer, Martin Ginkel, and Ernst Dieter Gilles

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
Bioinformatics 2008 24: i213-i219; doi:10.1093/bioinformatics/btn289 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Elisabeth Remy and Paul Ruet

From minimal signed circuits to the dynamics of Boolean regulatory networks
Bioinformatics 2008 24: i220-i226; doi:10.1093/bioinformatics/btn287 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, and Hidde de Jong

Temporal logic patterns for querying dynamic models of cellular interaction networks
Bioinformatics 2008 24: i227-i233; doi:10.1093/bioinformatics/btn275 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Aitor González, Claudine Chaouiya, and Denis Thieffry

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc
Bioinformatics 2008 24: i234-i240; doi:10.1093/bioinformatics/btn266 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

BIOINFORMATICS FOR DISEASES

Get checked abstract Predrag Radivojac, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, and Sean D. Mooney

Gain and loss of phosphorylation sites in human cancer
Bioinformatics 2008 24: i241-i247; doi:10.1093/bioinformatics/btn267 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Louis-Philippe Kronek and Anupama Reddy

Logical analysis of survival data: prognostic survival models by detecting high-degree interactions in right-censored data
Bioinformatics 2008 24: i248-i253; doi:10.1093/bioinformatics/btn265 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

AUTHOR INDEX

Author Index
Bioinformatics 2008 24: i254-i255; doi:10.1093/bioinformatics/btn399 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE

GENOME ANALYSIS

Get checked abstract Meng Li, Hyun-il Henry Paik, Curt Balch, Yoosung Kim, Lang Li, Tim H-M. Huang, Kenneth P. Nephew, and Sun Kim

Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells
Bioinformatics Advance Access published on June 6, 2008
Bioinformatics 2008 24: 1745-1748; doi:10.1093/bioinformatics/btn256 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, and Yidong Chen

A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
Bioinformatics Advance Access published on July 4, 2008
Bioinformatics 2008 24: 1749-1756; doi:10.1093/bioinformatics/btn321 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Duncan P. Brown

Efficient functional clustering of protein sequences using the Dirichlet process
Bioinformatics Advance Access published on May 29, 2008
Bioinformatics 2008 24: 1765-1771; doi:10.1093/bioinformatics/btn244 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract A. D. J. van Dijk, D. Bosch, C. J. F. ter Braak, A. R. van der Krol, and R. C. H. J. van Ham

Predicting sub-Golgi localization of type II membrane proteins
Bioinformatics Advance Access published on June 18, 2008
Bioinformatics 2008 24: 1779-1786; doi:10.1093/bioinformatics/btn309 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Ali Torkamani and Nicholas J. Schork

Predicting functional regulatory polymorphisms
Bioinformatics Advance Access published on June 18, 2008
Bioinformatics 2008 24: 1787-1792; doi:10.1093/bioinformatics/btn311 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Liam J. McGuffin

Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
Bioinformatics Advance Access published on June 25, 2008
Bioinformatics 2008 24: 1798-1804; doi:10.1093/bioinformatics/btn326 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Scott F. Saccone, Nancy L. Saccone, Gary E. Swan, Pamela A. F. Madden, Alison M. Goate, John P. Rice, and Laura J. Bierut

Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
Bioinformatics Advance Access published on June 19, 2008
Bioinformatics 2008 24: 1805-1811; doi:10.1093/bioinformatics/btn315 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, and Jean X. Gao

Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data
Bioinformatics Advance Access published on June 18, 2008
Bioinformatics 2008 24: 1812-1818; doi:10.1093/bioinformatics/btn316 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE

STRUCTURAL BIOINFORMATICS

Get checked abstract Yungki Park and Volkhard Helms

MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon
Bioinformatics Advance Access published on June 10, 2008
Bioinformatics 2008 24: 1819-1820; doi:10.1093/bioinformatics/btn255 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Brian W. Lambert, Joseph D. Terwilliger, and Kenneth M. Weiss

ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth
Bioinformatics Advance Access published on June 19, 2008
Bioinformatics 2008 24: 1821-1822; doi:10.1093/bioinformatics/btn317 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES

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