Bioinformatics

ECCB 2006 CONFERENCE PROCEEDINGS, JANUARY 21-24, EILAT, ISRAEL:

EDITORIALS:

ECCB 2006
Bioinformatics 2007 23: e1-e2; doi:10.1093/bioinformatics/btl631 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ECCB 2006 Organization
Bioinformatics 2007 23: e3-e4; doi:10.1093/bioinformatics/btl651 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

Get checked abstract Sebastian Böcker

Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
Bioinformatics 2007 23: e5-e11; doi:10.1093/bioinformatics/btl291 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yanay Ofran and Burkhard Rost

ISIS: interaction sites identified from sequence
Bioinformatics 2007 23: e13-e16; doi:10.1093/bioinformatics/btl303 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Huzefa Rangwala and George Karypis

Incremental window-based protein sequence alignment algorithms
Bioinformatics 2007 23: e17-e23; doi:10.1093/bioinformatics/btl297 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ariel S. Schwartz and Lior Pachter

Multiple alignment by sequence annealing
Bioinformatics 2007 23: e24-e29; doi:10.1093/bioinformatics/btl311 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dina Sokol, Gary Benson, and Justin Tojeira

Tandem repeats over the edit distance
Bioinformatics 2007 23: e30-e35; doi:10.1093/bioinformatics/btl309 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yanni Sun and Jeremy Buhler

Designing patterns for profile HMM search
Bioinformatics 2007 23: e36-e43; doi:10.1093/bioinformatics/btl323 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Abha Singh Bais, Steffen Grossmann, and Martin Vingron

Simultaneous alignment and annotation of cis-regulatory regions
Bioinformatics 2007 23: e44-e49; doi:10.1093/bioinformatics/btl305 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte, and T. Schiex

A comparative genome approach to marker ordering
Bioinformatics 2007 23: e50-e56; doi:10.1093/bioinformatics/btl321 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Matan Gavish, Amnon Peled, and Benny Chor

Genetic code symmetry and efficient design of GC-constrained coding sequences
Bioinformatics 2007 23: e57-e63; doi:10.1093/bioinformatics/btl317 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Filip Hermans and Elena Tsiporkova

Merging microarray cell synchronization experiments through curve alignment
Bioinformatics 2007 23: e64-e70; doi:10.1093/bioinformatics/btl320 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Macha Nikolski and David J. Sherman

Family relationships: should consensus reign?—consensus clustering for protein families
Bioinformatics 2007 23: e71-e76; doi:10.1093/bioinformatics/btl314 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Doron Lipson, Zohar Yakhini, and Yonatan Aumann

Optimization of probe coverage for high-resolution oligonucleotide aCGH
Bioinformatics 2007 23: e77-e83; doi:10.1093/bioinformatics/btl316 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chun Ye and Eleazar Eskin

Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
Bioinformatics 2007 23: e84-e90; doi:10.1093/bioinformatics/btl315 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, and Roded Sharan

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data
Bioinformatics 2007 23: e91-e98; doi:10.1093/bioinformatics/btl298 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, and Hans-Peter Lenhof

Electrostatic potentials of proteins in water: a structured continuum approach
Bioinformatics 2007 23: e99-e103; doi:10.1093/bioinformatics/btl312 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rafael J. Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled Edwards, Cheryl Arrowsmith, and Janet M. Thornton

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family
Bioinformatics 2007 23: e104-e109; doi:10.1093/bioinformatics/btl292 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract José C. Clemente, Kenji Satou, and Gabriel Valiente

Phylogenetic reconstruction from non-genomic data
Bioinformatics 2007 23: e110-e115; doi:10.1093/bioinformatics/btl307 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pawel Górecki and Jerzy Tiuryn

Inferring phylogeny from whole genomes
Bioinformatics 2007 23: e116-e122; doi:10.1093/bioinformatics/btl296 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller

Efficient parsimony-based methods for phylogenetic network reconstruction
Bioinformatics 2007 23: e123-e128; doi:10.1093/bioinformatics/btl313 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Matthias Bernt, Daniel Merkle, and Martin Middendorf

Using median sets for inferring phylogenetic trees
Bioinformatics 2007 23: e129-e135; doi:10.1093/bioinformatics/btl300 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Matan Ninio, Eyal Privman, Tal Pupko, and Nir Friedman

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
Bioinformatics 2007 23: e136-e141; doi:10.1093/bioinformatics/btl304 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Saharon Rosset

Efficient inference on known phylogenetic trees using Poisson regression
Bioinformatics 2007 23: e142-e147; doi:10.1093/bioinformatics/btl306 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tomer Hertz and Chen Yanover

Identifying HLA supertypes by learning distance functions
Bioinformatics 2007 23: e148-e155; doi:10.1093/Bioinformatics/btl324 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Keith Noto and Mark Craven

Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects
Bioinformatics 2007 23: e156-e162; doi:10.1093/bioinformatics/btl319 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Barak Raveh, Ofer Rahat, Ronen Basri, and Gideon Schreiber

Rediscovering secondary structures as network motifs—an unsupervised learning approach
Bioinformatics 2007 23: e163-e169; doi:10.1093/bioinformatics/btl290 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Eitan Hirsh and Roded Sharan

Identification of conserved protein complexes based on a model of protein network evolution
Bioinformatics 2007 23: e170-e176; doi:10.1093/bioinformatics/btl295 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Natasa Przulj

Biological network comparison using graphlet degree distribution
Bioinformatics 2007 23: e177-e183; doi:10.1093/bioinformatics/btl301 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Oleg Rokhlenko, Ydo Wexler, and Zohar Yakhini

Similarities and differences of gene expression in yeast stress conditions
Bioinformatics 2007 23: e184-e190; doi:10.1093/bioinformatics/btl308 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, and Marc Sturm

TOPP—the OpenMS proteomics pipeline
Bioinformatics 2007 23: e191-e197; doi:10.1093/bioinformatics/btl299 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, and Andrew Emili

Difference detection in LC-MS data for protein biomarker discovery
Bioinformatics 2007 23: e198-e204; doi:10.1093/bioinformatics/btl326 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fabian Birzele, Jan E. Gewehr, Gergely Csaba, and Ralf Zimmer

Vorolign—fast structural alignment using Voronoi contacts
Bioinformatics 2007 23: e205-e211; doi:10.1093/bioinformatics/btl294 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, and Dan Halperin

Prediction and simulation of motion in pairs of transmembrane -helices
Bioinformatics 2007 23: e212-e218; doi:10.1093/bioinformatics/btl325 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, and Adam Godzik

Using an alignment of fragment strings for comparing protein structures
Bioinformatics 2007 23: e219-e224; doi:10.1093/bioinformatics/btl310 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Etai Jacob and Ron Unger

A tale of two tails: why are terminal residues of proteins exposed?
Bioinformatics 2007 23: e225-e230; doi:10.1093/bioinformatics/btl318 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Annalisa Marsico, Dirk Labudde, Tanuj Sapra, Daniel J. Muller, and Michael Schroeder

A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy
Bioinformatics 2007 23: e231-e236; doi:10.1093/bioinformatics/btl293 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, and Peter Stoehr

EBIMed—text crunching to gather facts for proteins from Medline
Bioinformatics 2007 23: e237-e244; doi:10.1093/bioinformatics/btl302 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

EDITORIALS:

Alfonso Valencia, Alex Bateman, and Executive Editors

EDITORIAL
Bioinformatics 2007 23: 133; doi:10.1093/bioinformatics/btl635 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

SEQUENCE ANALYSIS:

Get checked abstract Richard J. Dixon, Ian C. Eperon, and Nilesh J. Samani

Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression
Bioinformatics Advance Access published on November 14, 2006
Bioinformatics 2007 23: 150-155; doi:10.1093/bioinformatics/btl575 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Michael Farrar

Striped Smith–Waterman speeds database searches six times over other SIMD implementations
Bioinformatics Advance Access published on November 16, 2006
Bioinformatics 2007 23: 156-161; doi:10.1093/bioinformatics/btl582 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xu Zhang and Tamer Kahveci

QOMA: quasi-optimal multiple alignment of protein sequences
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 162-168; doi:10.1093/bioinformatics/btl590 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

STRUCTURAL BIOINFORMATICS:

Get checked abstract Joo Chuan Tong, Tin Wee Tan, and Shoba Ranganathan

In silico grouping of peptide/HLA class I complexes using structural interaction characteristics
Bioinformatics Advance Access published on November 7, 2006
Bioinformatics 2007 23: 177-183; doi:10.1093/bioinformatics/btl563 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract J. R. de Haan, R. Wehrens, S. Bauerschmidt, E. Piek, R. C. van Schaik, and L. M. C. Buydens

Interpretation of ANOVA models for microarray data using PCA
Bioinformatics Advance Access published on November 14, 2006
Bioinformatics 2007 23: 184-190; doi:10.1093/bioinformatics/btl572 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andreas W. Schreiber and Ute Baumann

A framework for gene expression analysis
Bioinformatics Advance Access published on November 21, 2006
Bioinformatics 2007 23: 191-197; doi:10.1093/bioinformatics/btl591 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, and Cathy H. Wu

Dependence network modeling for biomarker identification
Bioinformatics Advance Access published on October 31, 2006
Bioinformatics 2007 23: 198-206; doi:10.1093/bioinformatics/btl553 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, and Richard H. Scheuermann

Modular organization of protein interaction networks
Bioinformatics Advance Access published on November 8, 2006
Bioinformatics 2007 23: 207-214; doi:10.1093/bioinformatics/btl562 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaotu Ma, Hyunju Lee, Li Wang, and Fengzhu Sun

CGI: a new approach for prioritizing genes by combining gene expression and protein–protein interaction data
Bioinformatics Advance Access published on November 10, 2006
Bioinformatics 2007 23: 215-221; doi:10.1093/bioinformatics/btl569 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Karin Deal, Jan Dvorak, and Olin D. Anderson

GenoProfiler: batch processing of high-throughput capillary fingerprinting data
Bioinformatics Advance Access published on October 2, 2006
Bioinformatics 2007 23: 240-242; doi:10.1093/bioinformatics/btl494 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nicolás Bellora, Domènec Farré, and M. Mar Albà

PEAKS: identification of regulatory motifs by their position in DNA sequences
Bioinformatics Advance Access published on November 10, 2006
Bioinformatics 2007 23: 243-244; doi:10.1093/bioinformatics/btl568 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Sinae Kim, Jerry Tsai, Ioannis Kagiampakis, Patricia LiWang, and Marina Vannucci

Detecting protein dissimilarities in multiple alignments using Bayesian variable selection
Bioinformatics Advance Access published on November 14, 2006
Bioinformatics 2007 23: 245-246; doi:10.1093/bioinformatics/btl566 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract R. Cathelin, F. Lopez, and Ch. Klopp

AGScan: a pluggable microarray image quantification software based on the ImageJ library
Bioinformatics Advance Access published on November 8, 2006
Bioinformatics 2007 23: 247-248; doi:10.1093/bioinformatics/btl564 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Reagan J. Kelly, Douglas M. Jacobsen, Yan V. Sun, Jennifer A. Smith, and Sharon L. R. Kardia

KGraph: a system for visualizing and evaluating complex genetic associations
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2007 23: 249-251; doi:10.1093/bioinformatics/btl510 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shaun Purcell, Mark J. Daly, and Pak C. Sham

WHAP: haplotype-based association analysis
Bioinformatics Advance Access published on November 21, 2006
Bioinformatics 2007 23: 255-256; doi:10.1093/bioinformatics/btl580 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

DATA AND TEXT MINING:

Get checked abstract J. A. Falkner, J. W. Falkner, and P. C. Andrews

ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 262-263; doi:10.1093/bioinformatics/btl573 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, and Jonas S. Almeida

PrepMS: TOF MS data graphical preprocessing tool
Bioinformatics Advance Access published on November 22, 2006
Bioinformatics 2007 23: 264-265; doi:10.1093/bioinformatics/btl583 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data
Bioinformatics 2007 23: 266; doi:10.1093/bioinformatics/btl576 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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