Volume 9, issue 1, December 2008
559 articles in this issue
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Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method
Authors
- Joseph W Foley
- Fumiaki Katagiri
- Content type: Methodology article
- Open Access
- Published: 29 November 2008
- Article: 508
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MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
Authors (first, second and last of 4)
- Jianguo Xia
- Trent C Bjorndahl
- David S Wishart
- Content type: Research article
- Open Access
- Published: 28 November 2008
- Article: 507
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c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
Authors
- Katerina Kechris
- Hao Li
- Content type: Methodology article
- Open Access
- Published: 28 November 2008
- Article: 506
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Use of normalization methods for analysis of microarrays containing a high degree of gene effects
Authors (first, second and last of 4)
- Terri T Ni
- William J Lemon
- Tao P Zhong
- Content type: Methodology article
- Open Access
- Published: 28 November 2008
- Article: 505
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Highly sensitive feature detection for high resolution LC/MS
Authors
- Ralf Tautenhahn
- Christoph Böttcher
- Steffen Neumann
- Content type: Research article
- Open Access
- Published: 28 November 2008
- Article: 504
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ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins
Authors
- Aarti Garg
- Gajendra PS Raghava
- Content type: Research article
- Open Access
- Published: 28 November 2008
- Article: 503
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Microarray-based gene set analysis: a comparison of current methods
Authors
- Sarah Song
- Michael A Black
- Content type: Methodology article
- Open Access
- Published: 27 November 2008
- Article: 502
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Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features
Authors (first, second and last of 5)
- Derek Huntley
- Y Amy Tang
- Neil Brockdorff
- Content type: Software
- Open Access
- Published: 27 November 2008
- Article: 501
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Prediction of glycosylation sites using random forests
Authors
- Stephen E Hamby
- Jonathan D Hirst
- Content type: Research article
- Open Access
- Published: 27 November 2008
- Article: 500
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Natural computation meta-heuristics for the in silico optimization of microbial strains
Authors (first, second and last of 8)
- Miguel Rocha
- Paulo Maia
- Isabel Rocha
- Content type: Research article
- Open Access
- Published: 27 November 2008
- Article: 499
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MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level
Authors (first, second and last of 6)
- Hélène Chiapello
- Annie Gendrault
- Meriem El Karoui
- Content type: Database
- Open Access
- Published: 27 November 2008
- Article: 498
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Clustering cancer gene expression data: a comparative study
Authors (first, second and last of 5)
- Marcilio CP de Souto
- Ivan G Costa
- Alexander Schliep
- Content type: Research article
- Open Access
- Published: 27 November 2008
- Article: 497
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Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes
Authors
- Josephine F Reyes
- Andrew R Francis
- Mark M Tanaka
- Content type: Research article
- Open Access
- Published: 27 November 2008
- Article: 496
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CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
Authors (first, second and last of 6)
- Matthew S Hestand
- Michiel van Galen
- Peter AC 't Hoen
- Content type: Software
- Open Access
- Published: 26 November 2008
- Article: 495
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ExonMiner: Web service for analysis of GeneChip Exon array data
Authors (first, second and last of 6)
- Kazuyuki Numata
- Ryo Yoshida
- Satoru Miyano
- Content type: Software
- Open Access
- Published: 26 November 2008
- Article: 494
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EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
Authors (first, second and last of 16)
- G Barton
- J Abbott
- SA Butcher
- Content type: Software
- Open Access
- Published: 25 November 2008
- Article: 493
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Structural descriptor database: a new tool for sequence-based functional site prediction
Authors
- Juliana S Bernardes
- Jorge H Fernandez
- Ana Tereza R Vasconcelos
- Content type: Database
- Open Access
- Published: 25 November 2008
- Article: 492
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Prediction of specificity-determining residues for small-molecule kinase inhibitors
Authors
- Daniel R Caffrey
- Elizabeth A Lunney
- Deborah J Moshinsky
- Content type: Methodology article
- Open Access
- Published: 25 November 2008
- Article: 491
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A comparison of four clustering methods for brain expression microarray data
Authors (first, second and last of 5)
- Alexander L Richards
- Peter Holmans
- Lesley Jones
- Content type: Research article
- Open Access
- Published: 25 November 2008
- Article: 490
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Determining gene expression on a single pair of microarrays
Authors
- Robert W Reid
- Anthony A Fodor
- Content type: Methodology article
- Open Access
- Published: 21 November 2008
- Article: 489
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Identifying differential correlation in gene/pathway combinations
Authors
- Rosemary Braun
- Leslie Cope
- Giovanni Parmigiani
- Content type: Methodology article
- Open Access
- Published: 18 November 2008
- Article: 488
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Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable
Authors (first, second and last of 4)
- Myron Peto
- Andrzej Kloczkowski
- Robert L Jernigan
- Content type: Research article
- Open Access
- Published: 18 November 2008
- Article: 487
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Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification
Authors
- Michael Gormley
- Aydin Tozeren
- Content type: Research article
- Open Access
- Published: 17 November 2008
- Article: 486
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CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
Authors
- Paolo Uva
- Emanuele de Rinaldis
- Content type: Software
- Open Access
- Published: 17 November 2008
- Article: 485
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Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Authors (first, second and last of 4)
- Jakub Orzechowski Westholm
- Feifei Xu
- Jan Komorowski
- Content type: Research article
- Open Access
- Published: 17 November 2008
- Article: 484
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mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
Authors (first, second and last of 6)
- Hwan Young Lee
- Injee Song
- Kyoung-Jin Shin
- Content type: Software
- Open Access
- Published: 17 November 2008
- Article: 483
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CellProfiler Analyst: data exploration and analysis software for complex image-based screens
Authors (first, second and last of 8)
- Thouis R Jones
- In Han Kang
- Anne E Carpenter
- Content type: Software
- Open Access
- Published: 15 November 2008
- Article: 482
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Gene set enrichment analysis for non-monotone association and multiple experimental categories
Authors (first, second and last of 6)
- Rongheng Lin
- Shuangshuang Dai
- Leping Li
- Content type: Methodology article
- Open Access
- Published: 14 November 2008
- Article: 481
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A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data
Authors (first, second and last of 5)
- Luca Corradi
- Marco Fato
- Livia Torterolo
- Content type: Software
- Open Access
- Published: 13 November 2008
- Article: 480
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Extension of the COG and arCOG databases by amino acid and nucleotide sequences
Authors
- Florian Meereis
- Michael Kaufmann
- Content type: Database
- Open Access
- Published: 13 November 2008
- Article: 479
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RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
Authors
- James K Hane
- Richard P Oliver
- Content type: Methodology article
- Open Access
- Published: 12 November 2008
- Article: 478
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Improved identification of conserved cassette exons using Bayesian networks
Authors (first, second and last of 6)
- Rileen Sinha
- Michael Hiller
- Rolf Backofen
- Content type: Research article
- Open Access
- Published: 12 November 2008
- Article: 477
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CoCoNUT: an efficient system for the comparison and analysis of genomes
Authors
- Mohamed I Abouelhoda
- Stefan Kurtz
- Enno Ohlebusch
- Content type: Software
- Open Access
- Published: 12 November 2008
- Article: 476
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Standardized high-throughput evaluation of cell-based compound screens
Authors
- Peter Frommolt
- Roman K Thomas
- Content type: Software
- Open Access
- Published: 12 November 2008
- Article: 475
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RNAalifold: improved consensus structure prediction for RNA alignments
Authors (first, second and last of 5)
- Stephan H Bernhart
- Ivo L Hofacker
- Peter F Stadler
- Content type: Methodology article
- Open Access
- Published: 11 November 2008
- Article: 474
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Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling
Authors (first, second and last of 5)
- Thora Pommerencke
- Thorsten Steinberg
- Niels Grabe
- Content type: Methodology article
- Open Access
- Published: 06 November 2008
- Article: 473
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Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data
Authors
- Tao Xu
- LinFang Du
- Yan Zhou
- Content type: Research article
- Open Access
- Published: 06 November 2008
- Article: 472
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Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes
Authors (first, second and last of 8)
- Inna Myslyuk
- Tirza Doniger
- Ron Unger
- Content type: Research article
- Open Access
- Published: 05 November 2008
- Article: 471
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MetaFIND: A feature analysis tool for metabolomics data
Authors
- Kenneth Bryan
- Lorraine Brennan
- Pádraig Cunningham
- Content type: Software
- Open Access
- Published: 05 November 2008
- Article: 470
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Gene set analyses for interpreting microarray experiments on prokaryotic organisms
Authors (first, second and last of 7)
- Nathan L Tintle
- Aaron A Best
- Ronald C Taylor
- Content type: Methodology article
- Open Access
- Published: 05 November 2008
- Article: 469
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A relation based measure of semantic similarity for Gene Ontology annotations
Authors (first, second and last of 4)
- Brendan Sheehan
- Aaron Quigley
- Simon Dobson
- Content type: Methodology article
- Open Access
- Published: 04 November 2008
- Article: 468
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Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
Authors
- Weijun Luo
- Kurt D Hankenson
- Peter J Woolf
- Content type: Research article
- Open Access
- Published: 03 November 2008
- Article: 467
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Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats
Authors (first, second and last of 6)
- Vladimir Paar
- Nenad Pavin
- Nils Paar
- Content type: Research article
- Open Access
- Published: 03 November 2008
- Article: 466
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QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR
Authors (first, second and last of 4)
- Samuel Arvidsson
- Miroslaw Kwasniewski
- Bernd Mueller-Roeber
- Content type: Software
- Open Access
- Published: 01 November 2008
- Article: 465
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Neutral network sizes of biological RNA molecules can be computed and are not atypically small
Authors
- Thomas Jörg
- Olivier C Martin
- Andreas Wagner
- Content type: Research article
- Open Access
- Published: 30 October 2008
- Article: 464
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Information-based methods for predicting gene function from systematic gene knock-downs
Authors (first, second and last of 4)
- Matthew T Weirauch
- Christopher K Wong
- Joshua M Stuart
- Content type: Research article
- Open Access
- Published: 29 October 2008
- Article: 463
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Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer
Authors
- Raffaele Giancarlo
- Davide Scaturro
- Filippo Utro
- Content type: Research article
- Open Access
- Published: 29 October 2008
- Article: 462
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minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
Authors
- Patrick E Meyer
- Frédéric Lafitte
- Gianluca Bontempi
- Content type: Software
- Open Access
- Published: 29 October 2008
- Article: 461
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A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
Authors (first, second and last of 5)
- Sabine Pérès
- Laurence Molina
- Franck Molina
- Content type: Software
- Open Access
- Published: 28 October 2008
- Article: 460