Volume 8, issue 1, December 2007
488 articles in this issue
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OReFiL: an online resource finder for life sciences
Authors
- Yasunori Yamamoto
- Toshihisa Takagi
- Content type: Database
- Open Access
- Published: 06 August 2007
- Article: 287
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CLUSS: Clustering of protein sequences based on a new similarity measure
Authors (first, second and last of 4)
- Abdellali Kelil
- Shengrui Wang
- Alain Fleury
- Content type: Software
- Open Access
- Published: 04 August 2007
- Article: 286
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miRAS: a data processing system for miRNA expression profiling study
Authors (first, second and last of 7)
- Feng Tian
- Huayue Zhang
- Xiangjun Liu
- Content type: Methodology article
- Open Access
- Published: 04 August 2007
- Article: 285
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Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
Authors
- Carson Andorf
- Drena Dobbs
- Vasant Honavar
- Content type: Correspondence
- Open Access
- Published: 03 August 2007
- Article: 284
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Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
Authors (first, second and last of 5)
- Xiangdong Liu
- Walter J Jessen
- Mario Medvedovic
- Content type: Research article
- Open Access
- Published: 03 August 2007
- Article: 283
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Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model
Authors
- Scott D Zuyderduyn
- Content type: Methodology article
- Open Access
- Published: 02 August 2007
- Article: 282
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Identification of discriminative characteristics for clusters from biologic data with InforBIO software
Authors (first, second and last of 4)
- Naoto Tanaka
- Masataka Uchino
- Hideaki Sugawara
- Content type: Software
- Open Access
- Published: 02 August 2007
- Article: 281
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PepBank - a database of peptides based on sequence text mining and public peptide data sources
Authors (first, second and last of 5)
- Timur Shtatland
- Daniel Guettler
- Ralph Weissleder
- Content type: Database
- Open Access
- Published: 01 August 2007
- Article: 280
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Combination of scoring schemes for protein docking
Authors
- Philipp Heuser
- Dietmar Schomburg
- Content type: Methodology article
- Open Access
- Published: 01 August 2007
- Article: 279
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Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants
Authors (first, second and last of 5)
- Erin P Price
- John Inman-Bamber
- Philip M Giffard
- Content type: Methodology article
- Open Access
- Published: 01 August 2007
- Article: 278
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Haplotype-based score test for linkage in nuclear families
Authors
- Chung Mo Nam
- Dae Ryong Kang
- Jinheum Kim
- Content type: Methodology article
- Open Access
- Published: 01 August 2007
- Article: 277
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AffyMAPSDetector: a software tool to characterize Affymetrix GeneChipâ„¢ expression arrays with respect to SNPs
Authors
- Sunita Kumari
- Lalit K Verma
- Jennifer W Weller
- Content type: Software
- Open Access
- Published: 30 July 2007
- Article: 276
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Large-scale integration of cancer microarray data identifies a robust common cancer signature
Authors
- Lei Xu
- Donald Geman
- Raimond L Winslow
- Content type: Research article
- Open Access
- Published: 30 July 2007
- Article: 275
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3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions
Authors (first, second and last of 9)
- Benjamin B Andken
- In Lim
- James O Deshler
- Content type: Database
- Open Access
- Published: 30 July 2007
- Article: 274
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The utility of MAS5 expression summary and detection call algorithms
Authors (first, second and last of 5)
- Stuart D Pepper
- Emma K Saunders
- Crispin J Miller
- Content type: Research article
- Open Access
- Published: 30 July 2007
- Article: 273
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A cis-regulatory logic simulator
Authors
- Robert D Zeigler
- Jason Gertz
- Barak A Cohen
- Content type: Methodology article
- Open Access
- Published: 27 July 2007
- Article: 272
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
Authors
- Markus Bauer
- Gunnar W Klau
- Knut Reinert
- Content type: Methodology article
- Open Access
- Published: 27 July 2007
- Article: 271
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Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets
Authors (first, second and last of 4)
- Guillaume Launay
- Raul Mendez
- Thomas Simonson
- Content type: Research article
- Open Access
- Published: 27 July 2007
- Article: 270
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Automating document classification for the Immune Epitope Database
Authors (first, second and last of 5)
- Peng Wang
- Alexander A Morgan
- Bjoern Peters
- Content type: Research article
- Open Access
- Published: 26 July 2007
- Article: 269
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msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
Authors
- Michael J Hickerson
- Eli Stahl
- Naoki Takebayashi
- Content type: Software
- Open Access
- Published: 26 July 2007
- Article: 268
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Classification of heterogeneous microarray data by maximum entropy kernel
Authors
- Wataru Fujibuchi
- Tsuyoshi Kato
- Content type: Research article
- Open Access
- Published: 26 July 2007
- Article: 267
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BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes
Authors (first, second and last of 4)
- Yingqin Luo
- Cong Fu
- Kui Lin
- Content type: Database
- Open Access
- Published: 25 July 2007
- Article: 266
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Semantic integration to identify overlapping functional modules in protein interaction networks
Authors (first, second and last of 4)
- Young-Rae Cho
- Woochang Hwang
- Aidong Zhang
- Content type: Methodology article
- Open Access
- Published: 24 July 2007
- Article: 265
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Using contextual and lexical features to restructure and validate the classification of biomedical concepts
Authors
- Jung-Wei Fan
- Hua Xu
- Carol Friedman
- Content type: Research article
- Open Access
- Published: 24 July 2007
- Article: 264
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Analysis and prediction of antibacterial peptides
Authors
- Sneh Lata
- BK Sharma
- GPS Raghava
- Content type: Methodology article
- Open Access
- Published: 23 July 2007
- Article: 263
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False positive reduction in protein-protein interaction predictions using gene ontology annotations
Authors
- Mahmoud A Mahdavi
- Yen-Han Lin
- Content type: Research article
- Open Access
- Published: 23 July 2007
- Article: 262
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Applying negative rule mining to improve genome annotation
Authors
- Irena I Artamonova
- Goar Frishman
- Dmitrij Frishman
- Content type: Methodology article
- Open Access
- Published: 21 July 2007
- Article: 261
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A procedure for identifying homologous alternative splicing events
Authors (first, second and last of 4)
- David Talavera
- Adam Hospital
- Xavier de la Cruz
- Content type: Methodology article
- Open Access
- Published: 19 July 2007
- Article: 260
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Reuse of structural domain–domain interactions in protein networks
Authors
- Benjamin Schuster-Böckler
- Alex Bateman
- Content type: Research article
- Open Access
- Published: 18 July 2007
- Article: 259
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Accelerated search for biomolecular network models to interpret high-throughput experimental data
Authors
- Suman Datta
- Bahrad A Sokhansanj
- Content type: Methodology article
- Open Access
- Published: 18 July 2007
- Article: 258
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Bayesian refinement of protein functional site matching
Authors (first, second and last of 5)
- Kanti V Mardia
- Vysaul B Nyirongo
- David R Westhead
- Content type: Research article
- Open Access
- Published: 17 July 2007
- Article: 257
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HoughFeature, a novel method for assessing drug effects in three-color cDNA microarray experiments
Authors
- Hongya Zhao
- Hong Yan
- Content type: Methodology article
- Open Access
- Published: 17 July 2007
- Article: 256
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The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments
Authors (first, second and last of 6)
- Mario Cannataro
- Giovanni Cuda
- Pierangelo Veltri
- Content type: Software
- Open Access
- Published: 15 July 2007
- Article: 255
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Progressive multiple sequence alignments from triplets
Authors
- Matthias Kruspe
- Peter F Stadler
- Content type: Methodology article
- Open Access
- Published: 15 July 2007
- Article: 254
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Difference-based clustering of short time-course microarray data with replicates
Authors
- Jihoon Kim
- Ju Han Kim
- Content type: Methodology article
- Open Access
- Published: 14 July 2007
- Article: 253
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Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
Authors (first, second and last of 5)
- Paolo Ferragina
- Raffaele Giancarlo
- Gabriel Valiente
- Content type: Research article
- Open Access
- Published: 13 July 2007
- Article: 252
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Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks
Authors
- Chang Sik Kim
- Content type: Research article
- Open Access
- Published: 13 July 2007
- Article: 251
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Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
Authors (first, second and last of 10)
- Curtis Huttenhower
- Avi I Flamholz
- Hilary A Coller
- Content type: Software
- Open Access
- Published: 12 July 2007
- Article: 250
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A novel ensemble learning method for de novo computational identification of DNA binding sites
Authors (first, second and last of 4)
- Arijit Chakravarty
- Jonathan M Carlson
- Robert H Gross
- Content type: Methodology article
- Open Access
- Published: 12 July 2007
- Article: 249
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Erratum to: Inference of miRNA targets using evolutionary conservation and pathway analysis
Authors (first, second and last of 4)
- Dimos Gaidatzis
- Erik van Nimwegen
- Mihaela Zavolan
- Content type: Erratum
- Open Access
- Published: 12 July 2007
- Article: 248
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HoxPred: automated classification of Hox proteins using combinations of generalised profiles
Authors
- Morgane Thomas-Chollier
- Luc Leyns
- Valérie Ledent
- Content type: Research article
- Open Access
- Published: 12 July 2007
- Article: 247
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Simcluster: clustering enumeration gene expression data on the simplex space
Authors (first, second and last of 5)
- Ricardo ZN Vêncio
- Leonardo Varuzza
- Ilya Shmulevich
- Content type: Software
- Open Access
- Published: 11 July 2007
- Article: 246
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Artificial neural network models for prediction of intestinal permeability of oligopeptides
Authors (first, second and last of 12)
- Eunkyoung Jung
- Junhyoung Kim
- Seung-Hoon Choi
- Content type: Research article
- Open Access
- Published: 11 July 2007
- Article: 245
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A survey of orphan enzyme activities
Authors
- Yannick Pouliot
- Peter D Karp
- Content type: Research article
- Open Access
- Published: 10 July 2007
- Article: 244
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Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
Authors (first, second and last of 5)
- Nikolai Daraselia
- Anton Yuryev
- Iaroslav Ispolatov
- Content type: Research article
- Open Access
- Published: 10 July 2007
- Article: 243
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Improving gene set analysis of microarray data by SAM-GS
Authors (first, second and last of 10)
- Irina Dinu
- John D Potter
- Yutaka Yasui
- Content type: Methodology article
- Open Access
- Published: 05 July 2007
- Article: 242
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Erratum to: Splice site identification using probabilistic parameters and SVM classification
Authors (first, second and last of 4)
- AKMA Baten
- BCH Chang
- Jason Li
- Content type: Erratum
- Open Access
- Published: 05 July 2007
- Article: 241
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Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data
Authors
- Randall Hulshizer
- Eric M Blalock
- Content type: Methodology article
- Open Access
- Published: 05 July 2007
- Article: 240
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Probabilistic prediction and ranking of human protein-protein interactions
Authors
- Michelle S Scott
- Geoffrey J Barton
- Content type: Research article
- Open Access
- Published: 05 July 2007
- Article: 239