![](https://media.springernature.com/w92/springer-static/cover/journal/12859/9/1.jpg)
Volume 9, issue 1, December 2008
559 articles in this issue
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GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords
Authors (first, second and last of 6)
- Zhong-Xi Huang
- Hui-Yong Tian
- Kai-Tai Yao
- Content type: Software
- Open Access
- Published: 13 July 2008
- Article: 308
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Conditional variable importance for random forests
Authors (first, second and last of 5)
- Carolin Strobl
- Anne-Laure Boulesteix
- Achim Zeileis
- Content type: Methodology article
- Open Access
- Published: 11 July 2008
- Article: 307
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Grammar-based distance in progressive multiple sequence alignment
Authors
- David J Russell
- Hasan H Otu
- Khalid Sayood
- Content type: Research article
- Open Access
- Published: 10 July 2008
- Article: 306
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MAID : An effect size based model for microarray data integration across laboratories and platforms
Authors (first, second and last of 8)
- Ivan Borozan
- Limin Chen
- Ian D McGilvray
- Content type: Methodology article
- Open Access
- Published: 10 July 2008
- Article: 305
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Investigating selection on viruses: a statistical alignment approach
Authors (first, second and last of 4)
- Saskia de Groot
- Thomas Mailund
- Jotun Hein
- Content type: Research article
- Open Access
- Published: 10 July 2008
- Article: 304
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A unified approach to false discovery rate estimation
Authors
- Korbinian Strimmer
- Content type: Methodology article
- Open Access
- Published: 09 July 2008
- Article: 303
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2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments
Authors
- Jens Allmer
- Sebastian Kuhlgert
- Michael Hippler
- Content type: Software
- Open Access
- Published: 07 July 2008
- Article: 302
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Deducing topology of protein-protein interaction networks from experimentally measured sub-networks
Authors (first, second and last of 6)
- Ling Yang
- Thomas M Vondriska
- Zhilin Qu
- Content type: Research article
- Open Access
- Published: 03 July 2008
- Article: 301
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A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data
Authors (first, second and last of 7)
- Liping Huang
- Wenying Zhu
- Arne C Bathke
- Content type: Research article
- Open Access
- Published: 02 July 2008
- Article: 300
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PseudoGeneQuest – Service for identification of different pseudogene types in the human genome
Authors
- Csaba Ortutay
- Mauno Vihinen
- Content type: Software
- Open Access
- Published: 02 July 2008
- Article: 299
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Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection
Authors (first, second and last of 4)
- Inkyung Jung
- Jaehyung Lee
- Dongsup Kim
- Content type: Research article
- Open Access
- Published: 01 July 2008
- Article: 298
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Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information
Authors
- Jing Hu
- Changhui Yan
- Content type: Research article
- Open Access
- Published: 27 June 2008
- Article: 297
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Re-searcher: a system for recurrent detection of homologous protein sequences
Authors
- Valdemaras Repšys
- Mindaugas Margelevičius
- Česlovas Venclovas
- Content type: Software
- Open Access
- Published: 27 June 2008
- Article: 296
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Systems biology driven software design for the research enterprise
Authors (first, second and last of 4)
- John Boyle
- Christopher Cavnor
- Ilya Shmulevich
- Content type: Methodology article
- Open Access
- Published: 25 June 2008
- Article: 295
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Relating gene expression data on two-component systems to functional annotations in Escherichia coli
Authors (first, second and last of 5)
- Anne M Denton
- Jianfei Wu
- Birgit M Prüß
- Content type: Research article
- Open Access
- Published: 25 June 2008
- Article: 294
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Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins
Authors
- Michael Hsing
- Artem Cherkasov
- Content type: Database
- Open Access
- Published: 25 June 2008
- Article: 293
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Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
Authors
- Dawei Liu
- Debashis Ghosh
- Xihong Lin
- Content type: Research article
- Open Access
- Published: 24 June 2008
- Article: 292
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Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
Authors (first, second and last of 7)
- Rob Jelier
- Peter AC 't Hoen
- Barend Mons
- Content type: Methodology article
- Open Access
- Published: 24 June 2008
- Article: 291
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SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis
Authors (first, second and last of 5)
- Jinho Yoo
- Youngbok Lee
- Yangseok Kim
- Content type: Software
- Open Access
- Published: 23 June 2008
- Article: 290
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Stability of gene contributions and identification of outliers in multivariate analysis of microarray data
Authors (first, second and last of 5)
- Florent Baty
- Daniel Jaeger
- Martin H Brutsche
- Content type: Methodology article
- Open Access
- Published: 20 June 2008
- Article: 289
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Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
Authors (first, second and last of 6)
- Jianchao Yao
- Chunqi Chang
- Stanley J Roux
- Content type: Research article
- Open Access
- Published: 18 June 2008
- Article: 288
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Partial mixture model for tight clustering of gene expression time-course
Authors
- Yinyin Yuan
- Chang-Tsun Li
- Roland Wilson
- Content type: Methodology article
- Open Access
- Published: 18 June 2008
- Article: 287
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Precise detection of rearrangement breakpoints in mammalian chromosomes
Authors (first, second and last of 4)
- Claire Lemaitre
- Eric Tannier
- Marie-France Sagot
- Content type: Research article
- Open Access
- Published: 18 June 2008
- Article: 286
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Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Authors
- Ryosuke LA Watanabe
- Enrique Morett
- Edgar E Vallejo
- Content type: Methodology article
- Open Access
- Published: 17 June 2008
- Article: 285
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Methods for evaluating gene expression from Affymetrix microarray datasets
Authors (first, second and last of 9)
- Ning Jiang
- Lindsey J Leach
- Zewei W Luo
- Content type: Research article
- Open Access
- Published: 17 June 2008
- Article: 284
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Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions
Authors (first, second and last of 5)
- Ki-Yeol Kim
- Dong Hyuk Ki
- Sun Young Rha
- Content type: Research article
- Open Access
- Published: 16 June 2008
- Article: 283
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The combination approach of SVM and ECOC for powerful identification and classification of transcription factor
Authors (first, second and last of 7)
- Guangyong Zheng
- Ziliang Qian
- Yixue Li
- Content type: Research article
- Open Access
- Published: 16 June 2008
- Article: 282
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PURE: A webserver for the prediction of domains in unassigned regions in proteins
Authors (first, second and last of 4)
- Chilamakuri CS Reddy
- Khader Shameer
- Ramanathan Sowdhamini
- Content type: Research article
- Open Access
- Published: 14 June 2008
- Article: 281
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Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification
Authors
- Manli Zhu
- Aleix M Martinez
- Content type: Methodology article
- Open Access
- Published: 14 June 2008
- Article: 280
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Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping
Authors (first, second and last of 6)
- Guohui Lin
- Zhipeng Cai
- Randy Goebel
- Content type: Research article
- Open Access
- Published: 13 June 2008
- Article: 279
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Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
Authors (first, second and last of 5)
- Oliver Keller
- Florian Odronitz
- Stephan Waack
- Content type: Software
- Open Access
- Published: 13 June 2008
- Article: 278
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Semantic role labeling for protein transport predicates
Authors (first, second and last of 4)
- Steven Bethard
- Zhiyong Lu
- Lawrence Hunter
- Content type: Research article
- Open Access
- Published: 11 June 2008
- Article: 277
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Discovering functional interaction patterns in protein-protein interaction networks
Authors
- Mehmet E Turanalp
- Tolga Can
- Content type: Research article
- Open Access
- Published: 11 June 2008
- Article: 276
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Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles
Authors
- Guangtao Ge
- G William Wong
- Content type: Methodology article
- Open Access
- Published: 11 June 2008
- Article: 275
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A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
Authors (first, second and last of 8)
- Armita Sheari
- Mehdi Kargar
- Sayed-Amir Marashi
- Content type: Research article
- Open Access
- Published: 11 June 2008
- Article: 274
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AMYPdb: A database dedicated to amyloid precursor proteins
Authors
- Sandrine Pawlicki
- Antony Le Béchec
- Christian Delamarche
- Content type: Database
- Open Access
- Published: 10 June 2008
- Article: 273
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SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles
Authors (first, second and last of 4)
- Paul D Yoo
- Yung Shwen Ho
- Albert Y Zomaya
- Content type: Research article
- Open Access
- Published: 10 June 2008
- Article: 272
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TiGER: A database for tissue-specific gene expression and regulation
Authors (first, second and last of 5)
- Xiong Liu
- Xueping Yu
- Jiang Qian
- Content type: Database
- Open Access
- Published: 09 June 2008
- Article: 271
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PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval
Authors
- Jimmy Lin
- Content type: Research article
- Open Access
- Published: 06 June 2008
- Article: 270
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Flexible boosting of accelerated failure time models
Authors
- Matthias Schmid
- Torsten Hothorn
- Content type: Methodology article
- Open Access
- Published: 06 June 2008
- Article: 269
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Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures
Authors (first, second and last of 4)
- Meng P Tan
- Erin N Smith
- Christodoulos A Floudas
- Content type: Methodology article
- Open Access
- Published: 06 June 2008
- Article: 268
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Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data
Authors
- Sudhakar Jonnalagadda
- Rajagopalan Srinivasan
- Content type: Research article
- Open Access
- Published: 06 June 2008
- Article: 267
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An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Authors (first, second and last of 6)
- Ari Rantanen
- Juho Rousu
- Esko Ukkonen
- Content type: Methodology article
- Open Access
- Published: 06 June 2008
- Article: 266
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StAR: a simple tool for the statistical comparison of ROC curves
Authors (first, second and last of 5)
- Ismael A Vergara
- Tomás Norambuena
- Francisco Melo
- Content type: Software
- Open Access
- Published: 05 June 2008
- Article: 265
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Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens
Authors (first, second and last of 7)
- Zheng Yin
- Xiaobo Zhou
- Stephen TC Wong
- Content type: Methodology article
- Open Access
- Published: 05 June 2008
- Article: 264
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GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors
Authors (first, second and last of 4)
- Chiara Parravicini
- Graziella Ranghino
- Piercarlo Fantucci
- Content type: Research article
- Open Access
- Published: 04 June 2008
- Article: 263
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Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
Authors (first, second and last of 4)
- Nak-Kyeong Kim
- Kannan Tharakaraman
- John L Spouge
- Content type: Research article
- Open Access
- Published: 04 June 2008
- Article: 262
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Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)
Authors (first, second and last of 7)
- Juan R González
- Josep L Carrasco
- Xavier Estivill
- Content type: Methodology article
- Open Access
- Published: 04 June 2008
- Article: 261
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GMDD: a database of GMO detection methods
Authors (first, second and last of 9)
- Wei Dong
- Litao Yang
- Dabing Zhang
- Content type: Database
- Open Access
- Published: 04 June 2008
- Article: 260