Volume 10, issue 1, December 2009
455 articles in this issue
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AtPIN: Arabidopsis thaliana Protein Interaction Network
Authors
- Marcelo M Brandão
- Luiza L Dantas
- Marcio C Silva-Filho
- Content type: Database
- Open Access
- Published: 31 December 2009
- Article: 454
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Classification across gene expression microarray studies
Authors (first, second and last of 4)
- Andreas Buness
- Markus Ruschhaupt
- Achim Tresch
- Content type: Research article
- Open Access
- Published: 30 December 2009
- Article: 453
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Skittle: A 2-Dimensional Genome Visualization Tool
Authors
- Josiah D Seaman
- John C Sanford
- Content type: Software
- Open Access
- Published: 30 December 2009
- Article: 452
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Predicting functional upstream open reading frames in Saccharomyces cerevisiae
Authors (first, second and last of 6)
- Selpi
- Christopher H Bryant
- Per Sunnerhagen
- Content type: Methodology article
- Open Access
- Published: 30 December 2009
- Article: 451
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A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
Authors (first, second and last of 7)
- Pedro T Monteiro
- Estelle Dumas
- Hidde de Jong
- Content type: Software
- Open Access
- Published: 30 December 2009
- Article: 450
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A white-box approach to microarray probe response characterization: the BaFL pipeline
Authors (first, second and last of 4)
- Kevin J Thompson
- Hrishikesh Deshmukh
- Jennifer W Weller
- Content type: Methodology article
- Open Access
- Published: 29 December 2009
- Article: 449
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Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling
Authors (first, second and last of 4)
- Johanna Mazur
- Daniel Ritter
- Lars Kaderali
- Content type: Research article
- Open Access
- Published: 28 December 2009
- Article: 448
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Next generation transcriptomes for next generation genomes using est2assembly
Authors (first, second and last of 4)
- Alexie Papanicolaou
- Remo Stierli
- David G Heckel
- Content type: Software
- Open Access
- Published: 24 December 2009
- Article: 447
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Data mining of enzymes using specific peptides
Authors
- Uri Weingart
- Yair Lavi
- David Horn
- Content type: Methodology article
- Open Access
- Published: 24 December 2009
- Article: 446
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LipocalinPred: a SVM-based method for prediction of lipocalins
Authors
- Jayashree Ramana
- Dinesh Gupta
- Content type: Methodology article
- Open Access
- Published: 24 December 2009
- Article: 445
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IRIS: a method for reverse engineering of regulatory relations in gene networks
Authors
- Sandro Morganella
- Pietro Zoppoli
- Michele Ceccarelli
- Content type: Software
- Open Access
- Published: 23 December 2009
- Article: 444
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MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data
Authors
- Thierry De Meeûs
- Jean-François Guégan
- Anatoly T Teriokhin
- Content type: Software
- Open Access
- Published: 23 December 2009
- Article: 443
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G+C content dominates intrinsic nucleosome occupancy
Authors
- Desiree Tillo
- Timothy R Hughes
- Content type: Research article
- Open Access
- Published: 22 December 2009
- Article: 442
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The Medicago truncatula gene expression atlas web server
Authors (first, second and last of 7)
- Ji He
- Vagner A Benedito
- Michael K Udvardi
- Content type: Database
- Open Access
- Published: 22 December 2009
- Article: 441
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ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly
Authors (first, second and last of 6)
- Marian Thieme
- Claudio Lottaz
- Peter J Oefner
- Content type: Software
- Open Access
- Published: 22 December 2009
- Article: 440
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svm PRAT: SVM-based Protein Residue Annotation Toolkit
Authors
- Huzefa Rangwala
- Christopher Kauffman
- George Karypis
- Content type: Software
- Open Access
- Published: 22 December 2009
- Article: 439
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A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
Authors
- Shyamal D Peddada
- David M Umbach
- Shawn F Harris
- Content type: Correspondence
- Open Access
- Published: 22 December 2009
- Article: 438
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Prediction of backbone dihedral angles and protein secondary structure using support vector machines
Authors
- Petros Kountouris
- Jonathan D Hirst
- Content type: Research article
- Open Access
- Published: 22 December 2009
- Article: 437
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PreDisorder: ab initio sequence-based prediction of protein disordered regions
Authors
- Xin Deng
- Jesse Eickholt
- Jianlin Cheng
- Content type: Software
- Open Access
- Published: 21 December 2009
- Article: 436
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In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana
Authors (first, second and last of 5)
- Damion Nero
- Manpreet S Katari
- Gloria M Coruzzi
- Content type: Methodology article
- Open Access
- Published: 21 December 2009
- Article: 435
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Identification of ATP binding residues of a protein from its primary sequence
Authors
- Jagat S Chauhan
- Nitish K Mishra
- Gajendra PS Raghava
- Content type: Research article
- Open Access
- Published: 19 December 2009
- Article: 434
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Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway
Authors (first, second and last of 4)
- Abhik Shah
- Toyoaki Tenzen
- Peter J Woolf
- Content type: Research article
- Open Access
- Published: 18 December 2009
- Article: 433
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Algorithms for locating extremely conserved elements in multiple sequence alignments
Authors
- Huei-Hun E Tseng
- Martin Tompa
- Content type: Research article
- Open Access
- Published: 18 December 2009
- Article: 432
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Discovering collectively informative descriptors from high-throughput experiments
Authors (first, second and last of 4)
- Clark D Jeffries
- William O Ward
- Fred A Wright
- Content type: Methodology article
- Open Access
- Published: 18 December 2009
- Article: 431
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WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Authors (first, second and last of 5)
- Wolfgang Gerlach
- Sebastian Jünemann
- Jens Stoye
- Content type: Software
- Open Access
- Published: 18 December 2009
- Article: 430
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A new permutation strategy of pathway-based approach for genome-wide association study
Authors (first, second and last of 5)
- Yan-Fang Guo
- Jian Li
- Hong-Wen Deng
- Content type: Methodology article
- Open Access
- Published: 18 December 2009
- Article: 429
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TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data
Authors (first, second and last of 8)
- Álvaro Cuadros-Inostroza
- Camila Caldana
- Matthew A Hannah
- Content type: Software
- Open Access
- Published: 16 December 2009
- Article: 428
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In silico method for systematic analysis of feature importance in microRNA-mRNA interactions
Authors (first, second and last of 7)
- Jiamin Xiao
- Yizhou Li
- Xuanmin Guang
- Content type: Research article
- Open Access
- Published: 16 December 2009
- Article: 427
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Prediction of protein-protein interaction sites using an ensemble method
Authors (first, second and last of 4)
- Lei Deng
- Jihong Guan
- Shuigeng Zhou
- Content type: Methodology article
- Open Access
- Published: 16 December 2009
- Article: 426
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Crossfit analysis: a novel method to characterize the dynamics of induced plant responses
Authors (first, second and last of 4)
- Jeroen J Jansen
- Nicole M van Dam
- Age K Smilde
- Content type: Methodology article
- Open Access
- Published: 16 December 2009
- Article: 425
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CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome
Authors
- Mikyung Lee
- Yangseok Kim
- Content type: Software
- Open Access
- Published: 16 December 2009
- Article: 424
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Comparison of phylogenetic trees through alignment of embedded evolutionary distances
Authors
- Kwangbom Choi
- Shawn M Gomez
- Content type: Methodology article
- Open Access
- Published: 15 December 2009
- Article: 423
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Quantitative comparison of microarray experiments with published leukemia related gene expression signatures
Authors (first, second and last of 7)
- Hans-Ulrich Klein
- Christian Ruckert
- Martin Dugas
- Content type: Research article
- Open Access
- Published: 15 December 2009
- Article: 422
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BLAST+: architecture and applications
Authors (first, second and last of 7)
- Christiam Camacho
- George Coulouris
- Thomas L Madden
- Content type: Software
- Open Access
- Published: 15 December 2009
- Article: 421
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Web-based interrogation of gene expression signatures using EXALT
Authors (first, second and last of 8)
- Jun Wu
- Qingchao Qiu
- Yajun Yi
- Content type: Software
- Open Access
- Published: 14 December 2009
- Article: 420
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Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences
Authors
- Yungki Park
- Content type: Research article
- Open Access
- Published: 14 December 2009
- Article: 419
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TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Authors (first, second and last of 4)
- Haiquan Li
- Vagner A Benedito
- Patrick Xuechun Zhao
- Content type: Research article
- Open Access
- Published: 14 December 2009
- Article: 418
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Graphle: Interactive exploration of large, dense graphs
Authors
- Curtis Huttenhower
- Sajid O Mehmood
- Olga G Troyanskaya
- Content type: Software
- Open Access
- Published: 14 December 2009
- Article: 417
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DescFold: A web server for protein fold recognition
Authors (first, second and last of 4)
- Ren-Xiang Yan
- Jing-Na Si
- Ziding Zhang
- Content type: Methodology article
- Open Access
- Published: 14 December 2009
- Article: 416
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Effects of normalization on quantitative traits in association test
Authors
- Liang Goh
- Von Bing Yap
- Content type: Research article
- Open Access
- Published: 14 December 2009
- Article: 415
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Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences
Authors
- Marcin J Mizianty
- Lukasz Kurgan
- Content type: Methodology article
- Open Access
- Published: 13 December 2009
- Article: 414
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Survival prediction from clinico-genomic models - a comparative study
Authors
- Hege M Bøvelstad
- Ståle Nygård
- Ørnulf Borgan
- Content type: Research article
- Open Access
- Published: 13 December 2009
- Article: 413
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The impact of measurement errors in the identification of regulatory networks
Authors (first, second and last of 4)
- André Fujita
- Alexandre G Patriota
- Satoru Miyano
- Content type: Methodology article
- Open Access
- Published: 13 December 2009
- Article: 412
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An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays
Authors
- Erdem Arslan
- Ian J Laurenzi
- Content type: Methodology article
- Open Access
- Published: 10 December 2009
- Article: 411
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Refining gene signatures: a Bayesian approach
Authors
- Amira Djebbari
- Aurélie Labbe
- Content type: Research article
- Open Access
- Published: 10 December 2009
- Article: 410
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An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
Authors (first, second and last of 5)
- Martin J Aryee
- José A Gutiérrez-Pabello
- John Quackenbush
- Content type: Research article
- Open Access
- Published: 10 December 2009
- Article: 409
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Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
Authors (first, second and last of 6)
- Bing Liu
- Jiuyong Li
- Gregory J Goodall
- Content type: Methodology article
- Open Access
- Published: 10 December 2009
- Article: 408
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Protein-protein docking using region-based 3D Zernike descriptors
Authors (first, second and last of 4)
- Vishwesh Venkatraman
- Yifeng D Yang
- Daisuke Kihara
- Content type: Research article
- Open Access
- Published: 09 December 2009
- Article: 407
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Erratum to: Disease candidate gene identification and prioritization using protein interaction networks
Authors
- Jing Chen
- Bruce J Aronow
- Anil G Jegga
- Content type: Erratum
- Open Access
- Published: 09 December 2009
- Article: 406