Bioinformatics -- Table of Contents (24 [20])

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Contents: Volume 24, Number 20, 15 October 2008   [Index by Author]

DISCOVERY NOTE

     SEQUENCE ANALYSIS

ORIGINAL PAPERS

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     STRUCTURAL BIOINFORMATICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

     SYSTEMS BIOLOGY

APPLICATIONS NOTE

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     PHYLOGENETICS

     GENE EXPRESSION

     GENETICS AND POPULATION ANALYSIS

     DATABASES AND ONTOLOGIES

LETTER TO THE EDITOR

     GENOME ANALYSIS

ERRATUM

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DISCOVERY NOTE

SEQUENCE ANALYSIS

Get checked abstract Antonina Andreeva and Henning Tidow: A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes
Bioinformatics Advance Access published on August 14, 2008
Bioinformatics 2008 24: 2277-2280; doi:10.1093/bioinformatics/btn431 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg, and Liming Cai: Fast and accurate search for non-coding RNA pseudoknot structures in genomes
Bioinformatics Advance Access published on August 7, 2008
Bioinformatics 2008 24: 2281-2287; doi:10.1093/bioinformatics/btn393 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

SEQUENCE ANALYSIS

Get checked abstract Edward Wijaya, Siu-Ming Yiu, Ngo Thanh Son, Rajaraman Kanagasabai, and Wing-Kin Sung: MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2288-2295; doi:10.1093/bioinformatics/btn420 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Qi Dai, Yanchun Yang, and Tianming Wang: Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2296-2302; doi:10.1093/bioinformatics/btn436 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract François Fauteux, Mathieu Blanchette, and Martina V. Strömvik: Seeder: discriminative seeding DNA motif discovery
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2303-2307; doi:10.1093/bioinformatics/btn444 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

Get checked abstract K. C. Dukka Bahadur and Dennis R. Livesay: Improving position-specific predictions of protein functional sites using phylogenetic motifs
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2308-2316; doi:10.1093/bioinformatics/btn454 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

PHYLOGENETICS

Get checked abstract Le Si Quang, Olivier Gascuel, and Nicolas Lartillot: Empirical profile mixture models for phylogenetic reconstruction
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2317-2323; doi:10.1093/bioinformatics/btn445 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

STRUCTURAL BIOINFORMATICS

Get checked abstract Vinay Pulim, Bonnie Berger, and Jadwiga Bienkowska: Optimal contact map alignment of protein–protein interfaces
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2324-2328; doi:10.1093/bioinformatics/btn432 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

Get checked abstract Tuo Zhang, Hua Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, and Lukasz Kurgan: Accurate sequence-based prediction of catalytic residues
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2329-2338; doi:10.1093/bioinformatics/btn433 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Ryan M. Bannen, Vanitha Suresh, George N. Phillips, Jr, Stephen J. Wright, and Julie C. Mitchell: Optimal design of thermally stable proteins
Bioinformatics Advance Access published on August 22, 2008
Bioinformatics 2008 24: 2339-2343; doi:10.1093/bioinformatics/btn450 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

GENE EXPRESSION

Get checked abstract Han Xu, Chia-Lin Wei, Feng Lin, and Wing-Kin Sung: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
Bioinformatics Advance Access published on July 29, 2008
Bioinformatics 2008 24: 2344-2349; doi:10.1093/bioinformatics/btn402 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Iuliana Ionita-Laza, Nan M. Laird, Benjamin A. Raby, Scott T. Weiss, and Christoph Lange: On the frequency of copy number variants
Bioinformatics Advance Access published on August 8, 2008
Bioinformatics 2008 24: 2350-2355; doi:10.1093/bioinformatics/btn421 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Meijuan Li, Cavan Reilly, and Timothy Hanson: A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations
Bioinformatics Advance Access published on August 27, 2008
Bioinformatics 2008 24: 2356-2362; doi:10.1093/bioinformatics/btn455 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, and Marek Kimmel: Model-based analysis of interferon-β induced signaling pathway
Bioinformatics Advance Access published on August 19, 2008
Bioinformatics 2008 24: 2363-2369; doi:10.1093/bioinformatics/btn400 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Juan Cui, Qi Liu, David Puett, and Ying Xu: Computational prediction of human proteins that can be secreted into the bloodstream
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2370-2375; doi:10.1093/bioinformatics/btn418 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Shuye Pu, Karen Ronen, James Vlasblom, Jack Greenblatt, and Shoshana J. Wodak: Local coherence in genetic interaction patterns reveals prevalent functional versatility
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2376-2383; doi:10.1093/bioinformatics/btn440 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, and Jason A. Papin: Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2384-2390; doi:10.1093/bioinformatics/btn451 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

APPLICATIONS NOTE

GENOME ANALYSIS

Get checked abstract Jasmina Bogojeska, Adrian Alexa, André Altmann, Thomas Lengauer, and Jörg Rahnenführer: Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2391-2392; doi:10.1093/bioinformatics/btn410 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS

SEQUENCE ANALYSIS

Get checked abstract Anika Jöcker, Fabian Hoffmann, Andreas Groscurth, and Heiko Schoof: Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2393-2394; doi:10.1093/bioinformatics/btn394 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Hui Jiang and Wing Hung Wong: SeqMap: mapping massive amount of oligonucleotides to the genome
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2395-2396; doi:10.1093/bioinformatics/btn429 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Yana Bromberg, Guy Yachdav, and Burkhard Rost: SNAP predicts effect of mutations on protein function
Bioinformatics Advance Access published on August 30, 2008
Bioinformatics 2008 24: 2397-2398; doi:10.1093/bioinformatics/btn435 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS

PHYLOGENETICS

Get checked abstract Thasso Griebel, Malte Brinkmeyer, and Sebastian Böcker: EPoS: a modular software framework for phylogenetic analysis
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 2399-2400; doi:10.1093/bioinformatics/btn364 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, and Tobias Müller: ProfDistS: (profile-) distance based phylogeny on sequence—structure alignments
Bioinformatics Advance Access published on August 21, 2008
Bioinformatics 2008 24: 2401-2402; doi:10.1093/bioinformatics/btn453 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Ádám Novák, István Miklós, Rune Lyngsø, and Jotun Hein: StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
Bioinformatics Advance Access published on August 27, 2008
Bioinformatics 2008 24: 2403-2404; doi:10.1093/bioinformatics/btn457 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

GENE EXPRESSION

Get checked abstract Wuming Gong, Yongliang Ren, Haiyan Zhou, Yejun Wang, Shuli Kang, and Tongbin Li: siDRM: an effective and generally applicable online siRNA design tool
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2405-2406; doi:10.1093/bioinformatics/btn442 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

GENETICS AND POPULATION ANALYSIS

Get checked abstract Jérôme Wojcik and Karl Forner: ExactFDR: exact computation of false discovery rate estimate in case-control association studies
Bioinformatics Advance Access published on July 28, 2008
Bioinformatics 2008 24: 2407-2408; doi:10.1093/bioinformatics/btn379 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

DATABASES AND ONTOLOGIES

Get checked abstract Jing Zhang, Tao Ma, Yanda Li, and Shao Li: dbNEI2.0: building multilayer network for drug–NEI–disease
Bioinformatics Advance Access published on July 25, 2008
Bioinformatics 2008 24: 2409-2411; doi:10.1093/bioinformatics/btn388 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Siyuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, and Yixue Li: MPSQ: a web tool for protein-state searching
Bioinformatics Advance Access published on August 12, 2008
Bioinformatics 2008 24: 2412-2413; doi:10.1093/bioinformatics/btn427 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Chaka Tang, Josephine F. Reyes, Fabio Luciani, Andrew R. Francis, and Mark M. Tanaka: spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex
Bioinformatics Advance Access published on August 18, 2008
Bioinformatics 2008 24: 2414-2415; doi:10.1093/bioinformatics/btn434 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, and Yixue Li: ITFP: an integrated platform of mammalian transcription factors
Bioinformatics Advance Access published on August 19, 2008
Bioinformatics 2008 24: 2416-2417; doi:10.1093/bioinformatics/btn439 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, and Jeffrey H. Chuang: cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation
Bioinformatics Advance Access published on August 20, 2008
Bioinformatics 2008 24: 2418-2419; doi:10.1093/bioinformatics/btn443 [Abstract] [Full Text] [Print PDF] [Request Permissions]

LETTER TO THE EDITOR

GENOME ANALYSIS

Get checked abstract Yang Xie: Comments on ‘On correcting the overestimation of the permutation-based false discovery rate estimator’
Bioinformatics Advance Access published on September 1, 2008
Bioinformatics 2008 24: 2420; doi:10.1093/bioinformatics/btn456 [Abstract] [Full Text] [Print PDF] [Request Permissions]

ERRATUM

Vladislav Vyshemirsky and Mark A. Girolami: Bayesian ranking of biochemical system models
Bioinformatics 2008 24: 2421; doi:10.1093/bioinformatics/btn475 [Extract] [Full Text] [Print PDF] [Request Permissions]