Bioinformatics -- Bioinformatics Advance Access

Bioinformatics Advance Access

Bioinformatics Advance Access articles are papers in manuscript form that have been accepted by the journal but have not been copyedited or formatted for publication. Copyediting may lead to minor differences between the Advance Access version and the final version of the paper; there may also be differences in the quality of the graphics. More information, including how to cite Advance Access papers, can be found on the Advance Access page.

Advance Access Articles By Date [View by Category]

To see an accepted manuscript, click its [Accepted Manuscript] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

10 February 2010

Abstract ORIGINAL PAPER
Fabian A. Buske, Mikael Bodén, Denis C. Bauer, and Timothy L. Bailey
Assigning roles to DNA regulatory motifs using comparative genomics
Bioinformatics Advance Access published on February 10, 2010.
doi:10.1093/bioinformatics/btq049
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

9 February 2010

Abstract ORIGINAL PAPER: Supriya Munshaw and Thomas B. Kepler
SoDA2: A Hidden Markov Model Approach for Inference of Immunoglobulin Rearrangements
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq056
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Brendan MacLean, Daniela M. Tomazela, Nicholas Shulman, Matthew Chambers, Gregory L. Finney, Barbara Frewen, Randall Kern, David L. Tabb, Daniel C. Liebler, and Michael J. MacCoss
Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq054
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract DISCOVERY NOTE: Liang Chen
A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq047
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Qiang Liu, Kevin K. Lin, Bogi Andersen, Padhraic Smyth, and Alexander Ihler
Estimating Replicate Time-Shifts Using Gaussian Process Regressio
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq022
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Antonio Reverter-Gomez, Nicholas J. Hudson, Shivashankar H. Nagaraj, Miguel Pérez-Enciso, and Brian P. Dalrymple
Regulatory Impact Factors: Unraveling the transcriptional regulation of complex traits from expression data
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq051
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Peter Krawitz, Christian Rödelsperger, Marten Jäger, Luke Jostins, Sebastian Bauer, and Peter N. Robinson
Microindel detection in short-read sequence data
Bioinformatics Advance Access published on February 9, 2010.
doi:10.1093/bioinformatics/btq027
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

7 February 2010

Abstract APPLICATIONS NOTE: Sébastien Loriot and Frédéric Cazals
Modeling Macro-Molecular Interfaces with Intervor
Bioinformatics Advance Access published on February 7, 2010.
doi:10.1093/bioinformatics/btq052
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Christian Rohr, Wolfgang Marwan, and Monika Heiner
Snoopy - a unifying Petri net framework to investigate biomolecular networks
Bioinformatics Advance Access published on February 7, 2010.
doi:10.1093/bioinformatics/btq050
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Jing Gao, V. Glenn Tarcea, Alla Karnovsky, Barbara R. Mirel, Terry E. Weymouth, Christopher W. Beecher, James D. Cavalcoli, Brian D. Athey, Gilbert S. Omenn, Charles F. Burant, and H. V. Jagadish
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
Bioinformatics Advance Access published on February 7, 2010.
doi:10.1093/bioinformatics/btq048
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

4 February 2010

Abstract ORIGINAL PAPER: Chia-Chin Wu, Shahab Asgharzadeh, Timothy J. Triche, and David Z. D'Argenio
Prediction of Human Functional Genetic Networks from Heterogeneous Data Using RVM-Based Ensemble Learning
Bioinformatics Advance Access published on February 4, 2010.
doi:10.1093/bioinformatics/btq044
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Marc Kirchner, Wiebke Timm, Peying Fong, Philine Wangemann, and Hanno Steen
Nonlinear Classification for On-The-Fly Fractional Mass Filtering and Targeted Precursor Fragmentation in Mass Spectrometry Experiments
Bioinformatics Advance Access published on February 4, 2010.
doi:10.1093/bioinformatics/btq036
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

3 February 2010

Abstract APPLICATIONS NOTE
William S. Bush, Scott M. Dudek, and Marylyn D. Ritchie
Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btp678
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jiangning Song, Hao Tan, Hongbin Shen, Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, and James C. Whisstock
Cascleave: towards more accurate prediction of caspase substrate cleavage sites
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq043
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Stefan R. Maetschke, Karin S. Kassahn, Jasmyn A. Dunn, Siew P. Han, Eva Z. Curley, Katryn J. Stacey, and Mark A. Ragan
A visual framework for sequence analysis using n-grams and spectral rearrangement
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq042
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Donovan H. Parks and Robert G. Beiko
Identifying biologically relevant differences between metagenomic communities
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq041
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Rodrigo Goya, Mark G.F. Sun, Ryan D. Morin, Gillian Leung, Gavin Ha, Kimberley C. Wiegand, Janine Senz, Anamaria Crisan, Marco A. Marra, Martin Hirst, David Huntsman, Kevin P. Murphy, Sam Aparicio, and Sohrab P. Shah
SNVMix: predicting single nucleotide variants from next generation sequencing of tumors
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq040
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract DISCOVERY NOTE: Stephen Cammer and Charles W. Carter Jr
Six Rossmannoid Folds, Including the Class I Aminoacyl-tRNA Syntheta-ses, Share a Partial Core with the Anticodon-Binding Domain of a Class II Aminoacyl-tRNA Synthetase
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq039
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Minghui Wang, Xiang Chen, and Heping Zhang
Maximal conditional chi-square importance in random forests
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq038
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Blaise Hanczar, Jianping Hua, Chao Sima, John Weinstein, Michael Bittner, and Edward R. Dougherty
Small-sample precision of ROC-related estimates
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq037
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin Karplus, and Julian Gough
Improving protein secondary structure prediction using a simple k-mer model
Bioinformatics Advance Access published on February 3, 2010.
doi:10.1093/bioinformatics/btq020
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

29 January 2010

Abstract ORIGINAL PAPER: Daniela Dunkler, Michael Schemper, and Georg Heinze
Gene selection in microarray survival studies under possibly non-proportional hazards
Bioinformatics Advance Access published on January 29, 2010.
doi:10.1093/bioinformatics/btq035
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Corin Yeats, Oliver C Redfern, and Christine Orengo
A fast and automated solution for accurately resolving protein domain architectures
Bioinformatics Advance Access published on January 29, 2010.
doi:10.1093/bioinformatics/btq034
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

28 January 2010

Abstract APPLICATIONS NOTE
Aaron R. Quinlan and Ira M. Hall
BEDTools: A flexible suite of utilities for comparing genomic features
Bioinformatics Advance Access originally published on January 28, 2010. This version published February 3, 2010.
doi:10.1093/bioinformatics/btq033
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Qianxing Mo and Faming Liang
A hidden Ising model for ChIP-chip data analysis
Bioinformatics Advance Access published on January 28, 2010.
doi:10.1093/bioinformatics/btq032
[Abstract] [Accepted Manuscript] [Request Permissions]

26 January 2010

Abstract APPLICATIONS NOTE: Paulo C Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria da Gloria da Costa Carvalho, Valmir C Barbosa, and John R Yates III
XDIA: Improving on the label-free data-independent analysis
Bioinformatics Advance Access published on January 26, 2010.
doi:10.1093/bioinformatics/btq031
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Idan Gabdank, Danny Barash, and Edward N. Trifonov
FineStr : a web server for single-base-resolution nucleosome positioning
Bioinformatics Advance Access published on January 26, 2010.
doi:10.1093/bioinformatics/btq030
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Paul F. O'Reilly, Lachlan J.M. Coin, and Clive J. Hoggart
invertFREGENE: Software for simulating inversions in population genetic data
Bioinformatics Advance Access published on January 26, 2010.
doi:10.1093/bioinformatics/btq029
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Anaïs Mottaz, Fabrice P.A. David, Anne-Lise Veuthey, and Yum L. Yip
Easy retrieval of Single Amino-acid Polymorphisms and phenotype information using SwissVar
Bioinformatics Advance Access published on January 26, 2010.
doi:10.1093/bioinformatics/btq028
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Matias Piipari, Thomas A. Down, Harpreet Saini, Anton Enright, and Tim J.P. Hubbard
iMotifs: an integrated sequence motif visualization and analysis environment
Bioinformatics Advance Access originally published on January 26, 2010. This version published February 4, 2010.
doi:10.1093/bioinformatics/btq026
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jörg Wicker, Kathrin Fenner, Lynda Ellis, Larry Wackett, and Stefan Kramer
Predicting Biodegradation Products and Pathways: A Hybrid Knowledge-Based and Machine Learning Based Approach
Bioinformatics Advance Access published on January 26, 2010.
doi:10.1093/bioinformatics/btq024
[Abstract] [Accepted Manuscript] [Request Permissions]

22 January 2010

Abstract ORIGINAL PAPER: Thomas W. Binsl, David J.C. Alders, Jaap Heringa, A.B. Johan Groeneveld, and Johannes H.G.M. van Beek
Computational Quantification of Metabolic Fluxes from a Single Isotope Snapshot: Application to an Animal Biopsy
Bioinformatics Advance Access published on January 22, 2010.
doi:10.1093/bioinformatics/btq018
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Mingyao Li, Muredach P. Reilly, Daniel J. Rader, and Li-San Wang
Correcting Population Stratification in Genetic Association Studies Using a Phylogenetic Approach
Bioinformatics Advance Access published on January 22, 2010.
doi:10.1093/bioinformatics/btq025
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Ozgur Demir-Kavuk, Henning Riedesel, and Ernst-Walter Knapp
Exploring classification strategies with the CoEPrA 2006 contest
Bioinformatics Advance Access published on January 22, 2010.
doi:10.1093/bioinformatics/btq021
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Frédéric Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard, Corinne Pinel, Delphine Ropers, Johannes Geiselmann, and Hidde de Jong
WellReader: A MATLAB Program for the Analysis of Fluorescence and Luminescence Reporter Gene Data
Bioinformatics Advance Access published on January 22, 2010.
doi:10.1093/bioinformatics/btq016
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

19 January 2010

Abstract APPLICATIONS NOTE: Arnaud Droit, Charles Cheung, and Raphael Gottardo
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments
Bioinformatics Advance Access published on January 19, 2010.
doi:10.1093/bioinformatics/btq023
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Guy Nimrod, Maya Schushan, András Szilágyi, Christina Leslie, and Nir Ben-Tal
iDBPs: A web server for the identification of DNA binding proteins
Bioinformatics Advance Access published on January 19, 2010.
doi:10.1093/bioinformatics/btq019
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Thomas Dan Otto, Marcos Catanho, Cristian Tristão, Márcia Bezerra, Renan Mathias Fernandes, Guilherme Steinberger Elias, Alexandre Capeletto Scaglia, Bill Bovermann, Viktors Berstis, Sergio Lifschitz, Antonio Basílio de Miranda, and Wim Degrave
ProteinWorldDB: Querying radical pairwise alignments among protein sets from complete genomes
Bioinformatics Advance Access published on January 19, 2010.
doi:10.1093/bioinformatics/btq011
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

16 January 2010

Abstract APPLICATIONS NOTE: Sergio Gálvez, David Díaz, Pilar Hernández, Francisco J. Esteban, Juan A. Caballero, and Gabriel Dorado
Next-Generation Bioinformatics: Using Many-Core Processor Architecture to Develop a Web Service for Sequence Alignment
Bioinformatics Advance Access published on January 16, 2010.
doi:10.1093/bioinformatics/btq017
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Royi Itzhack and Yoram Louzoun
Random Distance Dependent Attachment as a Model for Neural Network Generation in the Caenorhabditis Elegans
Bioinformatics Advance Access published on January 16, 2010.
doi:10.1093/bioinformatics/btq015
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Christian Schaefer, Avner Schlessinger, and Burkhard Rost
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be
Bioinformatics Advance Access published on January 16, 2010.
doi:10.1093/bioinformatics/btq012
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, and Brent T. Harris
Multifactor Dimensionality Reduction for Graphics Processing Units Enables Genome-wide Testing of Epistasis in Sporadic ALS
Bioinformatics Advance Access published on January 16, 2010.
doi:10.1093/bioinformatics/btq009
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

15 January 2010

Abstract ORIGINAL PAPER: Anastasios Markitsis and Yinglei Lai
A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes
Bioinformatics Advance Access published on January 15, 2010.
doi:10.1093/bioinformatics/btq001
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Karl Frank, Markus Gruber, and Manfred J. Sippl
COPS Benchmark: Interactive analysis of database search methods
Bioinformatics Advance Access published on January 15, 2010.
doi:10.1093/bioinformatics/btp712
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Heng Li and Richard Durbin
Fast and accurate long read alignment with Burrows-Wheeler transform
Bioinformatics Advance Access published on January 15, 2010.
doi:10.1093/bioinformatics/btp698
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

14 January 2010

Abstract ORIGINAL PAPER
Stefan Janssen and Robert Giegerich
Faster computation of exact RNA shape probabilities
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq014
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: E. Iannuccelli, F. Mompart, J. Gellin, Y. Lahbib-Mansais, M. Yerle, and T. Boudier
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq013
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Sriram Sankararaman, Fei Sha, Jack F. Kirsch, Michael I. Jordan, and Kimmen Sjölander
Active Site Prediction using Evolutionary and Structural Information
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq008
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Shashi B. Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, and Jeffrey Skolnick
PSiFR: An integrated resource for prediction of protein structure and function
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq006
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Vanathi Gopalakrishnan, Jonathan L. Lustgarten, Shyam Visweswaran, and Gregory F. Cooper
Bayesian Rule Learning for Biomedical Data Mining
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq005
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Gustavo A. de Souza, Magnus Ø. Arntzen, and Harald G. Wiker
MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
Bioinformatics Advance Access published on January 14, 2010.
doi:10.1093/bioinformatics/btq004
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

12 January 2010

Abstract APPLICATIONS NOTE
Tim Carver, Ulrike Böhme, Thomas D. Otto, Julian Parkhill, and Matthew Berriman
BamView: Viewing mapped read alignment data in the context of the reference sequence.
Bioinformatics Advance Access published on January 12, 2010.
doi:10.1093/bioinformatics/btq010
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

7 January 2010

Abstract APPLICATIONS NOTE: Sidhartha Chaudhury, Sergey Lyskov, and Jeffrey J. Gray
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
Bioinformatics Advance Access published on January 7, 2010.
doi:10.1093/bioinformatics/btq007
[Abstract] [Accepted Manuscript] [Request Permissions]

6 January 2010

Abstract APPLICATIONS NOTE
Ying Huang, Beifang Niu, Ying Gao, Limin Fu, and Weizhong Li
CD-HIT Suite: a web server for clustering and comparing biological sequences
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btq003
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Xinglong Wang, Jun'ichi Tsujii, and Sophia Ananiadou
Disambiguating the Species of Biomedical Named Entities Using Natural Language Parsers
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btq002
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Visotheary Ung, Guillaume Dubus, René Zaragüeta-Bagils, and Régine Vignes-Lebbe
Xper²: introducing e-Taxonomy
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btp715
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Christine Fong, Dennis C. Ko, Michael Wasnick, Matthew Radey, Samuel I. Miller, and Mitchell Brittnacher
GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btp714
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract REVIEW
Jason H. Moore, Folkert W. Asselbergs, and Scott M. Williams
Bioinformatics Challenges for Genome-Wide Association Studies
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btp713
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Ping-Shi Wu and Hans-Georg Müller
Functional Embedding for the Classification of Gene Expression Profiles
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btp711
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Yan Zhang and Vadim N. Gladyshev
dbTEU: a protein database of trace element utilization
Bioinformatics Advance Access published on January 6, 2010.
doi:10.1093/bioinformatics/btp705
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

3 January 2010

Abstract ORIGINAL PAPER: Victoria Martín-Requena, Javier Ríos, Maximiliano García, Sergio Ramírez, and Oswaldo Trelles
jORCA: Easily integrating bioinformatics web services
Bioinformatics Advance Access published on January 3, 2010.
doi:10.1093/bioinformatics/btp709
[Abstract] [Accepted Manuscript] [Supplementary Data] [Supplementary Data] [Request Permissions]

29 December 2009

Abstract APPLICATIONS NOTE: Ming-Huei Chen and Qiong Yang
GWAF: an R package for genome-wide association analyses with family data
Bioinformatics Advance Access published on December 29, 2009.
doi:10.1093/bioinformatics/btp710
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

23 December 2009

Abstract ORIGINAL PAPER: Qunyuan Zhang, Li Ding, David E. Larson, Daniel C. Koboldt, Michael D. McLellan, Ken Chen, Xiaoqi Shi, Aldi Kraja, Elaine R. Mardis, Richard K. Wilson, Ingrid B. Boreki, and Michael A. Province
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
Bioinformatics Advance Access published on December 23, 2009.
doi:10.1093/bioinformatics/btp708
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Benhuai Xie, Wei Pan, and Xiaotong Shen
Penalized Mixtures of Factor Analyzers with Application to Clustering High Dimensional Microarray Data
Bioinformatics Advance Access published on December 23, 2009.
doi:10.1093/bioinformatics/btp707
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Naama Tepper and Tomer Shlomi
Predicting Metabolic Engineering Knockout Strategies for Chemical Production: Accounting for Competing Pathways
Bioinformatics Advance Access published on December 23, 2009.
doi:10.1093/bioinformatics/btp704
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Yanbin Liu, Bin Hu, Chengxin Fu, and Xin Chen
DCDB: Drug Combination Database
Bioinformatics Advance Access published on December 23, 2009.
doi:10.1093/bioinformatics/btp697
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Ninad Dewal, Matthew L. Freedman, Thomas LaFramboise, and Itsik Pe'er
Power to Detect Selective Allelic Amplification in Genome-wide Scans of Tumor Data
Bioinformatics Advance Access published on December 23, 2009.
doi:10.1093/bioinformatics/btp694
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

22 December 2009

Abstract APPLICATIONS NOTE: Elena Y. Harris, Nadia Ponts, Aleksandr Levchuk, Karine Le Roch, and Stefano Lonardi
BRAT: Bisulfite-treated Reads Analysis Tool
Bioinformatics Advance Access published on December 22, 2009.
doi:10.1093/bioinformatics/btp706
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Shang-Hong Zhang and Ya-Zhi Huang
Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA
Bioinformatics Advance Access published on December 22, 2009.
doi:10.1093/bioinformatics/btp703
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Kelvin Xi Zhang and B.F. Francis Ouellette
Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence
Bioinformatics Advance Access published on December 22, 2009.
doi:10.1093/bioinformatics/btp701
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Kosaku Shinoda, Masaru Tomita, and Yasushi Ishihama
emPAI Calc -- for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry
Bioinformatics Advance Access published on December 22, 2009.
doi:10.1093/bioinformatics/btp700
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Kristian Kvilekval, Dmitry Fedorov, Boguslaw Obara, Ambuj Singh, and B.S. Manjunath
Bisque: A Platform for Bioimage Analysis and Management
Bioinformatics Advance Access published on December 22, 2009.
doi:10.1093/bioinformatics/btp699
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

21 December 2009

Abstract APPLICATIONS NOTE: Tin-Lap Lee, Yunmin Li, Hoi-Hung Cheung, Janek Claus, Sumeeta Singh, Chandan Sastry, Owen M. Rennert, Yun-Fai Chris Lau, and Wai-Yee Chan
GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development
Bioinformatics Advance Access published on December 21, 2009.
doi:10.1093/bioinformatics/btp695
[Abstract] [Accepted Manuscript] [Request Permissions]

18 December 2009

Abstract APPLICATIONS NOTE
Jared T. Simpson, Rebecca E. McIntyre, David J. Adams, and Richard Durbin
Copy number variant detection in inbred strains from short read sequence data
Bioinformatics Advance Access published on December 18, 2009.
doi:10.1093/bioinformatics/btp693
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, and Colin N. Dewey
RNA-Seq gene expression estimation with read mapping uncertainty
Bioinformatics Advance Access published on December 18, 2009.
doi:10.1093/bioinformatics/btp692
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

16 December 2009

Abstract APPLICATIONS NOTE
Peter Husemann and Jens Stoye
r2cat: Synteny Plots and Comparative Assembly
Bioinformatics Advance Access published on December 16, 2009.
doi:10.1093/bioinformatics/btp690
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Mingoo Kim, Sung Bum Cho, and Ju Han Kim
Mixture model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data
Bioinformatics Advance Access published on December 16, 2009.
doi:10.1093/bioinformatics/btp685
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, and Peter F. Stadler
RNAsnoop: Efficient Target Prediction for H/ACA snoRNAs
Bioinformatics Advance Access published on December 16, 2009.
doi:10.1093/bioinformatics/btp680
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

10 December 2009

Abstract APPLICATIONS NOTE
Cheng-Long Chuang, Jia-Hong Wu, Chi-Sheng Cheng, and Grace S. Shieh
WebPARE: Web-computing for inferring genetic or transcriptional interactions
Bioinformatics Advance Access published on December 10, 2009.
doi:10.1093/bioinformatics/btp684
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Matthew Horton, Natacha Bodenhausen, and Joy Bergelson
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.
Bioinformatics Advance Access published on December 10, 2009.
doi:10.1093/bioinformatics/btp682
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

9 December 2009

Abstract ORIGINAL PAPER: Tuping Zhou, Nanjiang Shu, and Sven Hovmöller
A Novel Method for Accurate One-dimensional Protein Structure Prediction Based on Fragment Matching
Bioinformatics Advance Access published on December 9, 2009.
doi:10.1093/bioinformatics/btp679
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Maureen A. Sartor, Vasudeva Mahavisno, Venkateshwar G. Keshamouni, James Cavalcoli, Zachary Wright, Alla Karnovsky, Rork Kuick, H.V. Jagadish, Barbara Mirel, Terry Weymouth, Brian Athey, and Gilbert S. Omenn
ConceptGen: a gene set enrichment and gene set relation mapping tool
Bioinformatics Advance Access published on December 9, 2009.
doi:10.1093/bioinformatics/btp683
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

26 November 2009

Abstract ORIGINAL PAPER: Daniel L. Mace, Nicole Varnado, Weiping Zhang, Erwin Frise, and Uwe Ohler
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images
Bioinformatics Advance Access published on November 26, 2009.
doi:10.1093/bioinformatics/btp658
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]