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.

4 July 2009

Abstract ORIGINAL PAPER
Zhihui Wang, Christina M. Birch, Jonathan Sagotsky, and Thomas S. Deisboeck
Cross-Scale, Cross-Pathway Evaluation using an Agent-Based Non-Small Cell Lung Cancer Model
Bioinformatics Advance Access published on July 4, 2009.
doi:10.1093/bioinformatics/btp416
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Magdalena Feldhahn, Pierre Dönnes, Philipp Thiel, and Oliver Kohlbacher
FRED - A Framework for T-cell Epitope Detection
Bioinformatics Advance Access published on July 4, 2009.
doi:10.1093/bioinformatics/btp409
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Stefan Jaeger, Qingfeng Song, and Su-Shing Chen
DYNAMIK: A Software Environment for Cell DYNAmics, Motility, and Information TracKing, with an Application to Ras Pathways
Bioinformatics Advance Access published on July 4, 2009.
doi:10.1093/bioinformatics/btp405
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Don Gilbert and Andreas Rechtsteiner
Comments on sequence normalization of tiling array expression
Bioinformatics Advance Access published on July 4, 2009.
doi:10.1093/bioinformatics/btp389
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

3 July 2009

Abstract APPLICATIONS NOTE: Lin Himmelmann and Dirk Metzler
TreeTime: An extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.
Bioinformatics Advance Access published on July 3, 2009.
doi:10.1093/bioinformatics/btp417
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Eva Grafahrend-Belau, Christian Klukas, Björn H. Junker, and Falk Schreiber
FBA-SimVis: Interactive visualisation of constraint-based metabolic models
Bioinformatics Advance Access published on July 3, 2009.
doi:10.1093/bioinformatics/btp408
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, and Herbert M. Sauro
Antimony: A modular model definition language
Bioinformatics Advance Access published on July 3, 2009.
doi:10.1093/bioinformatics/btp401
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Mieszko Lis, Maxim N. Artyomov, Srinivas Devadas, and Arup K. Chakraborty
Efficient stochastic simulation of reaction-diffusion processes via direct compilation
Bioinformatics Advance Access published on July 3, 2009.
doi:10.1093/bioinformatics/btp387
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

2 July 2009

Abstract ORIGINAL PAPER
Lee Zamparo and Theodore Perkins
Statistical lower bounds on protein copy number from fluorescence expression images
Bioinformatics Advance Access published on July 2, 2009.
doi:10.1093/bioinformatics/btp415
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Galina V. Glazko and Frank Emmert-Streib
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets
Bioinformatics Advance Access published on July 2, 2009.
doi:10.1093/bioinformatics/btp406
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Heinrich Magnus Manske and Dominic P. Kwiatkowski
SNP-o-matic
Bioinformatics Advance Access published on July 2, 2009.
doi:10.1093/bioinformatics/btp403
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Nestor Zaburannyy, Bohdan Ostash, and Victor Fedorenko
TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon
Bioinformatics Advance Access published on July 2, 2009.
doi:10.1093/bioinformatics/btp402
[Abstract] [Accepted Manuscript] [Request Permissions]

1 July 2009

Abstract APPLICATIONS NOTE
Andrew A. Pohl, Charles W. Sugnet, Tyson A. Clark, Kayla Smith, Pauline A. Fujita, and Melissa S. Cline
Affy Exon Tissues: Exon Levels in Normal Tissues in Human, Mouse, and Rat
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp414
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract DISCOVERY NOTE: Hiromi Nishida, Takayuki Motoyama, Shogo Yamamoto, Hiroyuki Aburatani, and Hiroyuki Osada
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp413
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Quan Long, Daniel MacArthur, Zemin Ning, and Chris Tyler-Smith
HI: Haplotype Improver using paired-end short reads
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp412
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Xiaofeng Dai, Olli Yli-Harja, and Andre S. Ribeiro
Determining noisy attractors of delayed stochastic Gene Regulatory Networks from multiple data sources
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp411
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Lauren M. Bragg and Glenn Stone
k-link EST Clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp410
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: A. H. M. Mahbub Latif, Frank Bretz, and Edgar Brunner
Robustness Considerations in Selecting Efficient Two–Color Microarray Designs
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp407
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: David S. DeLuca, Britta Eiz-Vesper, Nektarios Ladas, Barbara Anna-Maria Khattab, and Rainer Blasczyk
High throughput minor histocompatibility antigen prediction
Bioinformatics Advance Access published on July 1, 2009.
doi:10.1093/bioinformatics/btp404
[Abstract] [Accepted Manuscript] [Request Permissions]

29 June 2009

Abstract ORIGINAL PAPER: S. M. Wimalaratne, M. D. B. Halstead, C. M. Lloyd, E. J. Crampin, and P. F. Nielsen
Biophysical annotation and representation of CellML models
Bioinformatics Advance Access published on June 29, 2009.
doi:10.1093/bioinformatics/btp391
[Abstract] [Accepted Manuscript] [Request Permissions]

27 June 2009

Abstract APPLICATIONS NOTE
Aleksandar Stojmirovic and Yi-Kuo Yu
ITM Probe: analyzing information flow in protein networks
Bioinformatics Advance Access published on June 27, 2009.
doi:10.1093/bioinformatics/btp398
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Jong Hyun Kim, Woo-Cheol Kim, Michael S. Waterman, Sanghyun Park, and Lei M. Li
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome
Bioinformatics Advance Access published on June 27, 2009.
doi:10.1093/bioinformatics/btp399
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Victor M. Markowitz, Konstantinos Mavromatis, Natalia N. Ivanova, I-Min A. Chen, Ken Chu, and Nikos C. Kyrpides
IMG ER: A System for Microbial Genome Annotation Expert Review and Curation
Bioinformatics Advance Access originally published on June 27, 2009. This version published July 2, 2009.
doi:10.1093/bioinformatics/btp393
[Abstract] [Accepted Manuscript] [Request Permissions]

26 June 2009

Abstract ORIGINAL PAPER: Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, and Olga G. Troyanskaya
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp397
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Pierre Nicolas, Aurélie Leduc, Stéphane Robin, Simon Rasmussen, Hanne Jarmer, and Philippe Bessières
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp395
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, and Zemin Ning
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp394
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Neil Swainston and Pedro Mendes
libAnnotationSBML: a library for exploiting SBML annotations
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp392
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Zheng Rong Yang, Ganjana Lertmemongkolchai, Gladys Tan, Philip L. Felgner, and Richard Titball
A Genetic Programming Approach for Burkholderia Pseudomallei Diagnostic Pattern Discovery
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp390
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
David L. Gold, Jeffrey C. Miecznikowski, and Song Liu
Error control variability in pathway-based microarray analysis.
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp385
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Reid F. Thompson, Masako Suzuki, Kevin W. Lau, and John M. Greally
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp382
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Cenny Taslim, Jiejun Wu, Pearlly Yan, Greg Singer, Jeffrey Parvin, Tim Huang, Shili Lin, and Kun Huang
Comparative Study on ChIP-seq Data: Normalization and Binding Pattern Characterization
Bioinformatics Advance Access published on June 26, 2009.
doi:10.1093/bioinformatics/btp384
[Abstract] [Accepted Manuscript] [Supplementary Data] [Supplementary Data] [Request Permissions]

23 June 2009

Abstract ORIGINAL PAPER: Ali Torkamani and Nicholas J. Schork
Prestige Centrality-Based Functional Outlier Detection in Gene Expression Analysis
Bioinformatics Advance Access published on June 23, 2009.
doi:10.1093/bioinformatics/btp388
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Christophe N. Magnan, Arlo Randall, and Pierre Baldi
SOLpro: accurate sequence-based prediction of protein solubility
Bioinformatics Advance Access published on June 23, 2009.
doi:10.1093/bioinformatics/btp386
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Nava Whiteford, Tom Skelly, Christina Curtis, Matt E. Ritchie, Andrea Löhr, Alexander Wait Zaranek, Irina Abnizova, and Clive Brown
Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform
Bioinformatics Advance Access published on June 23, 2009.
doi:10.1093/bioinformatics/btp383
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Lianyi Han, Yanli Wang, and Stephen H. Bryant
A survey of across-target bioactivity results of small molecules in PubChem
Bioinformatics Advance Access published on June 23, 2009.
doi:10.1093/bioinformatics/btp380
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

19 June 2009

Abstract APPLICATIONS NOTE
Davide Rambaldi and Francesca D. Ciccarelli
FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci.
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp381
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinja, and Bertil Schmidt
SHREC: A short-read error correction method
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp379
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Bas E. Dutilh, Martijn A. Huynen, and Marc Strous
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp377
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Daniel C. Koboldt, Ken Chen, Todd Wylie, David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, and Li Ding
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp373
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur Chun-Chieh Shih
GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp372
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: E. Andrés Houseman, Brock C. Christensen, Margaret R. Karagas, Margaret R. Wrensch, Heather H. Nelson, Joseph L. Wiemels, Shichun Zheng, John K. Wiencke, Karl T. Kelsey, and Carmen J. Marsit
Copy number variation has little impact on bead-array-based measures of DNA methylation
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp364
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Gerald Quon and Quaid Morris
ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp378
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Xuerui Yang, Yang Zhou, Rong Jin, and Christina Chan
Reconstruct Modular Phenotype-Specific Gene Networks by Knowledge-Driven Matrix Factorization
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp376
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Lars Kaderali, Eva Dazert, Ulf Zeuge, Michael Frese, and Ralf Bartenschlager
Reconstructing Signaling Pathways from RNAi Data using Probabilistic Boolean Threshold Networks
Bioinformatics Advance Access published on June 19, 2009.
doi:10.1093/bioinformatics/btp375
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

17 June 2009

Abstract APPLICATIONS NOTE: Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, and Simon J. Puglisi
A Fast Hybrid Short Read Fragment Assembly Algorithm
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp374
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Henrik Bengtsson, Pratyaksha Wirapati, and Terence P. Speed
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp371
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Liang-Tsung Huang and M. Michael Gromiha
Reliable Prediction of Protein Thermostability Change upon Double Mutation from Amino Acid Sequence
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp370
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Nicolas Lartillot, Thomas Lepage, and Samuel Blanquart
PhyloBayes 3. A Bayesian software package for phylogenetic reconstruction and molecular dating
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp368
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Xiaowen Liu, Yonghua Han, Denis Yuen, and Bin Ma
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp366
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Yuliya Karpievitch, Jeff Stanley, Thomas Taverner, Jianhua Huang, Joshua N. Adkins, Charles Ansong, Fred Heffron, Thomas O. Metz, Wei-Jun Qian, Hyunjin Yoon, Richard D. Smith, and Alan R. Dabney
A Statistical Framework for Protein Quantitation in Bottom-Up MS-based Proteomics
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp362
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Thomas Sütterlin, Simone Huber, Hartmut Dickhaus, and Niels Grabe
Modeling Multi-Cellular Behavior in Epidermal Tissue Homeostasis via Finite State Machines in Multi-Agent Systems
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp361
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Chuan Lu and Ross D. King
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
Bioinformatics Advance Access published on June 17, 2009.
doi:10.1093/bioinformatics/btp360
[Abstract] [Accepted Manuscript] [Request Permissions]

15 June 2009

Abstract ORIGINAL PAPER: Lun Yang, Langlai Xu, and Lin He
A CitationRank Algorithm Inheriting Google Technology Designed to Highlight Genes Responsible for Serious Adverse Drug Reaction
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp369
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Inanç Birol, Shaun D Jackman, Cydney Nielsen, Jenny Q Qian, Richard Varhol, Greg Stazyk, Ryan D Morin, Yongjun Zhao, Martin Hirst, Jacqueline E Schein, Doug E Horsman, Joseph M Connors, Randy D Gascoyne, Marco A Marra, and Steven JM Jones
De novo Transcriptome Assembly with ABySS
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp367
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Kathleen F. Kerr
Commentson theAnalysisof Unbalanced Microarray Data
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp363
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Stan Pounds, Cheng Cheng, Xueyuan Cao, Kristine R. Crews, William Plunkett, Varsha Gandhi, Jeffrey Rubnitz, Raul C. Ribeiro, James R. Downing, and Jatinder Lamba
PROMISE: A Tool to Identify Genomic Features with a Specific Biologically Interesting Pattern of Associations with Multiple Endpoint Variables
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp357
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, M Baudis, and Tamer Kahveci
Inferring Progression Models for CGH data
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp365
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Rodrigo Gouveia-Oliveira, Francisco S Roque, Rasmus Wernersson, Thomas Sicheritz-Ponten, Peter W Sackett, Anne Mølgaard, and Anders G Pedersen
InterMap3D: predicting and visualizing co-evolving protein residues
Bioinformatics Advance Access published on June 15, 2009.
doi:10.1093/bioinformatics/btp335
[Abstract] [Accepted Manuscript] [Request Permissions]

10 June 2009

Abstract ORIGINAL PAPER: Yanglan Gan, Jihong Guan, and Shuigeng Zhou
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles
Bioinformatics Advance Access published on June 10, 2009.
doi:10.1093/bioinformatics/btp359
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Anna I Rissman, Bob Mau, Bryan S. Biehl, Aaron E. Darling, Jeremy D. Glasner, and Nicole T. Perna
Reordering contigs of draft genomes using the Mauve Aligner
Bioinformatics Advance Access published on June 10, 2009.
doi:10.1093/bioinformatics/btp356
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan Fokkink, Thilo Kielmann, Henri Bal, and Jaap Heringa
Executing Multicellular Differentiation: Quantitative Predictive Modelling of C. elegans Vulval Development
Bioinformatics Advance Access published on June 10, 2009.
doi:10.1093/bioinformatics/btp355
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Suparna Mitra, Bernhard Klar, and Daniel H. Huson
Visual and Statistical Comparison of Metagenomes
Bioinformatics Advance Access published on June 10, 2009.
doi:10.1093/bioinformatics/btp341
[Abstract] [Accepted Manuscript] [Request Permissions]

8 June 2009

Abstract ORIGINAL PAPER: A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, and J. Timmer
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp358
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Audrey Kauffmann, Tim F. Rayner, Helen Parkinson, Misha Kapushesky, Margus Lukk, Alvis Brazma, and Wolfgang Huber
Importing ArrayExpress datasets into R/Bioconductor.
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp354
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Caroline C. Friedel and Ralf Zimmer
Identifying the topology of protein complexes from affinity purification assays
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp353
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and 1000 Genome Project Data Processing Subgroup
The Sequence Alignment/Map (SAM) Format and SAMtools
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp352
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Ritwik Layek, Aniruddha Datta, Ranadip Pal, and Edward R. Dougherty
Adaptive Intervention in Probabilistic Boolean Networks
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp349
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Salvador Capella-Gutiérrez, José M. Silla-Martínez, and Toni Gabaldón
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp348
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Nils Hoffmann and Jens Stoye
ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp343
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Andrew F Neuwald
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp342
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, and Weiqun Peng
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Bioinformatics Advance Access published on June 8, 2009.
doi:10.1093/bioinformatics/btp340
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

3 June 2009

Abstract ORIGINAL PAPER
Taro L. Saito, Jun Yoshimura, Shin Sasaki, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kuroshu, and Shinichi Morishita
UTGB Toolkit for Personalized Genome Browsers
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp350
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Samuel Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold, and Matthew Berriman
ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp347
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Yong Wang, Ruslan I. Sadreyev, and Nick V. Grishin
PROCAIN server for remote protein sequence similarity search
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp346
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Woonghee Lee, William M. Westler, Arash Bahrami, Hamid R. Eghbalnia, and John L. Markley
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp345
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Kathryn E Holt, Yik Y Teo, Heng Li, Satheesh Nair, Gordon Dougan, John Wain, and Julian Parkhill
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp344
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Shanfeng Zhu, Jia Zeng, and Hiroshi Mamitsuka
Enhancing MEDLINE Document Clustering by Incorporating MeSH Semantic Similarity
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp338
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, and Jun Wang
SOAP2: an improved ultrafast tool for short read alignment
Bioinformatics Advance Access published on June 3, 2009.
doi:10.1093/bioinformatics/btp336
[Abstract] [Accepted Manuscript] [Request Permissions]

31 May 2009

Abstract ORIGINAL PAPER: Andrea Zen, Cesira de Chiara, Annalisa Pastore, and Cristian Micheletti
Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
Bioinformatics Advance Access published on May 31, 2009.
doi:10.1093/bioinformatics/btp339
[Abstract] [Accepted Manuscript] [Request Permissions]

26 May 2009

Abstract ORIGINAL PAPER
Jessica H Fong and Aron Marchler-Bauer
CORAL: Aligning conserved core regions across domain families
Bioinformatics Advance Access published on May 26, 2009.
doi:10.1093/bioinformatics/btp334
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Rodrigo Santamaría and Roberto Therón
Treevolution: visual analysis of phylogenetic trees
Bioinformatics Advance Access published on May 26, 2009.
doi:10.1093/bioinformatics/btp333
[Abstract] [Accepted Manuscript] [Request Permissions]

25 May 2009

Abstract ORIGINAL PAPER
Christoph Kaleta, Stephan Richter, and Peter Dittrich
Using Chemical Organization Theory for Model-Checking
Bioinformatics Advance Access published on May 25, 2009.
doi:10.1093/bioinformatics/btp332
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

21 May 2009

Abstract ORIGINAL PAPER: Kristin K. Nicodemus and James D. Malley
Predictor Correlation Impacts Machine Learning Algorithms: Implications for Genomic Studies
Bioinformatics Advance Access published on May 21, 2009.
doi:10.1093/bioinformatics/btp331
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, and G. Vriend
An Active Registry for Bioinformatics Web Services
Bioinformatics Advance Access published on May 21, 2009.
doi:10.1093/bioinformatics/btp329
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

19 May 2009

Abstract APPLICATIONS NOTE
Georgios A. Pavlopoulos, Charalampos N Moschopoulos, Sean D. Hooper, Reinhard Schneider, and Sophia Kossida
jClust: A clustering and visualization toolbox.
Bioinformatics Advance Access published on May 19, 2009.
doi:10.1093/bioinformatics/btp330
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

15 May 2009

Abstract ORIGINAL PAPER: Wandaliz Torres-García, Weiwen Zhang, George C. Runger, Roger H. Johnson, and Deirdre R. Meldrum
Integrative Analysis of Transcriptomic and Proteomic Data of Desulfovibrio vulgaris: a nonlinear model to predict abundance of undetected proteins
Bioinformatics Advance Access published on May 15, 2009.
doi:10.1093/bioinformatics/btp325
[Abstract] [Accepted Manuscript] [Request Permissions]

14 May 2009

Abstract ORIGINAL PAPER: Rene Hussong, Barbara Gregorius, Andreas Tholey, and Andreas Hildebrandt
Highly accelerated feature detection in proteomics data sets using modern graphics processing units
Bioinformatics Advance Access published on May 14, 2009.
doi:10.1093/bioinformatics/btp294
[Abstract] [Accepted Manuscript] [Request Permissions]

13 May 2009

Abstract APPLICATIONS NOTE: Rodriguez-Esteban Raul and Iossifov Ivan
Figure mining for biomedical research
Bioinformatics Advance Access published on May 13, 2009.
doi:10.1093/bioinformatics/btp318
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Chang H Seo, Kim Jeong-Rae, Kim Man-Sun, and Cho Kwang-Hyun
Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks
Bioinformatics Advance Access published on May 13, 2009.
doi:10.1093/bioinformatics/btp316
[Abstract] [Accepted Manuscript] [Request Permissions]

12 May 2009

Abstract APPLICATIONS NOTE: M Bahlo and C.J. Bromhead
Generating linkage mapping files from Affymetrix SNP chip data
Bioinformatics Advance Access published on May 12, 2009.
doi:10.1093/bioinformatics/btp313
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Guimei Liu, Limsoon Wong, and Hon Nian Chua
Complex Discovery from Weighted PPI Networks
Bioinformatics Advance Access published on May 12, 2009.
doi:10.1093/bioinformatics/btp311
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: GL Papadopoulos, P Alexiou, M Maragkakis, M Reczko, and AG Hatzigeorgiou
DIANA-mirPath: Integrating human and mouse microRNAs in pathways
Bioinformatics Advance Access published on May 12, 2009.
doi:10.1093/bioinformatics/btp299
[Abstract] [Accepted Manuscript] [Request Permissions]

7 May 2009

Abstract ORIGINAL PAPER: David S DeLuca, Elena Beisswanger, Joachim Wermter, Peter A Horn, Udo Hahn, and Rainer Blasczyk
MaHCO: An Ontology of the Major Histocompatibility Complex for Immunoinformatic Applications and Text Mining
Bioinformatics Advance Access published on May 7, 2009.
doi:10.1093/bioinformatics/btp306
[Abstract] [Accepted Manuscript] [Request Permissions]

6 May 2009

Abstract APPLICATIONS NOTE
Bo Peng and Christopher I Amos
Forward-time Simulations of Nonrandom Mating Populations using simuPOP
Bioinformatics Advance Access published on May 6, 2009.
doi:10.1093/bioinformatics/btp307
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Michael Matschiner and Walter Salzburger
TANDEM: integrating automated allele binning into genetics and genomics workflows
Bioinformatics Advance Access published on May 6, 2009.
doi:10.1093/bioinformatics/btp303
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Véronique Dupierris, Christophe Masselon, Magali Court, Sylvie Kieffer-Jaquinod, and Christophe Bruley
A toolbox for Validation of mass spectrometry peptides identification and Generation of database: IRMa
Bioinformatics Advance Access published on May 6, 2009.
doi:10.1093/bioinformatics/btp301
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: F Le Fèvre, S Smidtas, C Combe, M Durot, Florence d'Alché-Buc, and V Schachter
CycSim - an online tool for exploring and experimenting with genome-scale metabolic models
Bioinformatics Advance Access published on May 6, 2009.
doi:10.1093/bioinformatics/btp268
[Abstract] [Accepted Manuscript] [Request Permissions]

5 May 2009

Abstract ORIGINAL PAPER
Semin Lee and Tom L Blundell
Ulla: a program for calculating environment-specific amino acid substitution tables
Bioinformatics Advance Access published on May 5, 2009.
doi:10.1093/bioinformatics/btp300
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

4 May 2009

Abstract ORIGINAL PAPER: Tianwei Yu
apLCMS - Adaptive Processing of High-Resolution LC/MS Data
Bioinformatics Advance Access published on May 4, 2009.
doi:10.1093/bioinformatics/btp291
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, and Jun'ichi Tsujii
U-Compare: share and compare text mining tools with UIMA
Bioinformatics Advance Access published on May 4, 2009.
doi:10.1093/bioinformatics/btp289
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Qiong Cheng, Robert Harrison, and Alexander Zelikovsky
MetNetAligner: a web service tool for metabolic network alignments
Bioinformatics Advance Access published on May 4, 2009.
doi:10.1093/bioinformatics/btp287
[Abstract] [Accepted Manuscript] [Request Permissions]

28 April 2009

Abstract ORIGINAL PAPER
Michael Seifert, Jens Keilwagen, Marc Strickert, and Ivo Grosse
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data
Bioinformatics Advance Access published on April 28, 2009.
doi:10.1093/bioinformatics/btp276
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

27 April 2009

Abstract APPLICATIONS NOTE
Lasse Folkersen, Diego Diez, Craig E. Wheelock, Jesper Z. Haeggström, Susumu Goto, Per Eriksson, and Anders Gabrielsen
GeneRegionScan: a Bioconductor package for probe level analysis of specific, small regions of the genome
Bioinformatics Advance Access published on April 27, 2009.
doi:10.1093/bioinformatics/btp279
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Kévin Darty, Alain Denise, and Yann Ponty
VARNA: Interactive drawing and editing of the RNA secondary structure
Bioinformatics Advance Access published on April 27, 2009.
doi:10.1093/bioinformatics/btp250
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

23 April 2009

Abstract ORIGINAL PAPER
Sebastian J. Schultheiss, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, and Gunnar Rätsch
KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences
Bioinformatics Advance Access published on April 23, 2009.
doi:10.1093/bioinformatics/btp278
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

17 April 2009

Abstract APPLICATIONS NOTE
Stephan Saalfeld, Albert Cardona, Volker Hartenstein, and Pavel Tomancák
CATMAID: Collaborative Annotation Toolkit for Massive Amounts of Image Data
Bioinformatics Advance Access published on April 17, 2009.
doi:10.1093/bioinformatics/btp266
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

15 April 2009

Abstract APPLICATIONS NOTE: Claudia Andreini, Ivano Bertini, Gabriele Cavallaro, Gemma L. Holliday, and Janet M. Thornton
Metal-MACiE: a database of metals involved in biological catalysis
Bioinformatics Advance Access published on April 15, 2009.
doi:10.1093/bioinformatics/btp256
[Abstract] [Accepted Manuscript] [Request Permissions]

13 March 2009

Abstract ORIGINAL PAPER: Thomas Fober, Marco Mernberger, Gerhard Klebe, and Eyke Hüllermeier
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
Bioinformatics Advance Access published on March 13, 2009.
doi:10.1093/bioinformatics/btp144
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Utz J. Pape, Holger Klein, and Martin Vingron
Statistical detection of co-operative transcription factors with similarity adjustment
Bioinformatics Advance Access published on March 13, 2009.
doi:10.1093/bioinformatics/btp143
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

8 February 2009

Abstract ORIGINAL PAPER: Markus Riester, Peter F. Stadler, and Konstantin Klemm
FRANz: Reconstruction of wild multi-generation pedigrees
Bioinformatics Advance Access originally published on February 8, 2009. This version published February 10, 2009.
doi:10.1093/bioinformatics/btp064
[Abstract] [Accepted Manuscript] [Request Permissions]

2 February 2009

Abstract ORIGINAL PAPER
Steffen Heyne, Sebastian Will, Michael Beckstette, and Rolf Backofen
Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches
Bioinformatics Advance Access published on February 2, 2009.
doi:10.1093/bioinformatics/btp065
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE