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.

6 November 2009

Abstract ORIGINAL PAPER: Liam J. McGuffin and Daniel B. Roche
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
Bioinformatics Advance Access published on November 6, 2009.
doi:10.1093/bioinformatics/btp629
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Stefano Volinia, Rosa Visone, Marco Galasso, Elda Rossi, and Carlo M Croce
Identification of microRNA activity by Targets' Reverse EXpression
Bioinformatics Advance Access published on November 6, 2009.
doi:10.1093/bioinformatics/btp598
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

5 November 2009

Abstract APPLICATIONS NOTE: Ben D. MacArthur, Alexander Lachmann, Ihor R. Lemischka, and Avi Ma'ayan
GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data
Bioinformatics Advance Access published on November 5, 2009.
doi:10.1093/bioinformatics/btp628
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Brian Carrillo, Corey Yanofsky, Sylvie Laboissiere, Robert Nadon, and Robert E. Kearney
Methods for combining peptide intensities to estimate relative protein abundance
Bioinformatics Advance Access published on November 5, 2009.
doi:10.1093/bioinformatics/btp610
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

4 November 2009

Abstract ORIGINAL PAPER: Robert A. Forties and Ralf Bundschuh
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
Bioinformatics Advance Access published on November 4, 2009.
doi:10.1093/bioinformatics/btp627
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Axel Rasche and Ralf Herwig
ARH: Predicting Splice Variants from Genome-wide Data with Modified Entropy
Bioinformatics Advance Access published on November 4, 2009.
doi:10.1093/bioinformatics/btp626
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

3 November 2009

Abstract APPLICATIONS NOTE
Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, and Teresa M. Przytycka
SimBoolNet - A Cytoscape Plugin for Dynamic Simulation of Signaling Networks
Bioinformatics Advance Access published on November 3, 2009.
doi:10.1093/bioinformatics/btp617
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

30 October 2009

Abstract APPLICATIONS NOTE: Andrew L. Hipp and Marcial Escudero
MATICCE: mapping transitions in continuous character evolution
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp625
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L.S. Tang, and Weichuan Yu
Predictive rule inference for epistatic interaction detection in genome-wide association studies
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp622
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Runqing Yang, Xin Wang, Zeyuan Wu, Daniel R. Prows, and Min Lin
Bayesian Model Selection for Characterizing Genomic Imprinting Effects and Patterns
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp620
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Ji Qi, Fangqing Zhao, Anne Buboltz, and Stephan C. Schuster
inGAP: an integrated next-generation genome analysis pipeline
Bioinformatics Advance Access published on October 30, 2009.
doi:10.1093/bioinformatics/btp615
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

29 October 2009

LETTER TO THE EDITOR
Pawel Smialowski, Dmitrij Frishman, and Stefan Kramer
Pitfalls of supervised feature selection
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp621
[Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Tina Toni and Michael P. H. Stumpf
Simulation-based model selection for dynamical systems in systems and population biology
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp619
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, and Silke R. Sperling
MicroRazerS: Rapid alignment of small RNA reads
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp601
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Ranjit Randhawa, Clifford A. Shaffer, and John J. Tyson
Model Aggregation: a building-block approach to creating large macromolecular regulatory networks
Bioinformatics Advance Access published on October 29, 2009.
doi:10.1093/bioinformatics/btp581
[Abstract] [Accepted Manuscript] [Request Permissions]

27 October 2009

Abstract APPLICATIONS NOTE
W. Yu, M. Clyne, M.J. Khoury, and M. Gwinn
Phenopedia and Genopedia: Disease-centered and Gene-centered Views of the Evolving Knowledge of Human Genetic Associations
Bioinformatics Advance Access originally published on October 27, 2009. This version published October 30, 2009.
doi:10.1093/bioinformatics/btp618
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, and W. Evan Johnson
The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp614
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, and Judith A. J. Steen
Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp607
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Matti Pirinen
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
Bioinformatics Advance Access published on October 27, 2009.
doi:10.1093/bioinformatics/btp584
[Abstract] [Accepted Manuscript] [Request Permissions]

24 October 2009

Abstract ORIGINAL PAPER: Youngik Yang, Donald Gilbert, and Sun Kim
Annotation Confidence Score for Genome Annotation: A Genome Comparison Approach
Bioinformatics Advance Access published on October 24, 2009.
doi:10.1093/bioinformatics/btp613
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, and Xuegong Zhang
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Bioinformatics Advance Access published on October 24, 2009.
doi:10.1093/bioinformatics/btp612
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Erik Arner, Yoshihide Hayashizaki, and Carsten O. Daub
NGSView: an extensible open source editor for next-generation sequencing data
Bioinformatics Advance Access published on October 24, 2009.
doi:10.1093/bioinformatics/btp611
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

22 October 2009

Abstract DISCOVERY NOTE
Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp609
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Joshua Buckner, Justin Wilson, Mark Seligman, Brian Athey, Stanley Watson, and Fan Meng
The gputools package enables GPU computing in R
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp608
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Shuangge Ma, Yawei Zhang, Jian Huang, Xuesong Han, Theodore Holford, Qing Lan, Nathaniel Rothman, Peter Boyle, and Tongzhang Zheng
Identification of Non-Hodgkin's Lymphoma Prognosis Signatures Using the CTGDR Method
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp604
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Yun Niu, David Otasek, and Igor Jurisica
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I²D
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp602
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Abdoulaye Banire Diallo, Vladimir Makarenkov, and Mathieu Blanchette
Ancestors 1.0: A Web Server For Ancestral Sequence Reconstruction
Bioinformatics Advance Access published on October 22, 2009.
doi:10.1093/bioinformatics/btp600
[Abstract] [Accepted Manuscript] [Request Permissions]

21 October 2009

Abstract ORIGINAL PAPER: Mohammadmahdi R. Yousefi, Jianping Hua, Chao Sima, and Edward R. Dougherty
Reporting bias when using real data sets to analyze classification performance
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp605
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Bart P.P. van Houte and Jaap Heringa
Accurate confidence aware clustering of array CGH tumor profiles
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp603
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Christine Rousseau, Jacques Nicolas, and Mathieu Gonnet
CRISPI: a CRISPR Interactive database
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp586
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Troy Zerr, Gregory M. Cooper, Evan E. Eichler, and Deborah A. Nickerson
Targeted Interrogation of Copy Number Variation using SCIMMkit
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp606
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jian Yu, Yong Zhou, Isao Tanaka, and Min Yao
Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp599
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Yoshihiro Kawahara, Ryuichi Sakate, Akihiro Matsuya, Katsuhiko Murakami, Yoshiharu Sato, Hao Zhang, Takashi Gojobori, Takeshi Itoh, and Tadashi Imanishi
G-compass: A web-based comparative genome browser between human and other vertebrate genomes
Bioinformatics Advance Access published on October 21, 2009.
doi:10.1093/bioinformatics/btp594
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

16 October 2009

Abstract APPLICATIONS NOTE: Martijn J. Schuemie, Ning Kang, Maarten L. Hekkelman, and Jan A. Kors
GeneE: Gene and protein query expansion with disambiguation
Bioinformatics Advance Access published on October 16, 2009.
doi:10.1093/bioinformatics/btp597
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Christine Herold, Michael Steffens, Felix F. Brockschmidt, Max P. Baur, and Tim Becker
INTERSNP: Genome-wide Interaction Analysis Guided by A Priori Information
Bioinformatics Advance Access published on October 16, 2009.
doi:10.1093/bioinformatics/btp596
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Kevin R. Brown, David Otasek, Muhammad Ali, Michael McGuffin, Wing Xie, Baiju Devani, Ian Lawson van Toch, and Igor Jurisica
NAViGaTOR: Network Analysis, Visualization & Graphing Toronto
Bioinformatics Advance Access published on October 16, 2009.
doi:10.1093/bioinformatics/btp595
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

14 October 2009

Abstract ORIGINAL PAPER
Michael Beckstette, Robert Homann, Robert Giegerich, and Stefan Kurtz
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Bioinformatics Advance Access published on October 14, 2009.
doi:10.1093/bioinformatics/btp593
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Martin Schäfer, Holger Schwender, Sylvia Merk, Claudia Haferlach, Katja Ickstadt, and Martin Dugas
Integrated Analysis of Copy Number Alterations and Gene Expression: A Bivariate Assessment of Equally Directed Abnormalities
Bioinformatics Advance Access published on October 14, 2009.
doi:10.1093/bioinformatics/btp592
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Sarbashis Das, Anchal Vishnoi, and Alok Bhattacharya
ABWGAT: Anchor Based Whole Genome Analysis Tool.
Bioinformatics Advance Access published on October 14, 2009.
doi:10.1093/bioinformatics/btp587
[Abstract] [Accepted Manuscript] [Supplementary Data 1] [Request Permissions]

13 October 2009

LETTER TO THE EDITOR: Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, and David A. Fell
Response to comment on ’Can sugars be produced from fatty acids? A test case for pathway analysis tools’
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp591
[Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Mirjana Domazet-Loso and Bernhard Haubold
Efficient Estimation of Pairwise Distances between Genomes
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp590
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Qingliang Li, Yanli Wang, and Stephen H. Bryant
A novel method for mining highly imbalanced high-throughput screening data in PubChem
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp589
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Curtis Huttenhower, K. Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J. Forman, Olga G. Troyanskaya, and Hilary A. Coller
Detailing regulatory networks through large scale data integration
Bioinformatics Advance Access published on October 13, 2009.
doi:10.1093/bioinformatics/btp588
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

9 October 2009

Abstract ORIGINAL PAPER: Alfonso Ibáñez, Pedro Larrañaga, and Concha Bielza
Predicting citation count of Bioinformatics papers within four years of publication
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp585
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: I. M. Carr, J. I. Robinson, R. Dimitriou, A. F. Markham, A. W. Morgan, and D. T. Bonthron
Inferring relative proportions of DNA variants from sequencing electropherograms
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp583
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Xiaoxiao Kong and Cavan Reilly
A Bayesian approach to the alignment of mass spectra
Bioinformatics Advance Access published on October 9, 2009.
doi:10.1093/bioinformatics/btp582
[Abstract] [Accepted Manuscript] [Request Permissions]

7 October 2009

Abstract ORIGINAL PAPER
Magdalena A. Jonikas, Randall J. Radmer, and Russ B. Altman
Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models
Bioinformatics Advance Access published on October 7, 2009.
doi:10.1093/bioinformatics/btp576
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

6 October 2009

Abstract ORIGINAL PAPER: Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, and Kiyoshi Asai
CentroidAlign: Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-pairs Score
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp580
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Jacob F. Degner, John C. Marioni, Athma A. Pai, Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, and Jonathan K. Pritchard
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp579
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Stefan P. Albaum, Heiko Neuweger, Benjamin Fränzel, Sita Lange, Dominik Mertens, Christian Trötschel, Dirk Wolters, Jörn Kalinowski, Tim W. Nattkemper, and Alexander Goesmann
Qupe – a Rich Internet Application to take a Step Forward in the Analysis of Mass Spectrometry–Based Quantitative Proteomics Experiments
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp568
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Heidi Dvinge and Paul Bertone
HTqPCR: High-throughput analysis and visualization of quantitative real-time PCR data in R
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp578
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Pascal Gellert, Shizuka Uchida, and Thomas Braun
Exon Array Analyzer: a web interface for Affymetrix exon array analysis
Bioinformatics Advance Access originally published on October 6, 2009. This version published October 12, 2009.
doi:10.1093/bioinformatics/btp577
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: P. Gerlee, L. Lizana, and K. Sneppen
Pathway identification by network pruning in the metabolic network of Escherichia coli
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp575
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Ka-Lok Ng, Hsueh-Chuan Liu, and Shan-Chih Lee
ncRNAppi – A tool for identifying disease-related miRNA and siR-NA targeting pathways
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp574
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract DISCOVERY NOTE: Lior Shamir, Catherine A. Wolkow, and Ilya G. Goldberg
Quantitative measurement of aging using image texture entropy
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp571
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Jia Zeng, Reda Alhajj, and Douglas Demetrick
Adaptive multi-agent architecture for functional sequence motifs recognition
Bioinformatics Advance Access published on October 6, 2009.
doi:10.1093/bioinformatics/btp567
[Abstract] [Accepted Manuscript] [Request Permissions]

1 October 2009

Abstract APPLICATIONS NOTE
Dmitry A. Filatov
Processing and population genetic analysis of multigenic datasets with ProSeq3 software
Bioinformatics Advance Access published on October 1, 2009.
doi:10.1093/bioinformatics/btp572
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Victor X. Jin, Jeff Apostolos, Naga Satya Venkateswara Ra Nagisetty, and Peggy J. Farnham
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data
Bioinformatics Advance Access published on October 1, 2009.
doi:10.1093/bioinformatics/btp570
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Waqar Ali and Charlotte M. Deane
Functionally guided alignment of protein interaction networks for module detection
Bioinformatics Advance Access published on October 1, 2009.
doi:10.1093/bioinformatics/btp569
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

30 September 2009

Abstract ORIGINAL PAPER: Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster, and Francisco J. Planes
Computing the shortest elementary flux modes in genome-scale metabolic networks
Bioinformatics Advance Access published on September 30, 2009.
doi:10.1093/bioinformatics/btp564
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

29 September 2009

Abstract APPLICATIONS NOTE
Thomas C. Bishop
VDNA: The Virtual DNA plug-in for VMD
Bioinformatics Advance Access published on September 29, 2009.
doi:10.1093/bioinformatics/btp566
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract REVIEW: Panagiotis Alexiou, Manolis Maragkakis, Giorgos L Papadopoulos, Martin Reczko, and Artemis G Hatzigeorgiou
Lost in translation: an assessment and perspective for computational microRNA target identification.
Bioinformatics Advance Access published on September 29, 2009.
doi:10.1093/bioinformatics/btp565
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Kei Yura and Steven Hayward
The interwinding nature of protein-protein interfaces and its implication for protein complex formation
Bioinformatics Advance Access published on September 29, 2009.
doi:10.1093/bioinformatics/btp563
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Dario Ghersi and Roberto Sanchez
EASYMIFS & SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures
Bioinformatics Advance Access published on September 29, 2009.
doi:10.1093/bioinformatics/btp562
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

28 September 2009

Abstract ORIGINAL PAPER: Chris Kauffman and George Karypis
LIBRUS: Combined Machine Learning and Homology Information for Sequence-based Ligand-Binding Residue Prediction
Bioinformatics Advance Access published on September 28, 2009.
doi:10.1093/bioinformatics/btp561
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Nicolas Terrapon, Olivier Gascuel, Éric Maréchal, and Laurent Bréehélin
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
Bioinformatics Advance Access published on September 28, 2009.
doi:10.1093/bioinformatics/btp560
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Peter J Park, Sek Won Kong, Toma Tebaldi, Weil R Lai, Simon Kasif, and Isaac S Kohane
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.
Bioinformatics Advance Access published on September 28, 2009.
doi:10.1093/bioinformatics/btp559
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

25 September 2009

Abstract ORIGINAL PAPER: Hojung Nam, Bong Chul Chung, Younghoon Kim, KiYoung Lee, and Doheon Lee
Combining Tissue Transcriptomics and Urine Metabolomics for Breast Cancer Biomarker Identification
Bioinformatics Advance Access published on September 25, 2009.
doi:10.1093/bioinformatics/btp558
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Markus Leber, Volker Egelhofer, Ida Schomburg, and Dietmar Schomburg
Automatic assignment of reaction operators to enzymatic reactions
Bioinformatics Advance Access published on September 25, 2009.
doi:10.1093/bioinformatics/btp549
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Shashank Agarwal and Hong Yu
Automatically Classifying Sentences in Full-Text Biomedical Arti-cles into Introduction, Methods, Results and Discussion
Bioinformatics Advance Access published on September 25, 2009.
doi:10.1093/bioinformatics/btp548
[Abstract] [Accepted Manuscript] [Request Permissions]

23 September 2009

Abstract LETTER TO THE EDITOR: Karoline Faust, Didier Croes, and Jacques van Helden
In response to "Can sugars be produced from fatty acids? A test case for pathway analysis tools"
Bioinformatics Advance Access published on September 23, 2009.
doi:10.1093/bioinformatics/btp557
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Carl Herrmann, Sèverine Bérard, and Laurent Tichit
SimCT: a generic tool to visualize ontology based relationships for biological objects
Bioinformatics Advance Access published on September 23, 2009.
doi:10.1093/bioinformatics/btp553
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

22 September 2009

Abstract ORIGINAL PAPER: Mensur Dlakic
HHsvm: Fast and accurate classification of profile-profile matches identified by HHsearch
Bioinformatics Advance Access published on September 22, 2009.
doi:10.1093/bioinformatics/btp555
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Janne Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, and Esko Ukkonen
MOODS: fast search for position weight matrix matches in DNA sequences
Bioinformatics Advance Access published on September 22, 2009.
doi:10.1093/bioinformatics/btp554
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Darya Chudova, Alexander Ihler, Kevin K Lin, Bogi Andersen, and Padhraic Smyth
Bayesian detection of non-sinusoidal periodic patterns in circadian expression data
Bioinformatics Advance Access published on September 22, 2009.
doi:10.1093/bioinformatics/btp547
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

21 September 2009

Abstract ORIGINAL PAPER
Christian Blouin, Scott Perry, Allan Lavell, Edward Susko, and Andrew J. Roger
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier
Bioinformatics Advance Access published on September 21, 2009.
doi:10.1093/bioinformatics/btp552
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Jimin Song and Mona Singh
How and when should interactome-derived clusters be used to predict functional modules and protein function?
Bioinformatics Advance Access published on September 21, 2009.
doi:10.1093/bioinformatics/btp551
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

18 September 2009

Abstract APPLICATIONS NOTE: Richard Easty and Nikolay Nikolov
Client-side Integration of Life Science Literature Resources
Bioinformatics Advance Access published on September 18, 2009.
doi:10.1093/bioinformatics/btp550
[Abstract] [Accepted Manuscript] [Request Permissions]

17 September 2009

Abstract APPLICATIONS NOTE: Romina Oliva, Janet M. Thornton, and Marialuisa Pellegrini-Calace
PoreLogo: a new tool to analyse, visualise and compare channels in transmembrane proteins
Bioinformatics Advance Access published on September 17, 2009.
doi:10.1093/bioinformatics/btp545
[Abstract] [Accepted Manuscript] [Request Permissions]

16 September 2009

Abstract DISCOVERY NOTE: David Hiller, Hui Jiang, Weihong Xu, and Wing Hung Wong
Identifiability of isoform deconvolution from junction arrays and RNA-Seq
Bioinformatics Advance Access published on September 16, 2009.
doi:10.1093/bioinformatics/btp544
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Vera Afreixo, Carlos A. C. Bastos, Armando J. Pinho, Sara P. Garcia, and Paulo J. S. G. Ferreira
Genome analysis with inter-nucleotide distances
Bioinformatics Advance Access published on September 16, 2009.
doi:10.1093/bioinformatics/btp546
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE