Bioinformatics -- Bioinformatics Advance Access by Category

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 Category [View by date]

APPLICATIONS NOTE
ORIGINAL PAPER
DISCOVERY NOTE
REVIEW
ARTICLE

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.

APPLICATIONS NOTE

Abstract APPLICATIONS NOTE: André Wehe, Mukul S. Bansal, J. Gordon Burleigh, and Oliver Eulenstein
DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Bioinformatics Advance Access published on May 12, 2008.
doi:10.1093/bioinformatics/btn230
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Michiel Van Bel, Yvan Saeys, and Yves Van de Peer
FunSiP: A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA
Bioinformatics Advance Access published on May 12, 2008.
doi:10.1093/bioinformatics/btn225
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Miklós Csur ös
Malin: maximum likelihood analysis of intron evolution in eukaryotes
Bioinformatics Advance Access published on May 12, 2008.
doi:10.1093/bioinformatics/btn226
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E. Green, Michael Lachmann, and Janet Kelso
PatMaN: rapid alignment of short sequences to large databases
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn223
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Pan Du, Warren A. Kibbe, and Simon M. Lin
lumi: a pipeline for processing Illumina microarray
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn224
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca Wade, and Ursula Kummer
SYCAMORE - A SYstems biology Computational Analysis and MOdeling Research Environment
Bioinformatics Advance Access published on May 7, 2008.
doi:10.1093/bioinformatics/btn207
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, and Richard D. Smith
DAnTE: a statistical tool for quantitative analysis of -omics data
Bioinformatics Advance Access published on May 3, 2008.
doi:10.1093/bioinformatics/btn217
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: William Ritchie, François-Xavier Théodule, and Daniel Gautheret
Mireval: a web tool for simple microRNA prediction in genome sequences
Bioinformatics Advance Access published on May 3, 2008.
doi:10.1093/bioinformatics/btn137
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Samuel Neuenschwander, Frédéric Hospital, Frédéric Guillaume, and Jérôme Goudet
quantiNEMO: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Bioinformatics Advance Access published on May 1, 2008.
doi:10.1093/bioinformatics/btn219
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Carl Murie and Robert Nadon
A correction for estimating error when using the Local Pooled Error Statistical Test
Bioinformatics Advance Access published on May 1, 2008.
doi:10.1093/bioinformatics/btn211
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Martin Klammer, Sanjit Roopra, and Erik L. L. Sonnhammer
jSquid: a Java applet for graphical on-line network exploration
Bioinformatics Advance Access published on April 29, 2008.
doi:10.1093/bioinformatics/btn213
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Michael Y. Tolstorukov, Vidhu Choudhary, Wilma K. Olson, Victor B. Zhurkin, and Peter J. Park
nuScore: a web-interface for nucleosome positioning predictions
Bioinformatics Advance Access published on April 29, 2008.
doi:10.1093/bioinformatics/btn212
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, and David J. States
Cytoscape ESP: simple search of complex biological networks
Bioinformatics Advance Access published on April 28, 2008.
doi:10.1093/bioinformatics/btn208
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Michael J. Sweredoski and Pierre Baldi
PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half Sphere Exposure
Bioinformatics Advance Access published on April 28, 2008.
doi:10.1093/bioinformatics/btn199
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Frédéric Schütz and Mauro Delorenzi
MAMOT: Hidden MArkov MOdeling Tool
Bioinformatics Advance Access published on April 25, 2008.
doi:10.1093/bioinformatics/btn201
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Korbinian Strimmer
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Bioinformatics Advance Access published on April 25, 2008.
doi:10.1093/bioinformatics/btn209
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Margarita C Theodoropoulou, Pantelis G Bagos, Ioannis C Spyropoulos, and Stavros J Hamodrakas
gpDB: A database of GPCRs, G-proteins, Effectors and their interactions.
Bioinformatics Advance Access published on April 25, 2008.
doi:10.1093/bioinformatics/btn206
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Andreas Quandt, Patricia Hernandez, Alexandre Masselot, Céline Hernandez, Sergio Maffioletti, Cesare Pautasso, Ron D. Appel, and Frederique Lisacek
swissPIT: A novel approach for pipelined analysis of mass spectrometry data
Bioinformatics Advance Access published on April 23, 2008.
doi:10.1093/bioinformatics/btn139
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Gábor E. Tusnády, Lajos Kalmár, Hédi Hegyi, Péter Tompa, and István Simon
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
Bioinformatics Advance Access published on April 23, 2008.
doi:10.1093/bioinformatics/btn202
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Lixiao Wang and Uwe H. Sauer
OnD-CRF: predicting order and disorder in proteins using conditional random fields
Bioinformatics Advance Access published on April 21, 2008.
doi:10.1093/bioinformatics/btn132
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Bo Peng and Christopher I. Amos
Forward-time Simulations of Nonrandom Mating Populations using simuPOP
Bioinformatics Advance Access published on April 15, 2008.
doi:10.1093/bioinformatics/btn179
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol-Kyu Han, and Jeong-Hyeok Yoon
IDMap: facilitating the detection of potential leads with therapeutic targets
Bioinformatics Advance Access published on April 15, 2008.
doi:10.1093/bioinformatics/btn138
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Gilles Guillot, Filipe Santos, and Arnaud Estoup
Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface.
Bioinformatics Advance Access published on April 14, 2008.
doi:10.1093/bioinformatics/btn136
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Claus Lundegaard, Ole Lund, and Morten Nielsen
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
Bioinformatics Advance Access published on April 14, 2008.
doi:10.1093/bioinformatics/btn128
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Jonathan L. Lustgarten, Chad Kimmel, Henrik Ryberg, and William Hogan
EPO-KB: A searchable knowledge base of biomarker to protein links
Bioinformatics Advance Access published on April 9, 2008.
doi:10.1093/bioinformatics/btn125
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Jung-jae Kim, Piotr Pezik, and Dietrich Rebholz-Schuhmann
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline
Bioinformatics Advance Access published on April 9, 2008.
doi:10.1093/bioinformatics/btn117
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Thibaut Jombart
adegenet: a R package for the multivariate analysis of genetic markers
Bioinformatics Advance Access published on April 8, 2008.
doi:10.1093/bioinformatics/btn129
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
David J. States, Alex S. Ade, Zachary C. Wright, Aaron V. Bookvich, and Brian D. Athey
MiSearch Adaptive PubMed Search Tool
Bioinformatics Advance Access published on March 11, 2008.
doi:10.1093/bioinformatics/btn033
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

ORIGINAL PAPER

Abstract ORIGINAL PAPER: Håkan Viklund and Arne Elofsson
OCTOPUS:Improvingtopologypredictionbytwo-track ANN-basedpreferencescoresandanextended topologicalgrammar
Bioinformatics Advance Access published on May 12, 2008.
doi:10.1093/bioinformatics/btn221
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Junil Kim, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, and Kwang-Hyun Cho
Evolutionary design principles of modules that control cellular differentiation: Consequences for hysteresis and multistationarity
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn229
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: M. Zampieri, N. Soranzo, and C. Altafini
Discerning static and causal interactions in genome-wide reverse engineering problems
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn220
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Makio Tamura and Patrik D'haeseleer
Microbial Genotype-Phenotype Mapping by Class Association Rule Mining
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn210
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jiangning Song, Hao Tan, Kazuhiro Takemoto, and Tatsuya Akutsu
HSEpred: predict Half-Sphere Exposure from protein sequences
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn222
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Michael Hackenberg and Rune Matthiesen
Annotation-Modules: A tool for finding significant combinations of multisource annotations for gene lists
Bioinformatics Advance Access published on May 8, 2008.
doi:10.1093/bioinformatics/btn178
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Michael Bada and Lawrence Hunter
Identification of OBO Nonalignments and Its Implications for OBO Enrichment
Bioinformatics Advance Access published on May 7, 2008.
doi:10.1093/bioinformatics/btn194
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Bobbie-Jo M. Webb-Robertson, William R. Cannon, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, and Katrina M. Waters
A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Bioinformatics Advance Access published on May 3, 2008.
doi:10.1093/bioinformatics/btn218
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Istvan Bogdan, Jenny Rivers, Robert J Beynon, and Daniel Coca
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting
Bioinformatics Advance Access published on May 3, 2008.
doi:10.1093/bioinformatics/btn216
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Huaizhen Qin, Tao Feng, Scott A. Harding, Chung-Jui Tsai, and Shuanglin Zhang
An efficient method to identify differentially expressed genes in microarray experiments
Bioinformatics Advance Access published on May 3, 2008.
doi:10.1093/bioinformatics/btn215
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
John A. Capra and Mona Singh
Characterization and Prediction of Residues Determining Protein Functional Specificity
Bioinformatics Advance Access published on May 1, 2008.
doi:10.1093/bioinformatics/btn214
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Yong Li, Pankaj Agarwal, and Dilip Rajagopalan
A Global Pathway Crosstalk Network
Bioinformatics Advance Access published on April 23, 2008.
doi:10.1093/bioinformatics/btn200
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Hakim Tafer and Ivo L. Hofacker
RNAplex: a fast tool for RNA-RNA interaction search
Bioinformatics Advance Access published on April 23, 2008.
doi:10.1093/bioinformatics/btn193
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Rainer Malik, Erich A. Nigg, and Roman Körner
Comparative conservation analysis of the human mitotic phosphoproteome
Bioinformatics Advance Access published on April 20, 2008.
doi:10.1093/bioinformatics/btn197
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Takashi Ishida and Kengo Kinoshita
Prediction of disordered regions in proteins based on the meta approach
Bioinformatics Advance Access published on April 20, 2008.
doi:10.1093/bioinformatics/btn195
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Kaname Kojima, Masao Nagasaki, and Satoru Miyano
Fast grid layout algorithm for biological networks with sweep calculation
Bioinformatics Advance Access published on April 18, 2008.
doi:10.1093/bioinformatics/btn196
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Jonathan D. Wren
URL decay in MEDLINE – a 4-year follow-up study
Bioinformatics Advance Access published on April 15, 2008.
doi:10.1093/bioinformatics/btn127
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: D. Santoni, M. Pedicini, and F. Castiglione
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hyper-sensitivity reactions
Bioinformatics Advance Access published on April 14, 2008.
doi:10.1093/bioinformatics/btn135
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Haiyun Wang, Qi Wang, Xia Li, Bairong Sheng, Min Ding, and Ziyin Shen
Towards patterns tree of gene co-expression in eukaryotic species
Bioinformatics Advance Access published on April 10, 2008.
doi:10.1093/bioinformatics/btn134
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Anindya Bhattacharya and Rajat K. De
Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: Detecting varying patterns in expression profiles
Bioinformatics Advance Access published on April 10, 2008.
doi:10.1093/bioinformatics/btn133
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Marianne M. Lee, Michael K. Chan, and Ralf Bundschuh
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
Bioinformatics Advance Access published on April 10, 2008.
doi:10.1093/bioinformatics/btn130
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Chunqi Chang, Zhi Ding, Yeung Sam Hung, and Peter Chin Wan Fung
Fast Network Component Analysis (FastNCA) for gene regulatory network reconstruction from microarray data
Bioinformatics Advance Access published on April 9, 2008.
doi:10.1093/bioinformatics/btn131
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Daniel Dalevi and Niklas Eriksen
Expected Gene Order Distances and Model Selection in Bacteria
Bioinformatics Advance Access published on April 1, 2008.
doi:10.1093/bioinformatics/btn111
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, and Tim Beissbarth
Estimating Large Scale Signaling Networks through Nested Effect Models with Intervention Effects from Microarray Data
Bioinformatics Advance Access published on January 28, 2008.
doi:10.1093/bioinformatics/btm634
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

DISCOVERY NOTE

Abstract DISCOVERY NOTE: Jacob A. Tennessen
Positive selection drives a correlation between nonsynonymous/ synonymous divergence and functional divergence
Bioinformatics Advance Access published on April 28, 2008.
doi:10.1093/bioinformatics/btn205
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

REVIEW

Abstract REVIEW: Sridhar Hannenhalli
Eukaryotic transcription factor binding sites – modeling and integrative search methods
Bioinformatics Advance Access published on April 21, 2008.
doi:10.1093/bioinformatics/btn198
[Abstract] [Accepted Manuscript] [Request Permissions]