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 2008

Abstract ORIGINAL PAPER: Hiromi Arai, Satoru Watanabe, Takanori Kigawa, and Masayuki Yamamura
A new modeling method in feature construction for the HSQC spectra screening problem
Bioinformatics Advance Access published on July 4, 2008.
doi:10.1093/bioinformatics/btn345
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract REVIEW: Hanchuan Peng
Bioimage Informatics: A New Area of Engineering Biology
Bioinformatics Advance Access published on July 4, 2008.
doi:10.1093/bioinformatics/btn346
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová, and Jaroslav Koca
TRITON: a graphical tool for ligand-binding protein engineering
Bioinformatics Advance Access published on July 4, 2008.
doi:10.1093/bioinformatics/btn344
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, and Yidong Chen
A Probe-Density Based Analysis Method for Array CGH data: Simulation, Normalization and Centralization
Bioinformatics Advance Access published on July 4, 2008.
doi:10.1093/bioinformatics/btn321
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

3 July 2008

Abstract APPLICATIONS NOTE: Dominik Heider, Daniel Kessler, and Angelika Barnekow
Watermarking sexually reproducing diploid organisms
Bioinformatics Advance Access published on July 3, 2008.
doi:10.1093/bioinformatics/btn342
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew Bainbridge, and Steven J.M. Jones
FindPeaks 3.1: A Tool for Identifying Areas of Enrichment from Massively Parallel Short-Read Sequencing Technology
Bioinformatics Advance Access published on July 3, 2008.
doi:10.1093/bioinformatics/btn305
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

2 July 2008

Abstract ORIGINAL PAPER: Yung-Keun Kwon and Kwang-Hyun Cho
Coherent Coupling of Feedback Loops: A Design Principle of Cell Signaling Networks
Bioinformatics Advance Access published on July 2, 2008.
doi:10.1093/bioinformatics/btn337
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Yiqun Cao, Anna Charisi, Li-Chang Cheng, Tao Jiang, and Thomas Girke
ChemmineR: A Compound Mining Framework for R
Bioinformatics Advance Access published on July 2, 2008.
doi:10.1093/bioinformatics/btn307
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

1 July 2008

Abstract ORIGINAL PAPER: T. Theodosiou, N. Darzentas, L. Angelis, and C. A. Ouzounis
PuReD-MCL: a graph-based PubMed document clustering methodology
Bioinformatics Advance Access published on July 1, 2008.
doi:10.1093/bioinformatics/btn318
[Abstract] [Accepted Manuscript] [Request Permissions]

30 June 2008

Abstract APPLICATIONS NOTE
Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, and David Allouche
BioMAJ: A flexible framework for databanks synchronization and processing
Bioinformatics Advance Access published on June 30, 2008.
doi:10.1093/bioinformatics/btn325
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Heng Lian, William A. Thompson, Robert Thurman, John A. Stamatoyannopoulos, William Stafford Noble, and Charles E. Lawrence
Automated mapping of large-scale chromatin structure in ENCODE
Bioinformatics Advance Access published on June 30, 2008.
doi:10.1093/bioinformatics/btn335
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
David W. Ritchie, Dima Kozakov, and Sandor Vajda
Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions
Bioinformatics Advance Access published on June 30, 2008.
doi:10.1093/bioinformatics/btn334
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Kristoffer Forslund and Erik L.L. Sonnhammer
Predicting protein function from domain content
Bioinformatics Advance Access published on June 30, 2008.
doi:10.1093/bioinformatics/btn312
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

27 June 2008

Abstract ORIGINAL PAPER
Huai Li and Ming Zhan
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Bioinformatics Advance Access published on June 27, 2008.
doi:10.1093/bioinformatics/btn332
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Jiajian Liu and Gary D. Stormo
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
Bioinformatics Advance Access published on June 27, 2008.
doi:10.1093/bioinformatics/btn331
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, and Wen Gao
FlexStem: Improving Predictions of RNA Secondary Structures With Pseudoknots by Reducing the Search Space
Bioinformatics Advance Access published on June 27, 2008.
doi:10.1093/bioinformatics/btn327
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

25 June 2008

Abstract ORIGINAL PAPER: M.A. Marchisio and J. Stelling
Computational design of synthetic gene circuits with composable parts
Bioinformatics Advance Access published on June 25, 2008.
doi:10.1093/bioinformatics/btn330
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Shantanu Sharma, Feng Ding, and Nikolay V. Dokholyan
iFoldRNA: Three-dimensional RNA Structure Prediction and Folding
Bioinformatics Advance Access published on June 25, 2008.
doi:10.1093/bioinformatics/btn328
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Liam J. McGuffin
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
Bioinformatics Advance Access published on June 25, 2008.
doi:10.1093/bioinformatics/btn326
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Gyan P Srivastava, Juyuan Guo, Huidong Shi, and Dong Xu
PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands
Bioinformatics Advance Access published on June 25, 2008.
doi:10.1093/bioinformatics/btn320
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Frank T. Bergmann and Herbert M. Sauro
Comparing Simulation Results of SBML Capable Simulators
Bioinformatics Advance Access originally published on June 25, 2008. This version published June 30, 2008.
doi:10.1093/bioinformatics/btn319
[Abstract] [Accepted Manuscript] [Request Permissions]

23 June 2008

Abstract ORIGINAL PAPER: Han Zhang, Hsin-Chou Yang, and Yaning Yang
PoooL: An efficient method for estimating haplotype frequencies from large DNA pools
Bioinformatics Advance Access published on June 23, 2008.
doi:10.1093/bioinformatics/btn324
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Shuo Jiao and Shunpu Zhang
On correcting the overestimation of the permutation based false discovery rate estimator
Bioinformatics Advance Access published on June 23, 2008.
doi:10.1093/bioinformatics/btn310
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
E. Purdom, K.M. Simpson, M.D. Robinson, J.G. Conboy, A.V. Lapuk, and T.P Speed
FIRMA: a method for detection of alternative splicing from exon array data
Bioinformatics Advance Access published on June 23, 2008.
doi:10.1093/bioinformatics/btn284
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

21 June 2008

Abstract ORIGINAL PAPER
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, and Alejandro A. Schäffer
Database Indexing for Production MegaBLAST Searches
Bioinformatics Advance Access originally published on June 21, 2008. This version published June 23, 2008.
doi:10.1093/bioinformatics/btn322
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

19 June 2008

Abstract APPLICATIONS NOTE: Brian W Lambert, Joseph D Terwilliger, and Kenneth M Weiss
ForSim: A Tool for Exploring the Genetic Architecture of Complex Traits with Controlled Truth
Bioinformatics Advance Access published on June 19, 2008.
doi:10.1093/bioinformatics/btn317
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Scott F. Saccone, Nancy L. Saccone, Gary E. Swan, Pamela A.F. Madden, Alison M. Goate, John P. Rice, and Laura J. Bierut
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
Bioinformatics Advance Access published on June 19, 2008.
doi:10.1093/bioinformatics/btn315
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

18 June 2008

Abstract ORIGINAL PAPER: Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin Rosenblatt, and Jean X. Gao
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data
Bioinformatics Advance Access published on June 18, 2008.
doi:10.1093/bioinformatics/btn316
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, and Sergei L. Kosakovsky Pond
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
Bioinformatics Advance Access published on June 18, 2008.
doi:10.1093/bioinformatics/btn313
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Ali Torkamani and Nicholas J. Schork
Predicting Functional Regulatory Polymorphisms
Bioinformatics Advance Access published on June 18, 2008.
doi:10.1093/bioinformatics/btn311
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: A.D.J. van Dijk, D. Bosch, C. J. F. ter Braak, A.R. van der Krol, and R. C. H. J. van Ham
Predicting sub-Golgi localization of type II membrane proteins
Bioinformatics Advance Access published on June 18, 2008.
doi:10.1093/bioinformatics/btn309
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

17 June 2008

LETTER TO THE EDITOR: Khatun Jainab and Giddings Morgan
Response to "On E-values for Tandem MS Scoring Schemes"
Bioinformatics Advance Access published on June 17, 2008.
doi:10.1093/bioinformatics/btn252
[Accepted Manuscript] [Request Permissions]

LETTER TO THE EDITOR: Mark R. Segal
On E-values for Tandem MS Scoring Schemes
Bioinformatics Advance Access published on June 17, 2008.
doi:10.1093/bioinformatics/btn232
[Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Daniel J. Rigden and Michael Y. Galperin
Sequence analysis of GerM and SpoVS, uncharacterised bacterial ‘sporulation’ proteins with widespread phylogenetic distribution
Bioinformatics Advance Access published on June 17, 2008.
doi:10.1093/bioinformatics/btn314
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

16 June 2008

Abstract ORIGINAL PAPER
Lee A. Newberg
Memory-efficient dynamic programming backtrace and pairwise local sequence alignment
Bioinformatics Advance Access originally published on June 16, 2008. This version published June 17, 2008.
doi:10.1093/bioinformatics/btn308
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

13 June 2008

Abstract APPLICATIONS NOTE
Johannes Goll, Seesandra V Rajagopala, Shen C. Shiau, Hank Wu, Brian T. Lamb, and Peter Uetz
MPIDB: The microbial protein interaction database
Bioinformatics Advance Access published on June 13, 2008.
doi:10.1093/bioinformatics/btn285
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

12 June 2008

Abstract ORIGINAL PAPER: Francesco Pappalardo, Salvatore Musumeci, and Santo Motta
Modeling immune system control of atherogenesis
Bioinformatics Advance Access published on June 12, 2008.
doi:10.1093/bioinformatics/btn306
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Derek Greene, Gerard Cagney, Nevan Krogan, and Pádraig Cunningham
Ensemble Non-negative Matrix Factorization Methods for Clustering Protein-Protein Interactions
Bioinformatics Advance Access published on June 12, 2008.
doi:10.1093/bioinformatics/btn286
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

10 June 2008

Abstract APPLICATIONS NOTE: Yungki Park and Volkhard Helms
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon
Bioinformatics Advance Access published on June 10, 2008.
doi:10.1093/bioinformatics/btn255
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

9 June 2008

Abstract ORIGINAL PAPER: Tiago J.P. Sobreira and Arthur Gruber
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data
Bioinformatics Advance Access published on June 9, 2008.
doi:10.1093/bioinformatics/btn283
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Anne-Laure Boulesteix, Christine Porzelius, and Martin Daumer
Microarray-based classification and clinical predictors: On combined classifiers and additional predictive value
Bioinformatics Advance Access originally published on June 9, 2008. This version published June 11, 2008.
doi:10.1093/bioinformatics/btn262
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: J.Ramon Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, and Modesto Orozco
DNAlive: A tool for the physical analysis of DNA at the genomic scale
Bioinformatics Advance Access published on June 9, 2008.
doi:10.1093/bioinformatics/btn259
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

6 June 2008

Abstract DISCOVERY NOTE: Meng Li, Hyun-il Henry Paik, Curt Balch, Yoosung Kim, Lang Li, Tim H-M. Huang, Kenneth P. Nephew, and Sun Kim
Enriched Transcription Factor Binding Sites in Hypermethylated Gene Promoters in Drug Resistant Cancer Cells
Bioinformatics Advance Access published on June 6, 2008.
doi:10.1093/bioinformatics/btn256
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

5 June 2008

Abstract APPLICATIONS NOTE: Meizhuo Zhang, Rui Feng, Xiang Chen, Buqu Hu, and Heping Zhang
LOT: a Tool for Linkage Analysis of Ordinal Traits for Pedigree Data
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn258
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Christian Martin, Naryttza N. Diaz, Jörg Ontrup, and Tim W. Nattkemper
Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn257
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Kyoung-Jae Won, Albin Sandelin, Troels Torben Marstrand, and Anders Krogh
Modeling Promoter Grammars with Evolving Hidden Markov Models
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn254
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Marzio Pennisi, Roberto Catanuto, Francesco Pappalardo, and Santo Motta
Optimal vaccination schedules using Simulated Annealing
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn260
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
R. Schachtner, D. Lutter, P. Knollmüller, A. M. Tomé, F. J. Theis, G. Schmitz, M. Stetter, P. Gómez Vilda, and E. W. Lang
Knowledge - based Gene Expression Classification via Matrix Factorization
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn245
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract DISCOVERY NOTE: Andrew B. Conley, Jittima Piriyapongsa, and I. King Jordan
Retroviral promoters in the human genome
Bioinformatics Advance Access published on June 5, 2008.
doi:10.1093/bioinformatics/btn243
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

30 May 2008

Abstract APPLICATIONS NOTE: Carlos Morcillo-Suarez, Josep Alegre, Ricardo Sangros, Elodie Gazave, Rafael de Cid, Roger Milne, Jorge Amigo, Anna Ferrer-Admetlla, Andrés Moreno-Estrada, Michelle Gardner, Ferran Casals, Anna Pérez-Lezaun, David Comas, Elena Bosch, Francesc Calafell, Jaume Bertranpetit, and Arcadi Navarro
SNP Analysis To Results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data.
Bioinformatics Advance Access published on May 30, 2008.
doi:10.1093/bioinformatics/btn241
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Ludger Evers and Claudia-Martina Messow
Sparse kernel methods for high-dimensional survival data
Bioinformatics Advance Access published on May 30, 2008.
doi:10.1093/bioinformatics/btn253
[Abstract] [Accepted Manuscript] [Request Permissions]

29 May 2008

Abstract APPLICATIONS NOTE: James Thurmond, Hyejin Yoon, Carla Kuiken, Karina Yusim, Simon Perkins, James Theiler, Tanmoy Bhattacharya, Bette Korber, and Will Fischer
Web-based design and evaluation of T-cell vaccine candidates
Bioinformatics Advance Access published on May 29, 2008.
doi:10.1093/bioinformatics/btn251
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Christopher S. Miller and David Eisenberg
Using inferred residue contacts to distinguish between correct and incorrect protein models.
Bioinformatics Advance Access published on May 29, 2008.
doi:10.1093/bioinformatics/btn248
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Duncan P Brown
Efficient functional clustering of protein sequences using the Dirichlet process
Bioinformatics Advance Access published on May 29, 2008.
doi:10.1093/bioinformatics/btn244
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: Sebastian Bauer, Steffen Grossmann, Martin Vingron, and Peter N. Robinson
Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration
Bioinformatics Advance Access published on May 29, 2008.
doi:10.1093/bioinformatics/btn250