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.

17 March 2010

Abstract APPLICATIONS NOTE: Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, and Ralf Zimmer
HALO - A Java framework for precise transcript half-life determination
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq117
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE
Daron M. Standley, Reiko Yamashita, Akira R. Kinjo, Hiroyuki Toh, and Haruki Nakamura
SeSAW: balancing sequence and structural information in protein functional mapping
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq116
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER
Sebastian Briesemeister, Jörg Rahnenführer, and Oliver Kohlbacher
Going from where to why – interpretable prediction of protein subcellular localization
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq115
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Asif U Tamuri and Roman A Laskowski
ArchSchema: a tool for interactive graphing of related Pfam do-main architectures
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq119
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Pedro J. Ballester and John B.O. Mitchell
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq112
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract DISCOVERY NOTE: Andrew D. Fernandes and Gregory B. Gloor
Mutual Information is Critically Dependent on Prior Assumptions: Would the Correct Estimate of Mutual Information Please Identify Itself?
Bioinformatics Advance Access published on March 17, 2010.
doi:10.1093/bioinformatics/btq111
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

15 March 2010

Abstract DISCOVERY NOTE
Inbal Yomtovian, Nuttinee Teerakulkittipong, Byungkook Lee, John Moult, and Ron Unger
Composition Bias and the Origin of ORFan Genes
Bioinformatics Advance Access published on March 15, 2010.
doi:10.1093/bioinformatics/btq093
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

12 March 2010

Abstract ORIGINAL PAPER
Karoline Faust, Pierre Dupont, Jérôme Callut, and Jacques van Helden
Pathway discovery in metabolic networks by subgraph extraction
Bioinformatics Advance Access published on March 12, 2010.
doi:10.1093/bioinformatics/btq105
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Remco R. Bouckaert
DensiTree: Making Sense of Sets of Phylogenetic Trees
Bioinformatics Advance Access published on March 12, 2010.
doi:10.1093/bioinformatics/btq110
[Abstract] [Accepted Manuscript] [Request Permissions]

11 March 2010

Abstract APPLICATIONS NOTE
Sheng-Jian Xiao, Chi Zhang, and Zhi-Liang Ji
TiSGeD: a Database for Tissue-Specific Genes
Bioinformatics Advance Access published on March 11, 2010.
doi:10.1093/bioinformatics/btq109
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract ORIGINAL PAPER: Kim-Anh Lê Cao, Emmanuelle Meugnier, and Geoffrey J. McLachlan
Integrative mixture of experts to combine clinical factors and gene markers
Bioinformatics Advance Access published on March 11, 2010.
doi:10.1093/bioinformatics/btq107
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Vipin Narang, Ankush Mittal, and Wing-Kin Sung
Localized Motif Discovery in Gene Regulatory Sequences
Bioinformatics Advance Access published on March 11, 2010.
doi:10.1093/bioinformatics/btq106
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Yuichi Shiraishi, Shuhei Kimura, and Mariko Okada
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data
Bioinformatics Advance Access published on March 11, 2010.
doi:10.1093/bioinformatics/btq094
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

10 March 2010

Abstract APPLICATIONS NOTE
Jumamurat R Bayjanov, Roland J Siezen, and Sacha A.F.T van Hijum
PanCGHweb: a web-tool for genotype-calling in pangenome CGH data
Bioinformatics Advance Access published on March 10, 2010.
doi:10.1093/bioinformatics/btq103
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

9 March 2010

Abstract ORIGINAL PAPER: Yongjin Li and Jagdish C Patra
Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network
Bioinformatics Advance Access published on March 9, 2010.
doi:10.1093/bioinformatics/btq108
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

8 March 2010

Abstract ORIGINAL PAPER: Salih Tuna and Mahesan Niranjan
Reducing the algorithmic variability in transcriptome-based inference
Bioinformatics Advance Access published on March 8, 2010.
doi:10.1093/bioinformatics/btq104
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

5 March 2010

Abstract ORIGINAL PAPER: Manfred G Grabherr, Pamela Russell, Miriah Meyer, Evan Mauceli, Jessica Alföldi, Federica DiPalma, and Kerstin Lindblad-Toh
Genome-wide synteny through highly sensitive sequence alignment: Satsuma
Bioinformatics Advance Access published on March 5, 2010.
doi:10.1093/bioinformatics/btq102
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Frank Johannes, René Wardenaar, Maria Colomé-Tatché, Florence Mousson, Petra de Graaf, Michal Mokry, Victor Guryev, H.Th. Marc Timmers, Edwin Cuppen, and Ritsert C Jansen
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
Bioinformatics Advance Access published on March 5, 2010.
doi:10.1093/bioinformatics/btq087
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

4 March 2010

Abstract ORIGINAL PAPER
Jennifer Clarke, Pearl Seo, and Bertrand Clarke
Statistical expression deconvolution from mixed tissue samples
Bioinformatics Advance Access published on March 4, 2010.
doi:10.1093/bioinformatics/btq097
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

3 March 2010

Abstract LETTER TO THE EDITOR: Andrew D Johnson
An extended IUPAC nomenclature code for polymorphic nucleic acids
Bioinformatics Advance Access published on March 3, 2010.
doi:10.1093/bioinformatics/btq098
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, and Helen Parkinson
Modeling Sample Variables with an Experimental Factor Ontology
Bioinformatics Advance Access published on March 3, 2010.
doi:10.1093/bioinformatics/btq099
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
D Rebholz-Schuhmann, S Kavaliauskas, and P Pezik
PaperMaker: Validation of biomedical scientific publications
Bioinformatics Advance Access published on March 3, 2010.
doi:10.1093/bioinformatics/btq060
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

2 March 2010

Abstract ORIGINAL PAPER: Amin Moghaddas Gholami and Kurt Fellenberg
Cross-species common regulatory network inference without requirement for prior gene affiliation
Bioinformatics Advance Access published on March 2, 2010.
doi:10.1093/bioinformatics/btq096
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

1 March 2010

Abstract ORIGINAL PAPER: Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, and Satoru Miyano
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison
Bioinformatics Advance Access published on March 1, 2010.
doi:10.1093/bioinformatics/btq080
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE
Nobuhiko Tanaka, Kazunori Waki, Hideki Kaneda, Tomohiro Suzuki, Ikuko Yamada, Tamio Furuse, Kimio Kobayashi, Hiromi Motegi, Hideaki Toki, Maki Inoue, Osamu Minowa, Tetsuo Noda, Keizo Takao, Tsuyoshi Miyakawa, Aki Takahashi, Tsuyoshi Koide, Shigeharu Wakana, and Hiroshi Masuya
SDOP-DB: A comparative standardised-protocol database for mouse phenotypic analyses
Bioinformatics Advance Access published on March 1, 2010.
doi:10.1093/bioinformatics/btq095
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Chris Hemmerich, Aaron Buechlein, Ram Podicheti, Kashi V Revanna, and Qunfeng Dong
An Ergatis-based Prokaryotic Genome Annotation Web Server
Bioinformatics Advance Access published on March 1, 2010.
doi:10.1093/bioinformatics/btq090
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract APPLICATIONS NOTE: François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen, and Vincent Berry
ScripTree: scripting phylogenetic graphics
Bioinformatics Advance Access published on March 1, 2010.
doi:10.1093/bioinformatics/btq086
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

26 February 2010

Abstract ORIGINAL PAPER: Nawar Malhis and Steven JM Jones
High Quality SNP Calling Using Illumina Data at Shallow Coverage
Bioinformatics Advance Access published on February 26, 2010.
doi:10.1093/bioinformatics/btq092
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Wei-Yao Chou, Wei-I Chou, Tun-Wen Pai, Shu-Chuan Lin, Ting-Ying Jiang, Chuan-Yi Tang, and Margaret Dah-Tsyr Chang
Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate binding modules
Bioinformatics Advance Access published on February 26, 2010.
doi:10.1093/bioinformatics/btq084
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

25 February 2010

Abstract APPLICATIONS NOTE: Daniela Beisser, Gunnar W. Klau, Thomas Dandekar, Tobias Mueller, and Marcus Dittrich
BioNet: an R-Package for the Functional Analysis of Biological Networks
Bioinformatics Advance Access published on February 25, 2010.
doi:10.1093/bioinformatics/btq089
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Gerard Wong, Christopher Leckie, Kylie L. Gorringe, Izhak Haviv, Ian G. Campbell, and Adam Kowalczyk
Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations
Bioinformatics Advance Access published on February 25, 2010.
doi:10.1093/bioinformatics/btq088
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Sonja Zehetmayer and Martin Posch
Post-hoc power estimation in large-scale multiple testing problems
Bioinformatics Advance Access published on February 25, 2010.
doi:10.1093/bioinformatics/btq085
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Eduardo Corel, Florian Pitschi, and Burkhard Morgenstern
A min-cut Algorithm for the Consistency Problem in Multiple Sequence Alignment
Bioinformatics Advance Access published on February 25, 2010.
doi:10.1093/bioinformatics/btq082
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: David C Trudgian, Benjamin Thomas, Simon J McGowan, Benedikt M Kessler, Mogjiborahman Salek, and Oreste Acuto
CPFP: A central proteomics facilities pipeline
Bioinformatics Advance Access published on February 25, 2010.
doi:10.1093/bioinformatics/btq081
[Abstract] [Accepted Manuscript] [Request Permissions]

24 February 2010

Abstract APPLICATIONS NOTE: Sébastien Loriot, Frédéric Cazals, and Julie Bernauer
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
Bioinformatics Advance Access published on February 24, 2010.
doi:10.1093/bioinformatics/btq083
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Matthieu Muffato, Alexandra Louis, Charles-Edouard Poisnel, and Hugues Roest Crollius
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
Bioinformatics Advance Access published on February 24, 2010.
doi:10.1093/bioinformatics/btq079
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER: Peng Jiang and Mona Singh
SPICi: a fast clustering algorithm for large biological networks
Bioinformatics Advance Access published on February 24, 2010.
doi:10.1093/bioinformatics/btq078
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract DISCOVERY NOTE: David Golan, Carmit Levy, Brad Friedman, and Noam Shomron
Biased hosting of intronic microRNA genes
Bioinformatics Advance Access published on February 24, 2010.
doi:10.1093/bioinformatics/btq077
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Saket Navlakha and Carl Kingsford
The Power of Protein Interaction Networks for Associating Genes with Diseases
Bioinformatics Advance Access published on February 24, 2010.
doi:10.1093/bioinformatics/btq076
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

23 February 2010

Abstract ORIGINAL PAPER: Daniel Dahlmeier and Hwee Tou Ng
Domain Adaptation for Semantic Role Labeling in the Biomedical Domain
Bioinformatics Advance Access published on February 23, 2010.
doi:10.1093/bioinformatics/btq075
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract ORIGINAL PAPER
Yiqun Cao, Tao Jiang, and Thomas Girke
Accelerated Similarity Searching and Clustering of Large Compound Sets by Geometric Embedding and Locality Sensitive Hashing
Bioinformatics Advance Access published on February 23, 2010.
doi:10.1093/bioinformatics/btq067
[Abstract] [Accepted Manuscript] [Supplementary Data] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, and Shengqi Wang
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
Bioinformatics Advance Access published on February 23, 2010.
doi:10.1093/bioinformatics/btq064
[Abstract] [Accepted Manuscript] [Request Permissions]

21 February 2010

Abstract ORIGINAL PAPER: Dominik Skanda and Dirk Lebiedz
An optimal experimental design approach to model discrimination in dynamic biochemical systems
Bioinformatics Advance Access originally published on February 21, 2010. This version published March 1, 2010.
doi:10.1093/bioinformatics/btq074
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Joseph O. Dada, Irena Spasic, Norman W. Paton, and Pedro Mendes
SBRML: a markup language for associating systems biology data with models
Bioinformatics Advance Access published on February 21, 2010.
doi:10.1093/bioinformatics/btq069
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Song Zhang, Jing Cao, Y. Megan Kong, and Richard H Scheuermann
GO-Bayes: Gene Ontology-based over-representation analysis using a Bayesian approach
Bioinformatics Advance Access published on February 21, 2010.
doi:10.1093/bioinformatics/btq059
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER: Jing Zhu, Hui Xiao, Xiaopei Shen, Jing Wang, Jinfeng Zou, Lin Zhang, Da Yang, Wencai Ma, Chen Yao, Xue Gong, Min Zhang, Yang Zhang, and Zheng Guo
Viewing cancer genes from co-evolving gene modules
Bioinformatics Advance Access published on February 21, 2010.
doi:10.1093/bioinformatics/btq055
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

19 February 2010

Abstract ORIGINAL PAPER: Massimo Natale, Dario Bonino, Paolo Consoli, Tiziana Alberio, Rivka G Ravid, Mauro Fasano, and Enrico M Bucci
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease related protein DJ-1.
Bioinformatics Advance Access published on February 19, 2010.
doi:10.1093/bioinformatics/btq073
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

Abstract ORIGINAL PAPER
Lei Qu and Hanchuan Peng
A Principal Skeleton Algorithm for Standardizing Confocal Images of Fruit Fly Nervous Systems
Bioinformatics Advance Access published on February 19, 2010.
doi:10.1093/bioinformatics/btq072
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE
Jens Hollunder, Maik Friedel, Martin Kuiper, and Thomas Wilhelm
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.
Bioinformatics Advance Access published on February 19, 2010.
doi:10.1093/bioinformatics/btq071
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

Abstract APPLICATIONS NOTE: Fabian Schreiber, Peter Gumrich, Rolf Daniel, and Peter Meinicke
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics Advance Access published on February 19, 2010.
doi:10.1093/bioinformatics/btq070
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Armin O Schmitt, Jens Aßmus, Ralf H Bortfeldt, and Gudrun A Brockmann
CandiSNPer: a web-tool for the identification of candidate SNPs for causal variants
Bioinformatics Advance Access published on February 19, 2010.
doi:10.1093/bioinformatics/btq068
[Abstract] [Accepted Manuscript] [Request Permissions]

18 February 2010

Abstract ORIGINAL PAPER: Hugo Willy, Fushan Song, Zeyar Aung, See-Kiong Ng, and Wing-Kin Sung
SLiM on DIet: Finding Short Linear Motifs on Domain Interaction Interfaces in PDB
Bioinformatics Advance Access published on February 18, 2010.
doi:10.1093/bioinformatics/btq065
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

17 February 2010

Abstract ORIGINAL PAPER: Jin-Rui Xu and Yang Zhang
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics Advance Access published on February 17, 2010.
doi:10.1093/bioinformatics/btq066
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

16 February 2010

Abstract ORIGINAL PAPER: M. T. Cooling, V Rouilly, G Misirli, J Lawson, T Yu, J Hallinan, and A Wipat
Standard Virtual Biological Parts: A Repository of Modular Modeling Components for Synthetic Biology
Bioinformatics Advance Access published on February 16, 2010.
doi:10.1093/bioinformatics/btq063
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

15 February 2010

Abstract APPLICATIONS NOTE: Liang Liu and Lili Yu
Phybase: an R package for species tree analysis
Bioinformatics Advance Access published on February 15, 2010.
doi:10.1093/bioinformatics/btq062
[Abstract] [Accepted Manuscript] [Request Permissions]

Abstract APPLICATIONS NOTE: Ricard Garcia-Serna, Oleg Ursu, Tudor I. Oprea, and Jordi Mestres
iPHACE: integrative navigation in pharmacological space
Bioinformatics Advance Access published on February 15, 2010.
doi:10.1093/bioinformatics/btq061
[Abstract] [Accepted Manuscript] [Request Permissions]

12 February 2010

Abstract ORIGINAL PAPER: Christoph Lippert, Zoubin Ghahramani, and Karsten M. Borgwardt
Gene function prediction from synthetic lethality networks via ranking on demand
Bioinformatics Advance Access published on February 12, 2010.
doi:10.1093/bioinformatics/btq053
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]

11 February 2010

Abstract ORIGINAL PAPER
Zheng Wang, Jesse Eickholt, and Jianlin Cheng
MULTICOM: A Multi-Level Combination Approach to Protein Structure Prediction and its Assessments in CASP8
Bioinformatics Advance Access published on February 11, 2010.
doi:10.1093/bioinformatics/btq058
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

10 February 2010

Abstract ORIGINAL PAPER
Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics Advance Access published on February 10, 2010.
doi:10.1093/bioinformatics/btq057
[Abstract] [Accepted Manuscript] OPEN ACCESS ARTICLE

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

9 February 2010

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

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

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

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

7 February 2010

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

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

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

22 January 2010

Abstract APPLICATIONS NOTE: Frédéric Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard, Corinne Pinel, Delphine Ropers, Johannes Geiselmann, and Hidde de Jong
WellReader: A MATLAB Program for the Analysis of Fluorescence and Luminescence Reporter Gene Data
Bioinformatics Advance Access originally published on January 22, 2010. This version published March 5, 2010.
doi:10.1093/bioinformatics/btq016
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]