Volume 31, Issue 7, April 2015

DISCOVERY NOTES

GENOME ANALYSIS

Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens

Takahiro Tsukui and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 981–985, https://doi.org/10.1093/bioinformatics/btu753

• Abstract
• View article
• Supplementary data

GENE EXPRESSION

Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells

Peter Keane and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 986–990, https://doi.org/10.1093/bioinformatics/btu785

• Abstract
• View article
• Supplementary data

ORIGINAL PAPERS

PHYLOGENETICS

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

Graham Jones and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 991–998, https://doi.org/10.1093/bioinformatics/btu770

• Abstract
• View article
• Supplementary data

STRUCTURAL BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

David T. Jones and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 999–1006, https://doi.org/10.1093/bioinformatics/btu791

• Abstract
• View article
• Supplementary data

GENETICS AND POPULATION ANALYSIS

MGAS: a powerful tool for multivariate gene-based genome-wide association analysis

Sophie Van der Sluis and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1007–1015, https://doi.org/10.1093/bioinformatics/btu783

• Abstract
• View article
• Supplementary data

SYSTEMS BIOLOGY

Efficient searching and annotation of metabolic networks using chemical similarity

Dante A. Pertusi and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1016–1024, https://doi.org/10.1093/bioinformatics/btu760

• Abstract
• View article
• Supplementary data

Molecular principles of human virus protein–protein interactions

Rachita Ramachandra Halehalli and Hampapathalu Adimurthy Nagarajaram

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1025–1033, https://doi.org/10.1093/bioinformatics/btu763

• Abstract
• View article
• Supplementary data

HyDRA: gene prioritization via hybrid distance-score rank aggregation

Minji Kim and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1034–1043, https://doi.org/10.1093/bioinformatics/btu766

• Abstract
• View article
• Supplementary data

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

Koji Kyoda and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1044–1052, https://doi.org/10.1093/bioinformatics/btu767

• Abstract
• View article
• Supplementary data

Mechanotransduction map: simulation model, molecular pathway, gene set

Jennifer E. Dent and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1053–1059, https://doi.org/10.1093/bioinformatics/btu776

• Abstract
• View article
• Supplementary data

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

Haifen Chen and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1060–1066, https://doi.org/10.1093/bioinformatics/btu777

• Abstract
• View article
• Supplementary data

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data

Zhenqiu Liu and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1067–1074, https://doi.org/10.1093/bioinformatics/btu778

• Abstract
• View article
• Supplementary data

A logical model of HIV-1 interactions with the T-cell activation signalling pathway

Oyebode J. Oyeyemi and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1075–1083, https://doi.org/10.1093/bioinformatics/btu787

• Abstract
• View article
• Supplementary data

DATA AND TEXT MINING

Unsupervised discovery of information structure in biomedical documents

Douwe Kiela and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1084–1092, https://doi.org/10.1093/bioinformatics/btu758

• Abstract
• View article

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms

Christopher Y. Park and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1093–1101, https://doi.org/10.1093/bioinformatics/btu786

• Abstract
• View article
• Supplementary data

DATABASES AND ONTOLOGIES

A bio-inspired computing model for ovarian carcinoma classification and oncogene detection

Meng-Hsiun Tsai and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1102–1110, https://doi.org/10.1093/bioinformatics/btu782

• Abstract
• View article

BIOIMAGE INFORMATICS

Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning

Ying-Ying Xu and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1111–1119, https://doi.org/10.1093/bioinformatics/btu772

• Abstract
• View article
• Supplementary data

APPLICATIONS NOTES

GENOME ANALYSIS

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

Yuki Naito and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1120–1123, https://doi.org/10.1093/bioinformatics/btu743

• Abstract
• View article
• Supplementary data

SAMNetWeb: identifying condition-specific networks linking signaling and transcription

Sara J. C. Gosline and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1124–1126, https://doi.org/10.1093/bioinformatics/btu748

• Abstract
• View article

genomation: a toolkit to summarize, annotate and visualize genomic intervals

Altuna Akalin and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1127–1129, https://doi.org/10.1093/bioinformatics/btu775

• Abstract
• View article

SEQUENCE ANALYSIS

QuasR: quantification and annotation of short reads in R

Dimos Gaidatzis and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1130–1132, https://doi.org/10.1093/bioinformatics/btu781

• Abstract
• View article
• Supplementary data

PHYLOGENETICS

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP

Karen E. van Rens and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1133–1135, https://doi.org/10.1093/bioinformatics/btu755

• Abstract
• View article
• Supplementary data

STRUCTURAL BIOINFORMATICS

XenoSite server: a web-available site of metabolism prediction tool

Matthew K. Matlock and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1136–1137, https://doi.org/10.1093/bioinformatics/btu761

• Abstract
• View article

The Victor C++ library for protein representation and advanced manipulation

Layla Hirsh and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1138–1140, https://doi.org/10.1093/bioinformatics/btu773

• Abstract
• View article

SYSTEMS BIOLOGY

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data

Damian Fermin and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1141–1143, https://doi.org/10.1093/bioinformatics/btu788

• Abstract
• View article
• Supplementary data

BIOIMAGE INFORMATICS

NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei

Axel Poulet and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1144–1146, https://doi.org/10.1093/bioinformatics/btu774

• Abstract
• View article
• Supplementary data

DATA AND TEXT MINING

LigDig: a web server for querying ligand–protein interactions

Jonathan C. Fuller and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1147–1149, https://doi.org/10.1093/bioinformatics/btu784

• Abstract
• View article
• Supplementary data

Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms

Zeeshan Ahmed and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1150–1153, https://doi.org/10.1093/bioinformatics/btu796

• Abstract
• View article
• Supplementary data

LETTER TO THE EDITOR

SYSTEMS BIOLOGY

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi and others

Bioinformatics, Volume 31, Issue 7, April 2015, Pages 1154–1159, https://doi.org/10.1093/bioinformatics/btv013

• Abstract
• View article

CORRIGENDUM

MIRA: mutual information-based reporter algorithm for metabolic networks

A. Ercument Cicek and others

Bioinformatics, Volume 31, Issue 7, April 2015, Page 1160, https://doi.org/10.1093/bioinformatics/btv081

• Extract
• View article