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March 2014 Bioinformatics Papers of Note


Abba MC, Butti MD, et al.
BioPlat: a software for human cancer biomarker discovery.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

Dwibedi CK, Forsman M, et al.
CanSNPer: a hierarchical genotype classifier of clonal pathogens.
Bioinformatics. 2014 Mar 21. [Epub ahead of print]

Biswas A1, Fineran PC, Brown CM
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.
Bioinformatics. 2014 Mar 20. [Epub ahead of print]

Dopazo J, Florido JP, et al.
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing.
Bioinformatics. 2014 Mar 13. [Epub ahead of print]

Luo C1, Rodriguez-R LM, Konstantinidis KT.
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.
Nucleic Acids Res. 2014 Mar 3. [Epub ahead of print]

Hunt M, Newbold C, Berriman M, Otto TD
A comprehensive evaluation of assembly scaffolding tools.
Genome Biol. 2014 Mar 3;15(3):R42. [Epub ahead of print]

Gou J, Chen F, et al.
Stability SCAD: a powerful approach to detect interactions in large-scale genomic study.
BMC Bioinformatics. 2014 Mar 1;15:62. doi: 10.1186/1471-2105-15-62.

Wozniak M, Wong L, Tiuryn J.
eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.
BMC Bioinformatics. 2014 Mar 5;15(1):65. [Epub ahead of print]

Afzal Z, Bui C, et al.
Knowledge-based extraction of adverse drug events from biomedical text.
BMC Bioinformatics. 2014 Mar 4;15:64. doi: 10.1186/1471-2105-15-64.

Deveci M, Catalyürek UV, Toland AE.
mrSNP: software to detect SNP effects on microRNA binding.
BMC Bioinformatics. 2014 Mar 4;15:64. doi: 10.1186/1471-2105-15-64.

Allen AS, Guo H, et al.
An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data.
Hum Mutat. 2014 Mar 5. doi: 10.1002/humu.22537. [Epub ahead of print]

Ayyagari R, Biswas P, et al.
exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels.
Genomics. 2014 Mar 3. [Epub ahead of print]

Garrison EP, Marth GT, et al.
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping.
PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.

Boardman L, Dittmar RL, et al.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNAsequencing.
BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.

Mader M, Simon R, Kurtz S.
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.
J Clin Bioinforma. 2014 Mar 31;4(1):5. doi: 10.1186/2043-9113-4-5.

Porse BT, Sandelin A, et al.
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
BMC Bioinformatics. 2014 Mar 23;15:81. doi: 10.1186/1471-2105-15-81.

Armisén D, Byrne KP, et al.
SearchDOGS Bacteria: Automated identification of potentially missed genes in annotated bacterial genomes.
J Bacteriol. 2014 Mar 21. [Epub ahead of print].

Kermany AR, Oliver TR, et al.
TroX: A new method to learn about the genesis of aneuploidy from trisomic products of conception.
Bioinformatics. 2014 Mar 21. [Epub ahead of print].

Greshake B, Bayer PE, et al.
openSNP-A Crowdsourced Web Resource for Personal Genomics.
PLoS One. 2014 Mar 19;9(3):e89204. doi: 10.1371/journal.pone.0089204. eCollection 2014.

Koslicki D, Foucart S, Rosen G.
WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification.
PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.

Duffy P, Dinu V,et al.
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
Bioinformatics. 2014 Mar 27. [Epub ahead of print]

Chen F, Jeong JC, et al.
ST-analyzer: A web-based user interface for simulation trajectory analysis.
J Comput Chem. 2014 May 5;35(12):957-63. doi: 10.1002/jcc.23584. Epub 2014 Mar 17.

Chen F, Jeong JC, et al.
ST-analyzer: A web-based user interface for simulation trajectory analysis.
J Comput Chem. 2014 May 5;35(12):957-63. doi: 10.1002/jcc.23584. Epub 2014 Mar 17.

Bieri A, Braun T,et al.
openBEB: open biological experiment browser for correlative measurements.
BMC Bioinformatics. 2014 Mar 26;15(1):84. doi: 10.1186/1471-2105-15-84.

Berger E, Berger B,et al.
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.
PLoS Comput Biol. 2014 Mar 27. eCollection 2014..

Carey V, Gogarten S,et al.
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.
Bioinformatics. 2014 Mar 28. [Epub ahead of print]

Dimont E, Hide W,et al.
CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.
Bioinformatics. 2014 Mar 27. [Epub ahead of print]

Reinders MJ, Ridder Dd,et al.
SPiCE: a web-based tool for sequence-based protein classification and exploration.
BMC Bioinformatics. 2014 Mar 31;15(1):93. doi: 10.1186/1471-2105-15-93.

Filed under

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.