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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

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.