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January 2014 Bioinformatics Papers of Note


Kramer M, McCombie WR, et al.
FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
Bioinformatics. 2013 Jan 13. [Epub ahead of print]

Clarke AR, Khurana R, et al.
OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.
BMC Bioinformatics. 2014 Jan 15;15(1):15. [Epub ahead of print]

Choi I, Cho S, et al.
gsGator: an integrated web platform for cross-species gene set analysis.
BMC Bioinformatics. 2014 Jan 14;15(1):13. doi: 10.1186/1471-2105-15-13.

Berlanga-Taylor AJ, Heger A, et al.
CGAT: computational genomics analysis toolkit.
Bioinformatics. 2014 Jan 13. [Epub ahead of print]

Cher Soh K, Hadadi N, et al.
A computational framework for integration of lipidomics data into metabolic pathways.
Metab Eng. 2014 Jan 4. [Epub ahead of print]

Lee WP, Hsiao YT, Hwang WC.
Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.
BMC Syst Biol. 2014 Jan 16;8(1):5. doi: 10.1186/1752-0509-8-5.

Dang HX, Lawrence CB.
Allerdictor: fast allergen prediction using text classification techniques.
Bioinformatics. 2014 Jan 26. [Epub ahead of print]

Bendl J, Brezovsky J, et al.
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.
PLoS Comput Biol. Epub 2014 Jan 16.

Compton PD, Durbin KR, et al.
Autopilot: An Online Data Acquisition Control System for the Enhanced High-Throughput Characterization of Intact Proteins.
Anal Chem. 2014 Jan 23. [Epub ahead of print]

Wang T, Xie Y, Xiao G.
dCLIP: a computational approach for comparative CLIP-seq analyses.
Genome Biol. 2014 Jan 7;15(1):R11. [Epub ahead of print]

Arkin AP, Cambray G, et al.
D-Tailor: automated analysis and design of DNA sequences.
Bioinformatics. 2014 Jan 13. [Epub ahead of print]

Joshi KR, Dhiman H, Scaria V. tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. Database (Oxford). 2014 Jan 9.

Almeida J, Cole C, et al. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics. 2014 Jan 27;15(1):28. [Epub ahead of print]

Jia X, Ling Y, et al.
PanGP: A tool for quickly analyzing bacterial pan-genome profile.
Bioinformatics. 2014 Jan 13. [Epub ahead of print]

Pratas DR, Pinho AJ, Rodrigues JM.
XS: a FASTQ read simulator.
BMC Res Notes. 2014 Jan 16;7(1):40. [Epub ahead of print]

Bohnert R, Drewe P, et al.
Oqtans: The RNA-seq Workbench in the Cloud for Complete and Reproducible Quantitative Transcriptome Analysis.
Bioinformatics. 2014 Jan 11. [Epub ahead of print]

Lu X, Thomas RK, Peifer M.
CGARS: cancer genome analysis by rank sums.
Bioinformatics. 2014 Jan 26. [Epub ahead of print]

Ye C, Hsiao C, Bravo HC.
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.
Bioinformatics. 2014 Jan 9. [Epub ahead of print]

Jensen PA, Papin JA.
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Bioinformatics. 2014 Jan 26. [Epub ahead of print]

Cuesta SM, Furnham N, et al.
EC-BLAST: a tool to automatically search and compare enzyme reactions.
Nat Methods. Epub 2014 Jan 12.

Chen R, Choi B, et al.
A private DNA motif finding algorithm.
J Biomed Inform. 2014 Jan 9. [Epub ahead of print]

Chen X, Chen G, et al.
A Computational Framework to Infer Human Disease-Associated Long Noncoding RNAs.
PLoS One. 2014 Jan 2;9(1):e84408.

Dehm SM, Hwang TH, et al.
SHEAR: sample heterogeneity estimation and assembly by reference.
BMC Genomics. 2014 Jan 29;15(1):84. [Epub ahead of print].

Dutheil JY, Gaillard S, Stukenbrock EH.
SeqBench: Integrated solution for the management and analysis of exome sequencing data.
BMC Res Notes. 2014 Jan 20;7(1):43. doi: 10.1186/1756-0500-7-43.

Dander A, Fischer M, et al.
MafFilter: a highly flexible and extensible multiple genome alignment files processor.
BMC Genomics. 2014 Jan 22;15(1):53. doi: 10.1186/1471-2164-15-53.

Fumagalli M, Nielsen R, et al.
ngsTools: methods for population genetics analyses from Next-Generation Sequencing data.
Bioinformatics. 2014 Jan 23. [Epub ahead of print]

Ballester PJ, Leung KS, et al.
istar: A Web Platform for Large-Scale Protein-Ligand Docking.
PLoS One. 2014 Jan 24;9(1):e85678. doi: 10.1371/journal.pone.0085678. eCollection 2014.

Liu B, Li J, Liu C
Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.
J Biomed Inform. 2014 Jan 22.[Epub ahead of print]

Filed under

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.