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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]

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