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May's Bioinformatics Papers of Note


Fernández JM, Gómez-López G, et al.
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Bioinformatics. 2013 May 24. [Epub ahead of print]

Kuster B, Lemeer S, et al.
MScDB: A Mass Spectrometry-centric Protein Sequence Database for Proteomics.
J Proteome Res. 2013 May 14. [Epub ahead of print]

Guerrero RF, Kirkpatrick M, et al.
A sequential coalescent algorithm for chromosomal inversions.
Heredity (Edinb). 2013 May 1. [Epub ahead of print]

Antonov AV, Barlev NA, et al.
PPISURV: a novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome.
Oncogene 2013 May 20. [Epub ahead of print]

Afrasiabi C, Dineen D, et al.
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.
Nucleic Acids Res. 2013 May 18. [Epub ahead of print]

Deng HW, Duan J, et al.
CNV-TV: A robust method to discover copy number variation from short sequencing reads.
BMC Bioinformatics. 2013 May 2. [Epub ahead of print]

Birol I, Fejes AP, et al.
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.
BMC Bioinformatics. 2013 May 28. [Epub ahead of print]

Alfaro ME, Balhoff JP, et al.
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
BMC Bioinformatics. 2013 May 13. [Epub ahead of print]

Bacall F, Balcazar Vargas MP, et al.
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.
Nucleic Acids Res. 2013 May 2. [Epub ahead of print]

Alteyrac L, Bouchereau B, et al.
A universal open-source Electronic Laboratory Notebook.
Bioinformatics 2013 May 2. [Epub ahead of print]

Alcantara LC, Assel M, et al.
RegaDB: community-driven data management and analysis for infectious diseases.
Bioinformatics 2013 Jun 1;29(11):1477-1480. Epub 2013 May 2.

Cardoso J, Pereira R, et al.
TNA4OptFlux - a software tool for the analysis of strain optimization strategies.
BMC Res Notes. 2013 May 3;6:175. doi: 10.1186/1756-0500-6-175.

Azad MA, Baylay AJ, et al.
The Comprehensive Antibiotic Resistance Database.
Antimicrob Agents Chemother. 2013 May 6. [Epub ahead of print]

Dubé MP, Legault MA, et al.
pyGenClean: Efficient tool for genetic data clean up before association testing.
Bioinformatics. 2013 May 6. [Epub ahead of print]

Gao N, Tang J, Yang N.
Ancestral genome inference using a genetic algorithm approach.
PLoS One. 2013 May 2

Itoh T, Nakato R, Shirahige K.
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Genes Cells 2013 May 15. [Epub ahead of print]

Ballesteros-Villagrana E, Fu C, et al.
DrugMap Central (DMC), an on-line query and visualization tool to facilitate drug repositioning studies.
Bioinformatics. 2013 May 15. [Epub ahead of print]

Chen T, Jiang R, Zeng F.
PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data.
Nucleic Acids Res. 2013 May 21. [Epub ahead of print]

Bear KA, Nguyen AD, et al.
Clinical Genomic Database.
Proc Natl Acad Sci U S A. 2013 May 21. [Epub ahead of print]

Canzar S, Salzberg SL, et al.
GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms.
Bioinformatics 2013 May 10. [Epub ahead of print]

Chang Y, Jiang Y, et al.
HGPGD: The Human Gene Population Genetic Difference Database.
PLoS One. 2013 May 22

Berriman M, Hunt M, et al.
REAPR: a universal tool for genome assembly evaluation.
Genome Biol. 2013 May 27. [Epub ahead of print]

Filed under

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.