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In Print: Feb 18, 2011


Bioinformatics Tool-Related Papers of Note, January 2011

Alkan C, Eichler EE, Sajjadian S.
Limitations of next-generation genome sequence assembly.
Nat Methods. 2011 Jan;8(1):61-5. Epub 2010 Nov 21.

Breaker R, Weinberg Z.
R2R — software to speed the depiction of aesthetic consensus RNA secondary structures.
BMC Bioinformatics. 2011 Jan 4;12:3.

Linard B, Thompson J, Lecompte O, Poch O.
OrthoInspector: comprehensive orthology analysis and visual exploration.
BMC Bioinformatics. 2011 Jan 10;12:11.

Garny A, Miller A, Cowan D, Nickerson D, Nunns G, Lawson J, Cooling M, Halstead M, Hunter P, Nielsen P, Britten R, Wimalaratne S, Yu T.
Revision history aware repositories of computational models of biological systems.
BMC Bioinformatics. 2011 Jan 14;12(1):22.

Brazma A, Goncalves A, Tikhonov A, Kapushesky M.
A pipeline for RNA-seq data processing and quality assessment.
Bioinformatics. 2011 Jan 13.

Zhu D, Flemington E, Xu G, Deng N, Judeh T, Zhao Z.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Source Code Biol Med. 2011 Jan 13;6(1):2.

Jenkinson AM, Gel BM, Hermjakob H, Jimenez RC, Messeguer XP.
easyDAS: Automatic creation of DAS servers.
BMC Bioinformatics. 2011 Jan 18;12:23.

Ariyaratne PN, Sung WK.
PE-Assembler: de novo assembler using short paired-end reads.
Bioinformatics. 2011 Jan 15;27(2):167-74.

Yang J, Goddard ME, Visscher PM, Lee SH.
GCTA: A Tool for Genome-wide Complex Trait Analysis.
Am J Hum Genet. 2011 Jan 7;88(1):76-82.

Barton A, Martin P, Eyre S.
ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies.
Bioinformatics. 2011 Jan 1;27(1):144-6.

Futschik A, Kosiol C, Schlötterer C, De Maio N, Orozco-Terwengel P, Kofler R, Pandey RV, Nolte V.
PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals.
PLoS One. 2011 Jan 6;6(1):e15925

Piipari M, Down TA, Hubbard TJ.
Dalliance: interactive genome viewing on the web.
Bioinformatics. 2011 Jan 19. [Epub ahead of print]

Song H, Parkinson J, Lochovsky L, Provart NJ, On T, Xiong X.
Phylopro: A web based tool for the generation and visualization of phylogenetic profiles across Eukarya.
Bioinformatics. 2011 Jan 19. [Epub ahead of print]

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Deorowicz S, Grabowski S.
Compression of genomic sequences in FASTQ format.
Bioinformatics. 2011 Jan 19. [Epub ahead of print]

Eisen JA, Ladau J, Green JL, O'Dwyer JP, Pollard KS, Riesenfeld SJ, Kembel SW, Sharpton TJ.
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data.
PLoS Comput Biol. 2011 Jan 20;7(1):e1001061.

Glez-Peña D, Pisano DG, Fdez-Riverola F, Gómez-López G, Reboiro-Jato M.
PileLine: a toolbox to handle genome position information in next-generation sequencing studies.
BMC Bioinformatics. 2011 Jan 24;12(1):31.

Mathur A, Vidyarthi AS, Shankaracharya.
SWIFT MODELLER: A JAVA based GUI for molecular modeling.
J Mol Model. 2011 Jan 22. [Epub ahead of print]

Barnes C, Stan GB, Macdonald JT, Freemont PS, Kitney RI.
Computational design approaches and tools for synthetic biology.
Integr Biol (Camb). 2011 Feb 8;3(2):97-108.

Terfve C, Markowetz F, Rose JC, Wang X.
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
Bioinformatics. 2011 Jan 22. [Epub ahead of print]

Arkin AP, Chandonia JM, Huang YW.
WIST: Toolkit for rapid, customized LIMS development.
Bioinformatics. 2011 Feb 1;27(3):437-8.

Chen CC, Lan L, Feng S, Wang S.
GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits.
BMC Genet. 2011 Jan 21;12:12

Freudenberg JM, Medvedovic M, Joshi VK, Hu Z.
WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.
Source Code Biol Med. 2011 Jan 17;6:3

Lynch AG, Spyrou C, Cairns J, Smith ML, Stark R, Tavaré S.
BayesPeak - An R package for analysing ChIP-seq data.
Bioinformatics. 2011 Jan 17. [Epub ahead of print]

Wang C, Zhang D.
A novel compression tool for efficient storage of genome resequencing data.
Nucleic Acids Res. 2011 Jan 25. [Epub ahead of print]

Milosavljevic A, Miller CA, Coarfa C, Hampton O.
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS One. 2011 Jan 31;6(1):e16327.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.