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In Print: May 6, 2011


Bioinformatics Tool-Related Papers of Note, April 2011

Wang B, Jiang R, Bao S, Kwan W, Ma X, Song YQ.
Evaluation of next-generation sequencing software in mapping and assembly.
J Hum Genet. 2011 Apr 28. [Epub ahead of print]

Millard BL, Muhlich JL, Niepel M, Menden MP, Sorger PK.
Adaptive informatics for multifactorial and high-content biological data.
Nat Methods. 2011 Apr 28. [Epub ahead of print]

Wulf A, Benedicto CB, Dong LM, Clyne M, Khoury MJ, Schully SD, McCallum V, Yu W.
Cancer GAMAdb: database of cancer genetic associations from meta-analyses and genome-wide association studies.
Eur J Hum Genet. 2011 Apr 13. [Epub ahead of print]

Lapuk A, McPherson A, Collins C, Wu C, Hormozdiari F, Hach F, Hajirasouliha I, Shah S, Sahinalp SC, Volik S. Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.
Bioinformatics. 2011 Apr 9. [Epub ahead of print]

Suzek BE, Wu CH, Huang H, Zhang J, McGarvey PB, Mazumder R, Chen Y.
A comprehensive protein-centric ID mapping service for molecular data integration.
Bioinformatics. 2011 Apr 15;27(8):1190-1.

Maroulis D, Mylona E, Savelonas M, Kossida S.
A Computer-Based Technique for Automated Spot Detection in Proteomics Images.
IEEE Trans Inf Technol Biomed. 2011 Apr 7. [Epub ahead of print]

Chan AH, Kao WC, Song YS.
ECHO: A reference-free short-read error correction algorithm.
Genome Res. 2011 Apr 11. [Epub ahead of print]

Bikfalvi A, Stincone A, Falciani F, Antczak P, Bicknell R, Gupta R, Durant S.
A Computational Framework for Gene Regulatory Network Inference that Combines Multiple Methods and Datasets.
BMC Syst Biol. 2011 Apr 13;5(1):52. [Epub ahead of print]

Nesvizhskii AI, Vogel C, Marcotte EM, Choi H, Kwon T.
MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines.
J Proteome Res. 2011 Apr 29. [Epub ahead of print]

Sbano L, Kirkilionis M, Janus U.
Multi-scale genetic dynamic modelling I: an algorithm to compute generators.
Theory Biosci. 2011 Apr 13. [Epub ahead of print]

Machanick P, Bailey TL.
MEME-ChIP: motif analysis of large DNA datasets.
Bioinformatics. 2011 Apr 28. [Epub ahead of print]

Ali HH, Geng H, Iqbal J, Chan WC.
Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma.
BMC Med Genomics. 2011 Apr 12;4(1):32. [Epub ahead of print]

Wunsch Ii DC, Xu R.
BARTMAP: A viable structure for biclustering.
Neural Netw. 2011 Apr 12. [Epub ahead of print]

Tramontano A, Raimondo D, Leoni G, Floris M, Orsini M, Marcatili P.
MAISTAS: a tool for automatic structural evaluation of alternative splicing products.
Bioinformatics. 2011 Apr 15. [Epub ahead of print]

Zhang B, Bova GS, Yu G, Shih IM, Xu J, Wang Y.
BACOM: In Silico Detection of Genomic Deletion Types and Correction of Normal Cell Contamination in Copy Number Data.
Bioinformatics. 2011 Apr 15. [Epub ahead of print]

Niu B, Fu L, Wu S, Li W, Zhu Z.
FR-HIT, a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.
Bioinformatics. 2011 Apr 19. [Epub ahead of print]

Beaumont MA, Antao T.
Mcheza: A workbench to detect selection using dominant markers.
Bioinformatics. 2011 Apr 19. [Epub ahead of print]

Carneiro AR, Silva A, Baumbach J, Schneider MP, Ramos RT, Azevedo V.
Analysis of quality raw data of second generation sequencers with Quality Assessment Software.
BMC Res Notes. 2011 Apr 18;4(1):130. [Epub ahead of print]

Yoon BJ, Sahraeian SM.
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.
Nucleic Acids Res. 2011 Apr 22. [Epub ahead of print]

Laing C, Schlick T.
Computational approaches to RNA structure prediction, analysis, and design.
Curr Opin Struct Biol. 2011 Apr 20. [Epub ahead of print]

Nanduri B, Malone BM, McCarthy FM, Lawrence ML, Wang N, Burgess SC, Bridges SM, Sanders WS, Dandass YS.
The Proteogenomic Mapping Tool.
BMC Bioinformatics. 2011 Apr 22;12(1):115. [Epub ahead of print]

Norris Jr C, Liang H, Tsui KW, Zhang Q, Liang S, Ji Y, Yuan Y, Xu Y.
BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data.
Biometrics. 2011 Apr 22. doi: 10.1111/j.1541-0420.2011.01605.x. [Epub ahead of print]

Bielow C, Reinert K, Aiche S, Andreotti S.
MSSimulator: Simulation of Mass Spectrometry Data.
J Proteome Res. 2011 Apr 28. [Epub ahead of print]

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.