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In Print: Jul 8, 2011

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Bioinformatics Tool-Related Papers of Note, June 2011

Note: In addition to the below listing, papers for Nucleic Acids Research's annual web server issue are available here.


Paten B, Earl D, Haussler D, Zerbino D, Diekhans M, Nguyen N.
Cactus: Algorithms for genome multiple sequence alignment.
Genome Res. 2011 Jun 10. [Epub ahead of print]


Paulovich AG, Krasnoselsky A, Lin C, et al.
A targeted proteomics-based pipeline for verification of biomarkers in plasma.
Nat Biotechnol. 2011 Jun 19. [Epub ahead of print]


Gottlieb A, Ruppin E, Stein GY, Sharan R.
PREDICT: a method for inferring novel drug indications with application to personalized medicine.
Mol Syst Biol. 2011 Jun 7;7:496.


Papasian CJ, Deng HW, Shen H, Li J, Zhang L, Lin Y.
Comparative studies of de novo assembly tools for next-generation sequencing technologies.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]


Stamatakis A, Berger SA.
Aligning short reads to reference alignments and trees.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]


Ruden D, Nguyen T, Shi W.
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.
BMC Res Notes. 2011 Jun 6;4:171.


Marchini J, Donnelly P, Su Z.
HAPGEN2: simulation of multiple disease SNPs.
Bioinformatics. 2011 Jun 8. [Epub ahead of print]


Nieselt K, Symons S.
MGV: A generic graph viewer for comparative omics data.
Bioinformatics. 2011 Jun 11. [Epub ahead of print]


Schmidt B, Shi H, Liu W, Mueller-Wittig W.
Parallel mutual information estimation for inferring gene regulatory networks on GPUs.
BMC Res Notes. 2011 Jun 15;4(1):189.


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 Jun 16. [Epub ahead of print]


Alawi M, Beckstette M, Kurtz S.
CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.
J Integr Bioinform. 2011 Jun 21;8(2):155.


Van Rossum D, Bhardwaj G, Ko KD, et al.
Predicting protein folds with fold-specific PSSM libraries.
PLoS One. 2011;6(6):e20557.


Paradela A, Jones AR, Salazar E, et al.
The ProteoRed MIAPE web toolkit: A user-friendly framework to connect and share proteomics standards.
Mol Cell Proteomics. 2011 Jun 19. [Epub ahead of print]


Kohlhoff KJ, Sosnick MH, Altman RB, Pande VS, Hsu WT.
CAMPAIGN: An open-source library of GPU-accelerated data clustering algorithms.
Bioinformatics. 2011 Jun 27. [Epub ahead of print]


Bebek G, Koyuturk M, Ewing RM, Erten S.
DADA: degree-aware algorithms for network-based disease gene prioritization.
BioData Min. 2011 Jun 24;4(1):19.


Heider D, Hoffmann D.
Interpol: An R package for preprocessing of protein sequences.
BioData Min. 2011 Jun 17;4(1):16.


The Scan

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Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

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