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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

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.