Skip to main content
Premium Trial:

Request an Annual Quote

In Print: Jul 8, 2011


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

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

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

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.