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In Print: July’s Bioinformatics Papers of Note


Clark NR, Dannenfelser R, Ma'ayan A
Genes2FANs: connecting genes through functional association networks.
BMC Bioinformatics. 2012 Jul 2;13(1):156.

Hennessey J, Lai L, et al.
AraPath: a knowledgebase for pathway analysis in Arabidopsis.
Bioinformatics. 2012 Jul 3 [Epub ahead of print]

Chang D, Keinan A.
Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation.
PLoS Comput Biol. 2012 Jul;8(7):e1002600.

Abel O, Andersen PM, et al.
ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics.
Hum Mutat. 2012 Jul 2. [Epub ahead of print]

Bertram L, Lill CM
Developing the "next generation" of genetic association databases for complex diseases.
Hum Mutat. 2012 Jul 2. [Epub ahead of print]

Hall A, Hamer KM, et al.
Gemma: A resource for the re-use, sharing and meta-analysis of expression profiling data.
Bioinformatics. 2012 Jul 10. [Epub ahead of print]

Machado M, Magalhaes WC, et al.
A graph-based approach for designing extensible pipelines.
BMC Bioinformatics. 2012 Jul 12;13(1):163.

Huala E, Nepusz T, et al.
GFam: a platform for automatic annotation of gene families.
Nucleic Acids Res. 2012 Jul 11. [Epub ahead of print]

Ertl P, Rohde B.
The Molecule Cloud — compact visualization of large collections of molecules.
J Cheminform. 2012 Jul 6;4(1):12. [Epub ahead of print]

Buckler ES, Gore MA, et al.
GAPIT: Genome Association and Prediction Integrated Tool.
Bioinformatics. 2012 Jul 13 [Epub ahead of print]

Antipov D, Alekseyev MA, et al.
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly.
J Comput Biol. 2012 Jul 17 [Epub ahead of print]

Bhattacharya D, Dill DL, et al.
Gene expression commons: an open platform for absolute gene expression profiling.
PLoS One. 2012;7(7):e40321.

Asadi NB, Jiang H, et al.
Fast and Accurate Read Alignment for Resequencing.
Bioinformatics. 2012 Jul 18. [Epub ahead of print]

Schmitt-Kopplin P, Suhre K, et al.
MassTRIX Reloaded: Combined Analysis and Visualization of Transcriptome and Metabolome Data.
PLoS One. 2012;7(7):e39860.

Anderson GA, Brown JN, et al.
DanteR: an extensible R-based tool for quantitative analysis of-omics data.
Bioinformatics. 2012 Jul 19. [Epub ahead of print].

Marbach D, Stolovitzky G, et al.
Wisdom of crowds for robust gene network inference.
Nat Methods. 2012 Jul 15. [Epub ahead of print]

Cleland J, Kim R, et al.
SpliceSeq: A Resource for Analysis and Visualization of RNA-Seq Data on Alternative Splicing and Its Functional Impacts.
Bioinformatics. 2012 Jul 20. [Epub ahead of print]

Chen M, Ding D, et al.
atBioNet — an integrated network analysis tool for genomics and biomarker discovery.
BMC Genomics. 2012 Jul 20;13(1):325.

Kamphans T, Krawitz PM.
GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes.
Bioinformatics. 2012 Jul 23. [Epub ahead of print]

Jiang Q, Wang S, et al.
A novel hierarchical clustering algorithm for gene sequences.
BMC Bioinformatics. 2012 Jul 23;13(1):174. [Epub ahead of print]

Emmert-Streib F, Dehmer M, et al.
A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data.
Sci Rep. 2012;2:513. Epub 2012 Jul 20

Gottlieb A, Oron Y, et al.
INDI: a computational framework for inferring drug interactions and their associated recommendations.
Mol Syst Biol. 2012 Jul 17;8:592.

Filed under

The Scan

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The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.