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In Print: September's Bioinformatics Papers of Note


September's Bioinformatics Papers of Note

Bernstein BE, Birney E, et al.
An integrated encyclopedia of DNA elements in the human genome.
Nature. 2012 Sep 6;489(7414):57-74.

Allen AM, Barker GL, et al.
CerealsDB 2.0: an integrated resource for plant breeders and scientists.
BMC Bioinformatics. 2012 Sep 3;13(1):219.

Balasubramanian S, Gerstein MB, et al.
The GENCODE pseudogene resource.
Genome Biol. 2012 Sep 5;13(9):R51.

Campagna A, Delgado J, et al.
SAPIN: Structural Analysis for Protein Interaction Networks.
Bioinformatics. 2012 Sep 6 [Epub ahead of print]

Benz C, Collisson EA, et al.
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.
Bioinformatics. 2012 Sep 15;28(18):i640-i646.

Chan KC, Chiu RW, et al.
FetalQuant: Deducing Fractional Fetal DNA Concentration from Massively Parallel Sequencing of DNA in Maternal Plasma.
Bioinformatics. 2012 Sep 8 [Epub ahead of print]

Barber AE, Babbitt PC.
Pythoscape: A framework for generation of large protein similarity networks.
Bioinformatics. 2012 Sep 8 [Epub ahead of print]

Athanasiadis E, Cournia Z, Spyrou G.
ChemBioServer: A web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery.
Bioinformatics. 2012 Sep 8 [Epub ahead of print]

Broxholme J, Cazier JB, Holmes CC.
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.
Bioinformatics. 2012 Sep 8 [Epub ahead of print]

Bragin E, Chatzimichali EA, et al.
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.
Hum Mol Genet. 2012 Sep 8 [Epub ahead of print]

Eppig JT, Smith CL.
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.
Mamm Genome. 2012 Sep 9 [Epub ahead of print]

Altmann A, Azencott CA, et al.
GLIDE: GPU-Based Linear Regression for Detection of Epistasis.
Hum Hered. 2012 Sep 4;73(4):220-236. [Epub ahead of print]

Chen JY, Hou N, et al.
RhesusBase: a knowledgebase for the monkey research community.
Nucleic Acids Res. 2012 Sep 10 [Epub ahead of print]

Barann M, Ellinghaus D, et al.
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.
Nucleic Acids Res. 2012 Sep 10 [Epub ahead of print]

Chen T, Souaiaia T, Zhang Z.
FadE: whole genome methylation analysis for multiple sequencing platforms.
Nucleic Acids Res. 2012 Sep 10 [Epub ahead of print]

Assefa S, Auburn S, et al.
VarB: A Variation Browsing and analysis tool for variants derived from next-generation sequencing data.
Bioinformatics. 2012 Sep 13 [Epub ahead of print]

Bordenstein SR, Brucker RM, et al.
Insect Innate Immunity Database (IIID): An Annotation Tool for Identifying Immune Genes in Insect Genomes.
PLoS One. 2012;7(9):e45125. Epub 2012 Sep 12.

Huang J, Ma S, et al.
Incorporating group correlations in genome-wide association studies using smoothed group Lasso.
Biostatistics. 2012 Sep 17. [Epub ahead of print].

Ainsworth EA, Thimmapuram J, Yendrek CR.
The bench scientist's guide to statistical analysis of RNA-Seq data.
BMC Res Notes. 2012 Sep 14;5(1):506. [Epub ahead of print]

The Scan

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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.