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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

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.