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December 2014 Bioinformatics Papers of Note


Note: In addition to the below listing, papers for Nucleic Acids Research's annual database issue are available here.

Clarke R, Hou X, et al.
AISAIC: a software suite for accurate identification of significant aberrations in cancers.
Bioinformatics. 2013 Dec 13. [Epub ahead of print]

Brunner HG, Camilli F, et al.
Status quo of annotation of human disease variants.
BMC Bioinformatics. 2013 Dec 4;14:352. doi: 10.1186/1471-2105-14-352.

Hemann MT, Lauffenburger DA, et al.
Addressing genetic tumor heterogeneity through computationally predictive combination therapy.
Cancer Discov. 2013 Dec 6. [Epub ahead of print]

Achawanantakun R, Childs K, et al.
MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations.
Plant Physiol. 2013 Dec 6. [Epub ahead of print]

Berriman M, Estrada K, et al.
GARM: Genome Assembly, Reconciliation and Merging pipeline.
Curr Top Med Chem. 2013 Dec 3. [Epub ahead of print]

Chen Y, Jiang R, Wu X.
Integrating human omics data to prioritize candidate genes.
BMC Med Genomics. 2013 Dec 18;6:57. doi: 10.1186/1755-8794-6-57.

Tervo CJ, Reed JL.
BioMog: A Computational Framework for the De Novo Generation or Modification of Essential Biomass Components.
PLoS One. 2013 Dec 5;8(12):e81322. doi: 10.1371/journal.pone.0081322.

Hu J, Kehr B, Reinert K.
NetCoffee: A Fast and Accurate Global Alignment Approach to Identify Functionally Conserved Proteins in Multiple Networks.
Bioinformatics. 2013 Dec 13. [Epub ahead of print].

Bromley D, Daggett V,et al.
DIVE: A Data Intensive Visualization Engine.
Bioinformatics. 2013 Dec 13. [Epub ahead of print].

Li B, Wang G, Leal SM
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants.
Bioinformatics. 2013 Dec 17. [Epub ahead of print].

Deforce D, Proost S, et al.
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.
Genome Biol. 2013 Dec 13;14(12):R134. [Epub ahead of print]

Qureshi A, Thakur N, Kumar M.
VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.
J Transl Med. 2013 Dec 11;11:305. doi: 10.1186/1479-5876-11-305.

De Filippo MR, Giurato G, et al.
iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.
BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

Flicek P, Zerbino DR, et al..
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Bioinformatics. 2013 Dec 19. [Epub ahead of print]

Cheng J, Jiang X, et al..
A new computational strategy for predicting essential genes.
BMC Genomics. 2013 Dec 21;14(1):910. [Epub ahead of print]

Jorjani H, Zavolan M.
TSSer: An automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.
Bioinformatics. 2013 Dec 25. [Epub ahead of print]

Salzberg SL, Sobreira N, et al..
Diamund: Direct Comparison of Genomes to Detect Mutations.
Hum Mutat. 2013 Dec 25. doi: 10.1002/humu.22503. [Epub ahead of print]

El-Metwally S, Hamza T, et al..
Next-generation sequence assembly: four stages of data processing and computational challenges.
PLoS Comput Biol. Epub 2013 Dec 12.

Baheti S, Bhavsar JD, et al..
SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356.

Beck T, Brookes AJ, et al..
GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies.
Eur J Hum Genet. 2013 Dec 4. [Epub ahead of print]

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The Scan

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Not Always Trusted

In a new poll, slightly more than half of US adults have a great deal or quite a lot of trust in the Centers for Disease Control and Prevention, the Hill reports.

Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.