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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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