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In Print: December's Bioinformatics Papers of Note


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

Liu J, Manduchi E, et al.
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.

Database (Oxford). 2011 Dec 21;2011:bar045.Print 2011.

Holt C, Yandell M.
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

BMC Bioinformatics. 2011 Dec 22;12(1):491. [Epub ahead of print]

Biggin PC, Münz M.
JGromacs: a Java package for analyzing protein simulations

J Chem Inf Model. 2011 Dec 22. [Epub ahead of print]

Huang W, Li L, et al.
ART: a next-generation sequencing read simulator.

Bioinformatics 2011 Dec 23. [Epub ahead of print]

Berriman M, Carver T, et al.
Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

Bioinformatics 2011 Dec 22. [Epub ahead of print]

Biegert A, Hauser A, et al.
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Nat. Methods 2011 Dec 25. [Epub ahead of print]

Lloyd S, Snell QO.
Accelerated Large-Scale Multiple Sequence Alignment.

BMC Bioinformatics. 2011 Dec 7;12(1):466.

Peng B, San Lucas FA, et al.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

Bioinformatics. 2011 Dec 2. [Epub ahead of print]

San Lucas FA, Scheet P, et al.
Haploscope: a tool for the graphical display of haplotype structure in populations.

Genet Epidemiol. 2011 Dec 6. [Epub ahead of print]

Salzberg SL, Schatz MC, et al.
GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Genome Res. 2011 Dec 6. [Epub ahead of print]

Barthelson R, McFarlin AJ, et al.
Plantagora: modeling whole genome sequencing and assembly of plant genomes.

PLoS One. 2011;6(12):e28436. Epub 2011 Dec 12.

Durbin R, Simpson JT.
Efficient de novo assembly of large genomes using compressed data structures.

Genome Res. 2011 Dec 7. [Epub ahead of print]

Alkan C, Eichler EE, et al.
Detection of structural variants and indels within exome data.

Nat Methods. 2011 Dec 18. [Epub ahead of print]

Bardet AF, He Q, et al.
A computational pipeline for comparative ChIP-seq analyses.

Nat Protoc. 2011 Dec 15;7(1):45-61.

Ding L, Dooling DJ, et al..
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data.

Bioinformatics. 2011 Dec 6. [Epub ahead of print]

Chen Y, Gan J, et al.
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-Bruijn-graph.

Brief Funct Genomics. 2011 Dec 19. [Epub ahead of print]

Chen W, Lajoie GA, et al.
PEAKS DB: De novo sequencing assisted database search for sensitive and accurate peptide identification.

Mol Cell Proteomics. 2011 Dec 20. [Epub ahead of print]

Filed under

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.