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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

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.