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In Print: March's Bioinformatics Papers of Note


Langmead B, Salzberg SL.
Fast gapped-read alignment with Bowtie 2.

Nat Methods. 2012 Mar 4;9(4):357-9.

Craigen WJ, Graham BH, et al.
An integrated approach for classifying mitochondrial DNA variants: one clinical diagnostic laboratory's experience.

Genet Med. 2012 Mar 8. [Epub ahead of print].

Bicak M, Booth T, et al.
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

BMC Bioinformatics. 2012 Mar 19;13(1):42.

Hamilton CM, Junkins HA, et al.
Using PhenX measures to identify opportunities for cross-study analysis.

Hum Mutat. 2012 Mar 13. [Epub ahead of print].

Burriesci MS, Lehnert EM, Pringle JR.
Fulcrum: condensing redundant reads from high-throughput sequencing studies.

Bioinformatics. 2012 Mar 13. [Epub ahead of print]

Eltonsy N, Gabisi V, et al.
Detection algorithm for the validation of human cell lines.

Int J Cancer. 2012 Mar 15. [Epub ahead of print]

Brandt R, Bläker H, et al.
Optimized algorithm for Sanger sequencing-based EGFR mutation analyses in NSCLC biopsies.

Virchows Arch. 2012 Mar 15. [Epub ahead of print]

Blanchette M, Kam A, et al.
Phylo: a citizen science approach for improving multiple sequence alignment.

PLoS One. 2012;7(3):e31362.

Morgner N, Robinson CV.
Massign: an assignment strategy for maximizing information from the mass spectra of heterogeneous protein assemblies.

Anal Chem. 2012 Mar 20;84(6):2939-48.

Asghar W, Butt AR, et al.
GPU-based real-time detection and analysis of biological targets using solid-state nanopores.

Med Biol Eng Comput. 2012 Mar 25. [Epub ahead of print].

Gilles ED, Huard J, et al.
An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes.

FEBS J. 2012 Mar 24. [Epub ahead of print].

Estrada J, Gnad F, et al.
Proteus: a web-based, context-specific modelling tool for molecular networks.

Bioinformatics. 2012 Mar 15. [Epub ahead of print].

Adryan B, Zabet NR.
GRiP: a computational tool to simulate transcription factor binding in prokaryotes.

Bioinformatics. 2012 Mar 16. [Epub ahead of print].

Peterlongo P, Chikhi R.
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

BMC Bioinformatics. 2012 Mar 23;13(1):48. [Epub ahead of print].

Chanumolu SK, Chauhan RS, Rout C.
UniDrug-Target: a computational tool to identify unique drug targets in pathogenic bacteria.

PLoS One. 2012;7(3):e32833.

Archer J, Baillie G, et al.
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

BMC Bioinformatics. 2012 Mar 23;13(1):47.

Barfield RT, Conneely KN, et al.
MethLAB: A graphical user interface package for the analysis of array-based DNA methylation data.

Epigenetics. 2012 Mar 1;7(3):225-9

Andrio P, Cicin-Sain D, et al.
MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations.

Bioinformatics. 2012 Mar 21. [Epub ahead of print]

Hasty J, Mather WH, Tsimring LS
Fast stochastic algorithm for simulating evolutionary population dynamics.

Bioinformatics. 2012 Mar 21. [Epub ahead of print]

Lai D, Meyer IM, et al.
R-CHIE: a web server and R package for visualizing RNA secondary structures.

Nucleic Acids Res. 2012 Mar 19. [Epub ahead of print]

Davis RW, Gao H, et al.
JETTA: Junction and Exon Toolkits for Transcriptome Analysis.

Bioinformatics. 2012 Mar 19. [Epub ahead of print]

Herman L, Perola E, Weiss J.
Development of a rule-based method for the assessment of protein druggability.

J Chem Inf Model. 2012 Mar 26. [Epub ahead of print]

Cordeiro MN, Kleandrova VV, et al.
In silico discovery and virtual screening of multi-target inhibitors for proteins in Mycobacterium tuberculosis.

Comb Chem High Throughput Screen. 2012 Mar 28. [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.