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In Print: March's Bioinformatics Papers of Note

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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]


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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.