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In Print: Oct 22, 2010

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Bioinformatics Tool-Related Papers of Note, September 2010

Asbury TM, Mitman M, Tang J, Zheng WJ.
Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
BMC Bioinformatics. 2010 Sep 2;11:444.


Brodsky L, Kogan S, Benjacob E, Nevo E.
A binary search approach to whole-genome data analysis.
Proc Natl Acad Sci U S A. 2010 Sep 10. [Epub ahead of print]


Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ.
Drug off-target effects predicted using structural analysis in the context of a metabolic network model.
PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000938.


Cox MP, Peterson DA, Biggs PJ.
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
BMC Bioinformatics. 2010 Sep 27;11:485.


Demir E, Cary MP, Paley S, et al.
The BioPAX community standard for pathway data sharing.
Nat Biotechnol. 2010 Sep;28(9):935-42.


Edgar RC.
Search and clustering orders of magnitude faster than BLAST.
Bioinformatics. 2010 Oct 1;26(19):2460-1.


Gao M, Skolnick J.
iAlign: a method for the structural comparison of protein-protein interfaces.
Bioinformatics. 2010 Sep 15;26(18):2259-65.


Jia M, Choi SY, Reiners D, Wurtele ES, Dickerson JA.
MetNetGE: interactive views of biological networks and ontologies.
BMC Bioinformatics. 2010 Sep 17;11(1):469.


Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.
BioXSD: the common data-exchange format for everyday bioinformatics web services.
Bioinformatics. 2010 Sep 15;26(18):i540-6.


Kim T, Joo H.
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment.
BMC Bioinformatics. 2010 Sep 17;11(1):467.


Laing CR, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP.
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.
BMC Bioinformatics. 2010 Sep 15;11(1):461.


Martin ER, Kinnamon DD, Schmidt MA, Powell EH, Zuchner S, Morris RW.
SeqEM: An adaptive genotype-calling approach for next-generation sequencing studies.
Bioinformatics. 2010 Sep 21. [Epub ahead of print]


Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ.
Next generation tools for genomic data generation, distribution, and visualization.
BMC Bioinformatics. 2010 Sep 9;11:455.


Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y.
Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes.
PLoS One. 2010 Sep 24;5(9):e12651.


Schmitz-Hübsch DJ, Kurtz S.
MetaGenomeThreader: a software tool for predicting genes in DNA-sequences of metagenome projects.
Methods Mol Biol. 2010;668:325-38.


Shakya K, Ruskin HJ, Kerr G, Crane M, Becker J.
Comparison of microarray preprocessing methods.
Adv Exp Med Biol. 2010;680:139-47.


Soh D, Dong D, Guo Y, Wong L.
Consistency, comprehensiveness, and compatibility of pathway databases.
BMC Bioinformatics. 2010 Sep 7;11:449.


Staab P, Walossek J, Nellessen D, Grünberg R, Arndt KM, Müller KM.
SynBioWave — a real-time communication platform for molecular and synthetic biology.
Bioinformatics. 2010 Sep 13. [Epub ahead of print]


Sun Y, Zhang J, Braga-Neto UM, Dougherty ER.
BPDA — A Bayesian peptide detection algorithm for mass spectrometry.
BMC Bioinformatics. 2010 Sep 29;11(1):490.


Tian Z, Kuang R.
Integrative classification and analysis of multiple arrayCGH datasets with probe alignment.
Bioinformatics. 2010 Sep 15;26(18):2313-20.


Walker T, Grulke CM, Pozefsky D, Tropsha A.
Chembench: A cheminformatics workbench.
Bioinformatics. 2010 Sep 30. [Epub ahead of print]


Wohlgemuth G, Haldiya PK, Willighagen E, Kind T, Fiehn O.
The Chemical Translation Service (CTS) — a web-based tool to improve standardization of metabolomic reports.
Bioinformatics. 2010 Sep 9. [Epub ahead of print]


The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.