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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]


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