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Items: 18

1.

Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads.

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X, Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang da W.

BioData Min. 2016 Apr 5;9:13. doi: 10.1186/s13040-016-0090-8. eCollection 2016.

2.

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA.

Nat Commun. 2016 Feb 22;7:10740. doi: 10.1038/ncomms10740.

3.

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

Migliano AB, Romero IG, Metspalu M, Leavesley M, Pagani L, Antao T, Huang DW, Sherman BT, Siddle K, Scholes C, Hudjashov G, Kaitokai E, Babalu A, Belatti M, Cagan A, Hopkinshaw B, Shaw C, Nelis M, Metspalu E, Mägi R, Lempicki RA, Villems R, Lahr MM, Kivisild T.

Hum Biol. 2013 Feb-Jun;85(1-3):251-84.

PMID:
24297229
4.

A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q, Sherman BT, Hu X, Jones K, Raley C, Tran B, Munroe DJ, Stephens R, Liang D, Imamichi T, Kovacs JA, Lempicki RA, Huang DW.

J Data Mining Genomics Proteomics. 2013 Jul 31;4(3). pii: 16008.

5.

Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis.

Ma L, Huang DW, Cuomo CA, Sykes S, Fantoni G, Das B, Sherman BT, Yang J, Huber C, Xia Y, Davey E, Kutty G, Bishop L, Sassi M, Lempicki RA, Kovacs JA.

FASEB J. 2013 May;27(5):1962-72. doi: 10.1096/fj.12-224444. Epub 2013 Feb 7.

6.

DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

Jiao X, Sherman BT, Huang da W, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Bioinformatics. 2012 Jul 1;28(13):1805-6. doi: 10.1093/bioinformatics/bts251. Epub 2012 Apr 27.

7.

Gene duplications in prokaryotes can be associated with environmental adaptation.

Bratlie MS, Johansen J, Sherman BT, Huang da W, Lempicki RA, Drabløs F.

BMC Genomics. 2010 Oct 20;11:588. doi: 10.1186/1471-2164-11-588.

8.

Pre-gastrula expression of zebrafish extraembryonic genes.

Hong SK, Levin CS, Brown JL, Wan H, Sherman BT, Huang da W, Lempicki RA, Feldman B.

BMC Dev Biol. 2010 Apr 27;10:42. doi: 10.1186/1471-213X-10-42.

9.

Extracting biological meaning from large gene lists with DAVID.

Huang da W, Sherman BT, Zheng X, Yang J, Imamichi T, Stephens R, Lempicki RA.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 13:Unit 13.11. doi: 10.1002/0471250953.bi1311s27.

PMID:
19728287
10.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

11.

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Huang da W, Sherman BT, Lempicki RA.

Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.

12.

EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.

Barton G, Abbott J, Chiba N, Huang DW, Huang Y, Krznaric M, Mack-Smith J, Saleem A, Sherman BT, Tiwari B, Tomlinson C, Aitman T, Darlington J, Game L, Sternberg MJ, Butcher SA.

BMC Bioinformatics. 2008 Nov 25;9:493. doi: 10.1186/1471-2105-9-493.

13.

DAVID gene ID conversion tool.

Huang da W, Sherman BT, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Bioinformation. 2008 Jul 30;2(10):428-30.

14.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA.

BMC Bioinformatics. 2007 Nov 2;8:426.

15.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Genome Biol. 2007;8(9):R183.

16.

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W169-75. Epub 2007 Jun 18.

17.

Identifying biological themes within lists of genes with EASE.

Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA.

Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11.

18.

DAVID: Database for Annotation, Visualization, and Integrated Discovery.

Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA.

Genome Biol. 2003;4(5):P3. Epub 2003 Apr 3.

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