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Items: 25

1.

Software engineering for scientific big data analysis.

Grüning BA, Lampa S, Vaudel M, Blankenberg D.

Gigascience. 2019 May 1;8(5). pii: giz054. doi: 10.1093/gigascience/giz054.

2.

Child Weight Gain Trajectories Linked To Oral Microbiota Composition.

Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD.

Sci Rep. 2018 Sep 19;8(1):14030. doi: 10.1038/s41598-018-31866-9.

3.

Recommendations for the packaging and containerizing of bioinformatics software.

Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC; BioContainers Community, Perez-Riverol Y.

Version 2. F1000Res. 2018 Jun 14 [revised 2019 Jan 1];7. pii: ISCB Comm J-742. doi: 10.12688/f1000research.15140.2. eCollection 2018.

4.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D.

Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544. doi: 10.1093/nar/gky379.

5.

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D.

Mol Biol Evol. 2018 Jun 1;35(6):1372-1375. doi: 10.1093/molbev/msy084.

6.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2.

7.

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP.

Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18.

8.

Online resources for genomic analysis using high-throughput sequencing.

Blankenberg D, Taylor J, Nekrutenko A.

Cold Spring Harb Protoc. 2015 Feb 5;2015(4):324-35. doi: 10.1101/pdb.top083667.

PMID:
25655493
9.

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15474-9. doi: 10.1073/pnas.1409328111. Epub 2014 Oct 13.

10.

Dissemination of scientific software with Galaxy ToolShed.

Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N; Galaxy Team, Taylor J, Nekrutenko A.

Genome Biol. 2014 Feb 20;15(2):403. doi: 10.1186/gb4161.

11.

Analysis of next-generation sequencing data using Galaxy.

Blankenberg D, Hillman-Jackson J.

Methods Mol Biol. 2014;1150:21-43. doi: 10.1007/978-1-4939-0512-6_2.

PMID:
24743989
12.

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach.

Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A.

Biotechniques. 2014 Mar 1;56(3):134-141. doi: 10.2144/000114146. eCollection 2014.

13.

Wrangling Galaxy's reference data.

Blankenberg D, Johnson JE; Galaxy Team, Taylor J, Nekrutenko A.

Bioinformatics. 2014 Jul 1;30(13):1917-9. doi: 10.1093/bioinformatics/btu119. Epub 2014 Feb 28.

14.

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O.

Genetics. 2012 Dec;192(4):1249-69. doi: 10.1534/genetics.112.144204. Epub 2012 Oct 10.

15.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

16.

Using Galaxy to perform large-scale interactive data analyses.

Hillman-Jackson J, Clements D, Blankenberg D, Taylor J, Nekrutenko A; Galaxy Team.

Curr Protoc Bioinformatics. 2012 Jun;Chapter 10:Unit10.5. doi: 10.1002/0471250953.bi1005s38.

17.

Making whole genome multiple alignments usable for biologists.

Blankenberg D, Taylor J, Nekrutenko A; Galaxy Team.

Bioinformatics. 2011 Sep 1;27(17):2426-8. doi: 10.1093/bioinformatics/btr398. Epub 2011 Jul 19.

18.

Integrating diverse databases into an unified analysis framework: a Galaxy approach.

Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A; Galaxy Team.

Database (Oxford). 2011 Apr 29;2011:bar011. doi: 10.1093/database/bar011. Print 2011.

19.

Manipulation of FASTQ data with Galaxy.

Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team.

Bioinformatics. 2010 Jul 15;26(14):1783-5. doi: 10.1093/bioinformatics/btq281. Epub 2010 Jun 18.

20.

Galaxy: a web-based genome analysis tool for experimentalists.

Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J.

Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. doi: 10.1002/0471142727.mb1910s89.

21.

Using galaxy to perform large-scale interactive data analyses.

Taylor J, Schenck I, Blankenberg D, Nekrutenko A.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5. doi: 10.1002/0471250953.bi1005s19.

22.

28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ.

Genome Res. 2007 Dec;17(12):1797-808. Epub 2007 Nov 5.

23.

Quantitative sequence-function relationships in proteins based on gene ontology.

Sangar V, Blankenberg DJ, Altman N, Lesk AM.

BMC Bioinformatics. 2007 Aug 8;8:294.

24.

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A.

Genome Res. 2007 Jun;17(6):960-4.

25.

Galaxy: a platform for interactive large-scale genome analysis.

Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A.

Genome Res. 2005 Oct;15(10):1451-5. Epub 2005 Sep 16.

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