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Items: 1 to 20 of 69

1.

Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage.

Tyryshkina A, Coraor N, Nekrutenko A.

Bioinformatics. 2019 Jan 30. doi: 10.1093/bioinformatics/btz054. [Epub ahead of print]

PMID:
30698642
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.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

4.

Practical Computational Reproducibility in the Life Sciences.

Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J.

Cell Syst. 2018 Jun 27;6(6):631-635. doi: 10.1016/j.cels.2018.03.014.

5.

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.

6.

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.

7.

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Grüning BA, Rasche E, Rebolledo-Jaramillo B, Eberhard C, Houwaart T, Chilton J, Coraor N, Backofen R, Taylor J, Nekrutenko A.

PLoS Comput Biol. 2017 May 25;13(5):e1005425. doi: 10.1371/journal.pcbi.1005425. eCollection 2017 May.

8.

Streamlined analysis of duplex sequencing data with Du Novo.

Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A.

Genome Biol. 2016 Aug 26;17(1):180. doi: 10.1186/s13059-016-1039-4.

9.

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.

10.

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.

11.

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM.

Bioinformatics. 2015 Aug 15;31(16):2668-75. doi: 10.1093/bioinformatics/btv213. Epub 2015 Apr 16.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

Ten simple rules for reproducible computational research.

Sandve GK, Nekrutenko A, Taylor J, Hovig E.

PLoS Comput Biol. 2013 Oct;9(10):e1003285. doi: 10.1371/journal.pcbi.1003285. Epub 2013 Oct 24. No abstract available.

18.

The anatomy of successful computational biology software.

Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C.

Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. No abstract available.

19.

RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.

Bar-Yaacov D, Avital G, Levin L, Richards AL, Hachen N, Rebolledo Jaramillo B, Nekrutenko A, Zarivach R, Mishmar D.

Genome Res. 2013 Nov;23(11):1789-96. doi: 10.1101/gr.161265.113. Epub 2013 Aug 2.

20.

Web-based visual analysis for high-throughput genomics.

Goecks J, Eberhard C, Too T; Galaxy Team, Nekrutenko A, Taylor J.

BMC Genomics. 2013 Jun 13;14:397. doi: 10.1186/1471-2164-14-397.

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