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Items: 1 to 50 of 73

1.

Family reunion via error correction: an efficient analysis of duplex sequencing data.

Stoler N, Arbeithuber B, Povysil G, Heinzl M, Salazar R, Makova KD, Tiemann-Boege I, Nekrutenko A.

BMC Bioinformatics. 2020 Mar 4;21(1):96. doi: 10.1186/s12859-020-3419-8.

2.

Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees.

Zaidi AA, Wilton PR, Su MS, Paul IM, Arbeithuber B, Anthony K, Nekrutenko A, Nielsen R, Makova KD.

Proc Natl Acad Sci U S A. 2019 Dec 10;116(50):25172-25178. doi: 10.1073/pnas.1906331116. Epub 2019 Nov 22.

3.

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

Mei H, Arbeithuber B, Cremona MA, DeGiorgio M, Nekrutenko A.

Genome Biol Evol. 2019 Oct 1;11(10):3022-3034. doi: 10.1093/gbe/evz197.

4.

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV.

Mol Biol Evol. 2020 Jan 1;37(1):295-299. doi: 10.1093/molbev/msz197.

PMID:
31504749
5.

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

Tyryshkina A, Coraor N, Nekrutenko A.

Bioinformatics. 2019 Sep 15;35(18):3453-3460. doi: 10.1093/bioinformatics/btz054.

PMID:
30698642
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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
17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

NGS analyses by visualization with Trackster.

Goecks J, Coraor N; Galaxy Team, Nekrutenko A, Taylor J.

Nat Biotechnol. 2012 Nov;30(11):1036-9. doi: 10.1038/nbt.2404. No abstract available.

26.

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Nekrutenko A, Taylor J.

Nat Rev Genet. 2012 Sep;13(9):667-72. doi: 10.1038/nrg3305. Review.

PMID:
22898652
27.

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.

28.

Harnessing cloud computing with Galaxy Cloud.

Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J.

Nat Biotechnol. 2011 Nov 8;29(11):972-4. doi: 10.1038/nbt.2028. No abstract available.

29.

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD.

Genome Biol Evol. 2011;3:1096-106. doi: 10.1093/gbe/evr067. Epub 2011 Jul 29.

30.

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.

31.

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.

Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A.

Genome Biol. 2011;12(6):R59. doi: 10.1186/gb-2011-12-6-r59. Epub 2011 Jun 23.

32.

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.

33.

Galaxy CloudMan: delivering cloud compute clusters.

Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S4. doi: 10.1186/1471-2105-11-S12-S4.

34.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Goecks J, Nekrutenko A, Taylor J; Galaxy Team.

Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86. Epub 2010 Aug 25.

35.

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.

36.

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T.

Methods Mol Biol. 2010;628:275-96. doi: 10.1007/978-1-60327-367-1_15.

37.

Complete Khoisan and Bantu genomes from southern Africa.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM.

Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.

38.

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.

39.

Windshield splatter analysis with the Galaxy metagenomic pipeline.

Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

Genome Res. 2009 Nov;19(11):2144-53. doi: 10.1101/gr.094508.109. Epub 2009 Oct 9.

40.

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.

Han X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H.

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12741-6. doi: 10.1073/pnas.0902417106. Epub 2009 Jul 17.

41.

High-resolution mapping of evolutionary trajectories in a phage.

Dickins B, Nekrutenko A.

Genome Biol Evol. 2009 Aug 11;1:294-307. doi: 10.1093/gbe/evp029.

42.

Wheels within wheels: clues to the evolution of the Gnas and Gnal loci.

Wadhawan S, Dickins B, Nekrutenko A.

Mol Biol Evol. 2008 Dec;25(12):2745-57. doi: 10.1093/molbev/msn229. Epub 2008 Oct 8.

PMID:
18842685
43.

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.

44.
45.

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.

46.

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function.

Szklarczyk R, Heringa J, Pond SK, Nekrutenko A.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12807-12. Epub 2007 Jul 24.

47.

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.

48.

A first look at ARFome: dual-coding genes in mammalian genomes.

Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A.

PLoS Comput Biol. 2007 May;3(5):e91.

49.

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames.

Nekrutenko A, He J.

Trends Genet. 2006 Dec;22(12):645-8. Epub 2006 Oct 10. Review.

PMID:
17034899
50.

mNSC1 shows no evidence of protein-coding capacity.

Wilson C, Goetting-Minesky P, Nekrutenko A.

Gene. 2006 Mar 29;370:83-5. Epub 2006 Feb 14.

PMID:
16476528

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