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Research Output

2020

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

Stoler, N., Arbeithuber, B., Povysil, G., Heinzl, M., Salazar, R., Makova, K. D., Tiemann-Boege, I. & Nekrutenko, A., Mar 4 2020, In : BMC bioinformatics. 21, 1, 96.

Research output: Contribution to journalArticle

Open Access

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

Kosakovsky Pond, S. L., Poon, A. F. Y., Velazquez, R., Weaver, S., Hepler, N. L., Murrell, B., Shank, S. D., Magalis, B. R., Bouvier, D., Nekrutenko, A., Wisotsky, S., Spielman, S. J., Frost, S. D. W. & Muse, S. V., Jan 1 2020, In : Molecular biology and evolution. 37, 1, p. 295-299 5 p.

Research output: Contribution to journalArticle

2 Scopus citations
2019

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

Mei, H., Arbeithuber, B., Cremona, M. A., Degiorgio, M., Nekrutenko, A. & Li, W. H., Oct 1 2019, In : Genome biology and evolution. 11, 10, p. 3022-3034 13 p.

Research output: Contribution to journalArticle

Open Access

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

Zaidi, A. A., Wilton, P. R., Su, M. S. W., Paul, I. M., Arbeithuber, B., Anthony, K., Nekrutenko, A., Nielsen, R. & Makova, K. D., Dec 10 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 50, p. 25172-25178 7 p.

Research output: Contribution to journalArticle

Open Access

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

Tyryshkina, A., Coraor, N., Nekrutenko, A. & Wren, J., Sep 15 2019, In : Bioinformatics. 35, 18, p. 3453-3460 8 p.

Research output: Contribution to journalArticle

2 Scopus citations
2018

Biology needs evolutionary software tools: Let's build them right

Nekrutenko, A., Team, G., Goecks, J., Taylor, J. & Blankenberg, D., Jun 2018, In : Molecular biology and evolution. 35, 6, p. 1372-1375 4 p.

Research output: Contribution to journalArticle

4 Scopus citations

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Craig, S. J. C., Blankenberg, D., Parodi, A. C. L., Paul, I. M., Birch, L. L., Savage, J. S., Marini, M. E., Stokes, J. L., Nekrutenko, A., Reimherr, M., Chiaromonte, F. & Makova, K. D., Dec 1 2018, In : Scientific reports. 8, 1, 14030.

Research output: Contribution to journalArticle

7 Scopus citations

Community-Driven Data Analysis Training for Biology

Galaxy Training Network, Jun 27 2018, In : Cell Systems. 6, 6, p. 752-758.e1

Research output: Contribution to journalArticle

6 Scopus citations

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., Jun 27 2018, In : Cell Systems. 6, 6, p. 631-635 5 p.

Research output: Contribution to journalComment/debate

17 Scopus citations

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

Afgan, E., Baker, D., Batut, B., Van Den Beek, M., Bouvier, D., Ech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A. & Blankenberg, D., Jul 2 2018, In : Nucleic acids research. 46, W1, p. W537-W544

Research output: Contribution to journalArticle

415 Scopus citations
2017

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

Grüning, B. A., Rasche, E., Rebolledo-Jaramillo, B., Eberhard, C., Houwaart, T., Chilton, J., Coraor, N., Backofen, R., Taylor, J. & Nekrutenko, A., May 2017, In : PLoS computational biology. 13, 5, e1005425.

Research output: Contribution to journalArticle

22 Scopus citations
2016

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, J. T., Demchak, B., Hull, T., Ben-Artzi, G., Blankenberg, D., Barber, G. P., Lee, B. T., Kuhn, R. M., Nekrutenko, A., Segal, E., Ideker, T., Reich, M. & 3 others, Regev, A., Y Chang, H. & Mesirov, J. P., Feb 25 2016, In : Nature methods. 13, 3, p. 245-247 3 p.

Research output: Contribution to journalArticle

24 Scopus citations

Streamlined analysis of duplex sequencing data with Du Novo

Stoler, N., Arbeithuber, B., Guiblet, W., Makova, K. D. & Nekrutenko, A., Aug 26 2016, In : Genome biology. 17, 1, 180.

Research output: Contribution to journalArticle

10 Scopus citations

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., Jul 8 2016, In : Nucleic acids research. 44, W1, p. W3-W10

Research output: Contribution to journalArticle

825 Scopus citations
2015

Online resources for genomic analysis using high-throughput sequencing

Blankenberg, D. J., Taylor, J. & Nekrutenko, A., Jan 1 2015, In : Cold Spring Harbor Protocols. 2015, 4, p. 324-335 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

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

Tang, Y., Bouvier, E., Kwok, C. K., Ding, Y., Nekrutenko, A., Bevilacqua, P. C. & Assmann, S. M., Jan 19 2015, In : Bioinformatics. 31, 16, p. 2668-2675 8 p.

Research output: Contribution to journalArticle

24 Scopus citations
2014

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

Dickins, B., Rebolledo-Jaramillo, B., Su, M. S. W., Paul, I. M., Blankenberg, D., Stoler, N., Makova, K. D. & Nekrutenko, A., Mar 2014, In : BioTechniques. 56, 3, p. 134-141 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Dissemination of scientific software with Galaxy ToolShed

Blankenberg, D., Von Kuster, G., Bouvier, E., Baker, D., Afgan, E., Stoler, N., Taylor, J., Nekrutenko, A., Clements, D., Coraor, N., Eberhard, C., Francheteau, D., Goecks, J., Guerler, S., Jackson, J., Cooke, I., Johnson, J., Kirton, E., Cock, P., Chapman, B. & 2 others, Grüning, B. & Lazarus, R., Feb 20 2014, In : Genome biology. 15, 2, 403.

Research output: Contribution to journalLetter

87 Scopus citations

Erratum: The anatomy of successful computational biology software (Nature Biotechnology (2013) 31 (894-897))

Altschul, S., Demchak, B., Durbin, R., Gentleman, R., Krzywinski, M., Li, H., Nekrutenko, A., Robinson, J., Rasband, W., Taylor, J. & Trapnell, C., Jun 2014, In : Nature Biotechnology. 32, 6, 1 p.

Research output: Contribution to journalComment/debate

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

Rebolledo-Jaramillo, B., Su, M. S. W., Stoler, N., McElhoe, J. A., Dickins, B., Blankenberg, D., Korneliussen, T. S., Chiaromonte, F., Nielsen, R., Holland, M. M., Paul, I. M., Nekrutenko, A. & Makova, K. D., Oct 28 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15474-15479 6 p.

Research output: Contribution to journalArticle

95 Scopus citations

Wrangling Galaxy's reference data

Blankenberg, D., Johnson, J. E., Taylor, J. & Nekrutenko, A., Jul 1 2014, In : Bioinformatics. 30, 13, p. 1917-1919 3 p.

Research output: Contribution to journalArticle

18 Scopus citations
2013

A sustainable national gateway for biological computation

Taylor, J., Ropelewski, A., Zhang, Z., Nekrutenko, A., Palencia, J., Sanielevici, S., Coraor, N., Yanovich, J., Blood, P. D. & Budden, R., Aug 26 2013, Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 32. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Bar-Yaacov, D., Avital, G., Levin, L., Richards, A. L., Hachen, N., Rebolledo Jaramillo, B., Nekrutenko, A., Zarivach, R. & Mishmar, D., Nov 1 2013, In : Genome research. 23, 11, p. 1789-1796 8 p.

Research output: Contribution to journalArticle

32 Scopus citations

Ten Simple Rules for Reproducible Computational Research

Sandve, G. K., Nekrutenko, A., Taylor, J. & Hovig, E., Oct 1 2013, In : PLoS computational biology. 9, 10, e1003285.

Research output: Contribution to journalEditorial

265 Scopus citations

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., Oct 1 2013, In : Nature Biotechnology. 31, 10, p. 894-897 4 p.

Research output: Contribution to journalComment/debate

16 Scopus citations

Web-based visual analysis for high-throughput genomics

Goecks, J., Eberhard, C., Too, T., Nekrutenko, A. & Taylor, J., Jun 13 2013, In : BMC genomics. 14, 1, 397.

Research output: Contribution to journalArticle

29 Scopus citations
2012

A reference model for deploying applications in virtualized environments

Afgan, E., Baker, D., Nekrutenko, A. & Taylor, J., Aug 25 2012, In : Concurrency Computation Practice and Experience. 24, 12, p. 1349-1361 13 p.

Research output: Contribution to journalArticle

4 Scopus citations

Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses

Goecks, J., Afgan, E., Baker, D., Blankenberg, D., Coraor, N., Eberhard, C., Von Kuster, G., Lazarus, R., Li, K., McManus, S., Nekrutenko, A. & Taylor, J., Dec 1 2012, 2012 IEEE 8th International Conference on E-Science, e-Science 2012. 6404442. (2012 IEEE 8th International Conference on E-Science, e-Science 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility

Nekrutenko, A. & Taylor, J., Sep 1 2012, In : Nature Reviews Genetics. 13, 9, p. 667-672 6 p.

Research output: Contribution to journalReview article

176 Scopus citations

NGS analyses by visualization with Trackster

Goecks, J., Coraor, N., Nekrutenko, A. & Taylor, J., Nov 1 2012, In : Nature Biotechnology. 30, 11, p. 1036-1039 4 p.

Research output: Contribution to journalLetter

25 Scopus citations

Using galaxy to perform large-scale interactive data analyses

Hillman-Jackson, J., Clements, D., Blankenberg, D., Taylor, J., Nekrutenko, A. & Team, G., Jun 1 2012, In : Current Protocols in Bioinformatics. SUPPL.38, 10.5.

Research output: Contribution to journalArticle

86 Scopus citations
2011

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

Goto, H., Ryder, O. A., Fisher, A. R., Schultz, B., Pond, S. L. K., Nekrutenko, A. & Makova, K. D., Dec 1 2011, In : Genome biology and evolution. 3, 1, p. 1096-1106 11 p.

Research output: Contribution to journalArticle

42 Scopus citations

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

Goto, H., Dickins, B., Afgan, E., Paul, I. M., Taylor, J., Makova, K. D. & Nekrutenko, A., Jun 23 2011, In : Genome biology. 12, 6, R59.

Research output: Contribution to journalArticle

76 Scopus citations

Harnessing cloud computing with Galaxy Cloud

Afgan, E., Baker, D., Coraor, N., Goto, H., Paul, I., Makova, K. D., Nekrutenko, A. & Taylor, J., Nov 1 2011, In : Nature Biotechnology. 29, 11, p. 972-974 3 p.

Research output: Contribution to journalLetter

87 Scopus citations

Integrating diverse databases into an unified analysis framework: A Galaxy approach

Blankenberg, D., Coraor, N., Von Kuster, G., Taylor, J. & Nekrutenko, A., Dec 1 2011, In : Database. 2011, bar011.

Research output: Contribution to journalArticle

30 Scopus citations

Making whole genome multiple alignments usable for biologists

Blankenberg, D., Taylor, J. & Nekrutenko, A., Sep 1 2011, In : Bioinformatics. 27, 17, p. 2426-2428 3 p., btr398.

Research output: Contribution to journalArticle

28 Scopus citations
2010

Complete Khoisan and Bantu genomes from southern Africa

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., Burhans, R. & 28 others, Riemer, C., Wittekindt, N. E., Moorjani, P., Tindall, E. A., Danko, C. G., Teo, W. S., Buboltz, A. M., Zhang, Z., Ma, Q., Oosthuysen, A., Steenkamp, A. W., Oostuisen, H., Venter, P., Gajewski, J., Zhang, Y., Pugh, B. F., Makova, K. D., Nekrutenko, A., Mardis, E. R., Patterson, N., Pringle, T. H., Chiaromonte, F., Mullikin, J. C., Eichler, E. E., Hardison, R. C., Gibbs, R. A., Harkins, T. T. & Hayes, V. M., Feb 18 2010, In : Nature. 463, 7283, p. 943-947 5 p.

Research output: Contribution to journalArticle

262 Scopus citations

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

Goecks, J., Nekrutenko, A., Taylor, J., Afgan, E., Ananda, G., Baker, D., Blankenberg, D., Chakrabarty, R., Coraor, N., Goecks, J., Von Kuster, G., Lazarus, R., Li, K., Taylor, J. & Vincent, K., Aug 25 2010, In : Genome biology. 11, 8, R86.

Research output: Contribution to journalArticle

2388 Scopus citations

Galaxy: A web-based genome analysis tool for experimentalists

Blankenberg, D., Kuster, G. V., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. & Taylor, J., Feb 10 2010, In : Current Protocols in Molecular Biology. SUPPL. 89, p. 19.10.1-19.10.21

Research output: Contribution to journalReview article

948 Scopus citations

Galaxy CloudMan: Delivering cloud compute clusters

Afgan, E., Baker, D., Coraor, N., Chapman, B., Nekrutenko, A. & Taylor, J., Dec 21 2010, In : BMC bioinformatics. 11, SUPPL. 12, S4.

Research output: Contribution to journalArticle

125 Scopus citations

Manipulation of FASTQ data with galaxy

Blankenberg, D., Gordon, A., Von Kuster, G., Coraor, N., Taylor, J., Nekrutenko, A. & Team, G., Jun 18 2010, In : Bioinformatics. 26, 14, p. 1783-1785 3 p., btq281.

Research output: Contribution to journalArticle

349 Scopus citations

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

Bock, C., Von Kuster, G., Halachev, K., Taylor, J., Nekrutenko, A. & Lengauer, T., Jan 1 2010, Genetic Variation: Methods and Protocols. Humana Press Inc., p. 275-296 22 p. (Methods in Molecular Biology; vol. 628).

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Scopus citations
2009

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

Han, X., Wu, X., Chung, W. Y., Li, T., Nekrutenko, A., Altman, N. S., Chen, G. & Ma, H., Aug 4 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 31, p. 12741-12746 6 p.

Research output: Contribution to journalArticle

59 Scopus citations

Windshield splatter analysis with the Galaxy metagenomic pipeline

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J. & Nekrutenko, A., Nov 1 2009, In : Genome research. 19, 11, p. 2144-2153 10 p.

Research output: Contribution to journalArticle

49 Scopus citations
2008

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

Wadhawan, S., Dickins, B. & Nekrutenko, A., Dec 1 2008, In : Molecular biology and evolution. 25, 12, p. 2745-2757 13 p.

Research output: Contribution to journalArticle

8 Scopus citations
2007

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

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M. & 6 others, Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D. & Kent, W. J., Dec 2007, In : Genome research. 17, 12, p. 1797-1808 12 p.

Research output: Contribution to journalArticle

188 Scopus citations

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

Chung, W. Y., Wadhawan, S., Szklarczyk, R., Pond, S. K. & Nekrutenko, A., May 1 2007, In : PLoS computational biology. 3, 5, p. 855-861 7 p.

Research output: Contribution to journalArticle

44 Scopus citations

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, K. D., Hardison, R. C. & Nekrutenko, A., Jun 1 2007, In : Genome research. 17, 6, p. 960-964 5 p.

Research output: Contribution to journalArticle

107 Scopus citations

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

Szklarczyk, R., Heringa, J., Pond, S. K. & Nekrutenko, A., Jul 31 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 31, p. 12807-12812 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

Using galaxy to perform large-scale interactive data analyses.

Taylor, J., Schenck, I., Blankenberg, D. J. & Nekrutenko, A., Sep 1 2007, In : Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 10

Research output: Contribution to journalArticle