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Research Output 1998 2019

2019

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

Galaxies
Historical Data
Bioinformatics
Computational Biology
Random Forest
2018
3 Citations (Scopus)

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

Nekrutenko, A., Team, G., Goecks, J., Taylor, J. & Blankenberg, D., Jun 1 2018, In : Molecular biology and evolution. 35, 6, p. 1372-1375 4 p.

Research output: Contribution to journalArticle

life science
Software
Biological Science Disciplines
software
Biological Sciences
4 Citations (Scopus)

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

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

Research output: Contribution to journalArticle

Microbiota
Weight Gain
Growth
Bacteroidetes
Diet
1 Citation (Scopus)

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

Biological Science Disciplines
Web Browser
Research Personnel
Explosions
Internet
5 Citations (Scopus)

Practical Computational Reproducibility in the Life Sciences

Grüning, B., Chilton, J. M., 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

Biological Science Disciplines
Software
Technology
Workflow
Computational Biology
194 Citations (Scopus)

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. M., Clements, D., Coraor, N., Grüning, B. A., Guerler, A., Jackson, J. L., 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

Galaxies
Metabolomics
Genomics
2017
14 Citations (Scopus)

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. M., Coraor, N., Backofen, R., Taylor, J. & Nekrutenko, A., May 1 2017, In : PLoS computational biology. 13, 5, e1005425.

Research output: Contribution to journalArticle

Galaxies
Publications
Pipelines
researchers
Research Personnel
2016
18 Citations (Scopus)

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. J., 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

Workflow
Bioinformatics
Computational Biology
Biomedical Research
Software
5 Citations (Scopus)

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

Galaxies
duplex
Mitochondrial DNA
polymorphism
Noise
686 Citations (Scopus)

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

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D. J., Bouvier, D., Cech, M., Chilton, J. M., Clements, D., Coraor, N., Eberhard, C., Grüning, B., Guerler, A., Jackson, J. L., 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

Galaxies
Technology
Informatics
Biological Science Disciplines
DNA Sequence Analysis
2015
5 Citations (Scopus)

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

Research Personnel
Throughput
Informatics
Visualization
Availability
21 Citations (Scopus)

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

RNA Secondary Structure
RNA
Genome
Profiling
Genes
2014
6 Citations (Scopus)

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., Blankenberg, D. J., Stoler, N., Makova, K. D. & Nekrutenko, A., Jan 1 2014, In : BioTechniques. 56, 3, p. 134-141 8 p.

Research output: Contribution to journalArticle

Equipment Contamination
Contamination
Galaxies
Library Services
Polymorphism
77 Citations (Scopus)

Dissemination of scientific software with Galaxy ToolShed

Blankenberg, D. J., 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. L., 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

Galaxies
Software
software
freedom
analysis

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., Jan 1 2014, In : Nature Biotechnology. 32, 6, 1 p.

Research output: Contribution to journalComment/debate

Biotechnology
Computational Biology
Anatomy
Software

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

Maternal Age
Mitochondrial DNA
Germ Cells
Mothers
Mitochondrial Diseases
75 Citations (Scopus)

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., 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

Maternal Age
Mitochondrial DNA
Germ Cells
Mothers
Mitochondrial Diseases
17 Citations (Scopus)

Wrangling Galaxy's reference data

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

Research output: Contribution to journalArticle

Galaxies
Provenance
Reproducibility
Cache
Managers
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

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

Galaxies
Job analysis
Websites
Servers
Data storage equipment
29 Citations (Scopus)

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

16S Ribosomal RNA
Mitochondria
RNA
DNA
Mitochondrial DNA
220 Citations (Scopus)

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

biomedical research
Computational Biology
bioinformatics
Reproducibility of Results
reproducibility
15 Citations (Scopus)

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

Computational Biology
Anatomy
Software
27 Citations (Scopus)

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

Genomics
Web Browser
Genome
Research
2012
4 Citations (Scopus)

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

Reference Model
Infrastructure
Virtualization
Service Levels
Byproducts
4 Citations (Scopus)

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

Goecks, J., Afgan, E., Baker, D., Blankenberg, D. J., 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

Throughput
Software engineering
Assays
Visualization
Genomics
159 Citations (Scopus)

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

Precision Medicine
Biological Science Disciplines
Ecology
Research Personnel
Technology
24 Citations (Scopus)

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

Computer graphics
Data mining
Visualization
83 Citations (Scopus)

Using galaxy to perform large-scale interactive data analyses

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

Research output: Contribution to journalArticle

Galaxies
Microbial Genome
Research Personnel
Biomedical Technology
Informatics
2011
40 Citations (Scopus)

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

Equus przewalskii
High-Throughput Nucleotide Sequencing
horse
Horses
genetic variation
71 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

Mitochondrial Dynamics
Mitochondrial DNA
mitochondrial DNA
gene frequency
Gene Frequency
82 Citations (Scopus)

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

Galaxies
Cloud computing
Mitochondrial DNA
Internet
26 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

Galaxies
data analysis
Databases
genomics
Data Mining
27 Citations (Scopus)

Making whole genome multiple alignments usable for biologists

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

Research output: Contribution to journalArticle

Galaxies
Genome
Alignment
Genes
Graphical User Interface
2010
251 Citations (Scopus)

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

Southern Africa
Genome
Botswana
Medical History Taking
Exome
2304 Citations (Scopus)

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. J., 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

Galaxies
life science
Biological Science Disciplines
provenance
genomics
924 Citations (Scopus)

Galaxy: A web-based genome analysis tool for experimentalists

Blankenberg, D. J., 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

Research output: Contribution to journalReview article

Informatics
Web Browser
Genome
Molecular Biology
Software
122 Citations (Scopus)

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

Galaxies
Cloud computing
Web Browser
Research Personnel
Infrastructure
316 Citations (Scopus)

Manipulation of FASTQ data with galaxy

Blankenberg, D. J., 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

Galaxies
Sequencing
Manipulation
Pipelines
Filtering
10 Citations (Scopus)

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

Galaxies
Genome
Computational Biology
Programming Languages
Biological Science Disciplines
2009
56 Citations (Scopus)

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

High-Throughput Nucleotide Sequencing
Transcriptome
Genes
Gene Expression
Synaptotagmin II
49 Citations (Scopus)

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

Galaxies
Metagenomics
Statistical Data Interpretation
Workflow
Quality Control
2008
8 Citations (Scopus)

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

wheels
Mammals
imprinting
loci
genomic imprinting
2007
182 Citations (Scopus)

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. J., 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., Jan 1 2007, In : Genome research. 17, 12, p. 1797-1808 12 p.

Research output: Contribution to journalArticle

Vertebrates
Initiator Codon
Terminator Codon
Genome
Human Genome
42 Citations (Scopus)

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

Reading Frames
Genome
genome
Coding
Genes
104 Citations (Scopus)

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

Blankenberg, D. J., 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

Encyclopedias
DNA
Molecular Evolution
Manuscripts
Information Dissemination
13 Citations (Scopus)

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

Exons
Neoplasms
Reading Frames
Mutation
Alternative Splicing

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

Galaxies
Genes
Genome
Polymorphism
Single Nucleotide Polymorphism
2006
22 Citations (Scopus)

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

Nekrutenko, A. & He, J., Dec 1 2006, In : Trends in Genetics. 22, 12, p. 645-648 4 p.

Research output: Contribution to journalShort survey

Reading Frames
Overlapping Genes
Genes
Biological Phenomena
Proteins
2 Citations (Scopus)

mNSC1 shows no evidence of protein-coding capacity

Wilson, C., Goetting-Minesky, P. & Nekrutenko, A., Mar 29 2006, In : Gene. 370, 1-2, p. 83-85 3 p.

Research output: Contribution to journalArticle

Proteins
Genes
Reading Frames
DNA Transposable Elements
Cations
36 Citations (Scopus)
Duplicate Genes
Gene Networks
Gene Regulatory Networks
Divergence
Genes