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Research Output 1998 2019

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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
43 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

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

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

Research output: Contribution to journalArticle

Open Access
plasmid
plasmids
Plasmids
mutation
Mutation
42 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
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
113 Citations (Scopus)

Assessment of compositional heterogeneity within and between eukaryotic genomes

Nekrutenko, A. & Li, W. H., Dec 1 2000, In : Genome research. 10, 12, p. 1986-1995 10 p.

Research output: Contribution to journalArticle

Isochores
Genome
Base Composition
Eukaryota
Nucleotides
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
26 Citations (Scopus)

Bushbaby growth hormone is much more similar to nonprimate growth hormones than to rhesus monkey and human growth hormones

Adkins, R. M., Nekrutenko, A. & Li, W. H., Jan 1 2001, In : Molecular biology and evolution. 18, 1, p. 55-60 6 p.

Research output: Contribution to journalArticle

human growth
Human Growth Hormone
Macaca mulatta
somatotropin
Growth Hormone
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
255 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
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. 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

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

Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family

Nekrutenko, A., Hillis, D. M., Patton, J. C., Bradley, R. D. & Baker, R. J., Dec 1998, In : Molecular biology and evolution. 15, 12, p. 1674-1684 11 p.

Research output: Contribution to journalArticle

isocitrate dehydrogenase (NADP)
Isocitrate Dehydrogenase
isocitrate dehydrogenase
Arvicolinae
enzyme
62 Citations (Scopus)

Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence

Gu, Z., Wang, H., Nekrutenko, A. & Li, W. H., Dec 23 2000, In : Gene. 259, 1-2, p. 81-88 8 p.

Research output: Contribution to journalArticle

Nucleic Acid Repetitive Sequences
Base Composition
Human Genome
Y Chromosome
AT Rich Sequence
74 Citations (Scopus)

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

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

ETOPE: Evolutionary test of predicted exons

Nekrutenko, A., Chung, W. Y. & Li, W. H., Jul 1 2003, In : Nucleic acids research. 31, 13, p. 3564-3567 4 p.

Research output: Contribution to journalArticle

Exons
Expressed Sequence Tags
Computer Simulation
Open Reading Frames
Genome
316 Citations (Scopus)

Evolutionary analyses of the human genome

Li, W. H., Gu, Z., Wang, H. & Nekrutenko, A., Feb 15 2001, In : Nature. 409, 6822, p. 847-849 3 p.

Research output: Contribution to journalArticle

Human Genome
Gene Duplication
Regulator Genes
Genomics
History
43 Citations (Scopus)

Evolutionary dynamics of oncogenes and tumor suppressor genes: Higher intensities of purifying selection than other genes

Thomas, M. A., Weston, B., Joseph, M., Wu, W., Nekrutenko, A. & Tonellato, P. J., Jun 1 2003, In : Molecular biology and evolution. 20, 6, p. 964-968 5 p.

Research output: Contribution to journalArticle

selection intensity
tumor suppressor genes
oncogenes
Tumor Suppressor Genes
Oncogenes
45 Citations (Scopus)

Evolution of microsatellite alleles in four species of mice (genus Apodemus)

Makova, K. D., Nekrutenko, A. & Baker, R. J., Jan 1 2000, In : Journal Of Molecular Evolution. 51, 2, p. 166-172 7 p.

Research output: Contribution to journalArticle

Murinae
Apodemus
Microsatellite Repeats
allele
Alleles
2315 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
1315 Citations (Scopus)

Galaxy: A platform for interactive large-scale genome analysis

Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W. J. & Nekrutenko, A., Oct 1 2005, In : Genome research. 15, 10, p. 1451-1455 5 p.

Research output: Contribution to journalArticle

Galaxies
Genome
History
Research Personnel
Databases
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
1451 Citations (Scopus)

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S., Scott, G., Steffen, D., Worley, K. C., Burch, P. E., Okwuonu, G., Hines, S., Lewis, L., Deramo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R. & 216 others, Holt, R. A., Adams, M. D., Amanatides, P. G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C. A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C. L., Nguyen, T., Pfannkoch, C. M., Sitter, C., Sutton, G. G., Venter, J. C., Woodage, T., Smith, D., Lee, H. M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R. B., Dunn, D. M., Green, E. D., Blakesley, R. W., Bouffard, G. G., de Jong, P. J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C. M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W. C., Gibbs, R. A., Weinstock, G. M., Havlak, P. H., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X. Z., Li, B., Liu, Y., Qin, X., Cawley, S., Weinstock, G. M., Worley, K. C., Cooney, A. J., Gibbs, R. A., D'Souza, L. M., Martin, K., Wu, J. Q., Gonzalez-Garay, M. L., Jackson, A. R., Kalafus, K. J., McLeod, M. P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D. A., Zhang, Z., Bailey, J. A., Eichler, E. E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B. J., Young, J. M., Smith, D., Huang, H., Fechtel, K., Wang, H., Xing, H., Weinstock, K., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Albà, M. M., Abril, J. F., Guigo, R., Smit, A., Dubchak, I., Rubin, E. M., Couronne, O., Poliakov, A., Hübner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y. A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H. J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M. I., Kwitek, A. E., Lazar, J., Pasko, D., Tonellato, P. J., Twigger, S., Ponting, C. P., Duarte, J. M., Rice, S., Goodstadt, L., Beatson, S. A., Emes, R. D., Winter, E. E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R. C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T. D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S. M., Cooper, G. M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E. A., Venter, J. C., Payseur, B. A., Bourque, G., López-Otín, C., Puente, X. S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V. B., Caspi, A., Tesler, S. D. G., Pevzner, P. A., Haussler, S. C. D., Roskin, K. M., Baertsch, R., Clawson, H., Furey, T. S., Hinrichs, A. S., Karolchik, D., Kent, W. J., Rosenbloom, K. R., Trumbower, H., Weirauch, M., Cooper, D. N., Stenson, P. D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R. R., Taylor, M. S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. & Collins, F., Apr 1 2004, In : Nature. 428, 6982, p. 493-520 28 p.

Research output: Contribution to journalArticle

Genome
Human Genome
Karyotype
Biomedical Research
Proteins
13 Citations (Scopus)

Identification of novel exons from rat-mouse comparisons

Nekrutenko, A., Nov 1 2004, In : Journal Of Molecular Evolution. 59, 5, p. 703-708 6 p.

Research output: Contribution to journalArticle

exons
Rats
Exons
Genes
rodent
26 Citations (Scopus)

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

Galaxies
data analysis
Databases
genomics
Data Mining
19 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., 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
11 Citations (Scopus)

Isolation of binary species-specific PCR-based markers and their value for diagnostic applications

Nekrutenko, A., Makova, K. D. & Baker, R. J., May 16 2000, In : Gene. 249, 1-2, p. 47-51 5 p.

Research output: Contribution to journalArticle

Genome
Polymerase Chain Reaction
Nucleic Acid Repetitive Sequences
Ovum
Costs and Cost Analysis
16 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., Coraor, N., Backofen, R., Taylor, J. & Nekrutenko, A., May 2017, In : PLoS computational biology. 13, 5, e1005425.

Research output: Contribution to journalArticle

Galaxies
Publications
Pipelines
researchers
Research Personnel
27 Citations (Scopus)

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

Galaxies
Genome
Alignment
Genes
Graphical User Interface
328 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

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
80 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. 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
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
6 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
25 Citations (Scopus)

Oscillating evolution of a mammalian locus with overlapping reading frames: An XLαs/ALEX relay

Nekrutenko, A., Wadhawan, S., Goetting-Minesky, P. & Makova, K. D., Dec 1 2005, In : PLoS genetics. 1, 2, p. 197-204 8 p.

Research output: Contribution to journalArticle

Reading Frames
loci
protein
Proteins
Platyrrhini

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
37 Citations (Scopus)
Duplicate Genes
Gene Networks
Gene Regulatory Networks
Divergence
Genes
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
16 Citations (Scopus)

Reconciling the numbers: ESTs versus protein-coding genes

Nekrutenko, A., Jul 1 2004, In : Molecular Biology and Evolution. 21, 7, p. 1278-1282 5 p.

Research output: Contribution to journalArticle

Expressed Sequence Tags
Genes
protein
gene
Proteins
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
73 Citations (Scopus)

Signatures of domain shuffling in the human genome

Kaessmann, H., Zöllner, S., Nekrutenko, A. & Li, W. H., Nov 1 2002, In : Genome research. 12, 11, p. 1642-1650 9 p.

Research output: Contribution to journalArticle

Human Genome
Introns
Caenorhabditis elegans
Exons
Proteome
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
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
9 Citations (Scopus)

Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: Implications for evolutionary analysis of polyploids

Nekrutenko, A. & Baker, R. J., Mar 13 2003, In : Gene. 306, 1-2, p. 99-103 5 p.

Research output: Contribution to journalArticle

Gossypium
Polyploidy
Genome
Molecular Evolution
Diploidy
706 Citations (Scopus)

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

Galaxies
Technology
Informatics
Biological Science Disciplines
DNA Sequence Analysis
220 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., 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

Galaxies
Metabolomics
Genomics
147 Citations (Scopus)

The KA/KS ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study

Nekrutenko, A., Makova, K. D. & Li, W. H., Jan 26 2002, In : Genome research. 12, 1, p. 198-202 5 p.

Research output: Contribution to journalArticle

Exons
Genes
Proteins
Genomics
57 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
83 Citations (Scopus)

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

Galaxies
Microbial Genome
Research Personnel
Biomedical Technology
Informatics