Publications

In ascending order from 1998 to just about now:

  1. Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family. Nekrutenko A, Hillis DM, Patton JC, Bradley RD, Baker RJ. Mol Biol Evol. 1998
  2. Representational difference analysis to distinguish cryptic species. Nekrutenko A, Makova KD, Chesser RK, Baker RJ. Mol Ecol. 1999
  3. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. Nekrutenko A, Makova KD, Baker RJ. Gene. 2000
  4. Evolution of microsatellite alleles in four species of mice (genus Apodemus). Makova KD, Nekrutenko A, Baker RJ. J Mol Evol. 2000
  5. Assessment of compositional heterogeneity within and between eukaryotic genomes. Nekrutenko A, Li WH. Genome Res. 2000
  6. 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 WH. Gene. 2000
  7. Bushbaby growth hormone is much more similar to nonprimate growth hormones than to rhesus monkey and human growth hormones. Adkins RM, Nekrutenko A, Li WH. Mol Biol Evol. 2001
  8. Evolutionary analyses of the human genome. Li WH, Gu Z, Wang H, Nekrutenko A. Nature. 2001
  9. Transposable elements are found in a large number of human protein-coding genes. Nekrutenko A, Li WH. Trends Genet. 2001
  10. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Nekrutenko A, Makova KD, Li WH. Genome Res. 2002
  11. Signatures of domain shuffling in the human genome. Kaessmann H, Zöllner S, Nekrutenko A, Li WH. Genome Res. 2002
  12. Detection of gene duplications and block duplications in eukaryotic genomes. Li WH, Gu Z, Cavalcanti AR, Nekrutenko A. J Struct Funct Genomics. 2003
  13. Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids. Nekrutenko A, Baker RJ. Gene. 2003
  14. An evolutionary approach reveals a high protein-coding capacity of the human genome. Nekrutenko A, Chung WY, Li WH. Trends Genet. 2003
  15. Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes. Thomas MA, Weston B, Joseph M, Wu W, Nekrutenko A, Tonellato PJ. Mol Biol Evol. 2003
  16. ETOPE: Evolutionary test of predicted exons. Nekrutenko A, Chung WY, Li WH. Nucleic Acids Res. 2003
  17. Comparative genomics. Miller W, Makova KD, Nekrutenko A, Hardison RC. Annu Rev Genomics Hum Genet. 2004
  18. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, et al. Nature. 2004
  19. Reconciling the numbers: ESTs versus protein-coding genes. Nekrutenko A. Mol Biol Evol. 2004
  20. Identification of novel exons from rat-mouse comparisons. Nekrutenko A. J Mol Evol. 2004
  21. Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD. PLoS Genet. 2005
  22. Galaxy: a platform for interactive large-scale genome analysis. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Genome Res. 2005
  23. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. BMC Bioinformatics. 2006
  24. mNSC1 shows no evidence of protein-coding capacity. Wilson C, Goetting-Minesky P, Nekrutenko A. Gene. 2006
  25. Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames. Nekrutenko A, He J. Trends Genet. 2006
  26. 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
  27. 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
  28. 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
  29. Using galaxy to perform large-scale interactive data analyses. Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Curr Protoc Bioinformatics. 2007
  30. 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, et al. Genome Res. 2007
  31. Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench. Lazarus R, Taylor J, Qiu W, Nekrutenko A. Summit Transl Bioinform. 2008
  32. Wheels within wheels: clues to the evolution of the Gnas and Gnal loci. Wadhawan S, Dickins B, Nekrutenko A. Mol Biol Evol. 2008
  33. 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
  34. High-resolution mapping of evolutionary trajectories in a phage. Dickins B, Nekrutenko A. Genome Biol Evol. 2009
  35. 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
  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
  37. 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
  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
  39. 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, et al. Nature. 2010
  40. Manipulation of FASTQ data with Galaxy. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team.. Bioinformatics. 2010
  41. Galaxy CloudMan: delivering cloud compute clusters. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. BMC Bioinformatics. 2010
  42. 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
  43. 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
  44. 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
  45. Making whole genome multiple alignments usable for biologists. Blankenberg D, Taylor J, Nekrutenko A; Galaxy Team.. Bioinformatics. 2011
  46. 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
  47. 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
  48. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nekrutenko A, Taylor J. Nat Rev Genet. 2012
  49. NGS analyses by visualization with Trackster. Goecks J, Coraor N; Galaxy Team., Nekrutenko A, Taylor J. Nat Biotechnol. 2012
  50. Web-based visual analysis for high-throughput genomics. Goecks J, Eberhard C, Too T; Galaxy Team., Nekrutenko A, Taylor J. BMC Genomics. 2013
  51. Ten simple rules for reproducible computational research. Sandve GK, Nekrutenko A, Taylor J, Hovig E. PLoS Comput Biol. 2013
  52. 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
  53. 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
  54. 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
  55. 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
  56. Wrangling Galaxy’s reference data. Blankenberg D, Johnson JE; Galaxy Team., Taylor J, Nekrutenko A. Bioinformatics. 2014
  57. 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
  58. Online resources for genomic analysis using high-throughput sequencing. Blankenberg D, Taylor J, Nekrutenko A. Cold Spring Harb Protoc. 2015
  59. 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
  60. 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, et al. Nat Methods. 2016
  61. 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
  62. Streamlined analysis of duplex sequencing data with Du Novo. Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Genome Biol. 2016
  63. 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
  64. Biology Needs Evolutionary Software Tools: Let’s Build Them Right. Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D. Mol Biol Evol. 2018
  65. 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
  66. 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, et al. Cell Syst. 2018
  67. Family reunion via error correction: An efficient analysis of duplex sequencing data Stoler N, Arbeithuber B, Povysil M, Heinzl M, Salazar R, Makova K, Tiemann-Boege I, Nekrutenko A bioRxiv 2018
  68. Understanding trivial challenges of microbial genomics: An assembly example DeLariviere D, Mei H, Freeberg M, Taylor J, Nekrutenko A bioRxiv 2018
  69. 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
  70. 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
  71. Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage. Tyryshkina A, Coraor N, Nekrutenko A. Bioinformatics. 2019
  72. 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
  73. 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. PNAS 2019
  74. 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. 2019
  75. 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 Bioinf. 2020
  76. In memory of James Taylor: the birth of Galaxy. Nekrutenko A, Schatz MC. Genome Biol. 2020
  77. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. Nucleic Acids Res. 2020
  78. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. PLoS Pathog. 2020