Anton Nekrutenko - Publications

Affiliations: 
Pennsylvania State University, State College, PA, United States 
Area:
Bioinformatics Biology, Evolution and Development Biology, Genetics

67 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Scientific Reports. 8: 14030. PMID 30232389 DOI: 10.1038/s41598-018-31866-9  0.6
2018 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, ... ... Nekrutenko A, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research. PMID 29790989 DOI: 10.1093/nar/gky379  0.32
2018 Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D. Biology needs evolutionary software tools: Let's build them right. Molecular Biology and Evolution. PMID 29688462 DOI: 10.1093/molbev/msy084  0.32
2017 Grüning BA, Rasche E, Rebolledo-Jaramillo B, Eberhard C, Houwaart T, Chilton J, Coraor N, Backofen R, Taylor J, Nekrutenko A. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. Plos Computational Biology. 13: e1005425. PMID 28542180 DOI: 10.1371/journal.pcbi.1005425  0.32
2016 Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biology. 17: 180. PMID 27566673 DOI: 10.1186/s13059-016-1039-4  0.6
2016 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, ... ... Nekrutenko A, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. PMID 27137889 DOI: 10.1093/nar/gkw343  0.32
2016 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, ... ... Nekrutenko A, et al. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods. PMID 26780094 DOI: 10.1038/nmeth.3732  0.6
2015 Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo. Bioinformatics (Oxford, England). PMID 25886980 DOI: 10.1093/bioinformatics/btv213  0.6
2015 Blankenberg D, Taylor J, Nekrutenko A. Online resources for genomic analysis using high-throughput sequencing. Cold Spring Harbor Protocols. 2015: 324-35. PMID 25655493 DOI: 10.1101/pdb.top083667  0.6
2014 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. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15474-9. PMID 25313049 DOI: 10.1073/pnas.1409328111  0.6
2014 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, et al. Dissemination of scientific software with Galaxy ToolShed Genome Biology. 15. PMID 25001293 DOI: 10.1186/gb4161  0.6
2014 Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques. 56: 134-6, 138-41. PMID 24641477 DOI: 10.2144/000114146  0.6
2014 Blankenberg D, Johnson JE, Taylor J, Nekrutenko A. Wrangling Galaxy's reference data. Bioinformatics (Oxford, England). 30: 1917-9. PMID 24585771 DOI: 10.1093/bioinformatics/btu119  0.6
2013 Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. Plos Computational Biology. 9: e1003285. PMID 24204232 DOI: 10.1371/journal.pcbi.1003285  0.6
2013 Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The anatomy of successful computational biology software. Nature Biotechnology. 31: 894-7. PMID 24104757 DOI: 10.1038/nbt.2721  0.6
2013 Bar-Yaacov D, Avital G, Levin L, Richards AL, Hachen N, Rebolledo Jaramillo B, Nekrutenko A, Zarivach R, Mishmar D. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. Genome Research. 23: 1789-96. PMID 23913925 DOI: 10.1101/gr.161265.113  0.6
2013 Goecks J, Eberhard C, Too T, Nekrutenko A, Taylor J. Web-based visual analysis for high-throughput genomics. Bmc Genomics. 14: 397. PMID 23758618 DOI: 10.1186/1471-2164-14-397  0.6
2013 Taylor J, Ropelewski A, Zhang Z, Nekrutenko A, Palencia J, Sanielevici S, Coraor N, Yanovich J, Blood PD, Budden R. A sustainable national gateway for biological computation Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484817  0.6
2012 Goecks J, Coraor N, Nekrutenko A, Taylor J. NGS analyses by visualization with Trackster. Nature Biotechnology. 30: 1036-9. PMID 23138293 DOI: 10.1038/nbt.2404  0.6
2012 Nekrutenko A, Taylor J. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nature Reviews. Genetics. 13: 667-72. PMID 22898652 DOI: 10.1038/nrg3305  0.6
2012 Hillman-Jackson J, Clements D, Blankenberg D, Taylor J, Nekrutenko A. Using Galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.5. PMID 22700312 DOI: 10.1002/0471250953.bi1005s38  0.6
2012 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. Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses 2012 Ieee 8th International Conference On E-Science, E-Science 2012. DOI: 10.1109/eScience.2012.6404442  0.6
2012 Afgan E, Baker D, Nekrutenko A, Taylor J. A reference model for deploying applications in virtualized environments Concurrency Computation Practice and Experience. 24: 1349-1361. DOI: 10.1002/cpe.1836  0.6
2011 Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. Harnessing cloud computing with Galaxy Cloud. Nature Biotechnology. 29: 972-4. PMID 22068528 DOI: 10.1038/nbt.2028  0.6
2011 Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biology and Evolution. 3: 1096-106. PMID 21803766 DOI: 10.1093/gbe/evr067  0.6
2011 Blankenberg D, Taylor J, Nekrutenko A. Making whole genome multiple alignments usable for biologists. Bioinformatics (Oxford, England). 27: 2426-8. PMID 21775304 DOI: 10.1093/bioinformatics/btr398  0.6
2011 Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biology. 12: R59. PMID 21699709 DOI: 10.1186/gb-2011-12-6-r59  0.6
2011 Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A. Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database : the Journal of Biological Databases and Curation. 2011: bar011. PMID 21531983 DOI: 10.1093/database/bar011  0.6
2010 Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. Galaxy CloudMan: delivering cloud compute clusters. Bmc Bioinformatics. 11: S4. PMID 21210983 DOI: 10.1186/1471-2105-11-S12-S4  0.6
2010 Goecks J, Nekrutenko A, Taylor J, Afgan E, Ananda G, Baker D, Blankenberg D, Chakrabarty R, Coraor N, Von Kuster G, Lazarus R, Li K, Vincent K. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biology. 11. PMID 20738864 DOI: 10.1186/gb-2010-11-8-r86  0.6
2010 Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A. Manipulation of FASTQ data with Galaxy. Bioinformatics (Oxford, England). 26: 1783-5. PMID 20562416 DOI: 10.1093/bioinformatics/btq281  0.6
2010 Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T. Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods in Molecular Biology (Clifton, N.J.). 628: 275-96. PMID 20238087 DOI: 10.1007/978-1-60327-367-1_15  0.6
2010 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, ... ... Nekrutenko A, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/nature08795  0.6
2010 Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 19.10.1-21. PMID 20069535 DOI: 10.1002/0471142727.mb1910s89  0.6
2009 Dickins B, Nekrutenko A. High-resolution mapping of evolutionary trajectories in a phage. Genome Biology and Evolution. 1: 294-307. PMID 20333199 DOI: 10.1093/gbe/evp029  0.32
2009 Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. 19: 2144-53. PMID 19819906 DOI: 10.1101/gr.094508.109  0.6
2009 Han X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H. Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. 106: 12741-6. PMID 19617558 DOI: 10.1073/pnas.0902417106  0.6
2008 Wadhawan S, Dickins B, Nekrutenko A. Wheels within wheels: clues to the evolution of the Gnas and Gnal loci. Molecular Biology and Evolution. 25: 2745-57. PMID 18842685 DOI: 10.1093/molbev/msn229  0.6
2007 Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 10.5. PMID 18428782 DOI: 10.1002/0471250953.bi1005s19  0.6
2007 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, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/gr.6761107  0.6
2007 Szklarczyk R, Heringa J, Pond SK, Nekrutenko A. Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function. Proceedings of the National Academy of Sciences of the United States of America. 104: 12807-12. PMID 17652172 DOI: 10.1073/pnas.0703238104  0.6
2007 Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Research. 17: 960-4. PMID 17568012 DOI: 10.1101/gr.5578007  0.6
2007 Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A. A first look at ARFome: dual-coding genes in mammalian genomes. Plos Computational Biology. 3: e91. PMID 17511511 DOI: 10.1371/journal.pcbi.0030091  0.6
2006 Nekrutenko A, He J. Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames. Trends in Genetics : Tig. 22: 645-8. PMID 17034899 DOI: 10.1016/j.tig.2006.09.012  0.6
2006 Wilson C, Goetting-Minesky P, Nekrutenko A. mNSC1 shows no evidence of protein-coding capacity. Gene. 370: 83-5. PMID 16476528 DOI: 10.1016/j.gene.2005.11.016  0.6
2006 Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. Bmc Bioinformatics. 7: 46. PMID 16441884 DOI: 10.1186/1471-2105-7-46  0.6
2005 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. Galaxy: a platform for interactive large-scale genome analysis. Genome Research. 15: 1451-5. PMID 16169926 DOI: 10.1101/gr.4086505  0.6
2005 Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD. Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. Plos Genetics. 1: e18. PMID 16110341 DOI: 10.1371/journal.pgen.0010018  0.6
2004 Nekrutenko A. Identification of novel exons from rat-mouse comparisons. Journal of Molecular Evolution. 59: 703-8. PMID 15693626 DOI: 10.1007/s00239-004-2653-4  0.6
2004 Miller W, Makova KD, Nekrutenko A, Hardison RC. Comparative genomics. Annual Review of Genomics and Human Genetics. 5: 15-56. PMID 15485342 DOI: 10.1146/annurev.genom.5.061903.180057  0.6
2004 Nekrutenko A. Reconciling the numbers: ESTs versus protein-coding genes. Molecular Biology and Evolution. 21: 1278-82. PMID 15034132 DOI: 10.1093/molbev/msh125  0.6
2003 Li WH, Gu Z, Cavalcanti AR, Nekrutenko A. Detection of gene duplications and block duplications in eukaryotic genomes. Journal of Structural and Functional Genomics. 3: 27-34. PMID 12836682 DOI: 10.1023/A:1022644628861  0.6
2003 Nekrutenko A, Chung WY, Li WH. ETOPE: Evolutionary test of predicted exons. Nucleic Acids Research. 31: 3564-7. PMID 12824366 DOI: 10.1093/nar/gkg597  0.6
2003 Nekrutenko A, Chung WY, Li WH. An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends in Genetics : Tig. 19: 306-10. PMID 12801721 DOI: 10.1016/S0168-9525(03)00114-8  0.6
2003 Thomas MA, Weston B, Joseph M, Wu W, Nekrutenko A, Tonellato PJ. Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes. Molecular Biology and Evolution. 20: 964-8. PMID 12716985 DOI: 10.1093/molbev/msg110  0.6
2003 Nekrutenko A, Baker RJ. Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids. Gene. 306: 99-103. PMID 12657471 DOI: 10.1016/S0378-1119(03)00427-X  0.6
2002 Kaessmann H, Zöllner S, Nekrutenko A, Li WH. Signatures of domain shuffling in the human genome. Genome Research. 12: 1642-50. PMID 12421750 DOI: 10.1101/gr.520702  0.6
2002 Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Research. 12: 198-202. PMID 11779845 DOI: 10.1101/gr.200901  0.6
2001 Nekrutenko A, Li WH. Transposable elements are found in a large number of human protein-coding genes Trends in Genetics. 17: 619-621. PMID 11672845 DOI: 10.1016/S0168-9525(01)02445-3  0.6
2001 Li WH, Gu Z, Wang H, Nekrutenko A. Evolutionary analyses of the human genome. Nature. 409: 847-9. PMID 11237007 DOI: 10.1038/35057039  0.6
2001 Adkins RM, Nekrutenko A, Li WH. Bushbaby growth hormone is much more similar to nonprimate growth hormones than to rhesus monkey and human growth hormones. Molecular Biology and Evolution. 18: 55-60. PMID 11141192  0.6
2000 Gu Z, Wang H, Nekrutenko A, Li WH. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene. 259: 81-8. PMID 11163965 DOI: 10.1016/S0378-1119(00)00434-0  0.6
2000 Nekrutenko A, Li WH. Assessment of compositional heterogeneity within and between eukaryotic genomes Genome Research. 10: 1986-1995. PMID 11116093 DOI: 10.1101/gr.10.12.1986  0.6
2000 Makova KD, Nekrutenko A, Baker RJ. Evolution of microsatellite alleles in four species of mice (genus Apodemus). Journal of Molecular Evolution. 51: 166-72. PMID 10948273 DOI: 10.1007/s002390010077  0.6
2000 Nekrutenko A, Makova KD, Baker RJ. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. Gene. 249: 47-51. PMID 10831837 DOI: 10.1016/S0378-1119(00)00168-2  0.6
1999 Nekrutenko A, Makova KD, Chesser RK, Baker RJ. Representational difference analysis to distinguish cryptic species. Molecular Ecology. 8: 1235-8. PMID 10447864 DOI: 10.1046/j.1365-294X.1999.00682.x  0.6
1998 Nekrutenko A, Hillis DM, Patton JC, Bradley RD, Baker RJ. Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family. Molecular Biology and Evolution. 15: 1674-84. PMID 9866202  0.6
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