| Year |
Citation |
Score |
| 2024 |
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, ... ... Nekrutenko A, et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology. PMID 38278971 DOI: 10.1038/s41587-023-02100-3 |
0.771 |
|
| 2023 |
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, ... ... Nekrutenko A, et al. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. Biorxiv : the Preprint Server For Biology. PMID 37425881 DOI: 10.1101/2023.06.28.546576 |
0.78 |
|
| 2022 |
Lucaci AG, Zehr JD, Shank SD, Bouvier D, Ostrovsky A, Mei H, Nekrutenko A, Martin DP, Kosakovsky Pond SL. RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis. Plos One. 17: e0275623. PMID 36322581 DOI: 10.1371/journal.pone.0275623 |
0.358 |
|
| 2022 |
Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, ... ... Nekrutenko A, et al. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genomics. 2. PMID 35199087 DOI: 10.1016/j.xgen.2021.100085 |
0.356 |
|
| 2021 |
Mei H, Kosakovsky Pond S, Nekrutenko A. Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses. Molecular Biology and Evolution. PMID 34505896 DOI: 10.1093/molbev/msab265 |
0.345 |
|
| 2021 |
Mei H, Nekrutenko A. Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses. Biorxiv : the Preprint Server For Biology. PMID 34159333 DOI: 10.1101/2021.06.14.448413 |
0.344 |
|
| 2021 |
Larivière D, Wickham L, Keiler K, Nekrutenko A. Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses. Bmc Microbiology. 21: 168. PMID 34090324 DOI: 10.1186/s12866-021-02184-4 |
0.803 |
|
| 2021 |
Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, ... ... Nekrutenko A, et al. Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. Biorxiv : the Preprint Server For Biology. PMID 33791701 DOI: 10.1101/2021.03.25.437046 |
0.361 |
|
| 2021 |
Ostrovsky A, Hillman-Jackson J, Bouvier D, Clements D, Afgan E, Blankenberg D, Schatz MC, Nekrutenko A, Taylor J, Team TG, Lariviere D. Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update. Current Protocols. 1: e31. PMID 33583104 DOI: 10.1002/cpz1.31 |
0.807 |
|
| 2021 |
Povysil G, Heinzl M, Salazar R, Stoler N, Nekrutenko A, Tiemann-Boege I. Increased yields of duplex sequencing data by a series of quality control tools. Nar Genomics and Bioinformatics. 3: lqab002. PMID 33575654 DOI: 10.1093/nargab/lqab002 |
0.302 |
|
| 2020 |
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, ... ... Nekrutenko A, et al. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. Gigascience. 9. PMID 33079170 DOI: 10.1093/gigascience/giaa102 |
0.703 |
|
| 2020 |
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, et al. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. Plos Pathogens. 16: e1008643. PMID 32790776 DOI: 10.1371/Journal.Ppat.1008643 |
0.782 |
|
| 2020 |
Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research. PMID 32585001 DOI: 10.1093/Nar/Gkaa554 |
0.714 |
|
| 2020 |
Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research. PMID 32479607 DOI: 10.1093/nar/gkaa434 |
0.693 |
|
| 2020 |
Stoler N, Arbeithuber B, Povysil G, Heinzl M, Salazar R, Makova KD, Tiemann-Boege I, Nekrutenko A. Family reunion via error correction: an efficient analysis of duplex sequencing data. Bmc Bioinformatics. 21: 96. PMID 32131723 DOI: 10.1186/S12859-020-3419-8 |
0.654 |
|
| 2019 |
Zaidi AA, Wilton PR, Su MS, Paul IM, Arbeithuber B, Anthony K, Nekrutenko A, Nielsen R, Makova KD. Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. Proceedings of the National Academy of Sciences of the United States of America. PMID 31757848 DOI: 10.1073/Pnas.1906331116 |
0.585 |
|
| 2019 |
Mei H, Arbeithuber B, Cremona MA, DeGiorgio M, Nekrutenko A. A high resolution view of adaptive event dynamics in a plasmid. Genome Biology and Evolution. PMID 31539047 DOI: 10.1093/Gbe/Evz197 |
0.321 |
|
| 2019 |
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. HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies. Molecular Biology and Evolution. PMID 31504749 DOI: 10.1093/Molbev/Msz197 |
0.35 |
|
| 2019 |
Tyryshkina A, Coraor N, Nekrutenko A. Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage. Bioinformatics (Oxford, England). PMID 30698642 DOI: 10.1093/Bioinformatics/Btz054 |
0.373 |
|
| 2019 |
Larivière D, Don PK, Wickham L, Chiaromonte F, Keiler K, Nekrutenko A. Transposon insertion sequencing analysis in Galaxy F1000research. 8. DOI: 10.7490/F1000Research.1117141.1 |
0.413 |
|
| 2019 |
Craig S, Blankenberg D, Parodi A, Paul I, Birch L, Savage J, Marini M, Stokes J, Nekrutenko A, Reimherr M, Chiaromonte F, Makova K. 172. Child Weight Gain Trajectories Associated With Oral Microbiota Composition Biological Psychiatry. 85: S71. DOI: 10.1016/J.Biopsych.2019.03.186 |
0.703 |
|
| 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 |
0.72 |
|
| 2018 |
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, ... ... Nekrutenko A, et al. Community-Driven Data Analysis Training for Biology. Cell Systems. 6: 752-758.e1. PMID 29953864 DOI: 10.1016/J.Cels.2018.05.012 |
0.76 |
|
| 2018 |
Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J. Practical Computational Reproducibility in the Life Sciences. Cell Systems. 6: 631-635. PMID 29953862 DOI: 10.1016/J.Cels.2018.03.014 |
0.353 |
|
| 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 |
0.715 |
|
| 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 |
0.686 |
|
| 2018 |
Čech M, Chilton J, Grüning B, Rasche E, Soranzo N, Nekrutenko A, Bouvier D, Blankenberg D, Coraor N. Galaxy tool shed: tool discovery and repository management F1000research. 7. DOI: 10.7490/F1000Research.1115596.1 |
0.677 |
|
| 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 |
0.429 |
|
| 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 |
0.679 |
|
| 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 |
0.719 |
|
| 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 |
0.716 |
|
| 2016 |
Turaga N, Freeberg MA, Baker D, Chilton J, Team G, Nekrutenko A, Taylor J. A guide and best practices for R/Bioconductor tool integration in Galaxy F1000research. 5: 2757. DOI: 10.12688/F1000Research.9821.1 |
0.376 |
|
| 2016 |
Farkas CA, Fuentes F, Rebolledo B, Makova K, Nekrutenko A, Castro A, Pincheira R. Abstract B17: Role of Sall2 transcription factor under genotoxic stress: A transcriptomic approach Cancer Research. 76. DOI: 10.1158/1538-7445.Fbcr15-B17 |
0.557 |
|
| 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 |
0.747 |
|
| 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 |
0.735 |
|
| 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 |
0.704 |
|
| 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 |
0.779 |
|
| 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 |
0.708 |
|
| 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 |
0.37 |
|
| 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 |
0.317 |
|
| 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 |
0.366 |
|
| 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 |
0.322 |
|
| 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 |
0.421 |
|
| 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 |
0.726 |
|
| 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 |
0.323 |
|
| 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 |
0.644 |
|
| 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 |
0.631 |
|
| 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 |
0.723 |
|
| 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 |
0.63 |
|
| 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 |
0.727 |
|
| 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 |
0.371 |
|
| 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 |
0.424 |
|
| 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 |
0.713 |
|
| 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 |
0.484 |
|
| 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 |
0.665 |
|
| 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 |
0.75 |
|
| 2010 |
Afgan E, Baker D, Nekrutenko A, Taylor J. The elastic analysis with galaxy on the cloud Genome Biology. 11: 2. DOI: 10.1186/Gb-2010-11-S1-P2 |
0.441 |
|
| 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 |
0.335 |
|
| 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 |
0.794 |
|
| 2008 |
Lazarus R, Taylor J, Qiu W, Nekrutenko A. Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench. Summit On Translational Bioinformatics. 2008: 56-60. PMID 21347127 |
0.355 |
|
| 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 |
0.776 |
|
| 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 |
0.752 |
|
| 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 |
0.73 |
|
| 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 |
0.802 |
|
| 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 |
0.765 |
|
| 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 |
0.327 |
|
| 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 |
0.58 |
|
| 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 |
0.742 |
|
| 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 |
0.762 |
|
| 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 |
0.411 |
|
| 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 |
0.632 |
|
| 2004 |
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, ... ... Nekrutenko A, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426 |
0.664 |
|
| 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 |
0.373 |
|
| 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 |
0.376 |
|
| 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 |
0.38 |
|
| 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 |
0.424 |
|
| 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 |
0.552 |
|
| 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 |
0.308 |
|
| 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 |
0.608 |
|
| 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 |
0.345 |
|
| 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 |
0.405 |
|
| 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 |
0.358 |
|
| 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 |
0.394 |
|
| 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 |
0.663 |
|
| 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 |
0.687 |
|
| 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_1.X |
0.631 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A025894 |
0.623 |
|
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