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1

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

Blankenberg, D., Coraor, N., Von Kuster, G., Taylor, J., Nekrutenko, A.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

2

The anatomy of successful computational biology software

Altschul, Stephen, Demchak, Barry, Durbin, Richard, Gentleman, Robert, Krzywinski, Martin, Li, Heng, Nekrutenko, Anton, Robinson, James, Rasband, Wayne, Taylor, James, Trapnell, Cole

Journal:

Nature Biotechnology

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

3

Evolutionary analyses of the human genome

Li, Wen-Hsiung, Gu, Zhenglong, Wang, Haidong, Nekrutenko, Anton

Journal:

Year:

2001

Language:

english

File:

PDF, 119 KB

english, 2001

4

NGS analyses by visualization with Trackster

Goecks, Jeremy, Coraor, Nate, Team, The Galaxy, Nekrutenko, Anton, Taylor, James

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 663 KB

english, 2012

5

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,

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 753 KB

english, 2014

6

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

Nekrutenko, Anton, Team, Galaxy, Goecks, Jeremy, Taylor, James, Blankenberg, Daniel

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 466 KB

english, 2018

7

Ten Simple Rules for Reproducible Computational Research

Sandve, Geir Kjetil, Nekrutenko, Anton, Taylor, James, Hovig, Eivind, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 131 KB

english, 2013

8

Practical Computational Reproducibility in the Life Sciences

Grüning, Björn, Chilton, John, Köster, Johannes, Dale, Ryan, Soranzo, Nicola, van den Beek, Marius, Goecks, Jeremy, Backofen, Rolf, Nekrutenko, Anton, Taylor, James

Journal:

Year:

2018

Language:

english

File:

PDF, 431 KB

english, 2018

9

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., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S

Journal:

Genome Research

Year:

2007

Language:

english

File:

PDF, 1.14 MB

english, 2007

10

Windshield splatter analysis with the Galaxy metagenomic pipeline

Kosakovsky Pond, S., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W.-Y., Taylor, J., Nekrutenko, A.

Journal:

Genome Research

Year:

2009

Language:

english

File:

PDF, 1.05 MB

english, 2009

11

[IEEE 2012 IEEE 8th International Conference on E-Science (e-Science) - Chicago, IL, USA (2012.10.8-2012.10.12)] 2012 IEEE 8th International Conference on E-Science - Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses

Goecks, Jeremy, Team, The Galaxy, Nekrutenko, Anton, Taylor, James

Year:

2012

Language:

english

File:

PDF, 1.81 MB

english, 2012

12

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function

Szklarczyk, R., Heringa, J., Pond, S. K., Nekrutenko, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 634 KB

english, 2007

13

Evolution of Microsatellite Alleles in Four Species of Mice (GenusApodemus)

Kateryna D. Makova, Anton Nekrutenko, Robert J. Baker

Journal:

Journal of Molecular Evolution

Year:

2000

Language:

english

File:

PDF, 374 KB

english, 2000

14

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, K. D., Hardison, R. C., Nekrutenko, A.

Journal:

Genome Research

Year:

2007

Language:

english

File:

PDF, 612 KB

english, 2007

15

Galaxy CloudMan: delivering cloud compute clusters

Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 545 KB

english, 2010

16

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network

Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko, Kateryna D Makova

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 535 KB

english, 2006

17

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

Anton Nekrutenko, Kateryna D. Makova, Robert J. Baker

Journal:

Year:

2000

Language:

english

File:

PDF, 228 KB

english, 2000

18

The shrinkage of high-tenacity ftorlon fiber

N. D. Nekrutenko, A. A. Geller, B. E. Geller

Journal:

Fibre Chemistry

Year:

1975

Language:

english

File:

PDF, 123 KB

english, 1975

19

Family reunion via error correction: an efficient analysis of duplex sequencing data

Stoler, Nicholas, Arbeithuber, Barbara, Povysil, Gundula, Heinzl, Monika, Salazar, Renato, Makova, Kateryna D, Tiemann-Boege, Irene, Nekrutenko, Anton

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.20 MB

2020

20

Representational difference analysis to distinguish cryptic species

Anton Nekrutenko, Kateryna D. Makova, Ronald K. Chesser, Robert J. Baker

Journal:

Molecular Ecology

Year:

1999

Language:

english

File:

PDF, 286 KB

english, 1999

21

The elastic analysis with galaxy on the cloud

Enis Afgan, Dannon Baker, Anton Nekrutenko, James Taylor

Journal:

Year:

2010

Language:

english

File:

PDF, 165 KB

english, 2010

22

The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study

Journal:

Genome Research

Year:

2002

Language:

english

File:

PDF, 420 KB

english, 2002

23

Reconciling the Numbers: ESTs Versus Protein-Coding Genes

Journal:

Molecular Biology and Evolution

Year:

2004

Language:

english

File:

PDF, 148 KB

english, 2004

24

High-Resolution Mapping of Evolutionary Trajectories in a Phage

Dickins, B., Nekrutenko, A.

Journal:

Genome Biology and Evolution

Year:

2010

Language:

english

File:

PDF, 1.81 MB

english, 2010

25

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Jalili, Vahid, Afgan, Enis, Gu, Qiang, Clements, Dave, Blankenberg, Daniel, Goecks, Jeremy, Taylor, James, Nekrutenko, Anton

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 75 KB

2020

26

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.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 2.59 MB

english, 2013

27

Streamlined analysis of duplex sequencing data with Du Novo

Stoler, Nicholas, Arbeithuber, Barbara, Guiblet, Wilfried, Makova, Kateryna D., Nekrutenko, Anton

Journal:

Year:

2016

Language:

english

File:

PDF, 1.43 MB

english, 2016

28

Wheels within Wheels: Clues to the Evolution of the Gnas and Gnal Loci

Wadhawan, S., Dickins, B., Nekrutenko, A.

Journal:

Molecular Biology and Evolution

Year:

2008

Language:

english

File:

PDF, 865 KB

english, 2008

29

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.

Journal:

Molecular Biology and Evolution

Year:

1998

Language:

english

File:

PDF, 290 KB

english, 1998

30

mNSC1 shows no evidence of protein-coding capacity

Christina Wilson, Paula Goetting-Minesky, Anton Nekrutenko

Journal:

Year:

2006

Language:

english

File:

PDF, 84 KB

english, 2006

31

Making whole genome multiple alignments usable for biologists

Blankenberg, D., Taylor, J., Nekrutenko, A.

Journal:

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

32

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Craig, Sarah J. C., Blankenberg, Daniel, Parodi, Alice Carla Luisa, Paul, Ian M., Birch, Leann L., Savage, Jennifer S., Marini, Michele E., Stokes, Jennifer L., Nekrutenko, Anton, Reimherr, Matthew, C

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.71 MB

english, 2018

33

Identification of Novel Exons from Rat–Mouse Comparisons

Anton Nekrutenko

Journal:

Journal of Molecular Evolution

Year:

2004

Language:

english

File:

PDF, 153 KB

english, 2004

34

A reference model for deploying applications in virtualized environments

Enis Afgan, Dannon Baker, the Galaxy Team, Anton Nekrutenko, James Taylor

Journal:

Concurrency and Computation: Practice and Experience

Year:

2012

Language:

english

File:

PDF, 366 KB

english, 2012

35

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes

Chung, Wen-Yu, Wadhawan, Samir, Szklarczyk, Radek, Pond, Sergei Kosakovsky, Nekrutenko, Anton

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 227 KB

english, 2007

36

A high resolution view of adaptive event dynamics in a plasmid

Mei, Han, Arbeithuber, Barbara, Cremona, Marzia A, DeGiorgio, Michael, Nekrutenko, Anton, Li, Wen-Hsiung

Journal:

Genome Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 398 KB

english, 2019

37

’Gynandromorphic Effect‘ and the Optical Nature of Hidden Wing-pattern in Gonepteryx rhamni L. (Lepidoptera, Pieridae)

NEKRUTENKO, YURI P.

Journal:

Year:

1965

File:

PDF, 397 KB

1965

38

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Jeremy Goecks, Anton Nekrutenko, James Taylor

Journal:

Year:

2010

Language:

english

File:

PDF, 2.20 MB

english, 2010

39

Acetate fibre modified with dibutylphosphite

N. D. Nekrutenko, A. A. Geller, M. V. Polovnikova, B. E. Geller

Journal:

Fibre Chemistry

Year:

1975

Language:

english

File:

PDF, 83 KB

english, 1975

40

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.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 949 KB

english, 2009

41

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.

Journal:

Molecular Biology and Evolution

Year:

2001

Language:

english

File:

PDF, 204 KB

english, 2001

42

Detection of gene duplications and block duplications in eukaryotic genomes

Wen-Hsiung Li, Zhenglong Gu, Andre R. O. Cavalcanti, Anton Nekrutenko

Journal:

Journal of Structural and Functional Genomics

Year:

2003

Language:

english

File:

PDF, 77 KB

english, 2003

43

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Jalili, Vahid, Afgan, Enis, Gu, Qiang, Clements, Dave, Blankenberg, Daniel, Goecks, Jeremy, Taylor, James, Nekrutenko, Anton

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 1.86 MB

2020

44

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

Zhenglong Gu, Haidong Wang, Anton Nekrutenko, Wen-Hsiung Li

Journal:

Year:

2000

Language:

english

File:

PDF, 339 KB

english, 2000

45

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

Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian M Paul, James Taylor, Kateryna D Makova, Anton Nekrutenko

Journal:

Year:

2011

Language:

english

File:

PDF, 915 KB

english, 2011

46

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., Kosakovsky Pond, S. L., Nekrutenko, A., Makova, K. D.

Journal:

Genome Biology and Evolution

Year:

2011

Language:

english

File:

PDF, 516 KB

english, 2011

47

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

Dickins, Benjamin, Rebolledo-Jaramillo, Boris, Su, Marcia Shu-Wei, Paul, Ian M., Blankenberg, Daniel, Stoler, Nicholas, Makova, Kateryna D., Nekrutenko, Anton

Journal:

Year:

2014

Language:

english

File:

PDF, 2.62 MB

english, 2014

48

172. Child Weight Gain Trajectories Associated With Oral Microbiota Composition

Craig, Sarah, Blankenberg, Daniel, Parodi, Alice, Paul, Ian, Birch, Leann, Savage, Jennifer, Marini, Michele, Stokes, Jennifer, Nekrutenko, Anton, Reimherr, Matthew, Chiaromonte, Francesca, Makova, Ka

Journal:

Biological Psychiatry

Year:

2019

Language:

english

File:

PDF, 45 KB

english, 2019

49

Web-based visual analysis for high-throughput genomics

Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor

Journal:

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

50

COMPARATIVE GENOMICS

Miller, Webb, Makova, Kateryna D., Nekrutenko, Anton, Hardison, Ross C.

Journal:

Annual Review of Genomics and Human Genetics

Year:

2004

Language:

english

File:

PDF, 851 KB

english, 2004

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