N. D. Nekrutenko: search on Z-Library

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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

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

3

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

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

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

7

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

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

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

10

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

11

Degree of orientation stretching for ftorlon fibre determined by strain gauging

N. D. Nekrutenko, A. A. Geller, B. Kh. Yunusov, B. É. Geller

Journal:

Fibre Chemistry

Year:

1976

Language:

english

File:

PDF, 128 KB

english, 1976

12

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

13

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

14

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

15

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

16

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

17

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames

Anton Nekrutenko, Jianbin He

Journal:

Trends in Genetics

Year:

2006

Language:

english

File:

PDF, 610 KB

english, 2006

18

Transposable elements are found in a large number of human protein-coding genes

Anton Nekrutenko, Wen-Hsiung Li

Journal:

Trends in Genetics

Year:

2001

Language:

english

File:

PDF, 57 KB

english, 2001

19

An evolutionary approach reveals a high protein-coding capacity of the human genome

Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li

Journal:

Trends in Genetics

Year:

2003

Language:

english

File:

PDF, 447 KB

english, 2003

20

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

21

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

22

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

Nekrutenko, Anton, Taylor, James

Journal:

Nature Reviews Genetics

Year:

2012

Language:

english

File:

PDF, 685 KB

english, 2012

23

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

24

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

25

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

26

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

27

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

Anton Nekrutenko, Robert J. Baker

Journal:

Year:

2003

Language:

english

File:

PDF, 206 KB

english, 2003

28

’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

29

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

30

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

31

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

32

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

33

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

34

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

35

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

36

Erratum: 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:

2014

Language:

english

File:

PDF, 153 KB

english, 2014

37

Manipulation of FASTQ data with Galaxy

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

Journal:

Year:

2010

Language:

english

File:

PDF, 75 KB

english, 2010

38

[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

39

Online Resources for Genomic Analysis Using High-Throughput Sequencing

Blankenberg, Daniel, Taylor, James, Nekrutenko, Anton

Journal:

Cold Spring Harbor Protocols

Year:

2015

Language:

english

File:

PDF, 599 KB

english, 2015

40

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

41

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

42

ETOPE: evolutionary test of predicted exons

Journal:

Nucleic Acids Research

Year:

2003

Language:

english

File:

PDF, 268 KB

english, 2003

43

Reconciling the Numbers: ESTs Versus Protein-Coding Genes

Journal:

Molecular Biology and Evolution

Year:

2004

Language:

english

File:

PDF, 148 KB

english, 2004

44

Wrangling Galaxy's reference data

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

Journal:

Year:

2014

Language:

english

File:

PDF, 89 KB

english, 2014

45

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.

Journal:

Year:

2015

Language:

english

File:

PDF, 772 KB

english, 2015

46

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

47

Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay

Nekrutenko, Anton, Wadhawan, Samir, Goetting-Minesky, Paula, Makova, Kateryna D.

Journal:

Year:

2005

Language:

english

File:

PDF, 396 KB

english, 2005

48

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

49

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

50

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