Publications by authors named "Kateryna D Makova"

78Publications

Dynamic evolution of great ape Y chromosomes.

Proc Natl Acad Sci U S A 2020 Oct 5;117(42):26273-26280. Epub 2020 Oct 5.

Department of Biology, Penn State University, University Park, PA 16802;

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http://dx.doi.org/10.1073/pnas.2001749117DOI Listing
October 2020

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.

Mol Biol Evol 2020 Jul 28. Epub 2020 Jul 28.

Center for Medical Genomics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1093/molbev/msaa194DOI Listing
July 2020

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

BMC Bioinformatics 2020 Mar 4;21(1):96. Epub 2020 Mar 4.

Graduate Program in Bioinformatics and Genomics, The Huck Institutes for Life Sciences, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1186/s12859-020-3419-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057607PMC
March 2020

Pronounced somatic bottleneck in mitochondrial DNA of human hair.

Philos Trans R Soc Lond B Biol Sci 2020 01 2;375(1790):20190175. Epub 2019 Dec 2.

Department of Biology, Penn State University, University Park, PA, USA.

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http://dx.doi.org/10.1098/rstb.2019.0175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939377PMC
January 2020

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes.

PLoS Genet 2019 09 16;15(9):e1008369. Epub 2019 Sep 16.

Bioinformatics and Genomics Graduate Program, The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, PA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6772104PMC
September 2019

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.

BMC Genomics 2019 Aug 9;20(1):641. Epub 2019 Aug 9.

Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1186/s12864-019-5996-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688218PMC
August 2019

Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.

Bioinformatics 2019 11;35(22):4809-4811

Department of Biology, The Pennsylvania State University, State College, PA 16802, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853708PMC
November 2019

Functional data analysis for computational biology.

Bioinformatics 2019 09;35(17):3211-3213

Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736445PMC
September 2019

Investigating mitonuclear interactions in human admixed populations.

Nat Ecol Evol 2019 02 14;3(2):213-222. Epub 2019 Jan 14.

Department of Biology, The Pennsylvania State University, University Park, PA, USA.

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http://www.nature.com/articles/s41559-018-0766-1
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http://dx.doi.org/10.1038/s41559-018-0766-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925600PMC
February 2019

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.

Nat Commun 2018 11 2;9(1):4601. Epub 2018 Nov 2.

Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16802, USA.

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http://www.nature.com/articles/s41467-018-06910-x
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http://dx.doi.org/10.1038/s41467-018-06910-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214943PMC
November 2018

Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives.

Genes (Basel) 2018 Feb 26;9(3). Epub 2018 Feb 26.

Department of Biochemistry & Molecular Biology, Forensic Science Program, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.3390/genes9030124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867845PMC
February 2018

Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent.

Evol Appl 2017 09 22;10(8):784-791. Epub 2017 Jun 22.

Department of Biological Sciences and Museum Texas Tech University Lubbock TX USA.

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http://dx.doi.org/10.1111/eva.12475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680428PMC
September 2017

Y and W Chromosome Assemblies: Approaches and Discoveries.

Trends Genet 2017 04 22;33(4):266-282. Epub 2017 Feb 22.

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Genome Sciences Institute and Center for Medical Genomics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2017.01.008DOI Listing
April 2017

Streamlined analysis of duplex sequencing data with Du Novo.

Genome Biol 2016 08 26;17(1):180. Epub 2016 Aug 26.

Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1186/s13059-016-1039-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000403PMC
August 2016

Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.

DNA Res 2016 Dec 31;23(6):547-559. Epub 2016 Jul 31.

Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria

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http://dx.doi.org/10.1093/dnares/dsw038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144678PMC
December 2016

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

Mol Biol Evol 2016 10 12;33(10):2744-58. Epub 2016 Jul 12.

Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University Huck Institute of Genome Sciences, Pennsylvania State University

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http://dx.doi.org/10.1093/molbev/msw139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026258PMC
October 2016

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.

PLoS Comput Biol 2016 06 16;12(6):e1004956. Epub 2016 Jun 16.

Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911145PMC
June 2016

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

Genome Res 2015 May 30;25(5):736-49. Epub 2015 Mar 30.

Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Science Institute at the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;

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http://dx.doi.org/10.1101/gr.185892.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417121PMC
May 2015

The effects of chromatin organization on variation in mutation rates in the genome.

Nat Rev Genet 2015 Apr 3;16(4):213-23. Epub 2015 Mar 3.

Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1038/nrg3890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500049PMC
April 2015

Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes.

PLoS Genet 2014 Jul 17;10(7):e1004498. Epub 2014 Jul 17.

Department of Pathology, Gittlen Cancer Research Foundation, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America; Center for Medical Genomics, Penn State University, University Park, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102424PMC
July 2014

Genomic landscape of human, bat, and ex vivo DNA transposon integrations.

Mol Biol Evol 2014 Jul 22;31(7):1816-32. Epub 2014 Apr 22.

Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Biology, Penn State University, University Park, PA

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http://dx.doi.org/10.1093/molbev/msu138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069622PMC
July 2014

Segmenting the human genome based on states of neutral genetic divergence.

Proc Natl Acad Sci U S A 2013 Sep 19;110(36):14699-704. Epub 2013 Aug 19.

Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.1221792110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767554PMC
September 2013

Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells.

G3 (Bethesda) 2013 Mar 1;3(3):451-63. Epub 2013 Mar 1.

Intercollege Graduate Program in Genetics, Huck Institutes of Life Sciences, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA.

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http://dx.doi.org/10.1534/g3.112.005173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583453PMC
March 2013

Gene survival and death on the human Y chromosome.

Mol Biol Evol 2013 Apr 4;30(4):781-7. Epub 2012 Dec 4.

Statistics Department, University of California-Berkeley, California, USA.

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http://dx.doi.org/10.1093/molbev/mss267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603307PMC
April 2013

Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion.

PLoS Genet 2012 9;8(8):e1002842. Epub 2012 Aug 9.

Tulane Cancer Center, Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1002842
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http://dx.doi.org/10.1371/journal.pgen.1002842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415434PMC
December 2012

A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

Genome Res 2012 Jun 28;22(6):993-1005. Epub 2012 Mar 28.

The Integrative Biosciences Graduate Program, Bioinformatics and Genomics Option, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1101/gr.134395.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371707PMC
June 2012

Genome analyses substantiate male mutation bias in many species.

Bioessays 2011 Dec 18;33(12):938-45. Epub 2011 Oct 18.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, USA.

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http://doi.wiley.com/10.1002/bies.201100091
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http://dx.doi.org/10.1002/bies.201100091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600401PMC
December 2011

A matter of life or death: how microsatellites emerge in and vanish from the human genome.

Genome Res 2011 Dec 12;21(12):2038-48. Epub 2011 Oct 12.

Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.122937.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227094PMC
December 2011

Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes.

Evolution 2011 Oct 20;65(10):2800-15. Epub 2011 Jun 20.

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2011.01337.xDOI Listing
October 2011

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

Genome Biol 2011 23;12(6):R59. Epub 2011 Jun 23.

The Huck Institutes of Life Sciences and Department of Biology, Penn State University, 305 Wartik Lab, University Park, PA 16802, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-6-r59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218847PMC
December 2012

A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis.

Biol Direct 2011 Jun 13;6:30. Epub 2011 Jun 13.

Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, 2000, South Africa.

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http://dx.doi.org/10.1186/1745-6150-6-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142252PMC
June 2011

A genome-wide view of mutation rate co-variation using multivariate analyses.

Genome Biol 2011 22;12(3):R27. Epub 2011 Mar 22.

Center for Medical Genomics, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-r27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129677PMC
January 2012

Strong purifying selection at genes escaping X chromosome inactivation.

Mol Biol Evol 2010 Nov 9;27(11):2446-50. Epub 2010 Jun 9.

Center for Medical Genomics, Pennsylvania State University, University Park, USA.

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http://dx.doi.org/10.1093/molbev/msq143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981488PMC
November 2010

The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.

Genome Res 2010 May 10;20(5):600-13. Epub 2010 Mar 10.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.099044.109
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http://dx.doi.org/10.1101/gr.099044.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860162PMC
May 2010

Genomic analyses of sex chromosome evolution.

Annu Rev Genomics Hum Genet 2009 ;10:333-54

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.annualreviews.org/doi/10.1146/annurev-genom-08290
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http://dx.doi.org/10.1146/annurev-genom-082908-150105DOI Listing
October 2009

Evolution and survival on eutherian sex chromosomes.

PLoS Genet 2009 Jul 17;5(7):e1000568. Epub 2009 Jul 17.

Department of Biology, Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704370PMC
July 2009

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.

Genome Res 2009 Jul 5;19(7):1153-64. Epub 2009 Jun 5.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.088922.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704434PMC
July 2009

Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes.

Genome Biol 2009 28;10(1):R10. Epub 2009 Jan 28.

Center for Comparative Genomics and Bioinformatics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2009-10-1-r10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687787PMC
September 2009

Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee.

J Mol Evol 2009 Feb 14;68(2):134-44. Epub 2009 Jan 14.

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://link.springer.com/10.1007/s00239-008-9189-y
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http://dx.doi.org/10.1007/s00239-008-9189-yDOI Listing
February 2009

Horse domestication and conservation genetics of Przewalski's horse inferred from sex chromosomal and autosomal sequences.

Mol Biol Evol 2009 Jan 17;26(1):199-208. Epub 2008 Oct 17.

Department of Biology, The Pennsylvania State University, University Park, USA.

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http://dx.doi.org/10.1093/molbev/msn239DOI Listing
January 2009

Human-macaque comparisons illuminate variation in neutral substitution rates.

Genome Biol 2008 Apr 30;9(4):R76. Epub 2008 Apr 30.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2008-9-4-r76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643947PMC
April 2008

The genome-wide determinants of human and chimpanzee microsatellite evolution.

Genome Res 2008 Jan 21;18(1):30-8. Epub 2007 Nov 21.

Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.7113408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134767PMC
January 2008

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PLoS Comput Biol 2007 Sep 27;3(9):1772-82. Epub 2007 Jul 27.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0030176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976337PMC
September 2007

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Genome Res 2007 Jun;17(6):960-4

Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5578007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891355PMC
June 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Genomic environment predicts expression patterns on the human inactive X chromosome.

PLoS Genet 2006 Sep 3;2(9):e151. Epub 2006 Aug 3.

Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1584270PMC
September 2006

Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates.

J Mol Evol 2006 Oct 4;63(4):537-44. Epub 2006 Sep 4.

Department of Biology, Center for Comparative Genomics and Bioinformatics, 518A Mueller Lab, Penn State University, University Park, PA 16803, USA.

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http://link.springer.com/10.1007/s00239-005-0308-8
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http://dx.doi.org/10.1007/s00239-005-0308-8DOI Listing
October 2006

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

BMC Bioinformatics 2006 Jan 27;7:46. Epub 2006 Jan 27.

Department of Biology, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/1471-2105-7-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1403810PMC
January 2006

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.

Mol Biol Evol 2006 Mar 9;23(3):565-73. Epub 2005 Nov 9.

Department of Computer Science and Engineering, Penn State University, USA.

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http://academic.oup.com/mbe/article/23/3/565/1110290/Strong-
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http://dx.doi.org/10.1093/molbev/msj060DOI Listing
March 2006

Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay.

PLoS Genet 2005 Aug 12;1(2):e18. Epub 2005 Aug 12.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pgen.0010018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1186735PMC
August 2005

Comparative genomics.

Annu Rev Genomics Hum Genet 2004 ;5:15-56

The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1146/annurev.genom.5.061903.180057DOI Listing
November 2004

Insertions and deletions are male biased too: a whole-genome analysis in rodents.

Genome Res 2004 Apr;14(4):567-73

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1971104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383300PMC
April 2004

Divergence in the spatial pattern of gene expression between human duplicate genes.

Genome Res 2003 Jul;13(7):1638-45

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.1133803
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http://dx.doi.org/10.1101/gr.1133803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403737PMC
July 2003

Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum.

Nature 2002 Jul;418(6895):323-6

Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0425, USA.

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http://dx.doi.org/10.1038/nature00836DOI Listing
July 2002

Strong male-driven evolution of DNA sequences in humans and apes.

Nature 2002 Apr;416(6881):624-6

Department of Ecology and Evolution, University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.1038/416624aDOI Listing
April 2002

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.

Genome Res 2002 Jan;12(1):198-202

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.200901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155263PMC
January 2002