Michael Degiorgio

Michael Degiorgio

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Michael Degiorgio

Michael Degiorgio

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A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

Genome Biol Evol 2019 Oct;11(10):3022-3034

Department of Biochemistry and Molecular Biology, The Pennsylvania State University.

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https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe
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http://dx.doi.org/10.1093/gbe/evz197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827461PMC
October 2019

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore.

Cell 2019 Oct;179(3):736-749.e15

Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193107
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http://dx.doi.org/10.1016/j.cell.2019.09.019DOI Listing
October 2019

Localizing and Classifying Adaptive Targets with Trend Filtered Regression.

Mol Biol Evol 2019 02;36(2):252-270

Departments of Biology and Statistics, Pennsylvania State University,University Park, PA.

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http://dx.doi.org/10.1093/molbev/msy205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409434PMC
February 2019

Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism.

Mol Biol Evol 2019 01;36(1):177-199

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

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http://dx.doi.org/10.1093/molbev/msy202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530816PMC
January 2019

Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity.

Genetics 2018 12 12;210(4):1429-1452. Epub 2018 Oct 12.

Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802

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http://dx.doi.org/10.1534/genetics.118.301502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283157PMC
December 2018

Patterns of Genetic Coding Variation in a Native American Population before and after European Contact.

Am J Hum Genet 2018 05 26;102(5):806-815. Epub 2018 Apr 26.

Departments of Biology and Statistics, Pennsylvania State University, University Park, PA 16801, USA; Institute for CyberScience, Pennsylvania State University, University Park, PA 16801, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297183009
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http://dx.doi.org/10.1016/j.ajhg.2018.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986697PMC
May 2018

Fast and robust detection of ancestral selective sweeps.

Mol Ecol 2017 12 12;26(24):6871-6891. Epub 2017 Dec 12.

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

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http://dx.doi.org/10.1111/mec.14416DOI Listing
December 2017

An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy.

G3 (Bethesda) 2017 02 9;7(2):671-691. Epub 2017 Feb 9.

Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802

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http://dx.doi.org/10.1534/g3.116.037168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295611PMC
February 2017

Admixture and Ancestry Inference from Ancient and Modern Samples through Measures of Population Genetic Drift.

Hum Biol 2017 01;89(1):21-46

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

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January 2017

Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

Curr Biol 2016 12 17;26(23):3190-3194. Epub 2016 Nov 17.

Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, NW Washington, DC 20560-0163, USA; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC 20521, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.09.039DOI Listing
December 2016

A time transect of exomes from a Native American population before and after European contact.

Nat Commun 2016 11 15;7:13175. Epub 2016 Nov 15.

Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, Illinois 61820, USA.

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http://dx.doi.org/10.1038/ncomms13175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116069PMC
November 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

Genomic analyses inform on migration events during the peopling of Eurasia.

Authors:
Luca Pagani Daniel John Lawson Evelyn Jagoda Alexander Mörseburg Anders Eriksson Mario Mitt Florian Clemente Georgi Hudjashov Michael DeGiorgio Lauri Saag Jeffrey D Wall Alexia Cardona Reedik Mägi Melissa A Wilson Sayres Sarah Kaewert Charlotte Inchley Christiana L Scheib Mari Järve Monika Karmin Guy S Jacobs Tiago Antao Florin Mircea Iliescu Alena Kushniarevich Qasim Ayub Chris Tyler-Smith Yali Xue Bayazit Yunusbayev Kristiina Tambets Chandana Basu Mallick Lehti Saag Elvira Pocheshkhova George Andriadze Craig Muller Michael C Westaway David M Lambert Grigor Zoraqi Shahlo Turdikulova Dilbar Dalimova Zhaxylyk Sabitov Gazi Nurun Nahar Sultana Joseph Lachance Sarah Tishkoff Kuvat Momynaliev Jainagul Isakova Larisa D Damba Marina Gubina Pagbajabyn Nymadawa Irina Evseeva Lubov Atramentova Olga Utevska François-Xavier Ricaut Nicolas Brucato Herawati Sudoyo Thierry Letellier Murray P Cox Nikolay A Barashkov Vedrana Skaro Lejla Mulahasanovic Dragan Primorac Hovhannes Sahakyan Maru Mormina Christina A Eichstaedt Daria V Lichman Syafiq Abdullah Gyaneshwer Chaubey Joseph T S Wee Evelin Mihailov Alexandra Karunas Sergei Litvinov Rita Khusainova Natalya Ekomasova Vita Akhmetova Irina Khidiyatova Damir Marjanović Levon Yepiskoposyan Doron M Behar Elena Balanovska Andres Metspalu Miroslava Derenko Boris Malyarchuk Mikhail Voevoda Sardana A Fedorova Ludmila P Osipova Marta Mirazón Lahr Pascale Gerbault Matthew Leavesley Andrea Bamberg Migliano Michael Petraglia Oleg Balanovsky Elza K Khusnutdinova Ene Metspalu Mark G Thomas Andrea Manica Rasmus Nielsen Richard Villems Eske Willerslev Toomas Kivisild Mait Metspalu

Nature 2016 Oct 21;538(7624):238-242. Epub 2016 Sep 21.

Estonian Biocentre, Tartu, Estonia.

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http://dx.doi.org/10.1038/nature19792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164938PMC
October 2016

SweepFinder2: increased sensitivity, robustness and flexibility.

Bioinformatics 2016 06 15;32(12):1895-7. Epub 2016 Feb 15.

Department of Integrative Biology, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw051DOI Listing
June 2016

Detecting recent selective sweeps while controlling for mutation rate and background selection.

Mol Ecol 2016 Jan 7;25(1):142-56. Epub 2015 Sep 7.

Departments of Integrative Biology and Statistics, University of California, Berkeley, CA, USA.

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http://biorxiv.org/content/biorxiv/early/2015/04/30/018697.f
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http://doi.wiley.com/10.1111/mec.13351
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http://dx.doi.org/10.1111/mec.13351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082542PMC
January 2016

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Authors:
Maanasa Raghavan Matthias Steinrücken Kelley Harris Stephan Schiffels Simon Rasmussen Michael DeGiorgio Anders Albrechtsen Cristina Valdiosera María C Ávila-Arcos Anna-Sapfo Malaspinas Anders Eriksson Ida Moltke Mait Metspalu Julian R Homburger Jeff Wall Omar E Cornejo J Víctor Moreno-Mayar Thorfinn S Korneliussen Tracey Pierre Morten Rasmussen Paula F Campos Peter de Barros Damgaard Morten E Allentoft John Lindo Ene Metspalu Ricardo Rodríguez-Varela Josefina Mansilla Celeste Henrickson Andaine Seguin-Orlando Helena Malmström Thomas Stafford Suyash S Shringarpure Andrés Moreno-Estrada Monika Karmin Kristiina Tambets Anders Bergström Yali Xue Vera Warmuth Andrew D Friend Joy Singarayer Paul Valdes Francois Balloux Ilán Leboreiro Jose Luis Vera Hector Rangel-Villalobos Davide Pettener Donata Luiselli Loren G Davis Evelyne Heyer Christoph P E Zollikofer Marcia S Ponce de León Colin I Smith Vaughan Grimes Kelly-Anne Pike Michael Deal Benjamin T Fuller Bernardo Arriaza Vivien Standen Maria F Luz Francois Ricaut Niede Guidon Ludmila Osipova Mikhail I Voevoda Olga L Posukh Oleg Balanovsky Maria Lavryashina Yuri Bogunov Elza Khusnutdinova Marina Gubina Elena Balanovska Sardana Fedorova Sergey Litvinov Boris Malyarchuk Miroslava Derenko M J Mosher David Archer Jerome Cybulski Barbara Petzelt Joycelynn Mitchell Rosita Worl Paul J Norman Peter Parham Brian M Kemp Toomas Kivisild Chris Tyler-Smith Manjinder S Sandhu Michael Crawford Richard Villems David Glenn Smith Michael R Waters Ted Goebel John R Johnson Ripan S Malhi Mattias Jakobsson David J Meltzer Andrea Manica Richard Durbin Carlos D Bustamante Yun S Song Rasmus Nielsen Eske Willerslev

Science 2015 Aug 21;349(6250):aab3884. Epub 2015 Jul 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.aab3884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733658PMC
August 2015

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Authors:
Monika Karmin Lauri Saag Mário Vicente Melissa A Wilson Sayres Mari Järve Ulvi Gerst Talas Siiri Rootsi Anne-Mai Ilumäe Reedik Mägi Mario Mitt Luca Pagani Tarmo Puurand Zuzana Faltyskova Florian Clemente Alexia Cardona Ene Metspalu Hovhannes Sahakyan Bayazit Yunusbayev Georgi Hudjashov Michael DeGiorgio Eva-Liis Loogväli Christina Eichstaedt Mikk Eelmets Gyaneshwer Chaubey Kristiina Tambets Sergei Litvinov Maru Mormina Yali Xue Qasim Ayub Grigor Zoraqi Thorfinn Sand Korneliussen Farida Akhatova Joseph Lachance Sarah Tishkoff Kuvat Momynaliev François-Xavier Ricaut Pradiptajati Kusuma Harilanto Razafindrazaka Denis Pierron Murray P Cox Gazi Nurun Nahar Sultana Rane Willerslev Craig Muller Michael Westaway David Lambert Vedrana Skaro Lejla Kovačevic Shahlo Turdikulova Dilbar Dalimova Rita Khusainova Natalya Trofimova Vita Akhmetova Irina Khidiyatova Daria V Lichman Jainagul Isakova Elvira Pocheshkhova Zhaxylyk Sabitov Nikolay A Barashkov Pagbajabyn Nymadawa Evelin Mihailov Joseph Wee Tien Seng Irina Evseeva Andrea Bamberg Migliano Syafiq Abdullah George Andriadze Dragan Primorac Lubov Atramentova Olga Utevska Levon Yepiskoposyan Damir Marjanovic Alena Kushniarevich Doron M Behar Christian Gilissen Lisenka Vissers Joris A Veltman Elena Balanovska Miroslava Derenko Boris Malyarchuk Andres Metspalu Sardana Fedorova Anders Eriksson Andrea Manica Fernando L Mendez Tatiana M Karafet Krishna R Veeramah Neil Bradman Michael F Hammer Ludmila P Osipova Oleg Balanovsky Elza K Khusnutdinova Knut Johnsen Maido Remm Mark G Thomas Chris Tyler-Smith Peter A Underhill Eske Willerslev Rasmus Nielsen Mait Metspalu Richard Villems Toomas Kivisild

Genome Res 2015 Apr 13;25(4):459-66. Epub 2015 Mar 13.

Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;

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https://bib.irb.hr/datoteka/715300.2015_Genome_Res._Karmin-A
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http://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114
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http://dx.doi.org/10.1101/gr.186684.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381518PMC
April 2015

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).

Bioinformatics 2014 Oct 28;30(20):2962-4. Epub 2014 Jun 28.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184259PMC
October 2014

A model-based approach for identifying signatures of ancient balancing selection in genetic data.

PLoS Genet 2014 Aug 21;10(8):e1004561. Epub 2014 Aug 21.

Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America; Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America; Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pgen.1004561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140648PMC
August 2014

Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

Syst Biol 2014 Jan 29;63(1):66-82. Epub 2013 Aug 29.

Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; and Department of Mathematics and Statistics, University of New Mexico, 1 University of New Mexico, Albuquerque, NM 87131, USA.

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http://dx.doi.org/10.1093/sysbio/syt059DOI Listing
January 2014

Population structure in a comprehensive genomic data set on human microsatellite variation.

G3 (Bethesda) 2013 May 20;3(5):891-907. Epub 2013 May 20.

Department of Biology, Stanford University, Stanford, California 94305, USA.

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http://g3journal.org/lookup/doi/10.1534/g3.113.005728
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http://dx.doi.org/10.1534/g3.113.005728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656735PMC
May 2013

Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis.

Mol Biol Evol 2013 Feb 10;30(2):480-8. Epub 2012 Oct 10.

Department of Integrative Biology, University of California, Berkeley.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/mss233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548310PMC
February 2013

Coalescence-time distributions in a serial founder model of human evolutionary history.

Genetics 2011 Oct 20;189(2):579-93. Epub 2011 Jul 20.

Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1534/genetics.111.129296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189793PMC
October 2011

Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy.

Genetics 2010 Dec 5;186(4):1367-87. Epub 2010 Oct 5.

Center for Computational Medicine and Bioinformatics, Department of Human Genetics and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2218, USA.

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http://dx.doi.org/10.1534/genetics.110.121756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998318PMC
December 2010

Fast and consistent estimation of species trees using supermatrix rooted triples.

Mol Biol Evol 2010 Mar 15;27(3):552-69. Epub 2009 Oct 15.

Center for Computational Medicine and Bioinformatics, University of Michigan, USA.

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http://dx.doi.org/10.1093/molbev/msp250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877557PMC
March 2010

Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.

Proc Natl Acad Sci U S A 2009 Sep 17;106(38):16057-62. Epub 2009 Aug 17.

Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

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http://dx.doi.org/10.1073/pnas.0903341106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752555PMC
September 2009

An unbiased estimator of gene diversity in samples containing related individuals.

Mol Biol Evol 2009 Mar 6;26(3):501-12. Epub 2008 Nov 6.

Center for Computational Medicine and Biology, University of Michigan, USA.

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http://dx.doi.org/10.1093/molbev/msn254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915906PMC
March 2009

Properties of consensus methods for inferring species trees from gene trees.

Syst Biol 2009 Feb 4;58(1):35-54. Epub 2009 Jun 4.

Department of Human Genetics, 1241 East Catherine Street, University of Michigan, Ann Arbor, MI 48109-0618, USA.

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https://academic.oup.com/sysbio/article/58/1/35/1674751
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http://dx.doi.org/10.1093/sysbio/syp008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909780PMC
February 2009