Publications by authors named "Ripan S Malhi"

64Publications

Assessing the comparability of different DNA extraction and amplification methods in gut microbial community profiling.

Access Microbiol 2019 28;1(7):e000060. Epub 2019 Aug 28.

Department of Anthropology, Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1099/acmi.0.000060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7481737PMC
August 2019

Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.

Am J Phys Anthropol 2020 Sep 8;173(1):21-33. Epub 2020 Jul 8.

University of Illinois Urbana-Champaign, Urbana, Illinois, USA.

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http://dx.doi.org/10.1002/ajpa.24099DOI Listing
September 2020

Accurate Sex Identification of Ancient Elephant and Other Animal Remains Using Low-Coverage DNA Shotgun Sequencing Data.

G3 (Bethesda) 2020 04 9;10(4):1427-1432. Epub 2020 Apr 9.

Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana IL, 61801.

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http://dx.doi.org/10.1534/g3.119.400833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144076PMC
April 2020

Chaco Canyon Dig Unearths Ethical Concerns.

Hum Biol 2017 07;89(3):177-180

11 Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, Washington, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951383PMC
http://dx.doi.org/10.13110/humanbiology.89.3.01DOI Listing
July 2017

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

Advancing the ethics of paleogenomics.

Science 2018 04 26;360(6387):384-385. Epub 2018 Apr 26.

All affiliations and members of the SING Consortium are listed in the supplementary materials.

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http://dx.doi.org/10.1126/science.aaq1131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6150602PMC
April 2018

Race and diversity in U.S. Biological Anthropology: A decade of AAPA initiatives.

Am J Phys Anthropol 2018 01;165 Suppl 65:158-180

Department of Anthropology, Notre Dame.

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http://dx.doi.org/10.1002/ajpa.23382DOI Listing
January 2018

Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus).

Am J Phys Anthropol 2018 03 4;165(3):576-588. Epub 2018 Jan 4.

Department of Anthropology, University of Illinois at Urbana-Champaign, 109A Davenport Hall, 607 South Mathews Avenue, Urbana, Illinois 61801.

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http://dx.doi.org/10.1002/ajpa.23395DOI Listing
March 2018

Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens.

Mol Phylogenet Evol 2017 11 31;116:227-238. Epub 2017 Aug 31.

Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA.

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http://dx.doi.org/10.1016/j.ympev.2017.08.006DOI Listing
November 2017

2015 Gabriel W. Lasker Award.

Authors:
Ripan S Malhi

Hum Biol 2016 10;88(4):301

Executive Editor, Human Biology.

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October 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

ENGAGING NATIVE AMERICANS IN GENOMICS RESEARCH.

Am Anthropol 2015 Dec 4;117(4):743-744. Epub 2015 Dec 4.

Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801;

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http://dx.doi.org/10.1111/aman.12369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085287PMC
December 2015

Case Study on Ancestry Estimation in an Alaskan Native Family: Identity and Safeguards Against Reductionism.

Hum Biol 2015 Oct;87(4):338-351

1 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois.

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http://dx.doi.org/10.13110/humanbiology.87.4.0338DOI Listing
October 2015

Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus).

Am J Phys Anthropol 2017 Feb 5;162(2):241-254. Epub 2016 Oct 5.

Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.

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http://dx.doi.org/10.1002/ajpa.23113DOI Listing
February 2017

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d.

PLoS One 2015 28;10(10):e0141808. Epub 2015 Oct 28.

Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America; Carl R Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141808PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625051PMC
June 2016

Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.

Hum Biol 2015 Jan;87(1):71-84

2 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois.

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http://dx.doi.org/10.13110/humanbiology.87.1.0071DOI Listing
January 2015

Isotopic and genetic analyses of a mass grave in central California: Implications for precontact hunter-gatherer warfare.

Am J Phys Anthropol 2016 Jan 2;159(1):116-25. Epub 2015 Sep 2.

Department of Anthropology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL.

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http://dx.doi.org/10.1002/ajpa.22843DOI Listing
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

Anthropology. Response to Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

Science 2015 Feb;347(6224):835

Applied Paleoscience and DirectAMS, 10322 Northeast 190th Street, Bothell, WA 98011, USA.

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http://dx.doi.org/10.1126/science.1261188DOI Listing
February 2015

DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories.

J Hum Evol 2015 Feb 18;79:105-18. Epub 2014 Dec 18.

School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jhevol.2014.10.012DOI Listing
February 2015

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

J Hum Evol 2015 Feb 16;79:45-54. Epub 2014 Dec 16.

Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jhevol.2014.06.016DOI Listing
February 2015

Patterns of admixture and population structure in native populations of Northwest North America.

PLoS Genet 2014 Aug 14;10(8):e1004530. Epub 2014 Aug 14.

Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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https://rosenberglab.stanford.edu/papers/VerduEtAl2014-PlosG
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http://dx.plos.org/10.1371/journal.pgen.1004530
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http://dx.doi.org/10.1371/journal.pgen.1004530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133047PMC
August 2014

Early Americans: misstated results.

Science 2014 Jul 24;345(6195):390. Epub 2014 Jul 24.

Department of Anthropology and Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1126/science.345.6195.390-aDOI Listing
July 2014

Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans.

Science 2014 May;344(6185):750-4

Centre for AMS C, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Centre for GeoGenetics, Natural History Museum of Denmark, Geological Museum, Copenhagen, Denmark.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1252619
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http://dx.doi.org/10.1126/science.1252619DOI Listing
May 2014

The evolutionary history of SLC6A4 and the role of plasticity in Macaca.

Am J Phys Anthropol 2014 Apr 24;153(4):605-16. Epub 2013 Dec 24.

Department of Anthropology, University of Illinois, Urbana, IL, 61801.

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http://doi.wiley.com/10.1002/ajpa.22460
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http://dx.doi.org/10.1002/ajpa.22460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949201PMC
April 2014

Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys.

Am J Primatol 2011 Oct 31;73(10):1031-40. Epub 2011 May 31.

Department of Anthropology, University of Illinois Urbana-Champaign, USA.

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http://doi.wiley.com/10.1002/ajp.20969
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http://dx.doi.org/10.1002/ajp.20969DOI Listing
October 2011

The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta).

Primates 2011 Apr 5;52(2):129-38. Epub 2011 Jan 5.

Department of Anthropology, University of California, Davis, 330 Young Hall, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1007/s10329-010-0232-4DOI Listing
April 2011

Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas.

Am J Phys Anthropol 2010 Mar;141(3):494-7

Department of Anthropology, Animal Biology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, IL 61801, USA.

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http://doi.wiley.com/10.1002/ajpa.21238
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http://dx.doi.org/10.1002/ajpa.21238DOI Listing
March 2010

Multiple Asian pig origins revealed through genomic analyses.

Mol Phylogenet Evol 2010 Mar 10;54(3):680-6. Epub 2009 Nov 10.

Department of Animal Sciences, University of Illinois, 374 Edward R. Madigan Lab, 1201 West Gregory Drive, Urbana, IL 61801, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10557903090045
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http://dx.doi.org/10.1016/j.ympev.2009.11.004DOI Listing
March 2010

Diversification of porcine MHC class II genes: evidence for selective advantage.

Immunogenetics 2009 Feb 14;61(2):119-29. Epub 2009 Jan 14.

Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1007/s00251-008-0348-5DOI Listing
February 2009

MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics.

PLoS One 2007 May 9;2(5):e438. Epub 2007 May 9.

Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000438PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1859839PMC
May 2007

Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland.

Mol Phylogenet Evol 2006 Jul 17;40(1):148-54. Epub 2006 Apr 17.

Trace Genetics, Inc (a DNAPrint Genomics Company), 4655 Meade St., Suite 300, Richmond, CA 94804, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S105579030600070
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http://dx.doi.org/10.1016/j.ympev.2006.02.019DOI Listing
July 2006

Patterns of mtDNA diversity in northwestern North America.

Hum Biol 2004 Feb;76(1):33-54

Department of Anthropology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1353/hub.2004.0023DOI Listing
February 2004

Brief communication: Haplogroup X confirmed in prehistoric North America.

Am J Phys Anthropol 2002 Sep;119(1):84-6

Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109-0618, USA.

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http://dx.doi.org/10.1002/ajpa.10106DOI Listing
September 2002