Publications by authors named "Irene Gallego Romero"

26Publications

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.

Authors:
Heini M Natri Katalina S Bobowik Pradiptajati Kusuma Chelzie Crenna Darusallam Guy S Jacobs Georgi Hudjashov J Stephen Lansing Herawati Sudoyo Nicholas E Banovich Murray P Cox Irene Gallego Romero

PLoS Genet 2020 05 26;16(5):e1008749. Epub 2020 May 26.

Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia.

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May 2020

Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal.

Authors:
Kevin X Lau Elizabeth A Mason Joshua Kie David P De Souza Joachim Kloehn Dedreia Tull Malcolm J McConville Andrew Keniry Tamara Beck Marnie E Blewitt Matthew E Ritchie Shalin H Naik Daniela Zalcenstein Othmar Korn Shian Su Irene Gallego Romero Catrina Spruce Christopher L Baker Tracy C McGarr Christine A Wells Martin F Pera

Nat Commun 2020 05 15;11(1):2420. Epub 2020 May 15.

Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.

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May 2020

Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations.

Authors:
Burak Yelmen Mayukh Mondal Davide Marnetto Ajai K Pathak Francesco Montinaro Irene Gallego Romero Toomas Kivisild Mait Metspalu Luca Pagani

Mol Biol Evol 2019 08;36(8):1628-1642

Institute of Genomics, University of Tartu, Tartu, Estonia.

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August 2019

Impact of regulatory variation across human iPSCs and differentiated cells.

Authors:
Nicholas E Banovich Yang I Li Anil Raj Michelle C Ward Peyton Greenside Diego Calderon Po Yuan Tung Jonathan E Burnett Marsha Myrthil Samantha M Thomas Courtney K Burrows Irene Gallego Romero Bryan J Pavlovic Anshul Kundaje Jonathan K Pritchard Yoav Gilad

Genome Res 2018 01 5;28(1):122-131. Epub 2017 Dec 5.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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January 2018

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Authors:
Swapan Mallick Heng Li Mark Lipson Iain Mathieson Melissa Gymrek Fernando Racimo Mengyao Zhao Niru Chennagiri Susanne Nordenfelt Arti Tandon Pontus Skoglund Iosif Lazaridis Sriram Sankararaman Qiaomei Fu Nadin Rohland Gabriel Renaud Yaniv Erlich Thomas Willems Carla Gallo Jeffrey P Spence Yun S Song Giovanni Poletti Francois Balloux George van Driem Peter de Knijff Irene Gallego Romero Aashish R Jha Doron M Behar Claudio M Bravi Cristian Capelli Tor Hervig Andres Moreno-Estrada Olga L Posukh Elena Balanovska Oleg Balanovsky Sena Karachanak-Yankova Hovhannes Sahakyan Draga Toncheva Levon Yepiskoposyan Chris Tyler-Smith Yali Xue M Syafiq Abdullah Andres Ruiz-Linares Cynthia M Beall Anna Di Rienzo Choongwon Jeong Elena B Starikovskaya Ene Metspalu Jüri Parik Richard Villems Brenna M Henn Ugur Hodoglugil Robert Mahley Antti Sajantila George Stamatoyannopoulos Joseph T S Wee Rita Khusainova Elza Khusnutdinova Sergey Litvinov George Ayodo David Comas Michael F Hammer Toomas Kivisild William Klitz Cheryl A Winkler Damian Labuda Michael Bamshad Lynn B Jorde Sarah A Tishkoff W Scott Watkins Mait Metspalu Stanislav Dryomov Rem Sukernik Lalji Singh Kumarasamy Thangaraj Svante Pääbo Janet Kelso Nick Patterson David Reich

Nature 2016 Oct 21;538(7624):201-206. Epub 2016 Sep 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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October 2016

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs.

Authors:
Courtney K Burrows Nicholas E Banovich Bryan J Pavlovic Kristen Patterson Irene Gallego Romero Jonathan K Pritchard Yoav Gilad

PLoS Genet 2016 Jan 26;12(1):e1005793. Epub 2016 Jan 26.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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January 2016

Global diversity, population stratification, and selection of human copy-number variation.

Authors:
Peter H Sudmant Swapan Mallick Bradley J Nelson Fereydoun Hormozdiari Niklas Krumm John Huddleston Bradley P Coe Carl Baker Susanne Nordenfelt Michael Bamshad Lynn B Jorde Olga L Posukh Hovhannes Sahakyan W Scott Watkins Levon Yepiskoposyan M Syafiq Abdullah Claudio M Bravi Cristian Capelli Tor Hervig Joseph T S Wee Chris Tyler-Smith George van Driem Irene Gallego Romero Aashish R Jha Sena Karachanak-Yankova Draga Toncheva David Comas Brenna Henn Toomas Kivisild Andres Ruiz-Linares Antti Sajantila Ene Metspalu Jüri Parik Richard Villems Elena B Starikovskaya George Ayodo Cynthia M Beall Anna Di Rienzo Michael F Hammer Rita Khusainova Elza Khusnutdinova William Klitz Cheryl Winkler Damian Labuda Mait Metspalu Sarah A Tishkoff Stanislav Dryomov Rem Sukernik Nick Patterson David Reich Evan E Eichler

Science 2015 09 6;349(6253):aab3761. Epub 2015 Aug 6.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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September 2015

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.

Authors:
Irene Gallego Romero Bryan J Pavlovic Irene Hernando-Herraez Xiang Zhou Michelle C Ward Nicholas E Banovich Courtney L Kagan Jonathan E Burnett Constance H Huang Amy Mitrano Claudia I Chavarria Inbar Friedrich Ben-Nun Yingchun Li Karen Sabatini Trevor R Leonardo Mana Parast Tomas Marques-Bonet Louise C Laurent Jeanne F Loring Yoav Gilad

Elife 2015 Jun 23;4:e07103. Epub 2015 Jun 23.

Department of Human Genetics, University of Chicago, Chicago, United States.

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June 2015

Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions.

Authors:
Ibon Garitaonandia Hadar Amir Francesca Sesillo Boscolo Gerald K Wambua Heather L Schultheisz Karen Sabatini Robert Morey Shannon Waltz Yu-Chieh Wang Ha Tran Trevor R Leonardo Kristopher Nazor Ileana Slavin Candace Lynch Yingchun Li Ronald Coleman Irene Gallego Romero Gulsah Altun David Reynolds Stephen Dalton Mana Parast Jeanne F Loring Louise C Laurent

PLoS One 2015 25;10(2):e0118307. Epub 2015 Feb 25.

Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America; Department of Reproductive Medicine, UCSD Healthcare, 9500 Gilman Drive, Mail Code 0695, San Diego, CA 92093, United States of America.

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January 2016

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Authors:
Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H Sudmant Joshua G Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten I Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A Babiker Graciela Bailliet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M Bravi Francesca Brisighelli George B J Busby Francesco Cali Mikhail Churnosov David E C Cole Daniel Corach Larissa Damba George van Driem Stanislav Dryomov Jean-Michel Dugoujon Sardana A Fedorova Irene Gallego Romero Marina Gubina Michael Hammer Brenna M Henn Tor Hervig Ugur Hodoglugil Aashish R Jha Sena Karachanak-Yankova Rita Khusainova Elza Khusnutdinova Rick Kittles Toomas Kivisild William Klitz Vaidutis Kučinskas Alena Kushniarevich Leila Laredj Sergey Litvinov Theologos Loukidis Robert W Mahley Béla Melegh Ene Metspalu Julio Molina Joanna Mountain Klemetti Näkkäläjärvi Desislava Nesheva Thomas Nyambo Ludmila Osipova Jüri Parik Fedor Platonov Olga Posukh Valentino Romano Francisco Rothhammer Igor Rudan Ruslan Ruizbakiev Hovhannes Sahakyan Antti Sajantila Antonio Salas Elena B Starikovskaya Ayele Tarekegn Draga Toncheva Shahlo Turdikulova Ingrida Uktveryte Olga Utevska René Vasquez Mercedes Villena Mikhail Voevoda Cheryl A Winkler Levon Yepiskoposyan Pierre Zalloua Tatijana Zemunik Alan Cooper Cristian Capelli Mark G Thomas Andres Ruiz-Linares Sarah A Tishkoff Lalji Singh Kumarasamy Thangaraj Richard Villems David Comas Rem Sukernik Mait Metspalu Matthias Meyer Evan E Eichler Joachim Burger Montgomery Slatkin Svante Pääbo Janet Kelso David Reich Johannes Krause

Nature 2014 Sep;513(7518):409-13

1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany.

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September 2014

RNA-seq: impact of RNA degradation on transcript quantification.

Authors:
Irene Gallego Romero Athma A Pai Jenny Tung Yoav Gilad

BMC Biol 2014 May 30;12:42. Epub 2014 May 30.

Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 317, Chicago, IL 60637, USA.

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May 2014

Genome-wide analysis of cold adaptation in indigenous Siberian populations.

Authors:
Alexia Cardona Luca Pagani Tiago Antao Daniel J Lawson Christina A Eichstaedt Bryndis Yngvadottir Ma Than Than Shwe Joseph Wee Irene Gallego Romero Srilakshmi Raj Mait Metspalu Richard Villems Eske Willerslev Chris Tyler-Smith Boris A Malyarchuk Miroslava V Derenko Toomas Kivisild

PLoS One 2014 21;9(5):e98076. Epub 2014 May 21.

Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom; Estonian Biocentre, Tartu, Estonia.

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January 2015

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

Authors:
Andrea Bamberg Migliano Irene Gallego Romero Mait Metspalu Matthew Leavesley Luca Pagani Tiago Antao Da-Wei Huang Brad T Sherman Katharine Siddle Clarissa Scholes Georgi Hudjashov Elton Kaitokai Avis Babalu Maggie Belatti Alex Cagan Byrony Hopkinshaw Colin Shaw Mari Nelis Ene Metspalu Reedik Mägi Richard A Lempicki Richard Villems Marta Mirazon Lahr Toomas Kivisild

Hum Biol 2013 Feb-Jun;85(1-3):251-84

Department of Anthropology, University College London, London, UK.

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April 2015

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Authors:
Chandana Basu Mallick Florin Mircea Iliescu Märt Möls Sarah Hill Rakesh Tamang Gyaneshwer Chaubey Rie Goto Simon Y W Ho Irene Gallego Romero Federica Crivellaro Georgi Hudjashov Niraj Rai Mait Metspalu C G Nicholas Mascie-Taylor Ramasamy Pitchappan Lalji Singh Marta Mirazon-Lahr Kumarasamy Thangaraj Richard Villems Toomas Kivisild

PLoS Genet 2013 Nov 7;9(11):e1003912. Epub 2013 Nov 7.

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia ; Estonian Biocentre, Tartu, Estonia.

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November 2013

A general linear model-based approach for inferring selection to climate.

Authors:
Srilakshmi M Raj Luca Pagani Irene Gallego Romero Toomas Kivisild William Amos

BMC Genet 2013 Sep 22;14:87. Epub 2013 Sep 22.

Department of Zoology, University of Cambridge, Cambridge, UK.

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September 2013

Variation at diabetes- and obesity-associated Loci may mirror neutral patterns of human population diversity and diabetes prevalence in India.

Authors:
Srilakshmi M Raj Pradeep Halebeedu Jayarama S Kadandale Marta Mirazon Lahr Irene Gallego Romero Jamuna R Yadhav Mircea Iliescu Niraj Rai Federica Crivellaro Gyaneshwer Chaubey Richard Villems Kumarasamy Thangaraj Kalappagowda Muniyappa H Sharat Chandra Toomas Kivisild

Ann Hum Genet 2013 Sep 1;77(5):392-408. Epub 2013 Jul 1.

Department of Molecular Biology and Genetics, 101 Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA; Division of Biological Anthropology, Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.

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September 2013

Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool.

Authors:
Luca Pagani Toomas Kivisild Ayele Tarekegn Rosemary Ekong Chris Plaster Irene Gallego Romero Qasim Ayub S Qasim Mehdi Mark G Thomas Donata Luiselli Endashaw Bekele Neil Bradman David J Balding Chris Tyler-Smith

Am J Hum Genet 2012 Jul 21;91(1):83-96. Epub 2012 Jun 21.

Division of Biological Anthropology, University of Cambridge, UK.

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July 2012

Comparative studies of gene expression and the evolution of gene regulation.

Authors:
Irene Gallego Romero Ilya Ruvinsky Yoav Gilad

Nat Rev Genet 2012 Jun 18;13(7):505-16. Epub 2012 Jun 18.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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June 2012

A systematic survey of loss-of-function variants in human protein-coding genes.

Authors:
Daniel G MacArthur Suganthi Balasubramanian Adam Frankish Ni Huang James Morris Klaudia Walter Luke Jostins Lukas Habegger Joseph K Pickrell Stephen B Montgomery Cornelis A Albers Zhengdong D Zhang Donald F Conrad Gerton Lunter Hancheng Zheng Qasim Ayub Mark A DePristo Eric Banks Min Hu Robert E Handsaker Jeffrey A Rosenfeld Menachem Fromer Mike Jin Xinmeng Jasmine Mu Ekta Khurana Kai Ye Mike Kay Gary Ian Saunders Marie-Marthe Suner Toby Hunt If H A Barnes Clara Amid Denise R Carvalho-Silva Alexandra H Bignell Catherine Snow Bryndis Yngvadottir Suzannah Bumpstead David N Cooper Yali Xue Irene Gallego Romero Jun Wang Yingrui Li Richard A Gibbs Steven A McCarroll Emmanouil T Dermitzakis Jonathan K Pritchard Jeffrey C Barrett Jennifer Harrow Matthew E Hurles Mark B Gerstein Chris Tyler-Smith

Science 2012 Feb;335(6070):823-8

Wellcome Trust Sanger Institute, Hinxton, UK.

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February 2012

Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia.

Authors:
Mait Metspalu Irene Gallego Romero Bayazit Yunusbayev Gyaneshwer Chaubey Chandana Basu Mallick Georgi Hudjashov Mari Nelis Reedik Mägi Ene Metspalu Maido Remm Ramasamy Pitchappan Lalji Singh Kumarasamy Thangaraj Richard Villems Toomas Kivisild

Am J Hum Genet 2011 Dec;89(6):731-44

Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia.

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December 2011

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.

Authors:
Min Hu Qasim Ayub José Afonso Guerra-Assunção Quan Long Zemin Ning Ni Huang Irene Gallego Romero Lira Mamanova Pelin Akan Xin Liu Alison J Coffey Daniel J Turner Harold Swerdlow John Burton Michael A Quail Donald F Conrad Anton J Enright Chris Tyler-Smith Yali Xue

Hum Genet 2012 May 5;131(5):665-74. Epub 2011 Nov 5.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.

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May 2012

An Aboriginal Australian genome reveals separate human dispersals into Asia.

Authors:
Morten Rasmussen Xiaosen Guo Yong Wang Kirk E Lohmueller Simon Rasmussen Anders Albrechtsen Line Skotte Stinus Lindgreen Mait Metspalu Thibaut Jombart Toomas Kivisild Weiwei Zhai Anders Eriksson Andrea Manica Ludovic Orlando Francisco M De La Vega Silvana Tridico Ene Metspalu Kasper Nielsen María C Ávila-Arcos J Víctor Moreno-Mayar Craig Muller Joe Dortch M Thomas P Gilbert Ole Lund Agata Wesolowska Monika Karmin Lucy A Weinert Bo Wang Jun Li Shuaishuai Tai Fei Xiao Tsunehiko Hanihara George van Driem Aashish R Jha François-Xavier Ricaut Peter de Knijff Andrea B Migliano Irene Gallego Romero Karsten Kristiansen David M Lambert Søren Brunak Peter Forster Bernd Brinkmann Olaf Nehlich Michael Bunce Michael Richards Ramneek Gupta Carlos D Bustamante Anders Krogh Robert A Foley Marta M Lahr Francois Balloux Thomas Sicheritz-Pontén Richard Villems Rasmus Nielsen Jun Wang Eske Willerslev

Science 2011 Oct 22;334(6052):94-8. Epub 2011 Sep 22.

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

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October 2011

Herders of Indian and European cattle share their predominant allele for lactase persistence.

Authors:
Irene Gallego Romero Chandana Basu Mallick Anke Liebert Federica Crivellaro Gyaneshwer Chaubey Yuval Itan Mait Metspalu Muthukrishnan Eaaswarkhanth Ramasamy Pitchappan Richard Villems David Reich Lalji Singh Kumarasamy Thangaraj Mark G Thomas Dallas M Swallow Marta Mirazón Lahr Toomas Kivisild

Mol Biol Evol 2012 Jan 11;29(1):249-60. Epub 2011 Aug 11.

Department of Biological Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom.

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January 2012

Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.

Authors:
Gyaneshwer Chaubey Mait Metspalu Ying Choi Reedik Mägi Irene Gallego Romero Pedro Soares Mannis van Oven Doron M Behar Siiri Rootsi Georgi Hudjashov Chandana Basu Mallick Monika Karmin Mari Nelis Jüri Parik Alla Goverdhana Reddy Ene Metspalu George van Driem Yali Xue Chris Tyler-Smith Kumarasamy Thangaraj Lalji Singh Maido Remm Martin B Richards Marta Mirazon Lahr Manfred Kayser Richard Villems Toomas Kivisild

Mol Biol Evol 2011 Feb 26;28(2):1013-24. Epub 2010 Oct 26.

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.

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February 2011

Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations.

Authors:
Muthukrishnan Eaaswarkhanth Ikramul Haque Zeinab Ravesh Irene Gallego Romero Poorlin Ramakodi Meganathan Bhawna Dubey Faizan Ahmed Khan Gyaneshwer Chaubey Toomas Kivisild Chris Tyler-Smith Lalji Singh Kumarasamy Thangaraj

Eur J Hum Genet 2010 Mar 7;18(3):354-63. Epub 2009 Oct 7.

National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata, India.

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March 2010

CFTR mutations and reproductive outcomes in a population isolate.

Authors:
Irene Gallego Romero Carole Ober

Hum Genet 2008 Jan 28;122(6):583-8. Epub 2007 Sep 28.

Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 507C, Chicago, IL, 60637, USA.

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January 2008