Human Genomics and Evolution group at SVI

Publications

Below you can find a list of all of our publications. We are committed to carrying out high quality reproducible research, be that computational or molecular biology based. To that end we make source code and all data and protocols available on publication. Code repos should be available either here (older projects) or here (newer projects), and large data dumps associated with specific papers are on our figshare account. If you cannot find something, get in touch.

2025

Gene regulatory dynamics during craniofacial development in a carnivorous marsupial
Gene regulatory dynamics during craniofacial development in a carnivorous marsupial
Laura E Cook, Charles Y Feigin, John Hills, Davide M Vespasiani, Andrew J Pask, Irene Gallego Romero
eLife  ·  07 Jan 2025  ·  10.7554/eLife.103592.1
marsupials

2024

Using multiplexed functional data to reduce variant classification inequities in underrepresented populations
Using multiplexed functional data to reduce variant classification inequities in underrepresented populations
Moez Dawood, Shawn Fayer, Sriram Pendyala, Mason Post, Divya Kalra, …, Richard A. Gibbs, Lea M. Starita, Carla Daniela Robles-Espinoza, Willow Coyote-Maestas, Irene Gallego Romero
Genome Medicine  ·  03 Dec 2024  ·  doi:10.1186/s13073-024-01392-7
mave human-diversity
Public RNA-seq data are not representative of global human diversity
Public RNA-seq data are not representative of global human diversity
Irene Gallego Romero, Grace Rodenberg, Audrey M. Arner, Lani Li, Isobel J. Beasley, Ryan Rossow, Nicholas Ryan, Selina Wang, Amanda J. Lea
bioRxiv  ·  11 Oct 2024  ·  doi:10.1101/2024.10.11.617967
human-diversity metascience
The whole blood microbiome of Indonesians reveals translocated and pathogenic microbiota
The whole blood microbiome of Indonesians reveals translocated and pathogenic microbiota
Katalina Bobowik, Muhamad Fachrul, Chelzie Crenna Darusallam, Pradiptajati Kusuma, Herawati Sudoyo, Clarissa A. Febinia, Safarina G. Malik, Christine Wells, Irene Gallego Romero
bioRxiv  ·  06 May 2024  ·  doi:10.1101/2022.04.24.489025
indonesia microbiome
De novo transcriptome assembly and genome annotation of the fat-tailed dunnart Sminthopsis crassicaudata
De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)
Neke Ibeh, Charles Y. Feigin, Stephen R. Frankenberg, Davis J. McCarthy, Andrew J. Pask, Irene Gallego Romero
Gigabyte  ·  02 May 2024  ·  doi:10.46471/gigabyte.118
marsupials resource

2023

Increasing diversity of functional genetics studies to advance biological discovery and human health
Increasing diversity of functional genetics studies to advance biological discovery and human health
Sophia H.L. George, Alejandra Medina-Rivera, Youssef Idaghdour, Tuuli Lappalainen, Irene Gallego Romero
The American Journal of Human Genetics  ·  01 Dec 2023  ·  doi:10.1016/j.ajhg.2023.10.012
perspective human-diversity
Seeing humans through an evolutionary lens
Seeing humans through an evolutionary lens
Irene Gallego Romero
Science  ·  28 Apr 2023  ·  doi:10.1126/science.adh0745
perspective
Leveraging massively parallel reporter assays for evolutionary questions
Leveraging massively parallel reporter assays for evolutionary questions
Irene Gallego Romero, Amanda J. Lea
Genome Biology  ·  14 Feb 2023  ·  doi:10.1186/s13059-023-02856-6
mave human-evolution

2022

Denisovan introgression has shaped the immune system of present-day Papuans
Denisovan introgression has shaped the immune system of present-day Papuans
Davide M. Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Murray P. Cox, Irene Gallego Romero
PLOS Genetics  ·  08 Dec 2022  ·  doi:10.1371/journal.pgen.1010470
denisovan-introgression human-diversity
Genome-wide insights into human population structure
Genome-wide insights into human population structure
Irene Gallego Romero
Nature Reviews Genetics  ·  10 Mar 2022  ·  doi:10.1038/s41576-022-00469-6
perspective
Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries
Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries
Heini M. Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, …, Mait Metspalu, Herawati Sudoyo, Murray P. Cox, Irene Gallego Romero, Nicholas E. Banovich
The American Journal of Human Genetics  ·  01 Jan 2022  ·  doi:10.1016/j.ajhg.2021.11.017
indonesia human-diversity gene-regulation

2021

Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations
Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations
Navya Shukla, Bobbie Shaban, Irene Gallego Romero
Genome Biology and Evolution  ·  01 Nov 2021  ·  doi:10.1093/gbe/evab247
chimpanzee metascience
Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul
Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul
Nicolas Brucato, Mathilde André, Roxanne Tsang, Lauri Saag, Jason Kariwiga, …, Irene Gallego Romero, Mait Metspalu, Murray P Cox, Matthew Leavesley, François-Xavier Ricaut
Molecular Biology and Evolution  ·  12 Aug 2021  ·  doi:10.1093/molbev/msab238
papua-new-guinea human-evolution
Harnessing pluripotent stem cells as models to decipher human evolution
Harnessing pluripotent stem cells as models to decipher human evolution
Michael Dannemann, Irene Gallego Romero
The FEBS Journal  ·  30 Apr 2021  ·  doi:10.1111/febs.15885
review human-evolution ipscs
Transcriptomic profiles of i Plasmodium falciparum i and i Plasmodium vivax i -infected individuals in Indonesia
Transcriptomic profiles ofPlasmodium falciparumandPlasmodium vivax-infected individuals in Indonesia
Katalina Bobowik, Din Syafruddin, Chelzie Crenna Darusallam, Herawati Sudoyo, Christine Wells, Irene Gallego Romero
bioRxiv  ·  08 Jan 2021  ·  doi:10.1101/2021.01.07.425684
indonesia

2020

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Heini M. Natri, Katalina S. Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, …, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
PLOS Genetics  ·  26 May 2020  ·  doi:10.1371/journal.pgen.1008749
indonesia human-diversity gene-regulation

2019

Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations
Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations
Burak Yelmen, Mayukh Mondal, Davide Marnetto, Ajai K Pathak, Francesco Montinaro, Irene Gallego Romero, Toomas Kivisild, Mait Metspalu, Luca Pagani
Molecular Biology and Evolution  ·  05 Apr 2019  ·  doi:10.1093/molbev/msz037
human-evolution

2018

Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells
Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells
Irene Gallego Romero, Shyam Gopalakrishnan, Yoav Gilad
bioRxiv  ·  09 Nov 2018  ·  doi:10.1101/466631
chimpanzees ipscs

2017

Impact of regulatory variation across human iPSCs and differentiated cells
Impact of regulatory variation across human iPSCs and differentiated cells
Nicholas E. Banovich, Yang I. Li, Anil Raj, Michelle C. Ward, Peyton Greenside, …, Irene Gallego Romero, Bryan J. Pavlovic, Anshul Kundaje, Jonathan K. Pritchard, Yoav Gilad
Genome Research  ·  05 Dec 2017  ·  doi:10.1101/gr.224436.117
gene-regulation ipscs

2016

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, …, Kumarasamy Thangaraj, Svante Pääbo, Janet Kelso, Nick Patterson, David Reich
Nature  ·  21 Sep 2016  ·  doi:10.1038/nature18964
human-diversity

2015

Global diversity, population stratification, and selection of human copy-number variation
Global diversity, population stratification, and selection of human copy-number variation
Peter H. Sudmant, Swapan Mallick, Bradley J. Nelson, Fereydoun Hormozdiari, Niklas Krumm, …, Stanislav Dryomov, Rem Sukernik, Nick Patterson, David Reich, Evan E. Eichler
Science  ·  11 Sep 2015  ·  doi:10.1126/science.aab3761
human-diversity
A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Irene Gallego Romero, Bryan J Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C Ward, …, Mana Parast, Tomas Marques-Bonet, Louise C Laurent, Jeanne F Loring, Yoav Gilad
eLife  ·  23 Jun 2015  ·  doi:10.7554/eLife.07103
chimpanzee ipscs resource
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions
Ibon Garitaonandia, Hadar Amir, Francesca Sesillo Boscolo, Gerald K. Wambua, Heather L. Schultheisz, …, David Reynolds, Stephen Dalton, Mana Parast, Jeanne F. Loring, Louise C. Laurent
PLOS ONE  ·  25 Feb 2015  ·  doi:10.1371/journal.pone.0118307
ipscs
Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs
Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs
Courtney L. Kagan, Nicholas E Banovich, Bryan J Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K Pritchard, Yoav Gilad
Cold Spring Harbor Laboratory  ·  19 Jan 2015  ·  doi:10.1101/013888
ipscs gene-regulation

2014

Ancient human genomes suggest three ancestral populations for present-day Europeans
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, …, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
Nature  ·  01 Sep 2014  ·  doi:10.1038/nature13673
human-evolution
RNA-seq: impact of RNA degradation on transcript quantification
RNA-seq: impact of RNA degradation on transcript quantification
Irene Gallego Romero, Athma A Pai, Jenny Tung, Yoav Gilad
BMC Biology  ·  30 May 2014  ·  doi:10.1186/1741-7007-12-42
gene-expression methods
Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations
Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations
Alexia Cardona, Luca Pagani, Tiago Antao, Daniel J. Lawson, Christina A. Eichstaedt, …, Eske Willerslev, Chris Tyler-Smith, Boris A. Malyarchuk, Miroslava V. Derenko, Toomas Kivisild
PLoS ONE  ·  21 May 2014  ·  doi:10.1371/journal.pone.0098076
human-evolution

2013

The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
Chandana Basu Mallick, Florin Mircea Iliescu, Märt Möls, Sarah Hill, Rakesh Tamang, …, Lalji Singh, Marta Mirazon-Lahr, Kumarasamy Thangaraj, Richard Villems, Toomas Kivisild
PLoS Genetics  ·  07 Nov 2013  ·  doi:10.1371/journal.pgen.1003912
human-diversity
A general linear model-based approach for inferring selection to climate
A general linear model-based approach for inferring selection to climate
Srilakshmi M Raj, Luca Pagani, Irene Gallego Romero, Toomas Kivisild, William Amos
BMC Genetics  ·  22 Sep 2013  ·  doi:10.1186/1471-2156-14-87
methods
Variation at Diabetes- and Obesity-Associated Loci May Mirror Neutral Patterns of Human Population Diversity and Diabetes Prevalence in India
Variation at Diabetes- and Obesity-Associated Loci May Mirror Neutral Patterns of Human Population Diversity and Diabetes Prevalence in India
Srilakshmi M. Raj, Pradeep Halebeedu, Jayarama S Kadandale, Marta Mirazon Lahr, Irene Gallego Romero, …, Richard Villems, Kumarasamy Thangaraj, Kalappagowda Muniyappa, H. Sharat Chandra, Toomas Kivisild
Annals of Human Genetics  ·  01 Jul 2013  ·  doi:10.1111/ahg.12028
human-diversity india
Evolution of the Pygmy Phenotype: Evidence of Positive Selection from Genome-wide Scans in African, Asian, and Melanesian Pygmies
Evolution of the Pygmy Phenotype: Evidence of Positive Selection from Genome-wide Scans in African, Asian, and Melanesian Pygmies
Andrea Bamberg Migliano, Irene Gallego Romero, Mait Metspalu, Matthew Leavesley, Luca Pagani, …, Reedik Mägi, Richard A. Lempicki, Richard Villems, Marta Mirazon Lahr, Toomas Kivisild
Human Biology  ·  01 Jun 2013  ·  doi:10.3378/027.085.0313
human-evolution human-diversity

2012

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool
Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool
Luca Pagani, Toomas Kivisild, Ayele Tarekegn, Rosemary Ekong, Chris Plaster, …, Donata Luiselli, Endashaw Bekele, Neil Bradman, David J. Balding, Chris Tyler-Smith
The American Journal of Human Genetics  ·  01 Jul 2012  ·  doi:10.1016/j.ajhg.2012.05.015
human-diversity
Comparative studies of gene expression and the evolution of gene regulation
Comparative studies of gene expression and the evolution of gene regulation
Irene Gallego Romero, Ilya Ruvinsky, Yoav Gilad
Nature Reviews Genetics  ·  18 Jun 2012  ·  doi:10.1038/nrg3229
review gene-regulation
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
Daniel G. MacArthur, Suganthi Balasubramanian, Adam Frankish, Ni Huang, James Morris, …, Jeffrey C. Barrett, Jennifer Harrow, Matthew E. Hurles, Mark B. Gerstein, Chris Tyler-Smith
Science  ·  17 Feb 2012  ·  doi:10.1126/science.1215040
human-diversity

2011

Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia
Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia
Mait Metspalu, Irene Gallego Romero, Bayazit Yunusbayev, Gyaneshwer Chaubey, Chandana Basu Mallick, …, Ramasamy Pitchappan, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, Toomas Kivisild
The American Journal of Human Genetics  ·  01 Dec 2011  ·  doi:10.1016/j.ajhg.2011.11.010
human-evolution india human-diversity
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data
Min Hu, Qasim Ayub, José Afonso Guerra-Assunção, Quan Long, Zemin Ning, …, Michael A. Quail, Donald F. Conrad, Anton J. Enright, Chris Tyler-Smith, Yali Xue
Human Genetics  ·  05 Nov 2011  ·  doi:10.1007/s00439-011-1111-9
methods
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
Morten Rasmussen, Xiaosen Guo, Yong Wang, Kirk E. Lohmueller, Simon Rasmussen, …, Thomas Sicheritz-Pontén, Richard Villems, Rasmus Nielsen, Jun Wang, Eske Willerslev
Science  ·  07 Oct 2011  ·  doi:10.1126/science.1211177
human-diversity human-evolution
Herders of Indian and European Cattle Share Their Predominant Allele for Lactase Persistence
Herders of Indian and European Cattle Share Their Predominant Allele for Lactase Persistence
Irene Gallego Romero, Chandana Basu Mallick, Anke Liebert, Federica Crivellaro, Gyaneshwer Chaubey, …, Kumarasamy Thangaraj, Mark G. Thomas, Dallas M. Swallow, Marta Mirazón Lahr, Toomas Kivisild
Molecular Biology and Evolution  ·  11 Aug 2011  ·  doi:10.1093/molbev/msr190
human-evolution india lactase-persistence

2010

Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture
Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture
G. Chaubey, M. Metspalu, Y. Choi, R. Magi, I. G. Romero, …, M. B. Richards, M. M. Lahr, M. Kayser, R. Villems, T. Kivisild
Molecular Biology and Evolution  ·  26 Oct 2010  ·  doi:10.1093/molbev/msq288
human-diversity india

2009

Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations
Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations
Muthukrishnan Eaaswarkhanth, Ikramul Haque, Zeinab Ravesh, Irene Gallego Romero, Poorlin Ramakodi Meganathan, …, Gyaneshwer Chaubey, Toomas Kivisild, Chris Tyler-Smith, Lalji Singh, Kumarasamy Thangaraj
European Journal of Human Genetics  ·  07 Oct 2009  ·  doi:10.1038/ejhg.2009.168
human-diversity india

2008

How accurate is the current picture of human genetic variation
How accurate is the current picture of human genetic variation?
I G Romero, A Manica, J Goudet, L L Handley, F Balloux
Heredity  ·  03 Sep 2008  ·  doi:10.1038/hdy.2008.89
human-diversity human-evolution

2007

CFTR mutations and reproductive outcomes in a population isolate
CFTR mutations and reproductive outcomes in a population isolate
Irene Gallego Romero, Carole Ober
Human Genetics  ·  28 Sep 2007  ·  doi:10.1007/s00439-007-0432-1
cftr hutterites