Publications

Preprints

K. Bobowik, C. C. Darusallam, P. Kusuma, H. Sudoyo, C. A. Febinia, S. G. Malik, C. Wells and I. Gallego Romero, The whole blood microbiome of Indonesians reveals that environmental differences shape immune gene expression signatures, bioRxiv, doi: 10.1101/2022.04.24.489025. Full text available

I. Gallego Romero and A. Lea, Leveraging massively parallel reporter assays for evolutionary questions. arXiv: arXiv:2204.05857. Full text available

K. Bobowik, D. Syafruddin, C. C. Darusallam, H. Sudoyo, C. Wells and I. Gallego Romero, Transcriptomic profiles of Plasmodium falciparum and Plasmodium vivax-infected individuals in Indonesia. bioRxiv, doi: 10.1101/2021.01.07.425684. Full text available.

I. Gallego Romero, S. Gopalakrishnan and Y. Gilad, Widespread conservation of chromatin accessibility patterns and transcription factor binding activity in human and chimpanzee induced pluripotent stem cells. bioRxiv, doi: 10.1101/466631. Full text available.

2022

D. Vespasiani, G.S. Jacobs, L.E. Cook, N. Brucato, F.X. Ricaut, M. Leavesley, C. Kinipi, M.P. Cox and I. Gallego Romero. Denisovan introgression has shaped the immune system of present-day Papuans. PLOS Genetics, in press. Also available in bioRxiv, doi: 10.1101/2020.07.09.196444. Full text available.

H. M. Natri, G. Hudjashov, G. S. Jacobs, P. Kusuma, L. Saag, C C. Darusallam, M. Metspalu, H. Sudoyo, M. P. Cox*, I. Gallego Romero* and N. E. Banovich*, Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression. American Journal of Human Genetics, in press. Also available at bioRxiv, doi: 10.1101/2020.09.25.313726. * denotes equal contribution. Full text available.

 

2021

N. Shukla, B. Shaban and I. Gallego Romero, Genetic diversity in chimpanzee transcriptomics does not represent wild populations. Genome Biology and Evolution, in press. Also available at bioRxiv, doi:10.1101/2021.06.27.450107.

N. Brucato, M. André, R. Tsang, L. Saag, J. Kariwiga, K. Sesuki, T. Beni, W. Pomat, J. Muke, V. Meyer, A. Boland, J.F. Deleuze, H. Sudoyo, M. Mondal, L. Pagani, I. Gallego Romero, M. Metspalu, M.P. Cox, M. Leavesley and F.X. Ricaut, Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul . Molecular Biology and Evolution doi:10.1093/molbev/msab238. Full text available.

M. Dannemann and I. Gallego Romero. Harnessing pluripotent stem cells as models to decipher human evolution. The FEBS Journal, doi:10.1111/febs.15885. Full text available.

2020

H. Natri*, K. S. Bobowik*, P. Kusuma, C. C. Darusallam, G. S. Jacobs, G. Hudjashov, J.S. Lansing, H. Sudoyo, N.E. Banovich**, M.P. Cox**, I. Gallego Romero**. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLOS Genetics, 16(5): e1008749. doi:10.1371/journal.pgen.1008749. * and ** denote equal contributions. Full text available.

K.X. Lau, E.A. Mason, J. Kie, D.P. De Souza, J. Kloehn, D. Tull, M.J. McConville, A. Keniry, T. Beck, M.E. Blewitt, M.E. Ritchie, S.H. Naik, D. Zalcenstein, O. Korn, S. Su, I Gallego Romero, C. Spruce, C.L. Baker, T.C. McGarr, C.A. Wells, and M.F. Pera. Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal. Nature Communications, doi: 10.1038/s41467-020-16214-8.

2019

B. Yelmen, M. Mondal, D. Marnetto, A.K. Pathak, F. Montinaro, I. Gallego Romero, T. Kivisild, M. Metspalu and L. Pagani. Ancestry-specific analyses reveal differential demographic histories and opposite selective pressures in modern South Asian populations. Molecular Biology and Evolution, doi: 10.1093/molbev/msz037. Full text available.

2017

N. Banovich, Y. Li, A. Raj, M.C. Ward, P. Greenside, D. Calderon, P.Y. Tung, J.E. Burnett, M. Myrthil, S.M. Thomas, C.K. Burrows, I. Gallego Romero, B.J. Pavlovic, A. Kundaje, J.K. Pritchard and Y. Gilad. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Research, 2017. doi:10.1101/gr.224436.117. Full text available.

2016

S. Mallick, H. Li*, M. Lipson*, I. Mathieson*, M. Gymrek, F. Racimo, J.P. Spence, M. Zhao, N. Chennagiri, S. Nordenfelt, A. Tandon, P. Skoglund, I. Lazaridis, S. Sankararaman, Q. Fu, N. Rohland, G. Renaud, Y. Erlich, T. Willems, C. Gallo, G. Poletti, F. Balloux, G. van Driem, P. de Knifjj, I. Gallego Romero, A.R. Jha, D.M. Behar, C.M. Bravi, C. Capelli, T. Hervig, A. Moreno- Estrada, O.L. Posukh, E. Balanovska, O. Balanovsky, S. Karachanak-Yankova, H. Sahakyan, D. Toncheva, L. Yepiskoposyan, C. Tyler-Smith, Y. Xue, M.S. Abdullah, A. Ruiz-Linares, C.M. Beall, A. Di Rienzo, C. Jeong, E.B. Starikovskaya, E. Metspalu, J. Parik, R. Villems, B.M. Henn, U. Hodoglugil, R. Mahley, A. Sajantila, G. Stamatoyannopoulos, J.T. S. Wee, R. Khusainova, E. Khusnutdinova, S. Litvinov, G. Ayodo, D. Comas, M. Hammer, T. Kivisild, W. Klitz, C. Winkler, D. Labuda, M. Bamshad, L.B. Jorde, S.A. Tishko , W.S. Watkins, M. Metspalu, S. Dryomov, R. Sukernik, L. Singh, K. Thangaraj, Y.S. Song, S. Pääbo, J. Kelso, N. Patterson, and D. Reich. The landscape of human genome diversity. Nature, doi:10.1038/nature18964. * denotes equal contribution. Full text available.

C.L. Kagan*, N.E. Banovich*, B.J. Pavlovic, K. Patterson, I. Gallego Romero, J.K. Pritchard and Y. Gilad. Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs. PLoS Genetics, doi: 10.1371/journal.pgen.1005793. Also available at bioRxiv, doi: 10.1101/013888. * denotes equal contribution. Full text available.

2015

I. Gallego Romero*, B.J. Pavlovic*, I. Hernando-Herraez, X. Zhou, M.C. Ward, N.E. Banovich, C.L. Kagan, J.E. Burnett, C.H. Huang, A. Mitrano, C.I. Chavarria, I.F. Ben-Nun, Y. Li, K. Sabatini, T.R. Leonardo, M. Parast, T. Marques-Bonet, L..C. Laurent, J.F. Loring, and Y. Gilad. Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics. eLife, doi: 10.7554/eLife.07103. Also available at bioRxiv, doi: 10.1101/008862. * denotes equal contribution. Full text available.

P.H. Sudmant, S. Mallick, B.J. Nelson, F. Hormozdiari, N. Krumm, J. Huddleston, B.P. Coe, C. Baker1, S. Nordenfelt, M. Bamshad, L.B. Jorde, O.L. Posukh, H. Sahakyan, W.S. Watkins, L. Yepiskoposyan, M.S. Abdullah, C.M. Bravi, C. Capelli, T. Hervig, J.T.S. Wee, C. Tyler-Smith, G. van Driem, I. Gallego Romero, A.R. Jha, S. Karachanak-Yankova, D. Toncheva, D. Comas, B. Henn, T. Kivisild, A. Ruiz-Linares, A. Sajantila, E. Metspalu, J. Parik, R. Villems, E.B. Starikovskaya, G. Ayodo, C. Beall, A. Di Rienzo, M. Hammer, R. Khusainova, E. Khusnutdinova, W. Klitz, C. Winkler, D. Labuda, M. Metspalu, S.A. Tishkoff, S. Dryomov, R. Sukernik, N. Patterson, D. Reich, and E.E. Eichler. Global diversity, population stratification, and selection of human copy number variation. Science, doi: 10.1126/science.aab3761. Full text available.

I. Garitaonandia*, H. Amir*, F.S. Boscolo*, G.K. Wambua, H.L. Schultheisz, K. Sabatini, R. Morey, S. Waltz, Y-C. Wang, H. Tran, T.R. Leonardo, K. Nazor, I. Slavin, C. Lynch, Y. Li, R. Coleman, I. Gallego Romero, G. Altun, D. Reynolds, S. Dalton, M. Parast, J.F. Loring** and L.C. Laurent**. Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions. PLOSone, doi: 10.1371/journal.pone.0118307. * and ** denote equal contributions. Full text available.

2014

I. Gallego Romero, A. A. Pai, J. Tung and Y. Gilad. RNA-seq: Impact of RNA degradation on transcript quantification. BMC Biology, 12:42 doi:10.1186/1741-7007-12-42. Full text available.

A. Cardona, L. Pagani, T. Antão, D.J. Lawson, C.A. Eichstaedt, B. Yngvadottir, M. Than Than Shwe, J. Wee, I. Gallego Romero, S. Raj, M. Metspalu, R. Villems, E. Willerslev, C. Tyler-Smith, B.A. Malyarchuk, M.V, Derenko and T. Kivisild. Genome-wide analysis of cold adaption in indigenous Siberian populations. PLOSone, doi: 10.1371/journal.pone.0098076. Full text available.

I. Lazaridis, N. Patterson, A. Mittnik, G. Renaud, S. Mallick, P.H. Sudmant, J. Schraiber, S. Castellano, K. Kirsanow, C. Economou, R. Bollongino, K.I. Bos, S. Nordenfelt, C. de Filippo, K. Pruefer, A. Tandon, S. Sawyer, C. Posth, G. Ayodo, H.M.A. Babiker, E. Balanovska, O. Balanovsky, C. Beall, H. Ben-Ami, J. Bene, F. Berrada, F. Brighelli, G. Busby, F. Cali, C. Capelli, M. Churnosov, D.E.C. Cole, L. Damba, G. van Driem, S. Dryomov, S. Fedorova, M. Francken, I. Gallego Romero, X. Gebremedhin, M. Gubina, M. Hammer, B. Henn, U. Hodoglugil, A. Jha, R. Kittles, E. Khusnutdinova, T. Kivisild, V. Kučinskas, R. Kusainova, L. Kushniarevich, L. Laredj, S. Litvinov, T. Loukidis, R. Mahley, B. Melegh, E. Metspalu, T. Moen, J. Mountain, T. Nyambo, L. Ossipova, J. Parik, F. Platanov, O. Posukh, A. Di Rienzo, V. Romano, I. Rudan, R. Ruizbakiev, H. Sahakyan, A. Salas, M. Shriver, A. Tarekegn, D. Toncheva, S. Turdikulova, I. Uktveryte, O. Utevska, M. Voevoda, J. Wahl, P. Zalloua, L. Yeppiskoposyan, T. Zemunik, M. Thomas, S. Tishkoff, R. Villems, D. Comas, L. Singh, K. Thangaraj, R. Sukernik, M. Metspalu, M. Meyer, E.E. Eichler, J. Burger, M. Slatkin, S. Pääbo, J. Kelso, D. Reich, and J. Krause. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, doi: 10.1038/nature13673. Also available at bioRxiv, doi: 10.1101/001552. Full text available.

2013

A. Bamberg Migliano, I. Gallego Romero, M. Metspalu, M. Leavesley, L. Pagani, T. Antão, D.W. Huang, B.T. Sherman, K. Siddle, C. Scholes, G. Hudjashov, E. Kaitokai, H. Mandui, A. Babalu, M. Belatti, A. Cagan, B. Hopkinshaw, C. Shaw, K. Tabbada, M. Nelis, E. Metspalu, R. Mägi, R.A. Lempicki, R. Villems, M. Mirazón Lahr and T. Kivisild. Evolution of the pygmy phenotype: evidence of positive selection from genome-wide scans in African, Asian and Melanesian pygmies. Human Biology, 85(1-3):251-84. Link.

C. Basu Mallick*, F.M. Iliescu*, M. Möls, S. Hill, R. Tamang, G. Chaubey, R. Goto, S.Y.W Ho, I. Gallego Romero, F. Crivellaro, G. Hudjashov, N. Rai, M. Metspalu, C.G.N. Mascie-Taylor, R. Pitchappan, L. Singh, M. Mirazón Lahr, K. Thangaraj, R. Villems and T. Kivisild. The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent . PLoS Genetics, doi: 10.1371/journal.pgen.1003912. * denotes equal contribution. Full text available.

S.M. Raj, L. Pagani, I. Gallego Romero, T. Kivisild, and W. Amos. A general linear model-based approach for inferring selection to climate. BMC Genetics doi: 10.1186/1471-2156-14-87. Full text available.

S.M. Raj, P. Halebeedu, J.S. Kadandale, M. Mirazón Lahr, I. Gallego Romero, J.R. Yadhav, M. Iliescu, N. Rai, F. Crivellaro, G. Chaubey, R. Villems, K. Thangaraj, K. Muniyappa, H.S. Chandra, and T. Kivisild. Variation at Diabetes- and Obesity-Associated Loci May Mirror Neutral Patterns of Human Population Diversity and Diabetes Prevalence in India. Annals of Human Genetics, doi: 10.1111/ahg.12028. Full text available.

2012

I. Gallego Romero, I Ruvinsky and Y. Gilad. Comparative studies of gene expression and the evolution of gene regulation. Nature Reviews Genetics, doi: 10.1038/nrg3229. Link.

L. Pagani, T. Kivisild, A. Tarekegn, R. Ekong, C. Plaster, I. Gallego Romero, Q. Ayub, S.Q. Mehdi, M.G. Thomas, D. Luiselli, E. Bekele, N. Bradman, D.J. Balding and C. Tyler-Smith. Ethiopian Genetic Diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. American Journal of Human Genetics, doi: 10.1016/j.ajhg.2012.05.015. Full text available.

D.G. MacArthur, S. Balasubramanian, A. Frankish, N. Huang, J. Morris, K. Walter, L. Jostins, L. Habegger, J.K. Pickrell, S.B. Montgomery, C.A. Albers, Z.D. Zhang, D.F. Conrad, G. Lunter, H. Zheng, Q. Ayub, M.A. DePristo, E. Banks, M. Hu, R.E. Handsaker, J.A. Rosenfeld, M. Fromer, M. Jin, X. Jasmine Mu, E. Khurana, K. Ye, M. Kay, G.I. Saunders, M-M. Suner, T. Hunt, I.H.A. Barnes, C. Amid, D.R. Carvalho-Silva, A.H. Bignell, C. Snow, B. Yngvadottir, S. Bumpstead, D.N. Cooper, Y. Xue, I. Gallego Romero, 1000 Genomes Project Consortium, J. Wang, Y. Li, R.A. Gibbs, S.A. McCarroll, E.T. Dermitzakis, J.K. Pritchard, J.C. Barrett, J. Harrow, M.E. Hurles, M.B. Gerstein and C. Tyler-Smith. A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Science, doi: 10.1126/science.1215040. Full text available.

2011

M. Hu, Q. Ayub, J.A. Guerra-Assunção, Q. Long, Z. Ning, N. Huang, I. Gallego Romero, L. Mamanova, P. Akan, X. Liu, A.J. Coffey, D.J. Turner, H. Swerdlow, J. Burton, M.A. Quail, D.F. Conrad, A.J. Enright, C. Tyler-Smith and Y. Xue. Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Human Genetics, doi: 10.1007/s00439-011-1111-9. Link.

M. Metspalu*, I. Gallego Romero*, B. Yunusbayev*, G. Chaubey, C. Basu Mallick, G. Hudjashov, M. Nelis, R. Mägi, E. Metspalu, M. Remm, R. Pitchappan, L. Singh, K. Thangaraj, R. Villems, and T. Kivisild. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. American Journal of Human Genetics, doi: 10.1016/j.ajhg.2011.11.010. * denotes equal contribution. Full text available.

M. Rasmussen, X. Guo, Y. Wang, K.E. Lohmueller, S. Rasmussen, A. Albrechtsen, L. Skotte, S. Lindgreen, M. Metspalu, T. Jombart, T. Kivisild, W. Zhai, A. Eriksson, A. Manica, L. Orlando, F. De La Vega, S. Tridico, E. Metspalu, K. Nielsen, M.C. Avila-Arcos, J.V. Moreno-Mayar, C. Muller, J. Dortch, M.T. Gilbert, O. Lund, A. Wesolowska, M. Karmin, L.A. Weinert, B. Wang, J. Li, S. Tai, F. Xiao, T. Hanihara, G. van Driem, A.R. Jha, F.X. Ricaut, P. de Knijff, A.B. Migliano, I. Gallego Romero, K. Kristiansen, D.M. Lambert, S. Brunak, P. Forster, B. Brinkmann, O. Nehlich, M. Bunce, M. Richards, R. Gupta, C.D. Bustamante, A. Krogh, R. A. Foley, M.M. Lahr, F. Balloux, T. Sicheritz-Pontén, R. Villems, R. Nielsen, W. Jun and E. Willerslev. An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science, doi: 10.1126/science.1211177. Full text available.

I. Gallego Romero, C. Basu Mallick, A Liebert, F Crivellaro, G Chaubey, A Liebert, Y Ital, R. Pitchappan, M. Metspalu, M. Eaaswarkanth, R. Villems, L. Singh, K. Thangaraj, M. G. Thomas, D. Swallow, M Mirazón Lahr, and T. Kivisild. Herders of Indian and European cattle share their predominant allele for milk tolerance. Molecular Biology and Evolution, doi: 10.1093/molbev/msr190. Full text available.

2010-2008

G. Chaubey, M. Metspalu, Y. Choi, R. Maagi, I. Gallego Romero, P. Soares, M. van Oven, D. M. Behar, S. Rootsi, G. Hudjashov, C. Basu Mallick, M. Karmin, M. Nelis, J. Parik, A. G. Reddy, E. Metspalu, G. van Driem, Y. Xue, C. Tyler-Smith, K. Thangaraj, L. Singh, M. Remm, M. B. Richards, M. Mirazón Lahr, M. Kayser, R. Villems, and T. Kivisild. Population genetic structure in Indian Austroasiatic speakers: The role of landscape barriers and sex-specific admixture. Molecular Biology and Evolution, doi: 10.1093/molbev/msq288, 2010. Full text available.

M. Eaaswarkhanth, I. Haque, Z. Ravesh, I. Gallego Romero, P. R. Meganathan, B. Dubey, F. A. Khan, G. Chaubey, T. Kivisild, C. Tyler-Smith, L. Singh, and K. Thangaraj. Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations. European Journal of Human Genetics, 18(3):354-63, 2010. Full text available.

I. Gallego Romero, A. Manica, J. Goudet, L. J. Lawson-Handley, and F. Balloux. How accurate is the current picture of human genetic variation? Heredity, 102(2):120-6, 2009. Full text available.

I. Gallego Romero and C. Ober. CFTR mutations and reproductive outcomes in a population isolate. Human Genetics, 122(6):583-8, 2008. Full text available.