Michael DeGiorgio

Molecular Biology and Evolution 38:1209-1224 (2021)

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Molecular Biology and Evolution 37:3267-3291 (2020)

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Molecular Biology and Evolution 37:3023-3046 (2020)

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Genome Biology and Evolution 12:842-859 (2020)

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Genome Biology and Evolution 12:3977-3995 (2020)

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Genome Biology and Evolution 11:3022-3034 (2019)

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Molecular Biology and Evolution 36:252-270 (2019)

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Molecular Biology and Evolution 36:177-199 (2019)

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Genome Biology and Evolution 10:1333-1350 (2018)

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American Journal of Human Genetics 102:806-815 (2018)

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Molecular Biology and Evolution 34:2704-2715 (2017)

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Proceedings of the National Academy of Sciences of the United States of America 114:4093-4098 (2017)

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G3: Genes, Genomes, Genetics 7:671-691 (2017)

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Molecular Biology and Evolution 33:2744-2758 (2016)

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American Journal of Human Genetics 95:584-589 (2014)

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PLoS Genetics 10:e1004561 (2014) bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS)

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American Journal of Human Genetics 93:1072-1086 (2013)

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Molecular Biology and Evolution 30:1877-1888 (2013)

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G3: Genes, Genomes, Genetics 3:909-916 (2013)

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Molecular Biology and Evolution 30:480-488 (2013)

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Molecular Biology and Evolution 27:552-659 (2010)

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Proceedings of the National Academy of Sciences of the United States of America 106:16057-16062 (2009)

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Molecular Biology and Evolution 26:501-512 (2009)

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BalLeRMix+: Mixture model approaches for robust joint identification of both positive selection and long-term balancing selection

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X Cheng, M DeGiorgio

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Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals

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MR Mughal, M DeGiorgio

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Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

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WM Guiblet, M DeGiorgio, X Cheng, F Chiaromonte, KA Eckert, Y-F Huang, KD Makova

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Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data

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RH Adams, H Blackmon, M DeGiorgio

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PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments

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RH Adams, TA Castoe, M DeGiorgio

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Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data

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M DeGiorgio, R Assis

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Understanding the adaptive evolutionary history of South American ancient and modern populations via genomics

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J Lindo, M DeGiorgio

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Learning the properties of adaptive regions with functional data analysis

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MR Mughal, H Koch, J Huang, F Chiaromonte, M DeGiorgio

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VolcanoFinder: genomic scans for adaptive introgression

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D Setter*, S Mousset*, X Cheng, R Nielsen, M DeGiorgio, J Hermisson

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Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection

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A likelihood approach for uncovering selective sweep signatures from haplotype data

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AM Harris, M DeGiorgio

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Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels

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R Vegesna, M Tomaszkiewicz, OA Ryder, R Campos-Sanchez, P Medvedev, M DeGiorgio, KD Makova

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Identifying and classifying shared selective sweeps from multilocus data

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Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure

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H Koch, M DeGiorgio

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A high resolution view of adaptive events in a plasmid

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H Mei, B Arbeithuber, MA Cremona, M DeGiorgio, A Nekrutenko

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Large-scale whole-genome sequencing of three diverse Asian populations in Singapore

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D Wu, J Dou, X Chai, C Bellis, A Wilm, CC Shih, WWJ Soon, N Bertin, CB Lin, CC Khor, M DeGiorgio, S Cheng, L Bao, N Karnani, WYK Hwang, S Davila, P Tan, A Shabbir, A Moh, E-K Tan, JN Foo, LL Goh, KP Leong, RSY Foo, CSP Lam, AM Richards, C-Y Cheng, T Aung, TY Wong, HK Ng, SG10K Consortium

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Localizing and classifying adaptive targets with trend filtered regression

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Detection of shared balancing selection in the absence of trans-species polymorphism

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Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

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AM Harris, NR Garud, M DeGiorgio

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High levels of copy number variation of ampliconic genes across major human Y haplogroups

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D Ye, A Zaidi, M Tomaszkiewicz, K Anthony, C Liebowitz, M DeGiorgio, MD Shriver, KD Makova

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Patterns of genetic coding variation in a Native American population before and after European contact

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J Lindo, M Rogers, EK Mallot, B Petzelt, J Mitchell, D Archer, JS Cybulski, RS Malhi, M DeGiorgio

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Fast and robust detection of ancestral selective sweeps

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X Cheng, C Xu, M DeGiorgio

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Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation

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D Xu, P Pavlidis, RO Taskent, N Alachiotis, C Flanagan, M DeGiorgio, R Blekhman, S Ruhl, O Gokcumen

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Admixture and ancestry inference from ancient and modern samples through measures of population genetic drift

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Ancient individuals from the North American Northwest Coast reveal 10, 000 years of regional genetic continuity

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J Lindo, A Achilli, D Archer, C Valdiosera, B Petzelt, J Mitchell, R Worl, EJ Dixon, T Fifield, M Rasmussen, E Willerslev, J Cybulski, B Kemp, M DeGiorgio, RS Malhi

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An unbiased estimator of gene diversity with improved variance for samples containing related and inbred individuals of any ploidy

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Empty niches after extinctions increase population sizes of modern corals

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C Prada, B Hanna, AF Budd, C Woodley, J Schmutz, J Grimwood, R Iglesias-Prieto, JM Pandolfi, D Levitan, N Knowlton, H Kitano, M DeGiorgio*, M Medina*

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

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J Lindo, E Huerta-Sanchez, S Nakagome, M Rasmussen, B Petzelt, J Mitchell, JS Cybulski, E Willerslev, M DeGiorgio, RS Malhi

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Genomic analyses inform on migration events during the peopling of Eurasia

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L Pagani, DJ Lawson, E Jagoda, A Morseburg, A Eriksson, M Mitt, F Clemente, G Hudjashov, M DeGiorgio, L Saag, JD Wall, A Cardona, R Magi, MA Wilson Sayres, S Kaewert, C Inchley, CL Scheib, M Jarve, M Karmin, GS Jacobs, T Antao, FM Iliescu, A Kushniarevich, Q Ayub, C Tyler-Smith, Y Xue, B Yunusbayev, K Tambets, CB Mallick, L Saag, E Pocheshkhova, G Andriadze, C Muller, MC Westaway, DM Lambert, G Zoraqi, S Turdikulova, D Dalimova, Z Sabitov, GNN Sultana, J Lachance, S Tishkoff, K Momynaliev, J Isakova, LD Damba, M Gubina, P Nymadawa, I Evseeva, L Atramentova, O Utevska, F-X Ricaut, N Brucato, H Sudoyo, T Letellier, MP Cox, NA Barashkov, V Skaro, L Mulahasanovic, D Primorac, H Sahakyan, M Mormina, CA Eichstaedt, DV Lichman, S Abdullah, G Chaubey, JTS Wee, E Mihailov, A Karunas, S Litvinov, R Khusainova, N Ekomasova, V Akhmetova, I Khidiyatova, D Marjanovic, L Yepiskoposyan, DM Behar, E Balanovska, A Metspalu, M Derenko, B Malyarchuk, M Voevoda, SA Fedorova, LP Osipova, MM Lahr, P Gerbault, M Leavesley, AB Migliano, M Petraglia, O Balanovsky, EK Khusnutdinova, E Metspalu, MG Thomas, A Manica, R Nielsen, R Villems, E Willerslev, T Kivisild, M Metspalu

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Reverse transcription errors and RNA-DNA differences at short tandem repeats

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A Fungtammasan, M Tomaszkiewicz, R Campos-Sanchez, K Eckert, M DeGiorgio, KD Makova

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Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure

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M DeGiorgio, NA Rosenberg

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SweepFinder2: Increased sensitivity, robustness, and flexibility

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M DeGiorgio, CD Huber, MJ Hubisz, I Hellmann, R Nielsen

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

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CD Huber, M DeGiorgio, I Hellmann, R Nielsen

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

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M Raghavan*, M Steinrucken*, K Harris*, S Schiffels*, S Rasmussen*, M DeGiorgio*, A Albrechtsen*, C Valdiosera*, MC Avila-Arcos*, A-S Malaspinas*, A Eriksson, I Moltke, M Metspalu, JR Homburger, J Wall, OE Cornejo, JV Moreno-Mayar, TS Korneliussen, T Pierre, M Rasmussen, PF Campos, P de Barros Damgaard, ME Allentoft, J Lindo, E Metspalu, R Rodriguez-Varela, J Mansilla, C Henrickson, A Siguin-Orlando, H Malmstrom, T Safford Jr, SS Shingarpure, A Moreno-Esrada, M Karmin, K Tambets, A Bergstrom, Y Xue, V Warmuth, A Friend, J Singarayer, P Valdes, F Balloux, I Leboreiro, JL Vera, H Rangel-Villalobos, D Pettener, D Luiselli, LG Davis, E Heyer, CPE Zollikofer, MS Ponce de Leon, CI Smith, V Grimes, K-A Pike, M Deal, BT Fuller, B Arriaza, V Standen, MF Luz, F Ricaut, N Guidon, L Osipova, MI Voevoda, OL Posukh, O Balanovsky, M Lavryashina, Y Bogunov, E Khusnutdinova, M Gubina, E Balanovska, S Fedorova, S Litvinov, B Malyarchuk, M Derenko, MJ Mosher, D Archer, J Cybulski, B Petzelt, J Mitchell, R World, PJ Norman, P Parham, BM Kemp, T Kivisild, C Tyler-Smith, MS Sandhu, M Crawford, R Villems, DG Smith, MR Waters, T Goebel, JR Johnson, RS Malhi, M Jakobsson, DJ Meltzer, A Manica, R Durbin, CD Bustamante, YS Song, R Nielsen, E Willerslev

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

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M Karmin, L Saag, M Vicente, MA Wilson Sayres, M Jarve, U Gerst Talas, S Rootsi, A-M Ilumae, R Magi, M Mitt, L Pagani, T Puurand, Z Faltyskova, F Clemente, A Cardona, E Metspalu, H Sahakyan, B Yunusbayev, G Hudjashov, M DeGiorgio, E-L Loogvali, C Eichstaedt, M Eelmets, G Chaubey, K Tambets, S Litvinov, M Mormina, Y Xue, Q Ayub, G Zoraqi, T Sand Korneliussen, F Akhatova, J Lachance, S Tishkoff, K Momynaliev, F-X Ricaut, P Kusuma, H Razafindrazaka, D Pierron, MP Cox, G Nurun Nahar Sultana, R Willerslev, C Muller, M Westaway, D Lambert, V Skaro, L Kovacevic, S Turdikulova, D Dalimova, R Khusainova, N Trofimova, V Akhmetova, I Khidiyatova, DV Lichman, J Isakova, E Pocheshkhova, Z Sabitov, NA Barashkov, P Nymadawa, E Mihailov, J Wee Tien Seng, I Evseeva, A Bamberg Migliano, S Abdullah, G Andriadze, D Primorac, L Atramentova, O Utevska, L Yepiskoposyan, D Marjanovic, A Kushniarevich, DM Behar, C Gilissen, L Vissers, JA Veltman, E Balanovska, M Derenko, B Malyarchuk, A Metspalu, S Fedorova, A Eriksson, A Manica, FL Mendez, TM Karafet, KR Veeramah, NBradman, MF Hammer, LP Osipova, O Balanovsky, EK Khusnutdinova, K Johnsen, M Remm, MG Thomas, C Tyler-Smith, PA Underhill, E Willerslev, R Nielsen, M Metspalu, R Villems, T Kivisild

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Computational and statistical analyses of insertional polymorphic endogenous retroviruses in a non-model organism

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L Bao, D Elleder, R Malhotra, M DeGiorgio, T Maravegias, L Horvath, L Carrel, C Gillin, T Hron, H Fabryova, DR Hunter, M Poss

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A selective sweep on a deleterious mutation in CPT1A in Arctic populations

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FJ Clemente, A Cardona, CE Inchley, MB Peter, G Jacobs, L Pagani, DJ Lawson, T Antao, M Vicente, M Mitt, M DeGiorgio, Z Faltyskova, Y Xue, Q Ayub, M Szpak, R Magi, A Eriksson, A Manica, M Raghavan, M Rasmussen, S Rasmussen, E Willerslev, A Vidal-Puig, C Tyler-Smith, R Villems, R Nielsen, M Metspalu, B Malyarchuk, M Derenko, T Kivisild

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Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

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A-S Malaspinas, O Lao, H Schroeder, M Rasmussen, M Raghavan, I Moltke, PF Campos, F Santana Sagredo, S Rasmussen, VF Goncalves, A Albrechtsen, ME Allentoft, PLF Johnson, M Li, S Reis, DV Bernardo, M DeGiorgio, AT Duggan, M Bastos, Y Wang, J Stenderup, JV Moreno-Mayar, S Brunak, T Sicheritz-Ponten, E Hodges, GJ Hannon, L Orlando, TD Price, JD Jensen, R Nielsen, J Heinemeier, J Olsen, C Rodrigues-Carvalho, M Mirazon Lahr, WA Neves, M Kayser, T Higham, M Stoneking, SDJ Pena, E Willerslev

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The genetic prehistory of the New World Arctic

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M Raghavan, M DeGiorgio, A Albrechtsen, I Moltke, P Skogland, TS Korneliussen, B Grnnow, M Appelt, H Christian Gullv, TM Friesen, W Fitzhugh, H Malmstrom, S Rasmussen, J Olsen, L Melchior, BT Fuller, SM Fahrni, T Stafford Jr, V Grimes, MAP Renouf, J Cybulski, N Lynnerup, M Mirazon Lahr, K Britton, R Knecht, J Arneborg, M Metspalu, OE Cornejo, A-S Malaspinas, Y Wang, M Rasmussen, V Raghavan, TVO Hansen, E Khusnutdinova, T Pierre, K Dneprovsky, C Andreasen, H Lange, MG Hayes, J Coltrain, VA Spitsyn, A Gotherstrom, L Orlando, T Kivisild, R Villems, MH Crawford, FC Nielsen, J Dissing, J Heinemeier, M Meldgaard, C Bustamante, DH O'Rourke, M Jakobsson, MTP Gilbert, R Nielsen, E Willerslev

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

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M DeGiorgio, KE Lohmueller, R Nielsen

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A-S Malaspinas, O Tange, JV Moreno-Mayar, M Rasmussen, M DeGiorgio, Y Wang, CE Valdiosera, G Politis, E Willerslev, R Nielsen

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An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

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M DeGiorgio, J Syring, AJ Eckert, A Liston, R Cronn, DB Neale, NA Rosenberg

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Derived immune and ancestral pigmentation alleles in a 7, 000-year-old Mesolithic European

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I Olalde, ME Allentoft, F Sanchez-Quinto, G Santpere, CWK Chiang, M DeGiorgio, J Prado-Martinez, JA Rodriguez, S Rasmussen, J Quilez, O Ramirez, M Fernandez, ME Prada, JMV Encinas, R Nielsen, MG Netea, J Novembre, RA Sturm, P Sabeti, T Marques-Bonet, A Navarro, E Willerslev, C Lalueza-Fox

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The genome of a late Pleistocene human found at a Clovis burial site in western Montana

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M Rasmussen, SL Anzick, MR Waters, P Skoglund, M DeGiorgio, TW Stafford Jr, S Rasmussen, I Moltke, A Albrechtsen, SM Doyle, GD Poznik, V Gudmundsdottir, R Yadav, A-S Malaspinas, SS White V, M Allentoft, OE Cornejo, K Tambets, A Eriksson, P Heintzman, M Meiri, M Karmin, T Sand Korneliussen, TL Pierre, J Stenderup, L Saag, V Warmuth, M Cabrita Lopes, S Brunak, T Sicheritz-Ponten, I Barnes, M Collins, L Orlando, F Balloux, A Manica, M Metspalu, CD Bustamante, M Jakobsson, R Gupta, R Nielsen, E Willerslev

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

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M DeGiorgio, JH Degnan

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Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans

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M Raghavan, P Skoglund, KE Graf, M Metspalu, A Albrechtsen, I Moltke, S Rasmussen, TW Stafford Jr, L Orlando, E Metspalu, M Karmin, K Tambets, S Rootsi, R Magi, PF Campos, E Balanovska, O Balanovsky, E Khusnutdinova, S Litvinov, LP Osipova, SA Fedorova, MI Voevoda, M DeGiorgio, T Sicheritz-Ponten, S Brunak, S Demeshchenko, T Kivisild, R Villems, R Nielsen, M Jakobsson, E Willerslev

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Whole-exome sequencing of 2, 000 Danish individuals and the role of rare coding variants in type 2 diabetes

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KE Lohmueller, T Spars, Q Li, E Andersson, T Korneliussen, A Albrechtsen, K Banasik, N Grarup, I Hallgrimsdottir, K Kiil, TO Kilpelainen, NT Krarup, TH Pers, G Sanchez, Y Hu, M DeGiorgio, T Jrgensen, A Sandbk, T Lauritzen, S Brunak, K Kristiansen, Y Li, T Hansen, J Wang, R Nielsen, O Pedersen

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Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations

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E Huerta-Sanchez*, M DeGiorgio*, L Pagani*, A Tarekegn, R Ekong, T Antao, A Cardona, HE Montgomery, GL Cavalleri, PA Robbins, ME Weale, N Bradman, E Bekele, T Kivisild, C Tyler-Smith, R Nielsen

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Population structure in a comprehensive data set on human microsatellite variation

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TJ Pemberton, M DeGiorgio, NA Rosenberg

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

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

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M DeGiorgio, JH Degnan, NA Rosenberg

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

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M DeGiorgio*, I Jankovic*, NA Rosenberg

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Fast and consistent estimation of species trees using supermatrix rooted triples

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Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa

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M DeGiorgio, M Jakobsson, NA Rosenberg

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Properties of consensus methods for inferring species trees from gene trees

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JH Degnan, M DeGiorgio, D Bryant, NA Rosenberg

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An unbiased estimator of gene diversity in samples containing related individuals

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