{"id":60,"date":"2026-01-12T21:28:06","date_gmt":"2026-01-12T21:28:06","guid":{"rendered":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/?page_id=60"},"modified":"2026-11-10T20:26:48","modified_gmt":"2026-11-10T20:26:48","slug":"publications-2","status":"publish","type":"page","link":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/publications-2\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

* indicates equal contributions
\u2020 indicates corresponding author
Underline indicates DeGiorgio group m<\/p>\n\n\n\n

Preprints<\/strong><\/p>\n\n\n\n

Bacterial DNA invasian triggers transposable element proliferation and genome expansion<\/a>
ZP Cohen\u2020<\/sup>, L Perkin, PB Frandsen, M DeGiorgio\u2020<\/sup>, R Assis\u2020<\/sup>
bioRxiv<\/em><\/strong> doi:10.64898\/2026.07.14.738529 (2026)<\/p>\n\n\n\n

Recent positive selection implicates IP6K3<\/em> and MAPT<\/em> as metabolically relevant loci in South Asians<\/a>
E Pennarun*, B Banfalvi*, Y Li, V Bui, S Hodgson, M Bigossi, S Arnab, T Naimah, S Rison, D Stow, V Baskar, J Saravanan, V Radha, G&H Research Team, MDRF Research Team, V Mohan, M DeGiorgio, R Mohan Anjana, S Finer, M Fumagalli, MK Siddiqui\u2020<\/sup>
medRxiv<\/em><\/strong> doi:10.64898\/2026.03.12.26348237 (2026)<\/p>\n\n\n\n

Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil<\/a>
K Macias Calix, C Borges, AL Nascimento Oliveira, SC Albuquerque de Luna, CM Souza Cunha, AM Siqueira, AL Campelo dos Santos, M DeGiorgio, J Lindo, R Assis\u2020<\/sup>
bioRxiv<\/em><\/strong> doi:10.64898\/2025.12.10.693243 (2025)<\/p>\n\n\n\n

Journal publications<\/strong><\/p>\n\n\n\n

Prediction of chronic obstructive pulmonary disease using machine learning models<\/a>
S Ali, O Faqah, E Neubarth, MS Ashraf, M DeGiorgio, M Block, W Asghar\u2020<\/sup>
Scientific Reports<\/em><\/strong> accepted (2026)<\/p>\n\n\n\n

Negative frequency-dependent selection: a positive outlook with deep learning<\/a>
CG Santander*, AL Campelo dos Santos*, SP Arnab, M Fumagalli\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
Philosphical Transactions of the Royal Society B<\/em><\/strong> 381:20250170 (2026)<\/p>\n\n\n\n

Detecting positive selection by modeling structure within images of genetic variation<\/a>
MR Amin, SP Arnab, M Khan, M DeGiorgio\u2020<\/sup>
Genome Biology and Evolution<\/em><\/strong> 18:evag085 (2026)<\/p>\n\n\n\n

Identifying adaptive footprints in the presence of demographic uncertainty<\/a>
SP Arnab, M Khan, AL Campelo dos Santos, M Fumagalli, M DeGiorgio\u2020<\/sup>
Genome Biology and Evolution<\/em><\/strong> 18:evag075 (2026)<\/p>\n\n\n\n

AI solutions for evolutionary genomics of nonmodel species<\/a>
M DeGiorgio, SP Arnab, M Fumagalli\u2020<\/sup>
Evolution Letters<\/em><\/strong> 10:135-146 (2026)<\/p>\n\n\n\n

Discriminating models of trait evolution<\/a>
JR Lozanno, S Jangra, M DeGiorgio, R Assis, R Adams\u2020<\/sup>
Evolution<\/em><\/strong> 80:697-710 (2026)<\/p>\n\n\n\n

2025 Zuckerkandl Prize<\/a>
MG Behringer, M DeGiorgio, M Perez, DA Liberles\u2020<\/sup>
Journal of Molecular Evolution<\/em><\/strong> 94:1-2 (2026)<\/p>\n\n\n\n

Robust regression rescues poor phylogenetic decisions<\/a>
M Duncan, M DeGiorgio, R Assis\u2020<\/sup>, R Adams\u2020<\/sup>
BMC Ecology and Evolution<\/em><\/strong> 25:108 (2025)<\/p>\n\n\n\n

Genomic anomaly detection with functional data analysis<\/a>
R Kanjilal, AL Campelo dos Santos, SP Arnab, M DeGiorgio\u2020<\/sup>, R Assis\u2020<\/sup>
Genes<\/em><\/strong> 16:710 (2025)<\/p>\n\n\n\n

Pre-European contact leprosy in the Americas and its current persistence<\/a>
M Lopopolo*, C Avanzi*, S Duchene, P Luisi, A De Flamingh, GY Ponce-Soto, G Tressieres, S Neumeyer, F Lemoine, EA Nelson, M Iraeta-Orbegozo, JS Cybulski, J Mitchell, VT Marks, LB Adams, J Lindo, M DeGiorgio, N Ortiz, C Wiens, J Hiebert, A Bonifaz, GM De Oca, V Paredes-Solis, C Franco-Paredes, L Vera-Cabrera, JG Pereira Brunelli, M Jackson, JH Spencer, CG Salgado, X-Y Han, CM Pearce, AK Warren, PS Rosa, AJ De Finardi, A De FF Belone, C Ferreira, PN Suffys, AN Brum Fontes, SEG Vasconcellos, R Schaub, P Couppi\u00e9, KN Alsibai, R Hern\u00e1ndez-Castro, MS Miranda, I Estrada-Garcia, F Jurado-Santacruz, L Orlando, H Schroeder, L Quintana-Murci, M Del Papa, M Lahiri, RS Malhi, S Rasmussen, N Rascovan\u2020<\/sup>
Science<\/em><\/strong> doi:10.1126\/science.adu7144 (2025)<\/p>\n\n\n\n

Efficient detection and characterization of targets of natural selection using transfer learning<\/a>
SP Arnab, AL Campelo dos Santos, M Fumagalli, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 42:msaf094 (2025)<\/p>\n\n\n\n

A tale of too many trees: a conundrum for phylogenetic regression<\/a>
RH Adams\u2020<\/sup>, JR Lozano, M Duncan, J Green, R Assis*, M DeGiorgio*
Molecular Biology and Evolution<\/em><\/strong> 42:msaf032 (2025)<\/p>\n\n\n\n

TraitTrainR<\/em>: Accelerating large-scale simulation under models of trait evolution<\/a>
JR Lozano, M Duncan, DD McKenna, T Castoe, M DeGiorgio, RH Adams\u2020<\/sup>
Bioinformatics Advances<\/em><\/strong> 5:vbae196 (2025)<\/p>\n\n\n\n

Digital image processing to detect adaptive evolution<\/a>
MR Amin*, M Hasan*, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 41:msae242 (2024)<\/p>\n\n\n\n

Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times<\/a>
D First Rider, A Crop Eared Wolf, J Murray, A de Flamingh, AL Campelo dos Santos, F Lano\u00eb, MN Zedo\u00f1o, M DeGiorgio\u2020<\/sup>, J Lindo\u2020<\/sup>, RS Malhi\u2020<\/sup>
Science Advances<\/em><\/strong> 10:eadl6595 (2024)<\/p>\n\n\n\n

Predicting evolutionary targets and parameters of gene deletion from expression data<\/a>
AL Campelo dos Santos\u2020<\/sup>, M DeGiorgio*, R Assis*
Bioinformatics Advances<\/em><\/strong> 4:vbae002 (2024)<\/p>\n\n\n\n

Robust phylogenetic regression<\/a>
RH Adams\u2020<\/sup>, Z Cain, R Assis*, M DeGiorgio*
Systematic Biology<\/em><\/strong> 73:140-157 (2023)<\/p>\n\n\n\n

Tensor decomposition based feature extraction and classification to detect natural selection from genomic data<\/a>
MR Amin\u2020<\/sup>, M Hasan, SP Arnab, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 40:msad216 (2023)<\/p>\n\n\n\n

Likelihood-based tests of species trees<\/a>
RH Adams\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 40:msad159 (2023)<\/p>\n\n\n\n

Uncovering footprints of natural selection through spectral analysis of genomic summary statistics<\/a>
SP Arnab\u2020<\/sup>, MR Amin, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 40:msad157 (2023)<\/p>\n\n\n\n

Predicting expression divergence between single-copy orthologs in two species<\/a>
AA Piya, M DeGiorgio, R Assis\u2020<\/sup>
Genome Biology and Evolution<\/em><\/strong> 15:evad078 (2023)<\/p>\n\n\n\n

Genomic evidence for adaptation to tuberculosis in the Andes before European contact<\/a>
SK Joseph, NR Migliore, A Olivieri, A Torroni, AC Owings, M DeGiorgio, WG Ord\u00f3\u00f1ez, JJO Aguil\u00fa, F Gonz\u00e1lez-Andrade\u2020<\/sup>, A Achilli\u2020<\/sup>, J Lindo\u2020<\/sup>
iScience<\/em><\/strong> 26:106034 (2023)<\/p>\n\n\n\n

Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes<\/a>
AL Campelo dos Santos\u2020<\/sup>, HSL Sullasi, O Gokcumen, J Lindo\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
American Journal of Biological Anthropology<\/em><\/strong> 180:703-714 (2023)<\/p>\n\n\n\n

Genomic evidence for ancient human migration routes along South America’s Altantic coast<\/a>
AL Campelo dos Santos\u2020<\/sup>, A Owings, HSL Sullasi, O Gokcumen, M DeGiorgio\u2020<\/sup>, J Lindo\u2020<\/sup>
Proceedings of the Royal Society B: Biological Sciences<\/em><\/strong> 289:20221078 (2022)<\/p>\n\n\n\n

The roles of balancing selection and recombination in the evolution of rattlesnake venom<\/a>
DR Schield\u2020<\/sup>, BW Perry, RH Adams, ML Holding, ZL Nikolakis, SS Gopalan, CF Smith, JM Parker, JM Meik, M DeGiorgio, SP Mackessy, TA Castoe\u2020<\/sup>
Nature Ecology and Evolution<\/em><\/strong> 6:1367-1380 (2022)<\/p>\n\n\n\n

The genomic prehistory of the Indigenous people of Uruguay<\/a>
J Lindo\u2020<\/sup>, R De La Rosa, AL Campelo dos Santos, M Sans, M DeGiorgio, G Figueiro\u2020<\/sup>
PNAS Nexus<\/em><\/strong> 1:pgac047 (2022)<\/p>\n\n\n\n

A spatially aware likelihood test to detect sweeps from haplotype distributions<\/a>
M DeGiorgio\u2020<\/sup>, ZA Szpiech\u2020<\/sup>
PLoS Genetics<\/em><\/strong> 18:e1010134 (2022)<\/p>\n\n\n\n

Ancient and modern genomics of the Ohlone Indigenous population of California<\/a>
AL Severson, BF Byrd, EK Mallott, AC Owings, M DeGiorgio, A de Flamingh, C Nijmeh, MV Arellano, A Leventhal, NA Rosenberg\u2020<\/sup>, RS Malhi\u2020<\/sup>
Proceedings of the National Academy of Sciences of the United States of America<\/em><\/strong> 119:e2111533119 (2022)<\/p>\n\n\n\n

BalLeRMix+<\/em>: Mixture model approaches for robust joint identification of both positive selection and long-term balancing selection<\/a>
X Cheng\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
Bioinformatics<\/em><\/strong> 38:861-863 (2022)<\/p>\n\n\n\n

Properties and unbiased estimation of F<\/em>– and D<\/em>-statistics in samples containing related and inbred individuals<\/a>
MR Mughal\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
Genetics<\/em><\/strong> 220:iyab090 (2021)<\/p>\n\n\n\n

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome<\/a>
WM Guiblet, M DeGiorgio, X Cheng, F Chiaromonte, KA Eckert, Y-F Huang\u2020<\/sup>, KD Makova\u2020<\/sup>
Genome Research<\/em><\/strong> 31:1136-1149 (2021)<\/p>\n\n\n\n

Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data<\/a>
RH Adams, H Blackmon, M DeGiorgio\u2020<\/sup>
Systematic Biology<\/em><\/strong> 70:660-680 (2021)<\/p>\n\n\n\n

PhyloWGA<\/em>: chromosome-aware phylogenetic interrogation of whole genome alignments<\/a>
RH Adams\u2020<\/sup>, TA Castoe, M DeGiorgio\u2020<\/sup>
Bioinformatics<\/em><\/strong> 37:1923-1925 (2021)<\/p>\n\n\n\n

Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data<\/a>
M DeGiorgio\u2020<\/sup>, R Assis\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 38:1209-1224 (2021)<\/p>\n\n\n\n

Understanding the adaptive evolutionary history of South American ancient and modern populations via genomics<\/a>
J Lindo\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
Genes<\/em><\/strong> 12:360 (2021)<\/p>\n\n\n\n

Learning the properties of adaptive regions with functional data analysis<\/a>
MR Mughal\u2020<\/sup>, H Koch, J Huang, F Chiaromonte, M DeGiorgio\u2020<\/sup>
PLoS Genetics<\/em><\/strong> 16:e1008896 (2020)<\/p>\n\n\n\n

VolcanoFinder: genomic scans for adaptive introgression<\/a>
D Setter*, S Mousset*, X Cheng, R Nielsen, M DeGiorgio\u2020<\/sup>, J Hermisson\u2020<\/sup>
PLoS Genetics<\/em><\/strong> 16:e1008867 (2020)<\/p>\n\n\n\n

Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection<\/a>
X Cheng, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 37:3267-3291 (2020)<\/p>\n\n\n\n

A likelihood approach for uncovering selective sweep signatures from haplotype data<\/a>
AM Harris, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 37:3023-3046 (2020)<\/p>\n\n\n\n

Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels<\/a>
R Vegesna, M Tomaszkiewicz, OA Ryder, R Campos-S\u00e1nchez, P Medvedev, M DeGiorgio\u2020<\/sup>, KD Makova\u2020<\/sup>
Genome Biology and Evolution<\/em><\/strong> 12:842-859 (2020)<\/p>\n\n\n\n

Identifying and classifying shared selective sweeps from multilocus data<\/a>
AM Harris, M DeGiorgio\u2020<\/sup>
Genetics<\/em><\/strong> 215:143-171 (2020)<\/p>\n\n\n\n

Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure<\/a>
H Koch, M DeGiorgio\u2020<\/sup>
Genome Biology and Evolution<\/em><\/strong> 12:3977-3995 (2020)<\/p>\n\n\n\n

A high resolution view of adaptive events in a plasmid<\/a>
H Mei, B Arbeithuber, MA Cremona, M DeGiorgio, A Nekrutenko
Genome Biology and Evolution<\/em><\/strong> 11:3022-3034 (2019)<\/p>\n\n\n\n

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore<\/a>
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
Cell<\/em><\/strong> 3:736-749 (2019)<\/p>\n\n\n\n

Localizing and classifying adaptive targets with trend filtered regression<\/a>
MR Mughal, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 36:252-270 (2019)<\/p>\n\n\n\n

Detection of shared balancing selection in the absence of trans-species polymorphism<\/a>
X Cheng, M DeGiorgio\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 36:177-199 (2019)<\/p>\n\n\n\n

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity<\/a>
AM Harris, NR Garud, M DeGiorgio\u2020<\/sup>
Genetics<\/em><\/strong> 210:1419-1452 (2018)<\/p>\n\n\n\n

High levels of copy number variation of ampliconic genes across major human Y haplogroups<\/a>
D Ye, A Zaidi, M Tomaszkiewicz, K Anthony, C Liebowitz, M DeGiorgio, MD Shriver, KD Makova
Genome Biology and Evolution<\/em><\/strong> 10:1333-1350 (2018)<\/p>\n\n\n\n

Patterns of genetic coding variation in a Native American population before and after European contact<\/a>
J Lindo, M Rogers, EK Mallot, B Petzelt, J Mitchell, D Archer, JS Cybulski, RS Malhi\u2020<\/sup>, M DeGiorgio\u2020<\/sup>
American Journal of Human Genetics<\/em><\/strong> 102:806-815 (2018)<\/p>\n\n\n\n

Fast and robust detection of ancestral selective sweeps<\/a>
X Cheng, C Xu, M DeGiorgio\u2020<\/sup>
Molecular Ecology<\/em><\/strong> 26:6871-6891 (2017)<\/p>\n\n\n\n

Archaic hominin introgression in Africa contributes to functional salivary MUC7<\/em> genetic variation<\/a>
D Xu, P Pavlidis, RO Taskent, N Alachiotis, C Flanagan, M DeGiorgio, R Blekhman, S Ruhl, O Gokcumen
Molecular Biology and Evolution<\/em><\/strong> 34:2704-2715 (2017)<\/p>\n\n\n\n

Admixture and ancestry inference from ancient and modern samples through measures of population genetic drift<\/a>
AM Harris, M DeGiorgio\u2020<\/sup>
Human Biology<\/em><\/strong> 89:1 (2017)<\/p>\n\n\n\n

Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity<\/a>
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\u2020<\/sup>, M DeGiorgio\u2020<\/sup>, RS Malhi\u2020<\/sup>
Proceedings of the National Academy of Sciences of the United States of America<\/em><\/strong> 114:4093-4098 (2017)<\/p>\n\n\n\n

An unbiased estimator of gene diversity with improved variance for samples containing related and inbred individuals of any ploidy<\/a>
AM Harris, M DeGiorgio\u2020<\/sup>
G3: Genes, Genomes, Genetics<\/em><\/strong> 7:671-691 (2017)<\/p>\n\n\n\n

Empty niches after extinctions increase population sizes of modern corals<\/a>
C Prada\u2020<\/sup>, B Hanna, AF Budd, C Woodley, J Schmutz, J Grimwood, R Iglesias-Prieto, JM Pandolfi, D Levitan, N Knowlton, H Kitano, M DeGiorgio\u2020<\/sup>*, M Medina\u2020<\/sup>*
Current Biology<\/em><\/strong> 26:1-5 (2016)<\/p>\n\n\n\n

A time transect of exomes from a Native American population before and after European contact<\/a>
J Lindo, E Huerta-S\u00e1nchez, S Nakagome, M Rasmussen, B Petzelt, J Mitchell, JS Cybulski, E Willerslev, M DeGiorgio\u2020<\/sup>, RS Malhi\u2020<\/sup>
Nature Communications<\/em><\/strong> 7:13175 (2016)<\/p>\n\n\n\n

Genomic analyses inform on migration events during the peopling of Eurasia<\/a>
L Pagani, DJ Lawson, E Jagoda, A M\u00f6rseburg, A Eriksson, M Mitt, F Clemente, G Hudjashov, M DeGiorgio, L Saag, JD Wall, A Cardona, R M\u00e4gi, MA Wilson Sayres, S Kaewert, C Inchley, CL Scheib, M J\u00e4rve, 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 Marjanovi\u0107, 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
Nature<\/em><\/strong> 538:238-242 (2016)<\/p>\n\n\n\n

Reverse transcription errors and RNA-DNA differences at short tandem repeats<\/a>
A Fungtammasan, M Tomaszkiewicz, R Campos-Sanchez, K Eckert, M DeGiorgio\u2020<\/sup>, KD Makova\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 33:2744-2758 (2016)<\/p>\n\n\n\n

Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure<\/a>
M DeGiorgio\u2020<\/sup>, NA Rosenberg
Theoretical Population Biology<\/em><\/strong> 110:12-24 (2016)<\/p>\n\n\n\n

SweepFinder2<\/em>: Increased sensitivity, robustness, and flexibility<\/a>
M DeGiorgio\u2020<\/sup>, CD Huber, MJ Hubisz, I Hellmann, R Nielsen
Bioinformatics<\/em><\/strong> 32:1895-1897 (2016)<\/p>\n\n\n\n

Detecting recent selective sweeps while controlling for mutation rate and background selection<\/a>
CD Huber, M DeGiorgio, I Hellmann, R Nielsen
Molecular Ecology<\/em><\/strong> 25:142-156 (2015)<\/p>\n\n\n\n

Genomic evidence for the Pleistocene and recent population history of Native Americans<\/a>
M Raghavan*, M Steinr\u00fccken*, K Harris*, S Schiffels*, S Rasmussen*, M DeGiorgio*, A Albrechtsen*, C Valdiosera*, MC \u00c1vila-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 Rodr\u00edguez-Varela, J Mansilla, C Henrickson, A Siguin-Orlando, H Malmstr\u00f6m, T Safford Jr, SS Shingarpure, A Moreno-Esrada, M Karmin, K Tambets, A Bergstr\u00f6m, 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 Le\u00f3n, 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
Science<\/em><\/strong> 349:aab3884 (2015)<\/p>\n\n\n\n

A recent bottleneck of Y chromosome diversity coincides with a global change in culture<\/a>
M Karmin, L Saag, M Vicente, MA Wilson Sayres, M J\u00e4rve, U Gerst Talas, S Rootsi, A-M Ilum\u00e4e, R M\u00e4gi, M Mitt, L Pagani, T Puurand, Z Faltyskova, F Clemente, A Cardona, E Metspalu, H Sahakyan, B Yunusbayev, G Hudjashov, M DeGiorgio, E-L Loogv\u00e4li, 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
Genome Research<\/em><\/strong> 24:459-466 (2015)<\/p>\n\n\n\n

Computational and statistical analyses of insertional polymorphic endogenous retroviruses in a non-model organism<\/a>
L Bao, D Elleder, R Malhotra, M DeGiorgio, T Maravegias, L Horvath, L Carrel, C Gillin, T Hron, H F\u00e1bryov\u00e1, DR Hunter, M Poss
Computation<\/em><\/strong> 2:221-245 (2014)<\/p>\n\n\n\n

A selective sweep on a deleterious mutation in CPT1A<\/em> in Arctic populations<\/a>
FJ Clemente, A Cardona, CE Inchley, BM Peter, G Jacobs, L Pagani, DJ Lawson, T Ant\u00e3o, M Vicente, M Mitt, M DeGiorgio, Z Faltyskova, Y Xue, Q Ayub, M Szpak, R M\u00e4gi, 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
American Journal of Human Genetics<\/em><\/strong> 95:584-589 (2014)<\/p>\n\n\n\n

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil<\/a>
A-S Malaspinas, O Lao, H Schroeder, M Rasmussen, M Raghavan, I Moltke, PF Campos, F Santana Sagredo, S Rasmussen, VF Gon\u00e7alves, 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 Miraz\u00f3n Lahr, WA Neves, M Kayser, T Higham, M Stoneking, SDJ Pena, E Willerslev
Current Biology<\/em><\/strong> 24:R1035-R1037 (2014)<\/p>\n\n\n\n

The genetic prehistory of the New World Arctic<\/a>
M Raghavan, M DeGiorgio, A Albrechtsen, I Moltke, P Skogland, TS Korneliussen, B Gr\u00f8nnow, M Appelt, H Christian Gull\u00f8v, TM Friesen, W Fitzhugh, H Malmstr\u00f6m, 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 G\u00f6therstr\u00f6m, 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
Science<\/em><\/strong> 345: 345:1255832 (2014)<\/p>\n\n\n\n

A model-based approach for identifying signatures of ancient balancing selection in genetic data<\/a>
M DeGiorgio\u2020<\/sup>, KE Lohmueller, R Nielsen
PLoS Genetics<\/em><\/strong> 10:e1004561 (2014)<\/p>\n\n\n\n

bammds<\/em>: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS)<\/a>
A-S Malaspinas, O Tange, JV Moreno-Mayar, M Rasmussen, M DeGiorgio, Y Wang, CE Valdiosera, G Politis, E Willerslev, R Nielsen
Bioinformatics<\/em><\/strong> 30:2962-2964 (2014)<\/p>\n\n\n\n

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines<\/a>
M DeGiorgio\u2020<\/sup>, J Syring, AJ Eckert, A Liston, R Cronn, DB Neale, NA Rosenberg
BMC Evolutionary Biology<\/em><\/strong> 14:67 (2014)<\/p>\n\n\n\n

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European<\/a>
I Olalde, ME Allentoft, F S\u00e1nchez-Quinto, G Santpere, CWK Chiang, M DeGiorgio, J Prado-Mart\u00ednez, JA Rodr\u00edguez, S Rasmussen, J Quilez, O Ram\u00edrez, M Fern\u00e1ndez, ME Prada, JMV Encinas, R Nielsen, MG Netea, J Novembre, RA Sturm, P Sabeti, T Marqu\u00e8s-Bonet, A Navarro, E Willerslev, C Lalueza-Fox
Nature<\/em><\/strong> 507:225-228 (2014)<\/p>\n\n\n\n

The genome of a late Pleistocene human found at a Clovis burial site in western Montana<\/a>
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
Nature<\/em><\/strong> 506:225-229 (2014)<\/p>\n\n\n\n

Robustness to divergence time underestimation when inferring species trees from estimated gene trees<\/a>
M DeGiorgio, JH Degnan
Systematic Biology<\/em><\/strong> 63:66-82 (2014)<\/p>\n\n\n\n

Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans<\/a>
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 M\u00e4gi, 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
Nature<\/em><\/strong> 505:87-91 (2014)<\/p>\n\n\n\n

Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes<\/a>
KE Lohmueller, T Spars\u00f8, Q Li, E Andersson, T Korneliussen, A Albrechtsen, K Banasik, N Grarup, I Hallgrimsdottir, K Kiil, TO Kilpel\u00e4inen, NT Krarup, TH Pers, G Sanchez, Y Hu, M DeGiorgio, T J\u00f8rgensen, A Sandb\u00e6k, T Lauritzen, S Brunak, K Kristiansen, Y Li, T Hansen, J Wang, R Nielsen, O Pedersen
American Journal of Human Genetics<\/em><\/strong> 93:1072-1086 (2013)<\/p>\n\n\n\n

Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations<\/a>
E Huerta-S\u00e1nchez*\u2020<\/sup>, M DeGiorgio*\u2020<\/sup>, 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
Molecular Biology and Evolution<\/em><\/strong> 30:1877-1888 (2013)<\/p>\n\n\n\n

Population structure in a comprehensive data set on human microsatellite variation<\/a>
TJ Pemberton, M DeGiorgio, NA Rosenberg
G3: Genes, Genomes, Genetics<\/em><\/strong> 3:909-916 (2013)<\/p>\n\n\n\n

Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis<\/a>
M DeGiorgio\u2020<\/sup>, NA Rosenberg
Molecular Biology and Evolution<\/em><\/strong> 30:480-488 (2013)<\/p>\n\n\n\n

Coalescence-time distributions in a serial founder model of human evolutionary history<\/a>
M DeGiorgio\u2020<\/sup>, JH Degnan, NA Rosenberg
Genetics<\/em><\/strong> 189:579-593 (2011)<\/p>\n\n\n\n

Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy<\/a>
M DeGiorgio*\u2020<\/sup>, I Jankovic*, NA Rosenberg
Genetics<\/em><\/strong> 186:1367-1387 (2010)<\/p>\n\n\n\n

Fast and consistent estimation of species trees using supermatrix rooted triples<\/a>
M DeGiorgio\u2020<\/sup>, JH Degnan\u2020<\/sup>
Molecular Biology and Evolution<\/em><\/strong> 27:552-659 (2010)<\/p>\n\n\n\n

Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa<\/a>
M DeGiorgio, M Jakobsson, NA Rosenberg
Proceedings of the National Academy of Sciences of the United States of America<\/em><\/strong> 106:16057-16062 (2009)<\/p>\n\n\n\n

Properties of consensus methods for inferring species trees from gene trees<\/a>
JH Degnan, M DeGiorgio, D Bryant, NA Rosenberg
Systematic Biology<\/em><\/strong> 58:35-54 (2009)<\/p>\n\n\n\n

An unbiased estimator of gene diversity in samples containing related individuals<\/a>
M DeGiorgio\u2020<\/sup>, NA Rosenberg
Molecular Biology and Evolution<\/em><\/strong> 26:501-512 (2009)<\/p>\n","protected":false},"excerpt":{"rendered":"

* indicates equal contributions\u2020 indicates corresponding authorUnderline indicates DeGiorgio group m Preprints Bacterial DNA invasian triggers transposable element proliferation and […]<\/p>\n","protected":false},"author":101,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"normal-width-container","site-content-style":"boxed","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-60","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/60","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/users\/101"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/comments?post=60"}],"version-history":[{"count":19,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/60\/revisions"}],"predecessor-version":[{"id":423,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/60\/revisions\/423"}],"wp:attachment":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/media?parent=60"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}