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Items: 41

1.

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore.

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

Cell. 2019 Oct 17;179(3):736-749.e15. doi: 10.1016/j.cell.2019.09.019.

PMID:
31626772
2.

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

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

Genome Biol Evol. 2019 Oct 1;11(10):3022-3034. doi: 10.1093/gbe/evz197.

3.

Localizing and Classifying Adaptive Targets with Trend Filtered Regression.

Mughal MR, DeGiorgio M.

Mol Biol Evol. 2019 Feb 1;36(2):252-270. doi: 10.1093/molbev/msy205.

4.

Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism.

Cheng X, DeGiorgio M.

Mol Biol Evol. 2019 Jan 1;36(1):177-199. doi: 10.1093/molbev/msy202.

5.

Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity.

Harris AM, Garud NR, DeGiorgio M.

Genetics. 2018 Dec;210(4):1429-1452. doi: 10.1534/genetics.118.301502. Epub 2018 Oct 12.

PMID:
30315068
6.

High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups.

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

Genome Biol Evol. 2018 May 1;10(5):1333-1350. doi: 10.1093/gbe/evy086.

7.

Patterns of Genetic Coding Variation in a Native American Population before and after European Contact.

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

Am J Hum Genet. 2018 May 3;102(5):806-815. doi: 10.1016/j.ajhg.2018.03.008. Epub 2018 Apr 26.

8.
9.

Fast and robust detection of ancestral selective sweeps.

Cheng X, Xu C, DeGiorgio M.

Mol Ecol. 2017 Dec;26(24):6871-6891. doi: 10.1111/mec.14416. Epub 2017 Dec 12.

PMID:
29113018
10.

Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation.

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

Mol Biol Evol. 2017 Oct 1;34(10):2704-2715. doi: 10.1093/molbev/msx206.

11.

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

Lindo J, Achilli A, Perego UA, Archer D, Valdiosera C, Petzelt B, Mitchell J, Worl R, Dixon EJ, Fifield TE, Rasmussen M, Willerslev E, Cybulski JS, Kemp BM, DeGiorgio M, Malhi RS.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4093-4098. doi: 10.1073/pnas.1620410114. Epub 2017 Apr 4.

12.
13.

Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

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

Curr Biol. 2016 Dec 5;26(23):3190-3194. doi: 10.1016/j.cub.2016.09.039. Epub 2016 Nov 17.

14.

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

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

Nat Commun. 2016 Nov 15;7:13175. doi: 10.1038/ncomms13175.

15.

Genomic analyses inform on migration events during the peopling of Eurasia.

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

Nature. 2016 Oct 13;538(7624):238-242. doi: 10.1038/nature19792. Epub 2016 Sep 21.

16.

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

Fungtammasan A, Tomaszkiewicz M, Campos-Sánchez R, Eckert KA, DeGiorgio M, Makova KD.

Mol Biol Evol. 2016 Oct;33(10):2744-58. doi: 10.1093/molbev/msw139. Epub 2016 Jul 12.

17.

SweepFinder2: increased sensitivity, robustness and flexibility.

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

Bioinformatics. 2016 Jun 15;32(12):1895-7. doi: 10.1093/bioinformatics/btw051. Epub 2016 Feb 15.

PMID:
27153702
18.

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

DeGiorgio M, Rosenberg NA.

Theor Popul Biol. 2016 Aug;110:12-24. doi: 10.1016/j.tpb.2016.02.002. Epub 2016 Apr 13.

19.

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

Huber CD, DeGiorgio M, Hellmann I, Nielsen R.

Mol Ecol. 2016 Jan;25(1):142-56. doi: 10.1111/mec.13351. Epub 2015 Sep 7.

20.

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

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

Science. 2015 Aug 21;349(6250):aab3884. doi: 10.1126/science.aab3884. Epub 2015 Jul 21.

21.

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

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

Genome Res. 2015 Apr;25(4):459-66. doi: 10.1101/gr.186684.114. Epub 2015 Mar 13.

22.

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

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

Curr Biol. 2014 Nov 3;24(21):R1035-7. doi: 10.1016/j.cub.2014.09.078. Epub 2014 Oct 23.

23.

A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.

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

Am J Hum Genet. 2014 Nov 6;95(5):584-589. doi: 10.1016/j.ajhg.2014.09.016. Epub 2014 Oct 23.

24.

The genetic prehistory of the New World Arctic.

Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T Jr, Grimes V, Renouf MA, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TV, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O'Rourke DH, Jakobsson M, Gilbert MT, Nielsen R, Willerslev E.

Science. 2014 Aug 29;345(6200):1255832. doi: 10.1126/science.1255832.

25.

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

DeGiorgio M, Lohmueller KE, Nielsen R.

PLoS Genet. 2014 Aug 21;10(8):e1004561. doi: 10.1371/journal.pgen.1004561. eCollection 2014 Aug.

26.

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).

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

Bioinformatics. 2014 Oct 15;30(20):2962-4. doi: 10.1093/bioinformatics/btu410. Epub 2014 Jun 28.

27.

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

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

BMC Evol Biol. 2014 Mar 29;14:67. doi: 10.1186/1471-2148-14-67.

28.

The genome of a Late Pleistocene human from a Clovis burial site in western Montana.

Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E.

Nature. 2014 Feb 13;506(7487):225-9. doi: 10.1038/nature13025.

29.

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

Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C.

Nature. 2014 Mar 13;507(7491):225-8. doi: 10.1038/nature12960. Epub 2014 Jan 26.

30.

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

Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, Degiorgio M, Jørgensen T, Sandbæk A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O.

Am J Hum Genet. 2013 Dec 5;93(6):1072-86. doi: 10.1016/j.ajhg.2013.11.005. Epub 2013 Nov 27. Erratum in: Am J Hum Genet. 2014 Mar 6;94(3):479.

31.

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.

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

Nature. 2014 Jan 2;505(7481):87-91. doi: 10.1038/nature12736. Epub 2013 Nov 20.

32.

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

DeGiorgio M, Degnan JH.

Syst Biol. 2014 Jan 1;63(1):66-82. doi: 10.1093/sysbio/syt059. Epub 2013 Aug 29.

PMID:
23988674
33.

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

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

Mol Biol Evol. 2013 Aug;30(8):1877-88. doi: 10.1093/molbev/mst089. Epub 2013 May 10.

34.

Population structure in a comprehensive genomic data set on human microsatellite variation.

Pemberton TJ, DeGiorgio M, Rosenberg NA.

G3 (Bethesda). 2013 May 20;3(5):891-907. doi: 10.1534/g3.113.005728.

35.

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

DeGiorgio M, Rosenberg NA.

Mol Biol Evol. 2013 Feb;30(2):480-8. doi: 10.1093/molbev/mss233. Epub 2012 Oct 10.

36.

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

DeGiorgio M, Degnan JH, Rosenberg NA.

Genetics. 2011 Oct;189(2):579-93. doi: 10.1534/genetics.111.129296. Epub 2011 Jul 20.

37.

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

DeGiorgio M, Jankovic I, Rosenberg NA.

Genetics. 2010 Dec;186(4):1367-87. doi: 10.1534/genetics.110.121756. Epub 2010 Oct 5.

38.

Fast and consistent estimation of species trees using supermatrix rooted triples.

DeGiorgio M, Degnan JH.

Mol Biol Evol. 2010 Mar;27(3):552-69. doi: 10.1093/molbev/msp250. Epub 2009 Oct 15.

39.

Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.

DeGiorgio M, Jakobsson M, Rosenberg NA.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16057-62. doi: 10.1073/pnas.0903341106. Epub 2009 Aug 17.

40.

Properties of consensus methods for inferring species trees from gene trees.

Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA.

Syst Biol. 2009 Feb;58(1):35-54. doi: 10.1093/sysbio/syp008. Epub 2009 Jun 4.

41.

An unbiased estimator of gene diversity in samples containing related individuals.

DeGiorgio M, Rosenberg NA.

Mol Biol Evol. 2009 Mar;26(3):501-12. doi: 10.1093/molbev/msn254. Epub 2008 Nov 6.

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