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Items: 28

1.

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.

Gunz P, Tilot AK, Wittfeld K, Teumer A, Shapland CY, van Erp TGM, Dannemann M, Vernot B, Neubauer S, Guadalupe T, Fernández G, Brunner HG, Enard W, Fallon J, Hosten N, Völker U, Profico A, Di Vincenzo F, Manzi G, Kelso J, St Pourcain B, Hublin JJ, Franke B, Pääbo S, Macciardi F, Grabe HJ, Fisher SE.

Curr Biol. 2019 Mar 4;29(5):895. doi: 10.1016/j.cub.2019.02.008. No abstract available.

2.

admixr - R package for reproducible analyses using ADMIXTOOLS.

Petr M, Vernot B, Kelso J.

Bioinformatics. 2019 Jan 22. doi: 10.1093/bioinformatics/btz030. [Epub ahead of print]

PMID:
30668635
3.

Limits of long-term selection against Neandertal introgression.

Petr M, Pääbo S, Kelso J, Vernot B.

Proc Natl Acad Sci U S A. 2019 Jan 29;116(5):1639-1644. doi: 10.1073/pnas.1814338116. Epub 2019 Jan 15.

4.

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.

Gunz P, Tilot AK, Wittfeld K, Teumer A, Shapland CY, van Erp TGM, Dannemann M, Vernot B, Neubauer S, Guadalupe T, Fernández G, Brunner HG, Enard W, Fallon J, Hosten N, Völker U, Profico A, Di Vincenzo F, Manzi G, Kelso J, St Pourcain B, Hublin JJ, Franke B, Pääbo S, Macciardi F, Grabe HJ, Fisher SE.

Curr Biol. 2019 Jan 7;29(1):120-127.e5. doi: 10.1016/j.cub.2018.10.065. Epub 2018 Dec 13. Erratum in: Curr Biol. 2019 Mar 4;29(5):895.

5.

The genome of the offspring of a Neanderthal mother and a Denisovan father.

Slon V, Mafessoni F, Vernot B, de Filippo C, Grote S, Viola B, Hajdinjak M, Peyrégne S, Nagel S, Brown S, Douka K, Higham T, Kozlikin MB, Shunkov MV, Derevianko AP, Kelso J, Meyer M, Prüfer K, Pääbo S.

Nature. 2018 Sep;561(7721):113-116. doi: 10.1038/s41586-018-0455-x. Epub 2018 Aug 22.

6.

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.

Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE.

Science. 2018 Aug 3;361(6401):511-516. doi: 10.1126/science.aar8486.

PMID:
30072539
7.

The Predecessors Within . . .

Vernot B, Pääbo S.

Cell. 2018 Mar 22;173(1):6-7. doi: 10.1016/j.cell.2018.03.023.

8.

A high-coverage Neandertal genome from Vindija Cave in Croatia.

Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S.

Science. 2017 Nov 3;358(6363):655-658. doi: 10.1126/science.aao1887. Epub 2017 Oct 5.

9.

Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments.

Gittelman RM, Schraiber JG, Vernot B, Mikacenic C, Wurfel MM, Akey JM.

Curr Biol. 2016 Dec 19;26(24):3375-3382. doi: 10.1016/j.cub.2016.10.041. Epub 2016 Nov 10.

10.

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development.

Mora-Bermúdez F, Badsha F, Kanton S, Camp JG, Vernot B, Köhler K, Voigt B, Okita K, Maricic T, He Z, Lachmann R, Pääbo S, Treutlein B, Huttner WB.

Elife. 2016 Sep 26;5. pii: e18683. doi: 10.7554/eLife.18683.

11.

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB, Gittelman RM, Dannemann M, Grote S, McCoy RC, Norton H, Scheinfeldt LB, Merriwether DA, Koki G, Friedlaender JS, Wakefield J, Pääbo S, Akey JM.

Science. 2016 Apr 8;352(6282):235-9. doi: 10.1126/science.aad9416. Epub 2016 Mar 17.

12.

The phenotypic legacy of admixture between modern humans and Neandertals.

Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA.

Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149.

13.

Complex history of admixture between modern humans and Neandertals.

Vernot B, Akey JM.

Am J Hum Genet. 2015 Mar 5;96(3):448-53. doi: 10.1016/j.ajhg.2015.01.006. Epub 2015 Feb 12.

14.

Human evolution: genomic gifts from archaic hominins.

Vernot B, Akey JM.

Curr Biol. 2014 Sep 22;24(18):R845-R848. doi: 10.1016/j.cub.2014.07.079.

15.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA.

Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.

16.

Resurrecting surviving Neandertal lineages from modern human genomes.

Vernot B, Akey JM.

Science. 2014 Feb 28;343(6174):1017-21. doi: 10.1126/science.1245938. Epub 2014 Jan 29.

PMID:
24476670
17.

Exonic transcription factor binding directs codon choice and affects protein evolution.

Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA.

Science. 2013 Dec 13;342(6164):1367-72. doi: 10.1126/science.1243490.

18.

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.

Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA.

Cell. 2013 Aug 15;154(4):888-903. doi: 10.1016/j.cell.2013.07.020.

19.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D.

Bioinformatics. 2012 Sep 15;28(18):i409-i415. doi: 10.1093/bioinformatics/bts386.

20.

Personal and population genomics of human regulatory variation.

Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM.

Genome Res. 2012 Sep;22(9):1689-97. doi: 10.1101/gr.134890.111.

21.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

22.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

23.

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.

Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, Tishkoff SA.

Cell. 2012 Aug 3;150(3):457-69. doi: 10.1016/j.cell.2012.07.009. Epub 2012 Jul 26.

24.

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE.

Nature. 2012 Apr 4;485(7397):246-50. doi: 10.1038/nature10989.

25.

Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD).

Livstone MS, Oughtred R, Heinicke S, Vernot B, Huttenhower C, Durand D, Dolinski K.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 6:Unit 6.11. doi: 10.1002/0471250953.bi0611s33.

26.

Reconciliation with non-binary species trees.

Vernot B, Stolzer M, Goldman A, Durand D.

J Comput Biol. 2008 Oct;15(8):981-1006. doi: 10.1089/cmb.2008.0092.

27.

Reconciliation with non-binary species trees.

Vernot B, Stolzer M, Goldman A, Durand D.

Comput Syst Bioinformatics Conf. 2007;6:441-52.

28.

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

Durand D, Halldórsson BV, Vernot B.

J Comput Biol. 2006 Mar;13(2):320-35.

PMID:
16597243

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