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Items: 34

1.

Using herbaria to study global environmental change.

Lang PLM, Willems FM, Scheepens JF, Burbano HA, Bossdorf O.

New Phytol. 2018 Aug 30. doi: 10.1111/nph.15401. [Epub ahead of print]

PMID:
30160314
2.

nQuire: a statistical framework for ploidy estimation using next generation sequencing.

Weiß CL, Pais M, Cano LM, Kamoun S, Burbano HA.

BMC Bioinformatics. 2018 Apr 4;19(1):122. doi: 10.1186/s12859-018-2128-z.

3.

The rate and potential relevance of new mutations in a colonizing plant lineage.

Exposito-Alonso M, Becker C, Schuenemann VJ, Reiter E, Setzer C, Slovak R, Brachi B, Hagmann J, Grimm DG, Chen J, Busch W, Bergelson J, Ness RW, Krause J, Burbano HA, Weigel D.

PLoS Genet. 2018 Feb 12;14(2):e1007155. doi: 10.1371/journal.pgen.1007155. eCollection 2018 Feb.

4.

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana.

Exposito-Alonso M, Vasseur F, Ding W, Wang G, Burbano HA, Weigel D.

Nat Ecol Evol. 2018 Feb;2(2):352-358. doi: 10.1038/s41559-017-0423-0. Epub 2017 Dec 18.

5.

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America.

Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA.

Science. 2017 Aug 4;357(6350):512-515. doi: 10.1126/science.aam9425.

PMID:
28774930
6.

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana.

Durvasula A, Fulgione A, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C, Tsuchimatsu T, Burbano HA, Picó FX, Alonso-Blanco C, Hancock AM.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):5213-5218. doi: 10.1073/pnas.1616736114. Epub 2017 May 4.

7.

A Robust Framework for Microbial Archaeology.

Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J.

Annu Rev Genomics Hum Genet. 2017 Aug 31;18:321-356. doi: 10.1146/annurev-genom-091416-035526. Epub 2017 Apr 26. Review.

8.

Neandertal and Denisovan DNA from Pleistocene sediments.

Slon V, Hopfe C, Weiß CL, Mafessoni F, de la Rasilla M, Lalueza-Fox C, Rosas A, Soressi M, Knul MV, Miller R, Stewart JR, Derevianko AP, Jacobs Z, Li B, Roberts RG, Shunkov MV, de Lumley H, Perrenoud C, Gušić I, Kućan Ž, Rudan P, Aximu-Petri A, Essel E, Nagel S, Nickel B, Schmidt A, Prüfer K, Kelso J, Burbano HA, Pääbo S, Meyer M.

Science. 2017 May 12;356(6338):605-608. doi: 10.1126/science.aam9695. Epub 2017 Apr 27.

PMID:
28450384
9.

Extraction of ultrashort DNA molecules from herbarium specimens.

Gutaker RM, Reiter E, Furtwängler A, Schuenemann VJ, Burbano HA.

Biotechniques. 2017 Feb 1;62(2):76-79. doi: 10.2144/000114517.

10.

Reinforcing plant evolutionary genomics using ancient DNA.

Gutaker RM, Burbano HA.

Curr Opin Plant Biol. 2017 Apr;36:38-45. doi: 10.1016/j.pbi.2017.01.002. Epub 2017 Feb 1. Review.

PMID:
28160617
11.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

Weiß CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E, Gould BA, Stinchcombe JR, Krause J, Burbano HA.

R Soc Open Sci. 2016 Jun 22;3(6):160239. doi: 10.1098/rsos.160239. eCollection 2016 Jun.

12.

Ancient gene flow from early modern humans into Eastern Neanderthals.

Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S.

Nature. 2016 Feb 25;530(7591):429-33. doi: 10.1038/nature16544. Epub 2016 Feb 17.

13.

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data.

Weiß CL, Dannemann M, Prüfer K, Burbano HA.

Elife. 2015 Nov 3;4. pii: e10005. doi: 10.7554/eLife.10005.

14.

Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae.

Smith LM, Burbano HA, Wang X, Fitz J, Wang G, Ural-Blimke Y, Weigel D.

Plant J. 2015 Feb;81(4):597-610. doi: 10.1111/tpj.12754. Epub 2015 Jan 21.

15.

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L.

Science. 2014 Aug 29;345(6200):1074-1079. doi: 10.1126/science.1253714.

16.

Mining herbaria for plant pathogen genomes: back to the future.

Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S.

PLoS Pathog. 2014 Apr 24;10(4):e1004028. doi: 10.1371/journal.ppat.1004028. eCollection 2014 Apr. Review. No abstract available.

17.

Patterns of coding variation in the complete exomes of three Neandertals.

Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano HA, Renaud G, Stenzel U, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajković D, Kucan Ž, Gušic I, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andrés AM, Pääbo S.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6666-71. doi: 10.1073/pnas.1405138111. Epub 2014 Apr 21.

18.

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine.

Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, Thines M, Weigel D, Burbano HA.

Elife. 2013 May 28;2:e00731. doi: 10.7554/eLife.00731. Erratum in: Elife. 2013;2:e01108.

19.

DNA analysis of an early modern human from Tianyuan Cave, China.

Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2223-7. doi: 10.1073/pnas.1221359110. Epub 2013 Jan 22.

20.

Comparative population genomics of the ejaculate in humans and the great apes.

Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S.

Mol Biol Evol. 2013 Apr;30(4):964-76. doi: 10.1093/molbev/mst005. Epub 2013 Jan 16.

PMID:
23329688
21.

Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a.

Manavella PA, Koenig D, Rubio-Somoza I, Burbano HA, Becker C, Weigel D.

Plant Physiol. 2013 Feb;161(2):805-12. doi: 10.1104/pp.112.207068. Epub 2012 Nov 30.

22.

A recent evolutionary change affects a regulatory element in the human FOXP2 gene.

Maricic T, Günther V, Georgiev O, Gehre S, Curlin M, Schreiweis C, Naumann R, Burbano HA, Meyer M, Lalueza-Fox C, de la Rasilla M, Rosas A, Gajovic S, Kelso J, Enard W, Schaffner W, Pääbo S.

Mol Biol Evol. 2013 Apr;30(4):844-52. doi: 10.1093/molbev/mss271. Epub 2012 Nov 28.

PMID:
23197593
23.

Transcription factors are targeted by differentially expressed miRNAs in primates.

Dannemann M, Prüfer K, Lizano E, Nickel B, Burbano HA, Kelso J.

Genome Biol Evol. 2012;4(4):552-64. doi: 10.1093/gbe/evs033. Epub 2012 Mar 27.

24.

Annotation of primate miRNAs by high throughput sequencing of small RNA libraries.

Dannemann M, Nickel B, Lizano E, Burbano HA, Kelso J.

BMC Genomics. 2012 Mar 27;13:116. doi: 10.1186/1471-2164-13-116.

25.

Analysis of human accelerated DNA regions using archaic hominin genomes.

Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S.

PLoS One. 2012;7(3):e32877. doi: 10.1371/journal.pone.0032877. Epub 2012 Mar 7.

26.

A draft genome of Yersinia pestis from victims of the Black Death.

Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, Wood J, Earn DJ, Herring DA, Bauer P, Poinar HN, Krause J.

Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549. Erratum in: Nature. 2011 Dec 8;480(7376):278.

27.

Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection.

Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, Carlborg O, Hannon GJ, Pääbo S.

Heredity (Edinb). 2011 Sep;107(3):205-14. doi: 10.1038/hdy.2011.4. Epub 2011 Feb 9.

28.

Targeted investigation of the Neandertal genome by array-based sequence capture.

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S.

Science. 2010 May 7;328(5979):723-5. doi: 10.1126/science.1188046.

29.

A draft sequence of the Neandertal genome.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.

Science. 2010 May 7;328(5979):710-722. doi: 10.1126/science.1188021.

30.

The Neandertal genome and ancient DNA authenticity.

Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S.

EMBO J. 2009 Sep 2;28(17):2494-502. doi: 10.1038/emboj.2009.222. Epub 2009 Aug 6. Review.

31.

A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.

Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S.

Cell. 2008 Aug 8;134(3):416-26. doi: 10.1016/j.cell.2008.06.021.

32.

The derived FOXP2 variant of modern humans was shared with Neandertals.

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ, Hänni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Pääbo S.

Curr Biol. 2007 Nov 6;17(21):1908-12. Epub 2007 Oct 18.

33.

Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea.

Burbano HA, Andrade E.

Gene. 2007 Jul 1;396(1):75-83. Epub 2007 Mar 15.

PMID:
17433860
34.

Funders should allow for cost of publication.

Burbano HA.

Nature. 2006 Aug 31;442(7106):981. No abstract available.

PMID:
16943817

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