30.10.2014 - 15:28
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Publications

With the name of members of the group in italics. 

Selected recent publications

    • Key FM, Peter B, Dennis MY, Huerta-Sánchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM
      Selection on a Variant Associated with Improved Viral Clearance Drives Local Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)
      PLoS Genetics, October 2014. [Full text]
    • Key FM, Teixeira J, de Filippo C, Andrés AM
      Advantageous diversity maintained by balancing selection in humans.
      Current Opinion in Genetics & Development 29 (issue Genetics of Human Evolution):45-51 (2014). [PDF]
    • 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.
      Patterns of coding variation in the complete exomes of three Neandertals.
      PNAS 111:6666-71 (2014). [Full text]
    • Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J and Pääbo, S. 
      The complete genome sequence of a Neanderthal from the Altai Mountains.
      Nature 505:43–49 (2014). [Full text]
    • Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.
      Great ape genetic diversity and population history.
      Nature 499:471-5 (2013). [PubMed] [Full text]
    • Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ; NISC Comparative Sequencing Program, Green ED, Clark AG, Seixas S.
      Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity.
      Genome Biol Evol. 5:2512-23 (2013). [Full text]
    • Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ; NISC Comparative Sequencing Program, Clark AG, Green ED, Hurle B.
      Reproduction and immunity-driven natural selection in the human WFDC locus.
      Mol Biol Evol. 30:938-50 (2013). [PubMed] [PDF]
    • Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S.
      A High-Coverage Genome Sequence from an Archaic Denisovan Individual.
      Science 338:222-6 (2012). [PubMed] [Full text] [PDF]
    • Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karako E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S.
      The bonobo genome compared with the chimpanzee and human genomes.
      Nature, 486:527-31 (2012). [PubMed] [Full text]
    • Andrés AM.
      Balancing selection in the human genome.
      Encyclopedia of Life Sciences (2011). [Abstract] [Full Text] [PDF]
    • Andrés AM*, Dennis MY* , Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B; NISC Comparative Sequencing Program, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED.
      Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation.
      PLoS Genet. 2010 Oct 14;6(10):e1001157. [PubMed] [Full text] [PDF] [Supplementary Material]
      * Denotes equal contribution. 

     

     

    Selected publications before 2010

    • Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R.
      Targets of balancing selection in the human genome.
      Molecular Biology and Evolution, 26:2755-64 (2009). [PubMed] [Full text] [PDF] [Supplementary Material]
    • Castellano S*, Andrés AM*, Bosch E, Bayes M, Guigó R, Clark AG.
      Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.
      Molecular Biology and Evolution, 26:2031-40 (2009). [PubMed] [Full Text] [PDF] [Supplementary Material
      * Denotes equal contribution.

    • Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, and Clark AG.
      Darwinian and demographic forces affecting human protein coding genes.
      Genome Research, 19:838-49 (2009). [PubMed] [Full Text] [PDF] [Supplementary Material]

    • Andrés AM, Clark AG, Shimmin L, Boerwinkle E, Sing CF and Hixson JE.
      Understanding the accuracy of statistical haplotype inference with sequence data of known phase.
      Genetic Epidemiology, 31:659-71. (2007). [PubMed] [PDF].

    • Andrés AM, de Hemptinne C and Bertranpetit J.
      Heterogenetous rate of protein evolution in serotonin genes.
      Molecular Biology and Evolution, 24:2707-15 (2007). [PubMed] [Full text] [PDF] [Supplementary Material]

    • Soldevila M, Andrés AM, Helgason A, Ramírez-Soriano A, Marquès-Bonet T, Sigurdadóttir S, Calafell F, Navarro A, Stefánsson K and Bertranpetit J.
      The prion protein gene in humans revisited: lessons from a worldwide resequencing study.
      Genome Research, 16:231-9 (2006). [PubMed] [Full text] [PDF]

    • Andrés AM, Soldevila M, Navarro A, Kidd KK, Oliva B and Bertranpetit J.
      Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage.
      Human Genetics 115:377-86 (2004). [PubMed] [Full text] [PDF]

    • Andrés AM, Soldevila M, Lao O, Volpini V, Saitou N, Jacobs HT, Hayasaka I, Calafell F and Bertranpetit J.
      Comparative genetics of functional trinucleotide tandem repeats in humans and apes.
      Journal of Molecular Evolution 59:329-39 (2004). [PubMed] [Full text] [PDF]

    • Clarimón J, Andrés AM, Bertranpetit J and Comas D.
      Comparative analysis of Alu insertion sequences in the APP 5’flanking region in humans and other primates.
      Journal of Molecular Evolution 58:722-731 (2004). [PubMed] [Full text] [PDF

    • Soldevila M, Andrés AM, Blancher A, Calafell F, Ordoñez M, Pumarola M, Oliva B, Aramburu J and Bertranpetit J.
      Variation of the prion gene in chimpanzees and its implication for prion diseases.
      Neuroscience Letters 355:157-60 (2004). [PubMed] [Full text] [PDF]

    • Andrés AM, Soldevila M, Saitou N, Volpini V, Calafell F and Bertranpetit J.
      Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes.
      Neuroscience Letters 336:143-146 (2003). [PubMed] [Full text] [PDF]

    • Andrés AM, Lao O, Soldevila M, Calafell F and Bertranpetit J.
      Dynamics of CAG repeat loci revealed by the analysis of their variability.
      Human Mutation 21:61-70 (2003). [PubMed] [PDF]

    • Martínez-Arias R, Calafell R, Mateu E, Comas D, Andrés A and Bertranpetit J.
      Sequence variability of a human pseudogene.
      Genome Research 11:1071-1085 (2002). [PubMed] [Full text] [PDF]