Publications

 

  • Genetic adaptations to SIV across chimpanzee populations.
    Pawar H, Ostridge HJ, Schmidt JM, Andrés AM.
    Biorxiv 2022 May 25. https://doi.org/10.1101/2022.05.24.491624
  • Population dynamics and genetic connectivity in recent chimpanzee history.
    Fontserre C, … many authors … , Andrés AM, Hughes D, Kühl H, Lizano E, Arandjelovic M, Marques-Bonet T.
    Cell Genomics 2022 June 8; 6:100133. https://doi.org/10.1016/j.xgen.2022.100133
  • Inferring human evolutionary history.
    Rees J and Andrés AM.
    Science 2022 Feb 25;375(6583):817-818. doi: 10.1126/science.abo0498.
  • The Genomics of Human Local Adaptation.
    Rees JS, Castellano S, Andrés AM.
    Trends Genet. 2020 Jun;36(6):415-428. doi: 10.1016/j.tig.2020.03.006.
  • Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.
    Soto DC, Shew C, Mastoras M, Schmidt JM, Sahasrabudhe R, Kaya G, Andrés AM, Dennis MY.
    Genes (Basel). 2020 Mar 4;11(3):276. doi: 10.3390/genes11030276.
  • The impact of genetic adaptation on chimpanzee subspecies differentiation.
    Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM.
    PLoS Genet. 2019 Nov 25;15(11):e1008485. doi: 10.1371/journal.pgen.1008485.
  • Evolutionary and functional impact of common polymorphic inversions in the human genome.
    Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O’Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M.
    Nat Commun. 2019 Sep 17;10(1):4222. doi: 10.1038/s41467-019-12173-x.
  • Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions. Han S, Andrés AM, Marques-Bonet T, Kuhlwilm M.
    Genome Biol Evol. 2019 Apr 1;11(4):1178-1191. doi: 10.1093/gbe/evz047.
  • Immune Gene Diversity in Archaic and Present-day Humans.
    Reher D, Key FM, Andrés AM, Kelso J.
    Genome Biol Evol. 2019 Jan 1;11(1):232-241. doi: 10.1093/gbe/evy271.
  • Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.
    Key FM, Abdul-Aziz MA, Mundry R, Peter BM, Sekar A, D’Amato M, Dennis MY, Schmidt JM, Andrés AM.
    PLoS Genet. 2018 May 3;14(5):e1007298. doi: 10.1371/journal.pgen.1007298.
  • Signatures of Long-Term Balancing Selection in Human Genomes.
    Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM.
    Genome Biol Evol. 2018 Mar 1;10(3):939-955. doi: 10.1093/gbe/evy054.
  • A high-coverage Neandertal genome from Vindija Cave in Croatia.
    Prüfer K, de Filippo C, Grote S, Mafessoni F, 28 authors, Andrés AM, Kelso J, Meyer M, Pääbo S.
    Science, 358:655-658 (2017).
  • Natural selection in the great apes.
    Cagan A*, Theunert C*, Laayouni H*, Santpere G*, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J#, Andrés AM#.
    Molecular Biology and Evolution, 33:268-283 (2016).
  • Chimpanzee genomic diversity reveals ancient admixture with bonobos.
    de Manuel M*, Kuhlwilm M*, Frandsen P*, 25 authors, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C#, Marques-Bonet T#.
    Science, 354:477-481 (2016).
  • Human adaptation and population differentiation in the light of ancient genomes.
    Key FM, Fu Q, Romaine F, Lachmann M, Andrés AM.
    Nature Communications 7:10775-86 (2016).
  • Recent selective pressure changes in human genes previously affected by balancing selection.
    de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A, NISC Comparative Sequence Program, Parra G, Green ED, Andrés AM.
    Molecular Biology and Evolution, 33: 1435-1447 (2016).
  • Ancient gene flow from early modern humans into Eastern Neanderthals.
    Kuhlwilm M*, Gronau I*, Hubisz JM, de Filippo C, Prado J, Kircher M, Fu Q, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gusic I, Marques-Bonet T, Andrés AM, Viola B, Meyer M, Pääbo S, Siepel A and Castellano S.
    Nature 530: 429–433 (2016).
  • Danemann M, Andrés AM, Kelso J.
    Adaptive variation in human toll-like receptors is contributed by Neanderthal- and Denisova-like introgressed haplotypes.
    The American Journal of Human Genetics 98: 22–33 (2016).
  • Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andrés AM, Barbujani G, Hvilsom C, Marques-Bonet T.
    Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.
    Genome Biology and Evolution 8:2020-2030 (2016).
  • Teixeira J*, Filippo C*, Weihmann A, Meneu JR, Racimo F, Dannemann M, Nickel B, Fischer A, Halbwax M, Andre C, Atencia R, Meyer M, Parra G, Pääbo S and Andrés AM.
    Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos.
    Molecular Biology and Evolution, 32: 1186-1196 (2015).
  • White L, Romagné F, Erlebach E, Weihmann A, Parra G, Andrés AM, Castellano S.
    Genetic adaptation to levels of dietary selenium in recent human history.
    Molecular Biology and Evolution 32: 1507-1518 (2015).
  • Key FM, Peter B, Dennis M, Huerta-Sánchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM.
    Selection on a variant associated with improved viral clearance induced local, adaptive pseudogenization of interferon lambda 4 (IFNL4).
    PLoS Genetics 10:e1004681 (2014).
  • Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, 22 authors, Meyer M, Kelso J, Andrés AM, Pääbo S.
    Patterns of coding variation in the complete exomes of three Neandertals.
    Proc Natl Acad Sci USA, 111:6666-71 (2014).
  • Ferreira Z, Hurle B, Andrés AM, Kretzschmar W, Mullikin J, Cherukuri P, Cruz P, Gonder MK, Stone A, Tishkoff S, Swanson W, NISC Comparative Sequencing Program, Green E, Clark AG, Seixas S.
    Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity.
    Genome Biology and Evolution, 5:2512-2523. (2013).
  • Prado-Martinez J, Sudmant PH, Kidd JM, 66 authors, 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).
  • Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ, NISC Comparative Sequencing Program, Clark AG, Green ED and Hurle B. Reproduction and Immunity-Driven Natural Selection in the Human WFDC Locus.
    Molecular Biology and Evolution 30: 938-950 (2013).
  • Meyer M, Kircher M, Gansauge MT, Li H, 24 authors, 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). – Selected, Faculty of 1000 –
  • Prüfer K, Munch K, Hellmann I, Akagi K, 33 authors, Schierup MH, Andrés AM, Kelso J, Pääbo S.
    The bonobo genome compared with the chimpanzee and human genomes.
    Nature, 486:527-31 (2012).
  • 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 Genetics, 6:e1001157 (2010).
  • Andrés AM, Hubisz MJ, Indap A, Degenhartl J, Boyco AR, Gutenkunst RN, White T, Green ED, Bustamante CD, Clark AG, and Nielsen R.
    Targets of balancing selection in the human genome.
    Molecular Biology and Evolution, 26:2755-64 (2009). – Selected, Faculty of 1000 –
  • Castellano S*, Andrés AM*, Bosch E, Bayes M, Guigó R, and Clark AG.
    Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.
    Molecular Biology and Evolution, 26:2031-40 (2009).
  • 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). – Selected, Faculty of 1000 –
  • Andrés AM, de Hemptinne C, and Bertranpetit J.
    Heterogenetous rate of protein evolution in serotonin genes.
    Molecular Biology and Evolution, 24:2707-15 (2007).
  • 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).
  • Soldevila M, Andrés AM, Helgason A, Ramírez-Soriano A, Marqués-Bonet T, Sigurdadottir 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).
  • 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).
  • 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).
  • Soldevila M, Andrés AM, Blancher A, Calafell F, Ordoñnez M, Pumarola M, Oliva B, Aramburu J, and Bertranpetit J.
    Variation in the prion gene in chimpanzees and its implication for prion diseases.
    Neuroscience Letters 355:157-16 (2004).
  • Rovio AT, Abel J, Ahola AL, Andrés AM, 29 aditional authors, Jacobs HT.
    A prevalent POLG CAG microsatellite length allele in humans and African great apes.
    Mammalian Genome 15:492-502 (2004).
  • 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).
  • Soldevila M, Calafell F, Andrés AM, Yague J, Helgason A, Stefánsson K, and Bertranpetit J.
    Prion Susceptibility and Protective Alleles Exhibit Marked Geographic Differences.
    Human Mutation 22:104-5 (2003).
  • Lao O, Andrés AM, Mateu E, Bertranpetit J and Calafell F.
    Spatial patterns of cystic fibrosis mutation spectra in European populations.
    European Journal of Human Genetics 11:385-94 (2003).
  • 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).
  • 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 336:143-46 (2003).
  • Mateu E, Pérez-Lezaun A, Martínez-Arias R, Andrés A, Valles M, Bertranpetit J, and Calafell F.
    PKLR – GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldside populations.
    Human Genetics 110:532-544 (2002).
  • 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).