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Publications: Dr Matteo Fumagalli

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Mas-Sandoval A, Pope NS, Nielsen KN, Altinkaya I, Fumagalli M, Korneliussen TS ( 2024 ) . Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data . GigaScience vol. 11 ,
Korfmann K, Sellinger TPP, Freund F, Fumagalli M, Tellier A ( 2024 ) . Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent . Peer Community Journal vol. 4 ,
Mas-Sandoval A, Mathieson S, Fumagalli M ( 2023 ) . The genomic footprint of social stratification in admixing American populations . eLife vol. 12 ,
Mas-Sandoval A, Jin C, Fracassetti M, Fumagalli M ( 2023 ) . ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language . F1000Research vol. 11 , 126 - 126 .
Korfmann K, Gaggiotti OE, Fumagalli M ( 2023 ) . Deep Learning in Population Genetics . Genome Biology and Evolution vol. 15 , ( 2 )
Soraggi S, Rhodes J, Altinkaya I, Tarrant O, Balloux F, Fisher MC, Fumagalli M ( 2022 ) . HMMploidy: inference of ploidy levels from short-read sequencing data . Peer Community Journal vol. 2 ,
Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ormond L, Wang K, Hurtado M, Villegas V, Granja V et al. ( 2022 ) . Disentangling Signatures of Selection before and after European Colonization in Latin Americans . Molecular Biology and Evolution vol. 39 , ( 4 )
Gower G, Picazo PI, Fumagalli M, Racimo F ( 2021 ) . Detecting adaptive introgression in human evolution using convolutional neural networks . eLife vol. 10 ,
Isildak U, Stella A, Fumagalli M ( 2021 ) . Distinguishing between recent balancing selection and incomplete sweep using deep neural networks . Molecular Ecology Resources vol. 21 , ( 8 ) 2706 - 2718 .
Fumagalli M ( 2020 ) . Detecting loci under natural selection from temporal genomic data of selfing populations . Peer Community in Evolutionary Biology
Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T et al. ( 2020 ) . Inference of natural selection from ancient DNA . Evolution Letters vol. 4 , ( 2 ) 94 - 108 .
Torada L, Lorenzon L, Beddis A, Isildak U, Pattini L, Mathieson S, Fumagalli M ( 2019 ) . ImaGene: a convolutional neural network to quantify natural selection from genomic data . BMC Bioinformatics vol. 20 , ( Suppl 9 )
Wright AE, Rogers TF, Fumagalli M, Cooney CR, Mank JE ( 2019 ) . Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict . Molecular Ecology vol. 28 , ( 11 ) 2860 - 2871 .
Fumagalli M, Camus SM, Diekmann Y, Burke A, Camus MD, Norman PJ, Joseph A, Abi-Rached L et al. ( 2019 ) . Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism . eLife vol. 8 ,
Fox EA, Wright AE, Fumagalli M, Vieira FG ( 2019 ) . ngsLD: evaluating linkage disequilibrium using genotype likelihoods . Bioinformatics vol. 35 , ( 19 ) 3855 - 3856 .
Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V et al. ( 2019 ) . A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia . Nature Communications vol. 10 , ( 1 )
O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA et al. ( 2018 ) . Recent Asian origin of chytrid fungi causing global amphibian declines . Science vol. 360 , ( 6389 ) 621 - 627 .
Wright AE, Fumagalli M, Cooney CR, Bloch NI, Vieira FG, Buechel SD, Kolm N, Mank JE ( 2018 ) . Male‐biased gene expression resolves sexual conflict through the evolution of sex‐specific genetic architecture . Evolution Letters vol. 2 , ( 2 ) 52 - 61 .
Elfekih S, Etter P, Tay WT, Fumagalli M, Gordon K, Johnson E, De Barro P ( 2018 ) . Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories . PLOS ONE vol. 13 , ( 1 )
Lassalle F, Spagnoletti M, Fumagalli M, Shaw L, Dyble M, Walker C, Thomas MG, Migliano AB et al. ( 2017 ) . Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet . Molecular Ecology vol. 27 , ( 1 ) 182 - 195 .
Benazzo A, Trucchi E, Cahill JA, Delser PM, Mona S, Fumagalli M, Bunnefeld L, Cornetti L et al. ( 2017 ) . Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 45 ) e9589 - e9597 .
Fumagalli M, Balloux F ( 2017 ) . Chapter 11 Natural Selection Associated With Infectious Diseases . On Human Nature , Elsevier
Fumagalli M, Balloux F ( 2017 ) . Natural Selection Associated With Infectious Diseases . On Human Nature: Biology, Psychology, Ethics, Politics, and Religion ,
Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L et al. ( 2016 ) . Archaic Adaptive Introgression in TBX15/WARS2 . Molecular Biology and Evolution vol. 34 , ( 3 ) 509 - 524 .
Foote AD, Vijay N, Ávila-Arcos MC, Baird RW, Durban JW, Fumagalli M, Gibbs RA, Hanson MB et al. ( 2016 ) . Genome-culture coevolution promotes rapid divergence of killer whale ecotypes . Nature Communications vol. 7 , ( 1 )
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA et al. ( 2015 ) . Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments . Proceedings of the National Academy of Sciences of the United States of America vol. 112 , ( 50 ) e6889 - e6897 .
Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK et al. ( 2015 ) . Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse . Current Biology vol. 25 , ( 19 ) 2577 - 2583 .
Fumagalli M, Moltke I, Grarup N, Racimo F, Bjerregaard P, Jørgensen ME, Korneliussen TS, Gerbault P et al. ( 2015 ) . Greenlandic Inuit show genetic signatures of diet and climate adaptation . Science vol. 349 , ( 6254 ) 1343 - 1347 .
Vieira FG, Lassalle F, Korneliussen TS, Fumagalli M ( 2015 ) . Improving the estimation of genetic distances from Next‐Generation Sequencing data . Biological Journal of the Linnean Society vol. 117 , ( 1 ) 139 - 149 .
da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C et al. ( 2015 ) . Erratum: The origin and evolution of maize in the Southwestern United States . Nature Plants vol. 1 , ( 1 )
da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C et al. ( 2015 ) . The origin and evolution of maize in the Southwestern United States . Nature Plants vol. 1 , ( 1 )
Moltke I, Fumagalli M, Korneliussen TS, Crawford JE, Bjerregaard P, Jørgensen ME, Grarup N, Gulløv HC et al. ( 2014 ) . Uncovering the Genetic History of the Present-Day Greenlandic Population . American Journal of Human Genetics vol. 96 , ( 1 ) 54 - 69 .
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I et al. ( 2014 ) . Prehistoric genomes reveal the genetic foundation and cost of horse domestication . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 52 ) e5661 - e5669 .
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B et al. ( 2014 ) . Speciation with gene flow in equids despite extensive chromosomal plasticity . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 52 ) 18655 - 18660 .
Moltke I, Grarup N, Jørgensen ME, Bjerregaard P, Treebak JT, Fumagalli M, Korneliussen TS, Andersen MA et al. ( 2014 ) . A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes . Nature vol. 512 , ( 7513 ) 190 - 193 .
Fumagalli M, Sironi M ( 2014 ) . Human genome variability, natural selection and infectious diseases . Current Opinion in Immunology vol. 30 , 9 - 16 .
Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS et al. ( 2014 ) . Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears . Cell vol. 157 , ( 4 ) 785 - 794 .
Fumagalli M, Vieira FG, Linderoth T, Nielsen R ( 2014 ) . ngsTools: methods for population genetics analyses from next-generation sequencing data . Bioinformatics vol. 30 , ( 10 ) 1486 - 1487 .
Fumagalli M ( 2013 ) . Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences . PLOS ONE vol. 8 , ( 11 )
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sánchez E, Albrechtsen A, Nielsen R ( 2013 ) . Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data . Genetics vol. 195 , ( 3 ) 979 - 992 .
Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R ( 2013 ) . Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation . Genome Research vol. 23 , ( 11 ) 1852 - 1861 .
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E et al. ( 2013 ) . Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse . Nature vol. 499 , ( 7456 ) 74 - 78 .
Somel M, Sayres MAW, Jordan G, Huerta-Sanchez E, Fumagalli M, Ferrer-Admetlla A, Nielsen R ( 2013 ) . A Scan for Human-Specific Relaxation of Negative Selection Reveals Unexpected Polymorphism in Proteasome Genes . Molecular Biology and Evolution vol. 30 , ( 8 ) 1808 - 1815 .
Cagliani R, Guerini FR, Rubio‐Acero R, Baglio F, Forni D, Agliardi C, Griffanti L, Fumagalli M et al. ( 2013 ) . Long‐Standing Balancing Selection in the THBS4 Gene: Influence on Sex‐Specific Brain Expression and Gray Matter Volumes in Alzheimer Disease . Human Mutation vol. 34 , ( 5 ) 743 - 753 .
Cagliani R, Pozzoli U, Forni D, Cassinotti A, Fumagalli M, Giani M, Fichera M, Lombardini M et al. ( 2013 ) . Crohn's Disease Loci Are Common Targets of Protozoa-Driven Selection . Molecular Biology and Evolution vol. 30 , ( 5 ) 1077 - 1087 .
Fumagalli M, Fracassetti M, Cagliani R, Forni D, Pozzoli U, Comi GP, Marini F, Bresolin N et al. ( 2012 ) . An evolutionary history of the selectin gene cluster in humans . Heredity vol. 109 , ( 2 ) 117 - 126 .
Cagliani R, Guerini FR, Fumagalli M, Riva S, Agliardi C, Galimberti D, Pozzoli U, Goris A et al. ( 2012 ) . A Trans-Specific Polymorphism in ZC3HAV1 Is Maintained by Long-Standing Balancing Selection and May Confer Susceptibility to Multiple Sclerosis . Molecular Biology and Evolution vol. 29 , ( 6 ) 1599 - 1613 .
Cagliani R, Riva S, Marino C, Fumagalli M, D’Angelo MG, Riva V, Comi GP, Pozzoli U et al. ( 2011 ) . Variants in SNAP25 are targets of natural selection and influence verbal performances in women . Cellular and Molecular Life Sciences vol. 69 , ( 10 ) 1705 - 1715 .
Manry J, Laval G, Patin E, Fornarino S, Itan Y, Fumagalli M, Sironi M, Tichit M et al. ( 2011 ) . Evolutionary genetic dissection of human interferons . Journal of Experimental Medicine vol. 208 , ( 13 ) 2747 - 2759 .
Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Pattini L, Nielsen R ( 2011 ) . Correction: Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution . PLOS Genetics vol. 7 , ( 11 )
Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, Nielsen R ( 2011 ) . Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution . PLOS Genetics vol. 7 , ( 11 )
Cagliani R, Fumagalli M, Guerini FR, Riva S, Galimberti D, Comi GP, Agliardi C, Scarpini E et al. ( 2011 ) . Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis . Human Genetics vol. 131 , ( 1 ) 87 - 97 .
Cagliani R, Riva S, Fumagalli M, Biasin M, Caputo SL, Mazzotta F, Piacentini L, Pozzoli U et al. ( 2011 ) . A POSITIVELY SELECTED APOBEC3H HAPLOTYPE IS ASSOCIATED WITH NATURAL RESISTANCE TO HIV‐1 INFECTION . Evolution vol. 65 , ( 11 ) 3311 - 3322 .
Cagliani R, Riva S, Pozzoli U, Fumagalli M, Comi GP, Bresolin N, Clerici M, Sironi M ( 2011 ) . Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving . BMC Ecology and Evolution vol. 11 , ( 1 )
Sironi M, Guerini FR, Agliardi C, Biasin M, Cagliani R, Fumagalli M, Caputo D, Cassinotti A et al. ( 2011 ) . An Evolutionary Analysis of RAC2 Identifies Haplotypes Associated with Human Autoimmune Diseases . Molecular Biology and Evolution vol. 28 , ( 12 ) 3319 - 3329 .
Cagliani R, Riva S, Fumagalli M, Pozzoli U, Comi GP, Bresolin N, Clerici M, Sironi M ( 2010 ) . Balancing selection in the extended MHC region maintains a subset of alleles with opposite risk profile for different autoimmune diseases . Genome Biology vol. 11 , ( Suppl 1 )
Cagliani R, Riva S, Biasin M, Fumagalli M, Pozzoli U, Caputo SL, Mazzotta F, Piacentini L et al. ( 2010 ) . Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection . Human Molecular Genetics vol. 19 , ( 23 ) 4705 - 4714 .
Cagliani R, Fumagalli M, Biasin M, Piacentini L, Riva S, Pozzoli U, Bonaglia MC, Bresolin N et al. ( 2010 ) . Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene . Human Genetics vol. 128 , ( 6 ) 577 - 588 .
Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M ( 2010 ) . The landscape of human genes involved in the immune response to parasitic worms . BMC Ecology and Evolution vol. 10 , ( 1 )
Fumagalli M, Cagliani R, Riva S, Pozzoli U, Biasin M, Piacentini L, Comi GP, Bresolin N et al. ( 2010 ) . Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 Diabetes . Molecular Biology and Evolution vol. 27 , ( 11 ) 2555 - 2566 .
Torri F, Akelai A, Lupoli S, Sironi M, Amann‐Zalcenstein D, Fumagalli M, Dal Fiume C, Ben‐Asher E et al. ( 2010 ) . Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence . The FASEB Journal vol. 24 , ( 8 ) 3066 - 3082 .
Cagliani R, Fumagalli M, Riva S, Pozzoli U, Fracassetti M, Bresolin N, Comi GP, Sironi M ( 2010 ) . Polymorphisms in the CPB2 Gene Are Maintained by Balancing Selection and Result in Haplotype-Preferential Splicing of Exon 7 . Molecular Biology and Evolution vol. 27 , ( 8 ) 1945 - 1954 .
Fumagalli M, Cagliani R, Pozzoli U, Sironi M ( 2010 ) . Response to Wilson et al . American Journal of Human Genetics vol. 86 , ( 3 ) 493 - 495 .
Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M ( 2010 ) . Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach . PLOS Genetics vol. 6 , ( 2 )
Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Bresolin N, Sironi M ( 2010 ) . Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populations . Pharmacogenetics and Genomics vol. 20 , ( 2 ) 131 - 134 .
Pozzoli U, Fumagalli M, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M ( 2010 ) . The role of protozoa-driven selection in shaping human genetic variability . Trends in Genetics vol. 26 , ( 3 ) 95 - 99 .
Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M ( 2009 ) . A population genetics study of the Familial Mediterranean Fever gene: evidence of balancing selection under an overdominance regime . Genes & Immunity vol. 10 , ( 8 ) 678 - 686 .
Cagliani R, Fumagalli M, Pozzoli U, Riva S, Comi GP, Torri F, Macciardi F, Bresolin N et al. ( 2009 ) . Diverse Evolutionary Histories for β-adrenoreceptor Genes in Humans . American Journal of Human Genetics vol. 85 , ( 1 ) 64 - 75 .
Cagliani R, Fumagalli M, Pozzoli U, Riva S, Cereda M, Comi GP, Pattini L, Bresolin N et al. ( 2009 ) . A complex selection signature at the human AVPR1B gene . BMC Ecology and Evolution vol. 9 , ( 1 )
Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Riva S, Clerici M, Bresolin N, Sironi M ( 2009 ) . Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions . Journal of Experimental Medicine vol. 206 , ( 6 ) 1395 - 1408 .
Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M ( 2008 ) . Widespread balancing selection and pathogen-driven selection at blood group antigen genes . Genome Research vol. 19 , ( 2 ) 199 - 212 .
Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Menozzi G, Bresolin N, Sironi M ( 2008 ) . The signature of long-standing balancing selection at the human defensin β-1 promoter . Genome Biology vol. 9 , ( 9 )
Pozzoli U, Menozzi G, Fumagalli M, Cereda M, Comi GP, Cagliani R, Bresolin N, Sironi M ( 2008 ) . Both selective and neutral processes drive GC content evolution in the human genome . BMC Ecology and Evolution vol. 8 , ( 1 )
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