Publications
Publications of specific relevance to the Centre for Evolutionary and Functional Genomics
2025
The importance of small-island populations for the long-term survival of endangered large-bodied insular mammalsAninta SG Drinkwater R Carmagnini A Deere NJ Priyono DS Andayani N Winarni NL Supriatna J et al.
Proceedings of The National Academy of Sciences of The United States of America,
Proceedings of The National Academy of Sciences vol. 122 (26)
24-06-2025Efficient Detection and Characterization of Targets of Natural Selection Using Transfer LearningArnab SP dos Santos ALC Fumagalli M DeGiorgio M
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 42 (5)
30-04-2025 Efficient detection and characterization of targets of natural selection using transfer learningArnab SP dos Santos ALC Fumagalli M DeGiorgio M
,
Cold Spring Harbor Laboratory 07-03-2025 2024
Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta CoalescentKorfmann K Sellinger TPP Freund F Fumagalli M Tellier A
Peer Community Journal,
Peer Community In vol. 4
18-03-2024 2023
The genomic footprint of social stratification in admixing American populationsMas-Sandoval A Mathieson S Fumagalli M
Elife,
Elife vol. 12
01-12-2023 ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language.Mas-Sandoval A Jin C Fracassetti M Fumagalli M
F1000research vol. 11, 126-126.
14-07-2023 Deep Learning in Population GeneticsKorfmann K Gaggiotti OE Fumagalli M
Genome Biology and Evolution,
Oxford University Press (OUP) vol. 15 (2)
23-01-2023 ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia languageMas-Sandoval A Jin C Fracassetti M Fumagalli M
In
F1000res 01-01-2023 2022
HMMploidy: inference of ploidy levels from short-read sequencing dataSoraggi S Rhodes J Altinkaya I Tarrant O Balloux F Fisher MC Fumagalli M
Peer Community Journal,
Peer Community In vol. 2
14-10-2022 Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing dataMas-Sandoval A Pope NS Nielsen KN Altinkaya I Fumagalli M Korneliussen TS
Gigascience vol. 11
17-05-2022 Disentangling Signatures of Selection before and after European Colonization in Latin AmericansMendoza-Revilla J Chacón-Duque JC Fuentes-Guajardo M Ormond L Wang K Hurtado M Villegas V Granja V et al.
Molecular Biology and Evolution vol. 39 (4)
19-04-2022 2021
Detecting adaptive introgression in human evolution using convolutional neural networksGower G Picazo PI Fumagalli M Racimo F
Elife,
Elife vol. 10
25-05-2021 Distinguishing between recent balancing selection and incomplete sweep using deep neural networksIsildak U Stella A Fumagalli M
Molecular Ecology Resources,
Wiley vol. 21 (8), 2706-2718.
05-04-2021 2020
Detecting loci under natural selection from temporal genomic data of selfing populationsFumagalli M
Peer Community in Evolutionary Biology,
Peer Community In 26-10-2020 Inference of natural selection from ancient DNADehasque M Ávila‐Arcos MC Díez‐del‐Molino D Fumagalli M Guschanski K Lorenzen ED Malaspinas A Marques‐Bonet T et al.
Evolution Letters,
Oxford University Press (OUP) vol. 4 (2), 94-108.
01-04-2020 2019
ImaGene: a convolutional neural network to quantify natural selection from genomic dataTorada L Lorenzon L Beddis A Isildak U Pattini L Mathieson S Fumagalli M
Bmc Bioinformatics,
Springer Nature vol. 20 (Suppl 9)
01-11-2019 Genetic diversity of CHC22 clathrin impacts its function in glucose metabolismFumagalli M Camus SM Diekmann Y Burke A Camus MD Norman PJ Joseph A Abi-Rached L et al.
Elife,
Elife vol. 8
04-06-2019 Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflictWright AE Rogers TF Fumagalli M Cooney CR Mank JE
Molecular Ecology,
Wiley vol. 28 (11), 2860-2871.
01-06-2019 ngsLD: evaluating linkage disequilibrium using genotype likelihoodsFox EA Wright AE Fumagalli M Vieira FG
Bioinformatics,
Oxford University Press (OUP) vol. 35 (19), 3855-3856.
23-03-2019 A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in EurasiaAdhikari K Mendoza-Revilla J Sohail A Fuentes-Guajardo M Lampert J Chacón-Duque JC Hurtado M Villegas V et al.
Nature Communications,
Springer Nature vol. 10 (1)
21-01-2019 2018
Recent Asian origin of chytrid fungi causing global amphibian declinesO'Hanlon SJ Rieux A Farrer RA Rosa GM Waldman B Bataille A Kosch TA Murray KA et al.
Science,
American Association For The Advancement of Science (Aaas) vol. 360 (6389), 621-627.
11-05-2018 Male‐biased gene expression resolves sexual conflict through the evolution of sex‐specific genetic architectureWright AE Fumagalli M Cooney CR Bloch NI Vieira FG Buechel SD Kolm N Mank JE
Evolution Letters,
Oxford University Press (OUP) vol. 2 (2), 52-61.
01-04-2018 Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic historiesElfekih S Etter P Tay WT Fumagalli M Gordon K Johnson E De Barro P
Plos One,
Public Library of Science (Plos) vol. 13 (1)
24-01-2018 2017
Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to dietLassalle F Spagnoletti M Fumagalli M Shaw L Dyble M Walker C Thomas MG Migliano AB et al.
Molecular Ecology,
Wiley vol. 27 (1), 182-195.
14-12-2017 Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglersBenazzo A Trucchi E Cahill JA Delser PM Mona S Fumagalli M Bunnefeld L Cornetti L et al.
Proceedings of The National Academy of Sciences of The United States of America,
Proceedings of The National Academy of Sciences vol. 114 (45), e9589-e9597.
24-10-2017 Natural Selection Associated With Infectious DiseasesFumagalli M Balloux F
In
On Human Nature Biology Psychology Ethics Politics and Religion 177-191.
01-01-2017 Chapter 11 Natural Selection Associated With Infectious DiseasesFumagalli M Balloux F
In
On Human Nature,
Elsevier 177-191.
01-01-2017 2016
Archaic Adaptive Introgression in TBX15/WARS2Racimo F Gokhman D Fumagalli M Ko A Hansen T Moltke I Albrechtsen A Carmel L et al.
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 34 (3), 509-524.
21-12-2016 Genome-culture coevolution promotes rapid divergence of killer whale ecotypesFoote AD Vijay N Ávila-Arcos MC Baird RW Durban JW Fumagalli M Gibbs RA Hanson MB et al.
Nature Communications,
Springer Nature vol. 7 (1)
31-05-2016 2015
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environmentsLibrado P Der Sarkissian C Ermini L Schubert M Jónsson H Albrechtsen A Fumagalli M Yang MA et al.
Proceedings of The National Academy of Sciences of The United States of America,
Proceedings of The National Academy of Sciences vol. 112 (50), e6889-e6897.
23-11-2015 Evolutionary Genomics and Conservation of the Endangered Przewalski’s HorseDer Sarkissian C Ermini L Schubert M Yang MA Librado P Fumagalli M Jónsson H Bar-Gal GK et al.
Current Biology,
Elsevier vol. 25 (19), 2577-2583.
24-09-2015 Greenlandic Inuit show genetic signatures of diet and climate adaptationFumagalli M Moltke I Grarup N Racimo F Bjerregaard P Jørgensen ME Korneliussen TS Gerbault P et al.
Science,
American Association For The Advancement of Science (Aaas) vol. 349 (6254), 1343-1347.
18-09-2015 Improving the estimation of genetic distances from Next-Generation Sequencing dataVieira FG Lassalle F Korneliussen TS Fumagalli M
Biological Journal of The Linnean Society,
Oxford University Press (OUP) vol. 117 (1), 139-149.
30-03-2015 Erratum: The origin and evolution of maize in the Southwestern United Statesda Fonseca RR Smith BD Wales N Cappellini E Skoglund P Fumagalli M Samaniego JA Carøe C et al.
Nature Plants,
Springer Nature vol. 1 (1)
14-01-2015 The origin and evolution of maize in the Southwestern United Statesda Fonseca RR Smith BD Wales N Cappellini E Skoglund P Fumagalli M Samaniego JA Carøe C et al.
Nature Plants,
Springer Nature vol. 1 (1)
08-01-2015 2014
Uncovering the Genetic History of the Present-Day Greenlandic PopulationMoltke I Fumagalli M Korneliussen TS Crawford JE Bjerregaard P Jørgensen ME Grarup N Gulløv HC et al.
American Journal of Human Genetics,
Elsevier vol. 96 (1), 54-69.
31-12-2014 Prehistoric genomes reveal the genetic foundation and cost of horse domesticationSchubert M Jónsson H Chang D Der Sarkissian C Ermini L Ginolhac A Albrechtsen A Dupanloup I et al.
Proceedings of The National Academy of Sciences of The United States of America,
Proceedings of The National Academy of Sciences vol. 111 (52), e5661-e5669.
15-12-2014 Speciation with gene flow in equids despite extensive chromosomal plasticityJónsson H Schubert M Seguin-Orlando A Ginolhac A Petersen L Fumagalli M Albrechtsen A Petersen B et al.
Proceedings of The National Academy of Sciences of The United States of America,
Proceedings of The National Academy of Sciences vol. 111 (52), 18655-18660.
01-12-2014 A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetesMoltke I Grarup N Jørgensen ME Bjerregaard P Treebak JT Fumagalli M Korneliussen TS Andersen MA et al.
Nature,
Springer Nature vol. 512 (7513), 190-193.
18-06-2014 Human genome variability, natural selection and infectious diseasesFumagalli M Sironi M
Current Opinion in Immunology,
Elsevier vol. 30, 9-16.
29-05-2014 Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar BearsLiu S Lorenzen ED Fumagalli M Li B Harris K Xiong Z Zhou L Korneliussen TS et al.
Cell,
Elsevier vol. 157 (4), 785-794.
01-05-2014 ngsTools: methods for population genetics analyses from next-generation sequencing dataFumagalli M Vieira FG Linderoth T Nielsen R
Bioinformatics,
Oxford University Press (OUP) vol. 30 (10), 1486-1487.
23-01-2014 2013
Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics InferencesFumagalli M
Plos One,
Public Library of Science (Plos) vol. 8 (11)
18-11-2013 Quantifying Population Genetic Differentiation from Next-Generation Sequencing DataFumagalli M Vieira FG Korneliussen TS Linderoth T Huerta-Sánchez E Albrechtsen A Nielsen R
Genetics,
Oxford University Press (OUP) vol. 195 (3), 979-992.
01-11-2013 Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimationVieira FG Fumagalli M Albrechtsen A Nielsen R
Genome Research,
Cold Spring Harbor Laboratory vol. 23 (11), 1852-1861.
15-08-2013 Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horseOrlando L Ginolhac A Zhang G Froese D Albrechtsen A Stiller M Schubert M Cappellini E et al.
Nature,
Springer Nature vol. 499 (7456), 74-78.
26-06-2013 A Scan for Human-Specific Relaxation of Negative Selection Reveals Unexpected Polymorphism in Proteasome GenesSomel M Sayres MAW Jordan G Huerta-Sanchez E Fumagalli M Ferrer-Admetlla A Nielsen R
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 30 (8), 1808-1815.
22-05-2013 Long‐Standing Balancing Selection in the THBS4 Gene: Influence on Sex‐Specific Brain Expression and Gray Matter Volumes in Alzheimer DiseaseCagliani R Guerini FR Rubio‐Acero R Baglio F Forni D Agliardi C Griffanti L Fumagalli M et al.
Human Mutation,
Hindawi vol. 34 (5), 743-753.
02-04-2013 Crohn's Disease Loci Are Common Targets of Protozoa-Driven SelectionCagliani R Pozzoli U Forni D Cassinotti A Fumagalli M Giani M Fichera M Lombardini M et al.
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 30 (5), 1077-1087.
06-02-2013 2012
An evolutionary history of the selectin gene cluster in humansFumagalli M Fracassetti M Cagliani R Forni D Pozzoli U Comi GP Marini F Bresolin N et al.
Heredity,
Springer Nature vol. 109 (2), 117-126.
02-05-2012 A Trans-Specific Polymorphism in ZC3HAV1 Is Maintained by Long-Standing Balancing Selection and May Confer Susceptibility to Multiple SclerosisCagliani R Guerini FR Fumagalli M Riva S Agliardi C Galimberti D Pozzoli U Goris A et al.
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 29 (6), 1599-1613.
06-01-2012 2011
Variants in SNAP25 are targets of natural selection and influence verbal performances in womenCagliani R Riva S Marino C Fumagalli M D’Angelo MG Riva V Comi GP Pozzoli U et al.
Cellular and Molecular Life Sciences,
Springer Nature vol. 69 (10), 1705-1715.
23-12-2011 Evolutionary genetic dissection of human interferonsManry J Laval G Patin E Fornarino S Itan Y Fumagalli M Sironi M Tichit M et al.
Journal of Experimental Medicine,
Rockefeller University Press vol. 208 (13), 2747-2759.
12-12-2011 Correction: Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human EvolutionFumagalli M Sironi M Pozzoli U Ferrer-Admetlla A Pattini L Nielsen R
Plos Genetics,
Public Library of Science (Plos) vol. 7 (11)
21-11-2011 Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human EvolutionFumagalli M Sironi M Pozzoli U Ferrer-Admettla A Pattini L Nielsen R
Plos Genetics,
Public Library of Science (Plos) vol. 7 (11)
01-11-2011 Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysisCagliani R Fumagalli M Guerini FR Riva S Galimberti D Comi GP Agliardi C Scarpini E et al.
Human Genetics,
Springer Nature vol. 131 (1), 87-97.
07-07-2011 A POSITIVELY SELECTED APOBEC3H HAPLOTYPE IS ASSOCIATED WITH NATURAL RESISTANCE TO HIV‐1 INFECTIONCagliani R Riva S Fumagalli M Biasin M Caputo SL Mazzotta F Piacentini L Pozzoli U et al.
Evolution,
Oxford University Press (OUP) vol. 65 (11), 3311-3322.
28-06-2011 Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolvingCagliani R Riva S Pozzoli U Fumagalli M Comi GP Bresolin N Clerici M Sironi M
Bmc Ecology and Evolution,
Springer Nature vol. 11 (1)
17-06-2011 An Evolutionary Analysis of RAC2 Identifies Haplotypes Associated with Human Autoimmune DiseasesSironi M Guerini FR Agliardi C Biasin M Cagliani R Fumagalli M Caputo D Cassinotti A et al.
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 28 (12), 3319-3329.
16-06-2011 2010
Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infectionCagliani R Riva S Biasin M Fumagalli M Pozzoli U Caputo SL Mazzotta F Piacentini L et al.
Human Molecular Genetics,
Oxford University Press (OUP) vol. 19 (23), 4705-4714.
15-09-2010 Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 geneCagliani R Fumagalli M Biasin M Piacentini L Riva S Pozzoli U Bonaglia MC Bresolin N et al.
Human Genetics,
Springer Nature vol. 128 (6), 577-588.
02-09-2010 The landscape of human genes involved in the immune response to parasitic wormsFumagalli M Pozzoli U Cagliani R Comi GP Bresolin N Clerici M Sironi M
Bmc Ecology and Evolution,
Springer Nature vol. 10 (1)
31-08-2010 Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 DiabetesFumagalli M Cagliani R Riva S Pozzoli U Biasin M Piacentini L Comi GP Bresolin N et al.
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 27 (11), 2555-2566.
10-06-2010 Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidenceTorri F Akelai A Lupoli S Sironi M Amann‐Zalcenstein D Fumagalli M Dal Fiume C Ben‐Asher E et al.
The Faseb Journal,
Wiley vol. 24 (8), 3066-3082.
06-04-2010 Polymorphisms in the CPB2 Gene Are Maintained by Balancing Selection and Result in Haplotype-Preferential Splicing of Exon 7Cagliani R Fumagalli M Riva S Pozzoli U Fracassetti M Bresolin N Comi GP Sironi M
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 27 (8), 1945-1954.
17-03-2010 Response to Wilson et al.Fumagalli M Cagliani R Pozzoli U Sironi M
American Journal of Human Genetics,
Elsevier vol. 86 (3), 493-495.
01-03-2010 Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics ApproachFumagalli M Pozzoli U Cagliani R Comi GP Bresolin N Clerici M Sironi M
Plos Genetics,
Public Library of Science (Plos) vol. 6 (2)
19-02-2010 Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populationsCagliani R Fumagalli M Riva S Pozzoli U Comi GP Bresolin N Sironi M
Pharmacogenetics and Genomics,
Wolters Kluwer vol. 20 (2), 131-134.
01-02-2010 The role of protozoa-driven selection in shaping human genetic variabilityPozzoli U Fumagalli M Cagliani R Comi GP Bresolin N Clerici M Sironi M
Trends in Genetics,
Elsevier vol. 26 (3), 95-99.
25-01-2010 Balancing selection in the extended MHC region maintains a subset of alleles with opposite risk profile for different autoimmune diseasesCagliani R Riva S Fumagalli M Pozzoli U Comi GP Bresolin N Clerici M Sironi M
Genome Biology,
Springer Nature vol. 11 (Suppl 1)
01-01-2010 2009
A population genetics study of the Familial Mediterranean Fever gene: evidence of balancing selection under an overdominance regimeFumagalli M Cagliani R Pozzoli U Riva S Comi GP Menozzi G Bresolin N Sironi M
Genes & Immunity,
Springer Nature vol. 10 (8), 678-686.
13-08-2009 Diverse Evolutionary Histories for β-adrenoreceptor Genes in HumansCagliani R Fumagalli M Pozzoli U Riva S Comi GP Torri F Macciardi F Bresolin N et al.
American Journal of Human Genetics,
Elsevier vol. 85 (1), 64-75.
01-07-2009 A complex selection signature at the human AVPR1B geneCagliani R Fumagalli M Pozzoli U Riva S Cereda M Comi GP Pattini L Bresolin N et al.
Bmc Ecology and Evolution,
Springer Nature vol. 9 (1)
01-06-2009 Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditionsFumagalli M Pozzoli U Cagliani R Comi GP Riva S Clerici M Bresolin N Sironi M
Journal of Experimental Medicine,
Rockefeller University Press vol. 206 (6), 1395-1408.
25-05-2009 2008
Widespread balancing selection and pathogen-driven selection at blood group antigen genesFumagalli M Cagliani R Pozzoli U Riva S Comi GP Menozzi G Bresolin N Sironi M
Genome Research,
Cold Spring Harbor Laboratory vol. 19 (2), 199-212.
07-11-2008 Both selective and neutral processes drive GC content evolution in the human genomePozzoli U Menozzi G Fumagalli M Cereda M Comi GP Cagliani R Bresolin N Sironi M
Bmc Ecology and Evolution,
Springer Nature vol. 8 (1)
27-03-2008 The signature of long-standing balancing selection at the human defensin β-1 promoterCagliani R Fumagalli M Riva S Pozzoli U Comi GP Menozzi G Bresolin N Sironi M
Genome Biology,
Springer Nature vol. 9 (9)
01-01-2008 On the use of generative models for evolutionary inference of malaria vectors from genomic dataEneli AA Siu PC Perez MF Burt A Fumagalli M Mathieson S
In
Biorxiv Semi-supervised detection of natural selection with positive-unlabeled learningArnab SP dos Santos ALC Fumagalli M DeGiorgio M
In
Biorxiv Disentangling signatures of selection before and after European colonization in Latin AmericansMendoza-Revilla J Chacón-Duque JC Fuentes-Guajardo M Ormond L Wang K Hurtado M Villegas V Granja V et al.
In
Biorxiv HMMploidy: inference of ploidy levels from short-read sequencing dataSoraggi S Rhodes J Altinkaya I Tarrant O Balloux F Fisher MC Fumagalli M
In
Biorxiv Detecting adaptive introgression in human evolution using convolutional neural networksGower G Picazo PI Fumagalli M Racimo F
In
Biorxiv Distinguishing between recent balancing selection and incomplete sweep using deep neural networksIsildak U Stella A Fumagalli M
In
Biorxiv ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia languageMas-Sandoval A Jin C Fracassetti M Fumagalli M
Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta CoalescentKorfmann K Sellinger T Freund F Fumagalli M Tellier A
In
Biorxiv The genomic footprint of social stratification in admixing American populationsMas-Sandoval A Mathieson S Fumagalli M
In
Biorxiv Genetic diversity of CHC22 clathrin impacts its function in glucose metabolismFumagalli M Camus SM Diekmann Y Burke A Camus MD Norman PJ Joseph AP Abi-Rached L et al.
In
Biorxiv Sex-Biased Gene Expression Resolves Sexual Conflict through the Evolution of Sex-Specific Genetic ArchitectureWright AE Fumagalli M Cooney CR Bloch NI Vieira FG Buechel SD Kolm N Mank JE
In
Biorxiv Archaic adaptive introgression in TBX15/WARS2Racimo F Gokhman D Fumagalli M Ko A Hansen T Moltke I Albrechtsen A Carmel L et al.
In
Biorxiv The origin and evolution of maize in the American Southwestda Fonseca RR Smith BD Wales N Cappellini E Skoglund P Fumagalli M Samaniego JA Carøe C et al.
In
Biorxiv Genome-culture coevolution promotes rapid divergence in the killer whaleFoote AD Vijay N Ávila-Arcos MC Baird RW Durban JW Fumagalli M Gibbs RA Hanson MB et al.
In
Biorxiv The importance of small island populations for the long-term survival of endangered large-bodied insular mammalsAninta SG Drinkwater R Carmagnini A Deere NJ Priyono DS Andayani N Winarni NL Supriatna J et al.
In
Biorxiv
