Publications: Dr Matteo Fumagalli
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
)
Mas-Sandoval A, Pope NS, Nielsen KN, Altinkaya I, Fumagalli M, Korneliussen TS
(
2022
)
.
Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data
.
GigaScience
vol.
11
,
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
.
Grarup N, Moltke I, Jorgensen ME, Bjerregaard P, Treebak JT, Korneliussen TS, Andersen MA, Nielsen TS et al.
(
2014
)
.
A common Greenlandic <i>TBC1D4</i> variant confers muscle insulin resistance and type 2 diabetes
.
DIABETOLOGIA
.
vol.
57
,
S50
-
S50
.
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
)
Alippi C, Casagrande E, Fumagalli M, Scotti F, Piuri V, Valsecchi L
(
2002
)
.
An embedded system methodology for real-time analysis of railways track profile
.
Conference Record - IEEE Instrumentation and Measurement Technology Conference
.
vol.
1
,
747
-
751
.