List of works - Matteo Fumagalli

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

scientific article

A complex selection signature at the human AVPR1B gene

scientific article

A population genetics study of the familial Mediterranean fever gene: evidence of balancing selection under an overdominance regime

scientific article published on 13 August 2009

A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection.

scientific article

A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes

scientific article published on 22 May 2013

A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis.

scientific article published on 6 January 2012

An evolutionary analysis of RAC2 identifies haplotypes associated with human autoimmune diseases.

scientific article published on 16 June 2011

An evolutionary history of the selectin gene cluster in humans.

scientific article

Archaic Adaptive Introgression in TBX15/WARS2.

scientific article

Assessing the effect of sequencing depth and sample size in population genetics inferences

scientific article

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

scientific article

Both selective and neutral processes drive GC content evolution in the human genome

scientific article

Crohn's disease loci are common targets of protozoa-driven selection

scientific article published on 6 February 2013

Deep Learning in Population Genetics

scientific article published in 2023

Diverse evolutionary histories for beta-adrenoreceptor genes in humans

scientific article published on 02 July 2009

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

scientific article

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse

scientific article published on 22 September 2015

Evolutionary genetic dissection of human interferons

scientific article published on 12 December 2011

Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence

scientific article published on 6 April 2010

Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection

article

Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism.

scientific article published on 4 June 2019

Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populations

scientific article

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

scientific article

Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach

scientific article (publication date: 19 February 2010)

Greenlandic Inuit show genetic signatures of diet and climate adaptation

scientific article

HMMploidy: inference of ploidy levels from short-read sequencing data

scientific article published on 30 June 2021

Human genome variability, natural selection and infectious diseases

scientific article published on 29 May 2014

Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis.

scientific article

ImaGene: a convolutional neural network to quantify natural selection from genomic data

scientific article published on 22 November 2019

Improving the estimation of genetic distances from Next-Generation Sequencing data

article by Filipe G. Vieira et al published 30 March 2015 in Biological Journal of the Linnean Society

Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease.

scientific article

Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene

scientific article published on 2 September 2010

Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions

scientific article

Polymorphisms in the CPB2 Gene Are Maintained by Balancing Selection and Result in Haplotype-Preferential Splicing of Exon 7

article

Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes

scientific article published on 10 June 2010

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

scientific article

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

Quantifying population genetic differentiation from next-generation sequencing data

scientific article

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Recent Asian origin of chytrid fungi causing global amphibian declines.

scientific article

Response to Wilson et al

Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution

scientific article

Speciation with gene flow in equids despite extensive chromosomal plasticity

scientific article

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

scientific article published on 24 October 2017

The evolution of CHC22 clathrin influences its role in human glucose metabolism

The landscape of human genes involved in the immune response to parasitic worms ⬇️

scientific article published on August 31, 2010

The origin and evolution of maize in the Southwestern United States

scientific article

The role of protozoa-driven selection in shaping human genetic variability

scientific article published on 25 January 2010

The signature of long-standing balancing selection at the human defensin beta-1 promoter.

scientific article published on 25 September 2008

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

scientific article

Uncovering the genetic history of the present-day Greenlandic population. ⬇️

scientific article

Variants in SNAP25 are targets of natural selection and influence verbal performances in women

scientific article

Widespread balancing selection and pathogen-driven selection at blood group antigen genes

scientific article

ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

scientific article published in 2022

ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

scientific article published in 2023

ngsTools: methods for population genetics analyses from next-generation sequencing data

scientific article

List of works by Matteo Fumagalli

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

A complex selection signature at the human AVPR1B gene

A population genetics study of the familial Mediterranean fever gene: evidence of balancing selection under an overdominance regime

A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection.

A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes

A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis.

An evolutionary analysis of RAC2 identifies haplotypes associated with human autoimmune diseases.

An evolutionary history of the selectin gene cluster in humans.

Archaic Adaptive Introgression in TBX15/WARS2.

Assessing the effect of sequencing depth and sample size in population genetics inferences

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

Both selective and neutral processes drive GC content evolution in the human genome

Crohn's disease loci are common targets of protozoa-driven selection

Deep Learning in Population Genetics

Diverse evolutionary histories for beta-adrenoreceptor genes in humans

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse

Evolutionary genetic dissection of human interferons

Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence

Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection

Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism.

Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populations

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach

Greenlandic Inuit show genetic signatures of diet and climate adaptation

HMMploidy: inference of ploidy levels from short-read sequencing data

Human genome variability, natural selection and infectious diseases

Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis.

ImaGene: a convolutional neural network to quantify natural selection from genomic data

Improving the estimation of genetic distances from Next-Generation Sequencing data

Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease.

Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene

Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions

Polymorphisms in the CPB2 Gene Are Maintained by Balancing Selection and Result in Haplotype-Preferential Splicing of Exon 7

Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Quantifying population genetic differentiation from next-generation sequencing data

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Recent Asian origin of chytrid fungi causing global amphibian declines.

Response to Wilson et al

Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution

Speciation with gene flow in equids despite extensive chromosomal plasticity

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

The evolution of CHC22 clathrin influences its role in human glucose metabolism

The landscape of human genes involved in the immune response to parasitic worms ⬇️

The origin and evolution of maize in the Southwestern United States

The role of protozoa-driven selection in shaping human genetic variability

The signature of long-standing balancing selection at the human defensin beta-1 promoter.

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Uncovering the genetic history of the present-day Greenlandic population. ⬇️

Variants in SNAP25 are targets of natural selection and influence verbal performances in women

Widespread balancing selection and pathogen-driven selection at blood group antigen genes

ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

ngsTools: methods for population genetics analyses from next-generation sequencing data