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Dr Matteo Fumagalli

Matteo

Senior Lecturer in Genetics

Email: m.fumagalli@qmul.ac.uk
Telephone: +44 (0)20 7882 8342
Room Number: 5.01, Fogg Building
Website: https://mfumagalli.github.io/

Profile

I graduated in biomedical engineering from Politecnico di Milano - Italy (PhD, 2011). I then moved to UC Berkeley for a postdoc position with Professor Rasmus Nielsen funded by EMBO. In 2014 I returned to Europe as a research fellow with Professor Francois Balloux at UCL funded by HFSP and jointly supervised by Professor Frances Brodsky with funding from NIH. I moved to Imperial College London in 2016 and then became Lecturer in Quantitative Evolution at Silwood Park in 2017. I joined Queen Mary University of London as Senior Lecturer in Genetics in 2021. I am also an affiliated fellow at the Digital Environment Research Institute (DERI).

In my research, I use statistics and computer science to solve complex questions in human genetics and evolutionary biology. I am a strong advocate of open-source and open-access science initiatives such as Peer Community In. I often deliver outreach activities on human evolution at local communities and organise STEM-career events to secondary school pupils.

Undergraduate Teaching

Evolution (BIO113)

Essentials skills in biomedicine (BMD100)

Research projects (BIO600/BMD600)

Postgraduate Teaching

Statistics for Biologists (BIO724P)

Bioinformatics Software Development Group Project (BIO727P)

Statistics and Data Analysis (BIO773P)

Research projects (BIO702P)

 

Research

Research Interests:

Has evolution shaped our predisposition to disease?

As humans encountered new environments, adaptation shaped the genetic similarities and differences among populations through the action of natural selection. In a changing environment, previously beneficial mutations may have a detrimental effect and contribute to disease susceptibility. We investigate how much natural selection has maintained disease-associated genetic variants in human populations, as a result of exposure of new pathogens, diet regimes, or extreme environments.

How do we extract reliable information from biological experiments?

Whilst new high-throughput sequencing technologies allow for rapid generation of genomic data, the information they provide is associated with uncertainty and errors. We develop statistical methods and implement software for the bioinformatic analysis of genomic sequencing data. We are particularly interested in estimating population genetic parameters from low-coverage sequencing data of non-model systems.

Is Artificial Intelligence able to solve the unsolvable in evolutionary studies?

One of the main scientific advancements in recent years is the improved predictive power of Artificial Intelligence. We pioneer the use of machine learning algorithms for the inference of past demographic history, admixture events, and genes under positive and balancing selection from genomic data. We established the EvoGenomics.AI for the dissemination of new findings, including a review in the application of Artificial Intelligence in evolutionary genomics.

Publications

Google Scholar publication list 

  • Korfmann K, Sellinger TPP, Freund F et al. (publicationYear). Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent. nameOfConference


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  • Mas-Sandoval A, Mathieson S, Fumagalli M (publicationYear). The genomic footprint of social stratification in admixing American populations. nameOfConference


  • Mas-Sandoval A, Jin C, Fracassetti M et al. (2022). ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language.. nameOfConference


  • Korfmann K, Gaggiotti OE, Fumagalli M (2023). Deep Learning in Population Genetics. nameOfConference


  • Soraggi S, Rhodes J, Altinkaya I et al. (publicationYear). HMMploidy: inference of ploidy levels from short-read sequencing data. nameOfConference


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  • Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M et al. (2022). Disentangling Signatures of Selection before and after European Colonization in Latin Americans. nameOfConference


  • Mas-Sandoval A, Pope NS, Nielsen KN et al. (2022). Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data. nameOfConference


  • Gower G, Picazo PI, Fumagalli M et al. (publicationYear). Detecting adaptive introgression in human evolution using convolutional neural networks. nameOfConference


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  • Isildak U, Stella A, Fumagalli M (2021). Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. nameOfConference


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  • Fumagalli M (2020). Detecting loci under natural selection from temporal genomic data of selfing populations. nameOfConference


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  • Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D et al. (2020). Inference of natural selection from ancient DNA. nameOfConference


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  • Torada L, Lorenzon L, Beddis A et al. (2019). ImaGene: a convolutional neural network to quantify natural selection from genomic data. nameOfConference


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  • Wright AE, Rogers TF, Fumagalli M et al. (2019). Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict. nameOfConference


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  • Fumagalli M, Camus SM, Diekmann Y et al. (publicationYear). Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism. nameOfConference


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  • Fox EA, Wright AE, Fumagalli M et al. (2019). ngsLD: evaluating linkage disequilibrium using genotype likelihoods. nameOfConference


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  • Adhikari K, Mendoza-Revilla J, Sohail A et al. (publicationYear). A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. nameOfConference


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  • O'Hanlon SJ, Rieux A, Farrer RA et al. (2018). Recent Asian origin of chytrid fungi causing global amphibian declines. nameOfConference


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  • Wright AE, Fumagalli M, Cooney CR et al. (2018). Male‐biased gene expression resolves sexual conflict through the evolution of sex‐specific genetic architecture. nameOfConference


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  • Elfekih S, Etter P, Tay WT et al. (publicationYear). Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories. nameOfConference


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  • Lassalle F, Spagnoletti M, Fumagalli M et al. (2018). Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet. nameOfConference


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  • Benazzo A, Trucchi E, Cahill JA et al. (2017). Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers. nameOfConference


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  • Fumagalli M, Balloux F (2017). Chapter 11 Natural Selection Associated With Infectious Diseases. nameOfConference


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  • Fumagalli M, Balloux F (2017). Natural Selection Associated With Infectious Diseases. nameOfConference


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  • Racimo F, Gokhman D, Fumagalli M et al. (2017). Archaic Adaptive Introgression in TBX15/WARS2. nameOfConference


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  • Foote AD, Vijay N, Ávila-Arcos MC et al. (publicationYear). Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. nameOfConference


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  • Librado P, Der Sarkissian C, Ermini L et al. (2015). Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. nameOfConference


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  • Der Sarkissian C, Ermini L, Schubert M et al. (2015). Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse. nameOfConference


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  • Fumagalli M, Moltke I, Grarup N et al. (2015). Greenlandic Inuit show genetic signatures of diet and climate adaptation. nameOfConference


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  • Vieira FG, Lassalle F, Korneliussen TS et al. (2016). Improving the estimation of genetic distances from Next‐Generation Sequencing data. nameOfConference


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  • da Fonseca RR, Smith BD, Wales N et al. (publicationYear). Erratum: The origin and evolution of maize in the Southwestern United States. nameOfConference


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  • da Fonseca RR, Smith BD, Wales N et al. (publicationYear). The origin and evolution of maize in the Southwestern United States. nameOfConference


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  • Moltke I, Fumagalli M, Korneliussen TS et al. (2015). Uncovering the Genetic History of the Present-Day Greenlandic Population. nameOfConference


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  • Schubert M, Jónsson H, Chang D et al. (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. nameOfConference


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  • Jónsson H, Schubert M, Seguin-Orlando A et al. (2014). Speciation with gene flow in equids despite extensive chromosomal plasticity. nameOfConference


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  • Moltke I, Grarup N, Jørgensen ME et al. (2014). A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. nameOfConference


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  • Fumagalli M, Sironi M (2014). Human genome variability, natural selection and infectious diseases. nameOfConference


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  • Liu S, Lorenzen ED, Fumagalli M et al. (2014). Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. nameOfConference


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  • Fumagalli M, Vieira FG, Linderoth T et al. (2014). ngsTools: methods for population genetics analyses from next-generation sequencing data. nameOfConference


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  • Grarup N, Moltke I, Jorgensen ME et al. (2014). A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. nameOfConference

    DOI: doi

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  • Fumagalli M (publicationYear). Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences. nameOfConference


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  • Fumagalli M, Vieira FG, Korneliussen TS et al. (2013). Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data. nameOfConference


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  • Vieira FG, Fumagalli M, Albrechtsen A et al. (2013). Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. nameOfConference


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  • Orlando L, Ginolhac A, Zhang G et al. (2013). Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. nameOfConference


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  • Somel M, Sayres MAW, Jordan G et al. (2013). A Scan for Human-Specific Relaxation of Negative Selection Reveals Unexpected Polymorphism in Proteasome Genes. nameOfConference


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  • Cagliani R, Guerini FR, Rubio‐Acero R et al. (2013). Long‐Standing Balancing Selection in the THBS4 Gene: Influence on Sex‐Specific Brain Expression and Gray Matter Volumes in Alzheimer Disease. nameOfConference


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  • Cagliani R, Pozzoli U, Forni D et al. (2013). Crohn's Disease Loci Are Common Targets of Protozoa-Driven Selection. nameOfConference


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  • Fumagalli M, Fracassetti M, Cagliani R et al. (2012). An evolutionary history of the selectin gene cluster in humans. nameOfConference


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  • Cagliani R, Guerini FR, Fumagalli M et al. (2012). A Trans-Specific Polymorphism in ZC3HAV1 Is Maintained by Long-Standing Balancing Selection and May Confer Susceptibility to Multiple Sclerosis. nameOfConference


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  • Cagliani R, Riva S, Marino C et al. (2012). Variants in SNAP25 are targets of natural selection and influence verbal performances in women. nameOfConference


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  • Manry J, Laval G, Patin E et al. (2011). Evolutionary genetic dissection of human interferons. nameOfConference


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  • Fumagalli M, Sironi M, Pozzoli U et al. (publicationYear). Correction: Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. nameOfConference


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  • Fumagalli M, Sironi M, Pozzoli U et al. (2011). Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. nameOfConference


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  • Cagliani R, Fumagalli M, Guerini FR et al. (2012). Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis. nameOfConference


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  • Cagliani R, Riva S, Fumagalli M et al. (2011). A POSITIVELY SELECTED APOBEC3H HAPLOTYPE IS ASSOCIATED WITH NATURAL RESISTANCE TO HIV‐1 INFECTION. nameOfConference


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  • Cagliani R, Riva S, Pozzoli U et al. (2011). Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving. nameOfConference


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  • Sironi M, Guerini FR, Agliardi C et al. (2011). An Evolutionary Analysis of RAC2 Identifies Haplotypes Associated with Human Autoimmune Diseases. nameOfConference


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  • Cagliani R, Riva S, Fumagalli M et al. (2010). Balancing selection in the extended MHC region maintains a subset of alleles with opposite risk profile for different autoimmune diseases. nameOfConference


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  • Cagliani R, Riva S, Biasin M et al. (2010). Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection. nameOfConference


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  • Cagliani R, Fumagalli M, Biasin M et al. (2010). Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene. nameOfConference


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  • Fumagalli M, Pozzoli U, Cagliani R et al. (2010). The landscape of human genes involved in the immune response to parasitic worms. nameOfConference


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  • Fumagalli M, Cagliani R, Riva S et al. (2010). Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 Diabetes. nameOfConference


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  • Torri F, Akelai A, Lupoli S et al. (2010). Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence. nameOfConference


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  • Cagliani R, Fumagalli M, Riva S et al. (2010). Polymorphisms in the CPB2 Gene Are Maintained by Balancing Selection and Result in Haplotype-Preferential Splicing of Exon 7. nameOfConference


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  • Fumagalli M, Cagliani R, Pozzoli U et al. (2010). Response to Wilson et al.. nameOfConference


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  • Fumagalli M, Pozzoli U, Cagliani R et al. (publicationYear). Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach. nameOfConference


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  • Cagliani R, Fumagalli M, Riva S et al. (2010). Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populations. nameOfConference


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  • Pozzoli U, Fumagalli M, Cagliani R et al. (2010). The role of protozoa-driven selection in shaping human genetic variability. nameOfConference


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  • Fumagalli M, Cagliani R, Pozzoli U et al. (2009). A population genetics study of the Familial Mediterranean Fever gene: evidence of balancing selection under an overdominance regime. nameOfConference


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  • Cagliani R, Fumagalli M, Pozzoli U et al. (2009). Diverse Evolutionary Histories for β-adrenoreceptor Genes in Humans. nameOfConference


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  • Cagliani R, Fumagalli M, Pozzoli U et al. (2009). A complex selection signature at the human AVPR1B gene. nameOfConference


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  • Fumagalli M, Pozzoli U, Cagliani R et al. (2009). Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. nameOfConference


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  • Fumagalli M, Cagliani R, Pozzoli U et al. (2009). Widespread balancing selection and pathogen-driven selection at blood group antigen genes. nameOfConference


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  • Cagliani R, Fumagalli M, Riva S et al. (2008). The signature of long-standing balancing selection at the human defensin β-1 promoter. nameOfConference


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  • Pozzoli U, Menozzi G, Fumagalli M et al. (2008). Both selective and neutral processes drive GC content evolution in the human genome. nameOfConference


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Supervision

Yuemin Li (PhD student)

Amelia Eneli (EngD student)

Roudin Sarama (PhD student)

Janeesh Kaur Bansal (PhD student - secondary supervisor)

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Pui Chung Siu (Junior Research Assistant, 2023)

Collaborators

Michael DeGiorgio (Florida Atlantic University)

Sara Mathieson (Haverford College)

Austin Burt (Imperial College London)

Grants

NSFDEB-NERC: "Machine learning tools to discover balancing selection in genomes from spatial and temporal autocorrelations" 2023-2026

NERC Exploring the frontiers of environmental research: "Generative adversarial networks for demographic inferences of nonmodel species from genomic data" 2023

The Leverhulme Trust Research Grant: "A deep learning approach to quantify natural selection in Latin Americans" 2018-2022

Human Frontier Science Program postdoctoral fellowship 2014-2016

European Molecular Biology Organization postdoctoral fellowship 2012-2013

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