Dr Matteo FumagalliSenior Lecturer in GeneticsEmail: m.fumagalli@qmul.ac.ukTelephone: +44 (0)20 7882 8342Room Number: 5.01, Fogg BuildingWebsite: https://mfumagalli.github.io/ProfileTeachingResearchPublicationsSupervisionCollaboratorsGrantsProfileI 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 TeachingEvolution (BIO113) Essentials skills in biomedicine (BMD100) Research projects (BIO600/BMD600)Postgraduate TeachingStatistics for Biologists (BIO724P) Bioinformatics Software Development Group Project (BIO727P) Statistics and Data Analysis (BIO773P) Research projects (BIO702P) ResearchResearch 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.PublicationsGoogle Scholar publication list Mas-Sandoval A, Mathieson S, Fumagalli M (publicationYear). The genomic footprint of social stratification in admixing American populations. nameOfConference DOI: 10.7554/elife.84429 QMRO: qmroHref Mas-Sandoval A, Jin C, Fracassetti M et al. (2022). ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language.. nameOfConference DOI: 10.12688/f1000research.104368.2 QMRO: qmroHref Korfmann K, Gaggiotti OE, Fumagalli M (2023). Deep Learning in Population Genetics. nameOfConference DOI: 10.1093/gbe/evad008 QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/88202 Soraggi S, Rhodes J, Altinkaya I et al. (publicationYear). HMMploidy: inference of ploidy levels from short-read sequencing data. nameOfConference DOI: 10.24072/pcjournal.178 QMRO: qmroHref 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 DOI: 10.1093/molbev/msac076 QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/88203 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 DOI: 10.1093/gigascience/giac032 QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/88204 Gower G, Picazo PI, Fumagalli M et al. (publicationYear). Detecting adaptive introgression in human evolution using convolutional neural networks. nameOfConference DOI: 10.7554/elife.64669 QMRO: qmroHref Isildak U, Stella A, Fumagalli M (2021). Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. nameOfConference DOI: 10.1111/1755-0998.13379 QMRO: qmroHref Fumagalli M (2020). Detecting loci under natural selection from temporal genomic data of selfing populations. nameOfConference DOI: 10.24072/pci.evolbiol.100110 QMRO: qmroHref Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D et al. (2020). Inference of natural selection from ancient DNA. nameOfConference DOI: 10.1002/evl3.165 QMRO: qmroHref Torada L, Lorenzon L, Beddis A et al. (2019). ImaGene: a convolutional neural network to quantify natural selection from genomic data. nameOfConference DOI: 10.1186/s12859-019-2927-x QMRO: qmroHref Wright AE, Rogers TF, Fumagalli M et al. (2019). Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict. nameOfConference DOI: 10.1111/mec.15115 QMRO: qmroHref Fumagalli M, Camus SM, Diekmann Y et al. (publicationYear). Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism. nameOfConference DOI: 10.7554/elife.41517 QMRO: qmroHref Fox EA, Wright AE, Fumagalli M et al. (2019). ngsLD: evaluating linkage disequilibrium using genotype likelihoods.. nameOfConference DOI: 10.1093/bioinformatics/btz200 QMRO: qmroHref 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 DOI: 10.1038/s41467-018-08147-0 QMRO: qmroHref O'Hanlon SJ, Rieux A, Farrer RA et al. (2018). Recent Asian origin of chytrid fungi causing global amphibian declines. nameOfConference DOI: 10.1126/science.aar1965 QMRO: qmroHref 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 DOI: 10.1002/evl3.39 QMRO: qmroHref 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 DOI: 10.1371/journal.pone.0190555 QMRO: qmroHref 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 DOI: 10.1111/mec.14435 QMRO: qmroHref 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 DOI: 10.1073/pnas.1707279114 QMRO: qmroHref Fumagalli M, Balloux F (2017). Chapter 11 Natural Selection Associated With Infectious Diseases. nameOfConference DOI: 10.1016/b978-0-12-420190-3.00011-9 QMRO: qmroHref Fumagalli M, Balloux F (2017). Natural Selection Associated With Infectious Diseases. nameOfConference DOI: 10.1016/B978-0-12-420190-3.00011-9 QMRO: qmroHref Racimo F, Gokhman D, Fumagalli M et al. (2017). Archaic Adaptive Introgression in TBX15/WARS2. nameOfConference DOI: 10.1093/molbev/msw283 QMRO: qmroHref Foote AD, Vijay N, Ávila-Arcos MC et al. (publicationYear). Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. nameOfConference DOI: 10.1038/ncomms11693 QMRO: qmroHref 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 DOI: 10.1073/pnas.1513696112 QMRO: qmroHref Der Sarkissian C, Ermini L, Schubert M et al. (2015). Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse. nameOfConference DOI: 10.1016/j.cub.2015.08.032 QMRO: qmroHref Fumagalli M, Moltke I, Grarup N et al. (2015). Greenlandic Inuit show genetic signatures of diet and climate adaptation. nameOfConference DOI: 10.1126/science.aab2319 QMRO: qmroHref Vieira FG, Lassalle F, Korneliussen TS et al. (2016). Genetic Distances from NGS Data. nameOfConference DOI: 10.1111/bij.12511 QMRO: qmroHref da Fonseca RR, Smith BD, Wales N et al. (publicationYear). Erratum: The origin and evolution of maize in the Southwestern United States. nameOfConference DOI: 10.1038/nplants.2015.7 QMRO: qmroHref da Fonseca RR, Smith BD, Wales N et al. (publicationYear). The origin and evolution of maize in the Southwestern United States. nameOfConference DOI: 10.1038/nplants.2014.3 QMRO: qmroHref Moltke I, Fumagalli M, Korneliussen TS et al. (2015). Uncovering the Genetic History of the Present-Day Greenlandic Population. nameOfConference DOI: 10.1016/j.ajhg.2014.11.012 QMRO: qmroHref Schubert M, Jónsson H, Chang D et al. (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. nameOfConference DOI: 10.1073/pnas.1416991111 QMRO: qmroHref Jónsson H, Schubert M, Seguin-Orlando A et al. (2014). Speciation with gene flow in equids despite extensive chromosomal plasticity. nameOfConference DOI: 10.1073/pnas.1412627111 QMRO: qmroHref Moltke I, Grarup N, Jørgensen ME et al. (2014). A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. nameOfConference DOI: 10.1038/nature13425 QMRO: qmroHref Fumagalli M, Sironi M (2014). Human genome variability, natural selection and infectious diseases. nameOfConference DOI: 10.1016/j.coi.2014.05.001 QMRO: qmroHref Liu S, Lorenzen ED, Fumagalli M et al. (2014). Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. nameOfConference DOI: 10.1016/j.cell.2014.03.054 QMRO: qmroHref Fumagalli M, Vieira FG, Linderoth T et al. (2014). ngsTools: methods for population genetics analyses from next-generation sequencing data. nameOfConference DOI: 10.1093/bioinformatics/btu041 QMRO: qmroHref 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 QMRO: qmroHref Fumagalli M (publicationYear). Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences. nameOfConference DOI: 10.1371/journal.pone.0079667 QMRO: qmroHref Fumagalli M, Vieira FG, Korneliussen TS et al. (2013). Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data. nameOfConference DOI: 10.1534/genetics.113.154740 QMRO: qmroHref Vieira FG, Fumagalli M, Albrechtsen A et al. (2013). Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. nameOfConference DOI: 10.1101/gr.157388.113 QMRO: qmroHref Orlando L, Ginolhac A, Zhang G et al. (2013). Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. nameOfConference DOI: 10.1038/nature12323 QMRO: qmroHref 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 DOI: 10.1093/molbev/mst098 QMRO: qmroHref 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 DOI: 10.1002/humu.22301 QMRO: qmroHref Cagliani R, Pozzoli U, Forni D et al. (2013). Crohn's Disease Loci Are Common Targets of Protozoa-Driven Selection. nameOfConference DOI: 10.1093/molbev/mst020 QMRO: qmroHref Fumagalli M, Fracassetti M, Cagliani R et al. (2012). An evolutionary history of the selectin gene cluster in humans. nameOfConference DOI: 10.1038/hdy.2012.20 QMRO: qmroHref 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 DOI: 10.1093/molbev/mss002 QMRO: qmroHref Cagliani R, Riva S, Marino C et al. (2012). Variants in SNAP25 are targets of natural selection and influence verbal performances in women. nameOfConference DOI: 10.1007/s00018-011-0896-y QMRO: qmroHref Manry J, Laval G, Patin E et al. (2011). Evolutionary genetic dissection of human interferons. nameOfConference DOI: 10.1084/jem.20111680 QMRO: qmroHref 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 DOI: 10.1371/annotation/ca428083-dbcb-476a-956c-d7bb6e317cf7 QMRO: qmroHref 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 DOI: 10.1371/journal.pgen.1002355 QMRO: qmroHref 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 DOI: 10.1007/s00439-011-1053-2 QMRO: qmroHref Cagliani R, Riva S, Fumagalli M et al. (2011). A POSITIVELY SELECTED APOBEC3H HAPLOTYPE IS ASSOCIATED WITH NATURAL RESISTANCE TO HIV‐1 INFECTION. nameOfConference DOI: 10.1111/j.1558-5646.2011.01368.x QMRO: qmroHref 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 DOI: 10.1186/1471-2148-11-171 QMRO: qmroHref Sironi M, Guerini FR, Agliardi C et al. (2011). An Evolutionary Analysis of RAC2 Identifies Haplotypes Associated with Human Autoimmune Diseases. nameOfConference DOI: 10.1093/molbev/msr164 QMRO: qmroHref 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 DOI: 10.1186/gb-2010-11-s1-p38 QMRO: qmroHref 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 DOI: 10.1093/hmg/ddq401 QMRO: qmroHref Cagliani R, Fumagalli M, Biasin M et al. (2010). Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene. nameOfConference DOI: 10.1007/s00439-010-0884-6 QMRO: qmroHref Fumagalli M, Pozzoli U, Cagliani R et al. (2010). The landscape of human genes involved in the immune response to parasitic worms. nameOfConference DOI: 10.1186/1471-2148-10-264 QMRO: qmroHref 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 DOI: 10.1093/molbev/msq141 QMRO: qmroHref Torri F, Akelai A, Lupoli S et al. (2010). Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence. nameOfConference DOI: 10.1096/fj.09-152611 QMRO: qmroHref 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 DOI: 10.1093/molbev/msq082 QMRO: qmroHref Fumagalli M, Cagliani R, Pozzoli U et al. (2010). Response to Wilson et al.. nameOfConference DOI: 10.1016/j.ajhg.2010.01.032 QMRO: qmroHref Fumagalli M, Pozzoli U, Cagliani R et al. (publicationYear). Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach. nameOfConference DOI: 10.1371/journal.pgen.1000849 QMRO: qmroHref 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 DOI: 10.1097/fpc.0b013e3283333532 QMRO: qmroHref Pozzoli U, Fumagalli M, Cagliani R et al. (2010). The role of protozoa-driven selection in shaping human genetic variability. nameOfConference DOI: 10.1016/j.tig.2009.12.010 QMRO: qmroHref 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 DOI: 10.1038/gene.2009.59 QMRO: qmroHref Cagliani R, Fumagalli M, Pozzoli U et al. (2009). Diverse Evolutionary Histories for β-adrenoreceptor Genes in Humans. nameOfConference DOI: 10.1016/j.ajhg.2009.06.005 QMRO: qmroHref Cagliani R, Fumagalli M, Pozzoli U et al. (2009). A complex selection signature at the human AVPR1B gene. nameOfConference DOI: 10.1186/1471-2148-9-123 QMRO: qmroHref 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 DOI: 10.1084/jem.20082779 QMRO: qmroHref Fumagalli M, Cagliani R, Pozzoli U et al. (2009). Widespread balancing selection and pathogen-driven selection at blood group antigen genes. nameOfConference DOI: 10.1101/gr.082768.108 QMRO: qmroHref Cagliani R, Fumagalli M, Riva S et al. (2008). The signature of long-standing balancing selection at the human defensin β-1 promoter. nameOfConference DOI: 10.1186/gb-2008-9-9-r143 QMRO: qmroHref Pozzoli U, Menozzi G, Fumagalli M et al. (2008). Both selective and neutral processes drive GC content evolution in the human genome. nameOfConference DOI: 10.1186/1471-2148-8-99 QMRO: qmroHref Alippi C, Casagrande E, Fumagalli M et al. (2002). An embedded system methodology for real-time analysis of railways track profile. nameOfConference DOI: doi QMRO: qmroHref SupervisionYuemin Li (PhD student) Amelia Eneli (EngD student) Roudin Sarama (PhD student) Janeesh Kaur Bansal (PhD student - secondary supervisor) ---------------------------------------------------------- Pui Chung Siu (Junior Research Assistant, 2023)CollaboratorsMichael DeGiorgio (Florida Atlantic University) Sara Mathieson (Haverford College) Austin Burt (Imperial College London)GrantsNSFDEB-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