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  • Extended Figure 1Despite decades of research, many metabolic genes still lack known molecular substrates. To discover functions for “orphan” transporters and enzymes, we developed the GeneMAP resource. The paper is now out (July 2024) in Nature Genetics. This interdisciplinary study spanning genomics and metabolism also identified SLC25A48 as the long-sought mitochondrial choline transporter.
  • STATGEN2024The American Statistical Association (ASA) Section on Statistics in Genomics and Genetics (SSGG) had its first section conference (STATGEN 2024) on May 1-3, 2024 in Pittsburgh. We presented our work on single-cell and bulk-tissue transcriptomics in the session “Computational methods and platforms for genetic and omic data integration”.
  • single_cell_workshop.logoWe presented the single-cell RNA-Seq workshop at the International Genetic Epidemiology Society (2023) annual meeting.
  • Screenshot 2022-08-02 at 01-33-57 model_diagram.pdfWe present a new deep learning framework, HYFA (Hypergraph Factorisation), for multi-tissue gene expression imputation and cell-type signature inference — just out in Nature Machine Intelligence. The study was selected for the front cover of the July issue. HYFA represents multi-tissue gene expression in a hypergraph of individuals, metagenes, and tissues, and learns factorised representations via a specialised message passing neural network operating on the hypergraph. Through transfer learning on single-nucleus RNA-seq data, HYFA resolves cell-type signatures from bulk gene expression. HYFA may provide a unifying transcriptomic methodology for multi-tissue imputation and cell-type deconvolution.

    The hypergraph factorisation framework is flexible (supporting k-uniform hypergraphs of arbitrary node types) and may find application beyond computational genomics.

  • 2_GenSpotlightOur research was highlighted by NIH/NHGRI in the first Genomics Research Spotlight (“Artificial intelligence and machine learning becoming pervasive at NHGRI and in genomics” article) featuring a funded investigator-initiated research project.
  • FLVCR1A study, led by Kıvanç Birsoy and Timothy Kenny, identifying the major mammalian choline transporter is now out in Cell Metabolism. The study was selected by Cell Metabolism for preview. Combined genetic and biochemical screens provide “the answer to a long-standing question in lipid biology,” identifying the transporters for choline uptake critical for cell and tissue phospholipid homeostasis.
  • SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells has come out in Nature (October 2021). Led by Kıvanç Birsoy, it solves a long-standing mystery in metabolism and redox biology, with implications for our understanding of a range of human diseases. The study leverages organellar proteomics and metabolomics approaches and human transcriptome-wide association studies (TWAS).
  • pQTL_discoveryExcited to see Mapping the proteo-genomic convergence of human diseases finally out in Science (October 2021). Led by Claudia Langenberg, it “provides a framework to 1) connect etiologically related diseases, 2) provide biological context for new or emerging disorders, and 3) integrate different biological domains to establish mechanisms for known gene-disease links.”
  • NIH_Center_for_Scientific_ReviewDr Gamazon has been appointed a standing member of the NIH Biostatistical Methods and Research Design (BMRD) study section.
  • Contextualizing_NatCommsOur study Contextualizing genetic risk score for disease screening and rare variant discovery is out in Nature Communications. We investigate how common, small-effect polygenic burden (PB) and large-effect variants (LEVs) can inform disease risk stratification and prediction. The study develops a computational methodology on the use of genetic risk score for disease screening and rare variant discovery. The framework makes predictions on PB-based LEV screening for 36 complex traits, which we confirm in a large-scale biobank (UK Biobank) with available LEV information. Our observation on the enrichment of rare variant carriers in the lower tail of the polygenic risk score was first presented in the 2015 International Genetic Epidemiology Society meeting (Davis LK et al.).
  • We are excited to have Mariah Antopia and Elma Jashim in our group. Mariah is a recent recipient of the Barry Goldwater Scholarship, the nation’s preeminent scholarship in science, technology, engineering and mathematics. Elma is quickly becoming a prolific young scientist with authorship on several recent publications.
  • Dr Gamazon received the 2020-2021 Basic Research Award of the Division of Genetic Medicine, Department of Medicine.
  • figure1Our latest research on genetics and neurodegeneration with Zac Gerring and Eske Derks of QIMR Berghofer is out.
  • Reuters_healthCheck out this Reuters Health story about a new JAMA Psychiatry study on shared genetic factors between major psychiatric disorders and BMI.
  • Benson_Hall_VanderbiltWe are excited to design and teach the following graduate courses (Spring 2020) at Vanderbilt University:
    IGP 8002: Integrating Genomics and Phenomics: Characterizing Disease Mechanisms
    EPID 8332: Advanced Methods For Epidemiology
  • Vandy_BMEWe are super thrilled to be paired with students in a Senior Design group in Vanderbilt University’s Department of Biomedical Engineering for our project “Developing a Machine Learning Framework for Data Integration in Genomics and Precision Medicine” (PIs: Eric Gamazon and Sandra Zinkel).
  • ScienceNGOur recent paper on genetic mechanisms underlying neuropsychiatric disease (Nature Genetics 55, 933 (2019)) received coverage in Science (14 June 2019).
  • agnietenkapel-351720Congratulations to Andries Marees for successful defense of his PhD thesis! The ceremony was held at the Agnietenkapel, built in the 1400’s and considered the birthplace of the University of Amsterdam.
    Marees heeft onderzocht wat de genetische basis is van middelengebruik/verslaving. Hij wilde achterhalen welke genetische varianten een rol spelen in de kwetsbaarheid om verslaafd te raken.
  • eLife_LogoBid maintains mitochondrial cristae structure and protects against cardiac disease in an integrative genomics study is out in eLIFE and was showcased in eLife Digest. We identified a homeostatic role for Bid in the regulation of mitochondrial structure and function with implications for human cardiac disease, combining cell biology and human genetic studies and observations in a model system. Bid-/- mice hearts have increased fibrotic damage after acute stress, similar to post-myocardial-infarction damage observed in human patients. Proteomics studies suggest a possible defect in mitochondrial respiratory chain function. Through immunoprecipitation, Bid binds the matrix form of Mcl-1 (previously implicated in cristae stability), which can be altered with helix-6 mutant M148T (nonsynonymous variation in Bid’s membrane binding domain).
  • ClareHall_LogoDr Gamazon is now a Life Member of Clare Hall, a graduate college devoted to advanced studies within the University of Cambridge. Life Member designation allows him to return to the college at any time to participate in its intellectual life, facilitating his extensive research collaborations within the university.
  • FRSB_LogoDr Gamazon was elected Fellow of the Royal Society of Biology in July 2018.
  • ClareHall_LogoDr Gamazon has been elected to a Clare Hall Visiting Fellowship to advance his research and mentor graduate students in the University of Cambridge. Fellows become Life Members of Clare Hall, Cambridge.
  • UCambridgeDr Gamazon is a visiting researcher (Department of Medicine, MRC Biostatistics Unit, MRC Epidemiology Unit) in the University of Cambridge for much of the Lent and Easter term (2018).