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Siwei Chen

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Our lab strives to unlock the full potential of genomic data for genomic medicine: given near-complete genomic information from a patient, what can we reliably infer to improve their clinical care? We pursue this goal by developing foundational, scalable, and interpretable computational frameworks that guide us through the full 'genomic medicine cycle' – beginning with the discovery of disease-associated variants (variant-to-disease), progressing toward understanding their molecular mechanisms (variant-to-function), and culminating in translating these insights into improved patient care (variant-to-care).
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    Collapse Biography 
    Collapse education and training
    Cornell University, IthacaPhD05/2020Systems Biology
    Massachusetts General Hospital, BostonPostdoc08/2024Statistical Genetics
    Harvard Medical School, BostonInstructor08/2025Statistical Genetics

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Leu C, Avbersek A, Stevelink R, Custodio HM, Chen S, Speed D, Bennett CA, Jonsson L, Unnsteinsdóttir U, Jorgensen AL, Cavalleri GL, Delanty N, Craig JJ, Depondt C, Johnson MR, Koeleman BPC, Hassanin E, Omidvar ME, Krause R, Lerche H, Marson AG, O'Brien TJ, Sander JW, Sills GJ, Striano P, Zara F, Stefansson H, Stefansson K, May P, Neale BM, Lal D, Berkovic SF, Epi25 Collaborative, EpiPGX Consortium, Sisodiya SM. Genome-wide association meta-analyses of drug-resistant epilepsy. EBioMedicine. 2025 May; 115:105675. PMID: 40240269; PMCID: PMC12143209.
      Citations: 1     Fields:    Translation:Humans
    2. Sealock JM, Ivankovic F, Liao C, Chen S, Churchhouse C, Karczewski KJ, Howrigan DP, Neale BM. Tutorial: guidelines for quality filtering of whole-exome and whole-genome sequencing data for population-scale association analyses. Nat Protoc. 2025 Mar 28. PMID: 40155705.
      Citations:    Fields:    Translation:Humans
    3. Epi25 Collaborative. Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes. Nat Neurosci. 2024 Oct; 27(10):1864-1879. PMID: 39363051; PMCID: PMC11646479.
      Citations: 9     Fields:    Translation:Humans
    4. Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, Poterba T, Wilson MW, Tarasova Y, Phu W, Grant R, Yohannes MT, Koenig Z, Farjoun Y, Banks E, Donnelly S, Gabriel S, Gupta N, Ferriera S, Tolonen C, Novod S, Bergelson L, Roazen D, Ruano-Rubio V, Covarrubias M, Llanwarne C, Petrillo N, Wade G, Jeandet T, Munshi R, Tibbetts K, Genome Aggregation Database Consortium, O'Donnell-Luria A, Solomonson M, Seed C, Martin AR, Talkowski ME, Rehm HL, Daly MJ, Tiao G, Neale BM, MacArthur DG, Karczewski KJ. A genomic mutational constraint map using variation in 76,156 human genomes. Nature. 2024 Jan; 625(7993):92-100. PMID: 38057664; PMCID: PMC11629659.
      Citations: 503     Fields:    Translation:Humans
    5. International League Against Epilepsy Consortium on Complex Epilepsies. GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture. Nat Genet. 2023 09; 55(9):1471-1482. PMID: 37653029; PMCID: PMC10484785.
      Citations: 71     Fields:    Translation:HumansCells
    6. Bundalian L, Su YY, Chen S, Velluva A, Kirstein AS, Garten A, Biskup S, Battke F, Lal D, Heyne HO, Platzer K, Lin CC, Lemke JR, Le Duc D, Epi25 Collaborative. Epilepsies of presumed genetic etiology show enrichment of rare variants that occur in the general population. Am J Hum Genet. 2023 07 06; 110(7):1110-1122. PMID: 37369202; PMCID: PMC10357498.
      Citations:    Fields:    Translation:Humans
    7. Chen S, Liu Y, Zhang Y, Wierbowski SD, Lipkin SM, Wei X, Yu H. A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. Genome Res. 2022 01; 32(1):135-149. PMID: 34963661; PMCID: PMC8744679.
      Citations: 5     Fields:    Translation:Humans
    8. Chen S, Wang J, Cicek E, Roeder K, Yu H, Devlin B. De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. Mol Autism. 2020 10 08; 11(1):76. PMID: 33032641; PMCID: PMC7545940.
      Citations: 15     Fields:    Translation:HumansCells
    9. Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst. 2020 04 22; 10(4):333-350.e14. PMID: 32325033; PMCID: PMC7938770.
      Citations: 39     Fields:    Translation:Animals
    10. Pertesi M, Vallée M, Wei X, Revuelta MV, Galia P, Demangel D, Oliver J, Foll M, Chen S, Perrial E, Garderet L, Corre J, Leleu X, Boyle EM, Decaux O, Rodon P, Kolb B, Slama B, Mineur P, Voog E, Le Bris C, Fontan J, Maigre M, Beaumont M, Azais I, Sobol H, Vignon M, Royer B, Perrot A, Fuzibet JG, Dorvaux V, Anglaret B, Cony-Makhoul P, Berthou C, Desquesnes F, Pegourie B, Leyvraz S, Mosser L, Frenkiel N, Augeul-Meunier K, Leduc I, Leyronnas C, Voillat L, Casassus P, Mathiot C, Cheron N, Paubelle E, Moreau P, Bignon YJ, Joly B, Bourquard P, Caillot D, Naman H, Rigaudeau S, Marit G, Macro M, Lambrecht I, Cliquennois M, Vincent L, Helias P, Avet-Loiseau H, Moreno V, Reis RM, Varkonyi J, Kruszewski M, Vangsted AJ, Jurczyszyn A, Zaucha JM, Sainz J, Krawczyk-Kulis M, Watek M, Pelosini M, Iskierka-Jazdzewska E, Grzasko N, Martinez-Lopez J, Jerez A, Campa D, Buda G, Lesueur F, Dudzinski M, García-Sanz R, Nagler A, Rymko M, Jamroziak K, Butrym A, Canzian F, Obazee O, Nilsson B, Klein RJ, Lipkin SM, McKay JD, Dumontet C. Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma. Leukemia. 2019 09; 33(9):2324-2330. PMID: 30967618; PMCID: PMC6756025.
      Citations: 26     Fields:    Translation:Humans
    11. Chen S, Fragoza R, Klei L, Liu Y, Wang J, Roeder K, Devlin B, Yu H. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Nat Genet. 2018 07; 50(7):1032-1040. PMID: 29892012; PMCID: PMC6314957.
      Citations: 46     Fields:    Translation:Humans
    12. Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, Zhang J, Walsh MF, Nichols KE, Joseph V, Snyder C, Vachon CM, McKay JD, Wang SP, Jayabalan DS, Jacobs LM, Becirovic D, Waller RG, Artomov M, Viale A, Patel J, Phillip J, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager SL, Godley LA, Churpek J, Garber JE, Anderson KC, Daly MJ, Roeder RG, Dumontet C, Lynch HT, Mullighan CG, Camp NJ, Offit K, Klein RJ, Yu H, Cerchietti L, Lipkin SM. Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma. Cancer Res. 2018 05 15; 78(10):2747-2759. PMID: 29559475; PMCID: PMC5955848.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    13. Chen S, Beltrán JF, Esteban-Jurado C, Franch-Expósito S, Castellví-Bel S, Lipkin S, Wei X, Yu H. GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. Nucleic Acids Res. 2017 07 03; 45(W1):W207-W214. PMID: 28521008; PMCID: PMC5556704.
      Citations: 1     Fields:    Translation:Humans
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