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Louis J. Liu

Ph.D. Student
WCM & MSKCC
jil4030 (at) med.cornell.edu


About Me

Hi. I’m Louis (Jǐnruì).

I am currently a 3rd-year Ph.D. candidate of the Physiology, Biophysics and Systems Biology Program at Weill Cornell Graduate School of Medical Sciences in New York City, jointly advised by Dr. Christina Leslie and Dr. Kushal Dey from Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center (MSKCC). My research interests lie in studying gene regulation through integrative analysis of functional genomics and genetics data using machine learning and statistical approaches.

Prior to Cornell, I worked as a Senior Associate Scientist in computational immuno-oncology for a biotechnology company. I received my master’s degree in Biomedical Engineering from Johns Hopkins University focusing on bioinformatics research under Dr. Carlo Colantuoni and Dr. Brian Caffo. I received dual bachelor’s degrees in Bioengineering from University of Missouri and East China University of Science and Technology.

Research Interests

Publications

  1. A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development.
    S Sonthalia, R Adkins, J Orvis, G Li, X Blanco, A Casella, J Liu, G Stein-O’Brien, B Caffo, R Hertzano, A Mahurkar, J Gillis, J Werner, S Ma, N Micali, N Sestan, P Rakic, G Santpere, S Ament, C Colantuoni
    bioRxiv (Accepted, Nature Neuroscience), 2025 - journal

  2. Identifying Rheumatoid Arthritis Gene-regulatory Enhancers with RNA+ATAC Multiome Data.
    L Liu, T Park, S Mitra, M Smith, L. Donlin, K Dey, C Leslie
    ASHG, 2024 - conference

  3. A pan-cancer ex vivo drug screen database for next-generation pharmacogenomics and functional precision oncology.
    A Markus, K Pichotta, J Quinn, J White, C Tosh, J liu, E Coyne, W Tansey
    AACR, 2024 - conference

  4. Circulating tumor DNA (ctDNA) dynamics and survival outcomes in patients (pts) with advanced non-small cell lung cancer (aNSCLC) and high (>50%) programmed cell death-ligand 1 (PD-L1) expression, randomized to cemiplimab (cemi) vs chemotherapy (chemo).
    NI Vokes, DR Gandara, A Sezer, S Kilickap, M Gumus, I Bondarenko, M Özgüroğlu, M Gogishvili, HM Turk, I Cicin, D Bentsion, J Liu, N Giangreco, F Wang, S Li, I Lowy, J Pouliot, G Gullo, P Rietschel, V Jankovic
    ASCO, 2023 - conference

  5. Structured joint decomposition identifies reproducible cell states and their developmental progression across human neocortical development
    S Sonthalia, J Liu, H Chen, C Colantuoni
    CSHL, 2022 - conference

  6. Structured Joint Decomposition (SJD) identifies conserved molecular dynamics across collections of biologically related multi-omics data matrices
    H Chen, J Liu, S Sonthalia, G Stein-O’Brien, L Xiao, B Caffo, C Colantuoni
    bioRxiv, 2022 - journal

  7. Two-stage linked component analysis for joint decomposition of multiple biologically related data sets
    H Chen, B Caffo, G Stein-O’Brien, J Liu, B Langmead, C Colantuoni, L Xiao
    Biostatistics, 2022 - journal

  8. A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity
    W Zhang, PG Hawkins, J He, NT Gupta, J Liu, G Choonoo, SW Jeong, CR Chen, A Dhanik, M Dillon, R Deering, LE Macdonald, G Thurston, GS Atwal
    Science Advances, 2021 - journal

  9. Vibrational spectroscopy of sodalite: Theory and experiments.
    A Mofrad, C Peixoto, J Blumeyer, J Liu, H Hunt, K Hammond
    The Journal of Physical Chemistry C, 2018 - journal


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