Suhas Srinivasan

Publications

Peer-reviewed articles, preprints, book chapter, patent, theses and talks, listed newest first within each group.

* co-lead author · $ co-senior author · + equal contribution

Journal Articles

2026

  1. Mitochondrial Raf1 regulates glutamine catabolism

    Shanderson, Ferguson, Ducoli, Miao, Srinivasan, Siprashvili, Li, Velasco, Li, Hoang, Ye, Khavari

    Cell Reports, 2026 · 45(9):117975

  2. Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

    Jung+, Lopez-Pajares+, Donohue, Guo, Srinivasan, Siprashvili, Khavari

    Science Advances, 2026 · 12(33):eadz9441

  3. Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation

    Winge+, Jackrazi+, Porter, Srinivasan, Lopez-Pajares, Li, Pham, Houser, Cha, Meyers, Ko

    Science, 2026 · 392(6805):eaeb3900

  4. Bridging technical innovation and computational advances in studies of RNA–protein assemblies

    Ducoli, Srinivasan, Amjadi, Khavari

    Nature Reviews Genetics, 2026 · 27(6):462–484 · Review

  5. Autoantibody hotspots reveal the origin and impact of immunogenic XIST ribonucleoprotein complexes in autoimmune diseases

    Yan+, Lee+, Srinivasan, Ambriz, Shi, Dou, Davuluri, Nandyala, Woods, Leatherman, Zhao

    Journal of Clinical Investigation, 2026 · 136(7):e198291

  6. EcDNA-borne structural variants drive oncogenic fusion transcript amplification

    Yi+, Zhang+, Swinderman, Wang, Kanakaveti, Hung, Wong, Srinivasan, Curtis, Bhargava-Shah, Li

    Cell, 2026 · 189(3):906–921.e20

  7. Real-time spatiotemporal tracking of infectious outbreaks in confined environments with a host–pathogen agent-based system

    Srinivasan, King, Collins, Colubri, Korkin

    Proceedings of the National Academy of Sciences, 2026 · 123(4):e2422574123

2025

  1. Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis

    Porter+, Meyers+, Miao+, Reynolds+, Hong, Yang, Srinivasan, Mondal, Siprashvili, Fabo, Zhou, Nguyen, Ducoli, Meyers, Nguyen, Ko, Kellman, Elfaki, Guo, Winge, Jackrazi, Lopez-Pajares, Liu, Qu, Porter, Kim, Kim, Tao, Engreitz, Khavari

    Nature Communications, 2025 · 16:8387

  2. Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation

    Lopez-Pajares, Bhaduri, Zhao, Gowrishankar, Donohue, Guo, Siprashvili, Miao, Nguyen, Yang, Li, Tung, Shanderson, Winge, Meservey, Srinivasan, Meyers, Guerrero, Ji, Garcia, Tao, Gambhir, Long, Ye, Khavari

    Cell Stem Cell, 2025 · 32(5):795–810.e10

  3. irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA

    Ducoli+, Zarnegar+, Porter, Meyers, Miao, Riley, Srinivasan, Jackrazi, Yang, Li, Wang, Bertozzi, Flynn, Khavari

    Nature, 2025 · 641(8063):769–778

  4. Functional analysis of cancer-associated germline risk variants

    Kellman, Neela, Srinivasan, Siprashvili, Shanderson, Hong, Rao, Porter, Reynolds, Meyers, Guo, Yang, Zhao, Wozniak, Donohue, Shenoy, Ko, Nguyen, Mondal, Garcia, Elcavage, Elfaki, Abell, Tao, Montgomery, Khavari

    Nature Genetics, 2025 · 57(3):718–728

  5. DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs

    Miao+, Porter+, Siprashvili, Ferguson, Ducoli, Nguyen, Ko, Lopez-Pajares, Srinivasan, Hong, Yang, Cao, Meyers, Meyers, Tao, Wang, Khavari

    Cell Reports, 2025 · 44(1):115174

2024

  1. Xist ribonucleoproteins promote female sex-biased autoimmunity

    Dou, Zhao, Belk, Zhao, Casey, Chen, Li, Yu, Srinivasan, Abe, Kraft, Hellström, Sjöberg, Chang, Feng, Goldman, Shah, Petri, Chung, Fiorentino, Lundberg, Wutz, Utz, Chang

    Cell, 2024 · 187(3):733–749.e16

2023

  1. The extent of edgetic perturbations in the human interactome caused by population-specific mutations

    Cui, Srinivasan, Gao, Korkin

    Biomolecules, 2023 · 14(1):40

2022

  1. Unravelling psychiatric heterogeneity and predicting suicide attempts in women with trauma-related dissociation using artificial intelligence

    Srinivasan, Harnett, Zhang, Dahlgren, Jang, et al.

    European Journal of Psychotraumatology, 2022 · 13(2):2143693

2021

  1. Computational protein modeling and the next viral pandemic

    Narykov*, Srinivasan*, Korkin

    Nature Methods, 2021 · 18(5):444–445 · Comment

2020

  1. A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data

    Srinivasan, Leshchyk, Johnson, Korkin

    RNA, 2020 · 26(10):1303–1319

  2. Structural genomics of SARS-CoV-2 indicates evolutionary conserved functional regions of viral proteins

    Srinivasan, Cui, Gao, Liu, Lu, et al.

    Viruses, 2020 · 12(4):360 · Cover Feature

2019

  1. Enriching human interactome with functional mutations to detect high-impact network modules underlying complex diseases

    Cui, Srinivasan, Korkin

    Genes, 2019 · 10(11):933

  2. Assessment of network module identification across complex diseases

    Choobdar, Ahsen, Crawford, Tomasoni, Fang, Lamparter, Lin, Hescott, Hu, Mercer, Natoli, The DREAM Module Identification Challenge Consortium, et al.

    Nature Methods, 2019 · 16(9):843–852

Book Chapter

2021

  1. Structural genomics and interactomics of SARS-CoV-2

    Gao*, Lu*, Narykov*, Srinivasan*, Korkin

    Virus Bioinformatics (Chapman and Hall/CRC), 2021 · pp. 121–139 · Cover Feature

Preprints

2026

  1. Estrogen interactions with breast cancer risk variants in regulatory DNA

    Elfaki, Kellman, Meyers, Ducoli, Fu, Obbad, Mondal, Yang, Porter, Reynolds, Srinivasan, Nakase, Ota, Fabo, Meyers, Yang, Westerman, Kachuri, Khavari

    medRxiv, 2026

2025

  1. PLI Analyzer for data-driven validation of AI predicted biomolecular interfaces

    Liang*, Srinivasan*$, Chang$

    bioRxiv, 2025

  2. Thermal proteome profiling identifies glucose binding proteins involved in metabolic disease

    Meservey, Ferguson, Tien, Ducoli, Miao, Lu, Srinivasan, Lopez-Pajares, Porter, Cao, Wang

    bioRxiv, 2025 · Version 2 (January 2026)

Patent

2021

  1. System and method for monitoring machine anomalies via control data

    Zhang*, Srinivasan*

    US Patent 11,181,899 B2, 2021 · Granted 2021-11-23

Theses

2022

  1. Biological discovery via data science: Multigranular artificial intelligence approaches for cells, cerebra and cruise ships

    Srinivasan

    Doctoral dissertation, Worcester Polytechnic Institute, 2022

2013

  1. Code impact analyzer for improving software development practices

    Srinivasan

    Master's thesis, Birla Institute of Technology and Science, Pilani, 2013

Talks and Presentations

Invited Talks

2024

  1. Multigranular AI approaches for biological discovery

    Stony Brook University School of Medicine, 2024

  2. Modeling of infection dynamics with intelligent agents

    University of Texas at San Antonio, 2024

2022

  1. Transistors to transcription factors: Bioinformatics reimagined

    Stanford Research Computing Center, 2022

2019

  1. Deep learning for single-cell transcriptomics

    WPI Bioinformatics Seminars, 2019

Refereed Presentations

2026

  1. EcDNA-derived structural variants: A common pathway to oncogenic fusion transcript amplification in cancer

    Yi, Zhang, Swinderman, Wang, Kanakaveti, Hung, Wong, Srinivasan, Curtis, Bhargava-Shah, Li

    Cancer Research (abstract), 2026 · 86(1_Supplement):A007

2025

  1. Antigen hotspots reveal novel autoantibodies against XIST ribonucleoproteins in sex-biased autoimmune disease

    Yan, Lee, Srinivasan, Shi, Dou, Davuluri, Nandyala, Woods, Leatherman, Zhao, Reggiardo, Sawant, Thiam, Shah, Fiorentino, Chung, Chang

    Journal of Investigative Dermatology (abstract), 2025 · 145(8):S6

2024

  1. A large-scale TF-DNA interaction map in primary keratinocytes and its relation to skin disease-linked regulatory variants

    Porter, Reynolds, Miao, Meyers, Hong, Yang, Ducoli, Mondal, Siprashvili, Elfaki, Srinivasan, Khavari

    Journal of Investigative Dermatology (abstract), 2024 · 144(8):S71

2023

  1. XIST ribonucleoproteins promote female sex-biased autoimmunity

    Dou, Zhao, Belk, Zhao, Casey, Chen, Li, Yu, Srinivasan, Abe, Kraft, Hellström, Sjöberg, Chang, Feng, Goldman, Shah, Petri, Chung, Fiorentino, Lundberg, Wutz, Utz, Chang

    American College of Rheumatology Convergence, 2023

2021

  1. Unraveling tumor heterogeneity in triple-negative breast cancer at single-cell resolution

    Srinivasan, Leshchyk, Korkin

    Human Cell Atlas General Meeting, 2021

  2. Structural genomics and interactomics of SARS-CoV-2

    Srinivasan, Narykov, Cui, Gao, Liu, Lu, Mkandawire, Sun, Korkin

    ASBMB PDB50 Symposium, 2021

2019

  1. In-silico edgetic profiling of population-specific variation in human genome

    Cui, Srinivasan, Leshchyk, Korkin

    Cold Spring Harbor Laboratory, Biology of Genomes, 2019

  2. Real-time simulation of intelligent agents to study epidemiological outcomes

    Srinivasan, Korkin

    WPI Graduate Research and Innovation Exchange, 2019 · Second Place Award for Poster Presentation

2018

  1. Robust cell type profiling in single-cell RNA sequencing data through a de novo deep clustering approach

    Srinivasan, Johnson, Korkin

    Gordon Research Conference, Human Genetic Variation and Disease, 2018

  2. A hybrid deep clustering approach for robust cell type profiling

    Srinivasan, Johnson, Korkin

    WPI Graduate Research and Innovation Exchange, 2018 · First Place Award for Poster Presentation