Publications

Gene regulatory interactions limit the gene expression diversity [Link]
Orr Levy, Shubham Tripathi, Scott D. Pope, Yang Y. Liu, and Ruslan Medzhitov, Arxiv preprint (2023)

Regulation of chromatin transcription dynamics by DNA supercoiling [Link]
Sumitabha Brahmachari, Shubham Tripathi, José N Onuchic, and Herbert Levine, Biorxiv preprint (2023)

Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition [Link]
Yu-Chen Cheng, Yun Zhang, Shubham Tripathi, Harshavardhan BV, Mohit Kumar Jolly, Geoffrey Schiebinger, Herbert Levine, Thomas O. McDonald, and Franziska Michor, Biorxiv preprint (2023)

Systems immunology of regulatory T cells: can one circuit explain it all? [Link]
Shubham Tripathi, John S. Tsang, and Kyemyung Park, Trends in Immunology (2023)

Minimal frustration underlies the usefulness of incomplete regulatory network models in biology [Link]
Shubham Tripathi, David A. Kessler, and Herbert Levine, Proceedings of the National Academy of Sciences of the United States of America (2022)

Epigenetic factor competition reshapes the EMT landscape [Link]
M. Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D. Sontag, and Herbert Levine, Proceedings of the National Academy of Sciences of the United States of America (2022)

A Mechanistic Modeling Framework Reveals the Key Principles Underlying Tumor Metabolism [Link]
Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K. Bhattacharya, Benny Abraham Kaipparettu, and Herbert Levine, PLOS Computational Biology (2022)

DNA Supercoiling-mediated Collective Behavior of Co-transcribing RNA Polymerases [Link]
Shubham Tripathi, Sumitabha Brahmachari, José N. Onuchic, and Herbert Levine, Nucleic Acids Research (2021)

Identification of EMT Signaling Cross-talk and Gene Regulatory Networks by Single-cell RNA Sequencing [Link]
Abhijeet P. Deshmukh, Suhas V. Vasaikar, Katarzyna Tomczak, Shubham Tripathi, Petra den Hollander, Emre Arslan, Priyanka Chakraborty, Rama Soundararajan, Mohit Kumar Jolly, Kunal Rai, Herbert Levine, and Sendurai A. Mani, Proceedings of the National Academy of Sciences of the United States of America (2021)

Towards Decoding the Coupled Decision-Making of Metabolism and Epithelial-to-Mesenchymal Transition in Cancer [Link]
Dongya Jia, Jun Hyoung Park, Harsimran Kaur, Kwang Hwa Jung, Sukjin Yang, Shubham Tripathi, Madeline Galbraith, Youyuan Deng, Mohit Kumar Jolly, Benny Abraham Kaipparettu, José N. Onuchic, and Herbert Levine, British Journal of Cancer (2021)

Mathematical Modeling of Plasticity and Heterogeneity in EMT [Link]
Shubham Tripathi, Jianhua Xing, Herbert Levine, and Mohit Kumar Jolly, In: Campbell K., Theveneau E. (eds) The Epithelial-to Mesenchymal Transition. Methods in Molecular Biology, vol 2179. Humana, New York, NY. (2020)

Biological Networks Regulating Cell Fate Choice Are Minimally Frustrated [Link]
Shubham Tripathi, David A. Kessler, and Herbert Levine, Physical Review Letters (2020)

Epigenetic Feedback and Stochastic Partitioning During Cell Division can Drive Resistance to EMT [Link]
Wen Jia, Shubham Tripathi, Priyanka Chakraborty, Adithya Chedere, Annapoorni Rangarajan, Herbert Levine, and Mohit Kumar Jolly, Oncotarget (2020)

Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum [Link]
Priyanka Chakraborty, Jason T George, Shubham Tripathi, Herbert Levine, Mohit Kumar Jolly, Frontiers in Bioengineering and Biotechnology (2020)

A Mechanism for Epithelial-Mesenchymal Heterogeneity in a Population of Cancer Cells [Link]
Shubham Tripathi, Priyanka Chakraborty, Herbert Levine, and Mohit Kumar Jolly, PLOS Computational Biology (2020)

The Physics of Cellular Decision Making During Epithelial–Mesenchymal Transition [Link]
Shubham Tripathi, Herbert Levine, and Mohit Kumar Jolly, Annual Review of Biophysics (2020)

Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response [Link]
Dongya Jia, Xuefei Li, Federico Bocci, Shubham Tripathi, Youyuan Deng, Mohit Kumar Jolly, José N Onuchic, and Herbert Levine, Journal of Clinical Medicine (2019)

Analysis of Hierarchical Organization in Gene Expression Networks Reveals Underlying Principles of Collective Tumor Cell Dissemination and Metastatic Aggressiveness of Inflammatory Breast Cancer [Link]
Shubham Tripathi, Mohit Kumar Jolly, Wendy A. Woodward, Herbert Levine, and Michael W. Deem, Frontiers in Oncology (2018)

The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences [Link]
Shubham Tripathi and Michael W. Deem, Journal of Molecular Evolution (2018)

Hierarchy in Gene Expression is Predictive of Risk, Progression, and Outcome in Adult Acute Myeloid Leukemia [Link]
Shubham Tripathi and Michael W. Deem, Physical Biology (2015)