Publications

1.Herbert Levine, et al.(2024), Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition, PNAS, 121(32), e2406842121.

2. Herbert Levine, et al.(2024), RACER-m leverages structural features for sparse T cell specificity prediction. Science Advances, 10, eadl0161.

3. Herbert Levine, et al.(2024), Nucleosomes play a dual role in regulating transcription dynamics, PNAS, 121(28),e2319772121

4. Herbert Levine, et al.(2024), Machine learning meets physics: A two-way street, PNAS, 121(27), e2403580121 

5. Herbert Levine, et al.(2024), Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal transition plasticity (EMP), Translational Oncology, 39, 101837.

6.  Herbert Levine, et al.(2024), Computational modeling of cancer cell metabolism along the catabolic-anabolic axes, bioRxiv. https://doi.org/10.1101/2024.08.15.608169

7. Herbert Levine, David A. Kessler(2024), Pulse instabilities can shape virus-immune coevolution, Physical Review Research, 6(3), 033300.

8. Michele Di Pierro, et al.(2024), Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample, Cell, 187(7), 3541–3562.

9. M. W. Grunst, Z. Qin, E. Dodero-Rojas, S. Ding, J. Prevost, Y. Chen, Y. Hu, M. Pazgier, S. Wu, X. Xie, A. Finzi, J. N. Onuchic, P. C. Whitford, W. Mothes, W. Li. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science, 385, 757-765, 2024.

10. V. Singh, Y. Itoh, S. L. Del’Olio, A. Hassan, A. Naschberger, R. K. Flygaard, Y. Note, K. Izumikawa, S. Aibara, J. Andrell, P. C. Whitford, A. Barrientos, M. Taoka, A. Amunts. The complete structure of human mitoribosome, roles of mite-specific protein elements, cofactors and rRNA modifications. Nature Communications,15, 4272, 2024.

11. S. Byju, A. Hassan, P. C. Whitford. The energy landscape of the ribosome. Biopolymers, 115, e23570, 2024.

12. Y Tang, X Li, D Bi. Tunable Hyperuniformity in Cellular Structures. ArXiv preprint. 2024 arXiv:2408.08976.

13. Yang H, Nguyen AQ, Bi D, Buehler MJ, Guo M. Multicell-Fold: geometric learning in folding multicellular life. ArXiv preprint. 2024 Jul 22:arXiv:2407.07055v2.

14. Praver Gupta, Sayantani Kayal, Nobuyuki Tanimura, Shilpa P Pothapragada, Harish K Senapati, Padmashree Devendran, Yasuyuki Fujita, Dapeng Bi, Tamal Das. Mechanical imbalance between normal and transformed cells drives epithelial homeostasis through cell competition. bioRxiv 2024/6/22. 2023.09. 27.559723.

15. Y Tang, S Chen, MJ Bowick, D Bi. Cell Division and Motility Enable Hexatic Order in Biological Tissues. Physical review letters 132 (21), 218402.

16. G Cai, X Li, SS Lin, SJ Chen, NC Rodgers, KM Koning, D Bi, AP Liu. Matrix confinement modulates 3D spheroid sorting and burst-like collective migration. Acta biomaterialia 179, 192-206.

17. D Bi, S Fielding, M Hertaeg. Nonlinear elasticity and rheological response in epithelial tissues. Bulletin of the American Physical Society 2024.

18. Mohammad Nabizadeh, Farzaneh Nasirian, Xinzhi Li, Yug Saraswat, Rony Waheibi, Lilian C Hsiao, Dapeng Bi, Babak Ravandi, Safa Jamali. Network physics of attractive colloidal gels: Resilience, rigidity, and phase diagram. Proceedings of the National Academy of Sciences 121 (3), e2316394121.

19. MJ Hertaeg, SM Fielding, D Bi. Discontinuous shear thickening in biological tissue rheology. Physical Review X 14 (1), 011027.

20. Xiaofan Xie, Frank Sauer, Steffen Grosser, Jürgen Lippoldt, Enrico Warmt, Amit Das, Dapeng Bi, Thomas Fuhs, Josef A Käs. Effect of non-linear strain stiffening in eDAH and unjamming. Soft Matter 20 (9), 1996-2007.

21. Thibaut Divoux, Elisabeth Agoritsas, Stefano Aime, Catherine Barentin, Jean-Louis Barrat, Roberto Benzi, Ludovic Berthier, Dapeng Bi, Giulio Biroli, Daniel Bonn, Philippe Bourrianne, Mehdi Bouzid, Emanuela Del Gado, Hélène Delanoë-Ayari, Kasra Farain, Suzanne Fielding, Matthias Fuchs, Jasper van der Gucht, Silke Henkes, Maziyar Jalaal, Yogesh M Joshi, Anaël Lemaître, Robert L Leheny, Sébastien Manneville, Kirsten Martens, Wilson CK Poon, Marko Popović, Itamar Procaccia, Laurence Ramos, James A Richards, Simon Rogers, Saverio Rossi, Mauro Sbragaglia, Gilles Tarjus, Federico Toschi, Véronique Trappe, Jan Vermant, Matthieu Wyart, Francesco Zamponi, Davoud Zare. Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions. Soft Matter 20 (35), 6868-6888.

22. Marcela Sandoval-Velasco, Olga Dudchenko, Juan Antonio Rodríguez, Cynthia Pérez Estrada, Marianne Dehasque, Claudia Fontsere, Sarah ST Mak, Ruqayya Khan, Vinícius G Contessoto, Antonio B Oliveira Junior, Achyuth Kalluchi, Bernardo J Zubillaga Herrera, Jiyun Jeong, Renata P Roy, Ishawnia Christopher, David Weisz, Arina D Omer, Sanjit S Batra, Muhammad S Shamim, Neva C Durand, Brendan O’Connell, Alfred L Roca, Maksim V Plikus, Mariya A Kusliy, Svetlana A Romanenko, Natalya A Lemskaya, Natalya A Serdyukova, Svetlana A Modina, Polina L Perelman, Elena A Kizilova, Sergei I Baiborodin, Nikolai B Rubtsov, Gur Machol, Krisha Rath, Ragini Mahajan, Parwinder Kaur, Andreas Gnirke, Isabel Garcia-Treviño, Rob Coke, Joseph P Flanagan, Kelcie Pletch, Aurora Ruiz-Herrera, Valerii Plotnikov, Innokentiy S Pavlov, Naryya I Pavlova, Albert V Protopopov, Michele Di Pierro, Alexander S Graphodatsky, Eric S Lander, M Jordan Rowley, Peter G Wolynes, José N Onuchic, Love Dalén, Marc A Marti-Renom, M Thomas P Gilbert, Erez Lieberman Aiden. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 187 (14), 3541-3562. e51.

23. R Laghmach, M Di Pierro, D Potoyan. Illuminating the link between nuclear geometry and chromatin structure dynamics through 4D nucleus modeling. Bulletin of the American Physical Society.

24. L Burack, B Herrera, M Di Pierro. Abstract 1527 Informing models of in-silico DNA digestion. Journal of Biological Chemistry 300 (3).

25. R Laghmach, M Di Pierro, D Potoyan. Illuminating the link between nuclear geometry and chromatin structures through 4D nucleus modeling. Biophysical Journal 123 (3), 229a-230a.

26. M Di Pierro. Landscapes of genomic architecture across evolution. Biophysical Journal 123 (3), 327a.

27. R Laghmach, M Di Pierro, DA Potoyan. Four-dimensional mesoscale liquid model of nucleus resolves chromatin’s radial organization. PRX life 2 (1), 013006.

28. FR Adler, H Levine, A Brock. Cancer cell populations. Seminars in cancer biology 109, 8-9.

29. JT Park, H Levine. Mathematical Modeling of Drug-Induced Persistence in Cancer. Bulletin of the American Physical Society 2024.

30. Kishore Hari, Pradyumna Harlapur, Mohit Kumar Jolly, Herbert Levine, Herbert Levine, Aashna Saxena, Kushal Halder, Aishwarya Girish, Tanisha Malpani. Design principles of gene regulatory networks underlying low-dimensional cell-fate decision systems. Bulletin of the American Physical Society 2024.

31. DA Kessler, H Levine. Pulse instabilities can shape virus-immune coevolution. Physical Review Research 6 (3), 033300.

32. J Villela-Castrejon, H Levine, JN Onuchic, JT George, D Jia. Computational modeling of cancer cell metabolism along the catabolic-anabolic axes. bioRxiv, 2024.08. 15.608169.

33. Yu-Chen Cheng, Yun Zhang, Shubham Tripathi, BV Harshavardhan, Mohit Kumar Jolly, Geoffrey Schiebinger, Herbert Levine, Thomas O McDonald, Franziska Michor. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proceedings of the National Academy of Sciences 121 (32), e2406842121.

34. S Brahmachari, S Tripathi, JN Onuchic, H Levine. Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences 121 (28), e2319772121.

35. H Levine, Y Tu. Machine learning meets physics: A two-way street. Proceedings of the National Academy of Sciences 121 (27), e2403580121.

36. A Wang, X Lin, KN Chau, JN Onuchic, H Levine, JT George. RACER-m leverages structural features for sparse T cell specificity prediction. Science Advances 10 (20), eadl0161.

37. Javier Villela-Castrejon, Jason T George, Dongya Jia, Herbert Levine, José N Onuchic, Benny Abraham Kaipparettu. A phenotypic model for cancer metabolism. Cancer Research 84 (6_Supplement), 2349-2349.

38. Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Saumya Srivastava, Linlin Guo, Anusha Nathan, Rishov Chatterjee, Maneesh Jain, Wasim Nasser, Surinder Batra, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia. Dynamic phenotypic switching and group behavior help non-small cell lung cancer cells evade chemotherapy. Authorea Preprints, 2024.

39. K Hari, S Tripathi, V Anand, MK Jolly, H Levine. A multi-level formalism to capture the characteristics of hybrid phenotypes in Epithelial-Mesenchymal Plasticity. bioRxiv, 2024.11. 26.625479.

40. Madison Catalanotto, Joel Markus Vaz, Camille Abshire, Reneau Youngblood, Min Chu, Herbert Levine, Mohit Kumar Jolly, Ana-Maria Dragoi. Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal transition plasticity (EMP). Translational Oncology 39, 101837.

41. DA Ramirez, M Lu. Dissecting reversible and irreversible single cell state transitions from gene regulatory networks. bioRxiv.

42. A Katebi, X Chen, D Ramirez, S Li, M Lu. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. npj Systems Biology and Applications 10 (1), 38.

1.Hua Zheng, Wei Xie, Paul Whitford, Ailun Wang, Chunsheng Fang, Wandi Xu (2023). Structure and Function Dynamics Hybrid Modeling: RNA Degradation. Winter Simulation Conference 2023.

2. A. Hassan, S. Byju, F. C. Freitas, C. Roc, N. Pender, K. Nguyen, E. M. Kimbrough, J. Mattingly, R. L. Gonzalez Jr, R. J. Oliveira, C. M. Dunham, P. C. Whitford. Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome. Nucleic Acids Research, 2023, DOI: 10.1093/nar/gkac1211.

3. Junxiang Huang, Herbert Levine, and Dapeng Bi. Bridging the gap between collective motility and epithelial–mesenchymal transitions through the active finite voronoi model. Soft matter 19.48 (2023): 9389-9398.

4. Gupta P, Kayal S, Tanimura N, Pothapragada SP, Senapati HK, Devendran P, Fujita Y, Bi D, Das T. Mechanical imbalance between normal and transformed cells drives epithelial homeostasis through cell competition. bioRxiv. 2024 Jun:2023.09.27.559723.

5. Xinzhi Li, Dapeng Bi. Nature-inspired designs for disordered acoustic bandgap materials. 2023 Soft Matter Volume 19 Issue 42 Pages 8221-8227. Royal Society of Chemistry

6. Varghese Babu, HA Vinutha, Dapeng Bi, Srikanth Sastry. Discontinuous rigidity transition associated with shear jamming in granular simulations. 2023 Soft Matter Volume 19 Issue 48 Pages 9399-9404. Royal Society of Chemistry.

7. R Laghmach, M Di Pierro, DA Potoyan. 4D Mesoscale liquid model of nucleus resolves chromatin’s radial organization. bioRxiv, 2023.09. 21.558819.

8. Hannah L Harris, Huiya Gu, Moshe Olshansky, Ailun Wang, Irene Farabella, Yossi Eliaz, Achyuth Kalluchi, Akshay Krishna, Mozes Jacobs, Gesine Cauer, Melanie Pham, Suhas SP Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae Kim, Michael H Nichols, Eric S Davis, Dimos Gkountaroulis, Devika Udupa, Aviva Presser Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble, Guy Nir, Michele Di Pierro, Jeong-Sun Seo, Michael E Talkowski, Erez Lieberman Aiden, M Jordan Rowley. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nature Communications 14 (1), 3303.

9. Benjamin S Ruben, Sumitabha Brahmachari, Vinícius G Contessoto, Ryan R Cheng, Antonio B Oliveira Junior, Michele Di Pierro, José N Onuchic. Structural reorganization and relaxation dynamics of axially stressed chromosomes. Biophysical Journal 122 (9), 1633-1645.

10. W Lu, JN Onuchic, M Di Pierro. An associative memory Hamiltonian model for DNA and nucleosomes. PLOS Computational Biology 19 (3), e1011013.

11. A Das, R Cheng, D Potoyan, M Di Pierro. 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes. Biophysical Journal 122 (3), 76a-77a.

12. A Wang, M Di Pierro. Understanding the three-dimentional structures of chromatins at nucleosome resolution. Biophysical Journal 122 (3), 491a.

13. Vinícius G Contessoto, Olga Dudchenko, Erez Aiden, Peter G Wolynes, José N Onuchic, Michele Di Pierro. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature Communications 14 (326),

14. H Levine, C Kirkup, S Vilchez, S Srinivasan, M Lin, J Abel, M Drage, J Conway, A Khosla, A Taylor-Weiner. 2354P Computational pathology-derived features capture varied epithelial-mesenchymal transition (EMT) states. Annals of Oncology 34, S1197.

15. AS Moffett, Y Deng, H Levine. Modeling the role of immune cell conversion in the tumor-immune microenvironment. Bulletin of Mathematical Biology 85 (10), 93.

16. Mrinmoy Mukherjee, Oleksandr Chepizhko, Maria Chiara Lionetti, Stefano Zapperi, Caterina AM La Porta, Herbert Levine. Infiltration of tumor spheroids by activated immune cells. Physical Biology 20 (5), 056001.

17. H Levine. Conceptualizing life via non-equilibrium physics; is it enough?: Comment on “Unified representation of life’s basic properties by a 3-species stochastic cubic autocatalytic reaction-diffusion system of equations” by A.P. Muñuzuri and J. Pérez-Mercader. Physics of life reviews 45, 71-73.

18. JT George, H Levine. Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles. Elife 12, e82786.

19. Frederick R Adler, Alexander RA Anderson, Abhinav Bhushan, Paul Bogdan, Jose Javier Bravo-Cordero, Amy Brock, Yun Chen, Edna Cukierman, Kathleen E DelGiorno, Gerald V Denis, Meghan C Ferrall-Fairbanks, Zev Jordan Gartner, Ronald N Germain, Deborah M Gordon, Ginger Hunter, Mohit Kumar Jolly, Loukia Georgiou Karacosta, Karthikeyan Mythreye, Parag Katira, Rajan P Kulkarni, Matthew L Kutys, Arthur D Lander, Ashley M Laughney, Herbert Levine, Emil Lou, Pedro R Lowenstein, Kristyn S Masters, Dana Pe’er, Shelly R Peyton, Manu O Platt, Jeremy E Purvis, Gerald Quon, Jennifer K Richer, Nicole C Riddle, Analiz Rodriguez, Joshua C Snyder, Gregory Lee Szeto, Claire J Tomlin, Itai Yanai, Ioannis K Zervantonakis, Hannah Dueck. Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. Cell systems 14 (4), 252-257.

20. Prakash Kulkarni, H Steven Wiley, Herbert Levine, Herbert Sauro, Alexander Anderson, Stephen TC Wong, Aaron S Meyer, Puneeth Iyengar, Kevin Corlette, Kristin Swanson, Atish Mohanty, Supriyo Bhattacharya, Amit Patel, Vinay Jain, Ravi Salgia. Addressing the genetic/nongenetic duality in cancer with systems biology. Trends in Cancer 9 (3), 185-187.

21. Y Deng, H Levine, X Mao, LM Sander. Collective durotaxis in cell clusters. Physica D: Nonlinear Phenomena 445, 133637.

22. Y Zhang, H Levine, Y Zhao. Phase Field Modeling of Dictyostelium Discoideum Chemotaxis. arXiv preprint arXiv:2302.14854.

23. KN Chau, JT George, JN Onuchic, X Lin, H Levine. Contact map dependence of a T-cell receptor binding repertoire. Biophysical Journal 122 (3), 271a-272a.

24. M Galbraith, H Levine, JN Onuchic, D Jia. Decoding the coupled decision-making of the epithelial-mesenchymal transition and metabolic reprogramming in cancer. Iscience 26 (1).

25. Paras Jain, Sophia Corbo, Kulsoom Mohammad, Sarthak Sahoo, Santhalakshmi Ranganathan, Jason T George, Herbert Levine, Joseph Taube, Michael Toneff, Mohit Kumar Jolly. Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state. Journal of the Royal Society Interface 20 (198), 20220627.

26. S Tripathi, DA Kessler, H Levine. Minimal frustration underlies the usefulness of incomplete regulatory network models in biology. Proceedings of the National Academy of Sciences 120 (1), e2216109120.

27. J Huang, H Levine, D Bi. Bridging the gap between collective motility and epithelial–mesenchymal transitions through the active finite voronoi model. Soft matter 19 (48), 9389-9398.

28. H Levine, DI Goldman. Physics of smart active matter: integrating active matter and control to gain insights into living systems. Soft Matter 19 (23), 4204-4207.

29. M Mukherjee, H Levine. The alternate ligand Jagged enhances the robustness of Notch signaling patterns. Soft Matter 19 (26), 4859-4868.

30. B Clauss, M Lu. A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions. Iscience 26 (2).

31.C Caranica, M Lu. A data-driven optimization method for coarse-graining gene regulatory networks. Iscience 26 (2)

1. J Huang, JO Cochran, SM Fielding, MC Marchetti, D Bi. Shear-driven solidification and nonlinear elasticity in epithelial tissues. Physical Review Letters 128 (17), 178001.

2. S Brahmachari, VG Contessoto, M Di Pierro, JN Onuchic. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. S Brahmachari, VG Contessoto, M Di Pierro, JN Onuchic. Nucleic Acids Research 50 (8), 4258-4271

3. M Di Pierro. Landscapes of genomic architecture across evolution. Biophysical Journal 121 (3), 171a-172a.

4. R Laghmach, M Di Pierro, D Potoyan. A liquid state perspective on dynamics of chromatin compartments. Frontiers in Molecular Biosciences 8, 781981.

5. F. C. Freitas, S. Byju, A. Hassan, R. J. Oliveira, P. C. Whitford*. Quantifying biomolecular diffusion with a “spherical cow” model. American Journal of Physics. 90, 225-238, 2022

6. P. C. Whitford*, J. N. Onuchic. Probing the energy landscapes of biomolecular folding and function. In Physics of Molecular and Cellular Processes, pages 61-82. 2022

7. P. C. Whitford*. Energetic and structural properties of macromolecular assemblies. Submitted. In Physics of Molecular and Cellular Processes, pages 83-105. 2022

8. A. B. Oliveira Jr, V. G. Contessoto, A. Hassan, S. Byju, A. Wang, Y. Wang, E. Dodero-Rojas, U. Mohanty, J. K. Noel*, J. N. Onuchic*, P. C. Whitford*. SMOG2 and OpenSMOG: Extending the limits of structure-based models. Protein Science, 31, 158-172, 2022.

9. R. V. R. Dias, C. T. A. Ferreira, P. A. Jennings, P. C. Whitford, L. C. De Oliveira. Ask alphaC helix: A computational analysis of an essential region for conformational transitions. J. Phys. Chem. B, 2022. DOI: 10.1021/acs.jpcb.2c05408.

10. C. Markosian, D. I. Staquicini, P. Droga, E. Dodero-Rojas, J. H. Lubin, F. H. F. Tang, T. L. Smith, V. G. Contessoto, S. K. Libutti, Z. Wang, V. Cristini, S. D. Khare, P. C. Whitford, S. K. Burley, J. N. Onuchic, R. Pasqualini, W. Arap. Genetic and structural analysis of SARS-CoV-2 spike protein for universal epitope selection. Molecular Biology & Evolution. 39, msac091, 2022.

11. V. M. Oliveira, M. M. G. Dias, T. M. Avelino, N. B. Videira, F. B. da Silva, T. R. Doratioto, P. C. Whitford, V. B. P. Leite, A. C. M. Figueira. pH and the breast cancer recurrent mutation D538G affect the process of activation of Estrogen Receptor alpha. Biochemistry, 61, 455-463, 2022.

12. A. Hassan, P. C. Whitford*. Identifying strategies to experimentally probe multidimensional dynamics in the ribosome. J. Phys. Chem. B, 2022, DOI: 10.1021/acs.jpcb.2c05706

13. Y. Wang, A. Wang, U. Mohanty*, P. C. Whitford*. Precise steric features control aminoacyl-tRNA accommodation on the ribosome. J. Phys. Chem. B. 2022, DOI: 10.1021/acs.jpcb.205513.

14. A. Wang, M. Levi, U. Mohanty*, P. C. Whitford*. Diffuse ions coordinate dynamics in a ribonucleoprotein assembly. Journal of the American Chemical Society. 2022. DOI: 10.1021/jacs.2c04082

15. MA Al-Radhawi, S Tripathi, Y Zhang, ED Sontag, H Levine. Epigenetic factor competition reshapes the EMT landscape. Proceedings of the National Academy of Sciences 119 (42), e2210844119.

16. DA Kessler, H Levine. Introduction to Evolutionary Dynamics. Physics of Molecular and Cellular Processes, 237-253.

17. Y Deng, H Levine. Introduction to models of cell motility. Physics of molecular and cellular processes, 173-212.

18. KB Blagoev, H Levine. Physics of Molecular and Cellular Processes. Springer

19. DA Kessler, H Levine. Phenomenological approach to cancer cell persistence. Physical Review Letters 129 (10), 108101.

20. Y Chen, D Wu, H Levine. A physical model for dynamic assembly of human salivary stem/progenitor microstructures. Cells & Development 171, 203803.

21. W Jia, AS Duddu, MK Jolly, H Levine. Lack of correlation between landscape geometry and transition rates. The Journal of Physical Chemistry B 126 (30), 5613-5618.

22. K Ng Chau, JT George, JN Onuchic, X Lin, H Levine. Contact map dependence of a T-cell receptor binding repertoire. Physical Review E 106 (1), 014406.

23. S Tripathi, DA Kessler, H Levine. Minimal frustration underlies the usefulness of incomplete and inexact regulatory network models in biology. bioRxiv, 2022.06. 07.495167.

24. H Levine. Let the robotic games begin. Proceedings of the National Academy of Sciences 119 (17), e2204152119.

25. Samuel A Vilchez Mercedes, Federico Bocci, Mona Ahmed, Ian Eder, Ninghao Zhu, Herbert Levine, José N Onuchic, Mohit Kumar Jolly, Pak Kin Wong. Nrf2 modulates the hybrid epithelial/mesenchymal phenotype and Notch signaling during collective cancer migration. Frontiers in Molecular Biosciences 9, 807324.

26. P Esfahani, H Levine, M Mukherjee, B Sun. Three-dimensional cancer cell migration directed by dual mechanochemical guidance. Physical review research 4 (2), L022007.

27. Hiroko Masuda, Kenichi Harano, Sakiko Miura, Ying Wang, Yuko Hirota, Oi Harada, Mohit Kumar Jolly, Yuki Matsunaga, Bora Lim, Anita L Wood, Napa Parinyanitikul, Hee Jin Lee, Gyungyub Gong, Jason T George, Herbert Levine, Jangsoon Lee, Xiaoping Wang, Anthony Lucci, Arvind Rao, Brock L Schweitzer, O Rayne Lawrence, Robert S Seitz, Stephan W Morris, David R Hout, Seigo Nakamura, Savitri Krishnamurthy, Naoto T Ueno. Changes in triple-negative breast cancer molecular subtypes in patients without pathologic complete response after neoadjuvant systemic chemotherapy. JCO Precision Oncology 6, e2000368.

28. S Tripathi, S Brahmachari, JN Onuchic, H Levine. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic acids research 50 (3), 1269-1279.

29. Srinath Muralidharan, Sarthak Sahoo, Aryamaan Saha, Sanjay Chandran, Sauma Suvra Majumdar, Susmita Mandal, Herbert Levine, Mohit Kumar Jolly. Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial–hybrid–mesenchymal spectrum in cancer. Biomolecules 12 (2), 297.

30. Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine. A mechanistic modeling framework reveals the key principles underlying tumor metabolism. PLoS computational biology 18 (2), e1009841.

31. Veronika Te Boekhorst, Liying Jiang, Marius Mählen, Maaike Meerlo, Gina Dunkel, Franziska C Durst, Yanjun Yang, Herbert Levine, Boudewijn MT Burgering, Peter Friedl. Calpain-2 regulates hypoxia/HIF-induced plasticity toward amoeboid cancer cell migration and metastasis. Current Biology 32 (2), 412-427. e8.

32. W Jia, MK Jolly, H Levine. NRF2-dependent epigenetic regulation can promote the hybrid epithelial/mesenchymal phenotype. Frontiers in cell and developmental biology 9, 828250.

33. Susmita Mandal, Tanishq Tejaswi, Rohini Janivara, Syamanthak Srikrishnan, Pradipti Thakur, Sarthak Sahoo, Priyanka Chakraborty, Sukhwinder Singh Sohal, Herbert Levine, Jason T George, Mohit Kumar Jolly. Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts. Biomolecules 12 (1), 29.

34. Kenong Su, Ataur Katebi, Vivek Kohar, Benjamin Clauss, Danya Gordin, Zhaohui S Qin, R Krishna M Karuturi, Sheng Li, Mingyang Lu. NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity. Genome biology 23 (1), 270.

35. L Huang, B Clauss, M Lu. What makes a functional gene regulatory network? A circuit motif analysis. The Journal of Physical Chemistry B 126 (49), 10374-10383.

36. Dinesh Babu Uthaya Kumar, Efthymios Motakis, Marina Yurieva, Vivek Kohar, Jan Martinek, Te-Chia Wu, Johad Khoury, Jessica Grassmann, Mingyang Lu, Karolina Palucka, Naftali Kaminski, Jonathan L Koff, Adam Williams. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2022

1. Herbert Levine, et al.(2021), A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2, Cancers, 13(7), 1609.

2. Herbert Levine, et al.(2021), Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer, British Journal of Cancer https://doi.org/10.1038/s41416-021-01385-y

3. A. Hassan, S. Byju, P. C. Whitford. The energetics of subunit rotation in the ribosome. Biophysical Reviews. 13, 1029-1037, 2021.

4. F. C. Freitas, G. Fuchs, R. J. De Oliveira, P. C. Whitford. The dynamics of subunit rotation in a eukaryotic ribosome. Biophysica, 1, 204-221, 2021

5. D. I. Staquicini, F. H.F. Tang, C. Markosian, V. J. Yao, F. I. Staquicini, E. Dodero-Rojas, V. G. Contessoto, D. Davis, P. O’Brien, N. Habib, T. L. Smith, N. Bruiners, R. L. Sidman, M. L. Gennaro, E. C. Lattime, S. K. Libutti, P. C. Whitford, S. K. Burley, J. N. Onuchic, W. Arap, R. Pasqualini. Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlines cold-free supply chain. PNAS 118, e2105739118, 2021.

6. E. Dodero-Rojas, J. N. Onuchic, P. C. Whitford. Sterically-confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife, 10, e70362, 2021.

7. P. C. Whitford. Overview of the Biomolecular Association and Dynamics session at the 20th IUPAB congress, 45th Brazilian congress of SBBF, and the 50th annual meeting of SBBq. Biophysical Reviews. 13, 863-865, 2021

8. R Laghmach, M Di Pierro, DA Potoyan. The interplay of chromatin phase separation and lamina interactions in nuclear organization. Biophysical Journal 120 (22), 5005-5017.

9. Claire Hoencamp, Olga Dudchenko, Ahmed MO Elbatsh, Sumitabha Brahmachari, Jonne A Raaijmakers, Tom van Schaik, Ángela Sedeño Cacciatore, Vinícius G Contessoto, Roy GHP van Heesbeen, Bram van den Broek, Aditya N Mhaskar, Hans Teunissen, Brian Glenn St Hilaire, David Weisz, Arina D Omer, Melanie Pham, Zane Colaric, Zhenzhen Yang, Suhas SP Rao, Namita Mitra, Christopher Lui, Weijie Yao, Ruqayya Khan, Leonid L Moroz, Andrea Kohn, Judy St. Leger, Alexandria Mena, Karen Holcroft, Maria Cristina Gambetta, Fabian Lim, Emma Farley, Nils Stein, Alexander Haddad, Daniel Chauss, Ayse Sena Mutlu, Meng C Wang, Neil D Young, Evin Hildebrandt, Hans H Cheng, Christopher J Knight, Theresa LU Burnham, Kevin A Hovel, Andrew J Beel, Pierre-Jean Mattei, Roger D Kornberg, Wesley C Warren, Gregory Cary, José Luis Gómez-Skarmeta, Veronica Hinman, Kerstin Lindblad-Toh, Federica Di Palma, Kazuhiro Maeshima, Asha S Multani, Sen Pathak, Liesl Nel-Themaat, Richard R Behringer, Parwinder Kaur, René H Medema, Bas van Steensel, Elzo de Wit, José N Onuchic, Michele Di Pierro, Erez Lieberman Aiden, Benjamin D Rowland. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 372 (6545), 984-989.

10. RR Cheng, E Dodero-Rojas, M Di Pierro, JN Onuchic. Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility. bioRxiv, 2021.03. 25.437113

11. Vinícius G Contessoto, Ryan R Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F Mello, Erez Lieberman-Aiden, Peter G Wolynes, Michele Di Pierro, José N Onuchic. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Research 49 (D1), D172-D182.

12. Amit Das, Srikanth Sastry, Dapeng Bi. Controlled Neighbor Exchanges Drive Glassy Behavior, Intermittency, and Cell Streaming in Epithelial Tissues. Physical Review X 11 (4), 041037.

13. Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Saumya Srivastava, Linlin Guo, Anusha Nathan, Rishov Chatterjee, Maneesh Jain, Mohd W Nasser, Surinder Kumar Batra, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia. Dynamic phenotypic switching and group behavior help non-small cell lung cancer cells evade chemotherapy. Biomolecules 12 (1), 8

14. Sarthak Sahoo, Sonali Priyadarshini Nayak, Kishore Hari, Prithu Purkait, Susmita Mandal, Akash Kishore, Herbert Levine, Mohit Kumar Jolly. Immunosuppressive traits of the hybrid epithelial/mesenchymal phenotype. Frontiers in immunology 12, 797261

15. Jing Yang, Parker Antin, Geert Berx, Cedric Blanpain, Thomas Brabletz, Marianne Bronner, Kyra Campbell, Amparo Cano, Jordi Casanova, Gerhard Christofori, Shoukat Dedhar, Rik Derynck, Heide L Ford, Jonas Fuxe, Antonio Garcia de Herreros, Gregory J Goodall, Anna-Katerina Hadjantonakis, Ruby YJ Huang, Chaya Kalcheim, Raghu Kalluri, Yibin Kang, Yeesim Khew-Goodall, Herbert Levine, Jinsong Liu, Gregory D Longmore, Sendurai A Mani, Joan Massague, Roberto Mayor, David McClay, Keith E Mostov, Donald F Newgreen, M Angela Nieto, Alain Puisieux, Raymond Runyan, Pierre Savagner, Ben Stanger, Marc P Stemmler, Yoshiko Takahashi, Masatoshi Takeichi, Eric Theveneau, Jean Paul Thiery, Erik W Thompson, Robert A Weinberg, Elizabeth D Williams, Jianhua Xing, Binhua P Zhou, Guojun Sheng. Guidelines and definitions for research on epithelial-mesenchymal transition (vol 21, pg 341, 2020). NATURE REVIEWS MOLECULAR CELL BIOLOGY 22 (12), 834-834.

16. M Mukherjee, H Levine. Cluster size distribution of cells disseminating from a primary tumor. PLOS Computational Biology 17 (11), e1009011.

17. Y Deng, H Levine, X Mao, LM Sander. Collective motility and mechanical waves in cell clusters. The European Physical Journal E 44, 1-15.

18. E Teomy, DA Kessler, H Levine. Ordered hexagonal patterns via notch–delta signaling. Physical Biology 18 (6), 066006.

19. Anna-Katerina Hadjantonakis, Geert Berx, Masatoshi Takeichi, Antonio García de Herreros, Yoshiko Takahashi, Roberto Mayor, Robert A Weinberg, Jean Paul Thiery, Alain Puisieux, Yeesim Khew-Goodall, Elizabeth D Williams, Ruby Yun-Ju Huang, Joan Massagué, Binhua P Zhou, Pierre Savagner, Donald F Newgreen, Parker B Antin, Cédric Blanpain, Heide L Ford, Jordi Casanova, Amparo Cano, Rik Derynck, Kyra Campbell, Chaya Kalcheim, Yibin Kang, Jianhua Xing, Ben Z Stanger, Shoukat Dedhar, Raghu Kalluri, Gregory D Longmore, Guojun Sheng, Jing Yang, Thomas Brabletz, Herbert Levine, Sendurai A Mani, Marianne E Bronner, Keith E Mostov, Marc P Stemmler, Eric Theveneau, Gregory J Goodall, M Angela Nieto, Gerhard Christofori, Jonas Fuxe, David R McClay, Jinsong Liu, Erik W Thompson, Raymond B Runyan. Author Correction: Guidelines and definitions for research on epithelial–mesenchymal transition. Nature Reviews Molecular Cell Biology 22, 834-834.

20. C Floyd, H Levine, C Jarzynski, GA Papoian. Understanding cytoskeletal avalanches using mechanical stability analysis. Proceedings of the National Academy of Sciences 118 (41), e2110239118.

21. SA Vilchez Mercedes, F Bocci, H Levine, JN Onuchic, MK Jolly, PK Wong. Decoding leader cells in collective cancer invasion. Nature Reviews Cancer 21 (9), 592-604.

22. N Singh, T Bartol, H Levine, T Sejnowski, S Nadkarni. Author Correction: Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses. Communications Biology 4 (1), 969.

23. Juliana C Wortman, Ting-Fang He, Shawn Solomon, Robert Z Zhang, Anthony Rosario, Roger Wang, Travis Y Tu, Daniel Schmolze, Yuan Yuan, Susan E Yost, Xuefei Li, Herbert Levine, Gurinder Atwal, Peter P Lee, Clare C Yu. Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome. NPJ Breast Cancer 7 (1), 84.

24. 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, Herbert Levine. Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. British Journal of Cancer 124 (12), 1902-1911.

25. Grace G Bushnell, Abhijeet P Deshmukh, Petra den Hollander, Ming Luo, Rama Soundararajan, Dongya Jia, Herbert Levine, Sendurai A Mani, Max S Wicha. Breast cancer dormancy: need for clinically relevant models to address current gaps in knowledge. NPJ breast cancer 7 (1), 66.

26. 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, Sendurai A Mani. Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing. Proceedings of the National Academy of Sciences 118 (19), e2102050118.

27. V Kohar, D Gordin, A Katebi, H Levine, JN Onuchic, M Lu. Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics 37 (9), 1327-1329.

28. Xingcheng Lin, Jason T George, Nicholas P Schafer, Kevin Ng Chau, Michael E Birnbaum, Cecilia Clementi, José N Onuchic, Herbert Levine. Rapid assessment of T-cell receptor specificity of the immune repertoire. Nature computational science 1 (5), 362-373

29. R Salgia, P Kulkarni, H Levine, DT Loughlin. Quantifying cancer: More than just a numbers game. Trends in Cancer 7 (4).

30. JT George, H Levine. Implications of tumor–immune coevolution on cancer evasion and optimized immunotherapy. Trends in Cancer 7 (4), 373-383.

31. P Chakraborty, JT George, WA Woodward, H Levine, MK Jolly. Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum. Translational oncology 14 (4), 101026.

32. Y Deng, P Chakraborty, MK Jolly, H Levine. A theoretical approach to coupling the epithelial-mesenchymal transition (EMT) to extracellular matrix (ECM) stiffness via LOXL2 Cancers 13 (7), 1609.

33. J Kim, Y Cao, C Eddy, Y Deng, H Levine, WJ Rappel, B Sun. The mechanics and dynamics of cancer cells sensing noisy 3D contact guidance. Proceedings of the National Academy of Sciences 118 (10), e2024780118.

34. N Singh, T Bartol, H Levine, T Sejnowski, S Nadkarni. Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses. Communications Biology 4 (1), 241.

35. C Yu Clare, Juliana C Wortman, Ting-Fang He, Shawn Solomon, Robert Z Zhang, Anthony Rosario, Roger Wang, Travis Y Tu, Daniel Schmolze, Yuan Yuan, Susan E Yost, Xuefei Li, Herbert Levine, Gurinder Atwal, Peter P Lee. Physics approaches to the spatial distribution of immune cells in tumors. Reports on progress in physics 84 (2), 022601.

36. SC Tripathi, MK Jolly, SA Mani, H Levine. Characterizing the Multi-Faceted Dynamics of Tumor Cell Plasticity. Frontiers in Molecular Biosciences 7, 630276.

37. C Floyd, H Levine, C Jarzynski, GA Papoian. Data for: Understanding cytoskeletal avalanches using mechanical stability analysis (2021)

38. S NADKARNI, N SINGH, H Levine, T Sejnowski, T Bartol. Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses. Springer Nature

39. A Katebi, D Ramirez, M Lu. Computational systems‐biology approaches for modeling gene networks driving epithelial–mesenchymal transitions. Computational and systems oncology 1 (2), e1021.

40. V Kohar, D Gordin, A Katebi, H Levine, JN Onuchic, M Lu. Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics 37 (9), 1327-1329.

41. X Chen, H Ashoor, R Musich, J Wang, M Zhang, C Zhang, M Lu, S Li. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. Scientific Reports 11 (1), 376.

1. Herbert Levine, et al.(2020),Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum, Translational Oncology, 14, 101026

2. Ryan R Cheng, Vinicius G Contessoto, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, Jose N Onuchic (2020) Exploring chromosomal structural heterogeneity across multiple cell lines eLife 9:e60312

3. R Laghmach, M Di Pierro, DA Potoyan. Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes. Biophysical Journal 118 (9), 2130-2140.

4. S Brahmachari, V Contessoto, M Di Pierro, J Onuchic. Interplay of chromatin self-adhesion and lengthwise compaction on interchromosomal organization. Bulletin of the American Physical Society 65.

5. R Laghmach, M Di Pierro, D Potoyan. Nuclear chromatin patterns: modeling dynamics of intra-chromatin interactions and its impact on structure organization. Bulletin of the American Physical Society 65.

6. P. C. Whitford, W. Jiang, P. Serwer. Simulations of phase T7 capsid expansion reveal the role of molecular steric on dynamics. Viruses. 12, 1273, 2020.

7. M. Levi, K. Walak, A. Wang, U. Mohanty, P. C. Whitford. A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Nature Communications. 11, 5706, 2020.

8. MK Jolly, P Kulkarni, K Weninger, J Orban, H Levine. Phenotypic Plasticity. Response and Resistance in Castration-Resistant Prostate Cancer, 507.

9. D Schmolze, Y Yuan, SE Yost, X Li, H Levine, G Atwal, P Lee, CC Yu. Infiltrating the Tumor Microenvironment in Triple Negative Breast Cancer. Physics Of Cancer, The: Research Advances, 63.

10. Y Eliaz, F Nedelec, G Morrison, H Levine, MS Cheung. Insights from graph theory on the morphologies of actomyosin networks with multilinkers. Physical review E 102 (6), 062420.

11. Guangyuan Yu, Xuefei Li, Ting-Fang He, Tina Gruosso, Dongmei Zuo, Margarita Souleimanova, Valentina Muñoz Ramos, Atilla Omeroglu, Sarkis Meterissian, Marie-Christine Guiot, Li Yang, Yuan Yuan, Morag Park, Peter P Lee, Herbert Levine. Abstract PO-080: Predicting relapse in patients with triple negative breast cancer (TNBC) using a deep-learning approach. Cancer Research 80 (21_Supplement), PO-080-PO-080.

12. Guangyuan Yu, Xuefei Li, Ting-Fang He, Tina Gruosso, Dongmei Zuo, Margarita Souleimanova, Valentina Muñoz Ramos, Atilla Omeroglu, Sarkis Meterissian, Marie-Christine Guiot, Li Yang, Yuan Yuan, Morag Park, Peter P Lee, Herbert Levine. Predicting relapse in patients with triple negative breast cancer (TNBC) using a Deep-Learning approach. Frontiers in physiology 11, 511071.

13. S Tripathi, J Xing, H Levine, MK Jolly. Mathematical modeling of plasticity and heterogeneity in EMT. The Epithelial-to Mesenchymal Transition: Methods and Protocols, 385-413

14. Archana P Thankamony, Reshma Murali, Nitheesh Karthikeyan, Binitha Anu Varghese, Wee S Teo, Andrea McFarland, Daniel L Roden, Holly Holliday, Christina Valbirk Konrad, Aurelie Cazet, Eoin Dodson, Jessica Yang, Laura A Baker, Jason T George, Herbert Levine, Mohit Kumar Jolly, Alexander Swarbrick, Radhika Nair. Targeting the Id1-Kif11 axis in triple-negative breast cancer using combination therapy Biomolecules 10 (9), 1295

15. Jordan L Shivers, Jingchen Feng, Anne SG van Oosten, Herbert Levine, Paul A Janmey, Fred C MacKintosh. Compression stiffening of fibrous networks with stiff inclusions. Proceedings of the National Academy of Sciences 117 (35), 21037-21044.

16. B Huang, M Lu, M Galbraith, H Levine, JN Onuchic, D Jia. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. Journal of The Royal Society Interface 17 (169), 20200500.

17. S Tripathi, DA Kessler, H Levine. Biological networks regulating cell fate choice are minimally frustrated. Physical Review Letters 125 (8), 088101.

18. Dongya Jia, B Bishal Paudel, Corey E Hayford, Keisha N Hardeman, Herbert Levine, José N Onuchic, Vito Quaranta. Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype. Frontiers in Oncology 10, 1426.

19. Y Deng, H Levine, X Mao, LM Sander. Collective motility, mechanical waves, and durotaxis in cell clusters. arXiv preprint arXiv:2007.10488.

20. Wen Jia, Shubham Tripathi, Priyanka Chakraborty, Adithya Chedere, Annapoorni Rangarajan, Herbert Levine, Mohit Kumar Jolly. Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. Oncotarget 11 (27), 2611.

21. Y Yang, H Levine. Leader-cell-driven epithelial sheet fingering. Physical biology 17 (4), 046003

22. Juliana C Wortman, Ting-Fang He, Anthony Rosario, Roger Wang, Daniel Schmolze, Yuan Yuan, Susan E Yost, Xuefei Li, Herbert Levine, Gurinder Atwal, Peter Lee, Clare C Yu. Occupancy and Fractal Dimension Analyses of the Spatial Distribution of Cytotoxic (CD8+) T Cells Infiltrating the Tumor Microenvironment in Triple Negative Breast Cancer. Biophysical Reviews and Letters 15 (02), 83-98

23. H Levine, MK Jolly, P Kulkarni, V Nanjundiah. Phenotypic switching: implications in biology and medicine. Academic Press.

24. Jing Yang, Parker Antin, Geert Berx, Cédric Blanpain, Thomas Brabletz, Marianne Bronner, Kyra Campbell, Amparo Cano, Jordi Casanova, Gerhard Christofori, Shoukat Dedhar, Rik Derynck, Heide L Ford, Jonas Fuxe, Antonio García de Herreros, Gregory J Goodall, Anna-Katerina Hadjantonakis, Ruby YJ Huang, Chaya Kalcheim, Raghu Kalluri, Yibin Kang, Yeesim Khew-Goodall, Herbert Levine, Jinsong Liu, Gregory D Longmore, Sendurai A Mani, Joan Massagué, Roberto Mayor, David McClay, Keith E Mostov, Donald F Newgreen, M Angela Nieto, Alain Puisieux, Raymond Runyan, Pierre Savagner, Ben Stanger, Marc P Stemmler, Yoshiko Takahashi, Masatoshi Takeichi, Eric Theveneau, Jean Paul Thiery, Erik W Thompson, Robert A Weinberg, Elizabeth D Williams, Jianhua Xing, Binhua P Zhou, Guojun Sheng, EMT International Association (TEMTIA). Guidelines and definitions for research on epithelial–mesenchymal transition. Nature reviews Molecular cell biology 21 (6), 341-352.

25. Y Eliaz, F Nedelec, G Morrison, H Levine, MS Cheung. Multivalent actin-binding proteins augment the variety of morphologies in actomyosin networks. arXiv preprint. arXiv:2006.06503.

26. James Liman, Carlos Bueno, Yossi Eliaz, Nicholas P Schafer, M Neal Waxham, Peter G Wolynes, Herbert Levine, Margaret S Cheung. The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks. Proceedings of the National Academy of Sciences 117 (20), 10825-10831.

27. S Tripathi, H Levine, MK Jolly. The physics of cellular decision making during epithelial–mesenchymal transition. Annual Review of Biophysics 49 (1), 1-18.

28. Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Anusha Nathan, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia. Suppressing chemoresistance in lung cancer via dynamic phenotypic switching and intermittent therapy. bioRxiv, 2020.04. 06.028472

29. T Gruosso, M Park, H Levine, X Li. Mathematical modeling studies on spatial profiles of tumor-infiltrating T cells. CANCER IMMUNOLOGY RESEARCH 8 (4), 113-113

30. JT George, HR Garber, JJ Molldrem, H Levine. Co-evolution between tumor cells and immune system in the setting of T-cell immunotherapy. CANCER IMMUNOLOGY RESEARCH 8 (4), 110-110.

31. JT George, HR Garber, JJ Molldrem, H Levine. Abstract B59: Co-evolution between tumor cells and immune system in the setting of T-cell immunotherapy. Cancer Immunology Research 8 (4_Supplement), B59-B59.

32. T Gruosso, M Park, H Levine, X Li. Abstract B65: Mathematical modeling studies on spatial profiles of tumor-infiltrating T cells. Cancer Immunology Research 8 (4_Supplement), B65-B65.

33. P Chakraborty, JT George, S Tripathi, H Levine, MK Jolly. Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. Frontiers in bioengineering and biotechnology 8, 220.

34. S Tripathi, D Kessler, H Levine. Biological regulatory networks are minimally frustrated. Bulletin of the American Physical Society 65.

35. James Liman, Carlos Bueno, Yossi Eliaz, Nicholas Schafer, Neal Waxham, Peter Wolynes, Herbert Levine, Margaret Cheung. Avalanches in simulations of branched actomyosin networks with the Arp2/3 complex. Bulletin of the American Physical Society 65.

36. Y Deng, H Levine. Quasi-realistic modelling of expanding epithelial cell monolayer. Bulletin of the American Physical Society 65.

37. JT George, H Levine. A stochastic model of tumor-immune evasion predicts sustained coevolution and tumor antigen downregulation. CANCER IMMUNOLOGY RESEARCH 8 (3), 82-82.

38. JT George, H Levine. Abstract A104: A stochastic model of tumor-immune evasion predicts sustained coevolution and tumor antigen downregulation. Cancer Immunology Research 8 (3_Supplement), A104-A104.

39. JT George, H Levine. Sustained coevolution in a stochastic model of cancer–immune interaction. Cancer research 80 (4), 811-819.

40. Ayse Nihan Kilinc, Nami Sugiyama, Ravi Kiran Reddy Kalathur, Helena Antoniadis, Huseyin Birogul, Dana Ishay-Ronen, Jason T George, Herbert Levine, Mohit Kumar Jolly, Gerhard Christofori. Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial–mesenchymal plasticity and tumor metastasis. Oncogene 39 (7), 1498-1513.

41. Michael J O’Sullivan, Jennifer A Mitchel, Amit Das, Stephan Koehler, Herbert Levine, Dapeng Bi, Zachary D Nagel, Jin-Ah Park. Irradiation induces epithelial cell unjamming. Frontiers in Cell and Developmental Biology 8, 21.

42. S Tripathi, P Chakraborty, H Levine, MK Jolly. A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. PLoS computational biology 16 (2), e1007619.

43. Ana Rita Lourenco, Yi Ban, Michael J Crowley, Sharrell B Lee, Divya Ramchandani, Wei Du, Olivier Elemento, Jason T George, Mohit Kumar Jolly, Herbert Levine, Jianting Sheng, Stephen T Wong, Nasser K Altorki, Dingcheng Gao. Differential contributions of pre-and post-EMT tumor cells in breast cancer metastasis. Cancer research 80 (2), 163-169.

44. C Floyd, H Levine, C Jarzynski, GA Papoian. Hessian analysis enables prediction of cytoquake occurrence. arXiv preprint arXiv:2006.01884.

45. D Jia, MK Jolly, H Levine, JN Onuchic. Epithelial-mesenchymal transition in cancer. Phenotypic switching, 553-568.

46. Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Anusha Nathan, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia. Phenotypic switching and adaptive strategies of cancer cells in response to stress: insights from live cell imaging and mathematical modeling. bioRxiv, 028472.

47. B Huang, M Lu, M Galbraith, H Levine, JN Onuchic, D Jia. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. Journal of The Royal Society Interface 17 (169), 20200500

48. A Katebi, V Kohar, M Lu. Random parametric perturbations of gene regulatory circuit uncover state transitions in cell cycle. Iscience 23 (6).

49. D Ramirez, V Kohar, M Lu. Toward modeling context-specific EMT regulatory networks using temporal single cell RNA-Seq data. Frontiers in molecular biosciences 7, 54.