Publications: Pankaj Mehta
You can also visit my google scholar page.
Relevant code can be found here.
82. Krishna Rijal and Pankaj Mehta."A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits" arXiv.
81. Wenping Cui, Robert Marsland, and Pankaj Mehta. "Les Houches Lectures on Community Ecology: From Niche Theory to Statistical Mechanics" arXiv.
80. Emmy Blumenthal, Jason W Rocks, and Pankaj Mehta. Phase transition to chaos in complex ecosystems with non-reciprocal species-resource interactionsPhysical Review Letters 132.12: 127401 (2024) (Supporting Information)
79. Akshit Goyal, Jason W Rocks, Pankaj Mehta "A universal niche geometry governs the response of ecosystems to environmental perturbations" (2024) arXiv
78. Zhijie Feng, Robert Marsland III, Jason W Rocks, and Pankaj Mehta. Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems PLOS Computational Biology 20.2 (2024): e1011675.(2024)
77. Wenping Cui, Jason Rocks, and Pankaj Mehta. An elementary mean-field approach to the spectral densities of random matrix ensembles Physica A:Statistical Mechanics and its Applications 129608. (2024)
76. Jean C.C. Vila, Joshua Goldford, Sylvie Estrela, Djordje Bajic, Alicia Sanchez-Gorostiaga, Alejandro Damian-Serrano, Nanxi Lu, Robert Marsland III, Maria Rebolleda-Gomez, VPankaj Mehta, Alvaro Sanchez "Metabolic similarity and the predictability of microbial community assembly" (2023) bioRxiv
75. Xiaoyu Yang, Jason W. Rocks, Kaiyi Jiang, Andrew J. Walters, Kshitij Rai, Jing Liu, Jason Nguyen, Scott D. Olson, Pankaj Mehta, James J. Collins, Nichole M. Daringer, Caleb J. Bashor "Engineering synthetic phosphorylation signaling networks in human cells" (2023) bioRxiv
74. Laertis Ikonomou, Maria Yampolskya, and Pankaj Mehta Multipotent Embryonic Lung Progenitors: Foundational Units of In Vitro and In Vivo Lung Organogenesis Engineering Translational Models of Lung Homeostasis and Disease. Cham: Springer International Publishing, 2023. 49-70.(2023)
73. Claire L Burgess et al. Generation of human alveolar epithelial type I cells from pluripotent stem cells"Cell Stem Cell (2024).bioRxiv
72. Ronan O'Connel, Khsitij Raj, .., Jason W Rocks,..., Pankaj Mehta, Caleb Bashor. "Ultra-high throughput mapping of genetic design space" (2023) bioRxiv
71. Emmy Blumenthal and Pankaj Mehta Geometry of ecological coexistence and niche differentiation Phys. Rev. E 108, 044409 (2023)
70. Maria Yampolskaya, Michael Herriges, Laertis Ikonomou, Darrell Kotton, Pankaj Mehta scTOP: physics-inspired order parameters for cellular identification and visualization Development 150, dev201873 (2023)
69. Jason Rocks and Pankaj Mehta, "Integrating local energetics into Maxwell-Calladine constraint counting to design mechanical metamaterials" Physical Review E 110 (2), 025002 (2024) arXiv
68. Michael Herriges, Maria Yampolskaya et al. Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice Cell Stem Cell 30, 1217–1234 (2023) bioRxiv
67. Pankaj Mehta and Jason Rocks. "Thermodynamic origins of topological protection in nonequilibrium stochastic systems" (2022) arXiv
66. Jason Rocks and Pankaj Mehta. Bias-variance decomposition of overparameterized regression with random linear features. Physical Review E 106, 025304 (2022). (arXiv)
65. Pankaj Mehta and Robert Marsland III "Cross-feeding shapes both competition and cooperation in microbial ecosystems" (2021). arXiv or bioRxiv.
64. Chuqiao Huyan, Alex Golden, Xinwen Zhu, Pankaj Mehta, Allyson Sgro."Robust coordination of collective oscillatory signaling requires single-cell excitability and fold-change detection" (2021). bioRxiv
63. James Anibal, Alexandre Day, Erol Bahadiroglu, Liam O'Neill, Long Phan, Alec Peltekian, Amir Erez, Mariana Kaplan, Gregoire Altan-Bonnet, Pankaj Mehta. HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis PLoS Comp Bio 18(10): e1010349. (2022).
62. Alexander Golden, Allyson Sgro, and Pankaj Mehta. Arnold tongues in oscillator systems with nonuniform spatial driving. Physical Review E 103 042211 (2021).
61. Jason Rocks and Pankaj Mehta. "The Geometry of Over-parameterized Regression and Adversarial Perturbations" (2021) arXiv
60. Robert Marsland, Owen Howell, Andreas Mayer, and Pankaj Mehta. Tregs self-organize into a computing ecosystem and implement a sophisticated optimization algorithm for mediating immune response Proc. Natl. Acad. of Sci. 118, e2011709118 (2021). (Supporting Information)
59. Daniel Shams, Xingbo Yang, Pankaj Mehta, and David Schwab Spatial gradient sensing and chemotaxis via excitability in Dictyostelium discoideum Phys. Rev. E. 101, 062410 (2020).
58. Jason Rocks and Pankaj Mehta Memorizing without overfitting: Bias, variance, and interpolation in over-parameterized models . Phys. Rev. Research 4, 013201(2022) (Supporting Infomration). Chosen as Editors' Suggestion. See also arXiv
57. Robert Marsland and Pankaj Mehta "Data-driven modeling reveals a universal dynamic underlying the COVID-19 pandemic under social distancing" (2020) arXiv
56. Laertis Ikonomou et. al. Use of lung primordial progenitor in vivo signatures and similarity models improves fidelity of in vitro-derived respiratory lineages. Nature Communications 11, 635 (2020)
55. Owen Howell, Wenping Cui, Robert Marsland, Pankaj Mehta Machine Learning as Ecology. J. Phys. A: Math. Theor. 53 334001(2020). arXiv
54. Wenping Cui, Robert Marsland, Pankaj Mehta The effect of resource dynamics on species packing in diverse ecosystems Physical Review Letters 125, 048101 (2020). (Supporting Infomration). Also see Feature pick Synposis here.
53. Robert Marsland, Wenping Cui, Pankaj Mehta A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns Scientific Reports 10 3038 (2020)
52. Wenping Cui, Robert Marsland, Pankaj Mehta "Diverse communities behave like typical random ecosystems." (2019) arXiv
51. Robert Marsland, Wenping Cui, Josh Goldford, Pankaj Mehta The Community Simulator: A Python package for microbial ecology PLoS One 0230430 (2020) (Code on Github)
50. Robert Marsland, Wenping Cui, Pankaj Mehta The Minimum Environmental Perturbation Principle: A New Perspective on Niche Theory American Naturalist 196 p291 (2020) (Supporting Information).
49. Ching-Hao Wang, Caleb Bashor, Pankaj Mehta "The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks" (2018) (Arxiv)
48. Pankaj Mehta, Wenping Cui, Ching-Hao Wang, Robert Marsland III Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions. Physical Review E 99 052111 (2019)(Arxiv)
47. Robert Marsland III, Wenping Cui, Joshua Goldford, Alvaro Sanchez, Kirill Korolev, Pankaj Mehta. Available energy fluxes drive a phase transition in the diversity, stability, and functional structure of microbial communities PLoS Comp Bio 15(2): e1006793 (2019) (Arxiv)
46. Alexandre G. R. Day, Marin Bukov, Phillip Weinberg, Pankaj Mehta, Dries Sels The Glassy Phase of Optimal Quantum Control Phys. Rev. Lett. 122, 020601 (2019). SI. (Arxiv)
45. Pankaj Mehta, Marin Bukov, Ching-Hao Wang, Alexandre G.R. Day, Clint Richardson, Charles K. Fisher, David J. Schwab. A high-bias, low-variance introduction to Machine Learning for physicists. Physics reports (2019)(Paper and Notebooks)
44. Marin Bukov, Alexandre G. R. Day, Phillip Weinberg, Anatoli Polkovnikov, Pankaj Mehta, Dries Sels Broken Symmetry in a Correlated Quantum Control Landscape Phys Rev A. 97, 052114. (2018) (Arxiv)
43. Joshua E. Goldford, Nanxi Lu, Djordje Bajic, Sylvie Estrela, Mikhail Tikhonov, Alicia Sanchez-Gorostiaga, Daniel Segre, Pankaj Mehta*, Alvaro Sanchez* Emergent Simplicity in Microbial Community Assembly Science 361, 469-474 (2018). SI
42. Madhu Advani, Guy Bunin, Pankaj Mehta Statistical physics of community ecology: a cavity solution to MacArthur's consumer resource model Journal of Statistical Mechanics 3: 033406.(2018) (earlier arxiv version with different title.)
41. Marin Bukov, Alexandre GR Day, Dries Sels, Phillip Weinberg, Anatoli Polkovnikov, Pankaj Mehta.Reinforcement Learning in Different Phases of Quantum Control Physical Review X 8, 031086 (2018). (arxiv). Also see movies here.
40. Cui Wenping and Pankaj Mehta. Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting. PloS one, 13(8), e0202331 (2018).(arxiv with different name)
39. Sai Teja Pusuluri, Alex H. Lang, Pankaj Mehta, and Horacio E. Castillo Cellular reprogramming dynamics follow a simple 1D reaction coordinate. Physical biology 15, 016001 (2017)
38.Keri Dame et al. Thyroid Progenitors Are Robustly Derived from Embryonic Stem Cells through Transient, Developmental Stage-Specific Overexpression of Nkx2-1. Stem cell reports 8.2 216 (2017)
37. Ching-Hao Wang, Pankaj Mehta, Michael Elbaum. A thermodynamic paradigm for solution demixing inspired by nuclear transport in living cells. Physical Review Letters 118 158101 (2017).
36. Michael Kolodrubetz, Pankaj Mehta, Anatoli Polkovnikov. Geometry and non-adiabatic response in quantum and classical systems Physics Reports 697, 1-87 (2017)
35. Benjamin Dickens, Charles Fisher, and Pankaj Mehta. An analytically tractable model for community ecology with many species Physical Review E, 94, 022423 (2016) (arxiv)
34. Pankaj Mehta, Alex H. Lang, and David Schwab. Landauer in the age of synthetic biology: energy consumption and information processing in biochemical networks Journal of Statistical Physics. 162.5 (2016)
33. Pankaj Mehta and David Schwab. "An exact mapping from the Variational Renormalization Group to Deep Learning" (arxiv). code. Featured in Quanta Magazine and Wired.
32. Charles Fisher and Pankaj Mehta. Bayesian feature selection with strongly-regularizing priors maps to the Ising Model Neural Computation, 27, 2411–2422(2015). (arxiv)
31. Javad Noorbakhsh, David Schwab, Allyson Sgro, Thomas Gregor, Pankaj Mehta. Multiscale modeling of oscillations and spiral waves in Dictyostelium populations Physical Review E 91 (6), 062711 (2015)
30. A Wilson et al. Emergence of a developmental stage-dependent human liver disease signature demonstrated by directed differentiation of alpha-1 antitrypsin deficient iPS cells Stem Cells Report 4 1-15 (2015)
29. Charles Fisher and Pankaj Mehta. Fast Bayesian Feature Selection for High Dimensional Linear Regression in Genomics via the Ising Approximation Bioinformatics, 31(11), 2015, 1754–1761 (2015)
28. Allyson Sgro, David Schwab, Javad Noorbakhsh, Troy Mestler, Pankaj Mehta, Thomas Gregor. From Intracellular Signaling to Population Oscillations: Bridging Scales in Collective Behavior Molecular Systems Biology 11: 799 (2015). (arxiv)
27. Lin Chen, Javad Noorbakhsh, Rhys M. Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta, Gabor Balazsi. Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation Plos. Comp. Bio 12 e1003979 (2014)
26. Alex Lang, Charles Fisher, Thierry Mora, Pankaj Mehta. Thermodynamics of statistical inference by cells. Phys. Rev. Lett. 113, 148103 (2014). Supporting Information. (arxiv)
25. Charles Fisher and Pankaj Mehta. Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries using Sparse Linear Regression. PLoS One 9:e102451 (2014). (arxiv)
24. William R. Harcombe, William Riehl2, Ilija Dukovski, Brian R. Granger, Alex Betts, Alex H. Lang, Gracia Bonilla, Amrita Kar, Nicholas Leiby, Pankaj Mehta, Christopher J. Marx, Daniel Segré. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics Cell Reports 7, 1104–1115 (2014).
23. David J Schwab, Ilya Nemenman, Pankaj Mehta. Zipf's law and criticality in multivariate data without fine-tuning Phys. Rev. Lett. 113 68102 (2014). (arxiv)
22. Alket Mertiri, Hatice Altug, MK Hong, Pankaj Mehta, J Mertz, LD Ziegler, Shyamsunder Erramilli. Nonlinear Midinfrared Photothermal Spectroscopy Using Zharov Splitting and Quantum Cascade Lasers ACS Photonics 1, 696−702 (2014). (arxiv)
21. Charles Fisher and Pankaj Mehta. The transition between the niche and neutral regimes in ecology Proc. Natl. Acad Sci 36 13111–13116 (2014). (arxiv)
20. Ed Redznik, Pankaj Mehta, Daniel Segré.Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools PLoS computational biology 9 (8), e1003195 (2013).
19. Alex Lang, Hu Li, J.J. Collins, Pankaj Mehta. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLoS Computational Biology 10(8): e1003734 (2013). (arxiv)
18. Javad Noorbakhsh, Alex Lang, Pankaj Mehta. Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis PLOS One 8, e72676, (2013). (arxiv)
17. Pankaj Mehta and Anatoli Polkovnikov. Efficiency bounds for nonequilibrium heat engines Annals of Physics , 332, 110-126, (2013). (arxiv)
16. Pankaj Mehta and David Schwab. The Energetic Cost of Cellular Computation. Proc. Natl Acad. Sci 109(44), 17978-17982, (2012). (arxiv)
Highlighted by MIT technology review here; the Genome Web Daily Scan here; and Physics Today here.
15. David Schwab, Gabriel Plunk, Pankaj Mehta. Kuramoto model with coupling through an external medium. Chaos, 22(4), 043139-043139 (2012) arxiv
14. David Schwab, Ania Baetica, and Pankaj Mehta. Dynamical quorum-sensing and synchronization of nonlinear oscillators coupled through an external medium Physica D 241, 782 (2012).
13. SW Teng, JN. Schaffer, KC Tu, Pankaj Mehta, W Lu, N.P. Ong, BL Bassler, and NS Wingreen. Active Regulation of Receptor Ratios Controls Integration of Quorum Sensing Signals in Vibrio Harveyi. Molecular Systems Biology 7, 491 (2011). (see also Supporting Information)
12. Pankaj Mehta, David Schwab, and Anirvan Sengupta. Statistical mechanics of transcription-factor binding site discovery using Hidden Markov Models. Journal of Statistical Physics 142, 1187-1205 (2011)
11. Pankaj Mehta and Thomas Gregor. Approaching the molecular origins of collective dynamics in cell populations. Current Opinions in Genetics and Development. (2010)
10. SW Teng, Y. Wang, KC Tu, Pankaj Mehta, NS Wingreen, BL Bassler, NP Ong. Measurement of the copy number of the quorum-sensing regulator of bacterial cell. Biophys J. , 98(9):2024-31 (2010).
9. Pankaj Mehta, Sidhartha Goyal, Tao Long, Bonnie Bassler, Ned S Wingreen. Signal integration and information processing in bacterial quorum sensing. Molecular Systems Biology 5:325. (2009) . (see also Supporting Information )
8. Tao Long, CK Tu, Y Wang, Pankaj Mehta, NP Ong, BL Bassler, NS Wingreen. Quantifying the integration of multiple quorum-sensing signals in Vibrio harveyi with single-cell resolution. PLOS Biology 7(3): e100006.(2009) (see also Supporting Information)
7. Pankaj Mehta, Sidartha Goyal, Ned Wingreen. A quantitative comparison of sRNAs based and protein-based gene regulation Molecular Systems Biology 4, 221 (2008). (see also Supporting Information)
6. Pankaj Mehta, Ranjan Mukhopadhyay, Ned S Wingreen. Exponential sensitivity of noise-driven switching in genetic networks Physical Biology 5, 026005 (2008).
5. Pankaj Mehta and Natan Andrei Nonequilibrium quantum-impurities: from entropy production to information theory Phys. Rev. Lett. 100, 086804 (2008)
4. Pankaj Mehta and Natan Andrei Scattering approach to impurity thermodynamics (cond-mat/0702612).
3. E. Boulat, Pankaj Mehta, N. Andrei, E. Shimshoni, A. Rosch Heat Transport in Spin Ladders Physical Review B 75 , 245104 (2007)
2. Pankaj Mehta and Natan Andrei Nonequilibrium Transport in quantum impurity models (Bethe-Ansatz for open systems) Physical Reveiw Letters 96, 216802 (2006). (also see Errata)
1. Pankaj Mehta, L. Borda, G. Zarand, P. Coleman, N. Andrei. Regular and singular Fermi-liquid fixed points in quantum impurity models Physical Review B. 72, 0144320 (2005).