SELECTED WORK

Grants:

PI, NIH Grant R01 HG003470-01A2 “Locating Regulatory Elements in Genomes” Total amount $907,804, Period April ’06-May ’09 (extended to May ’11).
Co-PI, NSF PHY-1344069 “INSPIRE Track 1: Zero-One Laws at the Interface Between Physics, Engineering and Biology” Total amount $839,703, Period Oct ’13-Sept ’16 Rutgers Univ Subaward (Sengupta) about $311K.
PI, Simons Foundation-626323 “Neural Manifold Learning” Total amount $180,265, Period June ’19-May ’22.

Organization of Conferences, Workshops and Summer Schools:

“India and Abroad: A Conference on Condensed Matter Physics”,
S.N. Bose National Center for Basic Sciences, Calcutta, January 2-4, 2001.
Mini-workshop on “Dynamics, Adaptation and Fluctuations in Bio-networks”,
Part of the program on Bio-molecular Networks, KITP, Santa Barbara, March 24-27, 2003.
“Signaling, Gene Expression and Cell Fates”,
Aspen Center for Physics, Aspen, August 18-September 7, 2003.
“Transcriptional Regulation from Molecules to Systems and Beyond”, Rutgers University, Piscataway, June 21-25, 2004.
“Evolution and Robustness”,
Systems Biology Discussion Group, New York Academy of Science, Nov 3, 2004.
“Analyzing Complex Phenotypes”,
Systems Biology Discussion Group, New York Academy of Science, Sept 28, 2005.
“Integrated Data Analysis for High Throughput Biology”,
CSHL Summer Course, Cold Spring Harbor, June 14 - 27, 2006.
“Chromatin Dynamics, Gene Regulation and Silencing”, ICAM Workshop, Snowmass, August 10-13, 2006.
“Boulder School on Biological Physics”, Boulder, July 2007.
“DIMACS Workshop on Systems Biology and Translational Medicine”, Rutgers University, Piscataway, December 7, 2011.
“Winter School on Quantitative Systems Biology”, ICTP, Trieste, November 26-7 Dec, 2012.
“ICTP-ICTS Winter School on Quantitative Systems Biology”, ICTS, Bangalore, 9-20th Dec, 2013.
“11th Annual q-bio Conference”,
Rutgers University, New Brunswick, July 25-28, 2017 (local organizer).

Selected Talks (Spring of 2002 onward):

“Fermi Function, Support Vector Machines and Transcription Factor Binding Sites”, Invited Talk, APS March Meeting, Indianapolis, March 2002
“Fermi Function, Support Vector Machines and Transcription Factor Binding Sites”, IAS, Princeton, April 2002
“Fermi function, Support Vector Machines and Transcription Factor Binding Sites”, NEC Research Institute, Princeton, May 2002.
“Specificity and Robustness in Transcription Control Network”,
Invited talk, Gordon Research Conference on “Theoretical Biology and Biomathematics”, Tilton, June 2002.
“Unraveling Transcriptional Control Networks”, Colloquium, IBM, Almaden, October 2002.
“A Biophysical Approach to Transcription Factor Binding Site Discovery”, KITP program on “Biomolecular Networks”, Santa Barbara, February 2003.
“A Biophysical Approach to Transcription Factor Binding Site Discovery”, Lewis Sigler Institute, Princeton, September 2003.
“The Challenge of Understanding Bio-molecular Specificity”,
in “Workshop on Information Processing in the Biological Organism”, Bethesda, November 2003.
“Dissecting Transcriptional Control Networks”. IAS, Princeton, January 2004
“Biophysics and Bioinformatics of Protein-DNA Interaction”,
in “Systems Biology: Genomic Approaches to Transcriptional Regulation”, CSHL, Cold Spring Harbor, March 2004.
“Specificity of Protein-DNA Interaction in Transcription Control: Physics, Evolution and Bioinformatics”,
Invited Talk, APS March Meeting, Montreal, March 2004.
“Specificity of Protein-DNA Interaction in Transcription Control:
Physics, Evolution and Bioinformatics”,
Invited Talk, Rutgers Statistical Mechanics Meeting (#91), Piscataway, May 2004.
“Specificity of Protein-DNA Interaction in Transcription Control: Physics, Evolution and Bioinformatics”,
Duke University, Durham, November 2004.
“Classifiers for Detection of Regulatory Elements”,
Applied Mathematic Colloquium, Columbia University, New York, December 2004.
“Programmed Cell Death and Evolutionary Cheating”,
KITP program on “Networks of Growth, Death and Aging”, Santa Barbara, February 2005.
“Classifiers for Detection of Regulatory Elements”,
Courant Institute of Mathematical Sciences, New York University, New York, April 2005.
“Specificity in Signaling and Transcriptional Networks.”, Automated Biotechnology Group, Merck, North Wales, May 2005.
“SVMs and Probabilistic Approaches for Classifying Promoters”,
DIMACS Workshop on Machine Learning Approaches for Understanding Gene Regulation, Rutgers University, New Jersey, August 2005.
“Modeling Biochemical Circuits: A Tutorial for Engineers”,
Digital Technology Center, University of Minnesota, Minneapolis, April 2006.
“Detection of Regulatory Elements Utilizing Physical and Evolutionary Constraints ”, BCB 2006, Fourth Bertinoro Computational Biology Meeting, Bertinoro, Italy, June 2006.
“Phase Transitions in the State of the Genome”,
Physics Colloquium, Emory University, Atlanta, October 2006.
“Biological Information Processing in Signaling Cascades and in Transcriptional Control”, I2Lab Workshop: Frontiers in Quantum and Biological Information Processing,
University of Central Florida, Orlando, November 2006.
“Modeling Epigenetic Silencing”,
Invited Talk, International Conference of Bioinformatics, New Delhi, December 18 - 20, 2006 .
“Phase Transitions in the State of the Genome” Colloquium, TIFR, Mumbai, December 21, 2006.
“SVMs and Probabilistic Approaches for Classifying Promoters”,
Invited Talk, Computational Insights into Biological Systems, IISC, Bangalore, December 27, 2006.
“Dynamical Modeling in Genetic Networks, with Segment Polarity as an Example” and “Modeling Epigenetic Silencing”,
The Third Bangalore Benny Shilo Course in Developmental Biology,
NCBS, Bangalore, December 25, 2006- Jan 4, 2007.
“Geometry of Parameter Space in Regulatory Networks: Investigating Measures of Robustness”’ Design Principles in Biological Systems 2, Banbury Center, CSHL, Cold Spring Harbor, 6-8 May 2007.
“SVMs and Probabilistic Approaches for Classifying Promoters”, Invited Talk, Interface 07, Philadelphia, May 23-26, 2007.
“Motifs, PSSMs and all that”,
Integrated Data Analysis for High Throughput Biology, CSHL Course, June 2007.
“Optimal path to epigenetic switching”,
The First q-bio Conference on Cellular Information Processing, St. John’s College, Santa Fe, August 8-11, 2007.
“Modeling Epigenetic Silencing”,
Workshop: Deconstructing Biochemical Networks, Centre de Recherches Mathematiques, Universite de Montreal, Montreal, September 24-28, 2007.
“Phase Transitions in the State of the Genome”,
Physics Colloquium, Virginia Tech University, Blacksburg, November 16, 2007.
“Phase Transitions in the State of the Genome”,
Physics Colloquium, University of Toronto, Toronto, December 6, 2007.
“Modeling Epigenetic Silencing”,
Winter Conference on Decision Making in Single Cells, Aspen Center for Physics, Aspen, Jan 6-12, 2008.
“Modeling Epigenetic Silencing”,
Seminar, The Biocomplexity Institute, Indiana University, Bloomington, April 1, 2008.
“Action at a Distance in Eukaryotic Gene Regulation”, Physics Colloquium, CUNY, New York, April 16, 2008.
“Modeling Epigenetic Silencing”,
Design Principles in Biological Systems, Design Principles in Biological Systems,
The Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, April 21-25, 2008.
“Genomic Phase Transitions”,
Physics Colloquium, Ohio State University, Columbus, May 6, 2008.
“Epigenetic Chromatin Silencing”,
The Sixth Annual BioMaPS Summer School on Chromatin Structure and Gene Regulation, Rutgers University, Piscataway, June 9-13, 2008.
“Action at a Distance in Eukaryotic Gene Regulation”,
Center for Studies in Physics and Biology, Rockefeller University, New York, January 27, 2009.
“Bistability and Front Propagation in Epigenetic Silencing”,
IPCAT 2009: From Small Scale Dynamics To Understanding Systems Behavior, Centro Stefano Franscini, Ascona, 5-9 April 2009.
“Action at a Distance in Eukaryotic Gene Regulation”,
Physics Colloquium, Princeton University, Princeton, Feb 4, 2010.
“Rare Events and Epigenetic Switching”,
Rare Events in Biology, Princeton Center for Theoretical Science, Princeton University, Princeton, 3 - 4 February, 2010.
“Long-range Interactions: Enhancers and Insulators”,
OIST Summer School and Workshop: Quantitative Evolutionary and Comparative Genomics, Okinawa, May 24-June 4, 2010.
“Chromatin Architecture Dynamics and Long-range Regulatory Control”, Biophysics Talk, Princeton University, Princeton, April 11, 2011.
“Inferring Chromatin Conformation”,
DIMACS Workshop on Systems Biology and Translational Medicine, Rutgers University, Piscataway, December 7, 2011.
“High Dimensional Signals: Statistical Physics Methods in Analyzing Big Data Sets”, Neuroinformatics School. Marine Biology Lab, Woods Hole, August 23, 2012.
“Computational Analysis of ’Multi-C’ Data Reveals Dynamic Chromatin Loop Formation”, Dynamic Organization of Nuclear Function, CSHL, Cold Spring Harbor, September 28, 2012.
“Regulating Looping in Genome”, Colloquium, ICTS, Bengaluru, April 5, 2013.
“Chromatin Architecture Dynamics and Long-range Regulatory Control”, Statistical Mechanics Meeting 109, Rutgers University, Piscataway, May 13, 2013.
“Modeling Epigenetic Silencing”,
Mini-symposium on Quantitative Systems Biology-Pharmacology, Rutgers University, Piscataway, May 7, 2014.
“Compressed Sensing, Structured Sensing Matrices and Harmonic Analysis”,
NSF Workshop on Physical, Engineering and Biological Limits to Brain Measurements, Arlington, May 31, 2014.
“Regulating Looping in Genome”,
Mini-symposium “Applications of Statistical Physics in Quantitative Biology”, 9th European Conference on Mathematical and Theoretical Biology, Gothenburg, June 15-19, 2014.
“Polymer Models of Looping in Genome”,
Invited Talk, APS March Meeting, San Antonio, March 2015.
“First Passage Times and Relaxation Times in Biological Stochastic Processes ”, University of Delaware, Newark, Jan 2015.
“Large Random Matrices and Their Applications in Machine Learning”, IIT Madras, Chennai, Jan 2017.
“Large Random Matrices and Their Applications in Machine Learning”, ICTS, Bengaluru, Jan 2017.
“Neural Networks for Clustering and Manifold Learning via Spin Models”, Emergence in Disordered, Interacting and Living Systems: Abrahams@90, Aspen Center for Physics, Aspen, Aug 2017.
“Manifold Representation by an Unsupervised Neural Net: Biology, Mathematics and Computation”, Math and Data (MaD) Seminar, New York University, New York, Apr 2018.

Upcoming book:

Modeling Biochemical Networks
(with P. Mehta), Publisher: Oxford University Press.

List of Refereed Publications:

Systems Neuroscience and Machine Learning

N6. Critical Behavior and Universality Classes for an Algorithmic Phase Transition in Sparse Reconstruction (with M. Ramezanali and P. P. Mitra), accepted in J. Stat. Phys.
N5. Clustering is Semidefinitely not that Hard: Nonnegative SDP for Manifold Disentangling
(with M Tepper and D. B. Chklovskii), J. Mach. Learn. Res. 19, 3208-3237 (2018).
N4. Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networks (with M. Tepper, C. Pehlevan, A. Genkin, D. Chklovskii), Advances in Neural Information Processing Systems (NeurIPS) 7080-7090 (2018).
N3. Why Do Similarity Matching Objectives Lead to Hebbian/Anti-Hebbian Networks? (with C. Pehlevan and D. B. Chklovskii), Neural Computation 30, 84-124 (2018).
N2. Resource-efficient Perceptron Has Sparse Synaptic Weight Distribution
(with C. Pehlevan), 25th Signal Processing and Communications Applications Conference (SIU), 1-4 (2017).
N1. Mean Field Analysis of Sparse Reconstruction with Correlated Variables
(with M. Ramezanali and P. P. Mitra), 24th European Signal Processing Conference (EUSIPCO), 1267-1271 (2016).

Bioinformatics, Systems Biology and Evolution

B36. Translation Inhibition and Resource Balance in the TX-TL Cell-free Gene Expression System (with V. H. Nagaraj, J. M. Greene and E. D. Sontag), Synthetic Biology 2 , ysx005 (2017).
B35. Quantitative Analysis of Chromatin Interaction Changes upon a 4.3 Mb Deletion at Mouse 4E2 (with C. J. Zepeda-Mendoza, S. Mukhopadhyay, E. S. Wong, N. Harder, E. Splinter, E. de Wit,
M. A. Eckersley-Maslin, T. Ried, and R. Eils, K. Rohr, A. Mills, W. de Laat, P. Flieck
and D. L. Spector), BMC Genomics 16, 982 (2015).
B34. First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins (with W. Dai and R. M. Levy), Phys. Rev. Lett. 115, 048101 (2015).
B33. Breaking an Epigenetic Chromatin Switch: Curious Features of Hysteresis in Saccharomyces cerevisiae Telomeric Silencing (with V. Nagaraj, S. Mukhopadhyay and A. Dayarian), PLoS One 9, e113516 (2014).
B32. The Role of Multiple Marks in Epigenetic Silencing and the Emergence of a Stable Bivalent Chromatin State (with S. Mukhopadhyay), PLoS Comput. Biol. 9, e1003121 (2013).
B31. Titration and Hysteresis in Epigenetic Chromatin Silencing
(with A. Dayarian), Phys. Biol. 10, 036005 (2013).
B30. SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding
(with R. S. Roy, K. C. Chen and A. Schliep ), J. Comput. Biol. 19, 1162 (2012).
B29. Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin (with O. I. Kulaeva, G. Zheng, Y. S. Polikanov, A. V. Colasanti, N. Clauvelin,
S. Mukhopadhyay, V. M. Studitsky, and W. K. Olson), J. Biol. Chem. 287, 20248 (2012).
B28. Theoretical Analysis of the Role of Chromatin Interactions in Long-range Action of Enhancers and Insulators (with S. Mukhopadhyay, P. Schedl and V. M. Studitsky), PNAS 102, 19919 (2011).
B27. Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?
(with R. S. McIsaac, K. C. Huang and N. S. Wingreen), PLoS Comput. Biol. 7, e1002109 (2011).
B26. Regulated Antisense Transcription Controls Expression of Cell-type-specific Genes in Yeast, (with B. Gelfand, B., J. Mead, A. Bruning, N. Apostopoulos, V. H. Nagaraj and A. K. Vershon), Mol. Cell Biol. 31, 1701 (2011).
B25. Statistical Mechanics of Transcription-factor Binding Site Discovery Using Hidden Markov Models, (with P. Mehta, B. and D. J. Schwab),
J. Stat. Phys. 142, 1187 (2011).
B24. Locus Dependence in Epigenetic Chromatin Silencing
(with S. Mukhopadhyay and V. H. Nagaraj), Biosystems 102, 49 (2010).
B23. SOPRA: Scaffolding Algorithm for Paired Reads via Statistical Optimization (with A. Dayarian and T. P. Michael), BMC Bioinformatics 11, 345 (2010).
B22. OHMM: a Hidden Markov Model Accurately Predicting the Occupancy of a Transcription Factor with a Self-overlapping Binding Motif (with A. Drawid, N. Gupta, V. H. Nagaraj, and C. Gelinas), BMC Bioinformatics 10, 1 (2009).
B21. Inheritance of Epigenetic Chromatin Silencing
(with D. David-Rus, S. Mukhopadhyay and J. L. Lebowitz), J. Theor. Biol. 258, 112 (2009).
B20. Shape, Size and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks (with A. Dayarian, A., M. Chaves, E. D. Sontag), PLoS Comput. Biol. 5, e1000256 (2009).
B19. Better Estimation of Protein-DNA Interaction Parmeters Improve Prediction of Functional Sites
(with V. H. Nagaraj and R. A. OFlanagan), BMC Biotechnol. 8, 94 (2008).
B18. Geometry and Topology of Parameter Space: Investigating Measures of Robustness in Regulatory
Networks (with M. Chaves and E. D. Sontag), J. Math. Biol. 59, 315 (2008).
B17. Repression of BLNK and BCAP is Important for Lymphocyte Transformation by Rel/NF-κB
(with N. Gupta, J. Delrow, A. Drawid, G. Fan and C. Gelinas), Cancer Res. 68, 808 (2008). B16. Epigenetic Chromatin Silencing: Bistability and Front Propagation
(with M. Sedighi), Phys. Biol. 4, 246, (2007).
B15. Analysis of Escherichia coli Global Gene Expression Profiles in Response to Overexpression and Deletion of CspC and CspE
(with S. Phadtare, V. Tadigotla, W. H. Shin and K. Severinov), J. Bacteriol. 188, 2521, (2006).
B14. Thermodynamics and Kinetics Based Identification of Transcriptional Pauses
(with V. Tadigotla, D. O’Maoileidigh, V. Epshtein, R. Ebright, E. Nudler and A. Ruckenstein), PNAS 103, 4439 (2006).
B13. Quantitative Modeling and Data Analysis of SELEX Experiments (with M. Djordjevic),
Phys. Biol. 3, 13 (2005).
B12. Stochastic Evolutionary Dynamics at Two Levels (with A. Traulsen and M. Nowak),
J. Theor. Biol. 235, 393 (2005).
B11. Non-additivity in Protein-DNA binding (with R. O’Flanagan, G. Paillard and R. Lavery), Bioinformatics 21, 2254 (2005).
B10. G-protein Coupled Enzyme Cascades have Intrinsic Properties that Improve Signal Localization and Fidelity
(with P. Detwiller, S. Ramanathan and B. Shraiman),
Biophys. J. 88, 3063 (2005).
B9. Optimal Path to Epigenetic Switching
(with D. Marin Roma, R. O’Flanagan, A. Ruckenstein and R. Mukhopadhyay), Phys. Rev. E 71, 011902 (2005).
B8. Repression of the Yeast HO Gene by the MATα1 and MATa1 Homeodomain Proteins
(with J. Mathias, S. Hanlon, R. O’Flanagan and A. Vershon), Nucleic Acids Res. 32, 6469 (2004).
B7. Combined Analysis of Expression Data and Transcription Factor Binding Sites in the Yeast Genome
(with R. O’Flanagan, V. Nagaraj, A. Bruning, J. Mathias and A. Vershon),
BMC Genomics 5, 59 (2004).
B6. A Biophysical Approach to Transcription Factor Binding Site Discovery (with M. Djordjevic and B. Shraiman), Genome Res. 13, 2381 (2003).
B5. Stochastic Dynamics of Tumerogenesis
(with N. Komarova and M. Nowak), J. Theor. Biol. 223 433 (2003).
B4. Chromosomal Instability in Cancer
(with M. Nowak, N. Komarova, P. Jallepalli, I-M Shih, B. Vogelstein, C. Lengauer), PNAS 99, 166226 (2002).
B3. Specificity and Robustness in Transcription Control Networks (with M. Djorjevic and B. Shraiman), PNAS 99, 2072 (2002) .
B2. Engineering Aspects of Enzymatic Signal Transduction:
Photo-receptors in the Retina
(with P. Detwiller, S. Ramanathan and B. Shraiman), Biophys. J. 79, 2801 (2000).
B1. An O(n ln n) Algorithm for Finding Dissimilar Strings
(with S. Abbasi), Information Processing Letters 62, 135 (1997).

Applications: Communication and Computation

A8. Capacity of Multivariate Channels with Multiplicative Noise: Random Matrix Techniques and Large-N Expansions
(with P. P. Mitra), J. Stat. Phys.125 1223 (2006).
A7. Statistical Mechanics of Multi-antenna Communications: Replicas and Correlations (with A. Moustakas and S. Simon), Acta Physica Polonica B 36 2719 (2005).
A6. MIMO Capacity Through Correlated Channels in the Presence of Correlated Interferers and Noise: A (not so) Large N Analysis
(with A. Moustakas and S. Simon), IEEE Inform. Theory 49 2545 (2003). A5. Classical Analog of Quantum Search
(with L. Grover), Phys. Rev. A 65, 032319 (2002).
A4. Information Capacity of Nonlinear WDM Fiber Optical Transmission Line
(with J. Stark and P. P. Mitra), Opt. Fiber Technol. 7, 275 (2001). A3. Markov Random Field Models of Multicasting in Tree Networks
(with K. Ramanan , I. Ziedins and P. P. Mitra), Adv. Appl. Prob. 34, 58 (2002). A2. Communication Through a Diffusive Medium: Coherence and Capacity
(with A. L. Moustakas, H. U. Baranger, L. Balents and S. H. Simon), Science 287, 287 (2000). A1. Distributions of Singular Values of Some Random Matrices
(with P. P. Mitra), Phys. Rev. E 60, 3389 (1999).

Condensed Matter Physics

C11. Spin-cluster Model for the Low-temperature Phase of α′-NaV2O5 (with S. Trebst), Phys. Rev. B 62, R 14613 (2000).
C10. Hall Effect in the Perovskite Manganites
(with P. Majumdar and S. H. Simon), Phys. Rev. B 59, 4746 (1999).
C9. Overscreened Multi-channel SU(N) Kondo Model:
Large-N Solution and Conformal Field Theory
(with O. Parcollet, A. Georges and G. Kotliar), Phys. Rev. B 58, 3794 (1998).
C8. Spin in a Fluctating Field: The Bose (+Fermi) Kondo Models Phys. Rev. B 61, 4041 (2000).
C7. Kondo Quartet
(with A. Georges), Nucl. Phys. B (Proc. Suppl.) 58, 105 (1997).
C6. Overscreened Single Channel Kondo Problem (with Y. B. Kim), Phys. Rev. B 54, 14918 (1996).
C5. Hall Effect and Magnetoresistance in Copper-oxide Metals
(with G. Kotliar and C. M. Varma), Phys. Rev. B 53, 3573 (1996).
C4. Non-equilibrium Dynamics Following a Quench to the Critical Point in a Semi-infinite System
(with S. N. Majumdar), Phys. Rev. Lett. 76, 2394 (1996).
C3. Non Fermi Liquid Behaviour near a T = 0 Spin-glass Transition
(with A. Georges), Phys. Rev. B 52, 10295 (1995).
C2. Solution of the Two-channel Two Impurity Kondo Model
(with A. Georges), Phys. Rev. Lett. 74, 2808 (1995).
C1. On the Emery-Kivelson Solution of the Two Channel Kondo Model
(with A. Georges), Phys. Rev. B 49, 10020 (1994).

Strings, Random Surfaces and Matrix Models

S6. Target Space Interpretation of the New Moduli in Two Dimensional String Theory (with S. Mukherji and S. Mahapatra),Mod. Phys. Lett. A 7, 3119 (1992).
S5. Classical Solutions of 2-dimensional String Theory
(with G. Mandal and S. R. Wadia), Mod. Phys. Lett. A 6, 1685 (1991).
S4. Interactions and scattering in d = 1 string theory
(with G. Mandal and S. R. Wadia), Mod. Phys. Lett. A 6, 1465 (1991).
S3. Excitations and Interactions in d = 1 String Theory (with S. R. Wadia), Int. Jour. Mod. Phys. A 6, 1961 (1991).
S2. New Critical Behavior in d = 0 Large N Matrix Models
(with S. R. Das, A. Dhar and S. R. Wadia), Mod. Phys. Lett. A 5, 1041 (1990).
S1. Critical Behavior in Some D = 1 Large N Matrix Models
(with S. R. Das, A. Dhar and S. R. Wadia), Mod. Phys. Lett. A 5, 891 (1990).

Research: Text