Journal Publications

Peer-reviewed Archival Conference Papers

A Singh and P Bokes. Consequences of mRNA transport on stochastic variability in protein levels. Biophysical Journal, 103, 1087-1096, 2012.

RD Dar, B Razooky, A Singh, T Trimeloni, J McCollum, CD Cox, LS Weinberger and ML Simpson. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proceedings of the National Academy of Sciences, 109, 17454 -17459, 2012.

A Singh. Negative feedback through mRNA provides the best control of gene-expression noise. IEEE Transactions on NanoBiosciences, 11, 194-200, 2011.

K Franz, A Singh  and LS Weinberger. Studying noise in gene expression using HIV based lentiviral vectors. Methods in Enzymology, 497, 603-622,  2011.

A Singh  and JP Hespanha. Approximate moment dynamics for chemically reacting systems. IEEE Transactions on Automatic Control, 56, 414-418, 2011.

A Singh  and JP Hespanha. Stochastic hybrid systems for studying biochemical processes. Philosophical Transactions A of the Royal Society, 368, 4995-5011, 2010.

A Singh, B Razooky, CD Cox, ML Simpson and LS Weinberger. Transcriptional bursting in HIV-1 promoter creates high variability in proteins levels.  Biophysical Journal, 98, L32-L34, 2010.

A Singh  and JP Hespanha. Evolution of gene auto-regulation in the presence of noise. IET Systems Biology, 3, 368-378, 2009.

A Singh  and LS Weinberger. Noise in viral gene expression as a molecular switch for viral latency. Current Opinion in Microbiology, 12, 460-466, 2009.

A Singh, WW Murdoch and RM Nisbet. Skewed attacks, stability and host suppression. Ecology, 90, 1679-1686, 2009.

A Singh and JP Hespanha. Optimal feedback strength for noise suppression in auto-regulatory gene networks. Biophysical Journal, 96, 4013-4023, 2009.

A Singh and RM Nisbet. Variation in risk in single-species models. Mathematical Bioscience and Engineering, 5, 859-875, 2008.

A Singh and JP Hespanha. A derivative-matching approach to moment closure for the stochastic logistic model.  Bulletin of Math Biology, 69, 1909-1925, 2007.

A Singh and RM Nisbet. Semi-discrete host-parasitoid models.  Journal of Theoretical Biology, 247, 733-742, 2007.

JP Hespanha and A Singh. Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems.  Int. Journal of Robust and Nonlinear Control, 15, 669-689, 2005.

A Singh  and H. K. Khalil. Regulation of nonlinear systems using conditional integrators. International Journal of Robust and Nonlinear Control, 15, 339-362, 2005.

A Singh , R Mukherjee, K Turner and S Shaw. MEMS implementation of axial and follower end forces. Journal of Sound and Vibration, 286, 637–644, 2005.

A Singh, C Vargas and R Karmakar. Stochastic analysis and inference of a two-state genetic promoter model . American Control Conference, Washington, DC, 2013.

A Singh. Quantifying stochasticity in gene-expression models with extrinsic parameter fluctuations. IEEE Conference on Decision and Control, Maui, HI,  2012.

A Singh. Stochastic analysis of genetic feedback circuit controlling cell-fate decision in HIV. IEEE Conference on Decision and Control, Maui, HI,  2012.

A Singh. Genetic negative feedback circuits for filtering stochasticity in gene expression. IEEE Conference on Decision and Control, Orlando, FL, 2011.

A Singh and JP Hespanha. Reducing noise through translational control in an auto-regulatory gene network. American Control Conference, St. Louis, MO, 2009.

A Singh and JP Hespanha. Noise suppression in auto-regulatory gene networks. 47th IEEE Conference on Decision and Control, Cancun, Mexico, 2008.

A Singh and JP Hespanha. Scaling of stochasticity in gene cascades. American Control Conference, Seattle, WA, 2008.

A Singh and JP Hespanha. Stochastic analysis of gene regulatory networks using moment closure. American Control Conference, New York, NY, 2007.

A Singh and JP Hespanha. Moment closure techniques for stochastic models in population biology. American Control Conference, Minneapolis, MN, 2006.

A Singh and JP Hespanha. Lognormal moment closures for bio-chemical reactions. 45th

IEEE Conference on Decision and Control, San Diego, CA, 2006.

A Singh and JP Hespanha. Models for multi-specie chemical reactions using polynomial stochastic hybrid systems. 44th IEEE Conference on Decision and Control, Spain, 2005.

A Singh and JP Hespanha. Modeling chemical reactions with single reactant specie. In Proc. of the Workshop on Modeling and Control of Complex Systems, Cyprus, 2005.

A Singh and HK Khalil. State feedback regulation of nonlinear systems using conditional integrators. 43rd IEEE Conference on Decision and Control, Bahamas, 2004.

A Singh and JP Hespanha. Stochastic modeling of biochemical reactions. 25th Army Science Conference, Orlando, FL, 2006.

A Singh, B Razooky, RD Dar and LS Weinberger. Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Nature: Molecular Systems Biology, 8, 607, 2012.

Thesis, Book Chapters and Technical Reports

A Singh. Regulation of nonlinear systems using conditional integrators. MS Thesis in Electrical and Computer Engineering, Michigan State University, 2004.

A Singh. A mechanistic approach to tuning MEMS resonators. MS Thesis in Mechanical Engineering, Michigan State University, 2004.

A. Singh and JP Hespanha. Moment Closure for the Stochastic Logistic Model. Technical Report, University of California, Santa Barbara, 2006.

A Singh. Semi-discrete modeling of host-parasitoid population dynamics. MA Thesis in Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 2007.

A Singh. Stochastic modeling of chemical reactions and gene regulatory networks. Ph.D. Thesis in Electrical and Computer Engineering, University of California, Santa Barbara, 2008.

A Singh, C Vargas and R Karmakar. Stochastic analysis of genetic promoter architectures with memory. IEEE Conference on Decision and Control, Florence, Italy, 2013.

C Vargas, R Zurakowski and A Singh. Conditions for invasion of synapse-forming HIV variants. IEEE Conference on Decision and Control, Florence, Italy, 2013.

D Antunes and A Singh. Computing mRNA and protein statistical moments for a renewal model of stochastic gene-expression. IEEE Conference on Decision and Control, Florence, Italy, 2013.

A Singh and J Dennehy. Stochastic holin expression can account for lysis time variation in the bacteriophage lambda. Journal of the Royal Society Interface, 11, 20140140, 2014.

Z Fox and A Singh. Stochastic analysis of protein-mediated and microRNA-mediated feedback circuits in HIV. IFAC World Congress, Cape Town, South Africa, 2014.

C Vargas, L Cannon, A Singh and R Zurakowski. Optimal multi-drug approaches for reduction of the latent pool in HIV. IFAC World Congress, Cape Town, South Africa, 2014.

K Ghusinga and A Singh. Optimal first passage time in gene regulatory networks. IEEE Conference on Decision and Control, Los Angeles, CA, 2014.

D Antunes and A Singh. Quantifying gene expression variability arising from randomness in cell division times. Journal of Mathematical Biology, 2014. Online publication ahead of print.

B Daigle, M Soltani, L Petzold and A Singh. Inferring single-cell gene expression mechanisms using stochastic simulation. Bioinformatics, 31, 1428-1435, 2015.

M Soltani N. Kumar, R. Kulkarni and A Singh. Moment Closure Approximations in Genetic Negative Feedback Circuits. American Control Conference, Chicago, IL, 2015.

K Ghusinga, PW Fok and A Singh. Optimal feedback regulation for minimizing first-passage time variability in protein level. American Control Conference, Chicago, IL, 2015.

O Padovan-Merhar, G Nair, A Biaesch, A Mayer, S Scarfone, S Foley, A Wu, L Churchman, A Singh and A Raj. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular Cell, 58, 339–352, 2015.

SA Agrawal, D Anand, AD Siddam, A Kakrana, S Dash, DA Scheiblin, CA Dang, AM Terrell, SM Waters, A Singh, H Motohashi, M Yamamoto, SA Lachke. Compound mouse mutants of bZIP transcription factors Mafg and Mafk reveal a regulatory network of non-crystallin genes associated with cataract. Human Genetics, 134, 717-735, 2015.

M Soltani, C Vargas and A Singh. Conditional moment closure schemes for studying stochastic dynamics of genetic circuits. IEEE Trans. on Biomedical Systems and Circuits, 9, 518-526, 2015.

M Soltani, P Bokes, Z Fox and A Singh. Nonspecific transcription factor binding reduces variability in target protein expression for linear dose-response. Physical Biology, 12, 055002, 2015.

N. Kumar, A Singh and R. Kulkarni. Transcriptional bursting in gene expression: analytical results for general stochastic models. PLoS Computational Biology, 11, e1004292, 2015.

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A Borri, P Palumbo and and A Singh. Metabolic noise reduction for enzymatic reactions: the role of a negative feedback. IEEE Conference on Decision and Control, Osaka, Japan  2015.

K Ghusinga and A Singh. First-passage time for a stochastic gene expression model. IEEE Conference on Decision and Control, Osaka, Japan  2015.

P Kulkarni, N Rangarajan, Z Fox, A Singh and G Rangarajan. Disorder, oscillatory dynamics and state switching: the role of c-Myc. Journal of Theoretical Biology, 386, 105–114, 2015.

Please see my Google Scholar homepage for an updated list of publications

M Soltani and A Singh. Stochastic analysis of time-triggered linear stochastic hybrid systems. Technical Report, University of Delaware, 2016.

CA Vargas-Garcia, M Soltani and A Singh. Conditions for cell size homeostasis: A stochastic hybrid systems approach. IEEE Life Science Letters, 2, 47–50, 2016.

M Soltani and A Singh. Effects of cell-cycle-dependent expression on random fluctuations in protein levels. Royal Society Open Science, 3, 2016.

P Bokes and A Singh. Gene expression noise is affected differentially by feedback in burst frequency and burst size. Journal of Mathematical Biology, 74, 1483–1509, 2017.

K Ghusinga, JJ Dennehy and A Singh. First-passage time approach to controlling noise in the timing of intracellular events. Proceedings of the National Academy of Sciences, 114, 693–698, 2017.

A Borri, P Palumbo and A Singh. The impact of negative feedback in metabolic noise propagation. IET Systems Biology, 2016. DOI: 10.1049/iet-syb.2016.0003.

R Dar, S Schaffer, A Singh, B Razooky, M Simpson, A Raj and LS Weinberger. Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels. PLOS One, 11, e0158298, 2016

M Soltani and CA Vargas-Garcia, D Antunes and A Singh. Intercellular variability in protein levels from stochastic expression and noisy cell cycle processes. PLOS Computational Biology, 12, e1004972, 2016.

CA Vargas-Garcia, K Ghusinga and A Singh. A mechanistic stochastic framework for regulating bacterial cell division. Nature: Scientific Reports, 6, 30229, 2016.

B Emerick and A Singh. Host-feeding enhances stability of discrete-time host-parasitoid population dynamic models. Mathematical Bioscience, 272, 54--63, 2016.

M Soltani, T Platini and A Singh. Stochastic analysis of an incoherent feedforward genetic motif. American Control Conference, Boston, MA, 2016.

K Ghusinga and A Singh. Optimal regulation of protein degradation to schedule cellular events with precision. American Control Conference, Boston, MA, 2016.

J Conway, JJ Dennehy and A Singh. Optimizing phage lambda survival in a changing environment: stochastic model predictions. IEEE Conference on Decision and Control, Las Vegas, NV, 2016.

M Soltani and A Singh. Moment dynamics for a class of time-triggered stochastic hybrid systems. IEEE Conference on Decision and Control, Las Vegas, NV, 2016.

A Lamperski, K Ghusinga and A Singh. Stochastic optimal control using semidefinite programming for moment dynamics. IEEE Conference on Decision and Control, Las Vegas, NV, 2016.

CA Vargas-Garcia and A Singh. Hybrid systems approach to modeling stochastic dynamics of cell size. IEEE Conference on Decision and Control, Las Vegas, NV, 2016.

A Borri, P Palumbo and A Singh. Noise reduction for enzymatic reactions: a case study for stochastic product clearance. IEEE Conference on Decision and Control, Las Vegas, NV, 2016.

E Sontag and A Singh. Exact moment dynamics for feedforward nonlinear chemical reaction networks. IEEE Life Sciences Letters, 1, 26--29, 2015.

K Ghusinga, CA Vargas-Garcia, A Lamperski and A Singh. Exact lower and upper bounds on stationary moments in stochastic biochemical systems. Physical Biology, 2017.

M Soltani and A Singh. Moment-based analysis of stochastic hybrid systems with renewal transitions. Automatica, 84, 62-69, 2017.

S Shaffer, M Dunagin, S Torborg, E Torre, B Emert, C Krepler, M Beqiri, K Sproesser, P Brafford, M Xiao, E Eggan, I Anastopoulos, K Nathanson, CA Vargas-Garcia, A Singh, M Herlyn, A Raj. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature, 546, 431 - 435, 2017

S Modi, CA Vargas-Garcia, K Ghusinga and A Singh. Analysis of noise mechanisms in cell size control. Biophysical Journal, 112, 2408-2418, 2017.

M Soltani and A Singh. Stochastic analysis of linear time-invariant systems with renewal  transitions. American Control Conference, Seattle, WA, 2017.

K Ghusinga and A Singh. Effect of gene-expression bursts on stochastic timing of cellular events. American Control Conference, Seattle, WA, 2017.

CA Vargas-Garcia, C Agemabiese and A Singh. Optimal adsorption rate: Implications of  the shielding effect. American Control Conference, Seattle, WA, 2017.

A Singh and R Grima. Quantitative Biology: Theory, Computational Methods and Examples of Models. Editors: Bill Hlavacek, Brian Munsky and Lev Tsimring, MIT Press, 2017.

X Chen, M Ogura, K Ghusinga, A Singh and VM Preciado. Semidefinite bounds for moment dynamics: Application to epidemics on networks. IEEE Conference on Decision and Control, Melbourne, Australia, 2017.

A Singh. Modeling noise mechanisms in neuronal synaptic transmission. IEEE Conference on Decision and Control, Melbourne, Australia, 2017.

K Ghusinga, M Soltani, A Lamperski, S Dhople and A Singh. Approximate moment dynamics for polynomial and trigonometric stochastic systems. IEEE Conference on Decision and Control, Melbourne, Australia, 2017.

J Blotnick, CA Vargas-Garcia, JJ Dennehy, R Zurakowski and A Singh. The effect of multiplicity of infection on the temperateness of a bacteriophage: Implications for viral fitness. IEEE Conference on Decision and Control, Melbourne, Australia, 2017.

A Borri, P Palumbo and A Singh. Noise propagation in a class of metabolic networks. IEEE Conference on Decision and Control, Melbourne, Australia, 2017.