Works by Singh, Abhyudai

Results: 65

Priestia megaterium cells are primed for surviving lethal doses of antibiotics and chemical stress.

Published in:

Communications Biology, 2025, p. 1, doi. 10.1038/s42003-025-07639-2

By:

Guha, Manisha;
Singh, Abhyudai;
Butzin, Nicholas C.

Publication type:

Article

Transcriptional regulation of Sis1 promotes fitness but not feedback in the heat shock response.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.79444

By:

Garde, Rania;
Singh, Abhyudai;
Ali, Asif;
Pincus, David

Publication type:

Article

A comparative approach to stabilizing mechanisms between discrete- and continuous-time consumer-resource models.

Published in:

PLoS ONE, 2022, v. 17, n. 4, p. 1, doi. 10.1371/journal.pone.0265825

By:

Singh, Abhyudai

Publication type:

Article

Dynamics and consequences of the HTLV-1 proviral plus-strand burst.

Published in:

PLoS Pathogens, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.ppat.1010774

By:

Ramanayake, Saumya;
Moulding, Dale A.;
Tanaka, Yuetsu;
Singh, Abhyudai;
Bangham, Charles R. M.

Publication type:

Article

Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems.

Published in:

International Journal of Robust & Nonlinear Control, 2005, v. 15, n. 15, p. 669, doi. 10.1002/rnc.1017

By:

Hespanha, João Pedro;
Singh, Abhyudai

Publication type:

Article

Regulation of nonlinear systems using conditional integrators.

Published in:

International Journal of Robust & Nonlinear Control, 2005, v. 15, n. 8, p. 339, doi. 10.1002/rnc.996

By:

Singh, Abhyudai;
Khalil, Hassan K.

Publication type:

Article

Glycinergic Transmission in the Presence and Absence of Functional GlyT2: Lessons From the Auditory Brainstem.

Published in:

Frontiers in Synaptic Neuroscience, 2021, v. 13, p. 1, doi. 10.3389/fnsyn.2020.560008

By:

Brill, Sina E.;
Maraslioglu, Ayse;
Kurz, Catharina;
Kramer, Florian;
Fuhr, Martin F.;
Singh, Abhyudai;
Friauf, Eckhard

Publication type:

Article

Transcription coordinates histone amounts and genome content.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24451-8

By:

Claude, Kora-Lee;
Bureik, Daniela;
Chatzitheodoridou, Dimitra;
Adarska, Petia;
Singh, Abhyudai;
Schmoller, Kurt M.

Publication type:

Article

Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration.

Published in:

RNA Biology, 2021, v. 18, n. 9, p. 1310, doi. 10.1080/15476286.2020.1845504

By:

Begley, Victoria;
Jordán-Pla, Antonio;
Peñate, Xenia;
Garrido-Godino, Ana I.;
Challal, Drice;
Cuevas-Bermúdez, Abel;
Mitjavila, Adrià;
Barucco, Mara;
Gutiérrez, Gabriel;
Singh, Abhyudai;
Alepuz, Paula;
Navarro, Francisco;
Libri, Domenico;
Pérez-Ortín, José E.;
Chávez, Sebastián

Publication type:

Article

Understanding the liver under heat stress with statistical learning: an integrated metabolomics and transcriptomics computational approach.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5823-x

By:

Hubbard, Allen H.;
Zhang, Xiaoke;
Jastrebski, Sara;
Singh, Abhyudai;
Schmidt, Carl

Publication type:

Article

Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013014

By:

Zhang, Zhanhao;
Zabaikina, Iryna;
Nieto, Cesar;
Vahdat, Zahra;
Bokes, Pavol;
Singh, Abhyudai

Publication type:

Article

Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.pcbi.1013067

By:

Vahdat, Zahra;
Gambrell, Oliver;
Fisch, Jonas;
Friauf, Eckhard;
Singh, Abhyudai

Publication type:

Article

Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes.

Published in:

PLoS Computational Biology, 2016, v. 12, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004972

By:

Soltani, Mohammad;
Vargas-Garcia, Cesar A.;
Antunes, Duarte;
Singh, Abhyudai

Publication type:

Article

Distinct melanocyte subpopulations defined by stochastic expression of proliferation or maturation programs enable a rapid and sustainable pigmentation response.

Published in:

PLoS Biology, 2024, v. 22, n. 8, p. 1, doi. 10.1371/journal.pbio.3002776

By:

Aggarwal, Ayush;
Nasreen, Ayesha;
Sharma, Babita;
Sahoo, Sarthak;
Aswin, Keerthic;
Faruq, Mohammed;
Pandey, Rajesh;
Jolly, Mohit K.;
Singh, Abhyudai;
Gokhale, Rajesh S.;
Natarajan, Vivek T.

Publication type:

Article

Quantifying gene expression variability arising from randomness in cell division times.

Published in:

Journal of Mathematical Biology, 2015, v. 71, n. 2, p. 437, doi. 10.1007/s00285-014-0811-x

By:

Antunes, Duarte;
Singh, Abhyudai

Publication type:

Article

Transcriptional Bursting Explains the Noise–Versus–Mean Relationship in mRNA and Protein Levels.

Published in:

PLoS ONE, 2016, v. 11, n. 7, p. 1, doi. 10.1371/journal.pone.0158298

By:

Dar, Roy D.;
Shaffer, Sydney M.;
Singh, Abhyudai;
Razooky, Brandon S.;
Simpson, Michael L.;
Raj, Arjun;
Weinberger, Leor S.

Publication type:

Article

Efficient computation of stochastic cell-size transient dynamics.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3213-7

By:

Nieto-Acuna, Cesar Augusto;
Vargas-Garcia, Cesar Augusto;
Singh, Abhyudai;
Pedraza, Juan Manuel

Publication type:

Article

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 10, p. 1, doi. 10.1371/journal.pcbi.1010574

By:

Jia, Chen;
Singh, Abhyudai;
Grima, Ramon

Publication type:

Article

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009793

By:

Jia, Chen;
Singh, Abhyudai;
Grima, Ramon

Publication type:

Article

Density fluctuations, homeostasis, and reproduction effects in bacteria.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03348-2

By:

Nemati, Shahla;
Singh, Abhyudai;
Dhuey, Scott D.;
McDonald, Armando;
Weinreich, Daniel M.;
Vasdekis, Andreas. E.

Publication type:

Article

High Cooperativity in Negative Feedback can Amplify Noisy Gene Expression.

Published in:

Bulletin of Mathematical Biology, 2018, v. 80, n. 7, p. 1871, doi. 10.1007/s11538-018-0438-y

By:

Bokes, Pavol;
Lin, Yen Ting;
Singh, Abhyudai

Publication type:

Article

A Derivative Matching Approach to Moment Closure for the Stochastic Logistic Model.

Published in:

Bulletin of Mathematical Biology, 2007, v. 69, n. 6, p. 1909, doi. 10.1007/s11538-007-9198-9

By:

Singh, Abhyudai;
Hespanha, João Pedro

Publication type:

Article

Ploidy and Size at Multiple Scales in the Arabidopsis Sepal.

Published in:

Plant Cell, 2018, v. 30, n. 10, p. 2308, doi. 10.1105/tpc.18.00344

By:

Robinson, Dana O.;
Coate, Jeremy E.;
Singh, Abhyudai;
Hong, Lilan;
Bush, Max;
Doyle, Jeff J.;
Roeder, Adrienne H.K.

Publication type:

Article

Tradeoff between lag time and growth rate drives the plasmid acquisition cost.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38022-6

By:

Ahmad, Mehrose;
Prensky, Hannah;
Balestrieri, Jacqueline;
ElNaggar, Shahd;
Gomez-Simmonds, Angela;
Uhlemann, Anne-Catrin;
Traxler, Beth;
Singh, Abhyudai;
Lopatkin, Allison J.

Publication type:

Article

The dopamine membrane transporter plays an active modulatory role in synaptic dopamine homeostasis.

Published in:

Journal of Neuroscience Research, 2022, v. 100, n. 8, p. 1551, doi. 10.1002/jnr.24965

By:

Formisano, Rosaria;
Rosikon, Katarzyna D.;
Singh, Abhyudai;
Dhillon, Harbinder S.

Publication type:

Article

Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling.

Published in:

PLoS Pathogens, 2019, v. 15, n. 11, p. 1, doi. 10.1371/journal.ppat.1008164

By:

Miura, Michi;
Dey, Supravat;
Ramanayake, Saumya;
Singh, Abhyudai;
Rueda, David S.;
Bangham, Charles R. M.

Publication type:

Article

Inferring single-cell gene expression mechanisms using stochastic simulation.

Published in:

Bioinformatics, 2015, v. 31, n. 9, p. 1428, doi. 10.1093/bioinformatics/btv007

By:

Daigle Jr., Bernie J.;
Soltani, Mohammad;
Petzold, Linda R.;
Singh, Abhyudai

Publication type:

Article

Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00383-z

By:

Nieto, César;
Vargas-García, César Augusto;
Pedraza, Juan Manuel;
Singh, Abhyudai

Publication type:

Article

Author Correction: Disrupting cellular memory to overcome drug resistance.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48797-x

By:

Harmange, Guillaume;
Reyes Hueros, Raúl A.;
Schaff, Dylan L.;
Emert, Benjamin;
Saint-Antoine, Michael;
Kim, Laura C.;
Niu, Zijian;
Nellore, Shivani;
Fane, Mitchell E.;
Alicea, Gretchen M.;
Weeraratna, Ashani T.;
Simon, M. Celeste;
Singh, Abhyudai;
Shaffer, Sydney M.

Publication type:

Article

Disrupting cellular memory to overcome drug resistance.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41811-8

By:

Harmange, Guillaume;
Hueros, Raúl A. Reyes;
Schaff, Dylan L.;
Emert, Benjamin;
Saint-Antoine, Michael;
Kim, Laura C.;
Niu, Zijian;
Nellore, Shivani;
Fane, Mitchell E.;
Alicea, Gretchen M.;
Weeraratna, Ashani T.;
Simon, M. Celeste;
Singh, Abhyudai;
Shaffer, Sydney M.

Publication type:

Article

Cover Image.

Published in:

Synapse, 2020, v. 74, n. 1, p. N.PAG, doi. 10.1002/syn.22141

By:

Formisano, Rosaria;
Mersha, Mahlet D.;
Caplan, Jeff;
Singh, Abhyudai;
Rankin, Catharine H.;
Tavernarakis, Nektarios;
Dhillon, Harbinder S.

Publication type:

Article

Synaptic vesicle fusion is modulated through feedback inhibition by dopamine auto‐receptors.

Published in:

Synapse, 2020, v. 74, n. 1, p. N.PAG, doi. 10.1002/syn.22131

By:

Formisano, Rosaria;
Mersha, Mahlet D.;
Caplan, Jeff;
Singh, Abhyudai;
Rankin, Catharine H.;
Tavernarakis, Nektarios;
Dhillon, Harbinder S.

Publication type:

Article

Noise suppression in stochastic genetic circuits using PID controllers.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009249

By:

Modi, Saurabh;
Dey, Supravat;
Singh, Abhyudai

Publication type:

Article

Mixture distributions in a stochastic gene expression model with delayed feedback: a WKB approximation approach.

Published in:

Journal of Mathematical Biology, 2020, v. 81, n. 1, p. 343, doi. 10.1007/s00285-020-01512-y

By:

Bokes, Pavol;
Borri, Alessandro;
Palumbo, Pasquale;
Singh, Abhyudai

Publication type:

Article

Gene expression noise is affected differentially by feedback in burst frequency and burst size.

Published in:

Journal of Mathematical Biology, 2017, v. 74, n. 6, p. 1483, doi. 10.1007/s00285-016-1059-4

By:

Bokes, Pavol;
Singh, Abhyudai

Publication type:

Article

Microbial metabolic noise.

Published in:

WIREs: Mechanisms of Disease, 2021, v. 13, n. 3, p. 1, doi. 10.1002/wsbm.1512

By:

Vasdekis, Andreas E.;
Singh, Abhyudai

Publication type:

Article

Subcellular localization of the J-protein Sis1 regulates the heat shock response.

Published in:

Journal of Cell Biology, 2021, v. 220, n. 1, p. 1, doi. 10.1083/jcb.202005165

By:

Feder, Zoë A.;
Ali, Asif;
Singh, Abhyudai;
Krakowiak, Joanna;
Xu Zheng;
Bindokas, Vytas P.;
Wolfgeher, Donald;
Kron, Stephen J.;
Pincus, David

Publication type:

Article

Unraveling IFN-I response dynamics and TNF crosstalk in the pathophysiology of systemic lupus erythematosus.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1322814

By:

Van Eyndhoven, Laura C.;
Chouri, Eleni;
Matos, Catarina I.;
Pandit, Aridaman;
Radstake, Timothy R. D. J.;
Broen, Jasper C. A.;
Singh, Abhyudai;
Tel, Jurjen

Publication type:

Article

Identifying mechanisms of regulation to model carbon flux during heat stress and generate testable hypotheses.

Published in:

PLoS ONE, 2018, v. 13, n. 10, p. 1, doi. 10.1371/journal.pone.0205824

By:

Hubbard, Allen H.;
Zhang, Xiaoke;
Jastrebski, Sara;
Lamont, Susan J.;
Singh, Abhyudai;
Schmidt, Carl J.

Publication type:

Article

Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.

Published in:

PLoS Pathogens, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.ppat.1013155

By:

Ribis, John W.;
Nieto, César;
DiBenedetto, Nicholas V.;
Mehra, Anchal;
Kuhn, Pola;
Dong, Qiwen;
Nagawa, Irene;
El Meouche, Imane;
Aldridge, Bree B.;
Dunlop, Mary J.;
Tamayo, Rita;
Singh, Abhyudai;
Shen, Aimee

Publication type:

Article

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pcbi.1004292

By:

Kumar, Niraj;
Singh, Abhyudai;
Kulkarni, Rahul V.

Publication type:

Article

Compound mouse mutants of bZIP transcription factors Mafg and Mafk reveal a regulatory network of non-crystallin genes associated with cataract.

Published in:

Human Genetics, 2015, v. 134, n. 7, p. 717, doi. 10.1007/s00439-015-1554-5

By:

Agrawal, Smriti;
Anand, Deepti;
Siddam, Archana;
Kakrana, Atul;
Dash, Soma;
Scheiblin, David;
Dang, Christine;
Terrell, Anne;
Waters, Stephanie;
Singh, Abhyudai;
Motohashi, Hozumi;
Yamamoto, Masayuki;
Lachke, Salil

Publication type:

Article

Reversible Transitions in a Fluctuation Assay Modify the Tail of Luria–Delbrück Distribution.

Published in:

Axioms (2075-1680), 2023, v. 12, n. 3, p. 249, doi. 10.3390/axioms12030249

By:

Bokes, Pavol;
Hlubinová, Anna;
Singh, Abhyudai

Publication type:

Article

Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 18, p. 9905, doi. 10.1093/nar/gkad725

By:

Lyu, Zhihui;
Villanueva, Patricia;
O'Malley, Liam;
Murphy, Parker;
Augenstreich, Jacques;
Briken, Volker;
Singh, Abhyudai;
Ling, Jiqiang

Publication type:

Article

iSyTE 2.0: a database for expression-based gene discovery in the eye.

Published in:

Nucleic Acids Research, 2018, v. 46, n. D1, p. D875, doi. 10.1093/nar/gkx837

By:

Kakrana, Atul;
Yang, Andrian;
Anand, Deepti;
Djordjevic, Djordje;
Ramachandruni, Deepti;
Singh, Abhyudai;
Huang, Hongzhan;
Ho, Joshua W K;
Lachke, Salil A

Publication type:

Article

Asymmetric cell division requires specific mechanisms for adjusting global transcription.

Published in:

Nucleic Acids Research, 2017, v. 45, n. 21, p. 12401, doi. 10.1093/nar/gkx974

By:

Mena, Adriana;
Medina, Daniel A.;
García-Martínez, José;
Begley, Victoria;
Singh, Abhyudai;
Chávez, Sebastián;
Muñoz-Centeno, Mari C.;
Pérez-Ortín, José E.

Publication type:

Article

Fundamental limits of parasitoid-driven host population suppression: Implications for biological control.

Published in:

PLoS ONE, 2023, v. 18, n. 12, p. 1, doi. 10.1371/journal.pone.0295980

By:

Singh, Abhyudai

Publication type:

Article

Translation regulation by RNA stem-loops can reduce gene expression noise.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-024-05939-8

By:

Çelik, Candan;
Bokes, Pavol;
Singh, Abhyudai

Publication type:

Article

p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.

Published in:

Molecular Systems Biology, 2019, v. 15, n. 9, p. N.PAG, doi. 10.15252/msb.20188685

By:

Harton, Marie D;
Koh, Woo Seuk;
Bunker, Amie D;
Singh, Abhyudai;
Batchelor, Eric

Publication type:

Article

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability.

Published in:

Molecular Systems Biology, 2012, v. 8, n. 1, p. 1, doi. 10.1038/msb.2012.38

By:

Singh, Abhyudai;
Razooky, Brandon S;
Dar, Roy D;
Weinberger, Leor S

Publication type:

Article