Krishna Choudhary, PhD
Postdoctoral Scholar
Diabetes Center
School of Medicine

Publications (21)

Top publication keywords:
Quality ControlModels, GeneticSequence Analysis, RNAGene Expression Regulation, BacterialProgramming LanguagesRNA, MessengerEntorhinal CortexEscherichia coliGene Regulatory NetworksLac OperonSingle-Cell AnalysisGATA4 Transcription FactorRNAModels, NeurologicalSoftware

• Spontaneous persistent activity and inactivity in vivo reveals differential cortico-entorhinal functional connectivity.
  Nature communications 2024 Choudhary K, Berberich S, Hahn TTG, McFarland JM, Mehta MR
• A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors.
  Development (Cambridge, England) 2023 Krup AL, Winchester SAB, Ranade SS, Agrawal A, Devine WP, Sinha T, Choudhary K, Dominguez MH, Thomas R, Black BL, Srivastava D, Bruneau BG
• Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.
  Circulation 2022 Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van …
• Transcription factor protein interactomes reveal genetic determinants in heart disease.
  Cell 2022 Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, …
• Transient Cell Cycle Induction in Cardiomyocytes to Treat Subacute Ischemic Heart Failure.
  Circulation 2022 Abouleisa RRE, Salama ABM, Ou Q, Tang XL, Solanki M, Guo Y, Nong Y, McNally L, Lorkiewicz PK, Kassem KM, Ahern BM, Choudhary K, Thomas R, Huang Y, Juhardeen HR, Siddique A, Ifthikar Z, Hammad SK, …

Show all (16 more) Hide

• Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.
  Nature aging 2021 Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Aery Jones EA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, …
• Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.
  Nature aging 2021 Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Jones EAA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, …
• Introducing R as a smart version of calculators enables beginners to explore it on their own.
  F1000Research 2021 Choudhary K, Pico AR
• scNetViz: from single cells to networks using Cytoscape.
  F1000Research 2021 Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH
• Phenotypic Differences between the Alzheimer's Disease-Related hAPP-J20 Model and Heterozygous Zbtb20 Knock-Out Mice.
  eNeuro 2021 Gulbranson DR, Ho K, Yu GQ, Yu X, Das M, Shao E, Kim D, Zhang WJ, Choudhary K, Thomas R, Mucke L
• Urn models for stochastic gene expression yield intuitive insights into the probability distributions of single-cell mRNA and protein counts.
  Physical biology 2020 Choudhary K, Narang A
• Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP.
  Nature communications 2020 Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA
• Analytical Expressions and Physics for Single-Cell mRNA Distributions of the lac Operon of E. coli.
  Biophysical journal 2019 Choudhary K, Narang A
• Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.
  Genetics 2019 Lai YH, Choudhary K, Cloutier SC, Xing Z, Aviran S, Tran EJ
• dStruct: identifying differentially reactive regions from RNA structurome profiling data.
  Genome biology 2019 Choudhary K, Lai YH, Tran EJ, Aviran S
• Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.
  Nucleic acids research 2018 Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR
• Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.
  Quantitative biology (Beijing, China) 2017 Choudhary K, Deng F, Aviran S
• SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.
  Bioinformatics (Oxford, England) 2017 Choudhary K, Ruan L, Deng F, Shih N, Aviran S
• Metrics for rapid quality control in RNA structure probing experiments.
  Bioinformatics (Oxford, England) 2016 Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S
• Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments.
  PloS one 2014 Choudhary K, Oehler S, Narang A
• Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome.
  Systems and synthetic biology 2011 Grover A, Pande A, Choudhary K, Gupta K, Sundar D