Krishna Choudhary

Krishna Choudhary
University of California, San Francisco | UCSF · Department of Microbiology and Immunology

Doctor of Philosophy

About

32
Publications
5,889
Reads
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198
Citations
Citations since 2016
30 Research Items
193 Citations
201620172018201920202021202201020304050
201620172018201920202021202201020304050
201620172018201920202021202201020304050
201620172018201920202021202201020304050
Additional affiliations
September 2014 - December 2018
University of California, Davis
Position
  • PhD Student
July 2008 - July 2013
Indian Institute of Technology Delhi
Position
  • B. Tech & M. Tech

Publications

Publications (32)
Article
Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the single-cell count distributions of mRNA and protein molecules can yield valuable insights into mechanisms underlying gene expression. Solutions of chemical master equations are available for various kinetic schemes but, even for the basic...
Article
Full-text available
RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not ac...
Preprint
Full-text available
We obtain addition formulas for $_{p}F_{p}$ and $_{p+1}F_{p}$ generalized hypergeometric functions with general parameters. These are utilized in conjunction with integral representations of these functions to derive Kummer- and Euler-type transformations that express $_{p}F_{p}\left(x\right)$ and $_{p+1}F_p\left(x\right)$ in the form of sums of $_...
Preprint
Full-text available
Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify...
Article
Background GATA4 (GATA-binding protein 4), a zinc finger–containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is...
Article
Rapid technological advances in the past decades have enabled molecular biologists to generate large-scale and complex data with affordable resource investments, or obtain such data from public repositories. Yet, many graduate students, postdoctoral scholars, and senior researchers in the biosciences find themselves ill-equipped to analyze large-sc...
Article
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA...
Article
Background: The regenerative capacity of the heart after myocardial infarction (MI) is limited. Our previous study showed that ectopic introduction of Cdk1/CyclinB1 and Cdk4/CyclinD1 complexes (4F) promotes cardiomyocyte proliferation in 15-20% of infected cardiomyocytes in vitro and in vivo and improves cardiac function after MI in mice. Methods:...
Article
Congenital heart disease (CHD) is present in 1% of live births, yet despite large-scale genomic sequencing efforts, identification of causal mutations remains a challenge. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of GATA4 and TBX5, two transcription factors whose mutation cause CHDs. Defining the GATA4...
Article
Full-text available
The evident genetic, pathological and clinical heterogeneity of Alzheimer’s disease (AD) poses challenges for traditional drug development. We conducted a computational drug-repurposing screen for drugs to treat apolipoprotein E4 (APOE4)-related AD. We first established APOE genotype-dependent transcriptomic signatures of AD by analyzing publicly a...
Article
Full-text available
Rapid technological advances in the past decades have enabled molecular biologists to generate large-scale and complex data with affordable resource investments, or obtain such data from public repositories. Yet, many graduate students, postdoctoral scholars, and senior researchers in the biosciences find themselves ill-equipped to analyze large-sc...
Article
Full-text available
Single-cell RNA-sequencing (scRNA-seq) has revolutionized molecular biology and medicine by enabling high-throughput studies of cellular heterogeneity in diverse tissues. Applying network biology approaches to scRNA-seq data can provide useful insights into genes driving heterogeneous cell-type compositions of tissues. Here, we present scNetViz — a...
Article
Diverse gene products contribute to the pathogenesis of Alzheimer's disease (AD). Experimental models have helped elucidate their mechanisms and impact on brain functions. Human amyloid precursor protein (hAPP) transgenic mice from line J20 (hAPP-J20 mice) are widely used to simulate key aspects of AD. However, they also carry an insertional mutati...
Preprint
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains a challenge despite large-scale genomic sequencing efforts. We hypothesized that genetic determinants for CHDs may lie in protein interactomes of GATA4 and TBX5, two transcription factors that cause CHDs. Defining their interactomes in hum...
Preprint
Full-text available
The regenerative capacity of the heart after myocardial infarction (MI) is limited. Our previous study showed that ectopic introduction of Cdk1/CyclinB1 and Cdk4/CyclinD1 complexes (4F) promotes cardiomyocyte proliferation in 15-20% of infected cardiomyocytes in vitro and in vivo and improves cardiac function after MI. Here, we aim to identify the...
Article
Rationale: The regenerative capacity of the heart to repair itself after myocardial infarction (MI)is limited. Our previous study showed that ectopic introduction of Cdk1/CyclinB1 andCdk4/CyclinD1 complexes (4F) promotes cardiomyocyte proliferation in vitro and in vivo andimproves cardiac function after MI. However, its clinical application is limi...
Article
Myocardial infarction causes irreversible loss of cardiomyocytes (CMs) and often leads to heart failure. To replace the lost cells, we identified a combination of cell-cycle regulators that induces stable cytokinesis in adult post-mitotic cells. Specifically, adenoviral overexpression of cyclin-dependent kinase 1 (CDK1), CDK4, cyclin B1, and cyclin...
Article
Full-text available
RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal and tRNAs. Three proteins found in both complexes, Pop1, Pop6, and Pop7 are also telomerase-associated. Here, we determine how temperature sensitive POP1 and POP6 alleles affect yeast telomerase. At permissive temperatures, mutant Pop1/6 h...
Preprint
Full-text available
Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the count distributions of mRNA and protein molecules in single cells can yield valuable insights into mechanisms of gene regulation. Solutions of chemical master equations are available for various kinetic schemes but, even for the models of...
Article
Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for messenger RNA (mRNA) and protein distributions. The lac operon of Escherichia coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many oper...
Article
RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First,...
Preprint
Full-text available
Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for mRNA and protein distributions. The lac operon of E. coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many operons. Although this system...
Article
Full-text available
In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic...
Article
Background Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental adv...
Article
To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approach...
Article
Motivation: The diverse functionalities of RNA can be attributed to its capacity to form complex and varied structures. The recent proliferation of new structure probing techniques coupled with high-throughput sequencing has helped RNA studies expand in both scope and depth. Despite differences in techniques, most experiments face similar challeng...
Article
Full-text available
Although noisy gene expression is widely accepted, its mechanisms are subjects of debate, stimulated largely by single-molecule experiments. This work is concerned with one such study, in which Choi et al., 2008, obtained real-time data and distributions of Lac permease in E. coli. They observed small and large protein bursts in strains with and wi...
Article
Full-text available
Recent studies provide a glimpse of future potential therapeutic applications of custom-designed zinc finger proteins in achieving highly specific genomic manipulation. Custom-design of zinc finger proteins with tailor-made specificity is currently limited by the availability of information on recognition helices for all possible DNA targets. Howev...

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Projects

Project (1)
Project
Develop statistical methods and software to evaluate data quality and perform comparative analysis.