Jayaram Kancherla

Jayaram Kancherla
Genentech

Masters in Computer Science

About

34
Publications
7,342
Reads
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1,228
Citations
Citations since 2017
30 Research Items
1199 Citations
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Additional affiliations
January 2016 - October 2020
University of Maryland, College Park
Position
  • Researcher
August 2013 - December 2015
United States Environmental Protection Agency
Position
  • Fellow
September 2011 - August 2013
United States Environmental Protection Agency
Position
  • Researcher
Education
August 2009 - June 2011
North Carolina State University
Field of study
  • Computer Science
September 2005 - April 2009
Acharya Nagarjuna University
Field of study
  • Computer Science and Engineering

Publications

Publications (34)
Article
Full-text available
Motivation: Genomic data repositories like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Bioconductor's AnnotationHub and ExperimentHub etc., provide public access to large amounts of genomic data as flat files. Researchers often download a subset of data files from these repositories to perform exploratory data analysis....
Article
Full-text available
Large studies profiling microbial communities and their association with healthy or disease phenotypes are now commonplace. Processed data from many of these studies are publicly available but significant effort is required for users to effectively organize, explore and integrate it, limiting the utility of these rich data resources. Effective inte...
Article
Full-text available
Interactive and integrative data visualization tools and libraries are integral to exploration and analysis of genomic data. Web based genome browsers allow integrative data exploration of a large number of data sets for a specific region in the genome. Currently available web-based genome browsers are developed for specific use cases and datasets,...
Article
PURPOSE In this work, we introduce CDGnet (Cancer-Drug-Gene Network), an evidence-based network approach for recommending targeted cancer therapies. CDGnet represents a user-friendly informatics tool that expands the range of targeted therapy options for patients with cancer who undergo molecular profiling by including the biologic context via path...
Article
Background: Recent years have resulted in tremendous progress in understanding Alzheimer's disease (AD) via the generation and analysis of multi-omic data. In addition, the BRAIN initiative has been mapping gene expression in the normal brain. However, a barrier for the broad usage of these data has been limited access and the requirement for info...
Article
Full-text available
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals¹. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities t...
Article
Full-text available
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1–3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigen...
Article
Full-text available
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcripto...
Article
The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analy...
Article
Recent years have resulted in tremendous progress in understanding Alzheimer’s disease via the generation and analysis of multi‐omic data. In addition, the BRAIN initiative has been mapping gene expression in the normal brain, which is important in understanding disease. However, a barrier for the broad usage of these data has been limited access a...
Preprint
Full-text available
We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell tran...
Preprint
Full-text available
The gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, sorted, single cell/nucleus) and epigenomics data, from multiple species, time points and tissues in...
Article
Full-text available
The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analy...
Article
e14065 Background: It is becoming increasingly common for cancer patients to undergo molecular profiling of their tumors in order to see whether there are any actionable DNA, gene expression, or protein expression signatures. For example, individuals with ER+ or HER2+ breast cancer or KRAS wild type (non-mutated) colorectal cancer are prescribed sp...
Preprint
Full-text available
The primary motor cortex (M1) is essential for voluntary fine motor control and is functionally conserved across mammals. Using high-throughput transcriptomic and epigenomic profiling of over 450,000 single nuclei in human, marmoset monkey, and mouse, we demonstrate a broadly conserved cellular makeup of this region, whose similarity mirrors evolut...
Preprint
Full-text available
Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningfu...
Article
Full-text available
Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningfu...
Preprint
Full-text available
Genomic data repositories like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Bioconductor's AnnotationHub and ExperimentHub etc., provide public access to large amounts of genomic data as flat files. Researchers often download a subset of files data from these repositories to perform their data analysis. As these data repos...
Article
Motivation: Integrative analysis of genomic data that includes statistical methods in combination with visual exploration has gained widespread adoption. Many existing methods involve a combination of tools and resources: user interfaces that provide visualization of large genomic datasets, and computational environments that focus on data analyse...
Preprint
Full-text available
Single cell RNA sequencing (scRNA-seq) provides a rich view into the heterogeneity underlying a cell population. However single-cell data are usually noisy and very sparse due to the presence of dropout genes. In this work we propose an approach to impute missing gene expressions in single cell data using generative adversarial networks (GANs). By...
Preprint
Full-text available
In this work, we introduce CDGnet, an evidence-based network approach for recommending targeted cancer therapies, available as a user-friendly informatics tool. Our approach can be used to expand the range of options of targeted therapies for cancer patients who undergo molecular profiling. It considers biological pathway information specifically b...
Article
We developed the metagenomeFeatures R Bioconductor package along with annotation packages for three 16S rRNA databases (Greengenes, RDP, and SILVA) to facilitate working with 16S rRNA databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures f...
Preprint
Full-text available
We developed the metagenomeFeatures R Bioconductor package along with annotation packages for the three primary 16S rRNA databases (Greengenes, RDP, and SILVA) to facilitate working with 16S rRNA sequence databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databa...
Article
Knowledge of the ontogeny of Phase I and Phase II metabolizing enzymes may be used to inform children’s vulnerability based upon likely differences in internal dose from xenobiotic exposure. This might provide a qualitative assessment of toxicokinetic (TK) variability and uncertainty pertinent to early lifestages and help scope a more quantitative...
Preprint
Full-text available
Along with the survey techniques of 16S rRNA amplicon and whole-metagenome shotgun sequencing, an array of tools exists for clustering, taxonomic annotation, normalization, and statistical analysis of microbiome sequencing results. Integrative and interactive visualization that enables researchers to perform exploratory analysis in this feature ric...
Article
Full-text available
The U.S. Environmental Protection Agency’s (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches in order to support development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds...
Article
Full-text available
Background: Humans are exposed to thousands of man-made chemicals in the environment. Some chemicals mimic natural endocrine hormones and, thus, have the potential to be endocrine disruptors. Most of these chemicals have never been tested for their ability to interact with the estrogen receptor (ER). Risk assessors need tools to prioritize chemica...

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Projects

Projects (2)
Project
The Toxicity Forecaster ("ToxCast") project aims to identity potentially harmful chemicals among the thousands in our environment. ToxCast makes use of advances in vitro, high throughput testing, bioinformatics, and predictive mathematical modeling. (https://doi.org/10.1093/toxsci/kfl103) https://www.epa.gov/chemical-research/toxicity-forecasting
Archived project
This project was intended to be a demonstration of the use of predictive computational models on HTS data including ToxCast and Tox21 assays to prioritize a large chemical universe of ~32k unique structures for one specific molecular target – the estrogen receptor. CERAPP combined multiple computational models for prediction of estrogen receptor activity, and used the predicted results of these models to build a unique consensus model. The models were developed in collaboration between 17 groups in the U.S. and Europe and applied to predict the common set of chemicals to be prioritized. The final consensus predicted 4k chemicals as actives to be considered as high priority for further testing and ~6k as suspicious chemicals. This abstract does not necessarily reflect U.S. EPA policy