Nitesh Turaga

Nitesh Turaga
Carnegie Mellon University | CMU · Computational Biology Department

About

23
Publications
6,302
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1,735
Citations
Introduction
Nitesh does research in Bioinformatics, Computing in Mathematics, Natural Science, Engineering and Medicine and Algorithms. Their most recent publication is 'Bioconda: A sustainable and comprehensive software distribution for the life sciences'.

Publications

Publications (23)
Article
Full-text available
The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with othe...
Article
PURPOSE Institutional efforts toward the democratization of cloud-scale data and analysis methods for cancer genomics are proceeding rapidly. As part of this effort, we bridge two major bioinformatic initiatives: the Global Alliance for Genomics and Health (GA4GH) and Bioconductor. METHODS We describe in detail a use case in pancancer transcriptom...
Article
Full-text available
Motivation: Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected datasets and biological reasoning on the relevance of resulti...
Preprint
Full-text available
The Rocker Project provides widely-used Docker images for R across different application scenarios. This articles surveys downstream projects building upon Rocker and presents the current state of R packages for managing Docker images and controlling containers. These use cases and the variety of applications demonstrate the power of Rocker specifi...
Article
Full-text available
The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers. These use cases cover diverse topics such as package development, r...
Preprint
Full-text available
Background: Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected data sets and biological reasoning on the relevance of resulti...
Article
Full-text available
The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and analytical methods. Here, we detail the process we u...
Article
Full-text available
Solute carrier organic anion (SLCO) gene families encode organic anion transport proteins, which are transporters that up-take a number of substrates including androgens. Among them, high expression of SLCO2B1 is known to associate with the resistance to androgen deprivation therapy in prostate cancer (PCa). We hypothesized that high expression of...
Preprint
Full-text available
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 co...
Article
Purpose: To establish a novel panel of cancer-specific methylated genes for cancer detection and prognostic stratification of early stage non-small cell lung cancer (NSCLC). Experimental design: Identification of differentially methylated regions (DMRs) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utili...
Article
Full-text available
Clinically useful molecular tools to triage women for a biopsy upon referral to colposcopy are not available. We aimed to develop a molecular panel to detect cervical intraepithelial neoplasia (CIN) grade 2 or higher lesions (CIN2+) in women with abnormal cervical cytology and high-risk HPV (HPV+). We tested a biomarker panel in cervical epithelium...
Article
Full-text available
Galaxy provides a web-based platform for interactive, large-scale data analyses, which integrates bioinformatics tools written in a variety of languages. A substantial number of these tools are written in the R programming language, which enables powerful analysis and visualization of complex data. The Bioconductor Project provides access to these...
Article
We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV) and human genes that can discriminate between CIN2+ and normal/CIN1 patients in liquid prep samples and in Transrenal DNA (TrDNA) isolated from urine. Using Human DNA methylation arrays and massively parallel Next Generation Sequencing (NGS) for Discov...
Article
Full-text available
High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has le...
Article
Introduction: Head and neck squamous cell carcinoma (HNSCC) survival has steadily increased over the last 50 years, but the survival gap between African Americans (AAs) and Non-Latino Whites (NLWs) has remained practically unchanged. Most of the survival differences in HNSCC survival are due to HPV infection among oropharyngeal patients, which is m...
Code
Command-line utilities to assist in developing tools for the Galaxy Project. http://galaxyproject.org
Article
Introduction Several groups have identified hundreds of genes differentially methylated in head and neck squamous cell carcinoma (HNSCC) using genome-wide technologies. However, there is a paucity of studies examining differential methylation in HNSCC anatomic subsites. Objective Our principal objective is to determine DNA methylation differences b...
Article
Full-text available
Butyrylcholinesterase may have a role in a number of metabolic functions and could affect the expression of insulin resistance syndrome. We present our integrated work using clinical, biochemical and bioinformatic approaches to delineate the possible function of this enzyme. Initially, we constructed a phylogenic tree with nucleotides and amino aci...

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