Ninad Oak, Ph. D.
After completing my PhD in Genetics at Baylor College of Medicine, I joined St. Jude Children’s Research Hospital as a Bioinformatics Research Scientist. The focus of my current work is to identify the genetic basis of childhood cancer predisposition. During my PhD, I developed a bioinformatic tool, ADmiRE, to understand the impact of microRNA single nucleotide variation in human population and disease datasets.
Research Interests
- Cancer predisposition in childhood and adult cancers.
- Understanding the role of non-coding RNA (microRNA) sequence variation in human population and diseases.
In addition to doing science, I love to live-sketch scientific talks. You can find all of my picture summaries here.
Publications
An updated list of published and unpublished papers is listed in reverse chronological order.
- Oak N, Ghosh R, Huang KL, Wheeler DA, Ding L, Plon SE. Framework for microRNA variant annotation and prioritization using human population and disease datasets. Human Mutation. 2019; 40(1):73-89 PMID: 30302893
- Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, …, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018; 173(2):355-370.e14. NIHMSID: NIHMS957308 PMID: 29625052
- Ghosh R, Oak N, Plon SE. Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines. Genome biology. 2017; 18(1):225. PMID: 29179779, PMCID: PMC5704597
- Chandrani P, Upadhyay P, Iyer P, Tanna M, Shetty M, Raghuram GV, Oak N, Singh A, Chaubal R, Ramteke M, Gupta S, Dutt A. Integrated genomics approach to identify biologically relevant alterations in fewer samples. BMC genomics. 2015; 16:936. PMID: 26572163, PMCID: PMC4647579
- Oak N, Jayaraman VK. Identification of ligand binding pockets on nuclear receptors by machine learning methods. Protein and peptide letters. 2014; 21(8):808-14. PMID: 23855664
Highlights of PhD work ADmiRE: Annotative Database of miRNA Elements
- Annotation wrapper for adding comprehensive miRNA annotations to a user supplied list of variants (tab-separated format)
- Adds information for miRNA domains, gnomAD mean allele frequency percentiles, evolutionary conservation, etc.
- Published in Human Mutation
Scientific Coverage
- PLOS ECR blog coverage - A blog by Caitlin Grzeskowiak highlighting my sketchnote style of note-taking.