Ninad Oak, PhD

Ninad Oak, PhD

  • Bioinformatics Research Scientist

Departments

Divisions

Education

PhD  Baylor College of Medicine, Houston TX

MSc  Bioinformatics Center, University of Pune, Pune, India

BSc  Pravara Institute of Medical Sciences, Loni, India

Honors and Awards

  • 2011 Bioinformatics National CertificationGovt. of India, All India Rank 5
  • 2009-2011 G. N. Ramachandran FellowshipGovt. of India                      
  • 2009-2011 Dept. of Biotechnology Academic Fellowship, Govt. of India

About

I joined St. Jude as a bioinformatics research scientist in the Cancer Predisposition Division with a focus on understanding the germline predisposition to childhood and adult cancers. Prior to joining St. Jude, I worked with large-scale genomic projects such as The Cancer Genome Atlas (TCGA) to understand germline predisposition in adult cancers. I developed a bioinformatic tool, ADmiRE, to identify novel patterns of microRNA variation from large human population and adult cancer datasets.

Outside of research, I love to draw sketchnotes of many scientific talks and regularly post them on my Twitter (@ninadoak).

Research Interests

  • Development of bioinformatic workflows to optimize variant prioritization for germline cancer predisposition gene discovery
  • Understand functional consequences of causal genetic predisposition loci

Selected Publications

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. Hum Mutat. Jan 2019 ;40(1):73-89. doi: 10.1002/humu.23668. 2019 

Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA. Enrichment of Heterozygous Germline RECQL4 Loss-of-Function Variants in Pediatric Osteosarcoma. Cold Spring Harb Mol Case Stud. Oct 11 2019. doi: 10.1101/mcs.a004218.  2019

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell.  Apr 5 2018;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. 2018

Oak N, Plon SE. Insights from the 2018 Biology of Genomes meeting. Genome Biol. Sep 28, 2018 ;19(1):146. doi: 10.1186/s13059-018-1542-x. 2018

Ghosh R, Oak N, Plon SE. Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines. Genome Biol. Nov 28 2017 ;18(1):225. doi: 10.1186/s13059-017-1353-5. 2017 

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. Nov 14 2015;16:936. doi: 10.1186/s12864-015-2138-4. 2015

Oak N, Jayaraman VK. Identification of ligand binding pockets on nuclear receptors by machine learning methods. Protein Pept Lett. ;21(8):808-14. 2014

Last update: November 2019