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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
  • Determine mechanism of action for known cancer predisposition genes using functional genomic characterization of genetic mouse models

Selected Publications

Oak N, Cherniack AD, Mashl RJ, Hirsch FR, Ding L, Beroukhim R, Gümüş ZH, Plon SE, Huang KL. Ancestry-specific predisposing germline variants in cancer. Genome Med May 29;12(1):51, 2020. doi: 10.1186/s13073-020-00744-3. PMC7260738.

Nishii R, Baskin-Doerfler R, Yang W, Oak N, Zhao X, Yang W, Hoshitsuki K, Bloom M, Verbist KC, Burns MA, Li Z, Lin TN, Qian M, Moriyama T, Gastier-Foster JM, Rabin KR, Raetz E, Mullighan CG, Pui CH, Yeoh AEJ, Zhang J, Metzger M, Klco JM, Hunger SP, Newman S, Wu G, Loh ML, Nichols KE, Yang JJ. Molecular Basis of ETV6-Mediated Predisposition to Childhood Acute Lymphoblastic Leukemia. Blood 2020 Jul 21;. doi: 10.1182/blood.2020006164. [Epub ahead of print] PMC7819760.

Maciaszek JL, Oak N, Nichols KE. Recent advances in Wilms' tumor predisposition. Hum Mol Genet Oct 20;29(R2):R138-R149, 2020. doi: 10.1093/hmg/ddaa091. PMID: 32412586.

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

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

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;173(2):355-370.e14, 2018. doi: 10.1016/j.cell.2018.03.039.

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

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: February 2021