Ninad Oak, PhD

Lead Bioinformatics Research Scientist

Departments

Oncology Department

Divisions

Cancer Predisposition Division

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 Certification, Govt. of India, All India Rank 5
2009-2011 G. N. Ramachandran Fellowship, Govt. 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

Contact Information

Ninad Oak, PhD Cancer Presdisposition/Oncology MS 1135, Room IA6218.5 St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-3678

Email: ninad.oak@stjude.org
Phone: 901-595-7738

Selected Publications

Bloom M, Oak N, Baskin-Doerfler R, Feng R, Iacobucci I, Baviskar P, Zhao X, Stroh AN, Li C, Ozark P, Tillman H, Li Y, Verbist KC, Albeituni S, Scott DC, King MT, McKinney Freeman SL, Weiss MJ, Yang JJ, Nichols KE. ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice. Blood Adv. 2023 Jul 31:bloodadvances.2022009313. doi: 10.1182/bloodadvances.2022009313. Epub ahead of print. PMID: 37522715.

Albeituni S, Oak N, Tillman HS, Stroh A, Keenan C, Bloom M, Nichols KE. Cellular and transcriptional impacts of Janus kinase and/or IFN-gamma inhibition in a mouse model of primary hemophagocytic lymphohistiocytosis. Front Immunol. 2023 Apr 27;14:1137037. doi: 10.3389/fimmu.2023.1137037. PMID: 37228616; PMCID: PMC10204641.

McGee RB, Oak N, Harrison L, Xu K, Nuccio R, Blake AK, Mostafavi R, Lewis S, Taylor LM, Kubal M, Ouma A, Hines-Dowell SJ, Cheng C, Furtado LV, Nichols KE. Pathogenic Variants in Adult-Onset Cancer Predisposition Genes in Pediatric Cancer: Prevalence and Impact on Tumor Molecular Features and Clinical Management. Clin Cancer Res. 2023 Apr 3;29(7):1243-1251. doi: 10.1158/1078-0432.CCR-22-2482. PMID: 36693186.

Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K, Tithi SS, Goldin LR, Rotunno M, Caporaso N, Vogt A, Flamish D, Wyatt K, Liu J, Tucker M, Hahn CN, Brown AL, Scott HS, Mullighan C, Nichols KE, Metzger ML, McMaster ML, Yang JJ, Rampersaud E. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood. 2023 Mar 16;141(11):1293-1307. doi: 10.1182/blood.2022016056. PMID: 35977101; PMCID: PMC10082357.

Casado-Garcia A, Isidro-Hernandez M, Oak N, Mayado A, Mann-Ran C, Raboso-Gallego J, Aleman-Arteaga S, Buhles A, Sterker D, Sanchez EG, Martinez-Cano J, Blanco O, Orfao A, Alonso-Lopez D, De Las Rivas J, Riesco S, Prieto-Matos P, Gonzalez-Murillo A, Garcia Criado FJJ, Garcia Cenador MB, Radimerski T, Ramirez-Orellana M, Cobaleda C, Yang JJ, Vicente-Duenas C, Weiss A, Nichols KE, Sanchez-Garcia I. Transient inhibition of the JAK/STAT pathway prevents B-ALL development in genetically predisposed mice. Cancer Res Feb 7, 2022.

Salek M, Oak N, Hines MR, Maciaszek JL, Tatevossian R, Sharma A, Nichols KE, Campbell PK. Development of BRAFV600E-positive acute myeloid leukemia in a patient on long-term dabrafenib for multisystem LCH. Blood Adv Jan 7, 2021.

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: August 2023

Full list of publications