Ramakrishnan Rajagopalan, PhD, (Ramki) is the Director of Translational Bioinformatics in the Division of Genomic Diagnostics at CHOP and an Assistant Professor in the Department of Pathology and Laboratory Medicine at CHOP and the University of Pennsylvania. He uses cutting edge sequencing technologies and bioinformatics tools for advancing genomic diagnostics.

Education and Training

Graduate Degree

PhD in Biomedical Engineering - Drexel University, Philadelphia, PA
MS in Biomedical Engineering - Louisiana Tech University, Ruston, LA

Titles and Academic Titles

Director, Translational Bioinformatics

Assistant Professor with the Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania

Departments and Services




Rajagopalan R*, Gilbert MA*, McEldrew DA, Nassur JA, Loomes KM, Piccoli DA, Krantz ID, Conlin LK, Spinner NB. Genome sequencing increases diagnostic yield in clinically diagnosed Alagille syndrome patients with previously negative test results, Genetics In Medicine, 23(2): 323-330, 2020. *equal contributions

Rajagopalan R, Murrell JR, Luo M, Conlin LK. A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data, Genome Medicine, 12, Article number: 14 (2020).

Rajagopalan R, Tsai EA, Grochowski CM, Kelly SM, Loomes KM, Spinner NB, Devoto M. Exome sequencing in individuals with isolated Biliary Atresia, Scientific Reports, 10, Article number: 2709 (2020).

Zhao X, Lorent K, Escobar-Zarate D, Rajagopalan R, Loomes KM, Gillespie K, Mesaros C, Estrada MA, Blair I, Winkler JD, Spinner NB, Devoto M, Pack MA. Impaired redox and protein homeostasis as risk factors and therapeutic targets in toxin-induced biliary atresia, Gastroenterology, 159(3): 1068-1084, 2020.

Gilbert MA, Schultz-Rogers L, Rajagopalan R, Grochowski CM, Wilkins BJ, Biswas S, Conlin LK, Dhamija R, Pack MA, Klee EW, Piccoli DA, Spinner NB. Protein-elongating mutations in MYH11 are implicated in a dominantly-inherited smooth muscle dysmotility syndrome with severe esophageal, gastric, and intestinal disease, Human Mutation, 2020:1-20.


Uprety P, Curtis D, Elkan M, Fink J, Rajagopalan R, Zhao C, Bittinger K, Mitchell S, Ulloa ER, Hopkins S, Graf EH. Association of Enterovirus D68 with Acute Flaccid Myelitis, Philadelphia, Pennsylvania, USA, 2009-2018. Emerging Infectious Diseases, 25(9):1676-1672.

Levy-Sakin M, Pastor S, Mostovoy Y, Li L, Leung AKY, McCaffrey J, Young E, Lam ET, Hastie AR, Wong KHY, Chung CYL, Ma W, Sibert J, Rajagopalan R, Jin N, Chow EYC, Chu C, Poon A, Lin C, Naguib A, Wang WP, Cao H, Chan TF, Yip KY, Xiao M, Kwok PY. Genome maps across 26 human populations reveal population-specific patterns of structural variation, Nature Communications 10(1), 1025.

Berauer JP, Mezina AI, Okou DT, Sabo A, Muzny DM, Gibbs RA, Hegde MR, Chopra P, Cutler DJ, Perlmutter DH, Bull LN, Thompson RJ, Loomes KM, Spinner NB, Rajagopalan R, Guthery SL, Moore B, Yandell M, Harpavat S, Magee JC, Kamath BM, Molleston JP, Bezerra JA, Murray KF, Alonso EM, Rosenthal P, Squires RH, Wang KS, Finegold MJ, Russo P, Sherker AH, Sokol RJ, Karpen SJ; Childhood Liver Disease Research Network (ChiLDReN). Identification of PKD1L1 Gene Variants in Children with the Biliary Atresia Splenic Malformation Syndrome, Hepatology, 70(3):899-910.

Mills JA, Herrera PS, Kaur M, Leo L, McEldrew D, Tintos-Hernandez JA, Rajagopalan R, Gagne A, Zhang Z, Ortiz-Gonzalez XR, Krantz ID. NIPBL haploinsufficiency reveals a constellation of transcriptome disruptions in the pluripotent and cardiac states, Scientific Reports 8 (1), 1056.

Romasko EJ, Devkota B, Biswas S, Jayaraman V, Rajagopalan R, Dulik MC, Thom CS, Choi J, Jairam S, Scarano MI, Krantz ID, Spinner NB, Conlin LK, Lambert MP. Utility and limitations of exome sequencing in the molecular diagnosis of pediatric inherited platelet disorders, American Journal of Hematology, 93 (1), 8-16.


Young E, Pastor S, Rajagopalan R, McCaffrey J, Sibert J, Mak ACY, Kwok PY, Riethman H, Xiao M. High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres, Nucleic Acids Research, Epub Feb 9 2017.

Lurier EB, Dalton D, Dampier W, Raman P, Nassiri S, Ferraro NM, Rajagopalan R, Sarmady M, Spiller KL. Transcriptome analysis of IL-10-stimulated (M2c) macrophages by next-generation sequencing, Immunobiology, Jul;222(7):847-856.

Rajagopalan R, Grochowski CM, Gilbert MA, Falsey AM, Coleman K, Romero R, Loomes KM, Piccoli DA, Devoto M, Spinner NB. Compound heterozygous mutations in NEK8 in siblings with end-stage renal disease with hepatic and cardiac anomalies, American Journal of Medical Genetics, 170(3), 750-753.

Li MH, Abrudan JL, Dulik MC, Sasson A, Brunton J, Jayaraman V, Dugan N, Haley D, Rajagopalan R, Biswas S, Sarmady M, DeChene ET, Deardorff MA, Wilkens A, Noon SE, Scarano MI, Santani AB, White PS, Pennington J, Conlin LK, Spinner NB, Krantz ID, Vetter VL. Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death, Human Genomics 9(1).

Izumi K, Nakato R, Zhang Z, Edmondson AC, Noon S, Dulik MC, Rajagopalan R, Venditti CP, Gripp K, Samanich J, Zackai EH, Deardorff MA, Clark D, Allen JL, Dorsett D, Misulovin Z, Komata M, Bando M, Kaur M, Katou Y, Shirahige K, Krantz ID. Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking super elongation complex and cohesin, Nature Genetics 47(4), 338-344.

Tsai EA, Grochowski CM, Falsey AM, Rajagopalan R, Wendel D, Devoto M, Krantz ID, Loomes KM, Spinner NB. Heterozygous Deletion of FOXA2 Segregates with Disease in a Family with Heterotaxy, Panhypopituitarism, and Biliary Atresia, Human Mutation 36(6), 631-637.

Grochowski CM, Rajagopalan R, Falsey AM, Loomes KM, Piccoli DA, Krantz ID, Devoto M, Spinner NB. Exome sequencing reveals compound heterozygous mutations in ATP8B1 in a JAG1/ NOTCH2 mutation- negative patient with clinically diagnosed Alagille Syndrome, American Journal of Medical Genetics, 167A (4), 891-893.

Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John SE, Hebbar P, Behbehani K, Thanaraj TA. Genetic Substructure of Kuwaiti Population Reveals Migration History. PLoS ONE 8(9): e74913.

Gaynor JW, Jarvik GP, Gerdes M, Kim DS, Rajagopalan R, Bernbaum J, Wernovsky G, Nicolson SC, Spray TL, Clancy RR. Postoperative electroencephalographic seizures are associated with deficits in executive function and social behaviors at 4 years of age following cardiac surgery in infancy, The Journal of Thoracic and Cardiovascular Surgery, 146(1), 132-39.

Kim JH, Jarvik GP, Browning BL, Rajagopalan R, Gordon AS, Rieder MJ, Robertson PD, Nickerson DA, Fisher NA, Hopkins PM. Exome sequencing reveals novel rare variants in RYR1 and CACNA1S in 4 malignant hyper- thermia families, Anesthesiology, 119(5), 1054-1065.

Ganesh SK1, Tragante V, Guo W, Guo Y, Lanktree MB, Rajagopalan R et al. Loci influencing blood pressure identified using a cardiovascular gene-centric array, Human Molecular Genetics, 22(8), 1663-1678.

Guo Y, Lanktree MB, Taylor KC, Fairfax BP, Elbers CC, Rajagopalan R et al. Gene-centric meta-analyses of 108,912 individuals confirm known body mass index loci and reveal three novel signals, Human Molecular Genetics 22(1), 184-201.

Kim DS, Stanaway IB, Rajagopalan R, Bernbaum JC, Solot CB, Burnham N, Zackai EH, Clancy RR, Nicol- son SC, Gerdes M, Nickerson DA, Hakonarson H, Gaynor JW, Jarvik GP, Results of genome-wide analyses on neurodevelopmental phenotypes at four-year follow-up following cardiac surgery in infancy, PLoS ONE 7(9): e45936.

Asselbergs FW, Guo Y, van Iperen EP, Sivapalaratnam S, Tragante V, Rajagopalan R et al. Large-Scale Gene-Centric Meta-Analysis across 32 Studies Identifies Multiple Lipid Loci, AJHG 91(5), 823-828.

Saxena R, Elbers CC, Guo Y, Peter I, Gaunt TR, Rajagopalan R et al. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci, American Journal of Human Genetics, 90(3), 410-425.

Rosenthal EA, Ronald J, Rothstein J, Rajagopalan R, Ranchalis J, Wolfbauer G, Albers JJ, Brunzell JD, Mo- tulsky AG, Reider MJ, Nickerson DA, Wijsman EM, Jarvik GP, Linkage of phospholipid transfer protein activity to chromosome 19p in hyperlipidemic families and evidence of a role for LASS4, J. Lipid Res., 52, 1837-1846.


Ronald J, Rajagopalan R, Cerrato F, Nord AS, Hatsukami T, Kohler T, Marcovina S, Heagerty P, Jarvik GP, Genetic variation in LPAL2, LPA, and PLG predicts plasma lipoprotein(a) level and carotid artery disease risk, Stroke 2011;42;2-9.

Lanktree MB, Guo Y, Murtaza M, Glessner JT, Bailey SD, Rajagopalan R et al. J. Meta-analysis of dense gene-centric association studies reveals common and uncommon variants associated with height, Americal Journal of Human Genetics, 88(1), 6-18.


Fuller S, Rajagopalan R, Jarvik GP, Gerdes M, Bernbaum J, Wernovsky G, Clancy RR, Solot C, Nicolson SC, Spray TL, Gaynor JW, Deep Hypothermic Circulatory Arrest Does Not Impair Neurodevelopmental Outcome in School-Age Children After Infant Cardiac Surgery, The Annals of Thoracic Surgery, 2010, 90, 1985-1995.

Ronald J, Rajagopalan R, Ranchalis JE, Marshall JK, Hatsukami TS, Heagerty PJ, Jarvik GP, Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease, Lipids in Health and Disease, 8:52.

Jarvik GP, Rajagopalan R, Rosenthal EA, Wolfbauer G, McKinstry L, Vaze A, Brunzell J, Motulsky AG, Nickerson DA, Heagerty PJ, Wijsman EM, and Albers JJ, Genetic and non-genetic sources of variation in phospholipid transfer protein (PLTP) activity, J Lipid Res., 51(5):983-990.

Ober C, Nord AS, Thompson EE, Pan L, Tan Z, Cusanovich D, Sun Y, Nicolae R, Edelstein C, Schneider DH, Billstrand C, Pfaffinger D, Phillips N, Anderson RL, Philips B, Rajagopalan R, Hatsukami TS, Rieder MJ, Heagerty PJ, Nickerson DA, Abney M, Marcovina S, Jarvik GP, Scanu AM, Nicolae DL. Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q, J. Lipid Res., 50, 798-806.

Posters and Presentations


Rajagopalan R. Improving the current state of the art genetic diagnostic test, “Emerging innovators in collaborative research”, seminar series, Children’s Hospital of Philadelphia, Philadelphia PA: October 14, 2020.


Rajagopalan R. Systematic and comprehensive benchmarking of an exome sequencing based germline copy-number variant detection pipeline in a clinical setting, American College of Medical Genetics meeting, Seattle WA: April 4, 2019.

Rajagopalan R. Expanding the spectrum and classification of JAG1 mutations in ALGS and an update on THBS2 as a genetic modifier of liver disease severity, Biesecker Liver Center Meeting, Children’s Hospital of Philadelphia, Philadelphia, PA: June 6, 2019.

Awards and Honors

2020, Emerging Innovator in Collaborative Research, Children’s Hospital of Philadelphia
2017, 2nd prize, Abstract competition, Cancer Genomics Consortium meeting 2017
2015, Best poster award, Research poster day 2015, Children’s Hospital of Philadelphia

Editorial and Academic Positions

Editorial Positions

2020-present, Reviewer, Journal of Assisted Reproduction and Genetics
2020-present, Reviewer, Heliyon
2016-present, Reviewer, Human Mutation
2016-present, Reviewer, Oxford Bioinformatics