Publications

2026

T Lawler, J Long, R Welch, I Ong, O Ogunmuyiwa, R A Khatri, M Shrubsole, S Warren Andersen, “A Genome‐Wide Association Study of Colorectal Cancer Mortality Outcomes Among Individuals of African and Admixture Ancestry”, Molecular Carcinogenesis

C P Kerr, W J Jin, P Liu, J J Grudzinski, C A Ferreira, H Comas Rojas, A J Oñate, O Kwon, M Hyun, M B Idrissou, R Welch Schwartz, J M Vera, P A Clark, A Adeniyi, M Takashima, A K Erbe, A G Shea, M Powers, A N Pinchuk, C F Massey, C Choi, R Hernandez, B P Bednarz, I M Ong, J P Weichert, Z S Morris, “Priming versus propagating: distinct immune effects of alpha- versus beta-particle emitting radiopharmaceuticals when combined with immune checkpoint inhibition in mice”, Nature Communications, 17, 2044

2025

R Welch Schwartz, C L Zuleger, M A Newton, D M Vail, M R Albertini, I M Ong, “SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine”, MethodsX, 103733

U S Polaki, T E Gilpin, A T Patil, E Chiu, R Baker, P Liu, T S Pavletich, M Seifi, P M Mañán-Mejías, J Morrissey, J Port, R Welch Schwartz, I M Ong, D El-Rayes, M A Khalifa, P Hui, V L Horner, M Virumbrales-Muñoz, B K Erickson, L Barroilhet, S M McGregor, E H Bresnick, D R Matson, “Loss of GATA2 promotes invasion and predicts cancer recurrence and survival in uterine serous carcinoma”, JCI insight, 10-9, e187073

R Welch Schwartz, A Ahmed, R Hu, R J Kimple, P M Harari, I M Ong, S C Kerr, “Abstract B027: Spatial transcriptomic profiling of the head and neck cancer tumor microenvironment to guide design of microphysiological systems for reporting treatment response”, Cancer Research, 85-5_Supplement, B027-B027

2024

C Kerr, WJ Jin, P Liu, JJ Grudzinski, CA Ferreira, H Comas Rojas, AJ Onate, O Kwon, M Hyun, M Bio Idrissou, R Welch Schwartz, PA Clark, M Takashima, AG Shea, AN Pinchuk, R Hernandez, B Bednarz, IM Ong, J Weichert, Z Morris, “Tumor immunity following radiopharmaceutical+ checkpoint blockade varies with treatment sequence, radioisotope and tumor immunogenicity”. International Journal of Radiation Oncology, Biology, Physics, 120-2, S96

M R Albertini, C L Zuleger, E A Ranheim, O Shiyanbola, P M Sondel, Z S Morris, J Eickhoff, M A Newton, I M Ong, R Welch Schwartz, R Hayim, I D Kurzman, M Turek, D M Vail, “Administration of intratumoral GD2-directed interleukin-2 immunocytokine and local radiation therapy to activate immune rejection of spontaneous canine melanoma”, Melanoma research, 34-4, 307-318

C L Zuleger, R Welch Schwartz, I M Ong, M A Newton, D M Vail, M R Albertini, “Development of a next-generation sequencing protocol for the canine T cell receptor beta chain repertoire”, Veterinary immunology and immunopathology, 268, 110702

Critical assessment of genome interpretation consortium, “Critical assessment of genome interpretation consortium. CAGI, the critical assessment of genome interpretation, establishes progress and pprospects for computational genetic variant interpretation methods.”, Genome Biology, 25-1, 1-46

2023

D A Chasman, R Welch Schwartz, J Vazquez, M Chavarria, E T Jenkins, G E Lopez, C T Tyler, A K Stanic, I M Ong, “Proteogenomic and V (D) J analysis of human decidual T cells highlights unique transcriptional programming and clonal distribution”, The Journal of Immunology, 211-1, 154-162

L A Parlato, R Welch, I M Ong, J Long, Q Cai, M D Steinwandel, W J Blot, W Zheng, S Warren Andersen, “Genome-wide association study (GWAS) of circulating vitamin D outcomes among individuals of African ancestry”, The American Journal of Clinical Nutrition, 117-2, 308-316

R Welch, AR Y Collier, J Vazquez, S Banerjee, D Chasman, A Stanic-Kostic, I M Ong, “Single Cell Multi-Omic Analysis of Intervillous Lymphocytes in Preeclampsia”, REPRODUCTIVE SCIENCES, 30, 103A-104A

2022

M Albertini, C Zuleger, E Ranheim, O Shiyanbola, A Kosharek, P Sondel, Z Morris, J Eickhoff, M Newton, I Ong, R Welch Schwartz, R Hayim, S Adrianowycz, R Uyehara, I Kurzman, M Turek, D Vail, “Administration of intratumoral hu14. 18-IL2 immunocytokine and local radiation therapy to activate immune rejection of spontaneous canine melanoma”, Journal for ImmunoTherapy of Cancer, 10-Suppl 2

2021

J Vazquez, M Chavarria, D A Chasman, R Welch Schwartz, C T Tyler, G Lopez, R C Fisher, I M Ong, A K Stanic, “Multiomic analysis reveals decidual‐specific transcriptional programing of MAIT cells”, American Journal of Reproductive Immunology, 86-6, e13495

A LFV Assumpção, G Fu, D K Singh, Z Lu, A M Kuehnl, R Welch, I M Ong, R Wen, X Pan, “A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development”, Development, 148-7, dev197319

2020

The ENCODE Project Consortium, “Perspectives on ENCODE”, Nature, 583-7818, 693-698

The ENCODE Project Consortium, “Expanded encyclopaedias of DNA elements in the human and mouse genomes”, Nature, 583-7818, 699-710

2019

M R Eichelberg, R Welch, J T Guidry, A Ali, M Ohashi, K R Makielski, K McChesney, N Van Sciver, P F Lambert, S Keleș, S C Kenney, R S Scott, E Johannsen, “Epstein-Barr virus infection promotes epithelial cell growth by attenuating differentiation-dependent exit from the cell cycle”, MBio, 10-4, 10.1128/mbio. 01332-19

2017

R Welch, D Chung, J Grass, R Landick, S Keleş, “Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments”, Nucleic Acid Research, 45-15, e145-e145

A Kreimer, H Zeng, M D Edwards, Y Guo, K Tian, S Shin, R Welch, M Wainberg, R Mohan, N A Sinnott‐Armstrong, Y Li, G Eraslan, T Bin Amin, R Tewhey, P C Sabeti, J Goke, N S Mueller, M Kellis, A Kundaje, M A Beer, S Keles, D K Gifford, N Yosef, “Predicting gene expression in massively parallel reporter assays: A comparative study”, Human mutation, 38-9, 1240-1250

2016

A Wang, R Welch, B Zhao, T Ta, S Keleş, E Johannsen, “Epstein-Barr virus nuclear antigen 3 (EBNA3) proteins regulate EBNA2 binding to distinct RBPJ genomic sites”, Journal of virology, 90-6, 2906-2919

2015

X Zeng, B Li, R Welch, C Rojo, Y Zheng, C N Dewey, S Keleş, “Perm-seq: mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping”, PLoS computational biology, 11-10, e1004491