Chaim A. Schramm, Ph.D.

Chief, Integrative Bioinformatics of Immune Systems Core

Major Areas of Research

  • Single cell RNASeq and CITEseq analysis of innate and adaptive immune responses
  • Dynamics of IG and TR repertoires in response to vaccination and infection
  • Somatic hypermutation and antibody phylogenetics
  • Impact of IG genetics on immune outcomes

Program Description

The Integrative Bioinformatics of Immune Systems (IBIS) Core is the central bioinformatic resource for all repertoire and “omics” studies in the VRC, offering coordinated staffing and planning for multi-section and external collaborations, such as the ongoing SARS-CoV-2 response efforts. Specific research areas in the IBIS Core include transcriptomic analysis of both innate and adaptive immune cells, T cell receptor repertoire analysis, B cell receptor sequence and phylogenetic analysis, and analysis of immune cell population dynamics. In addition, we work closely with the Genome Analysis, Humoral Immunology, Structural Bioinformatics Cores, and the Vaccine Immunology Program to prioritize experiments and analyses that will best advance the scientific objectives of the VRC.

Biography

Dr. Schramm earned his Ph.D. from the University of Pennsylvania in 2012 and completed a postdoctoral fellowship at Columbia University prior to joining the VRC as a staff scientist in 2016. Dr. Schramm has been a pioneer in the longitudinal phylogenetic analysis of B cell clonal lineages and developed the SONAR analysis suite to facilitate those studies. He also has significant research interests in IG V gene substitution profiles and immunogenetics. As chief of the IBIS Core, Dr. Schramm designs and leads large-scale scRNASeq analyses of innate and adaptive immune cells dynamics in infection and vaccination. Beyond the VRC, Dr. Schramm is a founding member of the AIRR Community organization and serves as co-chair of the Software Working Group.

Selected Publications

Corbett KS, Gagne M, Wagner DA, Connell SO, Narpala SR, Flebbe DR, Andrew SF, Davis RL, Flynn B, Johnston TS, Stringham C, Lai L, Valentin D, Van Ry A, Flinchbaugh Z, Werner AP, Moliva JI, Sriparna M, O'Dell S, Schmidt SD, Tucker C, Choi A, Koch M, Bock KW, Minai M, Nagata BM, Alvarado GS, Henry AR, Laboune F, Schramm CA, Zhang Y, Wang L, Choe M, Boyoglu-Barnum S, Shi W, Lamb E, Nurmukhambetova ST, Provost SJ, Donaldson MM, Marquez J, Todd JM, Cook A, Dodson A, Pekosz A, Boritz E, Ploquin A, Doria-Rose N, Pessaint L, Andersen H, Foulds KE, Misasi J, Wu K, Carfi A, Nason MC, Mascola J, Moore IN, Edwards DK, Lewis MG, Suthar MS, Roederer M, McDermott A, Douek DC, Sullivan NJ, Graham BS, Seder RA. Protection against SARS-CoV-2 Beta Variant in mRNA-1273 Boosted Nonhuman Primates. bioRxiv [Preprint]. 2021 Aug:2021.08.11.456015.

Wang L, Zhou T, Zhang Y, Yang ES, Schramm CA, Shi W, Pegu A, Oloniniyi OK, Henry AR, Darko S, Narpala SR, Hatcher C, Martinez DR, Tsybovsky Y, Phung E, Abiona OM, Antia A, Cale EM, Chang LA, Choe M, Corbett KS, Davis RL, DiPiazza AT, Gordon IJ, Hait SH, Hermanus T, Kgagudi P, Laboune F, Leung K, Liu T, Mason RD, Nazzari AF, Novik L, O'Connell S, O'Dell S, Olia AS, Schmidt SD, Stephens T, Stringham CD, Talana CA, Teng IT, Wagner DA, Widge AT, Zhang B, Roederer M, Ledgerwood JE, Ruckwardt TJ, Gaudinski MR, Moore PL, Doria-Rose NA, Baric RS, Graham BS, McDermott AB, Douek DC, Kwong PD, Mascola JR, Sullivan NJ, Misasi J. Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Science. 2021 Aug;373(6556):eabh1766.

Mukhamedova M, Wrapp D, Shen CH, Gilman MSA, Ruckwardt TJ, Schramm CA, Ault L, Chang L, Derrien-Colemyn A, Lucas SAM, Ransier A, Darko S, Phung E, Wang L, Zhang Y, Rush SA, Madan B, Stewart-Jones GBE, Costner PJ, Holman LA, Hickman SP, Berkowitz NM, Doria-Rose NA, Morabito KM, DeKosky BJ, Gaudinski MR, Chen GL, Crank MC, Misasi J, Sullivan NJ, Douek DC, Kwong PD, Graham BS, McLellan JS, Mascola JR. Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses. Immunity. 2021 Apr;54(4):769-780.e6.

Roark RS, Li H, Williams WB, Chug H, Mason RD, Gorman J, Wang S, Lee FH, Rando J, Bonsignori M, Hwang KK, Saunders KO, Wiehe K, Moody MA, Hraber PT, Wagh K, Giorgi EE, Russell RM, Bibollet-Ruche F, Liu W, Connell J, Smith AG, DeVoto J, Murphy AI, Smith J, Ding W, Zhao C, Chohan N, Okumura M, Rosario C, Ding Y, Lindemuth E, Bauer AM, Bar KJ, Ambrozak D, Chao CW, Chuang GY, Geng H, Lin BC, Louder MK, Nguyen R, Zhang B, Lewis MG, Raymond DD, Doria-Rose NA, Schramm CA, Douek DC, Roederer M, Kepler TB, Kelsoe G, Mascola JR, Kwong PD, Korber BT, Harrison SC, Haynes BF, Hahn BH, Shaw GM. Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Science. 2021 Jan;371(6525):eabd2638.

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