My research lab focuses on developing novel computational methods to better understand the complex interactions between immune cells, their environment, and the microbiome. Our goal is to uncover clinically relevant insights and pave the way for new diagnostics and therapies that can improve human health.
Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus.
Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus. Cell Rep. 2022 09 13; 40(11):111341.
PMID: 36103821
Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer.
Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer. Nat Commun. 2022 07 13; 13(1):4053.
PMID: 35831288
Privacy preserving validation for multiomic prediction models.
Ahmed T, Carty MA, Wenric S, Dry JR, Salahudeen AA, Khan AA, Lefkofsky E, Stumpe MC, Pelossof R. Privacy preserving validation for multiomic prediction models. Brief Bioinform. 2022 05 13; 23(3).
PMID: 35388408
Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential.
Nakao T, Bick AG, Taub MA, Zekavat SM, Uddin MM, Niroula A, Carty CL, Lane J, Honigberg MC, Weinstock JS, Pampana A, Gibson CJ, Griffin GK, Clarke SL, Bhattacharya R, Assimes TL, Emery LS, Stilp AM, Wong Q, Broome J, Laurie CA, Khan AT, Smith AV, Blackwell TW, Codd V, Nelson CP, Yoneda ZT, Peralta JM, Bowden DW, Irvin MR, Boorgula M, Zhao W, Yanek LR, Wiggins KL, Hixson JE, Gu CC, Peloso GM, Roden DM, Reupena MS, Hwu CM, DeMeo DL, North KE, Kelly S, Musani SK, Bis JC, Lloyd-Jones DM, Johnsen JM, Preuss M, Tracy RP, Peyser PA, Qiao D, Desai P, Curran JE, Freedman BI, Tiwari HK, Chavan S, Smith JA, Smith NL, Kelly TN, Hidalgo B, Cupples LA, Weeks DE, Hawley NL, Minster RL. Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential. Sci Adv. 2022 Apr 08; 8(14):eabl6579.
PMID: 35385311
A pan-cancer organoid platform for precision medicine.
A pan-cancer organoid platform for precision medicine. Cell Rep. 2021 07 27; 36(4):109429.
PMID: 34320344
Improved integration of single-cell transcriptome and surface protein expression by LinQ-View.
Improved integration of single-cell transcriptome and surface protein expression by LinQ-View. Cell Rep Methods. 2021 Aug 23; 1(4):100056.
PMID: 35475142
Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection.
Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. Nat Commun. 2021 07 16; 12(1):4372.
PMID: 34272370
Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA.
Finkle JD, Boulos H, Driessen TM, Lo C, Blidner RA, Hafez A, Khan AA, Lozac'hmeur A, McKinnon KE, Perera J, Zhu W, Dowlati A, White KP, Tell R, Beaubier N. Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA. NPJ Precis Oncol. 2021 Jul 02; 5(1):63.
PMID: 34215841
Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination.
Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. PLoS Comput Biol. 2021 05; 17(5):e1008094.
PMID: 33939691
Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices.
Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung YJ, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf G, Montasser ME, Moon JY, Muzny D, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FF, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang YC, Chen YI, Choi WJ, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAV, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJ, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo JS, Smith AV, Tracy RP, Vasan RS, Kathiresan S, Cupples LA, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nat Commun. 2021 04 12; 12(1):2182.
PMID: 33846329