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Huimin Geng, PhD

Research and Clinical Interests

My research is focused on functional genomics and epigenomics of lymphoma and leukemia using computational approaches on high-resolution, genome-wide array and deep sequencing data, including gene expression, DNA copy number, transcription factor binding and DNA methylation. Applying bioinformatic methods coupled with in vitro and in vivo experiments, we are interested in identifying and evaluating new prognostic and disease-classification biomarkers and novel therapeutic targets for different forms of lymphoma and leukemia.

Selected Publications

  • Swaminathan S, Huang C, Geng H, Chen Z, Harvey R, Kang H, Ng C, Titz B, Hurtz C, Sadiyah M, Nowak D, Thoennissen GB, Rand V, Graeber TG, Koeffler PH, Carroll WL, Willman CL, Hall AG, Igarashi K, Melnick A, Müschen M. BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint. Nat Med 19(8):1014-22. (2013)
  • Wilkinson AC, Ballabio E, Geng H, North P, Tapia M, Kerry J, Biswas D, Roeder RG, Allis CD, Melnick A, Marella F, de Bruijn FTR, Milne TA. RUNX1 is a key target gene in t(4;11) leukemias and contributes to gene activation by interacting with the AF4-MLL complex. Cell Reports 3(1): 116–127 (2013)
  • Ramezani-Rad P, Geng H, Hurtz C, Chan LN, Chen Z, Jumaa H, Melnick A, Paietta E, Carroll WL, Willman CL, Lefebvre V, Müschen M. SOX4 enables oncogenic survival signals in acute lymphoblastic leukemia. Blood 121(1):148-55 (2013)
  • De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Wollcock B, Johnson N, Polo JM, Gascoyne RD, Melnick A, Michor F. Aberration in DNA methylation in B-Cell lymphomas has a complex origin and increases with disease severity. PLoS Genet. 9(1): e1003137 (2013)
  • Geng H, Brennan S, Milne TA, Chen WY, Li Y, Hurtz C, Kweon SM, Zick L, Shojaee S, Huang C, Neuberg D, Biswas D, Xin Y, Racevski, Ketterling RP, Luger SM, Lazarus H, Tallman MS, Rowe JM, Litzow MR, Guzman ML, Allis CD, Roeder RG, Müschen M, Paietta E, Elemento O, Melnick A. Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discovery 2(11): 1004-23 (2012)
  • Duy C, Hurtz C, Shojaee S, Cerchietti L, Geng H, Swaminathan S, Klemm L, Kweon SM, Nahar R, Braig M, Park E, Kim YM, Hofmann WK, Herzog S, Jumaa H, Koeffler HP, Yu JJ, Heisterkamp N, Graeber TG, Wu H, Ye BH, Melnick A, Müschen M. BCL6 enables Ph(+) acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition. Nature 473(7347): 384-8 (2011)
  • Geng H, Iqbal J, Chan WC, Ali HH. Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma. BMC Med Genomics 4: 32 (2011)
  • Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick A, Elemento O. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood 116(24): 5247-55 (2010)
  • Shaknovich R*, Geng H*, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood 116(20): e81-9. (2010) *equal contribution
  • Iqbal J, Kucuk C, Deleeuw RJ, Srivastava G, Tam W, Geng H, Klinkebiel D, Christman JK, Patel K, Cao K, Shen L, Dybkaer K, Tsui IF, Ali H, Shimizu N, Au WY, Lam WL, Chan WC. Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies. Leukemia 23(6): 1139-51 (2009)
  • Choi WW, Weisenburger DD, Greiner TC, Piris MA, Banham AH, Delabie J, Braziel RM, Geng H, Iqbal J, Lenz G, Vose JM, Hans CP, Fu K, Smith LM, Li M, Liu Z, Gascoyne RD, Rosenwald A, Ott G, Rimsza LM, Campo E, Jaffe ES, Jaye DL, Staudt LM, Chan WC. A new immunostain algorithm classifies diffuse large B-cell lymphoma into molecular subtypes with high accuracy. Clin Cancer Res. 15(17): 5494-502 (2009)
  • d'Amore F, Chan E, Iqbal J, Geng H, Young K, Xiao L, Hess MM, Sanger WG, Smith L, Wiuf C, Hagberg O, Fu K, Chan WC, Dave BJ. Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution. Clin Cancer Res. 14(22): 7180-7 (2008)
  • Geng H, Deng X, Ali HH. MPC: a knowledge-based framework for clustering under biological constraints. Int J Data Mining Bioinformatics 2(2): 95-120 (2008)
  • Dybkaer K, Iqbal J, Zhou G, Geng H, Xiao L, d'Amore F, Chan WC. Genome-wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways. BMC Genomics 8: 230 (2007)
  • Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 4(2): 217-39 (2006)
Huimin Geng, PhD
  • Assistant Adjunct Professor
  • Laboratory Medicine

Specialty Areas

  • Genomics and epigenomics of lymphoma and leukemia

Contact Information

  • 513 Parnassus Ave, Med Sci, 1457A
  • University of California San Francisco
  • San Francisco, CA 94143
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