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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 genome-wide array and deep sequencing data, including RNA-seq, Whole Exome-Seq, ChIP-seq, miRNA-seq and DNA methylation eRRBS-seq. 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

  • Chen Z, Shojaee S, Buchner M, Geng H, Lee JW, Klemm L, Titz B, Graeber TG, Park E, Tan YX, Satterthwaite A, Paietta E, Hunger SP, Willman CL, Melnick A, Loh ML, Jung JU, Coligan JE, Bolland S, Mak TW, Limnander A, Jumaa H, Reth M, Weiss A, Lowell CA & Müschen M. Signaling thresholds and negative B cell selection in acute lymphoblastic leukemia. Nature (2015). In press.
  • Geng H*, Hurtz C*, Lenz KB*, Chen Z, Baumjohann D, Thompson S, Goloviznina NA, Chen WY, Huan J, LaTocha D, Ballabio E, Gang X, Lee JW, Deucher A, Qi J, Park E, Huang C, Nahar R, Kweon SM, Shojaee S, Chan LN, Yu J, Kornblau SM, Bijl JJ, Ye BH, Ansel KM, Paietta E, Melnick A, Hunger SP, Kurre P, Tyner JW, Loh ML, Roeder RG, Burger JA, Milne T, Chang BH, & Müschen M. Self-enforcing feedback activation between BCL6 and tonic pre-B cell receptor signaling defines a distinct subtype of human acute lymphoblastic leukemia. Cancer Cell 27(3): 409–425 (2015). *Co-first authors
  • Kharabi-Masouleh B, Geng H, Hurtz C, Huang C, Chan LN, Ramezani-Rad P, Silveira VS, Cazzaniga V, Swaminathan S, Sun H, Koeffler HP, Melnick A, Glimcher LH & Müschen M. The plasma cell transcription factor XBP1 is required to mitigate the unfolded protein response in Ph+ ALL. Proc Natl Acad Sci. 111(21): E2219–28 (2014)
  • Huang C, Geng H, Boss I, Wang L & Melnick A. Cooperative transcriptional repression by BCL6 and BACH2 in germinal center B-cell differentiation. Blood 123(7):1012-20. (2014)
  • Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DM, Godley LA, Gascoyne RD, Melnick AM, Campagne F & Shaknovich R. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood 123(11):1699-708 (2014)
  • 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)
  • Chen WY, Zhang J, Geng H, Du Z, Nakadai T & Roeder RG. A TAF4 coactivator function for E proteins that involves enhanced TFIID binding. Genes & Dev. 27(14): 1596-1609 (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)
  • 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 Discov. 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) * Co-first authors
  • 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)

Additional Information

Huimin Geng, PhD
  • Associate Adjunct Professor
  • Laboratory Medicine

Specialty Areas

  • Bioinformatics, Genomics/Epigenomics in Lymphoma/Leukemia

Contact Information

Mailing/Shipping Address:

  • UCSF
  • Huimin Geng, PhD
  • Laboratory Medicine, Box 0451
  • 513 Parnassus Avenue, Room S-1457A
  • San Francisco, CA 94143

Web Site

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