Research Summary

My research is focused on functional genomics and epigenomics of lymphoma and leukemia, based on computational and statistical modeling and analysis of large-scale data derived from high-throughput microarray (gene expression, DNA methylation, ChIP-Chip, arrayCGH and SNP arrays) and next generation sequencing technologies (RNA-seq, Whole Exome-Seq, ChIP-seq and DNA methylation eRRBS-seq). Applying bioinformatics approaches, we are interested in identifying and evaluating 1) genetic and epigenetic abnormalities in the lymphomagenesis and leukemogenesis, 2) new biomarkers for prognosis and disease classification, and 3) novel therapeutic targets to develop precision medicine for different forms of lymphoma and leukemia. We have profiled 1000+ lymphoma and leukemia patient samples from LLMPP, COG, ECOG and other international consortiums and curated thousands of lymphoma and leukemia patient samples from public GEO, TCGA and TARGET datasets with different array and NGS platforms. Using these data, we have developed an integrative genomic and epigenomic metadata platform to study the master regulators and regulatory networks of hematopoietic malignancies. I have ongoing Intra- and Inter-Programmatic collaborations with numerous Cancer Center Members and Associate Members, including Markus Muschen, Neil Shah, James Rubenstein, Scott Kogan and Mignon Loh.

Education

University of Science & Technology of China, BS, 1999, School of the Gifted Young (Biophysics)
University of Nebraska at Omaha, MS, 2004, Computer Science
University of Nebraska Medical Center, PhD, 2008, Bioinformatics
Weill Cornell Medical College, Postdoc, 2008-2011, Computational Biology

Honors & Awards

  • 2004
    Best Poster Award, IEEE Computer Society Bioinformatics Conference (CSB'04), Stanford Univerisity, CA
  • 2005
    Kerrigan Research Minigrants Award, University of Nebraska at Omaha, Omaha, NE
  • 2007
    Best Poster Award, 2007 Nebraska Research and Innovation Conference, Omaha, NE
  • 2007
    Bukey Fellowship, University of Nebraska Medical Center, Omaha, NE
  • 2008
    Blanche Widaman Fellowship, University of Nebraska Medical Center, Omaha, NE
  • 2008
    Harris Award in Cancer Research, University of Nebraska Medical Center, Omaha, NE

Selected Publications

  1. Mazie Tsang, Joseph Cleveland, Miguel Carlos Cerejo, Huimin Geng, James L. Rubenstein Survival and Patient-Reported Outcomes of Older Adults with Primary Central Nervous System Lymphoma on Low-Dose Lenalidomide.  View on PubMed
  2. Lee J, Robinson ME, Ma N, Artadji D, Ahmed MA, Xiao G, Sadras T, Deb G, Winchester J, Cosgun KN, Geng H, Chan LN, Kume K, Miettinen TP, Zhang Y, Nix MA, Klemm L, Chen CW, Chen J, Khairnar V, Wiita AP, Thomas-Tikhonenko A, Farzan M, Jung JU, Weinstock DM, Manalis SR, Diamond MS, Vaidehi N, Müschen M IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells.  View on PubMed
  3. Fan H, Lu J, Guo Y, Li D, Zhang ZM, Tsai YH, Pi WC, Ahn JH, Gong W, Xiang Y, Allison DF, Geng H, He S, Diao Y, Chen WY, Strahl BD, Cai L, Song J, Wang GG BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis.  View on PubMed
  4. Fitch B, Roy R, Geng H, Montecino-Rodriguez E, Bengtsson H, Gaillard C, Hiam K, Casero D, Olshen AB, Dorshkind K, Kogan SC Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature.  View on PubMed
  5. Liu Y, Kong FZ, Xun XG, Dai L, Geng HX, Hu XL, Yu RC, Bao ZM, Zhou MJ Biokinetics and biotransformation of paralytic shellfish toxins in different tissues of Yesso scallops, Patinopecten yessoensis.  View on PubMed
  6. Chan LN, Murakami MA, Robinson ME, Caeser R, Sadras T, Lee J, Cosgun KN, Kume K, Khairnar V, Xiao G, Ahmed MA, Aghania E, Deb G, Hurtz C, Shojaee S, Hong C, Pölönen P, Nix MA, Chen Z, Chen CW, Chen J, Vogt A, Heinäniemi M, Lohi O, Wiita AP, Izraeli S, Geng H, Weinstock DM, Müschen M Signalling input from divergent pathways subverts B cell transformation.  View on PubMed
  7. Gang EJ, Kim HN, Hsieh YT, Ruan Y, Ogana HA, Lee S, Pham J, Geng H, Park E, Klemm L, Willman CL, Carroll WL, Mittelman SD, Orgel E, Oberley MJ, Parekh C, Abdel-Azim H, Bhojwani D, Wayne AS, De Arcangelis A, Georges-Labouesse E, Wayner E, Bonig H, Minasyan A, Ten Hoeve J, Graeber TG, Müschen M, Heisterkamp N, Kim YM Integrin a6 mediates the drug resistance of acute lymphoblastic B-cell leukemia.  View on PubMed
  8. Pi WC, Wang J, Shimada M, Lin JW, Geng H, Lee YL, Lu R, Li D, Wang GG, Roeder RG, Chen WY E2A-PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia.  View on PubMed
  9. Godfrey L, Crump NT, O'Byrne S, Lau IJ, Rice S, Harman JR, Jackson T, Elliott N, Buck G, Connor C, Thorne R, Knapp DJHF, Heidenreich O, Vyas P, Menendez P, Inglott S, Ancliff P, Geng H, Roberts I, Roy A, Milne TA H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells.  View on PubMed
  10. Brown MA, Edwards MA, Alshiraihi I, Geng H, Dekker JD, Tucker HO The lysine methyltransferase SMYD2 is required for normal lymphocyte development and survival of hematopoietic leukemias.  View on PubMed
  11. Jaewoong Lee, Kohei Kume, Zhengshan Chen, Gang Xiao, Kadriye Nehir Nehir Cosgun, Liting Chen, Lai N Chan, Lars Klemm, Chun-Wei David Chen, Ning Ma, Wing C. Chan, Stephen J Forman, Francesca Zammarchi, Patrick Van Berkel, Ari Melnick, Vu N Ngo, Huimin Geng, Selina M. Luger, Mark Litzow, Michael T McManus, Nagarajan Vaidehi, Elisabeth M. Paietta, Eric Meffre, David M. Weinstock, Markus Müschen Dynamic Assembly of a Feedback Complex to Regulate Oncogenic B-Cell Receptor-Signaling.  View on PubMed
  12. Kadriye Nehir Cosgun, Gauri Deb, Xin Yang, Gang Xiao, Teresa Sadras, Jaewoong Lee, Lai N Chan, Kohei Kume, Lu Yang, Huimin Geng, John Chan, Joo Y. Song, Hassan Jumaa, Andrew G. Polson, Hans Clevers, Markus Müschen Lgr5 Functions As a Critical Negative Regulator of Wnt/ß-Catenin Signaling and Is Essential for B-Lymphopoiesis and Malignant B-Cell Transformation.  View on PubMed
  13. Lili Pan, Chao Hong, Gang Xiao, Huimin Geng, Shaoyuan Wang, Markus Müschen Paraoxonase 2 Enables Initiation of B-ALL By Subverting Metabolic Gatekeeper Functions.  View on PubMed
  14. Choudhry P, Mariano MC, Geng H, Martin TG, Wolf JL, Wong SW, Shah N, Wiita AP DNA methyltransferase inhibitors upregulate CD38 protein expression and enhance daratumumab efficacy in multiple myeloma.  View on PubMed
  15. Hurtz C, Chan LN, Geng H, Ballabio E, Xiao G, Deb G, Khoury H, Chen CW, Armstrong SA, Chen J, Ernst P, Melnick A, Milne T, Müschen M Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia.  View on PubMed
  16. Rubenstein JL, Geng H, Vu K, Mannis G, Formaker P, Hwang J, Munster PN, Damato B Maintenance lenalidomide in primary CNS lymphoma.  View on PubMed
  17. Vu K, Mannis G, Hwang J, Geng H, Rubenstein JL Low-dose lenalidomide maintenance after induction therapy in older patients with primary central nervous system lymphoma.  View on PubMed
  18. Hatzi K, Geng H, Doane AS, Meydan C, LaRiviere R, Cardenas M, Duy C, Shen H, Vidal MNC, Baslan T, Mohammad HP, Kruger RG, Shaknovich R, Haberman AM, Inghirami G, Lowe SW, Melnick AM Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis.  View on PubMed
  19. Gaillard C, Surianarayanan S, Bentley T, Warr MR, Fitch B, Geng H, Passegué E, de Thé H, Kogan SC Identification of IRF8 as a potent tumor suppressor in murine acute promyelocytic leukemia.  View on PubMed
  20. Lu X, Fernando TM, Lossos C, Yusufova N, Liu F, Fontán L, Durant M, Geng H, Melnick J, Luo Y, Vega F, Moy V, Inghirami G, Nimer S, Melnick AM, Lossos IS PRMT5 interacts with the BCL6 oncoprotein and is required for germinal center formation and lymphoma cell survival.  View on PubMed

Go to UCSF Profiles, powered by CTSI