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.


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. Barry M, Wu F, Pati S, Chipman A, Geng H, Kozar R. Lyophilized plasma resuscitation downregulates inflammatory gene expression in a mouse model of sepsis. J Trauma Acute Care Surg. 2022 08 01; 93(2S Suppl 1):S119-S127.  View on PubMed
  2. Tarighat SS, Fei F, Joo EJ, Abdel-Azim H, Yang L, Geng H, Bum-Erdene K, Grice ID, von Itzstein M, Blanchard H, Heisterkamp N. Overcoming Microenvironment-Mediated Chemoprotection through Stromal Galectin-3 Inhibition in Acute Lymphoblastic Leukemia. Int J Mol Sci. 2021 Nov 10; 22(22).  View on PubMed
  3. Lai N. Chan, Christian Hurtz, Etienne Leveille, Kohei Kume, Mark E. Robinson, Huimin Geng, Kadriye Nehir Cosgun, Markus Müschen. Identification of BCL6 As Synthetic Lethality in RAS-Driven B-Cell Transformation. Blood. 2021 Nov 5; 138(Supplement 1):792-792.  View on PubMed
  4. Lai N. Chan, Mark A. Murakami, Christian Hurtz, Kohei Kume, Jaewoong Lee, Kadriye Nehir Cosgun, Huimin Geng, Shai Izraeli, David M. Weinstock, Markus Müschen. Leveraging Pathway-Interference to Overcome Drug-Resistance in Acute Lymphoblastic Leukemia. Blood. 2021 Nov 5; 138(Supplement 1):616-616.  View on PubMed
  5. Jaewoong Lee, Mark E. Robinson, Ning Ma, Kohei Kume, Dewan Artadji, Teresa Sadras, Kadriye Nehir Cosgun, Huimin Geng, Elisabeth M. Paietta, Maike Buchner, Nagarajan Vaidehi, David M. Weinstock, Markus Müschen. Structural Basis of Feedback Control of Oncogenic Signaling in B-Lymphoid Malignancies. Blood. 2021 Nov 5; 138(Supplement 1):355-355.  View on PubMed
  6. Geng H, Tsang M, Subbaraj L, Cleveland J, Chen L, Lu M, Sharma J, Vigneron DB, Kurhanewicz J, LaFontaine M, Luks T, Barshop BA, Gangoiti J, Villanueva-Meyer JE, Rubenstein JL. Tumor metabolism and neurocognition in CNS lymphoma. Neuro Oncol. 2021 10 01; 23(10):1668-1679.  View on PubMed
  7. Chan TY, Egbert CM, Maxson JE, Siddiqui A, Larsen LJ, Kohler K, Balasooriya ER, Pennington KL, Tsang TM, Frey M, Soderblom EJ, Geng H, Müschen M, Forostyan TV, Free S, Mercenne G, Banks CJ, Valdoz J, Whatcott CJ, Foulks JM, Bearss DJ, O'Hare T, Huang DCS, Christensen KA, Moody J, Warner SL, Tyner JW, Andersen JL. TNK1 is a ubiquitin-binding and 14-3-3-regulated kinase that can be targeted to block tumor growth. Nat Commun. 2021 09 09; 12(1):5337.  View on PubMed
  8. Drew WL, Miller S, Geng H, Ingebrigtsen D, Suslow LM and Suslow PS. Absence of Influenza and RSV Activity in the San
    Francisco Bay Area during the COVID-19 Pandemic, 2020-2021. J Adv Virol Res. 2021; 1(1):103.  View on PubMed
  9. Nix MA, Mandal K, Geng H, Paranjape N, Lin YT, Rivera JM, Marcoulis M, White KL, Whitman JD, Bapat SP, Parker KR, Ramirez J, Deucher A, Phojanokong P, Steri V, Fattahi F, Hann BC, Satpathy AT, Manglik A, Stieglitz E, Wiita AP. Surface Proteomics Reveals CD72 as a Target for In Vitro-Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL. Cancer Discov. 2021 08; 11(8):2032-2049.  View on PubMed
  10. Pan L, Hong C, Chan LN, Xiao G, Malvi P, Robinson ME, Geng H, Reddy ST, Lee J, Khairnar V, Cosgun KN, Xu L, Kume K, Sadras T, Wang S, Wajapeyee N, Müschen M. PON2 subverts metabolic gatekeeper functions in B cells to promote leukemogenesis. Proc Natl Acad Sci U S A. 2021 02 16; 118(7).  View on PubMed
  11. 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. Nature. 2020 12; 588(7838):491-497.  View on PubMed
  12. 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. Nat Genet. 2020 12; 52(12):1384-1396.  View on PubMed
  13. 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. Exp Hematol. 2020 10; 90:65-71.e1.  View on PubMed
  14. 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. Nature. 2020 07; 583(7818):845-851.  View on PubMed
  15. 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 α6 mediates the drug resistance of acute lymphoblastic B-cell leukemia. Blood. 2020 07 09; 136(2):210-223.  View on PubMed
  16. 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. Blood. 2020 07 02; 136(1):11-23.  View on PubMed
  17. 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. Leukemia. 2021 01; 35(1):90-106.  View on PubMed
  18. 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. Genes Immun. 2020 02; 21(2):119-130.  View on PubMed
  19. 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. Leukemia. 2020 03; 34(3):938-941.  View on PubMed
  20. 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. Genes Dev. 2019 09 01; 33(17-18):1265-1279.  View on PubMed

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