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    Huimin Geng, PhD

    TitleAssistant Professor
    SchoolUCSF School of Medicine
    DepartmentLaboratory Medicine
    Address513 Parnassus Ave, Med Sci
    San Francisco CA 94143
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      Collapse Biography 
      Collapse Education and Training
      University of Nebraska Medical CenterPh.D.Bioinformatics2008
      Weill Cornell Medical CollegePostdocInstitute for Computational Biomedicine2011
      Collapse Awards and Honors
      UCSF Academic Senate2016 - 2018Pilot for Junior Investigators in Basic and Clinical/Translational Sciences

      Collapse Overview 
      Collapse Overview
      Associate Member of the UCSF Helen Diller Family Comprehensive Cancer Center (Hematopoietic Malignancies Program)

      Collapse Interests
      Genomics, Epigenomics, Lymphoma, Leukemia, Bioinformatics (RNA-Seq, Whole Exome-Seq, ChIP-Seq, methylation eRRBS-Seq)

      Collapse ORNG Applications 
      Collapse Websites
      Collapse In The News

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre Ena X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM. CREBBP Inactivation Promotes the Development of HDAC3 Dependent Lymphomas. Cancer Discov. 2016 Oct 12. PMID: 27733359.
        View in: PubMed
      2. Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD, Melnick AM, et al. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest. 2016 Aug 2. PMID: 27482887.
        View in: PubMed
      3. Shojaee S, Chan LN, Buchner M, Cazzaniga V, Cosgun KN, Geng H, Qiu YH, von Minden MD, Ernst T, Hochhaus A, Cazzaniga G, Melnick A, Kornblau SM, Graeber TG, Wu H, Jumaa H, Müschen M. PTEN opposes negative selection and enables oncogenic transformation of pre-B cells. Nat Med. 2016 Apr; 22(4):379-87. PMID: 26974310.
        View in: PubMed
      4. Vieri M, Geng H, Patterson JB, Panse J, Wilop S, Samali A, Chevet E, Kharabi Masouleh B. Deregulated expression of the HSP40 family members Auxilin-1 and -2 is indicative of proteostasis imbalance and predicts patient outcome in Ph(+) leukemia. Exp Hematol Oncol. 2015; 5:5. PMID: 26862466.
        View in: PubMed
      5. Benito JM, Godfrey L, Kojima K, Hogdal L, Wunderlich M, Geng H, Marzo I, Harutyunyan KG, Golfman L, North P, Kerry J, Ballabio E, Chonghaile TN, Gonzalo O, Qiu Y, Jeremias I, Debose L, O'Brien E, Ma H, Zhou P, Jacamo R, Park E, Coombes KR, Zhang N, Thomas DA, O'Brien S, Kantarjian HM, Leverson JD, Kornblau SM, Andreeff M, Müschen M, Zweidler-McKay PA, Mulloy JC, Letai A, Milne TA, Konopleva M. MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199. Cell Rep. 2015 Dec 29; 13(12):2715-27. PMID: 26711339.
        View in: PubMed
      6. Shojaee S, Caeser R, Buchner M, Park E, Swaminathan S, Hurtz C, Geng H, Chan LN, Klemm L, Hofmann WK, Qiu YH, Zhang N, Coombes KR, Paietta E, Molkentin J, Koeffler HP, Willman CL, Hunger SP, Melnick A, Kornblau SM, Müschen M. Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia. Cancer Cell. 2015 Jul 13; 28(1):114-28. PMID: 26073130; PMCID: PMC4565502.
      7. Swaminathan S, Klemm L, Park E, Papaemmanuil E, Ford A, Kweon SM, Trageser D, Hasselfeld B, Henke N, Mooster J, Geng H, Schwarz K, Kogan SC, Casellas R, Schatz DG, Lieber MR, Greaves MF, Müschen M. Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia. Nat Immunol. 2015 Jul; 16(7):766-74. PMID: 25985233; PMCID: PMC4475638 [Available on 01/01/16].
      8. Cimmino L, Dawlaty MM, Ndiaye-Lobry D, Yap YS, Bakogianni S, Yu Y, Bhattacharyya S, Shaknovich R, Geng H, Lobry C, Mullenders J, King B, Trimarchi T, Aranda-Orgilles B, Liu C, Shen S, Verma AK, Jaenisch R, Aifantis I. TET1 is a tumor suppressor of hematopoietic malignancy. Nat Immunol. 2015 Jun; 16(6):653-62. PMID: 25867473; PMCID: PMC4545281.
      9. 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. Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia. Nature. 2015 May 21; 521(7552):357-61. PMID: 25799995; PMCID: PMC4441554 [Available on 11/21/15].
      10. Buchner M, Park E, Geng H, Klemm L, Flach J, Passegué E, Schjerven H, Melnick A, Paietta E, Kopanja D, Raychaudhuri P, Müschen M. Identification of FOXM1 as a therapeutic target in B-cell lineage acute lymphoblastic leukaemia. Nat Commun. 2015; 6:6471. PMID: 25753524; PMCID: PMC4366523.
      11. Geng H, Hurtz C, Lenz KB, Chen Z, Baumjohann D, Thompson S, Goloviznina NA, Chen WY, Huan J, LaTocha D, Ballabio E, Xiao G, Lee JW, Deucher A, Qi Z, Park E, Huang C, Nahar R, Kweon SM, Shojaee S, Chan LN, Yu J, Kornblau SM, Bijl JJ, Ye BH, Mark Ansel K, Paietta E, Melnick A, Hunger SP, Kurre P, Tyner JW, Loh ML, Roeder RG, Druker BJ, Burger JA, Milne TA, Chang BH, Müschen M. Self-enforcing feedback activation between BCL6 and pre-B cell receptor signaling defines a distinct subtype of acute lymphoblastic leukemia. Cancer Cell. 2015 Mar 9; 27(3):409-25. PMID: 25759025; PMCID: PMC4618684 [Available on 03/09/16].
      12. Béguelin W, Sawh S, Chambwe N, Chan FC, Jiang Y, Choo JW, Scott DW, Chalmers A, Geng H, Tsikitas L, Tam W, Bhagat G, Gascoyne RD, Shaknovich R. IL10 receptor is a novel therapeutic target in DLBCLs. Leukemia. 2015 Aug; 29(8):1684-94. PMID: 25733167.
        View in: PubMed
      13. Küçük C, Hu X, Jiang B, Klinkebiel D, Geng H, Gong Q, Bouska A, Iqbal J, Gaulard P, McKeithan TW, Chan WC. Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma. Clin Cancer Res. 2015 Apr 1; 21(7):1699-711. PMID: 25614448; PMCID: PMC4504988.
      14. Kharabi Masouleh B, Geng H, Hurtz C, Chan LN, Logan AC, Chang MS, Huang C, Swaminathan S, Sun H, Paietta E, Melnick AM, Koeffler P, Müschen M. Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. 2014 May 27; 111(21):E2219-28. PMID: 24821775; PMCID: PMC4040579.
      15. Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 2014 Mar 13; 123(11):1699-708. PMID: 24385541; PMCID: PMC3954051.
      16. Huang C, Geng H, Boss I, Wang L, Melnick A. Cooperative transcriptional repression by BCL6 and BACH2 in germinal center B-cell differentiation. Blood. 2014 Feb 13; 123(7):1012-20. PMID: 24277074; PMCID: PMC3924924.
      17. 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. 2013 Jul 15; 27(14):1596-609. PMID: 23873942; PMCID: PMC3731548.
      18. Swaminathan S, Huang C, Geng H, Chen Z, Harvey R, Kang H, Ng C, Titz B, Hurtz C, Sadiyah MF, Nowak D, Thoennissen GB, Rand V, Graeber TG, Koeffler HP, 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. 2013 Aug; 19(8):1014-22. PMID: 23852341; PMCID: PMC3954721.
      19. Cramer-Morales K, Nieborowska-Skorska M, Scheibner K, Padget M, Irvine DA, Sliwinski T, Haas K, Lee J, Geng H, Roy D, Slupianek A, Rassool FV, Wasik MA, Childers W, Copland M, Müschen M, Civin CI, Skorski T. Personalized synthetic lethality induced by targeting RAD52 in leukemias identified by gene mutation and expression profile. Blood. 2013 Aug 15; 122(7):1293-304. PMID: 23836560; PMCID: PMC3744994.
      20. Ruan J, Luo M, Wang C, Fan L, Yang SN, Cardenas M, Geng H, Leonard JP, Melnick A, Cerchietti L, Hajjar KA. Imatinib disrupts lymphoma angiogenesis by targeting vascular pericytes. Blood. 2013 Jun 27; 121(26):5192-202. PMID: 23632889; PMCID: PMC3695363.
      21. Wilkinson AC, Ballabio E, Geng H, North P, Tapia M, Kerry J, Biswas D, Roeder RG, Allis CD, Melnick A, de Bruijn MF, Milne TA. RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction. Cell Rep. 2013 Jan 31; 3(1):116-27. PMID: 23352661; PMCID: PMC3607232.
      22. Hsieh YT, Gang EJ, Geng H, Park E, Huantes S, Chudziak D, Dauber K, Schaefer P, Scharman C, Shimada H, Shojaee S, Klemm L, Parameswaran R, Loh M, Kang ES, Koo HH, Hofmann WK, Andrade J, Crooks GM, Willman CL, Müschen M, Papayannopoulou T, Heisterkamp N, Bönig H, Kim YM. Integrin alpha4 blockade sensitizes drug resistant pre-B acute lymphoblastic leukemia to chemotherapy. Blood. 2013 Mar 7; 121(10):1814-8. PMID: 23319569; PMCID: PMC3591800.
      23. De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, 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. 2013; 9(1):e1003137. PMID: 23326238; PMCID: PMC3542081.
      24. 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. 2013 Jan 3; 121(1):148-55. PMID: 23152540; PMCID: PMC3538327.
      25. Geng H, Brennan S, Milne TA, Chen WY, Li Y, Hurtz C, Kweon SM, Zickl L, Shojaee S, Neuberg D, Huang C, Biswas D, Xin Y, Racevskis J, 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 AM. Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discov. 2012 Nov; 2(11):1004-23. PMID: 23107779; PMCID: PMC3516186.
      26. Nahar R, Ramezani-Rad P, Mossner M, Duy C, Cerchietti L, Geng H, Dovat S, Jumaa H, Ye BH, Melnick A, Müschen M. Pre-B cell receptor-mediated activation of BCL6 induces pre-B cell quiescence through transcriptional repression of MYC. Blood. 2011 Oct 13; 118(15):4174-8. PMID: 21856866; PMCID: PMC3204735.
      27. 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. 2011 May 19; 473(7347):384-8. PMID: 21593872; PMCID: PMC3597744.
      28. 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. 2011; 4:32. PMID: 21486456; PMCID: PMC3086850.
      29. Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick AM, Elemento O. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood. 2010 Dec 9; 116(24):5247-55. PMID: 20736451; PMCID: PMC3012542.
      30. 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. 2010 Nov 18; 116(20):e81-9. PMID: 20610814; PMCID: PMC2993635.
      31. Iqbal J, Weisenburger DD, Greiner TC, Vose JM, McKeithan T, Kucuk C, Geng H, Deffenbacher K, Smith L, Dybkaer K, Nakamura S, Seto M, Delabie J, Berger F, Loong F, Au WY, Ko YH, Sng I, Armitage JO, Chan WC. Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma. Blood. 2010 Feb 4; 115(5):1026-36. PMID: 19965671; PMCID: PMC2817630.
      32. 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. 2009 Sep 1; 15(17):5494-502. PMID: 19706817.
        View in: PubMed
      33. 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. 2009 Jun; 23(6):1139-51. PMID: 19194464.
        View in: PubMed
      34. 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. 2008 Nov 15; 14(22):7180-7. PMID: 19010834.
        View in: PubMed
      35. Geng H, Ali HH, Chan WC. . A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling. In Ion Mandoiu, Raj Sunderraman and Alexander Zelikovsky (Eds.) Lecture Notes in Computer Science (LNCS). 2008; 4983:414-426. Springer, Heidelberg.
      36. Deng X, Geng H, Ali HH. A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data. Int J Bioinform Res Appl. 2008; 4(3):263-73. PMID: 18640903.
        View in: PubMed
      37. Geng H, Deng X, Ali HH. Message Passing Clustering (MPC): a knowledge-based framework for clustering under biological constraints. Int J Data Min Bioinform. 2008; 2(2):95-120. PMID: 18767349.
        View in: PubMed
      38. Dybkaer K, Iqbal J, Zhou G, Geng H, Xiao L, Schmitz A, 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. 2007; 8:230. PMID: 17623099; PMCID: PMC1959522.
      39. Deng X, Geng H, Ali HH. Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data. Cancer Inform. 2007; 3:183-202. PMID: 19455243; PMCID: PMC2675834.
      40. Deng X, Geng H, Bastola DR, Ali HH. Link test--A statistical method for finding prostate cancer biomarkers. Comput Biol Chem. 2006 Dec; 30(6):425-33. PMID: 17126079; PMCID: PMC1941704.
      41. Deng X, Geng H, Matache MT. Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes. Biosystems. 2007 Mar; 88(1-2):16-34. PMID: 16870321.
        View in: PubMed
      42. Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 2006 Apr; 4(2):217-39. PMID: 16819781.
        View in: PubMed
      43. Louis EE, Jr., Engberg SE, Lei R, Geng H, Sommer JA, Randriamampionona R, Randriamanana JC, Zaonarivelo JR, Andriantompohavana R, Randria G, Ramaromilanto B, Rakotoarisoa G, Rooney A, Brenneman RA. . Molecular and Morphological Analyses of the Sportive Lemurs (Family Megaladapidae: Genus Lepilemur) Reveals 11 Previously Unrecognized Species. Special Publications Museum of Texas Tech University. 2006; 49(SP):1-49.
      44. Deng X, Geng H, Ali H. EXAMINE: a computational approach to reconstructing gene regulatory networks. Biosystems. 2005 Aug; 81(2):125-36. PMID: 15951103.
        View in: PubMed
      45. Geng H, Deng X, Bastola DR, Ali HH. . On Clustering Biological Data Using Unsupervised and Semi-supervised Message Passing. Proceedings of IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE). 2005; 294-298.
      46. Deng X, Geng H, Ali H. Learning yeast gene functions from heterogeneous sources of data using hybrid weighted Bayesian networks. Proc IEEE Comput Syst Bioinform Conf. 2005; 25-34. PMID: 16447959.
        View in: PubMed
      47. Geng H, Deng X, Ali HH. . Mining Gene Microarray Data with Adaptive Feature Scaling. Proceedings of 4th IEEE International Conference on Electro Information Technology (EIT’05). 2005; 1-6.
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