Huimin Geng, PhD
Associate Professor
Laboratory Medicine
School of Medicine

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

Awards

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• Pilot for Junior Investigators in Basic and Clinical/Translational Sciences, UCSF Academic Senate, 2016-2018

Education & Training

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• Postdoc Computational Biomedicine Weill Cornell Medical College 2011
• Ph.D. Bioinformatics University of Nebraska Medical Center 2008
• MS Computer Science University of Nebraska at Omaha 2004
• BS BioPhysics, School of Gifted Young University of Science and Technology of China 1999

Interests

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• Bioinformatics (RNA-Seq
• Genomics
• Lymphoma
• methylation eRRBS-Seq
• Whole Exome-Seq
• Epigenomics
• Leukemia
• ChIP-Seq

Publications (92)

Top publication keywords:
Oncogene Proteins, FusionLymphoma, Large B-Cell, DiffusePrecursor Cells, B-LymphoidLymphoma, Non-HodgkinB-LymphocytesPrecursor Cell Lymphoblastic Leukemia-LymphomaFusion Proteins, bcr-ablMyeloid-Lymphoid Leukemia ProteinCentral Nervous System NeoplasmsProto-Oncogene Proteins c-bcl-6Germinal CenterLymphomaPrecursor B-Cell Lymphoblastic Leukemia-LymphomaGene Expression Regulation, LeukemicLeukemia

• Peripheral T-cell lymphomas expressing CD30 and CD15 expand the spectrum of anaplastic large cell lymphoma, ALK-negative.
  British journal of haematology 2024 Ganapathi KA, Nicolae A, Egan C, Geng H, Xi L, Pack SD, McFadden JR, Raffeld M, Jaffe ES, Pittaluga S
• CD46-Targeted Theranostics for PET and 225Ac-Radiopharmaceutical Therapy of Multiple Myeloma.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2024 Wadhwa A, Wang S, Patiño-Escobar B, Bidkar AP, Bobba KN, Chan E, Meher N, Bidlingmaier S, Su Y, Dhrona S, Geng H, Sarin V, VanBrocklin HF, Wilson DM, He J, Zhang L, Steri V, Wong SW, Martin TG, Seo Y,…
• Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells.
  bioRxiv : the preprint server for biology 2024 Kasap C, Izgutdina A, Patiño-Escobar B, Kang A, Chilakapati N, Akagi N, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Wicaksono G, …
• Local manufacturing processes contribute to variability in human mesenchymal stromal cell expansion while growth media supplements contribute to variability in gene expression and cell function: a Biomedical Excellence for Safer Transfusion (BEST) collaborative study.
  Cytotherapy 2023 Shaz BH, Schäfer R, Fontaine MJ, Norris PJ, McKenna DH, Jin P, Reems JA, Stroncek D, Tanashi M, Marks D, Geng H, Pati S, for Biomedical Excellence for Safer Transfusion (BEST)
• MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia.
  Nature communications 2023 Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts …

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• Artemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia.
  Frontiers in cell and developmental biology 2023 Ogana HA, Hurwitz S, Hsieh CL, Geng H, Müschen M, Bhojwani D, Wolf MA, Larocque J, Lieber MR, Kim YM
• Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling.
  bioRxiv : the preprint server for biology 2023 Lee J, Robinson ME, Sun R, Kume K, Ma N, Cosgun KN, Chan LN, Leveille E, Geng H, Vykunta VS, Shy BR, Marson A, Katz S, Chen J, Paietta E, Meffre E, Vaidehi N, Müschen M
• Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin beta receptor signaling.
  eLife 2023 Feng X, Sun R, Lee M, Chen X, Guo S, Geng H, Müschen M, Choi J, Pereira JP
• BTG1 mutation yields supercompetitive B cells primed for malignant transformation.
  Science (New York, N.Y.) 2023 Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B,…
• Lyophilized plasma resuscitation downregulates inflammatory gene expression in a mouse model of sepsis.
  The journal of trauma and acute care surgery 2022 Barry M, Wu F, Pati S, Chipman A, Geng H, Kozar R
• Overcoming Microenvironment-Mediated Chemoprotection through Stromal Galectin-3 Inhibition in Acute Lymphoblastic Leukemia.
  International journal of molecular sciences 2021 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
• Tumor metabolism and neurocognition in CNS lymphoma.
  Neuro-oncology 2021 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
• TNK1 is a ubiquitin-binding and 14-3-3-regulated kinase that can be targeted to block tumor growth.
  Nature communications 2021 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, …
• Absence of Influenza and RSV Activity in the San Francisco Bay Area during the COVID-19 Pandemic, 2020-2021
  J Adv Virol Res 2021 Drew WL, Miller S, Geng H, Ingebrigtsen D, Suslow LM and Suslow PS
• Surface Proteomics Reveals CD72 as a Target for In Vitro-Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL.
  Cancer discovery 2021 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…
• PON2 subverts metabolic gatekeeper functions in B cells to promote leukemogenesis.
  Proceedings of the National Academy of Sciences of the United States of America 2021 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
• IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells.
  Nature 2020 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,…
• BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis.
  Nature genetics 2020 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
• Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature.
  Experimental hematology 2020 Fitch B, Roy R, Geng H, Montecino-Rodriguez E, Bengtsson H, Gaillard C, Hiam K, Casero D, Olshen AB, Dorshkind K, Kogan SC
• Signalling input from divergent pathways subverts B cell transformation.
  Nature 2020 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,…
• Integrin α6 mediates the drug resistance of acute lymphoblastic B-cell leukemia.
  Blood 2020 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 …
• E2A-PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia.
  Blood 2020 Pi WC, Wang J, Shimada M, Lin JW, Geng H, Lee YL, Lu R, Li D, Wang GG, Roeder RG, Chen WY
• H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells.
  Leukemia 2020 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…
• The lysine methyltransferase SMYD2 is required for normal lymphocyte development and survival of hematopoietic leukemias.
  Genes and immunity 2020 Brown MA, Edwards MA, Alshiraihi I, Geng H, Dekker JD, Tucker HO
• DNA methyltransferase inhibitors upregulate CD38 protein expression and enhance daratumumab efficacy in multiple myeloma.
  Leukemia 2019 Choudhry P, Mariano MC, Geng H, Martin TG, Wolf JL, Wong SW, Shah N, Wiita AP
• Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia.
  Genes & development 2019 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
• Maintenance lenalidomide in primary CNS lymphoma.
  Annals of oncology : official journal of the European Society for Medical Oncology 2019 Rubenstein JL, Geng H, Vu K, Mannis G, Formaker P, Hwang J, Munster PN, Damato B
• Low-dose lenalidomide maintenance after induction therapy in older patients with primary central nervous system lymphoma.
  British journal of haematology 2019 Vu K, Mannis G, Hwang J, Geng H, Rubenstein JL
• Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis.
  Nature immunology 2018 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
• Identification of IRF8 as a potent tumor suppressor in murine acute promyelocytic leukemia.
  Blood advances 2018 Gaillard C, Surianarayanan S, Bentley T, Warr MR, Fitch B, Geng H, Passegué E, de Thé H, Kogan SC
• PRMT5 interacts with the BCL6 oncoprotein and is required for germinal center formation and lymphoma cell survival.
  Blood 2018 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
• Phase 1 investigation of lenalidomide/rituximab plus outcomes of lenalidomide maintenance in relapsed CNS lymphoma.
  Blood advances 2018 Rubenstein JL, Geng H, Fraser EJ, Formaker P, Chen L, Sharma J, Killea P, Choi K, Ventura J, Kurhanewicz J, Lowell C, Hwang J, Treseler P, Sneed PK, Li J, Wang X, Chen N, Gangoiti J, Munster PN, …
• Abstract 4975: Tumor metabolism and cognitive dysfunction in CNS lymphoma.
  Cancer Research 2018 Lakshmi Subbaraj, Huimin Geng, Jigyasa Sharma, Marisa LaFontaine, James L. Rubenstein
• Author Correction: Metabolic gatekeeper function of B-lymphoid transcription factors.
  Nature 2018 Chan LN, Chen Z, Braas D, Lee JW, Xiao G, Geng H, Cosgun KN, Hurtz C, Shojaee S, Cazzaniga V, Schjerven H, Ernst T, Hochhaus A, Kornblau SM, Konopleva M, Pufall MA, Cazzaniga G, Liu GJ, Milne TA, …
• B-Cell-Specific Diversion of Glucose Carbon Utilization Reveals a Unique Vulnerability in B Cell Malignancies.
  Cell 2018 Xiao G, Chan LN, Klemm L, Braas D, Chen Z, Geng H, Zhang QC, Aghajanirefah A, Cosgun KN, Sadras T, Lee J, Mirzapoiazova T, Salgia R, Ernst T, Hochhaus A, Jumaa H, Jiang X, Weinstock DM, Graeber TG, …
• CAMKs support development of acute myeloid leukemia.
  Journal of hematology & oncology 2018 Kang X, Cui C, Wang C, Wu G, Chen H, Lu Z, Chen X, Wang L, Huang J, Geng H, Zhao M, Chen Z, Müschen M, Wang HY, Zhang CC
• Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Pollock SB, Hu A, Mou Y, Martinko AJ, Julien O, Hornsby M, Ploder L, Adams JJ, Geng H, Müschen M, Sidhu SS, Moffat J, Wells JA
• Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia.
  Nature communications 2017 Stieglitz E, Mazor T, Olshen AB, Geng H, Gelston LC, Akutagawa J, Lipka DB, Plass C, Flotho C, Chehab FF, Braun BS, Costello JF, Loh ML
• BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells.
  Cancer discovery 2017 Valls E, Lobry C, Geng H, Wang L, Cardenas M, Rivas M, Cerchietti L, Oh P, Yang SN, Oswald E, Graham CW, Jiang Y, Hatzi K, Agirre X, Perkey E, Li Z, Tam W, Bhatt K, Leonard JP, Zweidler-McKay PA, …
• Metabolic gatekeeper function of B-lymphoid transcription factors.
  Nature 2017 Chan LN, Chen Z, Braas D, Lee JW, Xiao G, Geng H, Cosgun KN, Hurtz C, Shojaee S, Cazzaniga V, Schjerven H, Ernst T, Hochhaus A, Kornblau SM, Konopleva M, Pufall MA, Cazzaniga G, Liu GJ, Milne TA, …
• Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL.
  The Journal of experimental medicine 2017 Schjerven H, Ayongaba EF, Aghajanirefah A, McLaughlin J, Cheng D, Geng H, Boyd JR, Eggesbø LM, Lindeman I, Heath JL, Park E, Witte ON, Smale ST, Frietze S, Müschen M
• MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.
  Cell reports 2017 Kerry J, Godfrey L, Repapi E, Tapia M, Blackledge NP, Ma H, Ballabio E, O'Byrne S, Ponthan F, Heidenreich O, Roy A, Roberts I, Konopleva M, Klose RJ, Geng H, Milne TA
• MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation.
  Experimental hematology 2016 Godfrey L, Kerry J, Thorne R, Repapi E, Davies JO, Tapia M, Ballabio E, Hughes JR, Geng H, Konopleva M, Milne TA
• CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.
  Cancer discovery 2016 Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, …
• Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.
  The Journal of clinical investigation 2016 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, …
• PTEN opposes negative selection and enables oncogenic transformation of pre-B cells.
  Nature medicine 2016 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
• Corrigendum: Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia.
  Nature 2016 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,…
• Deregulated expression of the HSP40 family members Auxilin-1 and -2 is indicative of proteostasis imbalance and predicts patient outcome in Ph(+) leukemia.
  Experimental hematology & oncology 2016 Vieri M, Geng H, Patterson JB, Panse J, Wilop S, Samali A, Chevet E, Kharabi Masouleh B
• MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199.
  Cell reports 2015 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…
• Erratum: TET1 is a tumor suppressor of hematopoietic malignancy.
  Nature immunology 2015 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, …
• Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia.
  Cancer cell 2015 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…
• Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia.
  Nature immunology 2015 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
• TET1 is a tumor suppressor of hematopoietic malignancy.
  Nature immunology 2015 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, …
• Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia.
  Nature 2015 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,…
• Identification of FOXM1 as a therapeutic target in B-cell lineage acute lymphoblastic leukaemia.
  Nature communications 2015 Buchner M, Park E, Geng H, Klemm L, Flach J, Passegué E, Schjerven H, Melnick A, Paietta E, Kopanja D, Raychaudhuri P, 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 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…
• IL10 receptor is a novel therapeutic target in DLBCLs.
  Leukemia 2015 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
• Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2015 Küçük C, Hu X, Jiang B, Klinkebiel D, Geng H, Gong Q, Bouska A, Iqbal J, Gaulard P, McKeithan TW, Chan WC
• Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia.
  Proceedings of the National Academy of Sciences of the United States of America 2014 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
• Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes.
  Blood 2014 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
• Cooperative transcriptional repression by BCL6 and BACH2 in germinal center B-cell differentiation.
  Blood 2013 Huang C, Geng H, Boss I, Wang L, Melnick A
• A TAF4 coactivator function for E proteins that involves enhanced TFIID binding.
  Genes & development 2013 Chen WY, Zhang J, Geng H, Du Z, Nakadai T, Roeder RG
• BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint.
  Nature medicine 2013 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, …
• Personalized synthetic lethality induced by targeting RAD52 in leukemias identified by gene mutation and expression profile.
  Blood 2013 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, …
• Imatinib disrupts lymphoma angiogenesis by targeting vascular pericytes.
  Blood 2013 Ruan J, Luo M, Wang C, Fan L, Yang SN, Cardenas M, Geng H, Leonard JP, Melnick A, Cerchietti L, Hajjar KA
• RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction.
  Cell reports 2013 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
• Integrin alpha4 blockade sensitizes drug resistant pre-B acute lymphoblastic leukemia to chemotherapy.
  Blood 2013 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, …
• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.
  PLoS genetics 2013 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
• SOX4 enables oncogenic survival signals in acute lymphoblastic leukemia.
  Blood 2012 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
• Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia.
  Cancer discovery 2012 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,…
• Pre-B cell receptor-mediated activation of BCL6 induces pre-B cell quiescence through transcriptional repression of MYC.
  Blood 2011 Nahar R, Ramezani-Rad P, Mossner M, Duy C, Cerchietti L, Geng H, Dovat S, Jumaa H, Ye BH, Melnick A, Müschen M
• BCL6 enables Ph+ acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition.
  Nature 2011 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,…
• Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma.
  BMC medical genomics 2011 Geng H, Iqbal J, Chan WC, Ali HH
• EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis.
  Blood 2010 Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick AM, Elemento O
• DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma.
  Blood 2010 Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A
• Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma.
  Blood 2009 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, …
• A new immunostain algorithm classifies diffuse large B-cell lymphoma into molecular subtypes with high accuracy.
  Clinical cancer research : an official journal of the American Association for Cancer Research 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, …
• Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies.
  Leukemia 2009 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
• Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2008 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
• 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 Geng H, Ali HH, Chan WC
• A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data.
  International journal of bioinformatics research and applications 2008 Deng X, Geng H, Ali HH
• Message Passing Clustering (MPC): a knowledge-based framework for clustering under biological constraints.
  International journal of data mining and bioinformatics 2008 Geng H, Deng X, Ali HH
• 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 Dybkaer K, Iqbal J, Zhou G, Geng H, Xiao L, Schmitz A, d'Amore F, Chan WC
• Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data.
  Cancer informatics 2007 Deng X, Geng H, Ali HH
• Link test--A statistical method for finding prostate cancer biomarkers.
  Computational biology and chemistry 2006 Deng X, Geng H, Bastola DR, Ali HH
• Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes.
  Bio Systems 2006 Deng X, Geng H, Matache MT
• Joint learning of gene functions--a Bayesian network model approach.
  Journal of bioinformatics and computational biology 2006 Deng X, Geng H, Ali HH
• 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 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
• EXAMINE: a computational approach to reconstructing gene regulatory networks.
  Bio Systems 2005 Deng X, Geng H, Ali H
• Learning yeast gene functions from heterogeneous sources of data using hybrid weighted Bayesian networks.
  Proceedings. IEEE Computational Systems Bioinformatics Conference 2005 Deng X, Geng H, Ali H
• Mining Gene Microarray Data with Adaptive Feature Scaling
  Proceedings of 4th IEEE International Conference on Electro Information Technology (EIT’05) 2005 Geng H, Deng X, Ali HH
• On Clustering Biological Data Using Unsupervised and Semi-supervised Message Passing
  Proceedings of IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE) 2005 Geng H, Deng X, Bastola DR, Ali HH