California NanoSystems Institute
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Thomas Graeber, Ph.D.

Professor, Molecular & Medical Pharmacology
Member, California NanoSystems Institute, Crump Institute for Molecular Imaging
Research Fellow, Alfred P. Sloan Foundation

Ph.D., Stanford University

Contact Information:
Work Email Address:
Laboratory Address: Laboratory
4338 CNSI, Crump Institute
570 Westwood Plaza
Los Angeles, CA 90095
Office Address: Office
4341 CNSI, Crump Institute
570 Westwood Plaza,
Box 951770
Los Angeles, CA 90095
Lab Number: (310) 206-7054 Lab
Office Phone Number: (310) 206-6122 Office
Research Interests:

Systems biology of cancer and immune signaling and metabolism
My group is working to understand cancer signaling and metabolism from a systems view. We focus on developing genome-, proteome- and metabolome-wide assays, and applying these assays to measuring and computationally modeling aberrant function in cancer cells. Through collaboration with clinical scientists, we work directly with patient samples and aim to translate our discoveries to clinical applications. We collect high dimensionality data using mass spectrometry-based phosphoproteomic and metabolomic profiling. To integratively analyze this data, we develop computational approaches aimed at overlaying the raw data with known signaling and metabolic network structures. A point of emphasis is how cellular signaling and metabolism is rewired when cancers become resistant to molecularly targeted therapies (e.g. the mutant BRAF kinase inhibitor used in melanoma). Our results have pointed us to the contributions of feedback loops in maintaining cancer signaling and metabolism homeostasis, and we are exploring therapeutic approaches to perturbing these loops synergistically to disrupt cellular equilibrium and induce death in cancer cells. In modeling cancer, one of our goals is to identify minimal sets of informative components that best reflect the state of the cell and serve as molecular targets for diagnostics, imaging, and patient tailored treatment. As with all of systems biology, our research relies on an interdisciplinary approach that merges biology, chemistry, mathematics and computation / bioinformatics .

Additional Information:

Thomas Graeber is faculty in the Department of Molecular and Medical Pharmacology and a member of the Crump Institute for Molecular Imaging at UCLA, and is a Melanoma Research Alliance Established Investigator and an American Cancer Society Research Scholar. His background includes physics, cancer biology, signal transduction, metabolism, computational biology, proteomics, and metabolomics. His work builds experimental and computational approaches to studying cancer signaling and metabolism from a systems perspective. His work in cancer biology started with the discovery that hypoxia, a common feature of solid tumors, induces p53 protein levels, and that p53 deficient cells are less prone to undergo apoptosis in low oxygen conditions, conferring a survival advantage. These findings led to a model of hypoxia as a physiological selective force against apoptosis-competent cells in developing tumors, thus explaining the previously unaccounted for high frequency of p53 mutations in cancer. In computational biology, he developed an algorithm to identify potential autocrine signaling loops in cancer using gene expression microarray data. The algorithm integrates biological data (in this case, cognate ligand-receptor partners) into the analysis of raw gene expression data, and a number of leads from this method have been verified to play critical roles in cell signaling. His work in integrated signaling and metabolic networks has repeatedly pointed to the importance of negative and positive feedback loops in cancer phenotypes, and he is investigating approaches to therapeutically disrupting cancer-specific reliance on these feedback mechanisms.

Selected Publications:

Graham, NA, A Minasyan, A Lomova, A Cass, NG Balanis, M Friedman, S Chan, S Zhao, A Delgado, J Go, L Beck, C Hurtz, C Ng, R Qiao, J ten Hoeve, N Palaskas, H Wu, M Müschen, AS Multani, E Port, S Larson, N Schultz, D Braas, H Christofk, I Mellinghoff, & TG Graeber, Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures, Molecular Systems Biology, 2017, 13 (2), 914.
Chan Lai N, Chen Zhengshan, Braas Daniel, Lee Jae-Woong, Xiao Gang, Geng Huimin, Cosgun Kadriye Nehir, Hurtz Christian, Shojaee Seyedmehdi, Cazzaniga Valeria, Schjerven Hilde, Ernst Thomas, Hochhaus Andreas, Kornblau Steven M, Konopleva Marina, Pufall Miles A, Cazzaniga Giovanni, Liu Grace J, Milne Thomas A, Koeffler H Phillip, Ross Theodora S, Sanchez-Garcia Isidro, Borkhardt Arndt, Yamamoto Keith R, Dickins Ross A, Graeber Thomas G, Muschen Markus, Metabolic gatekeeper function of B-lymphoid transcription factors, Nature, 2017, 1-5.
Shin Daniel Sanghoon, Zaretsky Jesse M, Escuin-Ordinas Helena, Garcia-Diaz Angel, Hu-Lieskovan Siwen, Kalbasi Anusha, Grasso Catherine S, Hugo Willy, Sandoval Salemiz, Torrejon Davis Y, Palaskas Nicolaos, Rodriguez Gabriel Abril, Parisi Giulia, Azhdam Ariel, Chmielowski Bartosz, Cherry Grace, Seja Elizabeth, Berent-Maoz Beata, Shintaku I Peter, Le Dung T, Pardoll Drew M, Diaz Luis A, Tumeh Paul C, Graeber Thomas G, Lo Roger S, Comin-Anduix Begoña, Ribas Antoni, Primary Resistance to PD-1 Blockade Mediated by JAK1/2 Mutations, Cancer discovery, 2017, 7 (2), 188-201.
Momcilovic Milica, Bailey Sean T, Lee Jason T, Fishbein Michael C, Magyar Clara, Braas Daniel, Graeber Thomas, Jackson Nicholas J, Czernin Johannes, Emberley Ethan, Gross Matthew, Janes Julie, Mackinnon Andy, Pan Alison, Rodriguez Mirna, Works Melissa, Zhang Winter, Parlati Francesco, Demo Susan, Garon Edward, Krysan Kostyantyn, Walser Tonya C, Dubinett Steven M, Sadeghi Saman, Christofk Heather R, Shackelford David B, Targeted Inhibition of EGFR and Glutaminase Induces Metabolic Crisis in EGFR Mutant Lung Cancer, Cell reports, 2017, 18 (3), 601-610.
Titz Bjoern, Lomova Anastasia, Le Allison, Hugo Willy, Kong Xiangju, Ten Hoeve Johanna, Friedman Michael, Shi Hubing, Moriceau Gatien, Song Chunying, Hong Aayoung, Atefi Mohammad, Li Richard, Komisopoulou Evangelia, Ribas Antoni, Lo Roger S, Graeber Thomas G, JUN dependency in distinct early and late BRAF inhibition adaptation states of melanoma, Cell discovery, 2016, 2 (3), 16028.
Atefi Mohammad, Titz Bjoern, Tsoi Jennifer, Avramis Earl, Le Allison, Ng Charles, Lomova Anastasia, Lassen Amanda, Friedman Michael, Chmielowski Bartosz, Ribas Antoni, Graeber Thomas G, CRAF R391W is a melanoma driver oncogene, Scientific reports, 2016, 6 (4), 27454.
Drake Justin M, Paull Evan O, Graham Nicholas A, Lee John K, Smith Bryan A, Titz Bjoern, Stoyanova Tanya, Faltermeier Claire M, Uzunangelov Vladislav, Carlin Daniel E, Fleming Daniel Teo, Wong Christopher K, Newton Yulia, Sudha Sud, Vashisht Ajay A, Huang Jiaoti, Wohlschlegel James A, Graeber Thomas G, Witte Owen N, Stuart Joshua M, Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer, Cell, 2016, 166 (4), 1041-54.
Zaretsky Jesse M, Garcia-Diaz Angel, Shin Daniel S, Escuin-Ordinas Helena, Hugo Willy, Hu-Lieskovan Siwen, Torrejon Davis Y, Abril-Rodriguez Gabriel, Sandoval Salemiz, Barthly Lucas, Saco Justin, Homet Moreno Blanca, Mezzadra Riccardo, Chmielowski Bartosz, Ruchalski Kathleen, Shintaku I Peter, Sanchez Phillip J, Puig-Saus Cristina, Cherry Grace, Seja Elizabeth, Kong Xiangju, Pang Jia, Berent-Maoz Beata, Comin-Anduix Begoña, Graeber Thomas G, Tumeh Paul C, Schumacher Ton N M, Lo Roger S, Ribas Antoni, Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma, The New England journal of medicine, 2016, 375 (9), 819-29.
Krall Abigail S, Xu Shili, Graeber Thomas G, Braas Daniel, Christofk Heather R, Asparagine promotes cancer cell proliferation through use as an amino acid exchange factor, Nature communications, 2016, 7 (6), 11457.
Knight Deborah A, Ngiow Shin Foong, Li Ming, Parmenter Tiffany, Mok Stephen, Cass Ashley, Haynes Nicole M, Kinross Kathryn, Yagita Hideo, Koya Richard C, Graeber Thomas G, Ribas Antoni, McArthur Grant A, Smyth Mark J, Host immunity contributes to the anti-melanoma activity of BRAF inhibitors, The Journal of clinical investigation, 2016, 126 (1), 402-3.
Hong Candice Sun, Graham Nicholas A, Gu Wen, Espindola Camacho Carolina, Mah Vei, Maresh Erin L, Alavi Mohammed, Bagryanova Lora, Krotee Pascal A L, Gardner Brian K, Behbahan Iman Saramipoor, Horvath Steve, Chia David, Mellinghoff Ingo K, Hurvitz Sara A, Dubinett Steven M, Critchlow Susan E, Kurdistani Siavash K, Goodglick Lee, Braas Daniel, Graeber Thomas G, Christofk Heather R, MCT1 Modulates Cancer Cell Pyruvate Export and Growth of Tumors that Co-express MCT1 and MCT4, Cell reports, 2016, 14 (7), 1590-601.
Li Xiaoxiao, LeBlanc James, Elashoff David, McHardy Ian, Tong Maomeng, Roth Bennett, Ippoliti Andrew, Barron Gildardo, McGovern Dermot, McDonald Keely, Newberry Rodney, Graeber Thomas, Horvath Steve, Goodglick Lee, Braun Jonathan, Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease, Cellular and molecular gastroenterology and hepatology, 2016, 2 (5), 567-583.
Wu Ting-Hsiang, Sagullo Enrico, Case Dana, Zheng Xin, Li Yanjing, Hong Jason S, TeSlaa Tara, Patananan Alexander N, McCaffery J Michael, Niazi Kayvan, Braas Daniel, Koehler Carla M, Graeber Thomas G, Chiou Pei-Yu, Teitell Michael A, Mitochondrial Transfer by Photothermal Nanoblade Restores Metabolite Profile in Mammalian Cells, Cell metabolism, 2016, 23 (5), 921-9.
Sood Anup, Miller Alexandra M, Brogi Edi, Sui Yunxia, Armenia Joshua, McDonough Elizabeth, Santamaria-Pang Alberto, Carlin Sean, Stamper Aleksandra, Campos Carl, Pang Zhengyu, Li Qing, Port Elisa, Graeber Thomas G, Schultz Nikolaus, Ginty Fiona, Larson Steven M, Mellinghoff Ingo K, Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism, JCI insight, 2016, 1 (6), 921-9.
Shojaee Seyedmehdi, Chan Lai N, Buchner Maike, Cazzaniga Valeria, Cosgun Kadriye Nehir, Geng Huimin, Qiu Yi Hua, von Minden Marcus Dühren, Ernst Thomas, Hochhaus Andreas, Cazzaniga Giovanni, Melnick Ari, Kornblau Steven M, Graeber Thomas G, Wu Hong, Jumaa Hassan, Müschen Markus, PTEN opposes negative selection and enables oncogenic transformation of pre-B cells, Nature medicine, 2016, 22 (4), 379-87.
Court Colin M, Ankeny Jacob S, Sho Shonan, Hou Shuang, Li Qingyu, Hsieh Carolyn, Song Min, Liao Xinfang, Rochefort Matthew M, Wainberg Zev A, Graeber Thomas G, Tseng Hsian-Rong, Tomlinson James S, Reality of Single Circulating Tumor Cell Sequencing for Molecular Diagnostics in Pancreatic Cancer, The Journal of molecular diagnostics : JMD, 2016, 18 (5), 688-96.
Homet Moreno Blanca, Zaretsky Jesse M, Garcia-Diaz Angel, Tsoi Jennifer, Parisi Giulia, Robert Lidia, Meeth Katrina, Ndoye Abibatou, Bosenberg Marcus, Weeraratna Ashani T, Graeber Thomas G, Comin-Anduix Begoña, Hu-Lieskovan Siwen, Ribas Antoni, Response to Programmed Cell Death-1 Blockade in a Murine Melanoma Syngeneic Model Requires Costimulation, CD4, and CD8 T Cells, Cancer immunology research, 2016, 4 (10), 845-857.
Li Wei, Cohen Alexa, Sun Yin, Squires Jill, Braas Daniel, Graeber Thomas G, Du Lin, Li Gang, Li Zhen, Xu Xiang, Chen Xufeng, Huang Jiaoti, The Role of CD44 in Glucose Metabolism in Prostatic Small Cell Neuroendocrine Carcinoma, Molecular cancer research : MCR, 2016, 14 (4), 344-53.
TeSlaa Tara, Chaikovsky Andrea C, Lipchina Inna, Escobar Sandra L, Hochedlinger Konrad, Huang Jing, Graeber Thomas G, Braas Daniel, Teitell Michael A, alpha-Ketoglutarate Accelerates the Initial Differentiation of Primed Human Pluripotent Stem Cells, Cell metabolism, 2016, 24 (3), 485-93.
Fu Xudong, Chin Randall M, Vergnes Laurent, Hwang Heejun, Deng Gang, Xing Yanpeng, Pai Melody Y, Li Sichen, Ta Lisa, Fazlollahi Farbod, Chen Chuo, Prins Robert M, Teitell Michael A, Nathanson David A, Lai Albert, Faull Kym F, Jiang Meisheng, Clarke Steven G, Cloughesy Timothy F, Graeber Thomas G, Braas Daniel, Christofk Heather R, Jung Michael E, Reue Karen, Huang Jing, 2-Hydroxyglutarate Inhibits ATP Synthase and mTOR Signaling, Cell metabolism, 2015, 22 (3), 508-15.
Atefi Mohammad, Titz Bjoern, Avramis Earl, Ng Charles, Wong Deborah J L, Lassen Amanda, Cerniglia Michael, Escuin-Ordinas Helena, Foulad David, Comin-Anduix Begonya, Graeber Thomas G, Ribas Antoni, Combination of pan-RAF and MEK inhibitors in NRAS mutant melanoma, Molecular cancer, 2015, 14 (279), 27.
Inkeles Megan S, Scumpia Philip O, Swindell William R, Lopez David, Teles Rosane M B, Graeber Thomas G, Meller Stephan, Homey Bernhard, Elder James T, Gilliet Michel, Modlin Robert L, Pellegrini Matteo, Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis, The Journal of investigative dermatology, 2015, 135 (1), 151-9.
Goodwin Jonathan F, Kothari Vishal, Drake Justin M, Zhao Shuang, Dylgjeri Emanuela, Dean Jeffry L, Schiewer Matthew J, McNair Christopher, Jones Jennifer K, Aytes Alvaro, Magee Michael S, Snook Adam E, Zhu Ziqi, Den Robert B, Birbe Ruth C, Gomella Leonard G, Graham Nicholas A, Vashisht Ajay A, Wohlschlegel James A, Graeber Thomas G, Karnes R Jeffrey, Takhar Mandeep, Davicioni Elai, Tomlins Scott A, Abate-Shen Cory, Sharifi Nima, Witte Owen N, Feng Felix Y, Knudsen Karen E, DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis, Cancer cell, 2015, 28 (1), 97-113.
Ting Pamela Y, Damoiseaux Robert, Titz Björn, Bradley Kenneth A, Graeber Thomas G, Fernández-Vega Virneliz, Bannister Thomas D, Chase Peter, Nair Reji, Scampavia Louis, Hodder Peter, Spicer Timothy P, Colicelli John, Identification of small molecules that disrupt signaling between ABL and its positive regulator RIN1, PloS one, 2015, 10 (3), e0121833.
Hu-Lieskovan Siwen, Mok Stephen, Homet Moreno Blanca, Tsoi Jennifer, Robert Lidia, Goedert Lucas, Pinheiro Elaine M, Koya Richard C, Graeber Thomas G, Comin-Anduix Begoña, Ribas Antoni, Improved antitumor activity of immunotherapy with BRAF and MEK inhibitors in BRAF(V600E) melanoma, Science translational medicine, 2015, 7 (279), 279ra41.
Mok Stephen, Tsoi Jennifer, Koya Richard C, Hu-Lieskovan Siwen, West Brian L, Bollag Gideon, Graeber Thomas G, Ribas Antoni, Inhibition of colony stimulating factor-1 receptor improves antitumor efficacy of BRAF inhibition, BMC cancer, 2015, 15 (7552), 356.
Ploper Diego, Taelman Vincent F, Robert Lidia, Perez Brian S, Titz Björn, Chen Hsiao-Wang, Graeber Thomas G, von Euw Erika, Ribas Antoni, De Robertis Edward M, MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cells, Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (5), E420-9.
Thai Minh, Thaker Shivani K, Feng Jun, Du Yushen, Hu Hailiang, Ting Wu Ting, Graeber Thomas G, Braas Daniel, Christofk Heather R, MYC-induced reprogramming of glutamine catabolism supports optimal virus replication, Nature communications, 2015, 6 (1), 8873.
Chen Zhengshan, Shojaee Seyedmehdi, Buchner Maike, Geng Huimin, Lee Jae Woong, Klemm Lars, Titz Björn, Graeber Thomas G, Park Eugene, Tan Ying Xim, Satterthwaite Anne, Paietta Elisabeth, Hunger Stephen P, Willman Cheryl L, Melnick Ari, Loh Mignon L, Jung Jae U, Coligan John E, Bolland Silvia, Mak Tak W, Limnander Andre, Jumaa Hassan, Reth Michael, Weiss Arthur, Lowell Clifford A, Müschen Markus, Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia, Nature, 2015, 521 (7552), 357-61.
Ting Pamela Y, Johnson Christian W, Fang Cong, Cao Xiaoqing, Graeber Thomas G, Mattos Carla, Colicelli John, Tyrosine phosphorylation of RAS by ABL allosterically enhances effector binding, FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 2015, 29 (9), 3750-61.
Thai Minh, Graham Nicholas A, Braas Daniel, Nehil Michael, Komisopoulou Evangelia, Kurdistani Siavash K, McCormick Frank, Graeber Thomas G, Christofk Heather R, Adenovirus E4ORF1-induced MYC activation promotes host cell anabolic glucose metabolism and virus replication, Cell metabolism, 2014, 19 (4), 694-701.
Wong Deborah J L, Robert Lidia, Atefi Mohammad S, Lassen Amanda, Avarappatt Geetha, Cerniglia Michael, Avramis Earl, Tsoi Jennifer, Foulad David, Graeber Thomas G, Comin-Anduix Begonya, Samatar Ahmed, Lo Roger S, Ribas Antoni, Antitumor activity of the ERK inhibitor SCH772984 [corrected] against BRAF mutant, NRAS mutant and wild-type melanoma, Molecular cancer, 2014, 13 (11), 194.
Escuin-Ordinas Helena, Atefi Mohammad, Fu Yong, Cass Ashley, Ng Charles, Huang Rong Rong, Yashar Sharona, Comin-Anduix Begonya, Avramis Earl, Cochran Alistair J, Marais Richard, Lo Roger S, Graeber Thomas G, Herschman Harvey R, Ribas Antoni, COX-2 inhibition prevents the appearance of cutaneous squamous cell carcinomas accelerated by BRAF inhibitors, Molecular oncology, 2014, 8 (2), 250-60.
Robert Lidia, Tsoi Jennifer, Wang Xiaoyan, Emerson Ryan, Homet Blanca, Chodon Thinle, Mok Stephen, Huang Rong Rong, Cochran Alistair J, Comin-Anduix Begoña, Koya Richard C, Graeber Thomas G, Robins Harlan, Ribas Antoni, CTLA4 blockade broadens the peripheral T-cell receptor repertoire, Clinical cancer research : an official journal of the American Association for Cancer Research, 2014, 20 (9), 2424-32.
Graham Nicholas A, Graeber Thomas G, Complexity of metastasis-associated SDF-1 ligand signaling in breast cancer stem cells, Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (21), 7503-4.
Atefi Mohammad, Avramis Earl, Lassen Amanda, Wong Deborah J L, Robert Lidia, Foulad David, Cerniglia Michael, Titz Bjoern, Chodon Thinle, Graeber Thomas G, Comin-Anduix Begonya, Ribas Antoni, Effects of MAPK and PI3K pathways on PD-L1 expression in melanoma, Clinical cancer research : an official journal of the American Association for Cancer Research, 2014, 20 (13), 3446-57.
Mok Stephen, Koya Richard C, Tsui Christopher, Xu Jingying, Robert Lídia, Wu Lily, Graeber Thomas G, West Brian L, Bollag Gideon, Ribas Antoni, Inhibition of CSF-1 receptor improves the antitumor efficacy of adoptive cell transfer immunotherapy, Cancer research, 2014, 74 (1), 153-61.
Müller Judith, Krijgsman Oscar, Tsoi Jennifer, Robert Lidia, Hugo Willy, Song Chunying, Kong Xiangju, Possik Patricia A, Cornelissen-Steijger Paulien D M, Foppen Marnix H Geukes, Kemper Kristel, Goding Colin R, McDermott Ultan, Blank Christian, Haanen John, Graeber Thomas G, Ribas Antoni, Lo Roger S, Peeper Daniel S, Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma, Nature communications, 2014, 5 (3), 5712.
Zimman Alejandro, Titz Bjoern, Komisopoulou Evangelia, Biswas Sudipta, Graeber Thomas G, Podrez Eugene A, Phosphoproteomic analysis of platelets activated by pro-thrombotic oxidized phospholipids and thrombin, PloS one, 2014, 9 (1), e84488.
Anderson Jennifer L, Titz Björn, Akiyama Ryan, Komisopoulou Evangelia, Park Ann, Tap William D, Graeber Thomas G, Denny Christopher T, Phosphoproteomic profiling reveals IL6-mediated paracrine signaling within the Ewing sarcoma family of tumors, Molecular cancer research : MCR, 2014, 12 (12), 1740-54.
Tong Maomeng, McHardy Ian, Ruegger Paul, Goudarzi Maryam, Kashyap Purna C, Haritunians Talin, Li Xiaoxiao, Graeber Thomas G, Schwager Emma, Huttenhower Curtis, Fornace Albert J, Sonnenburg Justin L, McGovern Dermot P B, Borneman James, Braun Jonathan, Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism, The ISME journal, 2014, 8 (11), 2193-206.
Williams Kevin J, Argus Joseph P, Zhu Yue, Wilks Moses Q, Marbois Beth N, York Autumn G, Kidani Yoko, Pourzia Alexandra L, Akhavan David, Lisiero Dominique N, Komisopoulou Evangelia, Henkin Amy H, Soto Horacio, Chamberlain Brian T, Vergnes Laurent, Jung Michael E, Torres Jorge Z, Liau Linda M, Christofk Heather R, Prins Robert M, Mischel Paul S, Reue Karen, Graeber Thomas G, Bensinger Steven J, An Essential Requirement for the SCAP/SREBP Signaling Axis to Protect Cancer Cells from Lipotoxicity, Cancer research, 2013, 73 (9), 2850-2862.
Rohle Dan, Popovici-Muller Janeta, Palaskas Nicolaos, Turcan Sevin, Grommes Christian, Campos Carl, Tsoi Jennifer, Clark Owen, Oldrini Barbara, Komisopoulou Evangelia, Kunii Kaiko, Pedraza Alicia, Schalm Stefanie, Silverman Lee, Miller Alexandra, Wang Fang, Yang Hua, Chen Yue, Kernytsky Andrew, Rosenblum Marc K, Liu Wei, Biller Scott A, Su Shinsan M, Brennan Cameron W, Chan Timothy A, Graeber Thomas G, Yen Katharine E, Mellinghoff Ingo K, An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells, Science (New York, N.Y.), 2013, 340 (6132), 626-30.
Swaminathan Srividya, Huang Chuanxin, Geng Huimin, Chen Zhengshan, Harvey Richard, Kang Huining, Ng Carina, Titz Björn, Hurtz Christian, Sadiyah Mohammed Firas, Nowak Daniel, Thoennissen Gabriela B, Rand Vikki, Graeber Thomas G, Koeffler H Phillip, Carroll William L, Willman Cheryl L, Hall Andrew G, Igarashi Kazuhiko, Melnick Ari, Müschen Markus, BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint, Nature medicine, 2013, 19 (8), 1014-22.
Ahler Ethan, Sullivan William J, Cass Ashley, Braas Daniel, York Autumn G, Bensinger Steven J, Graeber Thomas G, Christofk Heather R, Doxycycline alters metabolism and proliferation of human cell lines, PloS one, 2013, 8 (5), e64561.
Knight Deborah A, Ngiow Shin Foong, Li Ming, Parmenter Tiffany, Mok Stephen, Cass Ashley, Haynes Nicole M, Kinross Kathryn, Yagita Hideo, Koya Richard C, Graeber Thomas G, Ribas Antoni, McArthur Grant A, Smyth Mark J, Host immunity contributes to the anti-melanoma activity of BRAF inhibitors, The Journal of clinical investigation, 2013, 123 (3), 1371-81.
McHardy Ian H, Goudarzi Maryam, Tong Maomeng, Ruegger Paul M, Schwager Emma, Weger John R, Graeber Thomas G, Sonnenburg Justin L, Horvath Steve, Huttenhower Curtis, McGovern Dermot Pb, Fornace Albert J, Borneman James, Braun Jonathan, Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships, Microbiome, 2013, 1 (1), 17.
Drake Justin M, Graham Nicholas A, Lee John K, Stoyanova Tanya, Faltermeier Claire M, Sud Sudha, Titz Björn, Huang Jiaoti, Pienta Kenneth J, Graeber Thomas G, Witte Owen N, Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinase targets, Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (49), E4762-9.
Zimman Alejandro, Berliner Judith A, Graeber Thomas G, Phosphoproteomic analysis of aortic endothelial cells activated by oxidized phospholipids, Methods in molecular biology (Clifton, N.J.), 2013, 1000 (3), 53-69.
Kidani Yoko, Elsaesser Heidi, Hock M Benjamin, Vergnes Laurent, Williams Kevin J, Argus Joseph P, Marbois Beth N, Komisopoulou Evangelia, Wilson Elizabeth B, Osborne Timothy F, Graeber Thomas G, Reue Karen, Brooks David G, Bensinger Steven J, Sterol regulatory element-binding proteins are essential for the metabolic programming of effector T cells and adaptive immunity, Nature immunology, 2013, 14 (5), 489-99.
Teles Rosane M B, Graeber Thomas G, Krutzik Stephan R, Montoya Dennis, Schenk Mirjam, Lee Delphine J, Komisopoulou Evangelia, Kelly-Scumpia Kindra, Chun Rene, Iyer Shankar S, Sarno Euzenir N, Rea Thomas H, Hewison Martin, Adams John S, Popper Stephen J, Relman David A, Stenger Steffen, Bloom Barry R, Cheng Genhong, Modlin Robert L, Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses, Science (New York, N.Y.), 2013, 339 (6126), 1448-53.
Koya Richard C, Mok Stephen, Otte Nicholas, Blacketor Kevin J, Comin-Anduix Begonya, Tumeh Paul C, Minasyan Aspram, Graham Nicholas A, Graeber Thomas G, Chodon Thinle, Ribas Antoni, BRAF inhibitor vemurafenib improves the antitumor activity of adoptive cell immunotherapy, Cancer research, 2012, 72 (16), 3928-37.
Tran Linh M, Chang Chun-Ju, Plaisier Seema, Wu Shumin, Dang Julie, Mischel Paul S, Liao James C, Graeber Thomas G, Wu Hong, Determining PTEN functional status by network component deduced transcription factor activities, PloS one, 2012, 7 (2), e31053.
Graham Nicholas A, Tahmasian Martik, Kohli Bitika, Komisopoulou Evangelia, Zhu Maggie, Vivanco Igor, Teitell Michael A, Wu Hong, Ribas Antoni, Lo Roger S, Mellinghoff Ingo K, Mischel Paul S, Graeber Thomas G, Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death, Molecular systems biology, 2012, 8 (16), 589.
Liu Philip T, Wheelwright Matthew, Teles Rosane, Komisopoulou Evangelia, Edfeldt Kristina, Ferguson Benjamin, Mehta Manali D, Vazirnia Aria, Rea Thomas H, Sarno Euzenir N, Graeber Thomas G, Modlin Robert L, MicroRNA-21 targets the vitamin D-dependent antimicrobial pathway in leprosy, Nature medicine, 2012, 18 (2), 267-73.
Schenk Mirjam, Krutzik Stephan R, Sieling Peter A, Lee Delphine J, Teles Rosane M B, Ochoa Maria Teresa, Komisopoulou Evangelia, Sarno Euzenir N, Rea Thomas H, Graeber Thomas G, Kim Soohyun, Cheng Genhong, Modlin Robert L, NOD2 triggers an interleukin-32-dependent human dendritic cell program in leprosy, Nature medicine, 2012, 18 (4), 555-63.
Drake Justin M, Graham Nicholas A, Stoyanova Tanya, Sedghi Amir, Goldstein Andrew S, Cai Houjian, Smith Daniel A, Zhang Hong, Komisopoulou Evangelia, Huang Jiaoti, Graeber Thomas G, Witte Owen N, Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression, Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (5), 1643-8.
Palaskas Nicolaos, Larson Steven M, Schultz Nikolaus, Komisopoulou Evangelia, Wong Justin, Rohle Dan, Campos Carl, Yannuzzi Nicolas, Osborne Joseph R, Linkov Irina, Kastenhuber Edward R, Taschereau Richard, Plaisier Seema B, Tran Chris, Heguy Adriana, Wu Hong, Sander Chris, Phelps Michael E, Brennan Cameron, Port Elisa, Huse Jason T, Graeber Thomas G, Mellinghoff Ingo K, 18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers, Cancer research, 2011, 71 (15), 5164-74.
Li Xiaoxiao, LeBlanc James, Truong Allison, Vuthoori Ravi, Chen Sharon S, Lustgarten Jonathan L, Roth Bennett, Allard Jeff, Ippoliti Andrew, Presley Laura L, Borneman James, Bigbee William L, Gopalakrishnan Vanathi, Graeber Thomas G, Elashoff David, Braun Jonathan, Goodglick Lee, A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface, PloS one, 2011, 6 (11), e26542.
Zuber Johannes, Rappaport Amy R, Luo Weijun, Wang Eric, Chen Chong, Vaseva Angelina V, Shi Junwei, Weissmueller Susann, Fellmann Christof, Fellman Christof, Taylor Meredith J, Weissenboeck Martina, Graeber Thomas G, Kogan Scott C, Vakoc Christopher R, Lowe Scott W, An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance, Genes & development, 2011, 25 (15), 1628-40.
Duy Cihangir, Hurtz Christian, Shojaee Seyedmehdi, Cerchietti Leandro, Geng Huimin, Swaminathan Srividya, Klemm Lars, Kweon Soo-mi, Nahar Rahul, Braig Melanie, Park Eugene, Kim Yong-mi, Hofmann Wolf-Karsten, Herzog Sebastian, Jumaa Hassan, Koeffler H Phillip, Yu J Jessica, Heisterkamp Nora, Graeber Thomas G, Wu Hong, Ye B Hilda, Melnick Ari, Müschen Markus, BCL6 enables Ph+ acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition, Nature, 2011, 473 (7347), 384-8.
Mulholland David J, Tran Linh M, Li Yunfeng, Cai Houjian, Morim Ashkan, Wang Shunyou, Plaisier Seema, Garraway Isla P, Huang Jiaoti, Graeber Thomas G, Wu Hong, Cell autonomous role of PTEN in regulating castration-resistant prostate cancer growth, Cancer cell, 2011, 19 (6), 792-804.
Rubbi Liudmilla, Titz Bjoern, Brown Lauren, Galvan Erica, Komisopoulou Evangelia, Chen Sharon S, Low Tracey, Tahmasian Martik, Skaggs Brian, Muschen Markus, Pellegrini Matteo, Graeber Thomas G, Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling, Science signaling, 2011, 4 (166), ra18.
Poulikakos Poulikos I, Persaud Yogindra, Janakiraman Manickam, Kong Xiangju, Ng Charles, Moriceau Gatien, Shi Hubing, Atefi Mohammad, Titz Bjoern, Gabay May Tal, Salton Maayan, Dahlman Kimberly B, Tadi Madhavi, Wargo Jennifer A, Flaherty Keith T, Kelley Mark C, Misteli Tom, Chapman Paul B, Sosman Jeffrey A, Graeber Thomas G, Ribas Antoni, Lo Roger S, Rosen Neal, Solit David B, RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E), Nature, 2011, 480 (7377), 387-90.
F. Remacle, T. G. Graeber and R. D. Levine., Whose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling, Journal of Statistical Physics, 2011, 144, 429-442.
Sun Jing, Masterman-Smith Michael D, Graham Nicholas A, Jiao Jing, Mottahedeh Jack, Laks Dan R, Ohashi Minori, DeJesus Jason, Kamei Ken-ichiro, Lee Ki-Bum, Wang Hao, Yu Zeta T F, Lu Yi-Tsung, Hou Shuang, Li Keyu, Liu Max, Zhang Nangang, Wang Shutao, Angenieux Brigitte, Panosyan Eduard, Samuels Eric R, Park Jun, Williams Dirk, Konkankit Vera, Nathanson David, van Dam R Michael, Phelps Michael E, Wu Hong, Liau Linda M, Mischel Paul S, Lazareff Jorge A, Kornblum Harley I, Yong William H, Graeber Thomas G, Tseng Hsian-Rong, A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens, Cancer research, 2010, 70 (15), 6128-38.
Alejandro Zimman, Sharon S Chen, Evangelia Komisopoulou, Bjoern Titz, Roxana Martínez-Pinna, Aarya Kafi, Judith A Berliner, Thomas G Graeber, Activation of Aortic Endothelial Cells by Oxidized Phospholipids: A Phosphoproteomic Analysis, Journal of Proteome Research, 2010, 9 (6), 2812-2824.
Fang Cong, Wang Yanju, Vu Nam T, Lin Wei-Yu, Hsieh Yao-Te, Rubbi Liudmilla, Phelps Michael E, Muschen Markus, Kim Yong-Mi, Chatziioannou Arion F, Tseng Hsian-Rong, Graeber Thomas G, Integrated microfluidic and imaging platform for a kinase activity radioassay to analyze minute patient cancer samples, Cancer Research, 2010, 70 (21), 8299-308.
Graeber, T. G., Heath, J. R., Skaggs, B. J., Phelps, M. E., Remacle, F., Levine, R. D., Maximal entropy inference of oncogenicity from phosphorylation signaling, Proc Natl Acad Sci U S A, 2010, 107 (13), 6112-6117.
Plaisier Seema B, Taschereau Richard, Wong Justin A, Graeber Thomas G, Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures, Nucleic acids research, 2010, 38 (17), e169.
Tumeh Paul C, Koya Richard C, Chodon Thinle, Graham Nicholas A, Graeber Thomas G, Comin-Anduix Begoña, Ribas Antoni, The impact of ex vivo clinical grade activation protocols on human T-cell phenotype and function for the generation of genetically modified cells for adoptive cell transfer therapy, Journal of immunotherapy (Hagerstown, Md. : 1997), 2010, 33 (8), 759-68.
B Titz, T Low, E Komisopoulou, S S Chen, L Rubbi and T G Graeber, The proximal signaling network of the BCR-ABL1 oncogene shows a modular organization, Oncogene, 2010, 29, 5895-5910.
Quinn Jeffrey A, Graeber C Thomas, Frackelton A Raymond, Kim Minsoo, Schwarzbauer Jean E, Filardo Edward J, Coordinate regulation of estrogen-mediated fibronectin matrix assembly and epidermal growth factor receptor transactivation by the G protein-coupled receptor, GPR30, Molecular endocrinology (Baltimore, Md.), 2009, 23 (7), 1052-64.
Lu Kan V, Zhu Shaojun, Cvrljevic Anna, Huang Tiffany T, Sarkaria Shawn, Ahkavan David, Dang Julie, Dinca Eduard B, Plaisier Seema B, Oderberg Isaac, Lee Yohan, Chen Zugen, Caldwell Jeremy S, Xie Yongmin, Loo Joseph A, Seligson David, Chakravari Arnab, Lee Francis Y, Weinmann Roberto, Cloughesy Timothy F, Nelson Stanley F, Bergers Gabriele, Graeber Thomas, Furnari Frank B, James C David, Cavenee Webster K, Johns Terrance G, Mischel Paul S, Fyn and SRC are effectors of oncogenic epidermal growth factor receptor signaling in glioblastoma patients, Cancer research, 2009, 69 (17), 6889-98.
Zimman Alejandro, Mouillesseaux Kevin P, Le Thang, Gharavi Nima M, Ryvkin Ann, Graeber Thomas G, Chen Tom T, Watson Andrew D, Berliner Judith A, Vascular endothelial growth factor receptor 2 plays a role in the activation of aortic endothelial cells by oxidized phospholipids, Arteriosclerosis, thrombosis, and vascular biology, 2007, 27 (2), 332-8.
Skaggs Brian J, Gorre Mercedes E, Ryvkin Ann, Burgess Michael R, Xie Yongming, Han Yun, Komisopoulou Evangelia, Brown Lauren M, Loo Joseph A, Landaw Elliot M, Sawyers Charles L, Graeber Thomas G, Phosphorylation of the ATP-binding loop directs oncogenicity of drug-resistant BCR-ABL mutants, Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (51), 19466-71.
Graeber Thomas G, Sawyers Charles L, Cross-species comparisons of cancer signaling, Nature genetics, 2005, 37 (1), 7-8.
Krutzik Stephan R, Tan Belinda, Li Huiying, Ochoa Maria Teresa, Liu Philip T, Sharfstein Sarah E, Graeber Thomas G, Sieling Peter A, Liu Yong-Jun, Rea Thomas H, Bloom Barry R, Modlin Robert L, TLR activation triggers the rapid differentiation of monocytes into macrophages and dendritic cells, Nature medicine, 2005, 11 (6), 653-60.
Pellegrini M, Graeber TG, Computational methods for protein function analysis, Focus on Protein Research, 2004.
Freedland Stephen J, Pantuck Allan J, Paik Sun H, Zisman Amnon, Graeber Thomas G, Eisenberg David, McBride William H, Nguyen David, Tso Cho-Lea, Belldegrun Arie S, Heterogeneity of molecular targets on clonal cancer lines derived from a novel hormone-refractory prostate cancer tumor system, The Prostate, 2003, 55 (4), 299-307.
Ellwood-Yen Katharine, Graeber Thomas G, Wongvipat John, Iruela-Arispe M Luisa, Zhang JianFeng, Matusik Robert, Thomas George V, Sawyers Charles L, Myc-driven murine prostate cancer shares molecular features with human prostate tumors, Cancer cell, 2003, 4 (3), 223-38.
Bleharski Joshua R, Li Huiying, Meinken Christoph, Graeber Thomas G, Ochoa Maria-Teresa, Yamamura Masahiro, Burdick Anne, Sarno Euzenir N, Wagner Manfred, Röllinghoff Martin, Rea Thomas H, Colonna Marco, Stenger Steffen, Bloom Barry R, Eisenberg David, Modlin Robert L, Use of genetic profiling in leprosy to discriminate clinical forms of the disease, Science (New York, N.Y.), 2003, 301 (5639), 1527-30.
Strong Michael, Graeber Thomas G, Beeby Morgan, Pellegrini Matteo, Thompson Michael J, Yeates Todd O, Eisenberg David, Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps, Nucleic acids research, 2003, 31 (24), 7099-109.
Matei Daniela, Graeber Thomas G, Baldwin Rae Lynn, Karlan Beth Y, Rao Jianyu, Chang David D, Gene expression in epithelial ovarian carcinoma, Oncogene, 2002, 21 (41), 6289-98.
Grutkoski Patricia S, Graeber C Thomas, Ayala Alfred, Simms H Hank, Paracrine suppression of apoptosis by cytokine-stimulated neutrophils involves divergent regulation of NF-kappaB, Bcl-X(L), and Bak, Shock (Augusta, Ga.), 2002, 17 (1), 47-54.
Graeber TG, Eisenberg D, Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles, Nature Genetics, 2001, 29 (3), 295-300.
Graeber TG, Shuai K, Rapid gene repression triggered by interleukin-6 at the onset of monocyte differentiation, Biochemical and Biophysical Research Communications, 2000, 267 (3), 863-9.
Graeber TG, Osmanian C, Jacks T, Housman DE, Koch CJ, Lowe SW, Giaccia AJ, Hypoxia-mediated selection of cells with diminished apoptotic potential in solid tumours, Nature, 1996, 379 (6560), 88-91.
Graeber TG, Peterson JF, Tsai M, Monica K, Fornace AJ, Giaccia AJ, Hypoxia induces accumulation of p53 protein, but activation of a G1-phase checkpoint by low-oxygen conditions is independent of p53 status, Molecular and Cellular Biology, 1994, 14 (9), 6264-77.