Thomas Graeber, Ph.D.

A Short Biography:

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.

Work Titles
Alfred P. Sloan Foundation Research Fellow, Alfred P. Sloan Foundation
California NanoSystems Institute Member, California NanoSystems Institute
UCLA Director, UCLA Metabolomics Center Professor, Molecular & Medical Pharmacology Member, Bioinformatics GPB Home Area Member, Cell & Developmental Biology GPB Home Area Member, Crump Institute for Molecular Imaging Member, Genetics & Genomics GPB Home Area Member, I3T Theme Member, Molecular Pharmacology GPB Home Area Member, Molecular, Cellular & Integrative Physiology GPB Home Area Member, Physics & Biology in Medicine GPB Home Area
Ph.D., Stanford University
Honors and Awards:
American Cancer Society Research Scholar

Contact Information:

Lab Number:

(310) 206-7054

Office Phone Number:

(310) 206-6122

Laboratory Address:

4338 CNSI, Crump Institute
570 Westwood Plaza
Los Angeles, CA 90095

Office Address:

4341 CNSI, Crump Institute
570 Westwood Plaza,
Box 951770
Los Angeles, CA 90095

Research Interest:

Systems biology of cancer 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.

Detailed Biography:

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.


A selected list of publications:

Balanis NG, Sheu KM, Esedebe FN, Patel SJ, Smith BA, Park JW, Alhani S, Gomperts BN, Huang J, Witte ON, Graeber TG.   Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies Cancer Cell, 2019; 36(1): 17-34.
J Tsoi, L Robert, K Paraiso, C Galvan, K Sheu, J Lay, DJL Wong, M Atefi, R Shirazi, X Wang, D Braas, CS Grasso, N Palaskas, A Ribas, TG Graeber   Multi-stage differentiation defines melanoma subtypes with differential vulnerability to drug-induced iron-dependent oxidative stress Cancer Cell, 2018; 33(5): 890-904.
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.
Xiao Gang, Chan Lai N, Klemm Lars, Braas Daniel, Chen Zhengshan, Geng Huimin, Zhang Qiuyi Chen, Aghajanirefah Ali, Cosgun Kadriye Nehir, Sadras Teresa, Lee Jaewoong, Mirzapoiazova Tamara, Salgia Ravi, Ernst Thomas, Hochhaus Andreas, Jumaa Hassan, Jiang Xiaoyan, Weinstock David M, Graeber Thomas G, Müschen Markus   B-Cell-Specific Diversion of Glucose Carbon Utilization Reveals a Unique Vulnerability in B Cell Malignancies Cell, 2018; 173(2): 470-484.e18.
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; 542(7642): 479-483.
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.
Grommes Christian, Pastore Alessandro, Palaskas Nicolaos, Tang Sarah S, Campos Carl, Schartz Derrek, Codega Paolo, Nichol Donna, Clark Owen, Hsieh Wan-Ying, Rohle Dan, Rosenblum Marc, Viale Agnes, Tabar Viviane S, Brennan Cameron W, Gavrilovic Igor T, Kaley Thomas J, Nolan Craig P, Omuro Antonio, Pentsova Elena, Thomas Alissa A, Tsyvkin Elina, Noy Ariela, Palomba M Lia, Hamlin Paul, Sauter Craig S, Moskowitz Craig H, Wolfe Julia, Dogan Ahmet, Won Minhee, Glass Jon, Peak Scott, Lallana Enrico C, Hatzoglou Vaios, Reiner Anne S, Gutin Philip H, Huse Jason T, Panageas Katherine S, Graeber Thomas G, Schultz Nikolaus, DeAngelis Lisa M, Mellinghoff Ingo K   Ibrutinib Unmasks Critical Role of Bruton Tyrosine Kinase in Primary CNS Lymphoma Cancer discovery, 2017; 7(9): 1018-1029.
Court Colin M, Ankeny Jacob S, Sho Shonan, Winograd Paul, Hou Shuang, Song Min, Wainberg Zev A, Girgis Mark D, Graeber Thomas G, Agopian Vatche G, Tseng Hsian-Rong, Tomlinson James S   Circulating Tumor Cells Predict Occult Metastatic Disease and Prognosis in Pancreatic Cancer Annals of surgical oncology, 2018; 25(4): 1000-1008.
Su Yapeng, Wei Wei, Robert Lidia, Xue Min, Tsoi Jennifer, Garcia-Diaz Angel, Homet Moreno Blanca, Kim Jungwoo, Ng Rachel H, Lee Jihoon W, Koya Richard C, Comin-Anduix Begonya, Graeber Thomas G, Ribas Antoni, Heath James R   Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance Proceedings of the National Academy of Sciences of the United States of America, 2017; 114(52): 13679-13684.
Flores Aimee, Schell John, Krall Abigail S, Jelinek David, Miranda Matilde, Grigorian Melina, Braas Daniel, White Andrew C, Zhou Jessica L, Graham Nicholas A, Graeber Thomas, Seth Pankaj, Evseenko Denis, Coller Hilary A, Rutter Jared, Christofk Heather R, Lowry William E   Lactate dehydrogenase activity drives hair follicle stem cell activation Nature cell biology, 2017; 19(9): 1017-1026.
Sho Shonan, Court Colin M, Winograd Paul, Lee Sangjun, Hou Shuang, Graeber Thomas G, Tseng Hsian-Rong, Tomlinson James S   Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications BMC cancer, 2017; 17(1): 457.
Garcia-Diaz Angel, Shin Daniel Sanghoon, Moreno Blanca Homet, Saco Justin, Escuin-Ordinas Helena, Rodriguez Gabriel Abril, Zaretsky Jesse M, Sun Lu, Hugo Willy, Wang Xiaoyan, Parisi Giulia, Saus Cristina Puig, Torrejon Davis Y, Graeber Thomas G, Comin-Anduix Begonya, Hu-Lieskovan Siwen, Damoiseaux Robert, Lo Roger S, Ribas Antoni   Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression Cell reports, 2017; 19(6): 1189-1201.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Graeber Thomas G, Sawyers Charles L   Cross-species comparisons of cancer signaling Nature genetics, 2005; 37(1): 7-8.
Pellegrini M, Graeber TG   Computational methods for protein function analysis Focus on Protein Research, 2004; .
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.
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.
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.
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.

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