Professional Summary
By combining classical thermal shift assays with modern quantitative proteomics and sample multiplexing, Dr. Van Vranken is able to assess changes in protein thermal stability of thousands of proteins in a single experiment. Using these methods, he is able to screen the proteome for drug-induced changes in protein thermal stability to determine the protein targets of compounds used for the treatment of cancer and other human disease.
Publications
Peer Reviewed Publications
Chakrabarty, Ram P; Van Vranken, Jonathan G; Aoi, Yuki; Poor, Taylor A; McElroy, Gregory S; Vasan, Karthik; Soliman, Shimaa H A; Iwanaszko, Marta; Grant, Rogan A; Howard, Benjamin C; Reczek, Colleen R; Chandel, Anjali D; Kahl, Michael; Xu, Zhaofa; Helmin, Kathryn A; Jin, Qiushi; Wang, Dongmei; Gao, Peng; Blum, Jenna L E; Sebo, Zachary L; Yue, Feng; Ma, Yongchao C; Davidson, Shawn M; Gygi, Steven P; Weinberg, Samuel E; Singer, Benjamin D; Han, SeungHye; Shilatifard, Ali; Chandel, Navdeep S (2026). Mitochondrial L-2-hydroxyglutarate is a physiological signalling metabolite. NatureMore Information
Cho, Juyeong; Danner, Rebecca; Kim, Woo Sung; Williams, Jonathan; Singh, Anshit; Han, Jiyoung A; Van Vranken, Jonathan G; Walker, Allison S; Rhoads, Timothy; Chaudhari, Snehal N (2026). Microbial metabolism of methotrexate produces a STAT3 signaling molecule that alleviates gut inflammation. bioRxiv : the preprint server for biologyMore Information
Nicholson, Rebekah J; Cedeño-Rosario, Luis; Maschek, J Alan; Lonergan, Trevor; Van Vranken, Jonathan G; Kruse, Angela R S; Stubben, Chris J; Wang, Liping; Stuart, Deborah; Alcantara, Queren A; Revelo, Monica P; Rutter, Kate; Pahulu, Mayette; Taloa, Jacob; Wu, Xuanchen; Kim, Juwan; Kim, Juna; Hall, Isaac; Clark, Amanda J; Parikh, Samir; Spraggins, Jeffrey; Romero, Donna; Blitzer, Jeremy T; Gygi, Steven P; Rutter, Jared; Holland, William L; Ramkumar, Nirupama; Summers, Scott A (2026). Therapeutic remodeling of the ceramide backbone prevents kidney injury. Cell metabolism, 38 (1) , 135-156.e10More Information
Zhao, Ting; He, Lingli; Wong, Lai Ping; Mei, Shenglin; Xia, Jun; Xu, Yanxin; Van Vranken, Jonathan G; Mazzola, Michael; Chen, Lei; Rhee, Catherine; Fang, Tiancheng; Fukushima, Tsuyoshi; Sayles, Leanne C; Diaz, Matthew; Gibbons, J Alex B; Mostoslavsky, Raul; Gygi, Steven P; Dou, Zhixun; Sykes, David B; Sadreyev, Ruslan I; Sweet-Cordero, E Alejandro; Scadden, David T (2025). Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming. Cell metabolism, 37 (8) , 1667-1681.e13More Information
Julian, Linda; Crozier, Lisa; Lukow, Devon; Mishra, Sanat; Swamy, Aditi; Hagenson, Ryan A; Sennhenn, Peter; Sausville, Erin L; Mendelson, Brianna; Chuaqui, Claudio; Qiao, Lu; Vasudevan, Anand; Lin, Kuan-Ting; Bhatia, Sonam; Bertomeu, Thierry; Chatr-Aryamontri, Andrew; Zhang, Li; Rees, Matthew G; Ronan, Melissa M; Roth, Jennifer A; Nottoli, Timothy; Bai, Suxia; Lakshmipathi, Jayalakshmi; Muthusamy, Viswanathan; Van Vranken, Jonathan G; Gygi, Steven P; Thompson, Sarah L; Smith, Joan C; Anderson, Kendall; Shah, Sanjana; Bindra, Ranjit S; Akerman, Martin; Spector, David L; Krainer, Adrian R; Sheltzer, Jason M (2025). On-target toxicity limits the efficacy of CDK11 inhibition against cancers with 1p36 deletions. bioRxiv : the preprint server for biologyMore Information
Cunningham, Corey N; Van Vranken, Jonathan G; Larios, Jakeline; Heyden, Katarina; Gygi, Steven P; Rutter, Jared (2025). A dual-purification system to isolate mitochondrial subpopulations. Journal of cell science, 138 (9) More Information
Sprenger, Hans-Georg; Mittenbühler, Melanie J; Sun, Yizhi; Van Vranken, Jonathan G; Schindler, Sebastian; Jayaraj, Abhilash; Khetarpal, Sumeet A; Smythers, Amanda L; Vargas-Castillo, Ariana; Puszynska, Anna M; Spinelli, Jessica B; Armani, Andrea; Kunchok, Tenzin; Ryback, Birgitta; Seo, Hyuk-Soo; Song, Kijun; Sebastian, Luke; O'Young, Coby; Braithwaite, Chelsea; Dhe-Paganon, Sirano; Burger, Nils; Mills, Evanna L; Gygi, Steven P; Paulo, Joao A; Arthanari, Haribabu; Chouchani, Edward T; Sabatini, David M; Spiegelman, Bruce M (2025). Ergothioneine controls mitochondrial function and exercise performance via direct activation of MPST. Cell metabolism, 37 (4) , 857-869.e9More Information
Dumesic, Phillip A; Wilensky, Sarah E; Bose, Symanthika; Van Vranken, Jonathan G; Gygi, Steven P; Spiegelman, Bruce M (2025). RBM43 controls PGC1α translation and a PGC1α-STING signaling axis. Cell metabolism, 37 (3) , 742-757.e8More Information
Van Vranken, Jonathan G; Li, Jiaming; Mintseris, Julian; Wei, Ting-Yu; Sniezek, Catherine M; Gadzuk-Shea, Meagan; Gygi, Steven P; Schweppe, Devin K (2024). Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays. eLife, 13More Information
Van Vranken, Jonathan G; Li, Jiaming; Mintseris, Julian; Wei, Ting-Yu; Sniezek, Catherine M; Gadzuk-Shea, Meagan; Gygi, Steven P; Schweppe, Devin K (2024). Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays. bioRxiv : the preprint server for biologyMore Information
Sprenger, Hans-Georg; Mittenbühler, Melanie J; Sun, Yizhi; Van Vranken, Jonathan G; Schindler, Sebastian; Jayaraj, Abhilash; Khetarpal, Sumeet A; Vargas-Castillo, Ariana; Puszynska, Anna M; Spinelli, Jessica B; Armani, Andrea; Kunchok, Tenzin; Ryback, Birgitta; Seo, Hyuk-Soo; Song, Kijun; Sebastian, Luke; O'Young, Coby; Braithwaite, Chelsea; Dhe-Paganon, Sirano; Burger, Nils; Mills, Evanna L; Gygi, Steven P; Arthanari, Haribabu; Chouchani, Edward T; Sabatini, David M; Spiegelman, Bruce M (2024). Ergothioneine boosts mitochondrial respiration and exercise performance via direct activation of MPST. bioRxiv : the preprint server for biologyMore Information
Ducommun, Serge; Jannig, Paulo R; Cervenka, Igor; Murgia, Marta; Mittenbühler, Melanie J; Chernogubova, Ekaterina; Dias, José M; Jude, Baptiste; Correia, Jorge C; Van Vranken, Jonathan G; Ocana-Santero, Gabriel; Porsmyr-Palmertz, Margareta; McCann Haworth, Sarah; Martínez-Redondo, Vicente; Liu, Zhengye; Carlström, Mattias; Mann, Matthias; Lanner, Johanna T; Teixeira, Ana I; Maegdefessel, Lars; Spiegelman, Bruce M; Ruas, Jorge L (2024). Mustn1 is a smooth muscle cell-secreted microprotein that modulates skeletal muscle extracellular matrix composition. Molecular metabolism, 82, 101912More Information
Ouyang, Yeyun; Jeong, Mi-Young; Cunningham, Corey N; Berg, Jordan A; Toshniwal, Ashish G; Hughes, Casey E; Seiler, Kristina; Van Vranken, Jonathan G; Cluntun, Ahmad A; Lam, Geanette; Winter, Jacob M; Akdogan, Emel; Dove, Katja K; Nowinski, Sara M; West, Matthew; Odorizzi, Greg; Gygi, Steven P; Dunn, Cory D; Winge, Dennis R; Rutter, Jared (2024). Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms. eLife, 13More Information
Yin, Terry C; Van Vranken, Jonathan G; Srivastava, Dhiraj; Mittal, Ayushi; Buscaglia, Paul; Moore, Autumn E; Verdinez, Jissele A; Graham, Aschleigh E; Walsh, Susan A; Acevedo, Michael A; Kerns, Robert J; Artemyev, Nikolai O; Gygi, Steven P; Sebag, Julien A (2023). Insulin sensitization by small molecules enhancing GLUT4 translocation. Cell chemical biology, 30 (8) , 933-942.e6More Information
Mitchell, Dylan C; Kuljanin, Miljan; Li, Jiaming; Van Vranken, Jonathan G; Bulloch, Nathan; Schweppe, Devin K; Huttlin, Edward L; Gygi, Steven P (2023). A proteome-wide atlas of drug mechanism of action. Nature biotechnology, 41 (6) , 845-857More Information
Mittenbühler, Melanie J; Jedrychowski, Mark P; Van Vranken, Jonathan G; Sprenger, Hans-Georg; Wilensky, Sarah; Dumesic, Phillip A; Sun, Yizhi; Tartaglia, Andrea; Bogoslavski, Dina; A, Mu; Xiao, Haopeng; Blackmore, Katherine A; Reddy, Anita; Gygi, Steven P; Chouchani, Edward T; Spiegelman, Bruce M (2023). Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues. Cell metabolism, 35 (3) , 535-549.e7More Information
Dumesic, Phillip A; Wilensky, Sarah E; Bose, Symanthika; Van Vranken, Jonathan G; Gygi, Steven P; Spiegelman, Bruce M (2023). RBM43 links adipose inflammation and energy expenditure through translational regulation of PGC1α. bioRxiv : the preprint server for biologyMore Information
Kam, Tae-In; Park, Hyejin; Chou, Shih-Ching; Van Vranken, Jonathan G; Mittenbühler, Melanie J; Kim, Hyeonwoo; A, Mu; Choi, Yu Ree; Biswas, Devanik; Wang, Justin; Shin, Yu; Loder, Alexis; Karuppagounder, Senthilkumar S; Wrann, Christiane D; Dawson, Valina L; Spiegelman, Bruce M; Dawson, Ted M (2022). Amelioration of pathologic α-synuclein-induced Parkinson's disease by irisin. Proceedings of the National Academy of Sciences of the United States of America, 119 (36) , e2204835119More Information
Van Vranken, Jonathan G; Li, Jiaming; Mitchell, Dylan C; Navarrete-Perea, José; Gygi, Steven P (2021). Assessing target engagement using proteome-wide solvent shift assays. eLife, 10More Information
Navarrete-Perea, Jose; Guerra-Moreno, Angel; Van Vranken, Jonathan; Isasa, Marta; Paulo, Joao A; Gygi, Steven P (2021). Iron Deficiency and Recovery in Yeast: A Quantitative Proteomics Approach. Journal of proteome research, 20 (5) , 2751-2761More Information
Li, Jiaming; Van Vranken, Jonathan G; Paulo, Joao A; Huttlin, Edward L; Gygi, Steven P (2020). Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. Journal of proteome research, 19 (5) , 2159-2166More Information
Li, Jiaming; Van Vranken, Jonathan G; Pontano Vaites, Laura; Schweppe, Devin K; Huttlin, Edward L; Etienne, Chris; Nandhikonda, Premchendar; Viner, Rosa; Robitaille, Aaron M; Thompson, Andrew H; Kuhn, Karsten; Pike, Ian; Bomgarden, Ryan D; Rogers, John C; Gygi, Steven P; Paulo, Joao A (2020). TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nature methods, 17 (4) , 399-404More Information
Nowinski, Sara M; Van Vranken, Jonathan G; Dove, Katja K; Rutter, Jared (2018). Impact of Mitochondrial Fatty Acid Synthesis on Mitochondrial Biogenesis. Current biology : CB, 28 (20) , R1212-R1219More Information
Van Vranken, Jonathan G; Nowinski, Sara M; Clowers, Katie J; Jeong, Mi-Young; Ouyang, Yeyun; Berg, Jordan A; Gygi, Jeremy P; Gygi, Steven P; Winge, Dennis R; Rutter, Jared (2018). ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. Molecular cell, 71 (4) , 567-580.e4More Information
Zurita Rendón, Olga; Fredrickson, Eric K; Howard, Conor J; Van Vranken, Jonathan; Fogarty, Sarah; Tolley, Neal D; Kalia, Raghav; Osuna, Beatriz A; Shen, Peter S; Hill, Christopher P; Frost, Adam; Rutter, Jared (2018). Vms1p is a release factor for the ribosome-associated quality control complex. Nature communications, 9 (1) , 2197More Information
Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P (2017). Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions. Proceedings of the National Academy of Sciences of the United States of America, 114 (27) , E5325-E5334More Information
Van Vranken, Jonathan G; Rutter, Jared (2016). The Whole (Cell) Is Less Than the Sum of Its Parts. Cell, 166 (5) , 1078-1079More Information
Van Vranken, Jonathan G; Jeong, Mi-Young; Wei, Peng; Chen, Yu-Chan; Gygi, Steven P; Winge, Dennis R; Rutter, Jared (2016). The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis. eLife, 5More Information
Van Vranken, Jonathan G; Rutter, Jared (2015). You Down With ETC? Yeah, You Know D!. Cell, 162 (3) , 471-3More Information
Van Vranken, Jonathan G; Na, Un; Winge, Dennis R; Rutter, Jared (2015). Protein-mediated assembly of succinate dehydrogenase and its cofactors. Critical reviews in biochemistry and molecular biology, 50 (2) , 168-80More Information
Schell, John C; Olson, Kristofor A; Jiang, Lei; Hawkins, Amy J; Van Vranken, Jonathan G; Xie, Jianxin; Egnatchik, Robert A; Earl, Espen G; DeBerardinis, Ralph J; Rutter, Jared (2014). A role for the mitochondrial pyruvate carrier as a repressor of the Warburg effect and colon cancer cell growth. Molecular cell, 56 (3) , 400-413More Information
Van Vranken, Jonathan G; Bricker, Daniel K; Dephoure, Noah; Gygi, Steven P; Cox, James E; Thummel, Carl S; Rutter, Jared (2014). SDHAF4 promotes mitochondrial succinate dehydrogenase activity and prevents neurodegeneration. Cell metabolism, 20 (2) , 241-52More Information
Bricker, Daniel K; Taylor, Eric B; Schell, John C; Orsak, Thomas; Boutron, Audrey; Chen, Yu-Chan; Cox, James E; Cardon, Caleb M; Van Vranken, Jonathan G; Dephoure, Noah; Redin, Claire; Boudina, Sihem; Gygi, Steven P; Brivet, Michèle; Thummel, Carl S; Rutter, Jared (2012). A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans. Science (New York, N.Y.), 337 (6090) , 96-100More Information