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.Nature, , More 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 biology, , More 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.e10 More 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.e13 More 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 biology, , More 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.e9 More 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.e8 More 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, , 13 , More 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 biology, , More 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 biology, , More 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 ,101912 More 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, , 13 , More 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.e6 More 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 ) ,845-857 More 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.e7 More 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 biology, , More 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 ) ,e2204835119 More 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, , 10 , More 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 ) ,2751-2761 More 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 ) ,2159-2166 More 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 ) ,399-404 More 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-R1219 More 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.e4 More 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 ) ,2197 More 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-E5334 More Information
Van Vranken, Jonathan G; Rutter, Jared (2016. ) The Whole (Cell) Is Less Than the Sum of Its Parts.Cell, , 166 (5 ) ,1078-1079 More 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, , 5 , More Information
Van Vranken, Jonathan G; Rutter, Jared (2015. ) You Down With ETC? Yeah, You Know D!.Cell, , 162 (3 ) ,471-3 More 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 ) ,168-80 More 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 ) ,400-413 More 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 ) ,241-52 More 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 ) ,96-100 More Information