Publications
Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns
Jordan A Berg, Youjia Zhou, Yeyun Ouyang, Ahmad A Cluntun, T Cameron Waller, Megan E Conway, Sara M Nowinski, Tyler Van Ry, Ian George, James E Cox, Bei Wang, Jared Rutter
Nature Cell Biology, 2023
Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase
Kevin G Hicks, Ahmad A Cluntun, Heidi L Schubert, Sean R Hackett, Jordan A Berg, Paul G Leonard, Mariana A Ajalla Aleixo, Youjia Zhou, Alex J Bott, Sonia R Salvatore, Fei Chang, Aubrie Blevins, Paige Barta, Samantha Tilley, Aaron Leifer, Andrea Guzman, Ajak Arok, Sarah Fogarty, Jacob M Winter, Hee-Chul Ahn, Karen N Allen, Samuel Block, Iara A Cardoso, Jianping Ding, Ingrid Dreveny, William C Gasper, Quinn Ho, Atsushi Matsuura, Michael J Palladino, Sabin Prajapati, Pengkai Sun, Kai Tittmann, Dean R Tolan, Judith Unterlass, Andrew P VanDemark, Matthew G Vander Heiden, Bradley A Webb, Cai-Hong Yun, Pengkai Zhao, Bei Wang, Francisco J Schopfer, Christopher P Hill, Maria Cristina Nonato, Florian L Muller, James E Cox, Jared Rutter
Science, 2023
Phosphate Starvation Signaling Increases Mitochondrial Membrane Potential through Respiration-independent Mechanisms
Yeyun Ouyang, Corey N Cunningham, Jordan A Berg, Ashish G Toshniwal, Casey E Hughes, Jonathan G Van Vranken, Mi-Young Jeong, Ahmad A Cluntun, Geanette Lam, Jacob M Winter, Emel Akdoǧan, Katja K Dove, Steven P Gygi, Cory D Dunn, Dennis R Winge, Jared Rutter
eLife, 2024
Collateral deletion of the mitochondrial AAA+ ATPase ATAD1 sensitizes cancer cells to proteasome dysfunction
Jacob M Winter, Heidi L Fresenius, Corey N Cunningham, Peng Wei, Heather R Keys, Jordan A Berg, Alex Bott, Tarun Yadav, Jeremy Ryan, Deepika Sirohi, Sheryl R Tripp, Paige Barta, Neeraj Agarwal, Anthony Letai, David M Sabatini, Matthew L Wohlever, Jared Rutter
eLife, 2022
The pyruvate-lactate axis modulates cardiac hypertrophy and heart failure
Ahmad A Cluntun*, Rachit Badolia*, Sandra Lettlova*, K Mark Parnell, Thirupura S Shankar, Nikolaos A Diakos, Kristofor A Olson, Iosif Taleb, Sean M Tatum, Jordan A Berg, Corey N Cunningham, Tyler Van Ry, Alex J Bott, Aspasia Thodou Krokidi, Sarah Fogarty, Sophia Skedros, Wojciech I Swiatek, Xuejing Yu, Bai Luo, Shannon Merx, Sutip Navankasattusas, James E Cox, Gregory S Ducker, William L Holland, Stephen H McKellar, Jared Rutter, Stavros G Drakos
Cell Metabolism, 2021
Regulation of tumor initiation by the mitochondrial pyruvate carrier
Claire L Bensard*, Dona R Wisidagama*, Kristofor A Olson, Jordan A Berg, Nathan M Krah, John C Schell, Sara M Nowinski, Sarah Fogarty, Alex J Bott, Peng Wei, Katja K Dove, Jason M Tanner, Vanja Panic, Ahmad Cluntun, Sandra Lettlova, Christian S Earl, David F Namnath, Karina Vázquez-Arreguín, Claudio J Villanueva, Dean Tantin, L Charles Murtaugh, Kimberley J Evason, Gregory S Ducker, Carl S Thummel, Jared Rutter
Cell Metabolism, 2020
XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Jordan A Berg, Jonathan R Belyeu, Jeffrey T Morgan, Yeyun Ouyang, Alex J Bott, Aaron R Quinlan, Jason Gertz, Jared Rutter
PLOS Computational Biology, 2020
Compartment and hub definitions tune metabolic networks for metabolomic interpretations
T Cameron Waller, Jordan A Berg, Alexander Lex, Brian E Chapman, Jared Rutter
GigaScience, 2020
Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis
Casey E Hughes, Troy K Coody, Mi-Young Jeong, Jordan A Berg, Dennis R Winge, Adam L Hughes
Cell, 2020
ACP acylation is an acetyl-CoA-dependent modification required for electron transport chain assembly
Jonathan G Van Vranken, Sara M Nowinski, Katie J Clowers, Mi-Young Jeong, Yeyun Ouyang, Jordan A Berg, Jeremy P Gygi, Steven P Gygi, Dennis R Winge, Jared Rutter
Molecular Cell, 2018
A PCR-based method for distinguishing between two common beehive bacteria, Paenibacillus larvae and Brevibacillus laterosporus
Jordan A Berg, Bryan D Merrill, Donald P Breakwell, Sandra Hope, Julianne H Grose
Applied and Environmental Microbiology, 2018
Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages
Jordan A Berg, Bryan D Merrill, Justin T Crockett, Kyle P Esplin, Marlee R Evans, Karli E Heaton, Jared A Hilton, Jonathan R Hyde, Morgan S McBride, Jordan T Schouten, Austin R Simister, Trever L Thurgood, Andrew T Ward, Donald P Breakwell, Sandra Hope, Julianne H Grose
PLOS ONE, 2016
Software
Metaboverse
A tool for visualizing and analyzing metabolic networks with reaction pattern recognition
XPRESSyourself
An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
Presentations
Oral Presentations
| Abcam Immunometabolism: Fundamentals to Prospective New Therapies | Selected Talk | 2022 |
| North American Mass Spectrometry Summer School | Flash Talk | 2022 |
| CSHL Biological Data Science | Selected Talk | 2020 |
| ISMB | Selected Talk | 2020 |
| EMBL/EMBO Epigenetics Meets Metabolism | Selected Talk | 2019 |
| CSHL Genome Informatics | Flash Talk | 2019 |
| UCSD Bioinformatics Seminar Series | Invited Talk | 2019 |
| ASM Tri-branch Meeting | Selected Talk | 2015 |
Poster Presentations
| Keystone Symposia: Mitochondrial Biochemistry in Health and Disease | Poster | 2022 |
| Keystone Symposia: Metabolic Decisions in Development and Disease | Poster | 2021 |
| Keystone Symposia: Tumor Metabolism and the Microenvironment | Poster | 2021 |
| Systems Approaches to Cancer Biology | Poster | 2020 |
| CSHL Genome Informatics | Poster | 2019 |
| RECOMB | Poster | 2018 |
| Frontiers in Metabolism | Poster | 2018 |