This study quantifies global PPI changes in skeletal muscle insulin resistance using PCP-MS and qXL-MS, revealing dysregulated interactions with chaperones and PDIA6.

Molecular Systems Biology · Jun 23, 2026Peer-reviewedBiochemistry

Rac1 deficiency reduces mitochondrial respiratory capacity, impairs fatty acid metabolism and causes muscle wasting

Lisbeth L. V. Møller, Steffen Henning Raun, Emma Frank, Andreas B. Jordy, Nicoline R. Andersen, Anders Gudiksen, Zakarias Kefil Jensen Ogueboule, Tang Cam Phung Pham, Jessica L. Braun, Esben N. Poulsen, Jeffrey Molendijk, Anders Karlsen, Jakob Agergaard, Sean Alec Newsom, Bryan C. Bergman, , Lykke Sylow

This study shows that Rac1 deficiency in muscle reduces mitochondrial function and fatty acid metabolism, leading to muscle wasting and highlights potential therapeutic targets for age-related muscle decline.

bioRxiv · Jun 17, 2026 · PreprintMolecular Biology

Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice

Jacob G. Smith, Jeffrey Molendijk, Ronnie Blazev, Wan Hsi Chen, Qing Zhang, Christopher Litwin, Carolina M. Greco, Paolo Sassone‐Corsi, Pura Muñoz‐Cánoves, Benjamin L. Parker, Kevin B. Koronowski

The paper investigates how Bmal1 rescue and time-restricted feeding affect liver and muscle proteomes in mice, finding BMAL1 has a greater impact than feeding cycles.

bioRxiv · Jun 12, 2023 · PreprintSystems Biology

Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function

Jeffrey Molendijk, Ronnie Blazev, Richard J. Mills, Yaan‐Kit Ng, Kevin I. Watt, Daryn Chau, Paul Gregorevic, Peter John Crouch, James B. W. Hilton, Leszek Lisowski, Peixiang Zhang, Karen Reue, Aldons Jake Lusis, James E. Hudson, David Ernest James, , Benjamin L. Parker

The paper identifies UFMylation as a negative regulator of skeletal muscle function through proteome-wide systems genetics in mice and validates it in a disease model.

eLife · Dec 6, 2022Peer-reviewedSystems Biology

CoffeeProt: An online tool for correlation and functional enrichment of proteome-wide systems genetics

Jeffrey Molendijk, Marcus Michael Seldin, Benjamin L. Parker

CoffeeProt is an open-source tool that integrates proteomics, genetics, and phenotypic data to identify functionally relevant genetic associations in mouse and human populations.

Nucleic Acids Research · Apr 22, 2021Peer-reviewedSystems Biology

Concurrent lipidomics and proteomics on malignant plasma cells from multiple myeloma patients: Probing the lipid metabolome

Ahmed Mohamed, Joel T Collins, Hui Jiang, Jeffrey Molendijk, Thomas M. Stoll, Federico Tesio Torta, Markus Rene Wenk, Robert J Bird, Paula V. Marlton, Peter N. Mollee, Kate Ann Markey, Michelle Mei Chih Hill

This study performs lipidomics and proteomics on plasma cells from multiple myeloma patients to identify metabolic changes associated with relapse.

PLoS ONE · Jan 8, 2020Peer-reviewedSystems Biology