Nick Thomas @NickTThomas
Postdoc in the Web Lab at the University of Kentucky Center for Muscle Biology Interested in outdoor recreation 🏃♂️🚲, science 🔬, and doggos 🐾 Lexington, KY Joined April 2021-
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Nick Thomas retweeted
“Myonuclear dynamics after skeletal muscle surgical injury” by undergrad Micah Goeke along with Drs. @PJKoopmansPhD and Nate Serrano. Seems like those non satellite cell-derived myonuclei are more active than we realize. #myotwitter faseb.onlinelibrary.wiley.com/doi/10.1096/fj…
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Very excited to share our paper showing altered myonuclear epigenetics and transcriptional output in response to ACL injury! Out now in @BioMedCentral Molecular Medicine! doi.org/10.1186/s10020… Thankful to work with an awesome crew! @ChrisFryPhD @KevinMurachPhD @yuan_wen16220
Thanks also to the rest of the team! Camille Brightwell, Thomas Carter, @AlexKeeble5 @saragonzalezve @ChristineLath @Allison_M_Owen
Exercise-associated microbial metabolites prevent skeletal muscle atrophy in adult female mice: rdcu.be/ftegi
Delayed molecular aging, preservation of energy metabolism and enhanced exercise response in exercise-trained human muscle | Nature Aging share.google/8FgRH6Kwzu7lgi…
@KevinMurachPhD @Mizzou @uacoehp Congrats and cheers to the next chapter!!
Nick Thomas retweeted
Carried by Dr. @RonaldGJones3, “the gigaMYC paper” as the trainees call it: “Transient MYC Mimicking the Exercise Response Orchestrates Multifaceted Skeletal Muscle Adaptations”. A huge collab that started many many years ago. Too many to thank! biorxiv.org/content/10.648…
Nick Thomas retweeted
Excited to share a new publication from the @ChrisFryPhD and @Allison_M_Owen labs! We identify senescent macrophages as contributors to quadriceps atrophy and PTOA following ligament injury. Proud to have contributed to this work with an amazing team. pubmed.ncbi.nlm.nih.gov/42348390/
Nick Thomas retweeted
How much biology can we recover from single-cell latent representations? 🧬 Latent spaces have become the backbone of modern single-cell analysis. They power atlas integration, foundation models, and increasingly perturbation prediction and Virtual Cell approaches. Yet there is a surprisingly basic question that has received little attention: 👉 How well can we reconstruct gene expression from these latent representations? In our new work, we introduce ReconEval, a benchmark for gene expression reconstruction across more than 100 million cells. We systematically evaluate three settings: 🔹 End-to-end reconstruction (PCA, autoencoders, VAEs) 🔹 Foundation model reconstruction (a new benchmark task for single-cell foundation models, asking how much gene-level information can be recovered from pretrained embeddings) 🔹 Latent shift reconstruction (evaluating reconstruction after perturbation prediction models operate in latent space) A few takeaways: 📊 Autoencoders (not VAEs) achieve the strongest stand-alone reconstruction performance. This is perhaps not surprising, as reconstruction is exactly their training objective. 🧠 Foundation model embeddings retain substantial recoverable gene-level information, although performance depends strongly on the decoder and pretraining strategy. 🔬 The optimal latent representation depends on the downstream task. What works best for reconstruction is not necessarily what works best after perturbation prediction. As the field moves toward increasingly sophisticated Virtual Cell models, reconstruction deserves more attention as an evaluation axis ie another task to evaluate. Ultimately, biological interpretation happens in gene expression space, not in latent coordinates. Congratulations to Xiaotong Fu for driving this project and to all collaborators involved in making this benchmark possible. 👏 📄 Preprint: biorxiv.org/content/10.648… 💻 Code: github.com/theislab/Recon… #SingleCell #ComputationalBiology #VirtualCell
Nick Thomas retweeted
New #SkeletalMuscle paper: Targeting muscle fibrosis using non-specific collagenase injections destabilizes the basal lamina and induces matrix remodeling. tinyurl.com/yk4fhxda
Nick Thomas retweeted
Short Report by @martacolosio et al. (@MVFranchi @PorcelliSimone @CWSundberg @re_re84) One half of the sprinting coin: the #oxygentransport cascade of a 91-yr-old female world-record sprinter ow.ly/a3G250Z7Z6M
Nick Thomas retweeted
New online! Single-cell four-omics with CHARM dlvr.it/TT1Fsx
Very happy with having had the opportunity to share our work on how aging influences behavior of satellite cell derived myonuclei! Big thanks to @BiochemExercise for organizing one of the best conference experiences I've had with great science from all! #IBEC2026
Nick Thomas retweeted
The skeletal muscle slow myosin heavy chain regulates mammalian metabolic homeostasis through the NRF2 pathway science.org/doi/10.1126/sc…
@MeaganKingren @archildrens @UAMS @TRI_UAMS Huge congrats Meagan!!
Nick Thomas retweeted
Multicellular senescence impairs skeletal muscle recovery following disuse in aging | Science Advances science.org/doi/10.1126/sc…
Nick Thomas retweeted
“Myonuclear Dynamics After Skeletal Muscle Surgical Injury” led by undergrad Micah Goeke and the newly minted Dr. @PJKoopmans biorxiv.org/content/10.648…
Nick Thomas retweeted
Lactate-driven mitochondrial pretenders hijack hippocampal function after excessive exercise dlvr.it/TSSC96
@KevinMurachPhD @RonaldGJones3 So awesome! Congrats Dr. Jones III!! May you carry the spirit of the blue dinosaur in your future endeavors
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@ChrisFryPhD
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Centre for Muscle Res...
@UniMelbCMR
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@GGouspillou
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