Benjamin L. Parker
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View article: eLife Assessment: The titin N2A-MARP signalosome constrains muscle longitudinal hypertrophy in response to stretch
eLife Assessment: The titin N2A-MARP signalosome constrains muscle longitudinal hypertrophy in response to stretch Open
View article: eLife Assessment: D-serine suppresses one-carbon metabolism by competing with mitochondrial L-serine transport
eLife Assessment: D-serine suppresses one-carbon metabolism by competing with mitochondrial L-serine transport Open
View article: Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain
Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain Open
Background Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these ge…
View article: Employing complementary fractionation‐based N‐terminomics approaches enhances the identification of legumain cleavage events in naïve and inflamed colon tissue
Employing complementary fractionation‐based N‐terminomics approaches enhances the identification of legumain cleavage events in naïve and inflamed colon tissue Open
The mammalian lysosomal protease legumain is often dysregulated in pathophysiological conditions including inflammation, neurodegeneration, and cancer, yet its proteolytic targets are poorly defined. To profile protease substrates, degrado…
View article: Skeletal muscle proteomics: considerations and opportunities
Skeletal muscle proteomics: considerations and opportunities Open
Skeletal muscle accounts for 30–40% of body weight and plays an indispensable role in maintaining movement and is also a central regulator of whole-body metabolism. As such, understanding the molecular mechanisms of skeletal muscle health …
View article: Bone marrow neutrophil progenitors suppress osteoclast formation in murine cortical and trabecular bone
Bone marrow neutrophil progenitors suppress osteoclast formation in murine cortical and trabecular bone Open
In inflammation, circulating neutrophils indirectly damage the skeleton by inducing formation of bone-resorbing osteoclasts. However, neutrophil progenitors in marrow have no known physiological function. A bone-protective role for the neu…
View article: Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS
Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS Open
View article: Embryonic stem cell factors DPPA2/4 facilitate a unique chromatin state in non-small cell lung cancer
Embryonic stem cell factors DPPA2/4 facilitate a unique chromatin state in non-small cell lung cancer Open
Summary Embryonic regulators are often re-expressed in cancers, however the functional and molecular significance of this is not always understood. The epigenetic priming factors Developmental Pluripotency Associated 2 and 4 (DPPA2/4) have…
View article: Phosphoproteomics Uncovers Exercise Intensity-Specific Skeletal Muscle Signaling Networks Underlying High-Intensity Interval Training in Healthy Male Participants
Phosphoproteomics Uncovers Exercise Intensity-Specific Skeletal Muscle Signaling Networks Underlying High-Intensity Interval Training in Healthy Male Participants Open
View article: Integrated liver-secreted and plasma proteomics identify a predictive model that stratifies MASH
Integrated liver-secreted and plasma proteomics identify a predictive model that stratifies MASH Open
Obesity is a major risk factor for metabolic-associated steatotic liver disease (MASLD), which can progress to metabolic-associated steatohepatitis (MASH). There are no validated non-invasive tests to stratify persons with obesity with a g…
View article: A selective inhibitor of oncogenic JNK signalling perturbs metastatic outgrowth of triple-negative breast cancer through metabolic blockade
A selective inhibitor of oncogenic JNK signalling perturbs metastatic outgrowth of triple-negative breast cancer through metabolic blockade Open
Summary Although c-Jun N-terminal Kinase (JNK) represents an attractive anti-cancer target, its pleiotropic functionality limits the use of direct JNK inhibitors. Here, we identify a distinct subcellular pattern of JNK activity as a therap…
View article: Clinical Validity of Autosomal Dominant<i>ALPK3</i>Loss-of-function Variants as a Cause of Hypertrophic Cardiomyopathy
Clinical Validity of Autosomal Dominant<i>ALPK3</i>Loss-of-function Variants as a Cause of Hypertrophic Cardiomyopathy Open
ALPK3 encodes the protein α-kinase 3, an essential cardiac-enriched atypical a-kinase that inserts in the nuclear envelope and the sarcomere M-band of cardiac myocytes, functioning to aid in myosin-mediated force buffering and sarcomere pr…
View article: Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies
Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies Open
View article: Neural Pathway Embedding Through Hierarchical Interchange Networks in Large Language Models
Neural Pathway Embedding Through Hierarchical Interchange Networks in Large Language Models Open
View article: eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug–diet interactions
eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug–diet interactions Open
Unraveling the complex interplay between nutrients and drugs via their effects on “omics” features could revolutionize our fundamental understanding of nutritional physiology, personalized nutrition, and, ultimately, human health span. Exp…
View article: Site-specific quantification of the<i>in vivo</i>UFMylome reveals myosin modification in ALS
Site-specific quantification of the<i>in vivo</i>UFMylome reveals myosin modification in ALS Open
UFMylation is a ubiquitin-like protein post-translational modification of Ubiquitin Fold Modifier 1 (UFM1) applied to substrate proteins. The UFMylation system is important for normal development and plays a critical role in a variety of c…
View article: Pathogenic hypothalamic extracellular matrix promotes metabolic disease
Pathogenic hypothalamic extracellular matrix promotes metabolic disease Open
View article: eLife assessment: A 2-hydroxybutyrate-mediated feedback loop regulates muscular fatigue
eLife assessment: A 2-hydroxybutyrate-mediated feedback loop regulates muscular fatigue Open
View article: Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription
Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription Open
The Hippo tumor suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs …
View article: ThunderBolt: An interactive data sharing and analysis platform for large-omics experiments
ThunderBolt: An interactive data sharing and analysis platform for large-omics experiments Open
Summary Mass-spectrometry (MS) datasets present a unique set of challenges that make in-depth bioinformatics analysis non-trivial, with analysis requiring both expertise and time. Often these datasets have unique structures that need to be…
View article: Phosphoproteomics uncovers exercise intensity-specific signaling networks underlying high-intensity interval training in human skeletal muscle
Phosphoproteomics uncovers exercise intensity-specific signaling networks underlying high-intensity interval training in human skeletal muscle Open
SUMMARY In response to exercise, protein kinases and signaling networks are rapidly engaged in skeletal muscle to maintain energy homeostasis. High-intensity interval training (HIIT) induces superior or similar health-promoting skeletal mu…
View article: Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response
Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response Open
Pancreatic ductal adenocarcinoma (PDAC) is characterized by increasing fibrosis, which can enhance tumor progression and spread. Here, we undertook an unbiased temporal assessment of the matrisome of the highly metastatic KPC ( Pdx1-Cre , …
View article: Real-time motion-enabling positron emission tomography of the brain of upright ambulatory humans
Real-time motion-enabling positron emission tomography of the brain of upright ambulatory humans Open
Background Mobile upright PET devices have the potential to enable previously impossible neuroimaging studies. Currently available options are imagers with deep brain coverage that severely limit head/body movements or imagers with upright…
View article: eLife assessment: Remodeling of skeletal muscle myosin metabolic states in hibernating mammals
eLife assessment: Remodeling of skeletal muscle myosin metabolic states in hibernating mammals Open
Full text Figures and data Peer review Side by side Abstract eLife assessment eLife digest Introduction Results Discussion Methods Data availability References Article and author information Metrics Abstract Hibernation is a period of meta…
View article: eLife Assessment: Remodelling of skeletal muscle myosin metabolic states in hibernating mammals
eLife Assessment: Remodelling of skeletal muscle myosin metabolic states in hibernating mammals Open
Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to deter…
View article: Ventricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies
Ventricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies Open
Background The left and right ventricles of the human heart are functionally and developmentally distinct such that genetic or acquired insults can cause dysfunction in one or both ventricles resulting in heart failure. The left ventricle …
View article: Personalized phosphoproteomics of skeletal muscle insulin resistance and exercise links MINDY1 to insulin action
Personalized phosphoproteomics of skeletal muscle insulin resistance and exercise links MINDY1 to insulin action Open
Summary Type 2 diabetes is preceded by a defective insulin response, yet our knowledge of the precise mechanisms is incomplete. Here, we investigate how insulin resistance alters signalling responses in skeletal muscle and how this is modi…
View article: eLife assessment: A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle
eLife assessment: A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle Open
Full text Figures and data Side by side Abstract eLife assessment eLife digest Introduction Results Discussion Materials and methods Data availability References Peer review Author response Article and author information Abstract An increa…
View article: Mitochondrial fusion and altered beta-oxidation drive muscle wasting in a Drosophila cachexia model
Mitochondrial fusion and altered beta-oxidation drive muscle wasting in a Drosophila cachexia model Open
View article: Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain
Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain Open
Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or products (isoforms) made by risk genes. However, how these genes …