M. Pan

Quantifiable Blood TCR Repertoire Components Associated with Immune Aging

The paper identifies age-associated TCR repertoire components using a new computational framework and links them to immune aging and clinical outcomes.

Association study of Plasmodium falciparum Acetyl-CoA Synthetase Mutations S868G and V949I with antimalarial drugs

This study investigates the association of PfACAS mutations S868G and V949I with antimalarial drug resistance using whole-genome sequencing and CRISPR/Cas9-engineered parasites.

Acetyl-CoA Synthetase Mutations S868G and V949I Do Not Confer Resistance to Antimalarial Drugs in vitro in Plasmodium falciparum.

This study investigates whether mutations in PfACAS confer antimalarial drug resistance by engineering parasite lines with these mutations and testing their drug susceptibility in vitro.

Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid.

The paper investigates RA's limited effect on primary neuroblastoma tumors but efficacy in clearing bone marrow cells, identifying BMP signaling as a key determinant of cell fate and RA sensitivity.

The segmented flavivirus Alongshan virus reduces mitochondrial mass via degrading STAT2 to suppress innate immune response

Characterization of the SARS-CoV-2 BA.5 Variants in H11-K18-hACE2 Hamsters

This study characterizes SARS-CoV-2 BA.5 variants in H11-K18 hACE2 golden hamsters, showing disease progression and severity similar to human infections, supporting the model's utility for research.

Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168

This study determines the cryo-EM structures of RNF168/UbcH5c-Ub/nucleosome complexes to elucidate the mechanism of H2A K13/K15 site-specific ubiquitination.

Rapid Prototyping of Thermoplastic Microfluidic 3D Cell Culture Devices by Creating Regional Hydrophilicity Discrepancy

This paper develops a method to rapidly prototype thermoplastic microfluidic devices for 3D cell culture by creating regional hydrophilicity discrepancies, enabling dynamic cell culture and drug screening.

Gender-based heterogeneity of FAHFAs in trained runners

The paper compares FAHFA levels in lean and overweight runners, finding gender-based differences and associations with body composition and metabolic factors.

Structural Visualization of HECT-type E3 ligase Ufd4 Accepting and Transferring Ubiquitin to Form K29/K48-branched Polyubiquitination

This study determines the structural mechanism of HECT-type E3 ligase Ufd4 in catalyzing K29/K48-branched polyubiquitination by capturing structural snapshots of Ub transfer cascades.

An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs.

The paper compares mesenchymal-like gene expression programs in neuroblastoma preclinical models and patient tumors using single-cell RNA-seq and identifies chemotherapy-induced changes in PDX and GEMM.

A CRISPR-drug perturbational map for identifying new compounds to combine with commonly used chemotherapeutics.

The paper uses CRISPR knockout screens to identify drug combinations that enhance the effectiveness of common chemotherapeutics in neuroblastoma cells.

Energy dependence of signalling dynamics and robustness in bacterial two component systems

This paper models energy flow through two variants of bacterial two-component systems to show how energy availability affects signal sensitivity, noise filtering, and response thresholds.

SBML to bond graphs: from conversion to composition

The paper presents a framework to convert SBML models into bond graphs to ensure physical plausibility and thermodynamic consistency in biochemical models.

Distinct bile salt hydrolase substrate preferences dictate C. difficile pathogenesis

The paper identifies bile salt hydrolase (BSH) substrate preferences and shows they inhibit C. difficile by altering bile acid pools in CDI models.

Glutamine deficiency in solid tumors confers resistance to ribosomal RNA synthesis inhibitors

The paper shows that glutamine deficiency in cancer cells prevents p53 activation by rRNA synthesis inhibitors, promoting survival during nutrient stress.

A semantics, energy-based approach to automate biomodel composition

The paper proposes an automated method to compose biosimulation models using semantic annotations and bond graphs, demonstrating it by integrating Ras-MAPK and EGFR models.

Metabolomic and transcriptomic analyses reveal the effects of grafting on anthocyanin synthesis in grapevine

This study investigates how grafting affects anthocyanin synthesis in grapevines by analyzing metabolomic and transcriptomic profiles across different grafting conditions.

Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1

This study reports cryo-EM structures of Ubr1 complexes to elucidate the mechanism of ubiquitination initiation and elongation using a single E2 enzyme.

Hierarchical semantic composition of biosimulation models using bond graphs

This paper introduces a method to compose biosimulation models using bond graphs and semantic annotations, demonstrating it on a human arterial circulation model to improve modularity and physical consistency.

Dual regulation of the actin cytoskeleton by CARMIL-GAP

This paper identifies CARMIL-GAP as a Dictyostelium protein that regulates actin dynamics by GAP activity on Rac1 and capping protein, showing its critical role in phagocytosis and chemotaxis.

Mycobacterium abscessus biofilms produce an ECM and have a distinct mycolic acid profile

This study characterizes the extracellular matrix and mycolic acid profile of Mycobacterium abscessus biofilms, revealing molecular changes linked to antibiotic resistance.

The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma.

This study identifies CX-5461 as a TOP2B inhibitor with selective activity in high-risk neuroblastoma but highlights safety concerns due to TOP2B off-target effects.

Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis

This paper develops algorithms to predict drug response and interactions in tuberculosis by analyzing transcriptome signatures of cell viability.

Mechanistic insight into substrate processing and allosteric inhibition of human p97

This study presents cryo-EM structures of human p97 complex with and without inhibitor NMS-873, revealing conformational changes and allosteric inhibition mechanisms.

Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis

The paper identifies PF-3845 as a novel inhibitor of Mycobacterium tuberculosis PheRS, showing selectivity over human PheRS and potential as an antibiotic lead.

Partial epithelial-to-mesenchymal transition is prognostic and associates with Slug in head and neck cancer

The paper identifies a partial epithelial-to-mesenchymal transition (p-EMT) signature in HNSCC linked to poor prognosis and Slug expression, showing its clinical relevance and mechanistic role in therapy resistance.

K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle

This study identifies sAB-K29, a tool to detect K29-linked polyubiquitin, and shows its role in proteotoxic stress response and cell cycle regulation.

A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3

The paper develops a ratiometric voltage indicator by fusing an improved red fluorescent protein to ASAP3, enabling motion artifact-free voltage imaging in motile cells.

CRISPR/Cpf1 mediated genome editing enhances Bombyx mori resistance to BmNPV

This study compares CRISPR/Cpf1 orthologs for genome editing efficiency and antiviral ability in silkworms, finding FnCpf1 more effective than SpCas9 against BmNPV.