İvet Bahar

The paper systematically assesses the functional impact of CPOX variants under different environmental conditions, revealing mercury-dependent variant effects and improving variant classification.

The paper reports cryo-EM structures of the Zn2+ ABC transporter ZnuB-ZnuC from E. coli, revealing a self-regulating mechanism via a zinc sensor.

This study presents X-ray structures of detemir in hexameric and dodecameric forms, revealing structural dynamics and identifying key residues involved in conformational changes and stability.

This study combines normal modes with weighted ensemble simulations to generate unbiased protein pathways efficiently.

The paper investigates how two small molecule activators of PP2A, ATUX-8385 and DBK-776, affect the structural stability of the PR65 scaffold using biophysical and computational methods.

The paper investigates how SMAPs bind to PR65, showing that S2 is a stable binding site while S1 is not, and that binding promotes an extended PR65 conformation favorable for PP2A holoenzyme assembly.

The paper links brain structure to function by showing that commute time, derived from diffusion MRI, correlates better with functional MRI data than other measures.

GraphVelo extends RNA velocity inference to multimodal data by using graph-based machine learning to preserve vector information across different data representations.

This study investigates the dynamics and interactions of the AlkB-AlkG electron transfer complex using computational methods, revealing how substrate binding and channeling modulate allosteric effects and electron transfer efficiency.

Rhapsody-2 is a machine learning tool that accurately predicts pathogenicity of single amino acid variants using sequence, structure, and dynamics features, achieving high performance across benchmark datasets.

The paper identifies NCOA7's role in lysosomal function and inflammatory sterol metabolism in PAH, showing its deficiency exacerbates disease through oxysterol/bile acid generation.

This paper shows that phosphorylation of Syntaxin1 at Ser14 is critical for non-vesicular dopamine release and AMPH-induced behaviors in Drosophila.

The paper uses elastic network modeling to identify sensor and effector genes in yeast that control information flow through long-range interactions.

The paper introduces dynamo, a framework for estimating RNA velocities and predicting cell fates using single-cell RNA-seq data, applied to various biological processes.

This study investigates how bile acid obeticholic acid (OCA) interacts with the dopamine transporter (DAT) and modulates its activity through non-competitive binding mechanisms.

Llamanade is an open-source pipeline that humanizes nanobodies using sequence and structural analysis, improving their translational potential for therapeutic applications.

This study investigates the effects of a DAT mutation linked to DTDS, showing impaired dopamine function and behavioral deficits in Drosophila, with potential therapeutic implications.

This paper introduces a method to jointly analyze two independent GWAS datasets with different phenotypes, addressing confounding factors and showing its utility in studying Alzheimer's disease and substance use disorder.

Modeling indicates N501Y strengthens ACE2 binding while K417N and E484K break two interface salt bridges, leaving 501.V2 affinity near wildtype but weakening several monoclonal antibodies.

This paper introduces a method to identify persistent structures in multiscale omics data, expanding cell type catalogs and revealing SARS-COV-2 protein interactions.

The paper performs a quantitative systems pharmacology analysis of 225 autophagy modulators to uncover their molecular mechanisms and regulatory pathways.

The paper introduces Rhapsody, a tool that predicts the pathogenicity of human missense variants by integrating sequence, structure, and dynamics data, outperforming existing methods.

This study shows that disulfide bridge formation in CaMKII disrupts its interaction with calmodulin in Parkinson's disease, linking oxidative stress to impaired Ca2+/CaM signaling.

The paper uses quantitative systems pharmacology to analyze 50 drugs of abuse, identifying new targets and pathways, with mTORC1 highlighted as a key effector in neuronal restructuring.

This paper builds a computational model to study how cells decide between autophagy and apoptosis under stress, revealing that cytoplasmic Ca2+ acts as a rheostat regulated by G-protein signaling and AMPK.

The paper uses a Gaussian Network Model (GNM) to predict chromosomal dynamics from Hi-C data, showing correlations with accessibility and gene coexpression.