Alex Zelter

The Findings Workflow: An agentic, collaborative, provenance-tracked framework for scientific data analysis with Claude Code

The paper introduces the Findings Workflow, a framework that enhances reproducibility and trust in LLM-assisted scientific analysis by structuring the process with provenance tracking and collaborative features.

Liver Fatty Acid Binding Protein (FABP1) Affects Cytochrome P450 2C9 (CYP2C9)-Mediated Metabolism in Human Liver Models

The paper shows that FABP1 affects CYP2C9-mediated drug metabolism in human liver models, improving prediction accuracy when included in physiologically based models.

A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice.

The paper presents two large-scale proteomics datasets from mice exposed to varying X-ray doses and time points, enabling biomarker discovery and machine learning applications for radiation exposure assessment.

Proteomic Profiling of Human Omental and Subcutaneous Adipose Tissue in Individuals with a Broad Range of BMI.

This study presents a comprehensive proteomic dataset of human omental and subcutaneous adipose tissue across a wide BMI range to uncover depot-specific biological changes associated with adiposity.

Is Protein Quantification and Physical Normalization Always Necessary in Proteomics?

This study investigates whether protein quantification and physical normalization are necessary in proteomics by comparing normalized and unnormalized sample inputs, showing that computational normalization can reduce variability in some cases.

Development and Validation of a Novel LC-MS/MS Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR)

This study develops and validates an LC-MS/MS method for absolute quantitation of RBP4 and TTR in serum and plasma, showing good linearity, precision, and correlation with ELISA.

Force transmission through the inner kinetochore is enhanced by centromeric DNA sequences

The paper shows that centromeric DNA sequences enhance force transmission through the inner kinetochore via the Okp1/Ame1 complex.

The molecular basis of integrated stress response silencing

This study determines the structure of the human E3 ligase SIFI, revealing its mechanism for ubiquitinating multiple substrates to silence the integrated stress response.

Limelight - An open, web-based tool for visualizing, sharing, and analyzing mass spectrometry data from DDA pipelines

DASH/Dam1 complex mutants stabilize ploidy by weakening kinetochore-microtubule attachments

The paper shows that missense mutations in kinetochore proteins reduce chromosome instability in histone-humanized yeast by weakening microtubule attachments, promoting euploidy.

A Stu2-mediated intrinsic tension-sensing pathway promotes chromosome biorientation in vivo

This study identifies a Stu2-mediated tension-sensing pathway that works with Aurora B to correct kinetochore attachments in vivo.

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

This paper summarizes current XL-MS practices, compares strategies, and proposes common protocols to establish best practice guidelines for accurate and reproducible results.

Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly

This study investigates the role of Spc110 N-terminal domains in stabilizing γ-tubulin small complex binding and γ-tubulin ring complex assembly through structural and biochemical analyses.