Neil L. Kelleher

This paper introduces a top-down mass spectrometry workflow with DMTm technology and a new software platform to achieve deeper proteoform sequencing and improved sequence coverage.

This paper introduces two plasma proteoform panels, PPA 526 and PPA 1514, using Individual Ion Mass Spectrometry to quantify proteoforms in human plasma with high reproducibility and disease discrimination capability.

This paper introduces Nuc-MS, a method to directly analyze chromatin reader-nucleosome interactions by disassembling complexes and identifying histone proteoforms involved in binding.

This study uses I2MS to analyze phosphorylation states of catenins in HEK cells, revealing their regulation by actomyosin contractility and identifying a phospho-code model for mechano-transduction.

The paper investigates how nucleosome context influences chromatin reader binding preferences using biochemical and genomic approaches, revealing that multivalent engagement often has regulatory effects beyond simple additivity.

This study compares single-molecule protein sequencing and individual ion mass spectrometry to analyze IL-6 proteoforms, showing combined coverage of 52% of the sequence.

This study shows that tau phosphorylation patterns influence microtubule stability, with specific phosphorylations impairing tau's ability to counteract destabilization, suggesting phosphorylation may respond to, rather than precede, MT instability.

This study shows replication stress reduces CENP-A nucleosome stability in S phase by disrupting ATRX and DAXX function, leading to centromere instability.

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

This paper evaluates YF2, a CREBBP/p300 activator, showing it enhances cytotoxicity and immune responses in B-cell lymphoma by restoring acetylation and altering the immune microenvironment.

This study maps the genome-wide binding of propionate and butyrate as acyl histone marks and shows their role in gene regulation and cell function.

This study uses top-down proteomics to identify plasma proteoform signatures that distinguish stages of liver cirrhosis progression.

This study uses engineered nanoparticles to enrich low-abundant proteins in human plasma, enabling top-down proteomics to detect proteoforms at lower concentrations and expand proteome depth.

MSModDetector identifies PTM patterns in individual ion mass spectrometry data by detecting mass shifts and using linear programming to infer modifications.

The paper constructs a coessential genetic network to map the dynamic cellular stress response across 625 cancer cell lines, identifying key regulators and modules involved in stress resilience.

The paper introduces two tools, BiG-SCAPE and CORASON, for analyzing biosynthetic gene clusters in large genomic datasets, demonstrating their utility through validation and discovery of new gene cluster families.

The paper uses linear programming to estimate modform distributions of proteins with multiple post-translational modifications, showing that combining bottom-up and top-down MS data reduces average modform range.

The paper uses a multi-modal proteomics approach to analyze PTMs of p53, revealing many modification sites but few distinct modified forms.

The paper introduces a synthetic biology approach to study nucleosome symmetry by creating asymmetric H3 heterodimers and demonstrates their utility in analyzing histone modification crosstalk.