Mengzhou Hu
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View article: Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics
Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics Open
View article: The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR
The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR Open
View article: Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization
Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization Open
Summary Cells are organized as a hierarchy of macromolecular assemblies, ranging from small protein complexes to entire organelles. Various technologies have been developed to elucidate subcellular architecture at different scales, such as…
View article: The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR
The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR Open
The protein tyrosine phosphatases (PTPs) TCPTP, PTPN22, and SHP1 are critical regulators of the activating phosphotyrosine (pY) site on the initiating T cell kinase, Lck Y394. Still, the broader implications of these phosphatases in T cell…
View article: Multimodal cell maps as a foundation for structural and functional genomics
Multimodal cell maps as a foundation for structural and functional genomics Open
View article: Evaluation of large language models for discovery of gene set function
Evaluation of large language models for discovery of gene set function Open
View article: Putting proteins in context
Putting proteins in context Open
View article: Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines Open
This article describes the Cell Maps for Artificial Intelligence (CM4AI) project and its goals, methods, standards, current datasets, software tools, status, and future directions. CM4AI is the Functional Genomics Data Generation Project i…
View article: Deep phosphotyrosine characterisation of primary murine T cells using Broad Spectrum Optimisation of Selective Triggering
Deep phosphotyrosine characterisation of primary murine T cells using Broad Spectrum Optimisation of Selective Triggering Open
Sequencing the tyrosine phosphoproteome using MS-based proteomics is challenging due to the low abundance of tyrosine phosphorylation in cells, a challenge compounded in scarce samples like primary cells or clinical samples. The broad-spec…
View article: Thought Graph: Generating Thought Process for Biological Reasoning
Thought Graph: Generating Thought Process for Biological Reasoning Open
We present the Thought Graph as a novel framework to support complex\nreasoning and use gene set analysis as an example to uncover semantic\nrelationships between biological processes. Our framework stands out for its\nability to provide a…
View article: Tools for assembling the cell: Towards the era of cell structural bioinformatics
Tools for assembling the cell: Towards the era of cell structural bioinformatics Open
Cells consist of large components, such as organelles, that recursively factor into smaller systems, such as condensates and protein complexes, forming a dynamic multi-scale structure of the cell. Recent technological innovations have pave…
View article: Evaluation of large language models for discovery of gene set function
Evaluation of large language models for discovery of gene set function Open
View article: Evaluation of large language models for discovery of gene set function
Evaluation of large language models for discovery of gene set function Open
Gene set analysis is a mainstay of functional genomics, but it relies on curated databases of gene functions that are incomplete. Here we evaluate five Large Language Models (LLMs) for their ability to discover the common biological functi…
View article: Mouse primary T cell phosphotyrosine proteomics enabled by BOOST
Mouse primary T cell phosphotyrosine proteomics enabled by BOOST Open
The Broad Spectrum Optimization of Selective Triggering (BOOST) approach was recently developed to increase the quantitative depth of the tyrosine phosphoproteome by mass spectrometry-based proteomics. While BOOST has been demonstrated in …
View article: Mass spectrometry profiling and quantitation of changes in circulating hormones secreted over time in Cancer borealis hemolymph due to feeding behavior
Mass spectrometry profiling and quantitation of changes in circulating hormones secreted over time in Cancer borealis hemolymph due to feeding behavior Open
View article: Exploring the Sexual Dimorphism of Crustacean Neuropeptide Expression Using <i>Callinectes sapidus</i> as a Model Organism
Exploring the Sexual Dimorphism of Crustacean Neuropeptide Expression Using <i>Callinectes sapidus</i> as a Model Organism Open
The impact of numerous diseases has been linked to differences in sex between organisms, including various neurological diseases. As neuropeptides are known to be key players in the nervous system, studying the variation of neuropeptidomic…
View article: Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in <i>Cancer borealis</i>
Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in <i>Cancer borealis</i> Open
The crab Cancer borealis nervous system is an important model for understanding neural circuit dynamics and modulation, but the identity of neuromodulatory substances and their influence on circuit dynamics in this system remains in…