Explanipedia

Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response Open

Jingru Fang, Dylan C. Lam, Clarence K. Mah, Herbert G. Tanner, Troy J. Comi , et al. · 2025

RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment …

Deep Learning of Functional Perturbations from Condensate Morphology Open

Anita Donlic, Troy J. Comi, Sofia A. Quinodoz, Nima Jaberi-Lashkari, Krist Helen Antunes , et al. · 2025

Biomolecular condensates compartmentalize the interior of living cells to spatiotemporally organize complex functions, yet linking molecular interactions within condensates to their mesoscale organization remains a major challenge. To brid…

Mapping and engineering RNA-driven architecture of the multiphase nucleolus Open

Sofia A. Quinodoz, Lifei Jiang, Aya A. Abu-Alfa, Troy J. Comi, Hongbo Zhao , et al. · 2025

Biomolecular condensates are key features of intracellular compartmentalization^1,2. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure in which ribosomal RNAs (rRNAs) are …

Genome-wide mapping of mesoscale neuronal RNA organization and condensation Open

Lindsay A. Becker, Sofia A. Quinodoz, Troy J. Comi, Ofer Kimchi, David A. Knowles , et al. · 2025

SUMMARY Subcellular RNA organization can affect critical cellular functions. However, our understanding of RNA microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack of technologies to comprehensiv…

Landscape of human protein-coding somatic mutations across tissues and individuals Open

Huixin Xu, Rob Bierman, Dayna T. Akey, Cooper Koers, Troy J. Comi , et al. · 2025

Although somatic mutations are fundamentally important to human biology, disease, and aging, many outstanding questions remain about their rates, spectrum, and determinants in apparently healthy tissues. Here, we performed high-coverage ex…

Jobstats: A Slurm-Compatible Job Monitoring Platform for CPU and GPU Clusters Open

Josko Plazonic, Jonathan D. Halverson, Troy J. Comi · 2023

Evolution of Human-Specific Alleles Protecting Cognitive Function of Grandmothers Open

Sudeshna Saha, Naazneen Khan, Troy J. Comi, Andrea Verhagen, Aniruddha Sasmal , et al. · 2022

The myelomonocytic receptor CD33 (Siglec-3) inhibits innate immune reactivity by extracellular V-set domain recognition of sialic acid (Sia)-containing “self-associated molecular patterns” (SAMPs). We earlier showed that V-set domain-defic…

Evolution of Human-specific Alleles Protecting Cognitive Function of Grandmothers Open

Sudeshna Saha, Naazneen Khan, Troy J. Comi, Andrea Verhagen, Aniruddha Sasmal , et al. · 2021

Summary Late-onset Alzheimer’s Disease (LOAD) pathology is rare in our closest living evolutionary relatives (chimpanzees), which also express much lower microglial levels of CD33(Siglec-3)–a myelomonocytic receptor inhibiting innate immun…

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks Open

Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash-Ahmed , et al. · 2020

Understanding the regulatory architecture of phenotypic variation is a fundamental goal in biology, but connections between gene regulatory network (GRN) activity and individual differences in behavior are poorly understood. We characteriz…

Author response: Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks Open

Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash-Ahmed , et al. · 2020

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks Open

Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash-Ahmed , et al. · 2020

Understanding the regulatory architecture of phenotypic variation is a fundamental goal in biology, but connections between gene regulatory network (GRN) activity and individual differences in behavior are poorly understood. We characteriz…

Species and sex differences in eye morphometry and visual responsivity of two crepuscular sweat bee species (<i>Megalopta</i>spp., Hymenoptera: Halictidae) Open

Beryl M. Jones, Brett Seymoure, Troy J. Comi, Ellis R. Loew · 2020

Visually dependent dim-light foraging has evolved repeatedly, broadening the ecological niches of some species. Many dim-light foraging lineages evolved from diurnal ancestors, requiring immense visual sensitivity increases to compensate f…

Lipid Heterogeneity between Astrocytes and Neurons Revealed by Single‐Cell MALDI‐MS Combined with Immunocytochemical Classification Open

Elizabeth K. Neumann, Troy J. Comi, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2019

Transcriptomics characterizes cells based on their potential molecular repertoire whereas direct mass spectrometry (MS) provides information on the actual compounds present within cells. Single‐cell matrix‐assisted laser desorption/ionizat…

Data for: Lipid heterogeneity between astrocytes and neurons revealed with single cell MALDI MS supervised by immunocytochemical classification Open

Elizabeth K. Neumann, Troy J. Comi, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2019

We have recently created an approach for high throughput single cell measurements using matrix assisted laser desorption / ionization mass spectrometry (MALDI MS) (J Am Soc Mass Spectrom. 2017, 28, 1919-1928. doi: 10.1007/s13361-017-1704-1…

Species and Sex Differences in Eye Morphology and Visual Sensitivity of Two Nocturnal Sweat Bee Species (Megalopta Spp., Hymenoptera: Halictidae) Open

Beryl M. Jones, Brett Seymoure, Troy J. Comi, Ellis R. Loew · 2019

Exploring the Fundamental Structures of Life: Non‐Targeted, Chemical Analysis of Single Cells and Subcellular Structures Open

Elizabeth K. Neumann, D. Thanh, Troy J. Comi, Jonathan V. Sweedler · 2018

Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares nume…

Multimodal Chemical Analysis of the Brain by High Mass Resolution Mass Spectrometry and Infrared Spectroscopic Imaging Open

Elizabeth K. Neumann, Troy J. Comi, Nicolás Spegazzini, Jennifer W. Mitchell, Stanislav S. Rubakhin , et al. · 2018

The brain functions through chemical interactions between many different cell types, including neurons and glia. Acquiring comprehensive information on complex, heterogeneous systems requires multiple analytical tools, each of which have u…

Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Open

Tong Si, Bin Li, Troy J. Comi, Yuwei Wu, Pingfan Hu , et al. · 2017

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-f…

MALDI MS Guided Liquid Microjunction Extraction for Capillary Electrophoresis–Electrospray Ionization MS Analysis of Single Pancreatic Islet Cells Open

Troy J. Comi, Monika A. Makurath, Marina C. Philip, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2017

The ability to characterize chemical heterogeneity in biological structures is essential to understanding cellular-level function in both healthy and diseased states, but these variations remain difficult to assess using a single analytica…

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling Open

Troy J. Comi, Elizabeth K. Neumann, D. Thanh, Jonathan V. Sweedler · 2017

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, d…

Development of enabling technologies for single cell analysis with mass spectrometry Open

Troy J. Comi · 2017

Mass spectrometry (MS) is an effective methodology for untargeted, label-free, highly multiplexed analyses of trace compounds based on their mass-to-charge ratios. For biological applications, these properties have generated interest in de…

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry Open

Troy J. Comi, D. Thanh, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2017

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local …

Single Cell Profiling Using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation Open

D. Thanh, Troy J. Comi, Sage J. B. Dunham, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2017

A high-throughput single cell profiling method has been developed for matrix-enhanced-secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, the…

Enhanced Temporal Resolution with Ion Channel-Functionalized Sensors Using a Conductance-Based Measurement Protocol Open

Mark T. Agasid, Troy J. Comi, S. Scott Saavedra, Craig A. Aspinwall · 2016

The binding of a target analyte to an ion channel (IC), which is readily detected electrochemically in a label-free manner with single-molecule selectivity and specificity, has generated widespread interest in using natural and engineered …

A one‐step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms Open

Bin Li, Troy J. Comi, Tong Si, Sage J. B. Dunham, Jonathan V. Sweedler · 2016

Matrix‐assisted laser desorption/ionization imaging of biofilms cultured on agar plates is challenging because of problems related to matrix deposition onto agar. We describe a one‐step, spray‐based application of a 2,5‐dihydroxybenzoic ac…

Single Cell Peptide Heterogeneity of Rat Islets of Langerhans Open

Erik T. Jansson, Troy J. Comi, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2016

Measuring the chemical composition of individual cells in mammalian organs can provide critical insights toward understanding the mechanisms leading to their normal and pathological function. In this work, single cell heterogeneity of isle…

On-Tissue Derivatization via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues Open

Qian Wu, Troy J. Comi, Bin Li, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2016

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is used for the multiplex detection and characterization of diverse analytes over a wide mass range directly from tissues. However, analyte coverage with M…

Metal-assisted polyatomic SIMS and laser desorption/ionization for enhanced small molecule imaging of bacterial biofilms Open

Sage J. B. Dunham, Troy J. Comi, Kyungwon Ko, Bin Li, Nameera Baig , et al. · 2016

Mass spectrometry imaging (MSI) has become an important analytical tool for many sectors of science and medicine. As the application of MSI expands into new areas of inquiry, existing methodologies must be adapted and improved to meet emer…

Photopolymerization of Dienoyl Lipids Creates Planar Supported Poly(lipid) Membranes with Retained Fluidity Open

Kristina S. Orosz, Ian W. Jones, John P. Keogh, Christopher M. Smith, Kaitlyn Renee Griffin , et al. · 2016

Polymerization of substrate-supported bilayers composed of dienoylphosphatidylcholine (PC) lipids is known to greatly enhance their chemical and mechanical stability; however, the effects of polymerization on membrane fluidity have not bee…

Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Open

Ta‐Hsuan Ong, David J. Kissick, Erik T. Jansson, Troy J. Comi, Elena V. Romanova , et al. · 2015

Cell-to-cell variability and functional heterogeneity are integral features of multicellular organisms. Chemical classification of cells into cell type is important for understanding cellular specialization as well as organismal function a…

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