Charles Demurjian

Understanding the spectrum of complex metastatic processes is important to the development of a comprehensive and cohesive understanding of cancer metastasis. The Metastasis Research Network (MetNet) supports collaborative, multidisciplinary projects that focus on several themes of the metastatic process and use integrative systems-level approaches.

MetNet is advancing the understanding of metastasis as a non-linear, dynamic, and emergent process, as well as revealing mechanistic insights of early ...

Shoulders Lab Collagen Publications

Endometriosis research done by the Griffith lab (MIT) and the Goods lab (Dartmouth)

ABSTRACT – OVERALL The primary focus of the MIT/DFCI Center for Systems Biology of Glioblastoma is to understand the intersections between neurons, immune cells, and tumor cells in this deadly tumor. The lack of response to immunotherapy strategies despite prominent infiltrates of immune cells in many GBM highlights the immuno- suppressive nature of the GBM microenvironment and the importance of more clearly understanding the dynamic interactions at the tumor/immune interface. Similarly, interactions ...

About

This project houses all the publicly available datasets generated by the Hi-IMPAcTB consortium over the course of its 7+ years.

What is Hi-IMPAcTB?

Hi-IMPAcTB is an ambitious endeavor bringing together a team of international, interdisciplinary researchers to improve our understanding of host-pathogen interactions in the context of tuberculosis (TB). Funded by a multi-center contract from the NIH, the long-term goal of the consortium is to enable principled vaccine design by improving ...

The MIT Superfund Research Program was created in 2017 to be responsive to communities who live near Superfund Sites. In particular, the MIT team leverages scientific research, community engagement, and educational experiences to support people who are concerned about hazardous chemicals in their environment.

Carcinogenic contaminants threaten the health of people living in the Mystic River Watershed (near the Olin, Industriplex, and Wells G&H Superfund sites) and members of Native American ...

Michael C. Chao, Michael R. Chase, Shoko Wakabayashi, Andrew Vickers, Byron Roman, Forrest Hopkins, Peter H. Culviner, Maximillan G. Marin, Pauline Maiello, Collin R. Dietrich, Zandrea Ambrose, Philana Ling Lin, Qingyun Liu, Sarah M. Fortune

DOI: https://doi.org/10.64898/2026.04.03.714442

Abstract: Whole genome sequencing of Mycobacterium tuberculosis (Mtb) populations from clinical samples has increasingly identified genes undergoing selection within and ...

Nina E Gubina, Lindsay B Volk, Anna F Dormitzer, Emily M Michelsen, Lee J Pribyl, Joshua J Corrigan, Esha D Dalvie, Amanda L Armijo, Monét Norales, Nicolette A Bugher, Kayla M Schonvisky, Desiree L Plata, Bevin P Engelward, Robert G Croy, John M Essigmann, Bogdan I Fedeles

DOI: https://doi.org/10.1093/narmme/ugag035

Abstract: N-Nitrosodimethylamine (NDMA) is classified as an animal and probable human carcinogen. Murine liver DNA adducts, mutations, MGMT and ...

Andrew W Simonson,1,2 Michael C Chao,3,4 E Grace Bothwell,1,2 Mark A Rodgers,1,2 Luke E Hood,1,2 Forrest Hopkins,3,4 Michael R Chase,3,4 Andrew J Vickers,3,4 Alex A Smith,1,2 Ryan J Kelly,1,2 Cassaundra L Ameel,1,2 Edwin Klein,5 Harris Chishti,1,2 Marshall Malin,1,2 H Jake Borish,1,2 Pauline Maiello,1,2 Charles A Scanga,1,2 Philana Ling Lin,2,6 Sarah M Fortune,3,4,7 JoAnne L Flynn1,2*

Mycobacterium tuberculosis (Mtb) remains endemic in much of the world, resulting in frequent exposures to the ...

Edward B. Irvine, Angel Nikolov, Mehak Z. Khan, Joshua M. Peters, Richard Lu, Jaimie Sixsmith, Aaron Wallace, Esther van Woudenbergh, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Patricia S. Grace, Galit Alter & Sarah M. Fortune

doi: https://doi.org/10.1101/2022.05.01.490220

Mounting evidence indicates that antibodies can contribute towards control of tuberculosis (TB). However, the underlying mechanisms ...

Krista M. Pullen, Ryan Finethy, Seung-Hyun B. Ko, Charlotte J. Reames, Christopher M. Sassetti, Douglas A. Lauffenburger

DOI: https://doi.org/10.1038/s41540-024-00487-6

Abstract:Numerous studies have identified similarities in blood transcriptomic signatures of mouse tuberculosis (TB) models and human disease phenotypes, such as type 1 interferon (IFN) production and innate immune cell activation, yet the pathophysiology observed in murine infection does not ...

Lee J. Pribyl, Jennifer E. Kay, Joshua J. Corrigan, Lindsay B. Volk, Monét Norales, Norah A. Owiti, Evan A. Kowal, Ishwar N. Kohale, Ilana S. Nazari, Matilda R. Swanson, Aimee C. Moise, Duanduan Ma, Stuart S. Levine, Emily Michelsen, Robert G. Croy, Timothy Ragan, Dorothea K. Torous, Svetlana L. Avlasevich, Stephen D. Dertinger, Sebastian E. Carrasco, Leona D. Samson, John M. Essigmann, Forest M. White, Bevin P. Engelward

DOI: https://www.biorxiv.org/content/10.1101/2025.10.01.679856v1 ...

Vincent L. Butty, Pranav Patel, Stuart S. Levine

DOI:

Abstract: DNA labelling fluorescent dyes such as ethidium bromide have long been considered to be highly mutagenic during DNA replication. While recent studies have pushed back on this narrative, the intercalative nature of these dyes continues to raise the possibility that these dyes can induce mutations. The iconPCR instrument by n6tec uses fluorescent dyes to measure amplification in real time and to ...

Lindsay B Volk, Monét Norales, Callie Karjane, Joshua J Corrigan, Alper J Alcaraz, Lee J Pribyl, Nicolette A Bugher, Megan Blawas, Isabella Dulski, Einthavy Arunachalam, Nina Gubina, Emily Michelsen, Kannammai Pichappan, Natalya Yakimchuk, Matilda Swanson, Duanduan Ma, Stuart S Levine, Desiree L Plata, Robert G Croy, Leona D Samson, John M Essigmann, Carole L Yauk, Sebastian E Carrasco, Bevin P Engelward

Abstract: N-Nitrosodimethylamine (NDMA) is a probable human carcinogen found in ...

Nicolette A. Bugher, Jonathan W. Zheng, Annabella S. Wardle, William H. Green, and Desiree L. Plata

DOI:

Abstract: N-nitrosamines are a class of carcinogenic industrial pollutants that lack well-characterized physicochemical properties. Classical approaches to determine octanol-water partition coefficients (Kow) values are laborious, slow, and challenged by experimental error. Alternative methods include quantum chemical estimation (e.g., COSMO-RS), quantitative ...

Megan D. Maerz, Mohau S. Makatsa, Allison N. Bucsan, Matthew S. Sutton, Emma Bishop, Ziwei Tian, Erik D. Layton, Mario Roederer, Alex K. Shalek, Robert A. Seder, Thomas J. Scriba, Chuangqi Wang, Patricia A. Darrah, and Chetan Seshadri

DOI: https://doi.org/10.1016/j.xcrm.2025.102536

γδ T cells expressing a Vδ1/3+ T cell receptor are enriched at mucosal surfaces, but their role in protection against Mycobacterium tuberculosis (Mtb) is largely unknown. We used ...

Marie

Elena Cambria, Adriana Blazeski, Eunkyung Clare Ko, Tran Thai, Shania Dantes, David A. Barbie, Sarah E. Shelton, Roger D. Kamm

https://www.biorxiv.org/content/10.1101/2025.01.10.632378v1

Abstract: Lung fibrosis, characterized by chronic and progressive scarring, has no cure. Hallmarks are the accumulation of myofibroblasts and extracellular matrix, as well as vascular remodeling. The crosstalk between myofibroblasts and vasculature is poorly understood, with ...

Abiola F. Ogunsola, Rocky Lai, Kelly Cavallo, Gillian L. Beamer, and Samuel M. Behar

DOI:

Abstract: Vaccine development for tuberculosis is a global priority. Our studies using Collaborative Cross (CC) mice show that genetic diversity influences the efficacy of BCG, the most widely used TB vaccine. BCG vaccination of CC042 mice reduces their lung bacillary burden and increases their survival following low-dose aerosol Mycobacterium tuberculosis infection ...

Mohau S. Makatsa, Emma Bishop, Allison N. Bucsan, Matthew Sutton, Chelsea Lehman, Molly Robertson, Krystle K.Q. Yu, Joshua M. Peters, Bryan D. Bryson, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Chetan Seshadri

DOI: https://doi.org/10.1016/j.mucimm.2025.10.011

Abstract: Intravenous (IV) vaccination with Bacillus Calmette–Guerin (BCG) mediates sterilizing immunity against Mycobacterium tuberculosis (Mtb) in rhesus macaques but the cellular mechanisms ...

Andrew W Simonson, Michael C Chao, Luke E Hood, Rachel A Donlan, Forrest Hopkins, Michael R Chase, Andrew J Vickers, Alanna Callendrello, Edwin Klein, H Jacob Borish, Marshall Malin, Pauline Maiello, Charles A Scanga, Philana Ling Lin, Sarah M Fortune, JoAnne L Flynn

DOI: https://doi.org/10.1101/2025.07.08.663727

Immunological memory elicited either through previous or ongoing M. tuberculosis (Mtb) infection provides a critical mechanism by which hosts protect ...

Marie Floryan, Elena Cambria, Adriana Blazeski, Mark F. Coughlin, Zhengpeng Wan, Giovanni Offeddu, Vinayak Vinayak, Aayush Kant, Vivek Shenoy, Roger D. Kamm

DOI:

Abstract: The incorporation of a functional perfusable microvascular network (MVN) is a common requirement for most organ on-chip-models. Long-term perfusion of MVNs is often required for the maturation of organ phenotypes and disease pathologies and to model the transport of cells and drugs entering ...

_Andrew W. Simonson, Joseph J. Zeppa, Allison N. Bucsan, Michael C. Chao, Supriya Pokkali, Forrest Hopkins, Michael R. Chase, Andrew J. Vickers, Matthew S. Sutton, Caylin G. Winchell, Amy J. Myers, Cassaundra L. Ameel, Ryan Kelly, Ben Krouse, Luke E. Hood, Jiaxiang Li, Chelsea C. Lehman, Megha Kamath, Jaime Tomko, Mark A. Rodgers, Rachel Donlan, Harris Chishti, H. Jacob Borish, Edwin Klein, Charles A. Scanga, Sarah Fortune, Philana Ling Lin, Pauline Maiello, Mario Roederer, Patricia A. Darrah, ...

Ze Gong, Koen van den Dries, Rodrigo A. Migueles-Ramírez, Paul W. Wiseman, Alessandra Cambi & Vivek B. Shenoy

DOI: https://doi.org/10.1038/s41467-023-38598-z

Abstract: Immune cells, such as macrophages and dendritic cells, can utilize podosomes, mechanosensitive actin-rich protrusions, to generate forces, migrate, and patrol for foreign antigens. Individual podosomes probe their microenvironment through periodic protrusion and retraction cycles (height ...

Kathryn M. Yammine, Sophia Mirda Abularach, Michael Xiong, Seo-yeon Kim, Agata A. Bikovtseva, Vincent L. Butty, Richard P. Schiavoni, John F. Bateman, Shireen R. Lamandé, and Matthew D. Shoulders

A dbGaP Submission is underway and metadata will be updated at the completion of submission. The remaining of the data and metadata are available here.

DOI: 10.1101/2024.11.07.622468.

Abstract:

Objectives Mutations in the procollagen-II gene (COL2A1) ...

This assay captures administrative and clinical metadata associated with patient study visits, serving as a structured data collection framework rather than a biological measurement assay. It records visit-level contextual information such as visit dates, timepoints, subject identifiers, clinical site details, and protocol-relevant annotations that are essential for linking experimental samples and assay results to their proper clinical context. This metadata layer ensures traceability and data ...

This assay captures metadata associated with tissue collection procedures, documenting critical provenance and contextual information for biological specimens obtained from study subjects. It records standardized parameters such as tissue type, anatomical source, collection method, preservation conditions, and relevant donor or sample identifiers to ensure traceability and reproducibility across downstream experimental workflows. This metadata serves as a foundational record linking collected ...

Flow cytometry is a laser-based, high-throughput single-cell analysis technique used to simultaneously measure multiple physical and fluorescent characteristics of cells or particles in suspension. This assay quantifies cell populations based on parameters such as cell size (forward scatter), granularity (side scatter), and fluorescence intensity of labeled surface or intracellular markers, enabling immunophenotyping, cell cycle analysis, viability assessment, and functional studies. Samples are ...

Flow cytometry is employed to quantitatively measure cell surface and/or intracellular markers, enabling characterization of cell populations based on fluorescence intensity and light scatter properties. This assay utilizes a flow cytometer to analyze individual cells in suspension, providing multi-parametric data on cell phenotype, viability, activation state, or other biological attributes as defined by the experimental panel. Samples are processed, stained with fluorescently labeled antibodies ...

This assay captures administrative and clinical metadata associated with patient study visits, serving as a structured data collection framework rather than a biological measurement assay. It records visit-level contextual information such as visit dates, timepoints, subject identifiers, clinical site details, and protocol-relevant annotations that are essential for linking experimental samples and assay results to their proper clinical context. This metadata layer ensures traceability and data ...

This assay captures metadata associated with tissue collection procedures, documenting critical provenance and contextual information for biological specimens obtained from study subjects. It records standardized parameters such as tissue type, anatomical source, collection method, preservation conditions, and relevant donor or sample identifiers to ensure traceability and reproducibility across downstream experimental workflows. This metadata serves as a foundational record linking collected ...

A titer assay designed to quantify the concentration or activity level of a specific biological agent (such as a virus, antibody, or other biomolecule) in a given sample, with results linked to associated experimental datasets for integrated analysis. The assay employs serial dilution methodology to determine the highest dilution at which a detectable response or activity is observed, providing a standardized endpoint titer value. Results are systematically recorded and cross-referenced with ...

This assay evaluates the binding affinity and interaction of test compounds or biological molecules (such as antibodies or Fc-fusion proteins) to Fc receptors (FcRs), which are critical mediators of immune effector functions including antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis. Binding interactions are quantified using established biochemical or biophysical detection methodologies, enabling characterization of Fc-FcR engagement relevant to the functional activity of ...

Antibody-dependent cellular phagocytosis measures immune cell uptake of antibody-coated targets. The assay quantifies phagocytic activity as an indicator of antibody function and cellular response. Input: Antibody-treated target cells and effector cells Output: Phagocytosis data file (e.g., fluorescence or imaging-based readouts).

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

A single cell expression matrix file contains processed gene expression counts for individual cells. It represents the normalized matrix used for downstream dimensionality reduction, clustering, or differential expression analysis. Each file integrates thousands of single-cell measurements into one dataset (many→1). Typical file types: .h5ad, .mtx, .csv

An antibody panel sample represents a curated collection of antibodies used for detection or labeling in assays. It defines the set of reagents applied to measure or visualize specific proteins, cells, or molecular targets. This sample type is used to link AB's together into a single UID

A non-human primate sample originates from an organism closely related to humans within the primate order. These samples are collected to study biological processes that share genetic and physiological similarities with human systems. Each reflects controlled collection and handling specific to the species and study design.

An antibody sample contains purified immune proteins that specifically recognize and bind to target molecules. These samples are used in experimental procedures that detect, label, or isolate biological components. Each antibody is defined by its binding specificity, source, and production method.

A bacteria sample represents a microbial strain used in an experiment, either as an infectious agent or as material isolated from another biological source. It serves as a basis for studying host interactions, gene expression, or microbial composition.

A tissue sample represents a portion of biological material collected from an organism. It serves as the source for downstream molecular, cellular, or histological analyses.

A bacteria sample represents a microbial strain used in an experiment, either as an infectious agent or as material isolated from another biological source. It serves as a basis for studying host interactions, gene expression, or microbial composition.

A DNA sample contains extracted genetic material isolated from a biological source. It serves as input for sequencing, amplification, or other genomic analyses.

A DNA sample contains extracted genetic material isolated from a biological source. It serves as input for sequencing, amplification, or other genomic analyses.

A sequencing file contains raw nucleotide sequence reads and their quality scores. It represents the digital output from a DNA or RNA sequencing run and serves as the starting point for downstream analyses such as alignment or variant calling. Typical file type: .fastq or .fastq.gz

A sequencing file contains raw nucleotide sequence reads and their quality scores. It represents the digital output from a DNA or RNA sequencing run and serves as the starting point for downstream analyses such as alignment or variant calling. Typical file type: .fastq or .fastq.gz

An antibody sample contains purified immune proteins that specifically recognize and bind to target molecules. These samples are used in experimental procedures that detect, label, or isolate biological components. Each antibody is defined by its binding specificity, source, and production method.

A digitally barcoded MTB matrix analysis file contains processed results from barcoded Mycobacterium tuberculosis tracking experiments. It represents summarized abundance or distribution data across bacterial lineages or host conditions. Each file aggregates results from multiple barcoded samples into one matrix (many→1). Typical file types: .csv, .xlsx

A flow cytometry file stores fluorescence and light-scattering measurements collected from individual cells or particles during cytometric analysis. It represents the digital output of a cytometer used to characterize cell populations and properties. Typical file type: .fcs

A flow cytometry analysis file contains processed results derived from raw cytometry data. It represents quantified cell populations, marker expression levels, or gating outcomes used for downstream statistical interpretation. Each file typically aggregates data from multiple raw samples into one analyzed dataset (many→1). Typical file types: .csv, .xlsx, .fcs

An antibody sample contains purified immune proteins that specifically recognize and bind to target molecules. These samples are used in experimental procedures that detect, label, or isolate biological components. Each antibody is defined by its binding specificity, source, and production method.

An imaging data file stores visual or spatial information captured from microscopy, radiography, or other imaging systems. It represents the raw or processed image output used for structural or morphological analysis. Typical file types: .tiff, .jpg, .png, .ome.tiff

An imaging data file stores visual or spatial information captured from microscopy, radiography, or other imaging systems. It represents the raw or processed image output used for structural or morphological analysis. Typical file types: .tiff, .jpg, .png, .ome.tiff

A patient visit record represents a specific encounter or collection event for a study participant. It provides temporal and contextual information linking biological samples or data files to a particular time point, condition, or intervention.

A single cell expression matrix file contains processed gene expression counts for individual cells. It represents the normalized matrix used for downstream dimensionality reduction, clustering, or differential expression analysis. Each file integrates thousands of single-cell measurements into one dataset (many→1). Typical file types: .h5ad, .mtx, .csv