NExtSEEK
Web page: https://nextseek.mit.edu/
Funding details: Related items
Projects: Hi-IMPAcTB, MIT SRP, MetNet, Cancer Systems Biology Consortium (CSBC), Endometriosis
Institutions: Massachusetts Institute of Technology
Projects: Hi-IMPAcTB, MetNet, MIT SRP
Institutions: MIT, Massachusetts Institute of Technology
Projects: Hi-IMPAcTB
Institutions: Massachusetts Institute of Technology
https://orcid.org/0000-0002-3455-2992
Projects: Hi-IMPAcTB, MIT SRP
Institutions: Massachusetts Institute of Technology
Researcher at BioMIcro Center, Data Management and Analysis Core; Massachusetts Institute of Technology
Projects: MIT SRP
Institutions: Massachusetts Institute of Technology
Projects: MIT SRP, Hi-IMPAcTB, MetNet
Institutions: Massachusetts Institute of Technology
Projects: Hi-IMPAcTB
Institutions: University of Toronto
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 ...
Programme: NExtSEEK
Public web page: Not specified
Shoulders Lab Collagen Publications
Programme: NExtSEEK
Public web page: Not specified
Endometriosis research done by the Griffith lab (MIT) and the Goods lab (Dartmouth)
Programme: NExtSEEK
Public web page: Not specified
Programme: NExtSEEK
Public web page: Not specified
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 ...
Programme: NExtSEEK
Public web page: Not specified
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 ...
Programme: NExtSEEK
Public web page: https://grantome.com/grant/NIH/75N93019C00071-0-9999-1
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 ...
Programme: NExtSEEK
Public web page: Not specified
ROR ID: Not specified
Department: Not specified
Country: 
United States
City: Not specified
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ROR ID: Not specified
Department: Not specified
Country: United States
City: Not specified
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ROR ID: Not specified
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Canada
City: Not specified
Web page: Not specified
Submitter: Charles Demurjian
Studies: Human cartilage model of the precocious osteoarthritis-inducing COL2A1 p...
Assays: All Metadata, Cell Imaging - Data Linked, Gene Expression Analysis - Data Linked, LC - MS/MS (Proteomics) - Data Linked, Library Creation - Metadata, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, Short Read Sequencing - Data Linked, iPSC Culture and Chondronoid Formation - Metadata
Submitter: Charles Demurjian
Studies: Structural and systems characterization of phosphorylation on metabolic ..., Validation and quantification of peptide antigens presented on MHCs usin...
Assays: All Metadata, ImmunoPeptideomics - Data Linked, Sample Processing - Metadata, SureQuant Analysis - Data Linked
Submitter: Charles Demurjian
Studies: Integrating endometrial proteomic and single cell transcriptomic pipelin..., Organoid co-culture model of the cycling human endometrium in a fully-de...
Assays: All Metadata, All Metadata, Cell Culture Imaging - Data Linked, Cell Culture and Organoid Generation - Metadata, DNA Extraction - Metadata, DNA Extraction - Metadata, Elisa - Data Linked, Gene Expression Analysis - Data Linked, Immunohistochemistry - Data Linked, Linear Mixed Model - Data Linked, Luminex - Data Linked, Mass Spectrometry Proteomics - Data Linked, Mass Spectrometry Proteomics Analysis - Data Linked, Patient Visit - Metadata, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Matrix Analysis - Data Linked, Single Cell Sequencing - Data Linked, Tissue Collection - Metadata, Tissue Collection - Metadata
Submitter: Charles Demurjian
Studies: Chemo-mechanical diffusion waves explain collective dynamics of immune c..., Chromatin conformation, gene transcription, and nucleosome remodeling as..., Confined cell migration along extracellular matrix space in vivo, Impact of fibrinogen, fibrin thrombi and thrombin on cancer cell extrava..., IntravChip: a vascularized and perfused microfluidic model of the primar..., Myofibroblasts reduce angiogenesis and vasculogenesis in a vascularized ..., Patient-specific vascularized tumor model: Blocking monocyte recruitment..., Personalized Vascularized Models of Breast Cancer Desmoplasia Reveal Bio..., Polyploidy of MDA-MB-231 cells drives increased extravasation with enhan..., Remodeling of self-assembled microvascular networks under long term flow, Utilizing convolutional neural networks for discriminating cancer and st...
Assays: All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, Cancer Cell Extravasation Analysis - Data Linked, Cancer Cell Extravasation Analysis - Data Linked, Cell Culture - Metadata, Cell Culture - Metadata, Cell Culture Imaging - Data Linked, Cell Culture Imaging Analysis - Data Linked, Cell Culture and Tumor Spheroid Creation - Metadata, Cell Culture and Tumor Spheroid Creation - Metadata, Cell Extraction - Metadata, Cell Imaging - Data Linked, Chromatin Sequencing Analysis - Data Linked, Clot Modeling Analysis - Data Linked, Convolutional Neural Network - Data Linked, Cytokine Luminex - Data Linked, Dendritic Cell Preparation - Metadata, Device Creation - Metadata, Device Creation - Metadata, Device Imaging - Data Linked, Device Imaging - Data Linked, Device Imaging - Data Linked, Device Imaging - Metadata, ELISA - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Fluorescence-Activated Cell Sorting - Data Linked, Gene Expression Analysis - Data Linked, Gene Expression Analysis - Data Linked, Imaging - Data Linked, Imaging Analysis - Data Attached, Imaging Analysis - Data Linked, Imaging Analysis - Data Linked, Imaging Analysis - Data Linked, Imaging Analysis - Data Linked, Intravital Microscopy, Library Creation - Metadata, Library Prep - Metadata, Library Prep - Metadata, Live Cell Imaging - Data Linked, Luminex - Data Linked, MVN Imaging Analysis - Data Linked, Mass Spectrometry Proteomics - Data Linked, Microfluidic Device Creation - Metadata, Microfluidic Device Creation - Metadata, Microfluidic Device Imaging - Data Linked, Microfluidic Network Formation - Metadata, Microfluidic Network Formation - Metadata, Microfluidic Network Imaging - Data Linked, Microvascular Network Formation - Metadata, Migration Assay Analysis - Data Linked, Modeling - Data Linked, Modeling - Data Linked, Permeability Analysis - Data Linked, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, RNA Extraction - Metadata, RNA Extraction - Metadata, Real Time RT-PCR - Data Linked, Real-time RT-PCR - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Tumoroid Formation - Metadata
Submitter: Dikshant Pradhan
Studies: Age and sex influence antibody profiles associated with tuberculosis pro..., Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restric..., BCG vaccination elicits protection against Mtb infection mediated by two..., BCG vaccination induces antibacterial effector functions among Vδ1/3 T c..., CD4+ T cells re-wire granuloma cellularity and regulatory networks to pr..., CD8+ lymphocytes are critical for early control of tuberculosis in macaques, Comparable Non-canonical T cell responses are associated with protection..., Fc-engineered antibodies promote neutrophil-dependent control of Mycobac..., Fc-engineered monoclonal antibodies drive antibody-dependent enhancement..., Fc-engineered monoclonal antibodies drive antibody-dependent enhancement..., High-dose intravenous BCG vaccination induces enhanced immune signaling ..., Humoral correlates of protection against Mycobacterium tuberculosis foll..., IFN-γ- GranzymeB + Natural killer cells are induced by IV BCG vaccinatio..., Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resis..., Intravenous BCG-mediated protection against tuberculosis requires CD4+ T..., Multi-modal data integration using Markov Field graphical networks predi..., Multimodal profiling of lung granulomas in macaques reveals cellular cor..., Population-level genome sequencing reveals distinct Mycobacterium tuberc..., Protection against disseminated disease following reinfection with Mycob..., Protection against reinfection with Mycobacterium tuberculosis extends a..., Robust IgM responses following intravenous vaccination with Bacille Calm..., Soloman placeholder, Specific CD4+ T cell phenotypes associate with bacterial control in peop..., Systematic deconstruction of myeloid cell signaling in tuberculosis gran..., Systems-level computational translation of mouse and human transcriptomi...
Assays: ADCD Analysis - Data Linked, ADFP Analysis - Data Linked, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, Anti-Microbial Assay – Metadata, Antibody Challenge - Metadata, Antibody Dependent Complement Deposition - Data Linked, Antibody Dependent Functional Profiling - Data Linked, Antibody Titer - Data Linked, Antibody Titer Analysis - Data Linked, Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis Analysis - Data Linked, Antibody-Dependent NK Cell Activation - Data Linked, Antibody-Dependent NK Cell Activation Analysis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis Analysis - Data Linked, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Survivability Restriction Assay - Data Linked, Bacterial Survivability Restriction Assay - Data Linked, Bacterial Survivability Restriction Assay: Validation Data - Data Attached, CITESEQ Analysis - Data Linked, Cell Extraction - Metadata, Cell Extraction: Validation Data - Metadata, Cell Isolation - Metadata, Cell Isolation - Metadata, Cell Sorting – Data Linked, DNA Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Digitally Barcoded Mtb Matrix Analysis - Data Linked, ELISA - Data Linked, ELISA Assay - Data Linked, FC Receptor Binding - Data Linked, FC Receptor Binding Analysis - Data Linked, FC Receptor Binding Assay - Data Linked, FC-Receptor Binding Assay - Data Linked, FCS Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Attached, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Processing – Data Attached, Flow Cytometry – Data Linked, Functional Assay – Metadata, Gene Expression Analysis - Data Linked, Gene Expression Analysis: Training Data - Data Linked, Gene Expression Analysis: Validation Data - Data Linked, Glycosylation Assay - Data Linked, Histology - Data Linked, Immunohistochemistry - Data Linked, Immunohistochemistry - Data Linked, Immunohistochemistry – Data Linked, Library Collection - Metadata, Library Creation - Metadata, Library Creation - Metadata, Library Creation - Metadata, Library Creation – Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep: Training Data - Metadata, Library Prep: Validation Data - Metadata, Linear Mixed Model - Data Linked, Luminex - Data Linked, Luminex Assay – Metadata, Luminex Data Processing – Data Attached, Mass Cytometry - Data Linked, Mass Cytometry - Data Linked, Mass Cytometry Analysis - Data Linked, Model Validation, Model Validation - Data Linked, Mouse Challenge – Metadata, NHP Necropsy – Metadata, NHP Tissue Collection – Metadata, PCR: Validation Data - Data Attached, PET-CT Scan - Data Linked, PET-CT Scan - Data Linked, PET-CT Scan - Data Linked, PET-CT Scan Analysis – Data Linked, PET-CT Scan – Data Linked, PET/CT Scan - Data Linked, PET/CT Scan - Data Linked, Pathogen Challenge and Antibody Depletion - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit – Metadata, Patient Visit – Metadata, RNA Extraction: Validation Data - Metadata, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing: Training Data - Data Linked, Short Read Sequencing: Validation Data - Data Linked, Single Cell Clustering - Data Linked, Single Cell Clustering Analysis - Data Linked, Single Cell Clustering Analysis – Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Matrix Analysis – Data Linked, Single Cell Sequencing – Data Linked, Tissue Colleciton - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection – Metadata, Tissue Collection: Training Data - Metadata, Tissue Extraction - Metadata, Titer Assay - Data Linked, Titer Assay - Data Linked, Titer Assay Analysis - Data Linked, TransCompR Cross Species Modeling - Data Linked, Variant Calling Analysis - Data Linked, Western Blot - Data Linked
Submitter: Dikshant Pradhan
Studies: Benthic fluxes of fluorescent dissolved organic material, salt and heat ..., Colorimetric Detection of Aqueous N-Nitrosodimethylamine via Photonitros..., CometChip Enables Parallel Analysis of Multiple DNA Repair Activities, DNA adduct and mutational profiles reveal the saturation point of cellul..., Early life exposure to N-nitrosamine drives genotoxicity, mutagenesis, a..., Electrochemical formation of N-nitrosodimethylamine in nitrite-impacted ..., Excision of mutagenic replication-blocking lesions suppresses cancer but..., Interaction of N-Nitroamines with Bincuelar Copper Complexs for Luminsec..., Low-level N-nitrosamine occurrence in disinfected drinking water and rel..., Molecular origins of mutational spectra produced by the environmental ca..., Novel In Vivo CometChip Reveals NDMA-Induced DNA Damage and Repair in Mu..., Optical Detection of Interleukin-6 using Liquid Janus Emulsions using Hy..., Partitioning parameters of N-nitrosamines: An intercomparison of determi..., Persistent interferon signaling and clonal expansion mark early events i..., Reversible Electrochemical Sensor for NDMA: Leveraging Molecularly Impri..., Sex and base excision repair as key susceptibility factors for alkylatio...
Assays: Absorption and Emission Spectroscopy - Data Linked, Absorption and Emission Spectroscopy Analysis - Data Linked, Agglutination Assay - Data Linked, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, Atomic Force Microscopy - Data Linked, Chemical Challenge, Chemical Challenge - Metadata, Chemical Challenge - Metadata, Chemical Simulations - Data Linked, Chemical Simulations - Data Linked, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Cleaved caspase-3 staining and analysis, Comet Chip - Data Linked, Comet Chip Analysis - Data Attached, Comet Chip Analysis - Data Attached, Crystallography - Data Linked, DNA Adduct Analysis - Data Linked, DNA Extraction - Metadata, DNA Extraction - Metadata, ELISA - Data Linked, Electrochemical Sensor Testing - Data Linked, Electron Paramagnetic Resonance - Data Linked, Experimental Physiochemical Measurement - Data Linked, Experimental Physiochemical Measurement Analysis - Data Linked, Extraction and Library Creation - Metadata, Field Water Sensor Run, Flow Cytometry, Flow Cytometry - Data Linked, Flow Cytometry Analysis, Flow Cytometry Analysis - Data Linked, Fourier Transform Infrared Spectroscopy - Data Linked, GPT Assay, GPT Assay - Data Attached, GPT Assay - Data Linked, GPT Assay - Data Linked, GPT Assay – Data Attached, Gel Permeation Chromatography - Data Linked, Gene Expression Analysis - Data Linked, Genome Alignment - Data Linked, Genome Alignment - Data Linked, High Resolution Mass Spectra - Data Linked, High Resolution Mass Spectra Analysis - Data Linked, HistoPathology Analysis, Illumina Sequencing - Data Linked, Imaging, Imaging - Data Linked, Imaging - Data Linked, Imaging Analysis - Data Linked, Imaging Analysis - Data Linked, Library Creation - Metadata, Library Prep - Metadata, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mass Spectrometry - Data Linked, Mass Spectrometry - Data Linked, Mass Spectrometry Analysis - Data Linked, Mass Spectrometry Analysis - Data Linked, Mass Spectrometry Processing – Data Linked, Mass Spectrometry – Data Linked, Mouse Challenge - Metadata, Mouse Necropsy – Metadata, Mutational Spectra Analysis - Data Linked, Mutational Spectra Analysis - Data Linked, Mutational Spectral Analysis - Data Attached, Necropsy - Metadata, Nuclear Magnetic Resonance - Data Linked, Nuclear Magnetic Resonance Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, PCR - Data Linked, Pendant Drop Tensiometry - Data Linked, Phosphoproteomics Analysis - Data Linked, Predictive Modeling - Data Linked, Protein Extraction - Metadata, RNA Extraction - Metadata, RNA Isolation - Metadata, RaDR - Data Linked, RaDR Image Machine Learning Analysis, RaDR Image Machine Learning Analysis – Data Attached, Sample Collection - Metadata, Sensor Creation - Metadata, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Single-crystal X-ray Crystallography - Data Linked, Solid Phase Extraction - Metadata, Spatial Transcriptomics - Data Linked, Spatial Transcriptomics Analysis - Data Linked, Tissue Collection, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Imaging, Tissue Imaging - Data Linked, Tissue Imaging – Metadata, Tissue Lysis – Metadata, Tissue Sectioning, Tissue Sectioning - Metadata, UV-Vis Spectroscopy - Data Linked, UV-Vis Spectroscopy Analysis - Data Linked, Water Quality Detection - Data Linked, Western Blot - Data Linked, Western Blot - Data Linked, Western Blot Analysis - Data Linked, Western Blot Analysis - Data Linked, X-ray Photoelectron Spectroscopy - Data Linked, γH2AX staining and analysis
Kay et al. 2026, DNA Repair 166 (2026) 103955 (DOI: 10.1016/j.dnarep.2026.103955; PMID: 42566817). A study of how sex and the Aag base-excision-repair gene modulate NDMA-induced liver damage, mutagenesis and tumourigenesis in mice. Reach out to Jenny Kay (kay@silentspring.org) with any questions.
**Abstract: ** N-Nitrosodimethylamine (NDMA) is present in food, water, and drugs and is considered a probable human carcinogen by the International Agency for Research on Cancer. The mechanism of ...
Submitter: Juanita Pardo Sanchez
Investigation: MIT SRP
Assays: Chemical Challenge, Cleaved caspase-3 staining and analysis, Flow Cytometry, Flow Cytometry Analysis, GPT Assay, HistoPathology Analysis, Imaging, RaDR Image Machine Learning Analysis, Tissue Collection, Tissue Imaging, Tissue Sectioning, γH2AX staining and analysis
Barathkumar Baskaran, Michelle Wang, Kristen A. Riedinger, Glen Andrew D. de Vera, Elijah E. Martin, Chad D. Vecitis, Desiree L. Plata
DOI: https://doi.org/10.1021/acs.est.6c00610
This work demonstrates formation of N-nitrosodimethylamine during electrochemical treatment of nitrite-impacted waters with mechanistic understanding to inform mitigation. ...
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 ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, Chemical Challenge - Metadata, DNA Extraction - Metadata, ELISA - Data Linked, GPT Assay - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mass Spectrometry Analysis - Data Linked, Mutational Spectra Analysis - Data Linked, PCR - Data Linked, RNA Extraction - Metadata, RaDR - Data Linked, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
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 ...
Riedinger, Kristen; Bugher, Nicolette; Wardle, Annabella; Vandiver, Kathleen; Baskaran, Barathkumar; Michael, Zion; de Vera, Glen Andrew; Plata, Desiree
N-Nitrosodimethylamine (NDMA) is a probable human carcinogen that can be formed in drinking water treatment systems as a byproduct of chloramination and chlorination. Occurrence of NDMA and other N-nitrosamines in the United States has not been assessed at health-relevant levels (i.e., low to sub-ng/L concentrations) using sensitive analytical ...
Angel Nikolov
Tuberculosis (TB) is the world’s deadliest infection by number of lives claimed. Thus, novel vaccination and therapeutic strategies are urgently needed to limit the spread of TB. Historically, immunologists have made extensive efforts to potentiate cell-mediated immune responses to control Mycobacterium tuberculosis (Mtb). However, emerging data illustrate that the humoral immune system also plays a role in microbial control of Mtb. Antibodies targeted against surface structures ...
Angel Nikolov
Tuberculosis (TB) is the world’s deadliest infection by number of lives claimed. Thus, novel vaccination and therapeutic strategies are urgently needed to limit the spread of TB. Historically, immunologists have made extensive efforts to potentiate cell-mediated immune responses to control Mycobacterium tuberculosis (Mtb). However, emerging data illustrate that the humoral immune system also plays a role in microbial control of Mtb. Antibodies targeted against surface structures ...
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 ...
Submitter: Jake Schissel
Investigation: IMPAcTB
Assays: All Metadata, Antibody Challenge - Metadata, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Survivability Restriction Assay - Data Linked, ELISA - Data Linked, Glycosylation Assay - Data Linked, Library Prep - Metadata, Luminex - Data Linked, Patient Visit - Metadata, Single Cell Clustering Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Extraction - Metadata
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 ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Survivability Restriction Assay: Validation Data - Data Attached, Cell Extraction: Validation Data - Metadata, Gene Expression Analysis: Training Data - Data Linked, Gene Expression Analysis: Validation Data - Data Linked, Library Prep: Training Data - Metadata, Library Prep: Validation Data - Metadata, PCR: Validation Data - Data Attached, RNA Extraction: Validation Data - Metadata, Short Read Sequencing: Training Data - Data Linked, Short Read Sequencing: Validation Data - Data Linked, Tissue Collection: Training Data - Metadata, TransCompR Cross Species Modeling - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, DNA Adduct Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Gene Expression Analysis - Data Linked, Imaging - Data Linked, Imaging Analysis - Data Linked, Library Creation - Metadata, Mouse Challenge - Metadata, Phosphoproteomics Analysis - Data Linked, Short Read Sequencing - Data Linked, Spatial Transcriptomics - Data Linked, Spatial Transcriptomics Analysis - Data Linked, Tissue Collection - Metadata, Western Blot - Data Linked, Western Blot Analysis - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, DNA Extraction - Metadata, GPT Assay - Data Linked, Genome Alignment - Data Linked, Imaging Analysis - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mutational Spectra Analysis - Data Linked, Protein Extraction - Metadata, RNA Isolation - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata, Tissue Imaging - Data Linked, Tissue Sectioning - Metadata, Western Blot - Data Linked, Western Blot Analysis - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, FCS Analysis - Data Linked, Flow Cytometry - Data Linked, Library Creation - Metadata, Mass Cytometry - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
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 ...
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
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 ...
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Creator: Charles Demurjian
Submitter: Charles Demurjian
DownloadCreator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Taïsha Joseph-Risch
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Taïsha Joseph-Risch
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Juanita Pardo Sanchez
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Taïsha Joseph-Risch
Creators: None
Submitter: Taïsha Joseph-Risch
Creators: None
Submitter: Taïsha Joseph-Risch
Creators: None
Submitter: Taïsha Joseph-Risch
Creators: None
Submitter: Taïsha Joseph-Risch
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Abstract (Expand)
Authors: J. E. Kay, J. J. Corrigan, L. B. Volk, A. L. Armijo, N. A. Owiti, L. J. Pribyl, I. S. Nazari, D. K. Torous, S. L. Avlasevich, R. G. Croy, D. N. Wadduwage, S. E. Carrasco, S. D. Dertinger, J. M. Essigmann, L. D. Samson, B. P. Engelward
Date Published: 4th Aug 2026
Publication Type: Journal Article
Abstract
Authors: Jennifer E. Kay, Joshua J. Corrigan, Amanda L. Armijo, Ilana S. Nazari, Ishwar N. Kohale, Dorothea K. Torous, Svetlana L. Avlasevich, Robert G. Croy, Dushan N. Wadduwage, Sebastian E. Carrasco, Stephen D. Dertinger, Forest M. White, John M. Essigmann, Leona D. Samson, Bevin P. Engelward
Date Published: 1st Mar 2021
Publication Type: Journal Article
