Author

M. Sirota

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 4 Cancer Biology· 3 Cell Biology· 2 Scientific Communication & Education· 1

Signature Assays, Organisms & Methods

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Organism:human· 9 Research Focus:cell type annotation· 8 Assay:bulk RNA-seq· 6 Research Focus:differential expression· 6 Approach:statistical model· 5 Approach:experimental assay· 4 Approach:deep learning· 3 Assay:scRNA-seq· 3

Frequent Co-Authors

K. Yu· 4 shared C. J. Ye· 2 shared C. Luck· 2 shared C. Wibrand· 2 shared D. Rychkov· 2 shared E. Flynn· 2 shared M. Kerwin· 2 shared M. M. Sarwal· 2 shared

Activity by Year

2019-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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4 shared papersCancer Biology

K. Yu

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics

G. Rabadam, C. Wibrand, E. Flynn, G. C. Hartoularos, Y. Sun, C. J. Ye, S. Kim, Z. J. Gartner, M. Sirota, J. Neely

This study uses single-cell transcriptomics to identify immune dysregulation in JDM, revealing coordinated type I interferon activity and B cell abnormalities.

bioRxiv · Nov 7, 2023Immunology

Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing

M. Binvignat, B. Miao, C. Wibrand, M. Yang, D. Rychkov, E. Flynn, J. Nititham, W. Tamaki, U. Khan, A. Carvidi, M. Krueger, E. Niemi, Y. Sun, G. K. Fragiadakis, J. Sellam, , M. Sirota

This study uses single-cell RNA sequencing of PBMCs from RA patients and controls to identify disease-associated cell subsets and gene signatures linked to RA disease activity.

bioRxiv · Oct 5, 2023 · PreprintImmunology

Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes

K. Yu, A. Basu, C. Yau, D. M. Wolf, H. Goodarzi, S. Bandyopadhyay, J. E. Korkola, G. L. Hirst, S. Asare, I-SPY 2 TRIAL, A. Demichele, N. Hylton, D. Yee, L. Esserman, L. van 't Veer, M. Sirota

This study uses computational drug repositioning to identify agents that can sensitize drug-resistant breast tumors, finding fulvestrant effective across multiple treatment and receptor subtypes.

bioRxiv · Mar 30, 2023Cell Biology

Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities

C. R. Schott, A. L. Koehne, L. C. Sayles, E. P. Young, C. Luck, K. Yu, A. G. Lee, M. R. Breese, S. G. Leung, A. T. Shah, H. Xu, H.-Y. Liu, A. Spillinger, I. H. Behroozfard, K. D. Marini, , E. A. Sweet-Cordero

The paper develops and characterizes new osteosarcoma PDX models with varying metastatic capacities to study disease biology and test therapeutic interventions.

bioRxiv · Jan 19, 2023Cancer Biology

Perturbations of the T-cell immune repertoire in kidney transplant rejection

T. Sigdel, P. A. Fields, J. Liberto, I. Damm, M. Kerwin, J. Hood, P. Towfighi, M. Sirota, H. Robins, M. M. Sarwal

This study examines T-cell repertoire changes in kidney transplant recipients to understand rejection mechanisms, finding lower pre-transplant T-cell fractions and higher TCR turnover during acute rejection.

bioRxiv · Aug 24, 2022Immunology

Novel Mechanism for Tubular Injury in Nephropathic Cystinosis

S. Sur, M. Kerwin, S. Pineda, P. Sansanwal, T. K. Sigdel, M. Sirota, M. M. Sarwal

This study identifies ATP6V0A1 downregulation in cystinosis as a key factor in tubular injury, showing that antioxidants like astaxanthin can restore mitochondrial function and autophagosome turnover.

bioRxiv · May 13, 2022Cell Biology

Transcriptional fidelity enhances cancer cell line selection in pediatric cancers

C. Luck, K. Yu, R. A. Okimoto, M. Sirota

This study evaluates how well cancer cell lines represent pediatric tumors using RNA-seq data, finding that most tumor types best correlate with cell lines of the closest disease type.

bioRxiv · Oct 1, 2021 · PreprintCancer Biology

Nurturing Diversity and Inclusion in AI in Biomedicine through a Virtual Summer Program for High School Students

T. Oskotsky, R. Bajaj, J. Burchard, T. B. Cavazos, I. Chen, W. Connell, S. Eaneff, T. Grant, I. Kanungo, K. Lindquist, D. J. Myers-Turnbull, Z. Z. C. Naing, A. Tang, B. Vora, J. X. Wang, , M. Sirota

The paper describes a virtual summer program for high school students aimed at increasing diversity in AI through biomedical education, showing improved knowledge and engagement in AI concepts.

bioRxiv · Mar 6, 2021Scientific Communication & Education

Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis

V. Sarin, K. Yu, I. D. Ferguson, O. Gugliemini, M. A. Nix, B. C. Hann, M. Sirota, A. P. Wiita

This study evaluates how well multiple myeloma cell lines represent patient tumors using transcriptomic correlation analysis, finding significant variation in their similarity to patient tumors.

bioRxiv · Nov 20, 2019Cancer Biology

Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis

J. Ashouri, L.-Y. Hsu, S. Yu, D. Rychkov, Y. Chen, D. Chang, M. Sirota, E. Hansen, L. Lattanza, J. Zikherman, A. Weiss

The paper identifies arthritogenic CD4 T cells in murine and human autoimmune arthritis using Nur77 as a marker of TCR signaling.

bioRxiv · Mar 12, 2019Immunology