I. Korsunsky

发表

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation

S. Raychaudhuri, L. Donlin, Aparna Nathan, 2020, bioRxiv.

Notch signaling drives synovial fibroblast identity and arthritis pathology

N. Hacohen, C. Nusbaum, P. Gregersen, 2020, Nature.

Mixed Effects Association of Single Cells Identifies an Expanded Th1-Skewed Cytotoxic Effector CD4+ T Cell Subset in Rheumatoid Arthritis

S. Raychaudhuri, E. Karlson, M. Weinblatt, 2018 .

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Joyce B. Kang, S. Raychaudhuri, F. Powrie, 2021, bioRxiv.

Distinct fibroblast subsets drive inflammation and damage in arthritis

S. Raychaudhuri, H. Perlman, D. Fearon, 2019, Nature.

Maternal oxytocin administration modulates gene expression in the brains of perinatal mice

C. Metz, A. Shih, I. Korsunsky, 2021, Journal of perinatal medicine.

A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history

J. Smoller, S. Raychaudhuri, S. Murphy, 2022, J. Am. Medical Informatics Assoc..

Persons with Chronic Spinal Cord Injury Have Decreased Natural Killer Cell and Increased Toll-Like Receptor/Inflammatory Gene Expression

P. Gregersen, I. Korsunsky, O. Bloom, 2018, Journal of neurotrauma.

Two microRNA signatures for malignancy and immune infiltration predict overall survival in advanced epithelial ovarian cancer

Annette Lee, P. Gregersen, A. Liew, 2017, Journal of Investigative Medicine.

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases.

Joyce B. Kang, S. Raychaudhuri, F. Powrie, 2022, Med.

TREC/KREC Levels and T and B Lymphocyte Subpopulations in COVID-19 Patients at Different Stages of the Disease

E. Tikhonova, I. Korsunsky, I. Kudryavtsev, 2022, Viruses.

A cellular and spatial map of salivary glands at single cell resolution reveals the functional basis of tertiary lymphoid structure formation in Sjogren’s syndrome

W. Ng, A. Filer, C. Buckley, 2022, bioRxiv.

Fast, sensitive, and accurate integration of single cell data with Harmony

Fan Zhang, Kamil Slowikowski, Soumya Raychaudhuri, 2018, bioRxiv.

IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies

M. Jackson, S. Raychaudhuri, S. Travis, 2021, Nature Medicine.

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation

S. Raychaudhuri, L. Donlin, Jessica I. Beynor, 2021, Genome medicine.

Maximizing statistical power to detect differentially abundant cell states with scPOST

Soumya Raychaudhuri, Aparna Nathan, Ilya Korsunsky, 2021, Cell reports methods.

Efficient and precise single-cell reference atlas mapping with Symphony

Soumya Raychaudhuri, Laurie Rumker, Joyce B. Kang, 2020, Nature Communications.

Maximizing statistical power to detect clinically associated cell states with scPOST

Soumya Raychaudhuri, Joyce B. Kang, Aparna Nathan, 2020, bioRxiv.

Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis

Joyce B. Kang, P. Gregersen, S. Raychaudhuri, 2022, bioRxiv.

Distinct fibroblast subsets drive inflammation and damage in arthritis

S. Raychaudhuri, H. Perlman, D. Fearon, 2019, Nature.

Presto scales Wilcoxon and auROC analyses to millions of observations

Soumya Raychaudhuri, Aparna Nathan, Ilya Korsunsky, 2019, bioRxiv.

Covarying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics

Joyce B. Kang, S. Raychaudhuri, S. Asgari, 2021, Nature Biotechnology.

Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis

Kamil Slowikowski, Elizabeth W Karlson, Soumya Raychaudhuri, 2018, Science Translational Medicine.

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

S. Raychaudhuri, Kamil Slowikowski, M. Gutierrez-Arcelus, 2019, Nature Communications.

CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data

Giancarlo Mauri, Giulio Caravagna, Bud Mishra, 2014, bioRxiv.

BioNetGen 2.2: advances in rule-based modeling

Dipak Barua, James R. Faeder, John A. P. Sekar, 2015, Bioinform..

Systems Biology of Cancer: A Challenging Expedition for Clinical and Quantitative Biologists

Bud Mishra, Ilya Korsunsky, Nancy Griffeth, 2014, Front. Bioeng. Biotechnol..

Molecular signatures in systemic lupus erythematosus: distinction between disease flare and infection

P. Gregersen, J. Sánchez-Guerrero, B. Diamond, 2016, Lupus Science & Medicine.

Efficient inference of cancer progression models

Giancarlo Mauri, Giulio Caravagna, Bud Mishra, 2014 .

Multimodal platform for assessing drug distribution and response in clinical trials.

Elizabeth C. Randall, Sankha S. Basu, J. Sarkaria, 2021, Neuro-oncology.

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

S. Raychaudhuri, Kamil Slowikowski, M. Gutierrez-Arcelus, 2019, Nature Communications.

IL-1-driven stromal-neutrophil interaction in deep ulcers defines a pathotype of therapy non-responsive inflammatory bowel disease

M. Jackson, S. Raychaudhuri, S. Travis, 2021, bioRxiv.

University of Birmingham Notch signalling drives synovial fibroblast identity and arthritis pathology

N. Hacohen, C. Nusbaum, P. Gregersen, 2020 .

Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response

Linda T. Nieman, N. Hacohen, Keren Yizhak, 2023, bioRxiv.

Adipocytes regulate fibroblast function, and their loss contributes to fibroblast dysfunction in inflammatory diseases

S. Raychaudhuri, L. Lynch, Fan Zhang, 2023, bioRxiv.

Next-Generation Sequencing of Human Antibody Repertoires for Exploring B-cell Landscape, Antibody Discovery and Vaccine Development

N. Chiorazzi, G. Ferrer, A. Mazzarello, 2020, Frontiers Research Topics.

Axes of inter-sample variability among transcriptional neighborhoods reveal disease-associated cell states in single-cell data

Joyce B. Kang, S. Raychaudhuri, S. Asgari, 2021, bioRxiv.

Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution

N. Chiorazzi, G. Ferrer, A. Mazzarello, 2017, Front. Immunol..

CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data

G. Mauri, B. Mishra, M. Antoniotti, 2014, bioRxiv.

Fast, sensitive, and accurate integration of single cell data with Harmony

Kamil Slowikowski, Soumya Raychaudhuri, Michael Brenner, 2019, Nature Methods.

Making inroads to precision medicine for the treatment of autoimmune diseases: Harnessing genomic studies to better diagnose and treat complex disorders

K. Kidd, A. Mammen, V. Nizet, 2023, Cambridge prisms. Precision medicine.

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation

S. Raychaudhuri, L. Donlin, Jessica I. Beynor, 2021, Genome Medicine.

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.

Martin J. Aryee, N. Hacohen, Keren Yizhak, 2024, Nature immunology.

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

Vitor R. C. Aguiar, José Alquicira-Hernández, K. Dey, 2023, Nature Genetics.