Author

Jonathan H. Chen

Broad InstituteORCID 0000-0001-6074-9302Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Organism:human· 2 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2 Research Focus:batch correction / integration· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Nir HacoheniD· 3 shared Adam L. Essene· 1 shared Alex K. ShalekiD· 1 shared Alexander SturmiD· 1 shared Alexandra–Chloé VillaniiD· 1 shared Alkes L. PriceiD· 1 shared Anat O Stemmer-RachamimoviD· 1 shared Andrea GannaiD· 1 shared

Activity by Year

2021-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersGenomics

Nir HacohenORCID

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3 papers

Recent·Most cited

Integrating spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns

Nghia Millard, Jonathan H. Chen, Mukta G. Palshikar, Karin Pelka, Maxwell Spurrell, Colles O. Price, Jiang He, Nir Hacohen, Soumya Raychaudhuri, Ilya Korsunsky

bioRxiv · Mar 7, 2024 · PreprintBioinformatics

Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Anna L. K. Gonye, Arvind Ravi, Monica B. Arniella, Irena Gushterova, Thomas James LaSalle, Emily M. Blaum, Keren Yizhak, Dennie Tompers Frederick, Tatyana Y. Sharova, Ignaty Leshchiner, Liudmila Elagina, , Nir Hacohen

The paper develops DNA- and RNA-based models combining immune and tumor features to predict outcomes of checkpoint inhibition in melanoma.

Cell Reports Medicine · Feb 1, 2022Peer-reviewedGenomics

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Toni Marie Delorey, Carly G.K. Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Stephen J. Fleming, Ayshwarya Subramanian, Daniel T. Montoro, Karthik A. Jagadeesh, Kushal K. Dey, Pritha Sen, Michal Slyper, Yered H. Pita-Juárez, , Alexandra–Chloé Villani

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

bioRxiv · Feb 25, 2021 · PreprintGenomics