Author

Daniel L. Abravanel

Broad InstituteORCID 0000-0002-0129-1618Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3 Genomics· 1

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Research Focus:cell type annotation· 4 Organism:human· 4 Organism:mouse· 3 Assay:spatial transcriptomics· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Approach:statistical model· 2 Research Focus:cell-cell communication· 1

Frequent Co-Authors

Aviv RegeviD· 3 shared Johanna KlughammeriD· 3 shared Judit Jané‐ValbuenaiD· 3 shared Julia WaldmaniD· 3 shared Michal SlyperiD· 3 shared Nikhil WagleiD· 3 shared Orit Rozenblatt–RoseniD· 3 shared Scott J. RodigiD· 3 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Aviv RegevORCID

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Author profile →

4 papers

Recent·Most cited

PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses

Yu-Chen Cheng, Hyemin Gu, Thomas O. McDonald, Wenbo Wu, Shubham Tripathi, Cristina Guarducci, Douglas Russo, Daniel L. Abravanel, Madeline Bailey, Yue Wang, Yun Zhang, Yannis Pantazis, Herbert Levine, Rinath M. Jeselsohn, Markos A. Katsoulakis, Franziska Michor A

Cell Systems · Aug 1, 2026Peer-reviewedBioinformatics

SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan M. Murray, Ralf Strasser, Jan Watter, Ofir Cohen, Orr Ashenberg, Daniel L. Abravanel, Judit Jané‐Valbuena, Simon Mages, Ana Lako, Karla E. Helvie, Orit Rozenblatt–Rosen, , Johanna Klughammer

SlideCNA detects spatial copy number alterations from Slide-seq data to identify sub-clones in metastatic breast cancer.

Genome biology · May 2, 2025Peer-reviewedBioinformatics

Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)

Charles S. Comiter, Xingjian Chen, Eeshit Dhaval Vaishnav, Koseki J. Kobayashi-Kirschvink, Metamia Ciampricotti, Ke Zhang, Jason Murray, Francesco Monticolo, Jianhuan Qi, Ryota Tanaka, Sonia E. Brodowska, Bo Li, Yiming Yang, Scott J. Rodig, Angeliki Karatza, , Aviv Regev

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

bioRxiv · Mar 21, 2023 · PreprintBioinformatics

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

Shahar Alon, Daniel Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G. Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun‐Chen Yao, Ho‐Jun Suk, , Kirsty Sawicka

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

Science · Jan 28, 2021Peer-reviewedGenomics