Author

Jose Melchor

Allen Institute for Brain Science

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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Neuroscience· 3 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Organism:mouse· 4 Research Focus:cell type annotation· 3 Research Focus:database / resource· 2 Assay:spatial transcriptomics· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:ChIP-seq· 1

Frequent Co-Authors

Cameron BielsteiniD· 4 shared Jocelin MaloneiD· 4 shared Zachary MadiganiD· 4 shared Alana A. OyamaiD· 3 shared Amanda GaryiD· 3 shared Anish Bhaswanth ChakkaiD· 3 shared Christina Alice PomiD· 3 shared Cindy Tzu-Ling HuangiD· 3 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersNeuroscience

Cameron BielsteinORCID

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4 papers

Recent·Most cited

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits

Avery C. Hunker, Morgan E. Wirthlin, Gursajan Gill, Nelson Johansen, Marcus J. Hooper, Victoria Omstead, Sara Vargas, M. Nathaly Lerma, Naz Taskin, Natalie Weed, Will Laird, Yemeserach M. Bishaw, Jacqueline L. Bendrick, Bryan B. Gore, Yoav Ben‐Simon, , Kara Ronellenfitch

The paper presents an enhancer AAV toolbox for targeting and perturbing striatal cell types and circuits in mice, with validated specificity and cross-species applicability.

Neuron · May 1, 2025Peer-reviewedNeuroscience

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

Yoav Ben‐Simon, Marcus J. Hooper, Sujatha Narayan, Tanya L. Daigle, Deepanjali Dwivedi, Sharon W. Way, Aaron Oster, David A. Stafford, John K. Mich, Michael J. Taormina, Refugio A. Martinez, Ximena Opitz-Araya, Jada R. Roth, Jason R. Alexander, Shona W. Allen, , Shea T. Ransford

The paper develops a toolkit of transgenic mouse lines and enhancer AAVs for selective targeting of cortical cell populations using transcriptomic and epigenomic data.

Cell · May 1, 2025Peer-reviewedNeuroscience

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

Naomi X. Martin, Paul A. Olsen, Jacob Quon, Jazmin Campos, Nasmil Valera Cuevas, Josh Nagra, Marshall VanNess, Zoe Maltzer, Emily C. Gelfand, Alana A. Oyama, Amanda Gary, Yimin Wang, Angela Alaya, Augustin Ruiz, Cade Reynoldson, , Jack Waters

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

bioRxiv · Dec 4, 2024 · PreprintBioinformatics

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Zizhen Yao, Cindy T. J. van Velthoven, Michael Kunst, Meng Zhang, Delissa McMillen, Changkyu Lee, Won Jung, Jeff Goldy, Aliya Abdelhak, Matthew Aitken, Katherine S. Baker, Pamela M. Baker, Eliza R. Barkan, Darren Bertagnolli, Ashwin A. Bhandiwad, , Xiaowei Zhuang

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

Nature · Dec 13, 2023Peer-reviewedNeuroscience