Author

A. J. Nirmal

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

Biology Disciplines

Click to filter author papers

Cancer Biology· 4 Cell Biology· 1 Immunology· 1 Pathology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 7 Research Focus:cell type annotation· 4 Research Focus:cell-cell communication· 4 Assay:spatial transcriptomics· 4 Approach:deep learning· 3 Research Focus:differential expression· 3 Approach:microscopy & imaging analysis· 3 Research Focus:spatial domain detection· 3

Frequent Co-Authors

P. K. Sorger· 6 shared S. Santagata· 5 shared Z. Maliga· 5 shared G. F. Murphy· 4 shared C. G. Lian· 3 shared Y.-A. Chen· 3 shared A. A. Chen· 2 shared C. A. Jacobson· 2 shared

Activity by Year

2020-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

6 shared papersCancer Biology

P. K. Sorger

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

I.-M. P. Launonen, E. P. Erkan, I. Niemiec, A. Junquera, M. Hincapie-Otero, D. Afenteva, Z. Liang, M. Salko, A. Szabo, F. Perez-Villatoro, M. M. Falco, Y. Li, G. Micoli, A. Nagaraj, U.-M. Haltia, , A. Farkkila

This study shows chemotherapy causes myeloid-driven spatial T-cell exhaustion in ovarian cancer by altering immune cell states and interactions, suggesting new immunotherapy approaches.

bioRxiv · Mar 19, 2024 · PreprintCancer Biology

Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours

C. Yapp, A. J. Nirmal, F. Y. Zhou, A. Y. H. Wong, J. Tefft, Y. D. Lu, Z. Shang, Z. Maliga, P. Montero Llopis, G. F. Murphy, C. Lian, G. Danuser, S. Santagata, P. K. Sorger

This paper introduces 3D CyCIF, a method for high-plex 3D profiling of cell states and immune niches in human tumors, revealing detailed spatial interactions and cytokine niches previously unattainable in thin sections.

bioRxiv · Nov 10, 2023 · PreprintCancer Biology

Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence

Z. Maliga, D. Y. Kim, A.-T. N. Bui, J.-R. Lin, A. K. Dewan, G. F. Murphy, A. J. Nirmal, C. G. Lian, P. K. Sorger, N. R. LeBoeuf

This study compares CyCIF and IHC for immune profiling in ICI-induced dAEs, finding CyCIF provides more detailed single-cell characterization of immune infiltrates.

bioRxiv · Apr 3, 2023 · PreprintImmunology

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data

S. Warchol, R. Krueger, A. J. Nirmal, G. Gaglia, J. Jessup, C. C. Ritch, J. Hoffer, J. L. Muhlich, M. Burger, T. L. Jacks, S. Santagata, P. K. Sorger, H. Pfister

Visinity analyzes spatial cell interactions in multiplexed tissue images to identify biological processes and immune-tumor interactions.

bioRxiv · May 9, 2022Cell Biology

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

A. J. Nirmal, Z. Maliga, T. Vallius, B. Quattrochi, A. A. Chen, C. A. Jacobson, R. J. Pelletier, C. Yapp, R. Arias-Camison, Y.-A. Chen, C. G. Lian, G. F. Murphy, S. Santagata, P. K. Sorger

The paper uses spatial techniques to study immune evasion and immunoediting in primary melanoma, finding localized immunosuppressive environments and coexistence of invasion and regression.

bioRxiv · May 23, 2021Cancer Biology

Micro-region transcriptomics of fixed human tissue using Pick-Seq

Z. Maliga, A. J. Nirmal, N. G. Ericson, S. A. Boswell, L. U'Ren, R. Podyminogin, J. Chow, Y.-A. Chen, A. A. Chen, D. M. Weinstock, C. G. Lian, G. F. Murphy, E. P. Kaldjian, S. Santagata, P. K. Sorger

Pick-Seq enables deep spatial transcriptomic profiling of fixed human tissue, revealing transcriptional differences in tumor invasion, proliferation, and immuno-editing.

bioRxiv · Mar 18, 2021 · PreprintCancer Biology

Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung

M. Kalocsay, Z. Maliga, A. J. Nirmal, R. J. Eisert, G. A. Bradshaw, I. H. Solomon, Y.-A. Chen, R. J. Pelletier, C. A. Jacobson, J. Mintseris, R. F. Padera, A. J. Martinot, D. H. Barouch, S. Santagata, P. Sorger

The paper uses multiplexed proteomics and imaging to compare inflammatory and thrombotic responses in resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans.

bioRxiv · Oct 14, 2020 · PreprintPathology