Author

Aïcha BenTaieb

GenentechORCID 0000-0002-7899-3327Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Approach:deep learning· 3 Organism:human· 3 Research Focus:cell-cell communication· 2 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2 Approach:statistical model· 2 Research Focus:database / resource· 1

Frequent Co-Authors

Tommaso BiancalaniiD· 3 shared Alma AnderssoniD· 2 shared David RichmondiD· 2 shared Gabriele ScaliaiD· 2 shared Graham HeimbergiD· 2 shared Héctor Corrada BravoiD· 2 shared Alsu M. MissarovaiD· 1 shared Anupriya TripathiiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersGenomics

Tommaso BiancalaniORCID

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3 papers

Recent·Most cited

Scoring gene importance by interpreting single-cell foundation models

Maxwell P. Gold, Miguel Reyes, Nathaniel Diamant, Tony Chien-Yen Kuo, Ehsan Hajiramezanali, Jane W. Newburger, Mary Beth F. Son, Pui Y. Lee, Gabriele Scalia, Aïcha BenTaieb, Sharookh B. Kapadia, Anupriya Tripathi, Héctor Corrada Bravo, Graham Heimberg, Tommaso Biancalani

The paper introduces SIGnature, a framework for scoring gene importance using attributions from scRNA-seq foundation models, and demonstrates its utility in identifying novel associations of the MS1 signature with hyperinflammatory conditions.

Nature Biotechnology · May 27, 2026Peer-reviewedBioinformatics

Spatial Decoding of Tertiary Lymphoid Structure Maturation in Non-Small Cell Lung Cancer Using Deep Neural Networks

Bob Chen, Conrad Foo, Alma Andersson, Brandon D. Kayser, Yiming Yang, Alsu M. Missarova, Priyanka Kulkarni, Jan-Christian Huetter, Sharmila Chatterjee, Youngmi J. Kim, Yan Liang, Emily Killinbeck, Sarah R. Murphy, Eloisa Fuentes, Jennifer Margaret Giltnane, , Lisa M. McGinnis

The paper develops a framework to decode TLS maturation in NSCLC using spatial omics data and deep learning, identifying two distinct spatial ecosystems linked to patient outcomes.

bioRxiv · Jan 20, 2026 · PreprintGenomics

Inferring cellular communication through mapping cells in space using Tangram 2

Hejin Huang, Alma Andersson, Sunny Z. Wu, Gabriele Scalia, Jenna L. Collier, Kam Hon Hoi, Sören Müller, Graham Heimberg, Héctor Corrada Bravo, Shreya Gaddam, Jan-Christian Hütter, Shannon J. Turley, David Richmond, Aïcha BenTaieb, Tommaso Biancalani

Tangram2 maps cell-to-cell communication by integrating spatial transcriptomics with single-cell RNA sequencing to identify gene expression changes driven by neighboring cell types.

bioRxiv · Sep 28, 2025 · PreprintGenomics