Author

Amirhossein Naghsh Nilchi

University of FreiburgORCID 0000-0003-1329-3044Unclaimed 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:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Approach:graph neural network· 1 Assay:protein structure· 1

Frequent Co-Authors

Andrew StubbsiD· 1 shared Ashleigh ListeriD· 1 shared Björn Andreas GrüningiD· 1 shared Cristóbal UauyiD· 1 shared David SwarbreckiD· 1 shared Gregory J. WickhamiD· 1 shared Hamed KhakzadiD· 1 shared Huihai WuiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Andrew StubbsORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 8, 2026

SIMORGH: Ensemble-Aware Geometric Deep Learning for Apo-State and Cryptic Ligand Binding Site Prediction

Omid Mokhtari, Amirhossein Naghsh Nilchi, Björn Andreas Grüning…·Hamed Khakzad

SIMORGH predicts ligand binding sites from apo proteins by integrating conformational ensembles, outperforming existing methods in ligand-free settings and identifying cryptic pockets.

DOI 10.64898/2026.10.02.756215

protein structuredeep learning

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BioinformaticsbioRxivPreprintSep 25, 2026

EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

Huihai Wu, Ashleigh Lister, Iain C. Macaulay…·Irene Papatheodorou

EISCA and EISTA are pipelines for single-cell and spatial transcriptomics analysis that provide standardized, modular workflows for data processing and downstream analysis.

DOI 10.64898/2026.09.02.748851

scRNA-seqspatial transcriptomics

𝕏 PostBluesky