Author

Songling Li

Research Institute for Microbial Diseases, The University of OsakaORCID 0000-0001-9554-2248Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:CITE-seq· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Approach:machine learning (classical)· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1

Frequent Co-Authors

Daron M. StandleyiD· 5 shared Ayan Sengupta· 3 shared Hendra Saputra IsmantoiD· 3 shared Jan WilamowskiiD· 2 shared Mara Anaís Llamas-CovarrubiasiD· 2 shared Shunsuke TeraguchiiD· 2 shared Soichiro Haruna· 2 shared Zichang XuiD· 2 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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5 shared papersBioinformatics

Daron M. StandleyORCID

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5 papers

Recent·Most cited

A germline shortcut in protein language model retrieval of adaptive immune receptors

Suyue Wang, Ayan Sengupta, Songling Li, Daron M. Standley

This paper benchmarks protein language models against sequence alignment methods for immune receptor retrieval, finding that alignments outperform PLMs at CDR3 level but PLMs match alignments at full variable domain by leveraging germline information.

bioRxiv · Jul 23, 2026 · PreprintBioinformatics

Accurate and scalable multi-disease classification from adaptive immune repertoires

Natnicha Jiravejchakul, Ayan Sengupta, Songling Li, Debottam Upadhyaya, Mara Anaís Llamas-Covarrubias, Florian Hauer, Soichiro Haruna, Daron M. Standley

This paper introduces FACTS, a scalable machine learning framework for multi-disease classification using TCR repertoires, achieving high accuracy and preserving biological signals.

bioRxiv · Aug 12, 2025 · PreprintBioinformatics

Fc-independent SARS-CoV-2 infection-enhancing antibodies decouple N-terminal and receptor-binding domains by cross-linking neighboring spikes

Floris J. van Eerden, Songling Li, Tina Lusiany, Hendra Saputra Ismanto, Tohru Terada, Christoph Gerle, Kanako Akamatsu, Mika Hirose, Fuminori Sugihara, David Virya Chen, Jun-ichi Kishikawa, Takayuki Kato, Yafei Liu, Masato Okada, Hisashi Arase, Daron M. Standley

This study shows that certain SARS-CoV-2 antibodies enhance infection by cross-linking spike proteins, causing NTD-RBD domain decoupling without needing the Fc region.

bioRxiv · Aug 21, 2024 · PreprintMolecular Biology

Robust diagnosis of infectious disease, autoimmunity and cancer from the paratope networks of adaptive immune receptors

Zichang Xu, Hendra Saputra Ismanto, Dianita S. Saputri, Soichiro Haruna, Guanqun Sun, Jan Wilamowski, Shunsuke Teraguchi, Ayan Sengupta, Songling Li, Daron M. Standley

This paper develops a novel representation of adaptive immune receptors to improve disease classification from blood samples, achieving higher accuracy for infectious disease, autoimmunity, and cancer.

bioRxiv · Nov 28, 2023 · PreprintBioinformatics

InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires

Jan Wilamowski, Zichang Xu, Hendra Saputra Ismanto, Songling Li, Shunsuke Teraguchi, Mara Anaís Llamas-Covarrubias, Xiuyuan Lu, Sho Yamasaki, Daron M. Standley

InterClone stores, searches, and clusters adaptive immune receptor repertoires, demonstrating its utility in analyzing SARS-CoV-2 antibodies and TCRs from different donor groups.

bioRxiv · Jul 31, 2022 · PreprintBioinformatics