PEPE: scalable extraction of multi-modal protein language model representations
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Author(s):
Jahn Zhong, Niccolò Cardente, Geir Kjetil Sandve, Habib Bashour, Maria Francesca Abbate, Victor Greiff
Published in:
Bioinformatics, Issue 42, 2026, ISSN 1367-4803
Publisher:
Oxford University Press (OUP)
DOI:
10.1093/BIOINFORMATICS/BTAG375
From virtual experiments to biomedical insight with synthetic data
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Author(s):
Margarida Victoriano, Milena Pavlović, Geir Kjetil Sandve, Hélder P. Oliveira, Artur Rocha, Victor Greiff
Published in:
Nature Machine Intelligence, Issue 8, 2026, ISSN 2522-5839
Publisher:
Springer Science and Business Media LLC
DOI:
10.1038/S42256-026-01244-6
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
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Author(s):
Maria Chernigovskaya, Khang Lê Quý, Maria Stensland, Sachin Singh, Rowan Nelson, Melih Yilmaz, Konstantinos Kalogeropoulos, Pavel Sinitcyn, Anand Patel, Natalie Castellana, Stefano Bonissone, Stian Foss, Jan Terje Andersen, Geir Kjetil Sandve, Timothy Patrick Jenkins, William S. Noble, Tuula A. Nyman, Igor Snapkow, Victor Greiff
Published in:
Cell Systems, Issue 16, 2026, ISSN 2405-4712
Publisher:
Elsevier BV
DOI:
10.1016/J.CELS.2025.101449
Identification of a type 1 diabetes–associated T cell receptor repertoire signature from the human peripheral blood
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Author(s):
Rawat, Puneet and Shapiro, Melanie R and Peters, Leeana D and Widrich, Michael and Mayer-Blackwell, Koshlan and Motwani, Keshav and Pavlovi{\'c}, Milena and Al Hajj, Ghadi and Posgai, Amanda L and Kanduri, Chakravarthi and others
Published in:
Science Advances, ISSN 2375-2548
Publisher:
Science Advances
DOI:
10.1126/SCIADV.ADX744
Training data composition determines machine learning generalization and biological rule discovery
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Author(s):
Eugen Ursu; Aygul Minnegalieva; Puneet Rawat; Maria Chernigovskaya; Robi Tacutu; Geir Kjetil Sandve; Philippe A. Robert; Victor Greiff
Published in:
Nature Machine Intelligence, 2025, ISSN 2522-5839
Publisher:
Nature Publishing Group
DOI:
10.1101/2024.06.17.599333
