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immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.
Weber CR, Akbar R, Yermanos A, Pavlović M, Snapkov I, Sandve GK, Reddy ST, Greiff V. Weber CR, et al. Among authors: greiff v. Bioinformatics. 2020 Jun 1;36(11):3594-3596. doi: 10.1093/bioinformatics/btaa158. Bioinformatics. 2020. PMID: 32154832 Free PMC article.
Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) …
Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region …
Modeling the Dynamics of T-Cell Development in the Thymus.
Robert PA, Kunze-Schumacher H, Greiff V, Krueger A. Robert PA, et al. Among authors: greiff v. Entropy (Basel). 2021 Apr 8;23(4):437. doi: 10.3390/e23040437. Entropy (Basel). 2021. PMID: 33918050 Free PMC article. Review.
Individualized VDJ recombination predisposes the available Ig sequence space.
Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V. Slabodkin A, et al. Among authors: greiff v. Genome Res. 2021 Dec;31(12):2209-2224. doi: 10.1101/gr.275373.121. Epub 2021 Nov 23. Genome Res. 2021. PMID: 34815307 Free PMC article.
In silico proof of principle of machine learning-based antibody design at unconstrained scale.
Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V. Akbar R, et al. Among authors: greiff v. MAbs. 2022 Jan-Dec;14(1):2031482. doi: 10.1080/19420862.2022.2031482. MAbs. 2022. PMID: 35377271 Free PMC article.
Reference-based comparison of adaptive immune receptor repertoires.
Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Weber CR, et al. Among authors: greiff v. Cell Rep Methods. 2022 Aug 22;2(8):100269. doi: 10.1016/j.crmeth.2022.100269. eCollection 2022 Aug 22. Cell Rep Methods. 2022. PMID: 36046619 Free PMC article.
88 results