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Page 1
Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.
Washburn JD, Varela JI, Xavier A, Chen Q, Ertl D, Gage JL, Holland JB, Lima DC, Romay MC, Lopez-Cruz M, de Los Campos G, Barber W, Zimmer C, Trucillo Silva I, Rocha F, Rincent R, Ali B, Hu H, Runcie DE, Gusev K, Slabodkin A, Bax P, Aubert J, Gangloff H, Mary-Huard T, Vanrenterghem T, Quesada-Traver C, Yates S, Ariza-Suárez D, Ulrich A, Wyler M, Kick DR, Bellis ES, Causey JL, Soriano Chavez E, Wang Y, Piyush V, Fernando GD, Hu RK, Kumar R, Timon AJ, Venkatesh R, Segura Abá K, Chen H, Ranaweera T, Shiu SH, Wang P, Gordon MJ, Amos BK, Busato S, Perondi D, Gogna A, Psaroudakis D, Chen CPJ, Al-Mamun HA, Danilevicz MF, Upadhyaya SR, Edwards D, de Leon N. Washburn JD, et al. Among authors: slabodkin a. Genetics. 2024 Nov 22:iyae195. doi: 10.1093/genetics/iyae195. Online ahead of print. Genetics. 2024. PMID: 39576009
Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.
Washburn JD, Varela JI, Xavier A, Chen Q, Ertl D, Gage JL, Holland JB, Lima DC, Romay MC, Lopez-Cruz M, de Los Campos G, Barber W, Zimmer C, Silva IT, Rocha F, Rincent R, Ali B, Hu H, Runcie DE, Gusev K, Slabodkin A, Bax P, Aubert J, Gangloff H, Mary-Huard T, Vanrenterghem T, Quesada-Traver C, Yates S, Ariza-Suárez D, Ulrich A, Wyler M, Kick DR, Bellis ES, Causey JL, Chavez ES, Wang Y, Piyush V, Fernando GD, Hu RK, Kumar R, Timon AJ, Venkatesh R, Abá KS, Chen H, Ranaweera T, Shiu SH, Wang P, Gordon MJ, Amos BK, Busato S, Perondi D, Gogna A, Psaroudakis D, Chen CPJ, Al-Mamun HA, Danilevicz MF, Upadhyaya SR, Edwards D, de Leon N. Washburn JD, et al. Among authors: slabodkin a. bioRxiv [Preprint]. 2024 Sep 19:2024.09.13.612969. doi: 10.1101/2024.09.13.612969. bioRxiv. 2024. Update in: Genetics. 2024 Nov 22:iyae195. doi: 10.1093/genetics/iyae195 PMID: 39345633 Free PMC article. Updated. Preprint.
MHC heterozygosity limits T cell receptor variability in CD4 T cells.
Brown AJ, White J, Shaw L, Gross J, Slabodkin A, Kushner E, Greiff V, Matsuda J, Gapin L, Scott-Browne J, Kappler J, Marrack P. Brown AJ, et al. Among authors: slabodkin a. Sci Immunol. 2024 Jul 12;9(97):eado5295. doi: 10.1126/sciimmunol.ado5295. Epub 2024 Jul 12. Sci Immunol. 2024. PMID: 38996008
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction.
Robert PA, Akbar R, Frank R, Pavlović M, Widrich M, Snapkov I, Slabodkin A, Chernigovskaya M, Scheffer L, Smorodina E, Rawat P, Mehta BB, Vu MH, Mathisen IF, Prósz A, Abram K, Olar A, Miho E, Haug DTT, Lund-Johansen F, Hochreiter S, Haff IH, Klambauer G, Sandve GK, Greiff V. Robert PA, et al. Among authors: slabodkin a. Nat Comput Sci. 2022 Dec;2(12):845-865. doi: 10.1038/s43588-022-00372-4. Epub 2022 Dec 19. Nat Comput Sci. 2022. PMID: 38177393
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: slabodkin a. MAbs. 2022 Jan-Dec;14(1):2031482. doi: 10.1080/19420862.2022.2031482. MAbs. 2022. PMID: 35377271 Free PMC article.
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. 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.
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.
Pavlović M, Scheffer L, Motwani K, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Haff IH, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML, Lund-Andersen C, Martini A, Minotto T, Pensar J, Rand K, Riccardi E, Robert PA, Rocha A, Slabodkin A, Snapkov I, Sollid LM, Titov D, Weber CR, Widrich M, Yaari G, Greiff V, Sandve GK. Pavlović M, et al. Among authors: slabodkin a. Nat Mach Intell. 2021 Nov;3(11):936-944. doi: 10.1038/s42256-021-00413-z. Epub 2021 Nov 16. Nat Mach Intell. 2021. PMID: 37396030 Free PMC article.