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White Papers and Case Studies

Publications

Publications by Abterra Bio founders and team members include:

[1] Gilchuk, Pavlo, et al. “Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma.” Frontiers in Immunology (2021): 2782. (Frontiers Immunol: 706757

[2] Bonissone SR, Lima T, Harris K, Davison L, Avanzino B, Trinklein N, et al. Serum Proteomics Expands on High-Affinity Antibodies in Immunized Rabbits Than Deep B-Cell Repertoire Sequencing Alone. BioRxiv (2020) 833871. doi: 10.1101/833871. (BioRxiv: 833871

[3] Cha, SW, Bonissone, S, Na, S, Pevzner, PA, Bafna, V (2017). The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics, 16, 12:2111-2124. (PubMed: 29046389

[4] Bonissone, Stefano R., and Pavel A. Pevzner. “Immunoglobulin classification using the colored antibody graph.” Journal of Computational Biology 23.6 (2016): 483-494. (PubMed: 27149636

[5] Y. Safonova, S. Bonissone, E. Kurpilyansky, E. Starostina, A. Lapidus, J. Stinson, L. DePalatis, W. Sandoval, J. Lill, and P. A. Pevzner. IgRepertoire Constructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, 31(12):53–61, Jun (2015) (PubMed: 26072509

[6] S. R. Bonissone, P. A. Pevzner, Research in Computational Molecular Biology, 44–59 (2015). (Springer

[7] Guthals, et al. (2012). Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics, 11, 10:1084-96. (PubMed: 22798278

[8] Castellana, NE, McCutcheon, K, Pham, VC, Harden, K, Nguyen, A, Young, J, Adams, C, Schroeder, K, Arnott, D, Bafna, V, Grogan, JL, Lill, JR (2011). Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin- antibody. Proteomics, 11, 3:395-405. (PubMed: 21268269) 

[9] Castellana, NE, et al. (2010). Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics, 9, 6:1260-70. (PubMed: 20164058)

[10] Bandeira, N, Pham, V, Pevzner, P, Arnott, D, Lill, JR (2008). Automated de novo protein sequencing of monoclonal antibodies. Nat. Biotechnol., 26, 12:1336-8. (PubMed: 19060866)

[11] Bandeira, N, et al. (2007). Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics, 6, 7:1123-34. (PubMed: 17446555)

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