Literature

We have compiled all of our white papers and case studies on one page for your convenience.

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Reptor

High-throughput Hybridoma Sequencing using NGS

Alicanto

• Alicanto Case Study: Discovery of high affinity anti-beta galactosidase rabbit antibodies
• Alicanto Case Study: Diverse VHH discovery from serum

Valens and Quorum Cloud

• Valens with CLIP Case Study: Confirmation of Leucine or Isoleucine presence in de novo antibody sequencing
• Molecular Networks: A deep dive into the world of small molecules

Reptor

• Clonal Hit-Expansion Case Study: NGS repertoires extend hits by finding more members of the same clone (Infographic)
• Enrichment of Memory B Cells for Antibody Discovery and Next-Generation Sequencing (Collaboration with Nanocellect Biomedical)

Publications by Abterra Bio founders and team members include:

Chen, Elaine, et al. “Systematic analysis of human antibody response to ebolavirus glycoprotein shows high prevalence of neutralizing public clonotypes.” Cell reports (2023): 42, 4 (PubMed: 37029928)

Tomasina, Florencia, et al. “De novo sequencing and construction of a unique antibody for the recognition of alternative conformations of cytochrome c in cells.” PNAS (2022): 119, 47 (PubMed: 36378644)

Deszynski, Piotr, et al. “INDI-integrated nanobody database for immunoinformatics.” Nucleic Acids Res (2022): 50 (PubMed: 34747487)

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)

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)

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)

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)

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)

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

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

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) 

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

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)

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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