Literature

We have compiled all of our posters, white papers, and case studies on one page for your convenience. Subscribe to our newsletter below for the download links. You can unsubscribe at any time!

ASHG Conference

• Deep Immune Repertoire Analysis of SARS-CoV-2 Antibodies from a Vaccinated Human Patient via Mass Spectrometry and
  Synthetic Long Reads

PepTalk Conference

• Deep Antibody Repertoire Sequencing of B Cells and Comparative Analysis Across Multiple Species – PepTalk 2020
• A next generation proteogenomic approach to discover rabbit monoclonal antibodies – PepTalk 2018

AE&T Conference

• Single domain antibody discovery in llama using NGS and mass spectrometry – AE&T 2019

ASMS Conference

• Quorum: untargeted metabolomics using tandem mass spectrometry and molecular networking – ASMS 2017
• Toward de novo sequencing of mixtures of antibodies – ASMS 2017

PEGS Boston Conference

• Automated sequencing of monoclonal antibodies – PEGS 2016
• Next-generation repertoire sequencing for mining single domain antibodies – PEGS 2021 Video (subscribe to access infographic)

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.
• Enrichment of Memory B Cells for Antibody Discovery and Next-Generation Sequencing

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)

Need more information? We’re here to answer any questions you have.