Characterizing immune repertoires by high throughput sequencing: strategies and applications
JJA Calis, BR Rosenberg - Trends in immunology, 2014 - cell.com
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized
receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These …
receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These …
The analysis of clonal expansions in normal and autoimmune B cell repertoires
U Hershberg, ET Luning Prak - … Transactions of the …, 2015 - royalsocietypublishing.org
Clones are the fundamental building blocks of immune repertoires. The number of different
clones relates to the diversity of the repertoire, whereas their size and sequence diversity …
clones relates to the diversity of the repertoire, whereas their size and sequence diversity …
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
Motivation: The diversity of the immune repertoire is initially generated by random
rearrangements of the receptor gene during early T and B cell development. Rearrangement …
rearrangements of the receptor gene during early T and B cell development. Rearrangement …
[HTML][HTML] Clustering-based identification of clonally-related immunoglobulin gene sequence sets
Background Clonal expansion of B lymphocytes coupled with somatic mutation and antigen
selection allow the mammalian humoral immune system to generate highly specific …
selection allow the mammalian humoral immune system to generate highly specific …
[HTML][HTML] Ontogeny of recognition specificity and functionality for the broadly neutralizing anti-HIV antibody 4E10
KAK Finton, D Friend, J Jaffe, M Gewe… - PLoS …, 2014 - journals.plos.org
The process of antibody ontogeny typically improves affinity, on-rate, and thermostability,
narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding …
narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding …
Sequencing and quantifying IgG fragments and antigen-binding regions by mass spectrometry
D de Costa, I Broodman, MM VanDuijn… - Journal of Proteome …, 2010 - ACS Publications
In cancer and autoimmune diseases, immunoglobulins with a specific molecular signature
that could potentially be used as diagnostic or prognostic markers are released into body …
that could potentially be used as diagnostic or prognostic markers are released into body …
Non-human animals that make single domain binding proteins
L MacDonald, AJ Murphy - US Patent 10,881,085, 2021 - Google Patents
Genetically modified non-human animals and methods and compositions for making and
using them are provided, wherein the genetic modification comprises (a) a deletion in an …
using them are provided, wherein the genetic modification comprises (a) a deletion in an …
Assigning and visualizing germline genes in antibody repertoires
Identifying the germline genes involved in immunoglobulin rearrangements is an essential
first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse …
first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse …
Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset
Motivation: Immunoglobulin heavy chain genes are formed by recombination of genes
randomly selected from sets of IGHV, IGHD and IGHJ genes. Utilities have been developed …
randomly selected from sets of IGHV, IGHD and IGHJ genes. Utilities have been developed …
[HTML][HTML] VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
IT Toby, MK Levin, EA Salinas, S Christley… - BMC …, 2016 - Springer
Background The genes that produce antibodies and the immune receptors expressed on
lymphocytes are not germline encoded; rather, they are somatically generated in each …
lymphocytes are not germline encoded; rather, they are somatically generated in each …