Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data

G Sturm, T Szabo, G Fotakis, M Haider, D Rieder… - …, 2020 - academic.oup.com
Advances in single-cell technologies have enabled the investigation of T-cell phenotypes
and repertoires at unprecedented resolution and scale. Bioinformatic methods for the …

The diagnostic, prognostic, and therapeutic potential of adaptive immune receptor repertoire profiling in cancer

LG Cowell - Cancer research, 2020 - AACR
Lymphocytes play a critical role in antitumor immune responses. They are directly targeted
by some therapies, and the composition and spatial organization of intratumor T-cell …

Exploiting B cell receptor analyses to inform on HIV-1 vaccination strategies

C Kreer, H Gruell, T Mora, AM Walczak, F Klein - Vaccines, 2020 - mdpi.com
The human antibody repertoire is generated by the recombination of different gene
segments as well as by processes of somatic mutation. Together these mechanisms result in …

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

E Smakaj, L Babrak, M Ohlin, M Shugay, B Briney… - …, 2020 - academic.oup.com
Antibody repertoires reveal insights into the biology of the adaptive immune system and
empower diagnostics and therapeutics. There are currently multiple tools available for the …

Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

N Nouri, SH Kleinstein - PLoS computational biology, 2020 - journals.plos.org
Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of
identifying and tracking B cell clonal expansions during adaptive immune responses …

The ADC API: a web API for the programmatic query of the AIRR data commons

S Christley, A Aguiar, G Blanck, F Breden… - Frontiers in big …, 2020 - frontiersin.org
The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group
that is establishing a clear set of community-accepted data and metadata standards; …

Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma

J Ostmeyer, E Lucas, S Christley, J Lea, N Monson… - PLoS …, 2020 - journals.plos.org
We previously showed, in a pilot study with publicly available data, that T cell receptor (TCR)
repertoires from tumor infiltrating lymphocytes (TILs) could be distinguished from adjacent …

Genotyping and copy number analysis of immunoglobin heavy chain variable genes using long reads

M Ford, E Haghshenas, CT Watson, SC Sahinalp - Iscience, 2020 - cell.com
One of the remaining challenges to describing an individual's genetic variation lies in the
highly heterogeneous and complex genomic regions that impede the use of classical …

The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data

JK Scott, F Breden - Current Opinion in Systems Biology, 2020 - Elsevier
Abstract Systems biology involves network-oriented, computational approaches to modeling
biological systems through analysis of big biological data. To contribute maximally to …

RDA COVID-19 Guidelines and Recommendations

NPC Hong, RDA COVID-19 Working Group - 2020 - research.ed.ac.uk
Data holds the potential to drive rapid response and informed decision-making during public
health emergencies. There is a need for timely and accurate collection, reporting and …