Tumor microenvironment: barrier or opportunity towards effective cancer therapy

A Tiwari, R Trivedi, SY Lin - Journal of biomedical science, 2022 - Springer
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …

Computational genomics tools for dissecting tumour–immune cell interactions

H Hackl, P Charoentong, F Finotello… - Nature Reviews …, 2016 - nature.com
Recent breakthroughs in cancer immunotherapy and decreasing costs of high-throughput
technologies have sparked intensive research into tumour–immune cell interactions using …

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data

NT Gupta, JA Vander Heiden, M Uduman… - …, 2015 - academic.oup.com
Advances in high-throughput sequencing technologies now allow for large-scale
characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic …

IgBLAST: an immunoglobulin variable domain sequence analysis tool

J Ye, N Ma, TL Madden, JM Ostell - Nucleic acids research, 2013 - academic.oup.com
The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes,
including the variable (V) gene, the diversity (D) gene and the joining (J) gene. Analysis of …

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized VJ and VDJ sequence analysis

X Brochet, MP Lefranc, V Giudicelli - Nucleic acids research, 2008 - academic.oup.com
Abstract IMGT/V-QUEST is the highly customized and integrated system for the standardized
analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide …

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

JA Vander Heiden, G Yaari, M Uduman… - …, 2014 - academic.oup.com
Driven by dramatic technological improvements, large-scale characterization of lymphocyte
receptor repertoires via high-throughput sequencing is now feasible. Although promising …

Practical guidelines for B-cell receptor repertoire sequencing analysis

G Yaari, SH Kleinstein - Genome medicine, 2015 - Springer
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being
applied to gain insights into the adaptive immune response in healthy individuals and in …

tcR: an R package for T cell receptor repertoire advanced data analysis

VI Nazarov, MV Pogorelyy, EA Komech, IV Zvyagin… - BMC …, 2015 - Springer
Abstract Background The Immunoglobulins (IG) and the T cell receptors (TR) play the key
role in antigen recognition during the adaptive immune response. Recent progress in next …

Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements

KJL Jackson, Y Liu, KM Roskin, J Glanville, RA Hoh… - Cell host & …, 2014 - cell.com
B cells produce a diverse antibody repertoire by undergoing gene rearrangements.
Pathogen exposure induces the clonal expansion of B cells expressing antibodies that can …

[HTML][HTML] Convergent antibody signatures in human dengue

P Parameswaran, Y Liu, KM Roskin, KKL Jackson… - Cell host & …, 2013 - cell.com
Dengue is the most prevalent mosquito-borne viral disease in humans, and the lack of early
prognostics, vaccines, and therapeutics contributes to immense disease burden. To identify …