PyPop: a mature open-source software pipeline for population genomics

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs E...

Full description

Bibliographic Details
Main Authors:	Alexander K. Lancaster, Richard M. Single, Steven J. Mack, Vanessa Sochat, Michael P. Mariani, Gordon D. Webster
Format:	Article
Language:	English
Published:	Frontiers Media S.A. 2024-04-01
Series:	Frontiers in Immunology
Subjects:	HLA MHC population genomics software bioinformatics
Online Access:	https://www.frontiersin.org/articles/10.3389/fimmu.2024.1378512/full

Similar Items

Complex Interactions between the Human Major Histocompatibility Complex (MHC) and Microbiota: Their Roles in Disease Pathogenesis and Immune System Regulation
by: Antonio Arnaiz-Villena, et al.
Published: (2024-08-01)

Current research status of HLA in immune‐related diseases
by: Bingnan Liu, et al.
Published: (2021-06-01)

Type 2 autoimmune hepatitis: Genetic susceptibility
by: Pascal Lapierre, et al.
Published: (2022-09-01)

The antibodies 3D12 and 4D12 recognise distinct epitopes and conformations of HLA-E
by: Simon Brackenridge, et al.
Published: (2024-03-01)

Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies
by: Matthew I. J. Raybould, et al.
Published: (2023-01-01)

Hilliard Seigler, M.D. and the origins of kidney transplantation and immunology at Duke
by: Stuart J. Knechtle, et al.
Published: (2023-05-01)

HLA Expression at the Maternal-Fetal Interface
by: Heinz Hutter, et al.
Published: (1998-01-01)

Comparison of NK alloreactivity prediction models based on KIR-MHC interactions in haematopoietic stem cell transplantation
by: Adèle Dhuyser, et al.
Published: (2023-03-01)

Immunogenetic Predisposition to SARS-CoV-2 Infection
by: Claudia Lehmann, et al.
Published: (2022-12-01)

Race/ethnicity-stratified fine-mapping of the MHC locus reveals genetic variants associated with late-onset asthma
by: Eunice Y. Lee, et al.
Published: (2023-06-01)

Secretogranin II influences the assembly and function of MHC class I in melanoma
by: Tamara Steinfass, et al.
Published: (2023-03-01)

Retinal vasculitis in HLA-A29 birdshot retinochoroiditis, particularities and imaging narrative of an under-estimated and diagnostic component of the disease
by: Jérôme Galand, et al.
Published: (2024-07-01)

Long-Term Human Immune Reconstitution, T-Cell Development, and Immune Reactivity in Mice Lacking the Murine Major Histocompatibility Complex: Validation with Cellular and Gene Expression Profiles
by: Milita Darguzyte, et al.
Published: (2024-10-01)

Characterization of genetic humanized mice with transgenic HLA DP401 or DRA but deficient in endogenous murine MHC class II genes upon Staphylococcus aureus pneumonia
by: Feng Li, et al.
Published: (2023-12-01)

Quantifying conformational changes in the TCR:pMHC-I binding interface
by: Benjamin McMaster, et al.
Published: (2024-12-01)

HLA and non-HLA polymorphisms in renal transplantation
by: Stéphanie Laperrousaz, et al.
Published: (2012-08-01)

Evaluating NetMHCpan performance on non-European HLA alleles not present in training data
by: Thomas Karl Atkins, et al.
Published: (2024-01-01)

Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods
by: Dinler A. Antunes, et al.
Published: (2024-02-01)

HLA Variation and SARS-CoV-2 Specific Antibody Response
by: Dawit Wolday, et al.
Published: (2023-03-01)

HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire
by: Maxim Shkurnikov, et al.
Published: (2023-01-01)

A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations
by: Alicia Sanchez-Mazas
Published: (2020-04-01)

HLA-DR expression in melanoma: from misleading therapeutic target to potential immunotherapy biomarker
by: Karim Amrane, et al.
Published: (2024-01-01)

Insights into PCSK9-LDLR Regulation and Trafficking via the Differential Functions of MHC-I Proteins HFE and HLA-C
by: Sepideh Mikaeeli, et al.
Published: (2024-05-01)

Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing
by: Maria Kalomoiri, et al.
Published: (2023-08-01)

DNA structural features and variability of complete MHC locus sequences
by: Trudy M. Wassenaar, et al.
Published: (2024-07-01)

The Avian MHC-Antigen System
by: Diana Wesselinova
Published: (2002-10-01)

Prediction of HLA genotypes from single-cell transcriptome data
by: Benjamin D. Solomon, et al.
Published: (2023-04-01)

A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability
by: Adrian Schmalen, et al.
Published: (2023-08-01)

Conserved biophysical compatibility among the highly variable germline-encoded regions shapes TCR-MHC interactions
by: Christopher T Boughter, et al.
Published: (2023-10-01)

LRMAHpan: a novel tool for multi-allelic HLA presentation prediction using Resnet-based and LSTM-based neural networks
by: Xue Mi, et al.
Published: (2024-11-01)

Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population
by: Wan-Hsuan Chou, et al.
Published: (2024-05-01)

Comprehensive Analysis of CD4+ T Cell Response Cross-Reactive to SARS-CoV-2 Antigens at the Single Allele Level of HLA Class II
by: You-Seok Hyun, et al.
Published: (2022-01-01)

Quantifying uncertainty of molecular mismatch introduced by mislabeled ancestry using haplotype-based HLA genotype imputation
by: Benedict M. Matern, et al.
Published: (2024-09-01)

Screening and validation of differentially expressed genes in polymyositis
by: Linmang Qin, et al.
Published: (2024-02-01)

Different MHC class I cell surface expression levels in diverse chicken lines, associations with B blood group, and proposed relationship to antigen-binding repertoire
by: Michael Kaiser, et al.
Published: (2025-01-01)

慢性HBV感染患者抗原表位特异性CTL与ALT水平无关
by: 邓洪, et al.
Published: (2006-01-01)

3D genome contributes to MHC-II neoantigen prediction
by: Mofan Feng, et al.
Published: (2024-09-01)

Critical Review of Existing MHC I Immunopeptidome Isolation Methods
by: Alexandr Kuznetsov, et al.
Published: (2020-11-01)

Population data on D6S2879 and D6S2806 markers located at HLA-DRB1 region in the Iranians: Identifying the signatures of balancing and directional selection
by: Mansoureh Tajadod, et al.
Published: (2011-12-01)

Variations in HLA-B cell surface expression, half-life and extracellular antigen receptivity
by: Brogan Yarzabek, et al.
Published: (2018-07-01)