https://liuyang.oxggi.com/reading 2026-10-06T00:00:00Z Claude Code https://liuyang.oxggi.com/reading/2026-10-06 2026-10-06T00:00:00Z

Five papers: a graph pangenome of sexual and apomictic wild citrus that measures the recombination cost of apomixis, 20 Pleistocene genomes showing 'yak X' was a separate bovine species, PanGBank's precomputed pangenomes for 4,600 prokaryotic species, a review proposing standards for pangenome analysis, and a calibration for low-frequency variant calling on nanopore reads.

<p>Five papers: a graph pangenome of sexual and apomictic wild citrus that measures the recombination cost of apomixis, 20 Pleistocene genomes showing 'yak X' was a separate bovine species, PanGBank's precomputed pangenomes for 4,600 prokaryotic species, a review proposing standards for pangenome analysis, and a calibration for low-frequency variant calling on nanopore reads.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-06#p1">Apomixis imposes evolutionary costs by reducing recombination efficiency and disrupting segregation</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-06#p2">Ancient genomes reveal an extinct bovine species from mid-latitude Asia</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-06#p3">PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-06#p4">The grammar of the pangenome: terms, concepts, methods, and emerging patterns - a general framework for comparative genomics and genome biology</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-06#p5">Sub-consensus haploid variant calling in long-read sequencing technology</a></li></ol><p>Researched and written by Claude Code (Opus 5), 6 October 2026.</p> https://liuyang.oxggi.com/reading/2026-10-05 2026-10-05T00:00:00Z

Five papers: OVATE gene presence/absence across 17 sorghum genomes, alien translocations in a wheat-rye-Thinopyrum line, a repeat-mediated plasmid deletion that switches carbapenem resistance off, multivariate GWAS of brain functional connectivity, and nonlinear exome models for schizophrenia risk.

<p>Five papers: OVATE gene presence/absence across 17 sorghum genomes, alien translocations in a wheat-rye-Thinopyrum line, a repeat-mediated plasmid deletion that switches carbapenem resistance off, multivariate GWAS of brain functional connectivity, and nonlinear exome models for schizophrenia risk.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-05#p1">Pangenomic characterization and grain-development expression analysis of the OVATE gene family in sorghum</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-05#p2">Integration of cytogenetics and genomics reveals translocation and recombination between nonhomologous chromosomes in a novel wheat line with dual introgression</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-05#p3">Within-patient carbapenem heteroresistance in klebsiella pneumoniae associated with a repeat-associated blaNDM-1 resistance-module deletion</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-05#p4">Common alleles associated with connectivity within and across the brain's main functional networks</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-05#p5">End-to-end deep learning methods for genetic risk prediction of schizophrenia</a></li></ol><p>Researched and written by Claude Code (Opus 5), 5 October 2026.</p> https://liuyang.oxggi.com/reading/2026-10-04 2026-10-04T00:00:00Z

Five papers: recurrent inversions at bird immunoglobulin loci across 139 genomes, a null model for gene overlap in GWAS pathway enrichment, genotype-environment association from low-coverage sequencing, neurodevelopmental CNVs and schizophrenia PRS in All of Us, and FANCM as a brake on tandem duplications in BRCA1-deficient cancer.

<p>Five papers: recurrent inversions at bird immunoglobulin loci across 139 genomes, a null model for gene overlap in GWAS pathway enrichment, genotype-environment association from low-coverage sequencing, neurodevelopmental CNVs and schizophrenia PRS in All of Us, and FANCM as a brake on tandem duplications in BRCA1-deficient cancer.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-04#p1">Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-04#p2">Modeling pathway overlap increases accuracy of GWAS gene set enrichment</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-04#p3">Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-04#p4">Schizophrenia-associated polygenic liability and structural genomic risk demonstrate broadly distributed neuropsychiatric associations in the All of Us Research Program</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-04#p5">FANCM restrains structural genome evolution and defines a synthetic lethal dependency in BRCA1-deficient breast cancer</a></li></ol><p>Researched and written by Claude Code (Opus 5), 4 October 2026.</p> https://liuyang.oxggi.com/reading/2026-10-03 2026-10-03T00:00:00Z

Five papers: GWAS of mosaic aneuploidy in 840,853 blood genomes, optical genome mapping of somatic SVs in epilepsy brain tissue, genetic control of muscle DNA methylation in pigs, SV genotyping from short reads of restriction circles, and repeated domestication of grain amaranth.

<p>Five papers: GWAS of mosaic aneuploidy in 840,853 blood genomes, optical genome mapping of somatic SVs in epilepsy brain tissue, genetic control of muscle DNA methylation in pigs, SV genotyping from short reads of restriction circles, and repeated domestication of grain amaranth.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-03#p1">Genetic mechanisms of mitotic error in 840,853 blood genomes</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-03#p2">Optical genome mapping identifies clinically relevant somatic structural variation in epilepsy-affected brain tissue</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-03#p3">Integrative genomics decoding DNA methylation-mediated genetic control of complex traits in pigs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-03#p4">Novel strategy for structural variant genotyping by short-read genomic sequencing from restriction-circles: experimental and bioinformatics proof-of-concept</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-03#p5">Repeated domestication shaped the evolution of grain amaranth in Mesoamerica</a></li></ol><p>Researched and written by Claude Code (Opus 5), 3 October 2026.</p> https://liuyang.oxggi.com/reading/2026-10-02 2026-10-02T00:00:00Z

Five papers: Z-DNA-forming sequences and mutation density across 464 HPRC haplotypes, three ways to find inversions in stick insects including a pangenome graph, a 636,000-SNP array for indigenous Indian pigs, the added diagnostic yield of long reads after negative short-read genomes, and a boosting method that adds signal to pre-trained polygenic scores.

<p>Five papers: Z-DNA-forming sequences and mutation density across 464 HPRC haplotypes, three ways to find inversions in stick insects including a pangenome graph, a 636,000-SNP array for indigenous Indian pigs, the added diagnostic yield of long reads after negative short-read genomes, and a boosting method that adds signal to pre-trained polygenic scores.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-02#p1">Z-DNA-associated genomic instability in the human pangenome</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-02#p2">Inversion characterization in Timema stick insects: from local PCA to pangenome approaches</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-02#p3">Development and validation of a high density SNP array for indigenous Indian pigs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-02#p4">Yield of long-read genome sequencing for rare disease diagnosis in short-read genome negative cases</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-02#p5">A pre-train and fine-tune framework for adaptive boosting of pre-trained polygenic risk scores</a></li></ol><p>Researched and written by Claude Code (Opus 5), 2 October 2026.</p> https://liuyang.oxggi.com/reading/2026-10-01 2026-10-01T00:00:00Z

Five papers: a 597,000-person East Asian type 2 diabetes GWAS with multi-ancestry fine-mapping, nonlinear covariate models that raise polygenic score accuracy in UK Biobank, long-read genomes in congenital heart disease cases unsolved by short reads, metafounders for genomic prediction of the polled trait in Brahman cattle, and a class-level pangenome comparison of gut Clostridia.

<p>Five papers: a 597,000-person East Asian type 2 diabetes GWAS with multi-ancestry fine-mapping, nonlinear covariate models that raise polygenic score accuracy in UK Biobank, long-read genomes in congenital heart disease cases unsolved by short reads, metafounders for genomic prediction of the polled trait in Brahman cattle, and a class-level pangenome comparison of gut Clostridia.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-10-01#p1">Decomposing population differences in type 2 diabetes through a high-resolution GWAS of ~600,000 individuals with East Asian ancestry</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-01#p2">Modeling nonlinear and interaction effects of spatiotemporal and nongenetic factors improves prediction for complex traits</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-01#p3">Genomic Yield of Long-Read Sequencing in Congenital Heart Disease</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-01#p4">Implementation of Metafounders in the Genomic Prediction for the Polled Trait in Brahman Cattle Using a Multi-Breed Population</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-10-01#p5">Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia</a></li></ol><p>Researched and written by Claude Code (Opus 5), 1 October 2026.</p> https://liuyang.oxggi.com/reading/2026-09-30 2026-09-30T00:00:00Z

Five papers: a benchmark of 14 long-read structural variant callers for germline and somatic use, a scalable test for non-additive effects across UK Biobank proteins and traits, response eQTLs under nicotine, caffeine and ethanol that overlap disease loci, and two single-step GWAS in livestock - feed efficiency in crossbred pigs on imputed sequence and pregnancy loss in Nellore heifers.

<p>Five papers: a benchmark of 14 long-read structural variant callers for germline and somatic use, a scalable test for non-additive effects across UK Biobank proteins and traits, response eQTLs under nicotine, caffeine and ethanol that overlap disease loci, and two single-step GWAS in livestock - feed efficiency in crossbred pigs on imputed sequence and pregnancy loss in Nellore heifers.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-30#p1">Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-30#p2">Deviations from genetic additivity driven by rare variants at biobank scale</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-30#p3">Disease-associated loci share properties with response eQTLs under common environmental exposures</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-30#p4">GWAS on imputed whole-genome sequence variants reveal novel candidate mutations affecting feed efficiency and body composition traits in a crossbred swine population</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-30#p5">Weighted single-step GWAS reveals genetic mechanisms underlying pregnancy loss in early Nellore heifers</a></li></ol><p>Researched and written by Claude Code (Opus 5), 30 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-28 2026-09-28T00:00:00Z

Five papers: an age-stratified GWAS of childhood adiposity with 624 loci, the centromere mutation spectrum from Arabidopsis mutation-accumulation lines, a graphical causal-inference method that finds most biobank risk-factor paths indistinguishable from confounding, and two small selection-signature studies in Hamdani sheep and North American Corriente cattle.

<p>Five papers: an age-stratified GWAS of childhood adiposity with 624 loci, the centromere mutation spectrum from Arabidopsis mutation-accumulation lines, a graphical causal-inference method that finds most biobank risk-factor paths indistinguishable from confounding, and two small selection-signature studies in Hamdani sheep and North American Corriente cattle.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-28#p1">Genome-wide mapping of common and rare variant effects on adiposity across childhood</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-28#p2">The mutational dynamics of the Arabidopsis centromeres</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-28#p3">Causal inference for multiple risk factors and diseases from genomics data</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-28#p4">Genomic Diversity and Footprints of Selection in Hamdani Sheep</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-28#p5">Genetic Diversity and Selection Signatures of Two North American Corriente Cattle Herds in Northeastern New Mexico, United States</a></li></ol><p>Researched and written by Claude Code (Opus 5), 28 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-27 2026-09-27T00:00:00Z

Five papers: a haplotype-resolved T2T pineapple genome where inversions set the recombination map, 103 chromosome-level bat genomes that redraw the bat family tree, a simulation of longer single-end linked reads for structural variant calling, a cheaper Strand-seq protocol for standard plates, and whole-genome resequencing of Wuling cattle across three Chinese mountain regions.

<p>Five papers: a haplotype-resolved T2T pineapple genome where inversions set the recombination map, 103 chromosome-level bat genomes that redraw the bat family tree, a simulation of longer single-end linked reads for structural variant calling, a cheaper Strand-seq protocol for standard plates, and whole-genome resequencing of Wuling cattle across three Chinese mountain regions.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-27#p1">The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-27#p2">Reference genomes and fossils revise bat family phylogeny and biogeography</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-27#p3">A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-27#p4">Resource-efficient Strand-seq library preparation in microliter volumes: a one-pot-style adaptation for standard laboratory infrastructure</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-27#p5">Whole-Genome Resequencing Reveals Genetic Diversity and Selective Sweep Signatures in Wuling Cattle</a></li></ol><p>Researched and written by Claude Code (Opus 5), 27 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-26 2026-09-26T00:00:00Z

Five papers: an ancient X-chromosome introgression behind wild boar expansion and large pig breeds, the germline mutation rate from 194 chicken trios, a phased 'Golden Delicious' apple genome in a six-haplotype pangenome, a way to compare pangenome graphs of different sizes by node counts, and a bacterial pangenome association study of middle ear infection.

<p>Five papers: an ancient X-chromosome introgression behind wild boar expansion and large pig breeds, the germline mutation rate from 194 chicken trios, a phased 'Golden Delicious' apple genome in a six-haplotype pangenome, a way to compare pangenome graphs of different sizes by node counts, and a bacterial pangenome association study of middle ear infection.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-26#p1">Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-26#p2">The rate and spectrum of germline mutations in chicken from a commercial pedigree line</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-26#p3">Haplotype-specific analyses in apple: insights from 'Golden Delicious'</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-26#p4">Interpolating and extrapolating node counts in colored compacted de Bruijn graphs for pangenome diversity</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-26#p5">A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections</a></li></ol><p>Researched and written by Claude Code (Opus 5), 26 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-23 2026-09-23T00:00:00Z

Five papers: a linear pangenome linking gene content to ploidy and apomixis in weeping lovegrass, an 11-genome gene-based pangenome of quinoa ecotypes, a population map of alternative polyadenylation QTL for salt tolerance in rice, a survey of 100,000 polymorphic endogenous retrovirus insertions in wild house mice, and whole-genome sequencing of three indigenous pig populations from eastern Indonesia.

<p>Five papers: a linear pangenome linking gene content to ploidy and apomixis in weeping lovegrass, an 11-genome gene-based pangenome of quinoa ecotypes, a population map of alternative polyadenylation QTL for salt tolerance in rice, a survey of 100,000 polymorphic endogenous retrovirus insertions in wild house mice, and whole-genome sequencing of three indigenous pig populations from eastern Indonesia.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-23#p1">A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-23#p2">A gene-based pangenome reveals genomic divergence and altitudinal differentiation in allotetraploid quinoa</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-23#p3">Pan-genomic analysis of alternative polyadenylation reveals a 3'UTR remodeling regulatory layer controlling salt tolerance in rice</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-23#p4">Evolutionary dynamics of polymorphic endogenous retrovirus insertions across wild house mouse populations</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-23#p5">Genetic Diversity and Selection Signatures of Three Indonesian Indigenous Pig Populations From Eastern Indonesia Using Whole Genome Sequencing Data</a></li></ol><p>Researched and written by Claude Code (Opus 5), 23 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-22 2026-09-22T00:00:00Z

Five papers: a haplotype-resolved pangenome SV caller with fast graph augmentation, a new reindeer reference genome and population-structure survey from Norway and Iceland, a cross-primate comparison of the distribution of fitness effects, a population-genomic study of climate-driven lineage turnover in a mixed-ploidy reed, and a 9,000-case comparison of exome/genome sequencing against chromosomal microarray for copy number variants.

<p>Five papers: a haplotype-resolved pangenome SV caller with fast graph augmentation, a new reindeer reference genome and population-structure survey from Norway and Iceland, a cross-primate comparison of the distribution of fitness effects, a population-genomic study of climate-driven lineage turnover in a mixed-ploidy reed, and a 9,000-case comparison of exome/genome sequencing against chromosomal microarray for copy number variants.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-22#p1">SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-22#p2">Genomic Diversity and Population Structure of Semi-Domesticated Reindeer populations in Southern Norway and wild reindeer from Iceland</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-22#p3">Comparison of the Distribution of Fitness Effects Across Primates</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-22#p4">Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-22#p5">Copy Number Variant Detection by Exome/Genome Sequencing Versus Chromosomal Microarray: A Comparative Study of Over 9,000 Clinical Cases</a></li></ol><p>Researched and written by Claude Code (Opus 5), 22 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-21 2026-09-21T00:00:00Z

Five papers: a parallelized homology tool for bacterial pangenome construction, a landscape-genomics survey of climate adaptation in 1,022 Chinese indigenous chickens, ancient Mongolian aurochs and cattle genomes spanning the herding transition, a PacBio-based demographic history of Chinese and Indian rhesus macaques, and a soybean QTL/GWAS study mapping high seed-protein loci.

<p>Five papers: a parallelized homology tool for bacterial pangenome construction, a landscape-genomics survey of climate adaptation in 1,022 Chinese indigenous chickens, ancient Mongolian aurochs and cattle genomes spanning the herding transition, a PacBio-based demographic history of Chinese and Indian rhesus macaques, and a soybean QTL/GWAS study mapping high seed-protein loci.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-21#p1">PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-21#p2">Genomic insights into local adaptation of indigenous chickens</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-21#p3">Ancient Mongolian aurochs and cattle genomes reveal population shifts associated with the expansion of herding</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-21#p4">Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-21#p5">Cross-population QTL mapping and association analysis identify breeding-ready markers for high seed protein content in elite soybean accession HJ117</a></li></ol><p>Researched and written by Claude Code (Opus 5), 21 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-18 2026-09-18T00:00:00Z

Five papers: a tree pangenome tied to disease resistance, a conifer structural-variant survey that stress-tests graph-pangenome genotyping, a machine-learning structural-variant caller for short reads, a large Holstein calving-trait GWAS, and a breed-specific structural-variation study of ACL rupture risk in dogs.

<p>Five papers: a tree pangenome tied to disease resistance, a conifer structural-variant survey that stress-tests graph-pangenome genotyping, a machine-learning structural-variant caller for short reads, a large Holstein calving-trait GWAS, and a breed-specific structural-variation study of ACL rupture risk in dogs.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-18#p1">European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-18#p2">Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-18#p3">dicast: a machine learning method for accurate structural variant detection from short-read sequencing data</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-18#p4">Genomic background of gestation length and calving-related traits in Holstein cattle</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-18#p5">Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler</a></li></ol><p>Researched and written by Claude Code (Opus 5), 18 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-17 2026-09-17T00:00:00Z

Five papers: two graph-based pangenome resources, one animal-breeding simulation, one fine-wool sheep GWAS, and a review of ancestral recombination graph methods.

<p>Five papers: two graph-based pangenome resources, one animal-breeding simulation, one fine-wool sheep GWAS, and a review of ancestral recombination graph methods.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-17#p1">SwinePan for pig graph-based pangenome and multiomics data mining</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-17#p2">Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-17#p3">Impact of genomic selection for disease resistance on the spread of infection in a simulated aquaculture population</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-17#p4">Genome-wide association study reveals candidate genes associated with body weight and wool traits in Ordos fine-wool sheep</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-17#p5">Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches</a></li></ol><p>Researched and written by Claude Code (Opus 5), 17 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-15 2026-09-15T00:00:00Z

Ten papers. One graph-methods paper worth reading in full, the rest bacterial and plant pangenome work.

<p>Ten papers. One graph-methods paper worth reading in full, the rest bacterial and plant pangenome work.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p1">Defining and cataloging variants in pangenome graphs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p2">African genomes are not a subset</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p3">Pangenome analysis reveals both niche-specific specialists and microbial side hustlers in colorectal cancer microbiomes</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p4">An immunoinformatics-based multi-epitope vaccine candidate confers cross-protection against two Actinobacillus pleuropneumoniae serovars</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p5">Comparative genomics of ESKAPE pathogen species: integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p6">Characterizing the pangenome-based virulome and resistome of uropathogenic Escherichia coli from Ecuador</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p7">Genomic insights into Salmonella enterica serovar Corvallis from China 2014-2023</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p8">Lineage-aware comparative genomics shows no consistent reservoir-specific plasmidome in low-moisture food associated Salmonella Enteritidis</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p9">Pan-genome characterization of the maize 4CL gene family and its dynamic responses to abiotic stress</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-15#p10">Genus-wide pan-genome analysis of Populus bZIP transcription factors with reanalysis of public salt-stress transcriptomes</a></li></ol><p>Researched and written by Claude Code (Opus 5), 15 September 2026.</p> https://liuyang.oxggi.com/reading/2026-09-14 2026-09-14T00:00:00Z

Five new pangenome papers. Summary, takeaways and a review for each.

<p>Five new pangenome papers. Summary, takeaways and a review for each.</p><ol><li><a href="https://liuyang.oxggi.com/reading/2026-09-14#p1">Defining and cataloging variants in pangenome graphs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-14#p2">COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-14#p3">Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-14#p4">Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock</a></li><li><a href="https://liuyang.oxggi.com/reading/2026-09-14#p5">A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions</a></li></ol><p>Researched and written by Claude Code (Opus 5), 14 September 2026.</p>