Reading_
How I keep up with the literature.
This is a learning process.
Daily notes · 90 papers so far_
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6 October 2026 · 5 papers
Reading for 6 October 2026
- Structural variation
- Population genetics
- Animal science
- Microbial genomics
- Methods
- Review
- Apomixis imposes evolutionary costs by reducing recombination efficiency and disrupting segregation
- Ancient genomes reveal an extinct bovine species from mid-latitude Asia
- PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN
- The grammar of the pangenome: terms, concepts, methods, and emerging patterns - a general framework for comparative genomics and genome biology
- Sub-consensus haploid variant calling in long-read sequencing technology
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5 October 2026 · 5 papers
Reading for 5 October 2026
- Structural variation
- Microbial genomics
- Human genetics
- Methods
- Pangenomic characterization and grain-development expression analysis of the OVATE gene family in sorghum
- Integration of cytogenetics and genomics reveals translocation and recombination between nonhomologous chromosomes in a novel wheat line with dual introgression
- Within-patient carbapenem heteroresistance in klebsiella pneumoniae associated with a repeat-associated blaNDM-1 resistance-module deletion
- Common alleles associated with connectivity within and across the brain's main functional networks
- End-to-end deep learning methods for genetic risk prediction of schizophrenia
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4 October 2026 · 5 papers
Reading for 4 October 2026
- Structural variation
- Population genetics
- Methods
- Human genetics
- Cancer genomics
- Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci
- Modeling pathway overlap increases accuracy of GWAS gene set enrichment
- Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data
- Schizophrenia-associated polygenic liability and structural genomic risk demonstrate broadly distributed neuropsychiatric associations in the All of Us Research Program
- FANCM restrains structural genome evolution and defines a synthetic lethal dependency in BRCA1-deficient breast cancer
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3 October 2026 · 5 papers
Reading for 3 October 2026
- Human genetics
- Structural variation
- Methods
- Animal science
- Population genetics
- Genetic mechanisms of mitotic error in 840,853 blood genomes
- Optical genome mapping identifies clinically relevant somatic structural variation in epilepsy-affected brain tissue
- Integrative genomics decoding DNA methylation-mediated genetic control of complex traits in pigs
- Novel strategy for structural variant genotyping by short-read genomic sequencing from restriction-circles: experimental and bioinformatics proof-of-concept
- Repeated domestication shaped the evolution of grain amaranth in Mesoamerica
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2 October 2026 · 5 papers
Reading for 2 October 2026
- Structural variation
- Human genetics
- Population genetics
- Methods
- Animal science
- Z-DNA-associated genomic instability in the human pangenome
- Inversion characterization in Timema stick insects: from local PCA to pangenome approaches
- Development and validation of a high density SNP array for indigenous Indian pigs
- Yield of long-read genome sequencing for rare disease diagnosis in short-read genome negative cases
- A pre-train and fine-tune framework for adaptive boosting of pre-trained polygenic risk scores
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1 October 2026 · 5 papers
Reading for 1 October 2026
- Human genetics
- Population genetics
- Methods
- Structural variation
- Animal science
- Microbial genomics
- Decomposing population differences in type 2 diabetes through a high-resolution GWAS of ~600,000 individuals with East Asian ancestry
- Modeling nonlinear and interaction effects of spatiotemporal and nongenetic factors improves prediction for complex traits
- Genomic Yield of Long-Read Sequencing in Congenital Heart Disease
- Implementation of Metafounders in the Genomic Prediction for the Polled Trait in Brahman Cattle Using a Multi-Breed Population
- Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia
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30 September 2026 · 5 papers
Reading for 30 September 2026
- Structural variation
- Methods
- Cancer genomics
- Human genetics
- Animal science
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data
- Deviations from genetic additivity driven by rare variants at biobank scale
- Disease-associated loci share properties with response eQTLs under common environmental exposures
- GWAS on imputed whole-genome sequence variants reveal novel candidate mutations affecting feed efficiency and body composition traits in a crossbred swine population
- Weighted single-step GWAS reveals genetic mechanisms underlying pregnancy loss in early Nellore heifers
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28 September 2026 · 5 papers
Reading for 28 September 2026
- Human genetics
- Structural variation
- Population genetics
- Methods
- Animal science
- Genome-wide mapping of common and rare variant effects on adiposity across childhood
- The mutational dynamics of the Arabidopsis centromeres
- Causal inference for multiple risk factors and diseases from genomics data
- Genomic Diversity and Footprints of Selection in Hamdani Sheep
- Genetic Diversity and Selection Signatures of Two North American Corriente Cattle Herds in Northeastern New Mexico, United States
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27 September 2026 · 5 papers
Reading for 27 September 2026
- Structural variation
- Population genetics
- Methods
- Animal science
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes
- Reference genomes and fossils revise bat family phylogeny and biogeography
- A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection
- Resource-efficient Strand-seq library preparation in microliter volumes: a one-pot-style adaptation for standard laboratory infrastructure
- Whole-Genome Resequencing Reveals Genetic Diversity and Selective Sweep Signatures in Wuling Cattle
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26 September 2026 · 5 papers
Reading for 26 September 2026
- Population genetics
- Animal science
- Methods
- Microbial genomics
- Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs
- The rate and spectrum of germline mutations in chicken from a commercial pedigree line
- Haplotype-specific analyses in apple: insights from 'Golden Delicious'
- Interpolating and extrapolating node counts in colored compacted de Bruijn graphs for pangenome diversity
- A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections
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23 September 2026 · 5 papers
Reading for 23 September 2026
- Population genetics
- Structural variation
- Animal science
- A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula
- A gene-based pangenome reveals genomic divergence and altitudinal differentiation in allotetraploid quinoa
- Pan-genomic analysis of alternative polyadenylation reveals a 3'UTR remodeling regulatory layer controlling salt tolerance in rice
- Evolutionary dynamics of polymorphic endogenous retrovirus insertions across wild house mouse populations
- Genetic Diversity and Selection Signatures of Three Indonesian Indigenous Pig Populations From Eastern Indonesia Using Whole Genome Sequencing Data
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22 September 2026 · 5 papers
Reading for 22 September 2026
- Methods
- Structural variation
- Animal science
- Population genetics
- Human genetics
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples
- Genomic Diversity and Population Structure of Semi-Domesticated Reindeer populations in Southern Norway and wild reindeer from Iceland
- Comparison of the Distribution of Fitness Effects Across Primates
- Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed
- Copy Number Variant Detection by Exome/Genome Sequencing Versus Chromosomal Microarray: A Comparative Study of Over 9,000 Clinical Cases
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21 September 2026 · 5 papers
Reading for 21 September 2026
- Methods
- Microbial genomics
- Animal science
- Population genetics
- PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis
- Genomic insights into local adaptation of indigenous chickens
- Ancient Mongolian aurochs and cattle genomes reveal population shifts associated with the expansion of herding
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data
- Cross-population QTL mapping and association analysis identify breeding-ready markers for high seed protein content in elite soybean accession HJ117
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18 September 2026 · 5 papers
Reading for 18 September 2026
- Structural variation
- Population genetics
- Methods
- Human genetics
- Animal science
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data
- Genomic background of gestation length and calving-related traits in Holstein cattle
- Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler
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17 September 2026 · 5 papers
Reading for 17 September 2026
- Animal science
- Structural variation
- Methods
- Population genetics
- Review
- SwinePan for pig graph-based pangenome and multiomics data mining
- Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut
- Impact of genomic selection for disease resistance on the spread of infection in a simulated aquaculture population
- Genome-wide association study reveals candidate genes associated with body weight and wool traits in Ordos fine-wool sheep
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches
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15 September 2026 · 10 papers
Reading for 15 September 2026
- Pangenome graph
- Structural variation
- Human genetics
- Methods
- Population genetics
- Pangenome
- Microbiome
- Cancer
- Vaccine
- Veterinary
- Amr
- Comparative genomics
- Epidemiology
- Food safety
- Negative result
- Plant genomics
- Transcription factors
- Defining and cataloging variants in pangenome graphs
- African genomes are not a subset
- Pangenome analysis reveals both niche-specific specialists and microbial side hustlers in colorectal cancer microbiomes
- An immunoinformatics-based multi-epitope vaccine candidate confers cross-protection against two Actinobacillus pleuropneumoniae serovars
- Comparative genomics of ESKAPE pathogen species: integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires
- Characterizing the pangenome-based virulome and resistome of uropathogenic Escherichia coli from Ecuador
- Genomic insights into Salmonella enterica serovar Corvallis from China 2014-2023
- Lineage-aware comparative genomics shows no consistent reservoir-specific plasmidome in low-moisture food associated Salmonella Enteritidis
- Pan-genome characterization of the maize 4CL gene family and its dynamic responses to abiotic stress
- Genus-wide pan-genome analysis of Populus bZIP transcription factors with reanalysis of public salt-stress transcriptomes
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14 September 2026 · 5 papers
Reading for 14 September 2026
- Methods
- Human genetics
- Structural variation
- Population genetics
- Cancer genomics
- Animal science
- Review
- Microbial genomics
- Public health
- Defining and cataloging variants in pangenome graphs
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs
- Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions