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About this wiki
This wiki is experimental. It is assembled by Tealc autonomously. The LLM is instructed to build pages about lab papers and topics of importance to the lab. Over time it is also expanding the wiki to include papers that we cite and are important to the lab too. The lab does try to review these pages and make corrections, but consider this wiki as a starting place rather than the final word on a topic.
— Heath
Topics State-of-understanding pages synthesized across many papers Updated each time a new paper with findings tagged to that topic is ingested. Contradictions between papers are flagged explicitly. 91 topics across 8 areas.
Bioinformatics & tools (26)
- Bioinformatics Methods
- Bioinformatics Tools
- Bisse
- Cavefish Genomics
- Chaining Algorithm
- Circadian rhythm evolution
- Flow Cytometry
- Genome Resequencing
- Genome Size Estimation
- Hybrid Sterility
- Inversions
- Long Read Sequencing
- Model Inadequacy
- Model Organism Databases
- Mutation Rate Bias
- Phylogenetic Comparative Methods
- Qtl Mapping
- Repeat Annotation
- Rna Seq
- Selection Theory
- Sequence Alignment
- Short Read Alignment
- Software Tools
- Speciation Genetics
- Trait Dependent Diversification
- Type I Error
Genome structure (6)
Insects & Coleoptera (7)
Karyotype evolution (9)
Population genetics (9)
Quantitative genetics & epistasis (10)
Sex chromosomes (9)
Papers Citable findings extracted from individual papers Verbatim quotes with page references, the reasoning for why each finding matters, and the counter-argument or limitation to watch for. 40 papers ingested.
- Chromosome-Level Reference Genome of an Endemic, Endangered Long-Armed Scarab (Cheirotonus formosanus): Discovery of a Putative Y-Linked Scaffold and Demographic History
- DirectRepeateR: An R package for annotating direct repeats in genome assemblies
- Drivers of achiasmatic meiosis: sexual antagonism versus heteromorphy-dependent aneuploidy across sex-chromosome divergence.
- Assessing the opportunity for selection to impact morphological traits in crosses between two Solanum species
- Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
- Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveals the origins of gene content reduction in Dendroctonus
- Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora
- Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera
- Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern.
- A reference quality genome assembly for the jewel scarab Chrysina gloriosa
- Wright was right: leveraging old data and new methods to illustrate the critical role of epistasis in genetics and evolution
- Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes)
- Retrogene survival is not impacted by linkage relationships
- CaveCrawler: an interactive analysis suite for cavefish bioinformatics
- Why not Y naught
- Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution
- Chromosome number evolves at equal rates in holocentric and monocentric clades
- Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects
- The probability of fusions joining sex chromosomes and autosomes: Sex Autosome Fusions
- Ghosts of a Structured Past: Impacts of Ancestral Patterns of Isolation-by-Distance on Divergence-Time Estimation
- The March of the Beetles: Epistatic Components Dominate Divergence in Dispersal Tendency in Tribolium castaneum
- Meiotic drive shapes rates of karyotype evolution in mammals
- A database of amphibian karyotypes
- Genome Size Estimation and Quantitative Cytogenetics in Insects
- Long-Term Fragility of Y Chromosomes Is Dominated by Short-Term Resolution of Sexual Antagonism.
- Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals
- Sex Determination, Sex Chromosomes, and Karyotype Evolution in Insects
- An information-theoretic approach to estimating the composite genetic effects contributing to variation among generation means: Moving beyond the joint-scaling test for line cross analysis
- Coleoptera Karyotype Database
- Y fuse? Sex chromosome fusions in fishes and reptiles.
- The evolutionary dynamics of haplodiploidy: genome architecture and haploid viability
- Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation
- Genomic origins of insect sex chromosomes
- The fragile Y hypothesis: Y chromosome aneuploidy as a selective pressure in sex chromosome and meiotic mechanism evolution
- Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis
- Ring Species and Speciation
- Fast and accurate short read alignment with Burrows-Wheeler transform.
- A role for a neo-sex chromosome in stickleback speciation.
- Sex differences in fitness and selection for centric fusions between sex-chromosomes and autosomes
- 10.1093/bioinformatics/bty191
Repositories Watched GitHub repositories — lab code and key collaborator repos Each repo page shows README summary, recent commit activity, and cross-links to the papers whose analyses live in that code. Private repos never render here.
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