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The Collaborative Cross Graphical Genome

https://doi.org/10.1101/858142
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00248-011-9880-1openalex-snapshot
The Salmonella enterica Pan-genome
inferredcites →https://doi.org/10.1007/s00335-015-9581-zopenalex-snapshot
Informatics resources for the Collaborative Cross and related mouse populations
inferredcites →https://doi.org/10.1007/s003359900998openalex-snapshot
Genotyping new BXD recombinant inbred mouse strains and comparison of BXD and consensus maps
inferredcites →https://doi.org/10.1016/j.ccell.2016.04.002openalex-snapshot
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
inferredcites →https://doi.org/10.1016/j.ccell.2016.07.015openalex-snapshot
DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias
inferredcites →https://doi.org/10.1016/j.cub.2018.05.058openalex-snapshot
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
inferredcites →https://doi.org/10.1016/j.mib.2008.09.006openalex-snapshot
Comparative genomics: the bacterial pan-genome
inferredcites →https://doi.org/10.1016/j.tig.2008.12.004openalex-snapshot
Estimating the size of the bacterial pan-genome
inferredcites →https://doi.org/10.1038/nature01262openalex-snapshot
Initial sequencing and comparative analysis of the mouse genome
inferredcites →https://doi.org/10.1038/nature10413openalex-snapshot
Mouse genomic variation and its effect on phenotypes and gene regulation
inferredcites →https://doi.org/10.1038/nbt.1596openalex-snapshot
Building the sequence map of the human pan-genome
inferredcites →https://doi.org/10.1038/ng.3257openalex-snapshot
Improved genome inference in the MHC using a population reference graph
inferredcites →https://doi.org/10.1038/ng.847openalex-snapshot
Subspecific origin and haplotype diversity in the laboratory mouse
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/s41586-018-0030-5openalex-snapshot
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
inferredcites →https://doi.org/10.1038/s41588-018-0223-8openalex-snapshot
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
inferredcites →https://doi.org/10.1073/pnas.0506758102openalex-snapshot
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”
inferredcites →https://doi.org/10.1093/bib/bbw089openalex-snapshot
Computational pan-genomics: status, promises and challenges
inferredcites →https://doi.org/10.1093/bioinformatics/bts217openalex-snapshot
GenomeRing: alignment visualization based on SuperGenome coordinates
inferredcites →https://doi.org/10.1093/bioinformatics/btu756openalex-snapshot
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
inferredcites →https://doi.org/10.1093/bioinformatics/btv603openalex-snapshot
Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btx170openalex-snapshot
EUPAN enables pan-genome studies of a large number of eukaryotic genomes
inferredcites →https://doi.org/10.1093/database/bar030openalex-snapshot
Ensembl BioMarts: a hub for data retrieval across taxonomic space
inferredcites →https://doi.org/10.1093/database/bau057openalex-snapshot
A novel multi-alignment pipeline for high-throughput sequencing data
inferredcites →https://doi.org/10.1099/mgen.0.000243openalex-snapshot
Pan-genome analyses of model fungal species
inferredcites →https://doi.org/10.1101/043430openalex-snapshot
Computational Pan-Genomics: Status, Promises and Challenges
inferredcites →https://doi.org/10.1101/gr.111310.110openalex-snapshot
Genetic analysis of complex traits in the emerging Collaborative Cross
inferredcites →https://doi.org/10.1101/gr.113886.110openalex-snapshot
Genetic analysis in the Collaborative Cross breeding population
inferredcites →https://doi.org/10.1101/gr.214155.116openalex-snapshot
Genome graphs and the evolution of genome inference
inferredcites →https://doi.org/10.1111/j.1601-183x.2009.00540.xopenalex-snapshot
High‐throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains
inferredcites →https://doi.org/10.1128/jvi.01034-19openalex-snapshot
Genetic Diversity of Collaborative Cross Mice Controls Viral Replication, Clinical Severity, and Brain Pathology Induced by Zika Virus Infection, Independently of Oas1b
inferredcites →https://doi.org/10.1145/2506583.2506645openalex-snapshot
Read Annotation Pipeline for High-Throughput Sequencing Data
inferredcites →https://doi.org/10.1186/1471-2156-5-7openalex-snapshot
A new set of BXD recombinant inbred lines from advanced intercross populations in mice
inferredcites →https://doi.org/10.1186/1471-2164-14-536openalex-snapshot
Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome
inferredcites →https://doi.org/10.1186/gb-2007-8-5-r71openalex-snapshot
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
inferredcites →https://doi.org/10.1186/gb-2007-8-6-r103openalex-snapshot
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
inferredcites →https://doi.org/10.1186/s12859-017-1678-9openalex-snapshot
Coordinates and intervals in graph-based reference genomes
inferredcites →https://doi.org/10.1186/s12864-016-2483-yopenalex-snapshot
Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice
inferredcites →https://doi.org/10.1186/s13015-018-0133-4openalex-snapshot
Coordinate systems for supergenomes
inferredcites →https://doi.org/10.1186/s13059-015-0587-3openalex-snapshot
Extending reference assembly models
inferredcites →https://doi.org/10.1371/journal.pbio.1000112openalex-snapshot
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
inferredcites →https://doi.org/10.1371/journal.pbio.1001091openalex-snapshot
Modernizing Reference Genome Assemblies
inferredcites →https://doi.org/10.1534/g3.111.001776openalex-snapshot
Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross
inferredcites →https://doi.org/10.1534/g3.111.001800openalex-snapshot
Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice
inferredcites →https://doi.org/10.1534/g3.119.400039openalex-snapshot
Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population
inferredcites →https://doi.org/10.1534/genetics.111.132597openalex-snapshot
High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
inferredcites →https://doi.org/10.1534/genetics.111.132639openalex-snapshot
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
inferredcites →https://doi.org/10.1534/genetics.114.161653openalex-snapshot
High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline
inferredcites →https://doi.org/10.1534/genetics.114.165886openalex-snapshot
RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations
inferredcites →https://doi.org/10.1534/genetics.116.197988openalex-snapshot
Structural Variation Shapes the Landscape of Recombination in Mouse
inferredcites →https://doi.org/10.1534/genetics.116.198838openalex-snapshot
Genomes of the Mouse Collaborative Cross
inferredcites →https://doi.org/10.3389/fgene.2019.00188openalex-snapshot
Identification of a Functional Non-coding Variant in the GABAA Receptor α2 Subunit of the C57BL/6J Mouse Reference Genome: Major Implications for Neuroscience Research

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41588-026-02604-zopenalex-snapshot
Non-Mendelian inheritance of DNA methylation patterns in mice
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