Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: paralogous ✕ Assay: genomic ✕ Clear

Comparative genomics of vertebrate Fox cluster loci.

PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups

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Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci

chimp sequences genomic blast molecular comparative
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic
From microarrays to genome duplications.

PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

tumor cancer plated saccharomyces comparative nonsense-mediated cell-based
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

genome genomic chromosome randomization
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

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Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

zebrafish sequence comparative cross-validation
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

Has reproduction · 93

Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Integration of cytogenetic landmarks into the draft sequence of the human genome.

PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

large-insert bac ml-2 dgap012 fluorescence sts array
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Comparative genomics of vertebrate Fox cluster loci.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

From microarrays to genome duplications.

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

Comparative genomics and understanding of microbial biology.

Integration of cytogenetic landmarks into the draft sequence of the human genome.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.