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).
-
Full-text index only
Genome-wide identification of human functional DNA using a neutral indel model.
PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups
A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently
-
Full-text index only
Genome structure in the vole bacillus, Mycobacterium microti, a member of the Mycobacterium tuberculosis complex with a low virulence for humans.
PMID 15133113 · PMC2964484 · Microbiology (Reading, England) · 2004 · 8 claims · 3 setups
Compared to M. tuberculosis H37Rv, 13 distinct deleted regions were identified across 12 M. microti strains, including RD1–RD10 also missing in M. bovis BCG.
-
Full-text index only
Genome informatics: taming the avalanche of genomic data.
PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups
Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown
-
Full-text index only
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.
PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups
Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters
-
Full-text index only
Patterns and rates of intron divergence between humans and chimpanzees.
PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups
Intron divergence (Ki) is strongly positively correlated with intron length
-
Full-text index only
Interpretation of genomic data: questions and answers.
PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups
The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.
-
Full-text index only
Comparing whole genomes using DNA microarrays.
PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups
DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.
-
Full-text index only
Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.
PMID 18269759 · PMC2291036 · BMC evolutionary biology · 2008 · 8 claims · 5 setups
The mouse Abp gene repertoire is twice as large as previously reported, comprising 30 Abpa and 34 Abpbg genes/pseudogenes
-
Has reproduction · 50
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups
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.
-
Full-text index only
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups
The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.
-
Full-text index only
MODBASE: a database of annotated comparative protein structure models and associated resources.
PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups
MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure
-
Has reproduction · 60
A comparative analysis of blastoid models through single-cell transcriptomics.
PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups
EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.
-
Has reproduction · 84
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.
PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups
The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus
-
Has reproduction · 67
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.
PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups
Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies
-
Has reproduction · 56
Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.
PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups
The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty
-
Has reproduction · 96
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.
PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups
gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory
-
Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
-
Full-text index only
Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.
PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups
Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.
-
Full-text index only
Protein length in eukaryotic and prokaryotic proteomes.
PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups
Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families
-
Full-text index only
Comprehensive splice-site analysis using comparative genomics.
PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups
Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.