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 39

System / cell line: shared ✕ Assay: comparative ✕ Clear

Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.

PMID 36345342 · PMC9636548 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 100

Comparative phosphoproteomics of hyperammonemic myotubes and exercise-model muscle identifies shared enriched pathways: PKA, calcium signaling, MAPK signaling, and protein homeostasis.

c2c12 hyperammonemic phosphoproteomics immunoblot comparative
POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.

PMID 15601531 · PMC3525001 · Human genomics · 2003 · 8 claims · 4 setups

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The MGR algorithm applied to human, mouse, cat and cattle comparative maps can impute an ancestral mammalian genome composed of conserved segments.

cat mammalian genome grimm-synteny comparative
More breast cancer genes?

PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

tumours five independent ataxia-telangiectasia comparative haplotype linkage
A comparative analysis of blastoid models through single-cell transcriptomics.

PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

Has reproduction · 60

EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov
The post-genomic era for a select few.

PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

takifugu physcomitrella coli vibrio comparative genetic dna-microarray
Comparative genomics of emerging human ehrlichiosis agents.

PMID 16482227 · PMC1366493 · PLoS genetics · 2006 · 8 claims · 5 setups

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Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins (OMP-1/P44/Msp2 family) facilitating antigenic variation

phagocytophilum representative concatenated rickettsiales whole-genome comparative phylogenetic
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

PMID 19781061 · PMC2768977 · Genome biology · 2009 · 8 claims · 7 setups

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The 027 genomes (CD196 and R20291) contain 234 additional genes compared to strain 630, spread across at least 50 regions of genetic difference, including a phage island, transposon genes, two-component response regulators, drug resistance genes and transporters

difficile toxin whole-genome toxin paloc
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups

Has reproduction · 89

Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.

wolbachia wbm differentially rna-seq comparative co-expression
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

Has reproduction · 84

The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus

mamiellales ostreococcus tauri shared comparative orthology synteny
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

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There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
Widespread ultraconservation divergence in primates.

PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

hg18 genome genes computed comparative snp gene
Protozoan genomics for drug discovery.

PMID 16151400 · PMC7096809 · Nature biotechnology · 2005 · 8 claims · 3 setups

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Complete genome sequences of five protozoan parasites (Theileria parva, T. annulata, Leishmania major, Trypanosoma brucei, T. cruzi) were reported, enabling comparative genomics.

theileria leishmania plasmodium whole-genome comparative
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
Of rats and men.

PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

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The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

rattus cftr fugu transgenic whole-genome comparative genome

Experiments

Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.

POCUS: mining genomic sequence annotation to predict disease genes.

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.

More breast cancer genes?

A comparative analysis of blastoid models through single-cell transcriptomics.

The post-genomic era for a select few.

Comparative genomics of emerging human ehrlichiosis agents.

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Comparative genomics search for losses of long-established genes on the human lineage.

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

Patterns of evolutionary constraints on genes in humans.

Widespread ultraconservation divergence in primates.

Protozoan genomics for drug discovery.

Bias of selection on human copy-number variants.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

Of rats and men.