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 36

System / cell line: monkey ✕ Clear

Asthma investigators begin to reap the fruits of genomics.

PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

monkey models lung inbred cdna oligonucleotide northern
Longitudinal analysis of early stage sarcopenia in aging rhesus monkeys.

PMID 18983905 · PMC2693938 · Experimental gerontology · 2009 · 8 claims · 6 setups

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mtDNA deletion mutations induce ETS enzyme abnormalities (COXneg/SDHhyp phenotypes) linked to intra-fiber atrophy and fiber loss

rhesus vastus muscle single dual hematoxylin immunohistochemistry
The SARS-CoV-2 subgenome landscape and its novel regulatory features.

PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

Has reproduction · 84

Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

vero caco-2 sars-cov-2 ngs nanopore northern
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 8 setups

Has reproduction · 84

ChIRP-MS of SARS-CoV-2 RNA in infected Huh7.5 and Vero E6 cells identifies a comprehensive set of 309 host proteins that bind the viral RNA during active infection

huh7.5 vero schmidt lung chirp-ms chirp-rna-seq sds-page
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Developments in CORG: a gene-centric comparative genomics resource.

PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

upstream gene overlapping c-fos pairwise sequence comparative
G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

PMID 19846439 · PMC2788932 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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G-compass is a web-based tool that displays two corresponding genomic regions from human and another vertebrate species simultaneously in parallel, without requiring client installation.

genome hg18 blastz comparison
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

Has reproduction · 84

COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

animal same coexpression gene rnaseq-based microarray-based pathway
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups

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Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin

rabbit gtm66 myoc myocilin cdna sds-page transfection
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

genomic rmrp family non-finnish sequencing comparative microsatellite
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

hmlh1 same cos-7 hela ese splice minigene
Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

PMID 16968793 · PMC1865081 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 7 setups

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Homozygous StAR missense mutations Val187Met and Arg188Cys cause a novel, milder form of lipoid CAH ('non-classic lipoid CAH') presenting at 2-4 years of age rather than in infancy

blood cos-1 bacteria mitochondria sequencing cell-based recombinant
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

wallaby squirrel deer clouded overgo bac comparative
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

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The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

Asthma investigators begin to reap the fruits of genomics.

Longitudinal analysis of early stage sarcopenia in aging rhesus monkeys.

The SARS-CoV-2 subgenome landscape and its novel regulatory features.

Heterogeneous genomic molecular clocks in primates.

Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Developments in CORG: a gene-centric comparative genomics resource.

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

Getting positive about selection.

Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.