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 194

System / cell line: conserved ✕ Clear

Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
An analysis of human microRNA and disease associations.

PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

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MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

literature-derived diseases mirnas mirna literature bipartite mirna
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups

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18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.

genitalium clinical selected 246-bp bioinformatics pcr plasmid
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

PMID 18515835 · PMC2475620 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Yeast Med2, Med3/Pgd1 and Med5/Nut1 (Tail module) are homologs of human Med29, Med27 and Med24, respectively

eukaryotic med genuine psi-blast mafft pssm-based
Genomic organization of zebrafish microRNAs.

PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

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Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

zebrafish candidate hairpin blast secondary comparative
Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

PMID 18312668 · PMC2275272 · BMC genomics · 2008 · 8 claims · 5 setups

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The conventional TCR loci (TRA/D, TRB, TRG) in opossum are highly conserved in organization and complexity with those of eutherian mammals.

monodelphis 23-day-old trav trbv comparative rt-pcr phylogenetic
The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

neisseria streptococcus coli vibrio reverse pan-genomic comparative
Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

patients unaffected sanger restriction
VISTA Enhancer Browser--a database of tissue-specific human enhancers.

PMID 17130149 · PMC1716724 · Nucleic acids research · 2007 · 8 claims · 2 setups

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Comparative genome analysis can identify candidate human enhancer elements whose tissue-specific in vivo activity can then be experimentally validated in transgenic mice.

genomic genome transgenic comparative
Mice and more.

PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

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A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

cftr ciona embryonic chromosome comparative genome bac-based
VectorBase: a home for invertebrate vectors of human pathogens.

PMID 17145709 · PMC1751530 · Nucleic acids research · 2007 · 8 claims · 5 setups

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VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens

anopheles aedes translated automated first-pass
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

Has reproduction · 70

Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

ihh additional chd7 sanger targeted rt-pcr
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

single glabripennis amino whole-genome gene busco
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups

Has reproduction · 91

De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads

whole-body cultripes expression-filtered bulk novo transcriptome
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

Has reproduction · 91

SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

deep co-assembled surf_17 surf_5 whole-genome novo 16s
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

Has reproduction · 72

Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

holacanthella duospinosa genome transcriptome phylogenomics
The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 8 claims · 8 setups

Has reproduction · 90

Phage Mimer is the first described lytic ssDNA (Microviridae) phage targeting Pectobacterium

phage conserved gpg cscl-gradient-purified whole-genome comparative intergenomic

Experiments

Comparative genomic analysis of prion genes.

An analysis of human microRNA and disease associations.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

The dystrobrevin-binding protein 1 gene: features and networks.

Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

Genomic organization of zebrafish microRNAs.

Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Mice and more.

VectorBase: a home for invertebrate vectors of human pathogens.

Web-based resources for comparative genomics.

Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.