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 21

System / cell line: transcripts ✕ Assay: conservation ✕ Clear

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

Full-text index only

Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
lncEvo: automated identification and conservation study of long noncoding RNAs.

PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

Has reproduction · 61

lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

chimp assembled pairwise raw bulk lncrna comparative
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding
Alternative splicing and bioinformatic analysis of human U12-type introns.

PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

Full-text index only

The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

hela hek293 genome jnk2 rt-pcr minigene bioinformatic
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

Full-text index only

MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

Full-text index only

3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

bovine cow coding blast-based ensembl gene
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

Full-text index only

Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

Full-text index only

A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

est gene worm fly blat-based transcription comparative
The dystrobrevin-binding protein 1 gene: features and networks.

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

Full-text index only

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
Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

Full-text index only

50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

genomic α-gal cos-7 transcripts pcr southern microsatellite
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

Full-text index only

ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

Full-text index only

Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

Full-text index only

A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

genome transcripts tissues proteins comparative taf250 cpg
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

Full-text index only

Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.

PMID 30303955 · PMC6179187 · PLoS neglected tropical diseases · 2018 · 7 claims · 6 setups

Has reproduction · 94

Rhodnius prolixus genome harbors four putative piwi orthologs (three piwi genes plus one ago3 ortholog), and core piRNA pathway components are expressed during previtellogenic oogenesis

rhodnius piwi paired-end parental rt-pcr
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups

Has reproduction · 73

Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course

dissected five anterior midguts rnaseq rt-qpcr

Experiments

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

lncEvo: automated identification and conservation study of long noncoding RNAs.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

Alternative splicing and bioinformatic analysis of human U12-type introns.

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

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

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.