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 45

System / cell line: alternative ✕ Assay: sequence ✕ Clear

Mitochondrial diversity within modern human populations.

PMID 17439969 · PMC1888801 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

Modern humans show extremely low divergence from the mitochondrial consensus sequence, differing on average by only 21.6 nucleotide sites

full-length mitochondrial mtdna additional sequence site-by-site regional
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

Full-text index only

Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Finding signals that regulate alternative splicing in the post-genomic era.

PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

Full-text index only

Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

intron-containing genome brain-specific cell-free computational comparative selex
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

Full-text index only

Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
Integrating alternative splicing detection into gene prediction.

PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

Full-text index only

An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

arabidopsis araset thaliana transcript-to-genome initio comparative
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

Full-text index only

Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
BIPASS: BioInformatics Pipeline Alternative Splicing Services.

PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

Full-text index only

BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

transcript aligned pre-computed user-submitted sequence alternative database
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

Full-text index only

Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

Full-text index only

PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

Full-text index only

Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
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
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

Full-text index only

Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

Full-text index only

GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr
Visualizing the genome: techniques for presenting human genome data and annotations.

PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

Full-text index only

Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation
SVC: structured visualization of evolutionary sequence conservation.

PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

Full-text index only

SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

orthologous exonic tblastx blastn sliding-window
In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

Full-text index only

Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription
The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

PMID 11178241 · PMC138858 · Genome biology · 2000 · 8 claims · 4 setups

Full-text index only

The V. cholerae O1 (El Tor) genome consists of two chromosomes with asymmetrically distributed gene functions

vibrio whole-genome microarray expression
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

Full-text index only

The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
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

Has reproduction · 96

gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

avian comparative correlation robustness
High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

PMID 16086836 · PMC1190179 · BMC medical genetics · 2005 · 8 claims · 6 setups

Full-text index only

IVS2-2A>G allele frequency does not differ significantly between hearing-impaired cases and controls among Hispanics and Caucasians (p=0.45)

genomic mitochondrial slc26a5 pcr sequence splice

Experiments

Mitochondrial diversity within modern human populations.

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Finding signals that regulate alternative splicing in the post-genomic era.

Does distance matter? Variations in alternative 3' splicing regulation.

Integrating alternative splicing detection into gene prediction.

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

BIPASS: BioInformatics Pipeline Alternative Splicing Services.

Genome informatics: taming the avalanche of genomic data.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Splicing bioinformatics to biology.

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

Mutation analysis of the MDM4 gene in German breast cancer patients.

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

Visualizing the genome: techniques for presenting human genome data and annotations.

SVC: structured visualization of evolutionary sequence conservation.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

Twin peaks: the draft human genome sequence.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.