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 19

System / cell line: alignment ✕ Assay: exact ✕ Clear

Using ESTs to improve the accuracy of de novo gene prediction.

PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

elegans genome chromosome novo gene partial
Versatile and open software for comparing large genomes.

PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Designating eukaryotic orthology via processed transcription units.

PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

ortholog blat exon-intron blast-based
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

nasal genomic ib3-1 western pcr fisher's
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
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
FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

PMID 42102720 · PMC13201080 · GigaScience · 2026 · 8 claims · 6 setups

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A pipeline combining IDF transformation, sparse random projection (SRP), and NNDescent (the FEDRANN strategy) enables accurate overlap detection across diverse long-read datasets

real same chromosome genome overlap exact simulated
Ensembl 2006.

PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

cow ensembl snps genome gene whole-genome pairwise
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

genome sequences automatic manual sequence
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Ecotype diversity and conversion in Photobacterium profundum strains.

PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 77

No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

photobacterium profundum predicted orthologous whole-genome pulsed-field comparative
RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

PMID 41222189 · PMC12857227 · GigaScience · 2026 · 8 claims · 8 setups

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RNA-SeqEZPZ is the first open-source tool offering a point-and-click interface with interactive plots, spanning raw FASTQ reads through differential gene and pathway analysis.

generic paired-end aligned gene bulk adapter read
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

Has reproduction · 91

An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

gossypium longicalyx nine diploids whole-genome wgs read
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based

Experiments

Using ESTs to improve the accuracy of de novo gene prediction.

Versatile and open software for comparing large genomes.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Designating eukaryotic orthology via processed transcription units.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

Predicting failure rate of PCR in large genomes.

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

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

Ensembl 2006.

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Ecotype diversity and conversion in Photobacterium profundum strains.

RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

Database resources of the National Center for Biotechnology Information.

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.