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 27

System / cell line: predicted ✕ Assay: likelihood ✕ Clear

Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

Full-text index only

27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

blood-derived family brca1 direct multiplex boadicea
A computational screen for type I polyketide synthases in metagenomics shotgun data.

PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

Full-text index only

A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

Full-text index only

169 gene products in the Ciona genome were identified as putative GPCRs

ciona sequence molecular est
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

Full-text index only

466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

Full-text index only

A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

Full-text index only

Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

Full-text index only

The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

Has reproduction · 94

The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

casei orthogroups unclassified selected whole-genome comparative pairwise
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

Full-text index only

A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

PMID 18325125 · PMC2311284 · Virology journal · 2008 · 8 claims · 6 setups

Full-text index only

H3N2 was the prevalent influenza A strain in Denmark from 1999 to 2006, except the 2000–2001 season when H1N1 dominated

danish representative h3n2 influenza phylogenetic complete haemagglutination
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

paired lung tissue-pair pooled hiv-1 maximum statistical
Web-based resources for comparative genomics.

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

Full-text index only

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
A model-based approach to selection of tag SNPs.

PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

Full-text index only

The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

hapmap encode enr112 tag cross-validated entropy tagged
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

Full-text index only

CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

Full-text index only

Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

Full-text index only

Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

brasiliensis gp43 ratio codon-based mutational
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

Full-text index only

Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
PhylomeDB: a database for genome-wide collections of gene phylogenies.

PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

Full-text index only

PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

seed homologous trimmed homology sequence neighbor
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat

Experiments

Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

A computational screen for type I polyketide synthases in metagenomics shotgun data.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

Genome-wide survey of allele-specific splicing in humans.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Web-based resources for comparative genomics.

A model-based approach to selection of tag SNPs.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Prediction and assessment of splicing alterations: implications for clinical testing.

PhylomeDB: a database for genome-wide collections of gene phylogenies.

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.