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 14

System / cell line: full ✕ Assay: repeat ✕ Clear

Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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The human genome encodes at least 71 kelch-repeat proteins

genome yeast kelch-repeat full-length blast blastp cross-referencing
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Molecular archeology of L1 insertions in the human genome.

PMID 12372140 · PMC134481 · Genome biology · 2002 · 8 claims · 4 setups

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TSDfinder, a new algorithm, refines RepeatMasker-identified L1 boundaries by locating poly(A) tails, TSDs, and inversion breakpoints

genome tsd 50-nt full-length repeat sequence repeat-content
The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

peripheral brca1 same simulated fluorescent cox weighted
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

Has reproduction · 57

ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

arabidopsis pacbio randomly illumina pacbio nanopore
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

Has reproduction · 90

Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

cephalopholis analysis next-generation pacbio ont
Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

Has reproduction · 85

First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

liver-derived muscle heart pooled 10x oxford hi-c
PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

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All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

vcjd scjd scottish controls pcr-rflp full chi-squared
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

bombyx whole-genome snp novo
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

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COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

cancer tumour manual semi-automated candidate
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp

Experiments

Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Molecular archeology of L1 insertions in the human genome.

The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

'Genome design' model and multicellular complexity: golden middle.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.