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 490

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Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

asian fgf5 woolly savanna pcr structural blast
Helicobacter Pylori's plasticity zones are novel transposable elements.

PMID 19727398 · PMC2731543 · PloS one · 2009 · 8 claims · 8 setups

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Plasticity zones are a novel class of transposable elements (named TnPZs), flanked by direct repeats of 5'AAGAATG and inserted at multiple discrete chromosomal sites

pylori shimaa model mammalian pcr-based genome pcr
Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

PMID 19682372 · PMC2735741 · BMC evolutionary biology · 2009 · 7 claims · 7 setups

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Major NLRP genes duplicated before the divergence of mammals, with lineage-specific duplications in primates (NLRP7, NLRP11) and rodents (Nlrp1, Nlrp4, Nlrp9)

mammalian cattle oocyte-expressed genome phylogenetic syntenic functional
QUANT: a long-term multi-city commercial air sensor dataset for performance evaluation.

PMID 39168987 · PMC11339295 · Scientific data · 2024 · 7 claims · 7 setups

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The QUANT dataset is the most extensive open-access evaluation of commercial air quality sensor systems on a global scale to date

main wider maqs low-cost reference-grade meteorological
IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

Has reproduction · 30

Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

mapped simulated rna-seq ict1 computational benchmarking 3'-seq
TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

PMID 41494038 · PMC12788660 · PLoS computational biology · 2026 · 8 claims · 6 setups

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TEPEAK identifies and characterizes polymorphic TEs in populations without any prior TE sequence or loci information, using only a chromosome-level reference assembly.

horse pooled sequences consensus whole-genome insertion hierarchical
Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin.

PMID 41568968 · PMC12915303 · Applied and environmental microbiology · 2026 · 8 claims · 7 setups

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Cluster analysis of 18S (and similarly 16S) community data revealed three clusters corresponding to depth zones: photic zone, deep chlorophyll maximum (DCM), and aphotic zone

seawater sterivex-filtered extracted log-transformed metabarcoding hydrographic extraction
RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

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RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq
Cancer genome standards for long-read sequencing using cancer cell line mixtures.

PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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Long-read variant calling tools achieve recall rates comparable to short-read gold standards

colo829 same whole-genome short-read 5mc
ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.

PMID 42208531 · PMC13261933 · Stem cell reports · 2026 · 8 claims · 8 setups

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ZFHX4 is a super-enhancer-controlled transcription factor induced during mDAN specification

ipsc-derived smnpcs postmortem cut&tag bulk shrna
CTCF's loop-independent functions prevail over chromatin looping in the acute degradation system.

PMID 41191909 · PMC13107559 · Protein & cell · 2026 · 8 claims · 8 setups

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CTCF regulates Ppa2 and Zbtb39 expression through mechanisms independent of chromatin looping

ctcf-aid mescs rna-seq chip-seq western
Systems biology of gene regulation fulfills its promise.

PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

unspecified embryonic five yeast chip-chip chip-pet computational
Developments in CORG: a gene-centric comparative genomics resource.

PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

upstream gene overlapping c-fos pairwise sequence comparative
Transcriptome maps of general eukaryotic RNA degradation factors.

PMID 31135339 · PMC6570525 · eLife · 2019 · 8 claims · 3 setups

Has reproduction · 60

Transcriptome-wide PAR-CLIP binding profiles of 30 RNA degradation factors reveal their distribution across different RNA classes.

saccharomyces par-clip western crac
Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

sporadic tumour tumour-derived pcr loss semi-quantitative
Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

PMID 15175115 · PMC425576 · BMC genetics · 2004 · 6 claims · 3 setups

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The SLC22A1LS gene is paternally imprinted (i.e., only the maternal allele is expressed).

genomic pcr cdna pcr-sscp sequencing
Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

PMID 15719063 · PMC548953 · PLoS biology · 2005 · 8 claims · 3 setups

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Discovery-based genomics research can be integrated into an undergraduate curriculum, engaging large numbers of students in professional-quality research without compromising didactic training

drosophila genomic flp p-element molecular
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

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PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

genome chip-chip comparative
Analysis of DAX1 (NR0B1) and steroidogenic factor-1 (NR5A1) in children and adults with primary adrenal failure: ten years' experience.

PMID 16684822 · PMC1865080 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 3 setups

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DAX1 mutations are a relatively frequent cause of adrenal failure in 46,XY phenotypic boys with adrenal hypoplasia

genomic direct targeted
Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

patients unaffected sanger restriction

Experiments

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

Helicobacter Pylori's plasticity zones are novel transposable elements.

Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

QUANT: a long-term multi-city commercial air sensor dataset for performance evaluation.

IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin.

RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

Cancer genome standards for long-read sequencing using cancer cell line mixtures.

ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.

CTCF's loop-independent functions prevail over chromatin looping in the acute degradation system.

Systems biology of gene regulation fulfills its promise.

Developments in CORG: a gene-centric comparative genomics resource.

Transcriptome maps of general eukaryotic RNA degradation factors.

Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Analysis of DAX1 (NR0B1) and steroidogenic factor-1 (NR5A1) in children and adults with primary adrenal failure: ten years' experience.

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.