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 16

System / cell line: contigs ✕ Assay: poly ✕ Clear

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
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

Has reproduction · 66

S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

Has reproduction · 67

Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

anas duck million random illumina read novo
ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.

PMID 41626876 · PMC12862641 · Genome biology and evolution · 2026 · 7 claims · 8 setups

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High-quality chromosome-level reference genomes were assembled for four previously unsequenced Culex species

whole-organism assembled annotated individual pacbio hi-c poly
De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

PMID 24586345 · PMC3929608 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 59

A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.

calanus pooled raw combined bulk extraction read
The genome sequence of True's beaked whale, Mesoplodon mirus True, 1913 (Artiodactyla: Ziphiidae).

PMID 41625987 · PMC12853023 · Wellcome open research · 2026 · 8 claims · 8 setups

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A genome assembly is presented for an individual female Mesoplodon mirus (True's beaked whale)

mesoplodon pacbio hi-c sequencing
A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

simulated same repeat whole-genome genome
The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.

PMID 41625985 · PMC12859430 · Wellcome open research · 2026 · 8 claims · 8 setups

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The Phakellia ventilabrum genome assembly spans 211.92 Mb with 99.97-99.98% scaffolded into 25 chromosomal pseudomolecules

phakellia pacbio genome microbial pacbio hi-c sequencing
The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.

PMID 41913758 · PMC13033139 · Wellcome open research · 2026 · 6 claims · 7 setups

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Genome assembly of Anodontia alba (buttercup lucine) with total length 1,862.85 Mb, 99.28% scaffolded into 18 chromosomal pseudomolecules

anodontia microbial pacbio hi-c sequencing
The genome sequence of the chocolate mining bee, Andrena scotica Perkins, 1916 (Hymenoptera: Andrenidae).

PMID 41960580 · PMC13058575 · Wellcome open research · 2026 · 7 claims · 8 setups

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A haploid chromosome-level genome assembly was generated for a male Andrena scotica (chocolate mining bee) specimen.

andrena pacbio hi-c rna-seq
The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).

PMID 41993727 · PMC13080331 · Wellcome open research · 2026 · 8 claims · 8 setups

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The Lamellibrachia columna genome assembly spans 879.73 Mb, with 99.96% scaffolded into 15 chromosomal pseudomolecules

lamellibrachia columna filtered assembled pacbio hi-c sequencing
The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.

PMID 42232316 · PMC13224822 · Wellcome open research · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly was produced for the sponge Rhopaloeides odorabile using the Tree of Life pipeline

rhopaloeides odorabile-associated odorabile recovered pacbio hi-c sequencing
The genome sequence of the Scarce Hook-tip, Sabra harpagula (Esper, 1786) (Lepidoptera: Drepanidae).

PMID 42255361 · PMC13234554 · Wellcome open research · 2026 · 8 claims · 8 setups

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The Sabra harpagula genome assembly has a total length of 377.24 Mb

sabra pacbio hi-c sequencing
Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups

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L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.

genome database l1-td ncbi genome-wide blast pairwise
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.

PMID 42116832 · PMC13157608 · Wellcome open research · 2026 · 7 claims · 8 setups

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Aurelia sp. 4 chromosomal genome assembly has a total length of 462.10 Mb with 99.99% of sequence scaffolded into 21 chromosomal pseudomolecules

aurelia microbial pacbio hi-c rna-seq

Experiments

Molecular archeology of L1 insertions in the human genome.

RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.

De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

The genome sequence of True's beaked whale, Mesoplodon mirus True, 1913 (Artiodactyla: Ziphiidae).

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.

The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.

The genome sequence of the chocolate mining bee, Andrena scotica Perkins, 1916 (Hymenoptera: Andrenidae).

The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).

The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.

The genome sequence of the Scarce Hook-tip, Sabra harpagula (Esper, 1786) (Lepidoptera: Drepanidae).

Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

Bases and spaces: resources on the web for accessing the draft human genome.

The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.