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).
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Advancing codon language modeling with synonymous codon constrained masking.
PMID 41736545 · PMC12956333 · Nucleic acids research · 2026 · 8 claims · 7 setups
SynCodonLM introduces synonymous codon-constrained masking, restricting masked-codon prediction to only synonymous codon options via logit masking before softmax
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Has reproduction · 88
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.
PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups
C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.
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Has reproduction · 90
Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs.
PMID 32515737 · PMC7282809 · eLife · 2020 · 8 claims · 3 setups
Both cohesin conversion and Scc2-dependent de novo loading mechanisms generate cohesion in S. cerevisiae, each requiring a distinct set of replisome-associated proteins.
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Has reproduction · 86
Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.
PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 8 claims · 8 setups
HPVN24 is E. coli APEC serotype O78:H9, sequence type ST23
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Has reproduction
Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.
PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups
SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates
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Has reproduction · 57
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
ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads
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Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.
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Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature.
PMID 35300606 · PMC8932150 · BMC plant biology · 2022 · 7 claims · 8 setups
Combined SGS+TGS full-length transcriptome sequencing generated 41,016 high-quality potato transcripts, including 15,189 putative new transcripts
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A chromosome-level reference genome and pangenome for barn swallow population genomics.
PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups
A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data
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The vertebrate genome annotation (Vega) database.
PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups
Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.