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).

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

  PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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  An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

  lung hpl1d rrna external pcr rt-pcr quantitative

• Retentive Network promotes efficient RNA language modeling of long sequences.

  PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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  RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

  million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna

• Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium leading to nanophthalmos.

  PMID 41746734 · PMC13043084 · JCI insight · 2026 · 8 claims · 8 setups

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  The dG-MYRF C-terminal frameshift variant undergoes normal homotrimerization, cleavage, and nuclear localization but shows reduced steady-state levels of the C-terminal cleavage product and decreased transcriptional activation of target genes.

  arpe-19 myrf rpe e17.5 immunofluorescence computational cycloheximide

• Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).

  PMID 41824659 · PMC13089509 · Plant physiology · 2026 · 7 claims · 8 setups

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  A near-complete telomere-to-telomere genome assembly of E. cheiri was generated (244.33 Mb, 6 chromosomes)

  cheiri brassicaceae illumina pacbio hi-c

• Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

  PMID 41842971 · PMC13132380 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  PRC2i/EZH2i alone or combined with AR inhibitors induce diverse cell state programs (CSPs) that increase tumor cell invasion, metastasis, and drug resistance despite only modest suppression of tumor growth.

  lncap pca pdx clinical viability tumor ic50

• An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.

  PMID 41934284 · PMC13232507 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  A high-quality chromosome-scale genome assembly and annotation of S. verrucosum accession CPC54 was produced, improving on prior assemblies

  verrucosum pacbio oxford hi-c

• Germline sequence variation within the ribosomal DNA is associated with human complex traits.

  PMID 41966685 · PMC13261666 · Cell genomics · 2026 · 8 claims · 5 setups

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  Germline rDNA sequence variant frequencies associate with multiple human complex traits in the UK Biobank, independently of rDNA copy number

  biobank genomes synthetic 28s whole-genome short-read genome-wide

• Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

  PMID 42062553 · PMC13259927 · Nature methods · 2026 · 8 claims · 6 setups

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  Xenium data show strong consistency across patients and technical replicates, with little technical variation between platforms

  ffpe matched xenium xenium single-nucleus immunohistochemistry

• TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.

  PMID 42098613 · PMC13196189 · BMC genomic data · 2026 · 6 claims · 8 setups

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  Developed a unified, evidence-based annotation pipeline integrating RNA-seq and homology data applied to six Trichoderma species, producing 'TrichoBase', a standardized genomic resource

  trichoderma fungal genome average repeat

• SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

  PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

  elegans expressed soluble crystallized recombinant solubility purification

• iRefIndex: a consolidated protein interaction database with provenance.

  PMID 18823568 · PMC2573892 · BMC bioinformatics · 2008 · 6 claims · 3 setups

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  A reproducible key (ROG) for each protein interactor and a corresponding key (RIG) for each interaction record can be generated by anyone using only primary sequence, taxonomy identifier, and the SHA-1 algorithm (SEGUID).

  sequence nine interactor seguid parsing mapping

• Bioinformatic Analysis of Differentially Expressed Long Non-Coding RNAs in Skeletal Muscle Following Aerobic and Resistance Exercise.

  PMID 41595529 · PMC12840796 · Genes · 2026 · 8 claims · 3 setups

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  Distinct lncRNA expression profiles exist in skeletal muscle between acute AE and RE, suggesting modality-specific lncRNA roles in exercise adaptation.

  skeletal aggregated bulk database

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated

• SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

  PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

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  SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

  genomic ncbi laboratory primer genomic

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction · 94

  ~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements

  tuberosum orthologous novo synteny orthologous

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative