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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Has reproduction · 94
A Deluge of Complex Repeats: The Solanum Genome.
PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups
~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements
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Has reproduction · 81
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.
PMID 32681306 · PMC7599172 · Current genetics · 2020 · 7 claims · 7 setups
A machine-learning (Random Forest) approach trained on transposon insertion features can predict gene essentiality genome-wide in yeast species
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Has reproduction · 80
Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.
PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups
α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination
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Has reproduction · 80
Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.
PMID 38909031 · PMC11193758 · Scientific data · 2024 · 7 claims · 8 setups
A chromosome-level genome of P. ornatus was assembled spanning 2.65 Gb with contig N50 of 51.05 Mb, with 99.11% of sequence anchored to 73 chromosomes
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Has reproduction · 62
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.
PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 8 claims · 4 setups
MultiDeNA pipeline combines PWM, diPWM, BaMM and InMoDe models to train, evaluate, threshold, and classify ChIP-seq peaks for TFBS structural heterogeneity
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Has reproduction · 81
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.
PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups
USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression
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Has reproduction · 71
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.
PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups
DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue
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Has reproduction · 77
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups
spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.
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Has reproduction · 71
Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.
PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 7 setups
R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', Wolbachia)
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Has reproduction · 81
Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.
PMID 41860215 · PMC13101498 · Applied and environmental microbiology · 2026 · 7 claims · 6 setups
Offshore Lake Michigan bacterioplankton show higher expression of DOM, N, and P acquisition/transporter genes than nearshore bacterioplankton
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Has reproduction · 82
Landscape of allele-specific transcription factor binding in the human genome.
PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups
A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.
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Has reproduction · 71
Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.
PMID 35338551 · PMC9241371 · Plant biotechnology journal · 2022 · 7 claims · 8 setups
Almost all centromeric sequences and 45S ribosomal DNA repeat arrays are absent from the MorexV3 pseudomolecules
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Has reproduction · 67
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.
PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups
Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines
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Has reproduction · 95
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups
P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)
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Has reproduction · 63
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.
PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups
Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA
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Has reproduction · 59
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.
PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups
Short-term stress and long-term adaptations share common metabolic pathways
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Has reproduction · 61
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
PMID 35584008 · PMC9465075 · Microbial genomics · 2022 · 8 claims · 7 setups
RegulonDB 11.0 is a radical upgrade offering access to more than 2000 high-throughput datasets on transcriptional regulation in E. coli K-12.
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Has reproduction · 93
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.
PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups
Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species
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Has reproduction
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.
PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups
Retrotransposons mobilize via a copy-and-paste mechanism involving transcription of an RNA intermediate and reinsertion as a cDNA copy, unlike DNA transposons which cut-and-paste.
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Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.