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 · 85
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.
PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups
Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.
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Has reproduction · 71
Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.
PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups
A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).
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Has reproduction · 61
lncEvo: automated identification and conservation study of long noncoding RNAs.
PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups
lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Has reproduction · 91
Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.
PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups
A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.
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Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.
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Has reproduction · 50
Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.
PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups
2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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Has reproduction · 76
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups
The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.
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Has reproduction · 79
Enhanced protein isoform characterization through long-read proteogenomics.
PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups
A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.
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Has reproduction · 87
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups
mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.
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Has reproduction · 92
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.
PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups
A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)
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Has reproduction · 23
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.
PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups
The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies
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Has reproduction · 50
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups
Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.
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Has reproduction · 59
Nucleosome regulatory dynamics in response to TGFβ.
PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups
SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.
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Has reproduction · 77
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.
PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 7 setups
HIV-1 recurrently integrates into genes that are proximal to super-enhancer (SE) genomic elements in both patients and in vitro T cell cultures.
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Has reproduction · 68
Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.
PMID 26618080 · PMC4655093 · PeerJ · 2015 · 6 claims · 6 setups
Phylogenetic analyses of full mitochondrial gene sets recover siphonophores as the first diverging clade within Hydroidolina, a well-supported Leptothecata–Filifera III–IV clade, and a second clade of Aplanulata–Capitata s.s.–Filifera I–II.
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Has reproduction · 72
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.
PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups
A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.
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Has reproduction · 78
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.
PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups
A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.