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).

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

  PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

  Has reproduction · 95

  transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

  piper assembled longum predicted rna-seq novo transcriptome

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

  PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

  Full-text index only

  HERV expression differs between primary and metastatic cutaneous melanoma

  tcga-skcm metastatic normal selected bulk consensus orf

• 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

  Has reproduction · 81

  A machine-learning (Random Forest) approach trained on transposon insertion features can predict gene essentiality genome-wide in yeast species

  saccharomyces schizosaccharomyces candida computational transposon random

• 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

  Has reproduction · 50

  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

  flower roots analysis parental high-throughput quantitative pcr

• 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

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Bayesian prediction of RNA translation from ribosome profiling.

  PMID 28126919 · PMC5389577 · Nucleic acids research · 2017 · 8 claims · 4 setups

  Has reproduction · 62

  Rp-Bp is an unsupervised Bayesian approach that uses a two-component 'high-low-low' mixture model to predict translated ORFs from ribosome profiles

  hek293 ribo-seq ribosome proteomics quantitative

• Enhanced protein isoform characterization through long-read proteogenomics.

  PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups

  Has reproduction · 79

  A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization

  jurkat jurkat-derived long-read transcript orf

• 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

  Full-text index only

  Combined SGS+TGS full-length transcriptome sequencing generated 41,016 high-quality potato transcripts, including 15,189 putative new transcripts

  potato pacbio illumina physiological

• A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.

  PMID 41513996 · PMC12872441 · Nature microbiology · 2026 · 8 claims · 7 setups

  Full-text index only

  The global cellular tRNA pool is not substantially altered during APMV infection, despite the virus encoding its own tRNA genes.

  acanthamoeba apmv rna-seq ribo-seq mim-trna-seq

• Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR.

  PMID 41771837 · PMC12953643 · Signal transduction and targeted therapy · 2026 · 8 claims · 8 setups

  Full-text index only

  KLF15 transcriptional activity shows the most significant change among TFs in pathological cardiomyocytes during progressive hypertrophic remodeling, reflecting less effective repression of disease-associated genes.

  ventricular heart cardiomyocytes cardiomyocyte single-cell rt-qpcr bulk

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups

  Has reproduction · 87

  A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)

  euglena gracilis consensus bulk in-house novo

• ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

  PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

  Full-text index only

  ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

  sequences parsed bacillus anopheles large-scale sequence orf

• Homeodomain protein Sxi1α independently controls cell-cell fusion and gene expression during sexual reproduction in Cryptococcus deneoformans.

  PMID 41818280 · PMC13001979 · PLoS genetics · 2026 · 8 claims · 8 setups

  Full-text index only

  Sxi1α has a previously unrecognized inhibitory role in same-sex (α-α) cell-cell fusion during unisexual reproduction

  sxi1α cerevisiae deneoformans sxi1αδ alphafold3 yeast crispr