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).

• DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

  PMID 41055236 · PMC12505516 · RNA biology · 2025 · 7 claims · 5 setups

  Has reproduction · 100

  DeepRNA-Reg, a recurrent neural network-based algorithm, predicts differentially enriched sites in paired HITS-CLIP datasets and outperforms dCLIP 1.7.

  dgcr8 mir-23 deeprna-reg ago2 gene flow

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

  PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups

  Full-text index only

  A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight

  recombinant target coli x-ray differential analytical

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae.

  PMID 37240377 · PMC10218906 · International journal of molecular sciences · 2023 · 7 claims · 8 setups

  Full-text index only

  HyperTRIBE was successfully established in S. cerevisiae by fusing an RBP to the hyper-active catalytic domain of human ADAR2 (E488Q), marking target transcripts with A-to-G editing events detectable by high-throughput sequencing

  cerevisiae khd1 wild-type bfr1-heterozygous hypertribe western meme

• The role of medical structural genomics in discovering new drugs for infectious diseases.

  PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

  bacteria plasmodium candidate burkholderia high-throughput animal compound-target

• 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

• MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

  PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

  Full-text index only

  High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

  high ovarian mir-29a mirna unsupervised significance

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

  Full-text index only

  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

  camellia sinensis small genome mirna

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups

  Has reproduction · 90

  Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.

  luad differentially bulk mirna-seq microarray

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

  PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups

  Has reproduction · 90

  Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.

  global ndama target illumina whole-genome array genotype

• Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

  PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

  cerevisiae cycle reanalysis statistical optimal

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 7 setups

  Has reproduction · 95

  Mineralocorticoid (DOCA) effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule (DCT2) cells.

  kidney doca-salt serum heart single-nucleus bulk physiology

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 5 setups

  Has reproduction · 100

  A network-based approach integrating RNA-seq and cell-shape imaging data identifies data-derived signaling networks specific to cell-shape regulation in breast cancer.

  breast representative kinases bulk high-throughput immunofluorescence

• Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

  PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.

  top100h decoys i-tasser non-homologous statistical rdcc comparative

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

  Full-text index only

  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Next-generation high-density self-assembling functional protein arrays.

  PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

  Full-text index only

  A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

  test high-density amine-coated array picogreen anti-gst fluorescently

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 7 claims · 5 setups

  Has reproduction · 75

  Short- and long-term HL responses in Arabidopsis leaves are driven by distinct transcriptional programs, with duration of HL treatment as the primary factor separating transcriptomic clusters.

  arabidopsis bulk hierarchical correlation