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).

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.

  mrc5 calu-3 nasopharyngeal sars-cov-2-infected bulk clinical term

• Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

  PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

  mg-thymoma colon exon fluorescent reverse

• Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.

  PMID 34871442 · PMC8682771 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 58

  RPS6 becomes progressively dephosphorylated on ribosomes as they translate along an mRNA CDS

  hela mef phospho-rps6-selective 80s immunoblotting

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 6 setups

  Has reproduction · 79

  CLSM6A, a CNN-based model set, predicts single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  clsm6a learned last-layer computational model-based propagation-based

• Computation of haplotypes on SNPs subsets: advantage of the "global method".

  PMID 17067372 · PMC1636337 · BMC genetics · 2006 · 6 claims · 4 setups

  Full-text index only

  The global method for subhaplotyping always yields a lower error rate than the direct method across datasets and SNP subset sizes

  gh1 apoe coalescent-model-simulated griv computational genetic

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

  tissues conditions randomized est-based mirna randomization

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

  PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

  Full-text index only

  Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

  normal genome-wide same omim microarray sage computational

• Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

  PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

  globally same computational publicly y-str snp supervised

• The stem cell population of the human colon crypt: analysis via methylation patterns.

  PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

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  A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

  colon computational simulated bisulfite coalescent posterior

• Fractional ridge regression: a fast, interpretable reparameterization of ridge regression.

  PMID 33252656 · PMC7702219 · GigaScience · 2020 · 7 claims · 2 setups

  Has reproduction · 84

  Ridge regression can be reparameterized in terms of the fraction γ between the L2-norms of the regularized and unregularized coefficient solutions (fractional ridge regression, FRR).

  synthetic brain benchmarking general

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 8 claims · 5 setups

  Has reproduction · 78

  A comprehensive genome-wide gene regulatory network resource for A. fumigatus (GRAsp) was constructed from 18 RNA-seq datasets using MERLIN-P-TFA.

  aspergillus fumigatus bulk computational chip-seq-based

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• Large-scale structural analysis of the core promoter in mammalian and plant genomes.

  PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.

  core-promoter arabidopsis rice computational adaptive linear

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

  PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

  Full-text index only

  A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

  α5+ computational k562 embryonic ligand tandem hierarchical

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational