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).

• Wiggle-predicting functionally flexible regions from primary sequence.

  PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

  Full-text index only

  A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

  hiv bovine calmodulin nonredundant gaussian gnm support

• Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

  PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

  hepg2 computational same bead-based integer comparative

• Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models.

  PMID 36536288 · PMC9762025 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 4 setups

  Has reproduction · 93

  Structural equation models can decompose the total genetic effect on a production trait into a direct host genetic effect and an indirect effect exerted through the microbiota.

  rabbits cecal host bayesian 16s snp

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.

  bca meta-geo tcga-blca tcga bulk rna-seq somatic

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

  Full-text index only

  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups

  Has reproduction · 32

  A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).

  tcga-luad geo bulk expression methylation

• Cis sequence effects on gene expression.

  PMID 17727713 · PMC2077339 · BMC genomics · 2007 · 6 claims · 4 setups

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  Approximately one in four genes (8 of 30, 26.7%) exhibit statistically significant cis sequence effects on gene expression in this study, consistent with a literature-wide weighted average of 26.2%

  lymphoblastoid genomic oligonucleotide gene candidate snp

• Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer.

  PMID 18690643 · PMC3970323 · Proteomics · 2008 · 8 claims · 5 setups

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  N-linked glycan biosynthetic enzyme transcript profiles in normal mouse and human ovarian tissue are similar, indicating species conservation

  ovarian qrt-pcr lectin con

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

  PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 88

  Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.

  hm450k seven annotated illumina beadarray model-based

• 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

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

  Full-text index only

  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• The genomic analysis of lactic acidosis and acidosis response in human cancers.

  PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

  mammary hmec gene breast gene real-time bayesian

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

  Full-text index only

  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  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.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

  PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 7 claims · 6 setups

  Has reproduction · 48

  The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.

  tcga-coad ncbi-geo colon c57bl bulk gene immune

• miR-4478 Accelerates Nucleus Pulposus Cells Apoptosis Induced by Oxidative Stress by Targeting MTH1.

  PMID 36130054 · PMC9897280 · Spine · 2023 · 7 claims · 8 setups

  Has reproduction · 100

  miR-4478 is upregulated in nucleus pulposus tissues from IVDD patients and is degeneration-degree-associated

  annulus tissues npcs mirna quantitative fluorescence

• Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.

  PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups

  Has reproduction · 59

  Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort

  pancreatic rna-seq liver tumor bulk machine multi-label

• Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.

  PMID 37614318 · PMC10442647 · Frontiers in pharmacology · 2023 · 8 claims · 8 setups

  Has reproduction · 87

  A six-lncRNA prognostic signature (LINC02428, LINC02163, AC008549.1, AC115619.1, CASC9, LINC02362) predicts overall survival in HCC patients

  hcc tcga paired snu-449 lncrna sequencing univariate