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).

Publications 1.3k Datasets 392.5k Experiments 42

System / cell line: biological ✕ Assay: prediction ✕ Clear

Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

Has reproduction · 88

Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

daf-2 wild-type same dauer developmental lifespan brood
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Optimized mixed Markov models for motif identification.

PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

Full-text index only

OMiMa can incorporate more than NNSplice's pairwise dependencies

simulated regulatory splice biological motif pairwise
Reconstruction of human protein interolog network using evolutionary conserved network.

PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

Full-text index only

A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

ppi sequences interaction predicted interolog orthology quasi-clique
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

Has reproduction · 83

170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

afb1 breast training candidate computational bulk weighted
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

Full-text index only

P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

sequences orthomcl yeast orthomcl jaccard phylogenetic
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

Full-text index only

The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
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
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
Systems biology in human health and disease.

PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups

Full-text index only

High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.

her2 biological prostate model quantitative combinatorial genome-wide
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 83

188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

blood degs peripheral hub microarray kegg cibersort
Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.

PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups

Has reproduction · 81

Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells

h460 nsclc swath-ms western machine
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 76

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.

pyronema confluens fungal whole-genome k-mer rna-seq
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

Full-text index only

159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

pooled sequenced analysis predicted small bioinformatic qrt-pcr
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

Has reproduction · 50

829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

sycon ciliatum sponges differential go-term genome
Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

PMID 38883333 · PMC11179850 · Horticulture research · 2024 · 7 claims · 7 setups

Full-text index only

A haplotype-resolved telomere-to-telomere (T2T) genome of plum (P. salicina cv. 'Fengtangli') was assembled into two gap-free haplotypes of 251.25 and 251.29 Mb.

plum four appm genes pacbio hi-c k-mer
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

Full-text index only

Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

Full-text index only

Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

peripheral patients mody young-onset pcr microsatellite variant

Experiments

Inferring combinatorial regulation of transcription in silico.

Optimized mixed Markov models for motif identification.

Reconstruction of human protein interolog network using evolutionary conserved network.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Dissecting microregulation of a master regulatory network.

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

Systems biology in human health and disease.

Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.