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 48

System / cell line: matrix ✕ Assay: classification ✕ Clear

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

genome protein-protein genes artificial kappa clustering gene
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

PMID 18834544 · PMC2575220 · BMC bioinformatics · 2008 · 8 claims · 8 setups

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128 discriminating 4-mer motifs combined with an SVM (RBF kernel, LIBSVM) can distinguish promoter from non-promoter DNA sequences

plant drosophila promoter same 4-mer tata blast
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.

PMID 42026624 · PMC13238118 · Genome biology · 2026 · 8 claims · 6 setups

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SEAGALL combines a geometry-regularised autoencoder (GRAE) to embed cells and build a cell-cell graph with a graph attention network (GAT) classifier and GNNExplainer-based XAI to identify features driving cell type/phenotype.

count same scchip-seq ten count latent classification
Much ado about nothing: modeling amino acid replacement with predicted protein structures.

PMID 42036821 · PMC13171170 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 7 setups

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AFSM was constructed from over 660,000 structural alignments across ~21,000 proteins (297 InterPro families), following the BLOSUM log-odds methodology.

proteins balibase pfam cath structural sequence remote
Structural evolution of the protein kinase-like superfamily.

PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

bank representative same kinase comparative manual structure-annotated
An SVM-based system for predicting protein subnuclear localizations.

PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

single-localization multi-localization same svm sequence
Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

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Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

human-mouse high aarm orthologous content pairwise
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

Has reproduction · 30

MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

simplified genome-scale cerevisiae coli minspan spearman comparative
ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

lines chromosome embryonic transcription chip-seq chromhmm hi-c
Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data.

PMID 41758825 · PMC12948085 · PloS one · 2026 · 8 claims · 6 setups

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AI-based predictive models built on unannotated scRNA-seq data (cell-by-gene expression matrices) can classify melanoma patients as ICI responders vs. non-responders

cd45+ scrna-seq independent scrna-seq single-gene-level pathway-level
Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

Has reproduction · 90

A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

monocytes natural hematopoietic leukemia atac-seq hierarchical
Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

pdb obligatory same psi-blast solvent residue
Bayesian prediction of microbial oxygen requirement.

PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

Has reproduction · 76

A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

bacterial selected predicted pfam-a genome gene domain
BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.

PMID 41896736 · PMC13147680 · BMC microbiology · 2026 · 7 claims · 8 setups

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BaGPipe is an automated, reproducible Nextflow pipeline that integrates pre-processing, Pyseer-based association analysis, and downstream visualisation into a unified bacterial GWAS workflow

streptococcus staphylococcus aureus pneumoniae bacterial read amr
RaMBat: Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects.

PMID 41571436 · PMC13060657 · Molecular oncology · 2026 · 7 claims · 5 setups

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RaMBat achieves a median accuracy of 99% across 13 independent benchmark datasets, significantly outperforming state-of-the-art MB subtyping methods and conventional ML classifiers

medulloblastoma gse85217 ger microarray bulk intrasample
Predicting FOX gene candidates for oxic nitrogen fixation using multi-omic machine learning and comparative bioinformatics.

PMID 41764348 · PMC13056922 · Scientific reports · 2026 · 8 claims · 6 setups

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Random Forest, XGBoost, and logistic regression classifiers can meaningfully differentiate literature-validated FOX genes from conserved non-essential genes, with Random Forest achieving the best ROC-AUC (~0.80)

anabaena diazotrophic gene-level trained bulk quantitative transcription-start-site-derived
Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

PMID 42004709 · PMC13089224 · PeerJ · 2026 · 8 claims · 8 setups

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GPD2 and GPD3 cluster into distinct WGCNA co-expression modules (magenta and black, respectively) with contrasting temporal expression profiles

chlamydomonas genes normalized gpd bulk weighted gene

Experiments

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.

Much ado about nothing: modeling amino acid replacement with predicted protein structures.

Structural evolution of the protein kinase-like superfamily.

An SVM-based system for predicting protein subnuclear localizations.

Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data.

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

Protein expression patterns in primary carcinoma of the vagina.

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

Bayesian prediction of microbial oxygen requirement.

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.

RaMBat: Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects.

Predicting FOX gene candidates for oxic nitrogen fixation using multi-omic machine learning and comparative bioinformatics.

Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.