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 21

System / cell line: gold-standard ✕ Clear

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

PMID 18487273 · PMC2447794 · Nucleic acids research · 2008 · 8 claims · 7 setups

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PolySearch supports more than 50 different classes of queries against nearly a dozen types of text, abstract, or bioinformatic databases

manually biomedical text feature real-life
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
Detection of alternative splicing: deep sequencing or deep learning?

PMID 41520225 · PMC12790623 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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Sequence-based deep learning tools (AlphaGenome, SpliceAI, DeepSplice) show potential for initial hypothesis development and as additional filters in standard RNA-seq pipelines, especially when sequencing depth is limited.

dilated dcm sequence subsampled bulk rna-seq deep
Cancer genome standards for long-read sequencing using cancer cell line mixtures.

PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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Long-read variant calling tools achieve recall rates comparable to short-read gold standards

colo829 same whole-genome short-read 5mc
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 · 7 claims · 6 setups

Has reproduction · 78

MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.

aspergillus fumigatus bulk computational chip-seq-based
Detection of germline BRCA1 mutations by Multiple-Dye Cleavase Fragment Length Polymorphism (MD-CFLP) method.

PMID 11556835 · PMC2375072 · British journal of cancer · 2001 · 6 claims · 4 setups

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MD-CFLP can detect DNA sequence alterations (single-base substitutions, small insertions/deletions) in BRCA1 fragments longer than 1 kb

brca1 direct pcr multiple-dye
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

PMID 16034025 · PMC1179732 · Nucleic acids research · 2005 · 7 claims · 4 setups

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Partial EC numbers are semantically ambiguous, and databases that assign a gene to all reactions sharing the same partial EC number make a faulty inference, causing systematic misannotation.

e.coli biocyc vimss specific database comparative manual
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups

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DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.

individual pooled individuals gatk-called whole-genome overlapped simulated
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

gastrulating gastrula gold-standard embryo single-cell computational promoter
DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

Has reproduction · 80

DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

synthetic partially embryonic mesc glycosylase dmn-seq ultrafast
High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

Has reproduction · 85

SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

atlantic low-coverage genotyping genome
Foster thy young: enhanced prediction of orphan genes in assembled genomes.

PMID 34928390 · PMC9023268 · Nucleic acids research · 2022 · 8 claims · 6 setups

Has reproduction · 84

Each of the five tested gene prediction pipelines under-predicts orphan genes, as few as 11% detected under one scenario

arabidopsis initio evidence-based combined
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

yeast yeast-related interaction random dictionary-based manual graph
Information-based methods for predicting gene function from systematic gene knock-downs.

PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.

caenorhabditis elegans saccharomyces interference computational genome-wide
A comparative study of techniques for differential expression analysis on RNA-Seq data.

PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 58

edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 7 claims · 6 setups

Has reproduction · 50

MEDUSA correctly identifies more species than MEGAN 6 CE, especially less abundant species.

bovine simulated cami datasets read host-sequence metagenome
Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

asian random subjects unrelated arms-pcr msei sanger

Experiments

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Detection of alternative splicing: deep sequencing or deep learning?

Cancer genome standards for long-read sequencing using cancer cell line mixtures.

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

Detection of germline BRCA1 mutations by Multiple-Dye Cleavase Fragment Length Polymorphism (MD-CFLP) method.

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

Foster thy young: enhanced prediction of orphan genes in assembled genomes.

Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

Information-based methods for predicting gene function from systematic gene knock-downs.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.