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 15

System / cell line: prediction ✕ Assay: sequence-based ✕ Clear

CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

pubmed genes same randomly geneseeker evoc disease
Genome bioinformatic analysis of nonsynonymous SNPs.

PMID 17708757 · PMC1978506 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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Structure- and sequence-based prediction tools can generally distinguish disease-causing mutations from neutral ones

gene modelled nssnps automated fold relative
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

mitoproteome orthologous liver mitochondrial sequence-based computational literature
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

Has reproduction · 24

MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

environmental quality-filtered assembled predicted metagenomic metagenome gene
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Wiggle-predicting functionally flexible regions from primary sequence.

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

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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
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

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PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

genome chip-chip comparative
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

Has reproduction

An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

udn blood skin snvs whole-genome bulk splice-altering
Evolutionary trace annotation of protein function in the structural proteome.

PMID 20036248 · PMC2831211 · Journal of molecular biology · 2010 · 8 claims · 7 setups

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ET-ranked residue clusters can be used to build 3D templates that predict GO function in enzymes and non-enzymes alike, without prior knowledge of functional mechanism.

structural pdb pairs annotated evolutionary template support
Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

PMID 19918099 · PMC4155129 · Antiviral therapy · 2009 · 8 claims · 6 setups

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Primary integrase inhibitor resistance mutations (T66I, E92Q, G140S, Y143C/H/R, Q148H/R/K, N155S/H) were absent in 342 drug-naive individuals, indicating these sites are highly constrained.

plasma genomic viral aligned bulk sequence-based quantitative
Targeted capture and massively parallel sequencing of 12 human exomes.

PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

hapmap unrelated na18507 randomly targeted array-based molecular
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification

Experiments

CRSD: a comprehensive web server for composite regulatory signature discovery.

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

Genome bioinformatic analysis of nonsynonymous SNPs.

Aggregation propensity of the human proteome.

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

Genome informatics: taming the avalanche of genomic data.

Wiggle-predicting functionally flexible regions from primary sequence.

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

Evolutionary trace annotation of protein function in the structural proteome.

Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

Targeted capture and massively parallel sequencing of 12 human exomes.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.