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).

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

  PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

  Has reproduction · 62

  E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

  preimplantation genome erna bulk computational motif

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.

  PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Has reproduction · 74

  SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.

  pairs nanostring st-sc osmfish_zeisel st-sc 5-fold spatially

• snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

  PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs

  whole-genome genome computational gene northern

• 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

• ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

  PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups

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  ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)

  30-node web-based cluster simulated computational web comparison

• Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

  PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

  genome chimpanzee genomic pcr computational triple pcr

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Computational identification of transcriptional regulatory elements in DNA sequence.

  PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy

  saccharomyces generic pwm-based pwm

• TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

  PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.

  promoter tred-retrieved computational literature relational

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical literature and molecular data according to user-defined terms, linking PubMed and GEO.

  pubmed invasive geo cancer semantic computational gene

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy.

  PMID 19094986 · PMC3388947 · Experimental eye research · 2009 · 8 claims · 3 setups

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  Three lead hhRz candidates (CUC↓266, CUC↓1411, AUA↓1414) significantly knock down human RHO protein expression relative to control (p<0.05)

  rho expression secondary western dicistronic

• Pre-implantation embryo metabolism identified by PEMA reveals endogenous lactate insufficiency contributes to pre-implantation development arrest.

  PMID 42272466 · PMC13247451 · Fundamental research · 2026 · 7 claims · 7 setups

  Has reproduction

  PEMA, a Ribo-seq-weighted computational framework, characterizes metabolic states of human and mouse pre-implantation embryos more accurately than Compass

  8-cell ch3pn pre-implantation computational single-embryo cut&tag

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• 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

• 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

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative