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).

• DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

  PMID 41055236 · PMC12505516 · RNA biology · 2025 · 7 claims · 5 setups

  Has reproduction · 100

  DeepRNA-Reg, a recurrent neural network-based algorithm, predicts differentially enriched sites in paired HITS-CLIP datasets and outperforms dCLIP 1.7.

  dgcr8 mir-23 deeprna-reg ago2 gene flow

• Inferring combinatorial regulation of transcription in silico.

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

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  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

• Accurate splice site prediction using support vector machines.

  PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

  Full-text index only

  Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

  nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 6 setups

  Has reproduction · 79

  CLSM6A, a CNN-based model set, predicts single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  clsm6a learned last-layer computational model-based propagation-based

• Reference based annotation with GeneMapper.

  PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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  GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

  orthologous human-mouse chicken encode reference-based multi-species reciprocal

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

  PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

  Full-text index only

  AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

  chromosome genomic training ghmm-based sequence parameter

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

  Full-text index only

  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

  PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

  real combined pre-mirna training random independent repeated

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature

• Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

  PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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  A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

  pre-mirnas test conserved-hairpin cross-species secondary svm cross-species

• PromoterPlot: a graphical display of promoter similarities by pattern recognition.

  PMID 15980503 · PMC1160174 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PromoterPlot is a web-based tool that displays and processes TransFac transcription factor search results as an interactive SVG page

  under set transcription microarray proteomics

• Integrating alternative splicing detection into gene prediction.

  PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

  arabidopsis araset thaliana transcript-to-genome initio comparative

• JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

  PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

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  Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

  encode genes invertebrate initio comparative training

• 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

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  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

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term