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 46

System / cell line: pairwise ✕ Assay: prediction ✕ Clear

Optimized mixed Markov models for motif identification.

PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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OMiMa can incorporate more than NNSplice's pairwise dependencies

simulated regulatory splice biological motif pairwise
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

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P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

sequences orthomcl yeast orthomcl jaccard phylogenetic
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
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

genome tissues novo pairwise rt-pcr
OPTIC: orthologous and paralogous transcripts in clades.

PMID 17933761 · PMC2238935 · Nucleic acids research · 2008 · 6 claims · 7 setups

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OPTIC is a database providing gene predictions and orthology assignments for three clades: amniotes (human, dog, mouse, opossum, platypus, chicken), 12 Drosophila species, and 4 Caenorhabditis nematodes.

drosophila translated gene orthologous homology-based all-against-all tree-based
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

chicken predicted human-chicken cdna comparative blastp pairwise
Towards alignment independent quantitative assessment of homology detection.

PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

curated homologene swiss-prot fruit signalp homologene-based fhom
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
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
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
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

eukaryotic homo sequence species pairwise algorithm low-complexity
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

Has reproduction · 87

TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

testseta bprna-new ts-inter individual jaccard pca ensemble
Pegasys: software for executing and integrating analyses of biological sequences.

PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

eukaryotic formatted genomic input initio sequence gene
Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

proteomes predicted long prokaryotic coiled-coil all-against-all sequence
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

pax6 brain yeast sequence yeast semi-quantitative
Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

orfs predicted modeled representative homology transmembrane intrinsic
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome

Experiments

Optimized mixed Markov models for motif identification.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Reference based annotation with GeneMapper.

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

OPTIC: orthologous and paralogous transcripts in clades.

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

Towards alignment independent quantitative assessment of homology detection.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

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

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

Conservation, variability and the modeling of active protein kinases.

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

Pegasys: software for executing and integrating analyses of biological sequences.

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.