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).

• DBD--taxonomically broad transcription factor predictions: new content and functionality.

  PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.

  proteomes eukaryotic genomes hmm-based comparative heatmap

• Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

  PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

  predicted non-masked genome interpro hmm tblastn inter-species

• Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

  PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

  blood-derived four patients col2a1 targeted clinical transthoracic

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• 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

• Discovering cancer genes by integrating network and functional properties.

  PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

  genes gene colon ppi pfam term

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing

• Small molecule splicing modulators that disrupt O-GlcNAc homeostasis.

  PMID 41526361 · PMC12894984 · Nature communications · 2026 · 8 claims · 7 setups

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  Kinase inhibitors GSK690693 and Y-33075 act as splicing modulators that disrupt O-GlcNAc homeostasis by simultaneously downregulating both OGT and OGA

  hct116 recombinant hek293t high-content western udp-glo

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• CancerGenes: a gene selection resource for cancer genome projects.

  PMID 17088289 · PMC1781153 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  CancerGenes is a gene list-centric web resource that combines expert-annotated gene lists with data from public databases (Entrez Gene, Ensembl BioMart, Kim et al. promoter data, Sanger COSMIC) to support gene selection for cancer re-sequencing projects.

  genes chip-on-chip literature entrez

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

  PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  169 gene products in the Ciona genome were identified as putative GPCRs

  ciona sequence molecular est

• Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts.

  PMID 41848149 · PMC12999062 · Microbial genomics · 2026 · 8 claims · 8 setups

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  Seven single-cell genomes assembled from uncultured environmental Bodo cells represent three potentially novel Bodo species

  uncultured environmental single-cell bodo single-cell fluorescence-activated whole-genome

• Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

  PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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  The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

  schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

  PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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  An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

  anopheles gambiae reanocds05 initio full-length rt-pcr

• Prominent neuroleptic sensitivity in a case of early-onset Alzheimer disease due to presenilin-1 G206A mutation.

  PMID 18797263 · PMC4867177 · Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology · 2008 · 8 claims · 8 setups

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  A patient with the PS-1 G206A mutation developed prominent extrapyramidal signs (EPS) shortly after starting the atypical neuroleptic risperidone, which resolved completely after the drug was discontinued.

  cerebrospinal genomic brain blood elisa genetic apoe

• Evolution of a distinct chromatin regulatory landscape in brown algae.

  PMID 41896322 · PMC13076208 · Nature ecology & evolution · 2026 · 8 claims · 6 setups

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  Brown algae lost DNA methyltransferases (DNMT1, DNMT3, DNMT5) early in their evolution, retaining only DNMT2/TRDMT homologues

  ectocarpus histone same computational mass western chip-seq