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).

• Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

  PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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  High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

  canine osteosarcoma independent third oligonucleotide cross-species quantitative

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• In silico segmentations of lentivirus envelope sequences.

  PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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  C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

  eiav hiv hmm-based hmm artificial

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• Diversity of the parB and repA genes of the Burkholderia cepacia complex and their utility for rapid identification of Burkholderia cenocepacia.

  PMID 18328098 · PMC2324101 · BMC microbiology · 2008 · 8 claims · 7 setups

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  repA sequences show distinct clustering of B. cenocepacia relative to other Bcc species, enabling design of a species-specific multiplex PCR

  burkholderia six bcc panel pcr phylogenetic multilocus

• Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

  PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

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  A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

  α5+ computational k562 embryonic ligand tandem hierarchical

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation

• Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

  PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

  Has reproduction · 67

  Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

  frugiperda satellite million contigs comparative homology divergence

• Columba: an integrated database of proteins, structures, and annotations.

  PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.

  pdb database sequence secondary

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• 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

• Application of functional genomics to primate endometrium: insights into biological processes.

  PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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  Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

  endometrial uterus whole-genome cdna oligonucleotide

• Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

  PMID 17982171 · PMC2238866 · Nucleic acids research · 2008 · 6 claims · 5 setups

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  StellaBase Disease houses homology data for 155,904 invertebrate isoforms of human disease genes across four model systems, including 14,874 predicted Nematostella genes

  nematostella blastp est snp

• Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

  PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)

  arabidopsis rice promoter cross-species ldss sequence distribution

• 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

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular