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 81

System / cell line: proteins ✕ Assay: species ✕ Clear

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

hadv-37 predicted select genome cpg global
Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

Has reproduction · 80

928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

burkholderia pseudomallei bulk tmt-based rt-qpcr
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

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Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
SNP-VISTA: an interactive SNP visualization tool.

PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets

abo homologous acid snp multi-species blast-based
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
Reconstructing the evolution of the mitochondrial ribosomal proteome.

PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.

proteomes eukaryotic aligned alignments iterative hmm-based neighbor-joining
Assessing the gene space in draft genomes.

PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

caenorhabditis toxoplasma homo briggsae cegma blast tblastn
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
Structural organization and interactions of transmembrane domains in tetraspanin proteins.

PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

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TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence
Protein length in eukaryotic and prokaryotic proteomes.

PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families

eukaryotic proteins genomic cog comparative orthology domain
Protein function assignment through mining cross-species protein-protein interactions.

PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

sapiens cross-species majority simple
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

PMID 15608248 · PMC539979 · Nucleic acids research · 2005 · 7 claims · 5 setups

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RefSeq provides a curated, non-redundant, explicitly linked collection of genomic, transcript and protein sequences spanning prokaryotes, eukaryotes and viruses.

refseq honey sequence computational conserved
NCBI Reference Sequences: current status, policy and new initiatives.

PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

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RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

microbial bacterial prokaryotic refseq spliced structural functional
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
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
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
Genomic signatures of human versus avian influenza A viruses.

PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

throat clinical 401-genome avian rt-pcr immunofluorescent sequence
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

Experiments

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

SNP-VISTA: an interactive SNP visualization tool.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

Reconstructing the evolution of the mitochondrial ribosomal proteome.

Assessing the gene space in draft genomes.

Phylogenetic analysis of RhoGAP domain-containing proteins.

Structural organization and interactions of transmembrane domains in tetraspanin proteins.

Protein length in eukaryotic and prokaryotic proteomes.

Protein function assignment through mining cross-species protein-protein interactions.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

NCBI Reference Sequences: current status, policy and new initiatives.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

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

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

Genomic signatures of human versus avian influenza A viruses.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Novel insights into adipogenesis from omics data.