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 55

System / cell line: orf ✕ Assay: sequence ✕ Clear

Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

mgc cloned orfs genome gateway orf blat
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

sequences parsed bacillus anopheles large-scale sequence orf
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

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All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

vcjd scjd scottish controls pcr-rflp full chi-squared
Proteomics data repositories.

PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

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The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

multi-organism yeast proteomes cerevisiae tandem yeast fluorescence
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
A biomedically enriched collection of 7000 human ORF clones.

PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

genes mgc plasmid literature pcr sequence
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

Has reproduction · 24

MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

environmental quality-filtered assembled predicted metagenomic metagenome gene
What the Phage: a scalable workflow for the identification and analysis of phage sequences.

PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

Has reproduction · 76

WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

assembled illumina phage-predicted predicted multitool metagenome gene
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
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
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Candida albicans genome sequence: a platform for genomics in the absence of genetics.

PMID 15239821 · PMC463275 · Genome biology · 2004 · 8 claims · 5 setups

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Publication of the complete diploid C. albicans genome sequence will accelerate research into the pathogenesis of Candida infections

candida sc5314 whole-genome fingerprinting multi-locus
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
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
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

Experiments

Evidence for a novel gene associated with human influenza A viruses.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

Proteomics data repositories.

A genome annotation-driven approach to cloning the human ORFeome.

A biomedically enriched collection of 7000 human ORF clones.

MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

What the Phage: a scalable workflow for the identification and analysis of phage sequences.

Comparative genomics and understanding of microbial biology.

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Gene losses during human origins.

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

Species-specific protein sequence and fold optimizations.

Candida albicans genome sequence: a platform for genomics in the absence of genetics.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

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

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.