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).

• In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

  PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

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  Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

  canine tissues hg-u133a probes microarray sequence ortholog

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

  Has reproduction · 94

  ~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

  tuberosum orthologous identified de-novo genome-wide transcriptional

• A surrogate-based approach for post-genomic partner identification.

  PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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  Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

  biotinylated tnf-β analysis secondary phage sequence secondary

• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

  PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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  A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

  jurkat computational immunoblotting structural protein-protein

• ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

  PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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  ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

  genome cytomegalovirus six probabilistic 5-fold directional

• 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

• A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

  PMID 20019893 · PMC2794658 · Molecular vision · 2009 · 7 claims · 7 setups

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  A novel missense mutation c.92T>C (p.I31T) in GJA8 causes autosomal dominant congenital nuclear cataract in this Chinese family

  family genomic unrelated gja8 clinical microsatellite sequencing

• 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

• Tandem repeats modify the structure of human genes hosted in segmental duplications.

  PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

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  Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

  genome genomic est paired genome-wide comparative cnv

• Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

  PMID 19649175 · PMC2718852 · Molecular vision · 2009 · 8 claims · 6 setups

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  A heterozygous missense mutation c.607G>A in exon 6 of CRYBB2, causing p.Val187Met, is the probable causative mutation for congenital nuclear cataract in this family

  genomic basotho pcr restriction secondary

• Autoantibody profiling for the study and treatment of autoimmune disease.

  PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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  Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

  serum antigen-antibody antigens fetal spotted elisa microarray

• Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

  PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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  Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

  huge brain pre-mrna greater genomic rt-pcr quantitative

• CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

  PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups

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  CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

  a498 frozen normal proteomics flow immunohistochemistry

• Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

  PMID 17517123 · PMC1899181 · BMC genomics · 2007 · 8 claims · 4 setups

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  A new method combining known LRR structures, multiple sequence alignment, and secondary structure prediction identifies and aligns LRRs in TLRs more accurately than PFAM/InterPro/SMART

  tlrs lrr-containing tlr2 mammalian comparative structural secondary

• Two novel myocilin mutations in a Chinese family with primary open-angle glaucoma.

  PMID 18776955 · PMC2530518 · Molecular vision · 2008 · 7 claims · 4 setups

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  Two novel MYOC mutations, Pro13Leu (38C→T) and Gln337Stop (1009C del), are likely responsible for POAG pathogenesis in this pedigree

  genomic family myoc pcr-rflp sequencing clinical

• A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

  PMID 18618005 · PMC2447816 · Molecular vision · 2008 · 6 claims · 4 setups

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  A heterozygous c.327C>A transversion in exon 3 of CRYGC causes a nonsense mutation (C109X) that cosegregates with autosomal dominant congenital nuclear cataract in a Chinese family.

  genomic type family γc-crystallin pcr comparative clinical

• Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

  PMID 18515835 · PMC2475620 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Yeast Med2, Med3/Pgd1 and Med5/Nut1 (Tail module) are homologs of human Med29, Med27 and Med24, respectively

  eukaryotic med genuine psi-blast mafft pssm-based

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

  PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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  An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

  lung hpl1d rrna external pcr rt-pcr quantitative

• Evaluating native-like structures of RNA-protein complexes through the deep learning method.

  PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 67

  DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

  bound-bound unbound-bound unbound-unbound bacillus structure interface secondary