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).

• Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

  PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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  Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

  genomic phylogenetic direct high

• Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

  PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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  FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

  cerevisiae elegans randomized computational randomized microarray

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene

• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

  PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

  chromosome genomic pbmc multi-species phylogenetic bisulphite

• Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

  PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups

  Has reproduction · 30

  Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.

  facs-purified ipsc-derived core bulk single-cell facs

• Downstream high-speed plasma jet generation as a direct consequence of shock reformation.

  PMID 35105885 · PMC8807623 · Nature communications · 2022 · 7 claims · 6 setups

  Has reproduction · 67

  High-speed downstream jets at Earth's bow shock are generated as a direct consequence of shock reformation.

  earth's mms mms2 upstream in-situ cross-correlation reduced

• Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

  PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

  Has reproduction · 54

  In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

  analysis microarray rna-seq quantitative

• The cohesin complex: sequence homologies, interaction networks and shared motifs.

  PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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  Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

  smc1 smc3 mmip1 smc psi-blast phylogenetic sequence

• Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

  PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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  The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

  bac heart ccs genomic genomic rt-pcr transcription

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• The evolution and genomic landscape of CGB1 and CGB2 genes.

  PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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  CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

  genomic great cgb1 chimpanzee pcr population hka

• taxize: taxonomic search and retrieval in R.

  PMID 24555091 · PMC3901538 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 30

  taxize is an open-source R package (on CRAN) giving simple programmatic access to taxonomic data from 13 web data sources.

  package session name identifier upstream

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

  PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

  orthologous literature sequence pairwise

• Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

  PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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  A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

  drosophila genome melanogaster real-time comparative gfp

• Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

  PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

  genome synthetic c-kit87 c-kit genome-wide circular molecular

• Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

  PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

  placenta five lines huh7 5'-race rt-pcr real-time

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

  PMID 17553156 · PMC2394752 · Genome biology · 2007 · 8 claims · 6 setups

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  154 positive and 88 negative modulators of NFκB signaling were identified from genomic screens

  hek-293t tissues gain-of-function loss-of-function glucocorticoid