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).

• Alternative polyadenylation of cyclooxygenase-2.

  PMID 15872218 · PMC1088970 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The human COX-2 gene undergoes alternative polyadenylation using proximal and distal polyadenylation signals

  cox-2 ht29 hela bioinformatics western rnase

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

  PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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  The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

  elegans whole-genome rnase pharmacological

• 52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

  PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

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  The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

  molt-4 placental placenta fetal cdna genomic race

• Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

  PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

  sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

• Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

  PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 8 claims · 7 setups

  Has reproduction · 95

  254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.

  ostreatus ccef00389 genome bulk computational

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

  PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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  IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

  igvh germline non-igv immunogenetics flow cdna bioinformatic

• Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

  PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

  ensembl genomic simulation pcr maldi-tof

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

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  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

  PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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  CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

  unrelated genomic mtmr2 array quantitative sanger

• Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

  PMID 33402206 · PMC7784341 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Disome-seq sequences mRNA fragments protected by two stacked (collided) ribosomes, detecting ribosome collisions at codon resolution.

  saccharomyces yeast disome-seq monosome-seq mrna-seq

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• Comparative genomic analysis of three Leishmania species that cause diverse human disease.

  PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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  L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

  infantum major braziliensis leishmania whole-genome comparative pcr