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).

• GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.

  PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 67

  GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.

  chm13 chm1 hg02723 genome sunk haplotype

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

  Full-text index only

  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

• Evolutionary toggling of the MAPT 17q21.31 inversion region.

  PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

  chimpanzee lymphoblastoid donor whole-genome reciprocal bac

• High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

  PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

  salmonella sequenced typhi whole-genome snp-based selection

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

  PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

  Full-text index only

  DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

  extremely families genome sanger case-control family-based

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing