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).

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

  Full-text index only

  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Thirty years into the genomics era: tumor viruses led the way.

  PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes

  sv40 bacteriophage epstein-barr aids-associated restriction recombinant sequencing

• Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome.

  PMID 33294007 · PMC7691466 · Evolutionary applications · 2020 · 7 claims · 8 setups

  Has reproduction · 84

  Lingcod comprise two distinct genetic clusters separated latitudinally at a break near Point Reyes off Northern California, with a high frequency of admixed individuals near the break.

  ophiodon single lingcod subset radseq genome bayesian

• Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

  PMID 18053125 · PMC2235865 · BMC genomics · 2007 · 7 claims · 4 setups

  Full-text index only

  A second-generation virtual RLGS (vRLGS) system predicts DNA fragment migration using sequence characteristics plus fragment length, and is applicable to any sequenced genome and enzyme combination

  peripheral genome restriction virtual

• DNA sequencing: bench to bedside and beyond.

  PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

  bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• Human genomic variation.

  PMID 11178257 · PMC138878 · Genome biology · 2000 · 8 claims · 7 setups

  Full-text index only

  Lewontin's 1972 analysis of 17 blood-group/protein loci found 85% of human genetic variation lies within individuals of a nation/tribe, 8% between populations within races, and only 6% between races

  populations individuals composite genome blood-group marker mitochondrial

• Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

  PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

  Full-text index only

  Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

  genomic anonymized dried pcr-restriction direct molecular

• A novel mutation in GRK1 causes Oguchi disease in a consanguineous Pakistani family.

  PMID 19753316 · PMC2742643 · Molecular vision · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel nonsense mutation (c.614C>A; p.S205X) in exon 1 of GRK1 causes disease in family RP19

  affected family rp19 selected genome-wide microsatellite direct

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• Cryptosporidium: genomic and biochemical features.

  PMID 19187778 · PMC2819285 · Experimental parasitology · 2010 · 8 claims · 8 setups

  Full-text index only

  C. parvum lacks a plastid and mitochondrial genome, unlike other apicomplexans, limiting plastid-targeted drug strategies

  parvum yeast recombinant gp40 pulsed-field happy genome

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

  Full-text index only

  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 8 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture introduced by stocking, especially with the Atlantic lineage.

  salmo brown subset five ddrad-seq read population

• Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.

  PMID 38909031 · PMC11193758 · Scientific data · 2024 · 6 claims · 5 setups

  Has reproduction · 80

  A chromosome-level genome of P. ornatus spanning 2.65 Gb was assembled with a contig N50 of 51.05 Mb, anchoring 99.11% of sequences to 73 chromosomes.

  ornatus wgs hi-c rna-seq

• The DNA sequence of the human X chromosome.

  PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

  Full-text index only

  The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

  pac selected chromosome clone-based shotgun comparative

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

  Full-text index only

  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• High-density SNP genotyping to define beta-globin locus haplotypes.

  PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

  Full-text index only

  RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

  genomic rflp subset rflp high-density haploview

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

  Full-text index only

  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c