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).

• 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

• Genome-wide scans for loci under selection in humans.

  PMID 16004726 · PMC3525256 · Human genomics · 2005 · 8 claims · 4 setups

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  Natural selection and population demographic history both distort patterns of genetic variation relative to the standard neutral model, so single-locus tests cannot unambiguously distinguish selection from demography.

  african-american european-american populations simulated tajima's fst coalescent

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.

  PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups

  Has reproduction · 80

  α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination

  rhizobium core same site intragenic nucleotide

• Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

  PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

  Has reproduction · 51

  K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

  uniflora whole-genome phylogenomic population

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• 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

• Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

  PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

  Has reproduction · 90

  Weak selection conferred by stem cell variation created before birth can reliably yield clonal hematopoiesis later in life.

  hscs simulated methylation single-cell

• Molecular epidemiology of DFNB1 deafness in France.

  PMID 15070423 · PMC385234 · BMC medical genetics · 2004 · 8 claims · 7 setups

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  35delG remains the most common pathogenic GJB2 mutation in the studied French (Languedoc Roussillon) population despite being less frequent than in other Mediterranean populations

  gjb2 dried genomic deaf dhplc pcr-mediated pcr-dhplc

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

  PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

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  BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

  genomic pedigrees first-degree study pcr pedigree-based age

• mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

  PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

  mitochondrial aligned compilation sequence multi-locus

• 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

• 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

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Mutation analysis of the MDM4 gene in German breast cancer patients.

  PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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  Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

  german bilateral mdm4 lymphoid direct rflp-based splice

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast