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).

Publications 1.3k Datasets 392.5k Experiments 40

System / cell line: population ✕ Assay: phylogenetic ✕ Clear

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
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

Has reproduction · 93

Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based
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
Updated three-stage model for the peopling of the Americas.

PMID 18797500 · PMC2527656 · PloS one · 2008 · 8 claims · 3 setups

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Removing nine non-Native American mtDNA sequences eliminates the previously reported early (~40 kya) expansion signal for the proto-Amerind population

native mitochondrial new bayesian mtdna molecular
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
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

Has reproduction · 95

Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

wheat hordeum bulk-segregated interval novo
Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups

Has reproduction · 89

Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.

coli st372 core draft whole-genome core population
Melanesian mtDNA complexity.

PMID 17327912 · PMC1803017 · PloS one · 2007 · 8 claims · 5 setups

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Among-group mtDNA variation in Northern Island Melanesia is structured by island, island size, and language affiliation.

populations near mtdna mtdna analysis coalescence
Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups

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ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets

software authors sequence polymorphism phylogenetic
In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups

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The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India

mtdna mitochondrial partial hvs1
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Sequence variation in the human transcription factor gene POU5F1.

PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

genomic multi-species inferred international resequencing comparative haplotype
Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

Has reproduction · 86

Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

clover-associated plasmids plasmidome replicons long-read k-mer genome
Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.

PMID 17331239 · PMC1810519 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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The majority (85%) of Saudi Arab mtDNA lineages have a western Asia (Eurasian) provenance

saudi mtdna rflp complete
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
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat

Experiments

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

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

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

Updated three-stage model for the peopling of the Americas.

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).

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

Melanesian mtDNA complexity.

Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

Gene losses during human origins.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Sequence variation in the human transcription factor gene POU5F1.

Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.

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

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.