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).
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Has reproduction · 84
An accurate method for identifying recent recombinants from unaligned sequences.
PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups
A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.
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Analysis of concordance of different haplotype block partitioning algorithms.
PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups
Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.
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Importance sampling for the infinite sites model.
PMID 18976228 · PMC2832804 · Statistical applications in genetics and molecular biology · 2008 · 7 claims · 2 setups
A new importance sampling proposal distribution for the ISM, derived from a new result on exact sampling from a single segregating site, generally shows greater efficiency than the GT and SD proposals.
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Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.
PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups
8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.
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Processing and population genetic analysis of multigenic datasets with ProSeq3 software.
PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups
ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets
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Lineage specific recombination rates and microevolution in Listeria monocytogenes.
PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups
Recombination is more prevalent in lineage II than in lineage I
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Analysis of chimpanzee history based on genome sequence alignments.
PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups
Bonobos and common chimpanzees separated approximately 1.29 million years ago
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Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.
PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups
NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.
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The stem cell population of the human colon crypt: analysis via methylation patterns.
PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups
A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.
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Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.
PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups
Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo
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Simple models of genomic variation in human SNP density.
PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups
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.
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Sex-biased evolutionary forces shape genomic patterns of human diversity.
PMID 18818765 · PMC2538571 · PLoS genetics · 2008 · 7 claims · 5 setups
X-linked diversity is higher than the neutral expectation (0.75) relative to autosomal diversity in all six sampled human populations
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In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.
PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups
The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India
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Absence of the TAP2 human recombination hotspot in chimpanzees.
PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups
The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.
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Genome-wide scans for loci under selection in humans.
PMID 16004726 · PMC3525256 · Human genomics · 2005 · 8 claims · 4 setups
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.
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Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.
PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups
The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).