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).

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

  PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

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  Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

  simulated simulation-based simulated

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  >700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

  w1118 dgrp drosophila dgrp-796 bulk high uas-rnai

• An accurate method for identifying recent recombinants from unaligned sequences.

  PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  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.

  simulated dblα coalescent comparative recombinant

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• Collisionless relaxation of a disequilibrated current sheet and implications for bifurcated structures.

  PMID 34145266 · PMC8213726 · Nature communications · 2021 · 6 claims · 4 setups

  Has reproduction · 95

  Collisionless transitions among four single-particle orbit classes are responsible for the relaxation/equilibration of a disequilibrated current sheet.

  disequilibrated harris earth's particle-in-cell single-particle spacecraft

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Sequence polymorphisms cause many false cis eQTLs.

  PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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  Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

  lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl

• 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

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  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).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Genetic drift acts strongly on influenza virus populations within acute human infections but is obscured by other factors within acutely infected swine.

  PMID 42027246 · PMC13100903 · Virus evolution · 2026 · 8 claims · 4 setups

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  Within-host human IAV populations have a very small effective population size (N_E = 49, 95% CI [28, 84])

  within-host swine simulated population diffusion simulation

• 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

• Emergence of recombinant forms of HIV: dynamics and scaling.

  PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

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  A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

  cd4+ scid-hu splenocytes computational single-round replication-competent proviral