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).
-
Full-text index only
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups
A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.
-
Full-text index only
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.
PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups
Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently
-
Full-text index only
Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.
PMID 18829526 · PMC2692251 · Cancer research · 2008 · 7 claims · 6 setups
Global association of HuR and AUF1 with target mRNAs changes substantially and largely reciprocally between MCT-1-transformed and nontransformed MCF10A cells
-
Full-text index only
Technical challenges in using human induced pluripotent stem cells to model disease.
PMID 19951687 · PMC2921621 · Cell stem cell · 2009 · 8 claims · 8 setups
hiPSCs generated from patient somatic cells (skin, blood) can be differentiated into disease-relevant cell types to model disease pathogenesis in vitro
-
Full-text index only
The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.
PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups
GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures
-
Full-text index only
Iterative pruning PCA improves resolution of highly structured populations.
PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups
ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data
-
Full-text index only
Bayesian coestimation of phylogeny and sequence alignment.
PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups
Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.
-
Full-text index only
Bcipep: a database of B-cell epitopes.
PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups
Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases
-
Full-text index only
The many uses of a genome sequence.
PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups
Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction
-
Full-text index only
From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.
PMID 19840938 · PMC2787308 · The Journal of biological chemistry · 2009 · 8 claims · 8 setups
γ-Glutamyl transpeptidase (GGT) activity in rat liver shows biphasic changes during azo dye-induced hepatocarcinogenesis, mirroring the oncofetal expression pattern of α-fetoprotein
-
Full-text index only
Metabolomics: what's happening downstream of DNA.
PMID 15159214 · PMC1242000 · Environmental health perspectives · 2004 · 8 claims · 4 setups
Metabolomics studies the full set of metabolites in biological samples (urine, saliva, blood plasma) and could offer a cheap, rapid, effective way to diagnose illness and monitor therapy.
-
Has reproduction · 100
Topological approximate Bayesian computation for parameter inference of an angiogenesis model.
PMID 35191485 · PMC9048691 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 3 setups
TDA summary statistics can be combined with ABC to infer parameters (ρ, χ) of the Anderson–Chaplain angiogenesis model
-
Has reproduction · 62
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments.
PMID 32093613 · PMC7041296 · BMC genomics · 2020 · 7 claims · 5 setups
Equivalent Change Enrichment Analysis (ECEA), built on a new gene-level statistic called the Equivalent Change Index (ECI), identifies pathways with non-random distributions of equivalently or inversely changed genes across two experiments.
-
Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups
TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene
-
Has reproduction · 40
On the holobiont 'predictome' of immunocompetence in pigs.
PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups
Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall
-
Has reproduction · 64
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups
metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes
-
Has reproduction · 85
NETISCE: a network-based tool for cell fate reprogramming.
PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups
NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.
-
Full-text index only
Environmental genome project: focusing on differences to understand the whole.
PMID 12460813 · PMC1241127 · Environmental health perspectives · 2002 · 8 claims · 4 setups
The EGP has generated a working list of more than 550 environmentally responsive genes involved in pathways such as metabolism, DNA repair, and cell cycle control as candidates for SNP resequencing.
-
Full-text index only
Linking disease-associated genes to regulatory networks via promoter organization.
PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups
Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks
-
Full-text index only
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.
PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups
Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.