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 406

System / cell line: phylogenetic ✕ Clear

PhyloRef: A Semi-Automated Workflow for eDNA Reference Database Curation via Phylogenetic Anomaly Detection.

PMID 41766741 · PMC12946455 · Ecology and evolution · 2026 · 8 claims · 5 setups

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PhyloRef is a Snakemake-based, semi-automated, phylogeny-guided workflow for eDNA reference database curation

chondrichthyes actinopterygii mitochondrial aligned phylogenetic sequence automated
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

pad phylogenetic est est-based
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Having a BLAST with bioinformatics (and avoiding BLASTphemy).

PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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BLAST is the most widely used tool for searching biological sequences for regions of local similarity

superfamilies blocks query pairwise phylogenetic sequence heuristic
An XML-based system for synthesis of data from disparate databases.

PMID 16501185 · PMC1513665 · Journal of the American Medical Informatics Association : JAMIA · 2006 · 8 claims · 2 setups

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An XML-based data management framework (built on Mobius) supports integration of disparate data sources and large data sets for biomedical research applications.

snp swisprot phylogenetic integration
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

PMID 41911220 · PMC13048486 · PLoS computational biology · 2026 · 8 claims · 5 setups

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WEPP is a pathogen-agnostic pipeline that uses phylogenetic placement of sequencing reads onto mutation-annotated trees (MATs) to identify candidate haplotypes and estimate their abundances

sars-cov-2 mutation-annotated simulated synthetic real-world
Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

Has reproduction · 87

Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

leaf trimmed species concatenated genome novo reference-assisted
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

Has reproduction · 94

Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

novel casei genomes selected whole-genome maximum-likelihood pairwise
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

Has reproduction · 91

SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

deep co-assembled surf_17 surf_5 whole-genome novo 16s
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

Has reproduction · 98

Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

clinical dnaa isogenic h37rv genome-wide structural deep-sequencing
Identification of functional SNPs in the 5-prime flanking sequences of human genes.

PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

flanking synthetic genomic cloned comparative electrophoretic rflp
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

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GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

synthetic eukaryotic simulated 16-species analytical comparative simulation
Bushes in the tree of life.

PMID 17105342 · PMC1637082 · PLoS biology · 2006 · 8 claims · 8 setups

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Bush-shaped clades, produced by short internal stems and long external branches, resist phylogenetic resolution regardless of the amount of conventional data collected.

chimpanzee elephant coelacanth metazoan multi-gene rare nuclear
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
The human phylome.

PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

proteome proteins neighbor-joining maximum bayesian
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
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

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Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation

Experiments

PhyloRef: A Semi-Automated Workflow for eDNA Reference Database Curation via Phylogenetic Anomaly Detection.

A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

Protein co-evolution, co-adaptation and interactions.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

An XML-based system for synthesis of data from disparate databases.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

Bushes in the tree of life.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

The human phylome.

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.