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 31

System / cell line: alignment ✕ Assay: ancestral ✕ Clear

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

personal genomic pcr-validated unrelated short-read pcr sanger
Genome-wide identification of human functional DNA using a neutral indel model.

PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

chromosome human-mouse genome individual whole-genome probabilistic comparative
Benchmarking tools for the alignment of functional noncoding DNA.

PMID 14736341 · PMC344529 · BMC bioinformatics · 2004 · 8 claims · 4 setups

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Global alignment tools (Avid, ClustalW, Lagan, Needle, DiAlign-G) typically have higher sensitivity over entire noncoding sequences and within constrained blocks than local tools

simulated melanogaster sapiens sequence pairwise genome
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups

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A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches

genome boreoeutherian ferungulate marker-presence whole-genome ancestral combinatorial
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
Mitochondrial diversity within modern human populations.

PMID 17439969 · PMC1888801 · Nucleic acids research · 2007 · 8 claims · 5 setups

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Modern humans show extremely low divergence from the mitochondrial consensus sequence, differing on average by only 21.6 nucleotide sites

full-length mitochondrial mtdna additional sequence site-by-site regional
Evolutionary toggling of the MAPT 17q21.31 inversion region.

PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

chimpanzee lymphoblastoid donor whole-genome reciprocal bac
Long-range regulation is a major driving force in maintaining genome integrity.

PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

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Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

opossum genome comparative identification statistical
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
EGenBio: a data management system for evolutionary genomics and biodiversity.

PMID 17118150 · PMC1683573 · BMC bioinformatics · 2006 · 7 claims · 7 setups

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EGenBio is a web-based system for integrated management, filtering, curation, and visualization of large-scale genomic sequences, alignments, and phylogenetic trees for evolutionary genomics and biodiversity research.

vertebrate sequence mutant phylogenetic sequence coevolution saturation
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species
Variation resources at UC Santa Cruz.

PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

chimpanzee affymetrix hapmap perlegen snp fixed linkage
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

genome chimpanzee genomic pcr computational triple pcr
Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

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Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

hcv-1a phylogenetic sequence nucleotide
Ensembl 2009.

PMID 19033362 · PMC2686571 · Nucleic acids research · 2009 · 8 claims · 6 setups

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Ensembl provides comprehensive, consistently annotated genome information for chordate genomes with automatically generated genesets and comparative genomics data

horse mammalian chromosome ensembl post-gene-build genome gerp
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

Experiments

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Genome-wide identification of human functional DNA using a neutral indel model.

Benchmarking tools for the alignment of functional noncoding DNA.

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

Phylogenetic analysis of RhoGAP domain-containing proteins.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Mitochondrial diversity within modern human populations.

Evolutionary toggling of the MAPT 17q21.31 inversion region.

Long-range regulation is a major driving force in maintaining genome integrity.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

EGenBio: a data management system for evolutionary genomics and biodiversity.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

Variation resources at UC Santa Cruz.

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

Ensembl 2009.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

Web-based resources for comparative genomics.