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 29

System / cell line: chimpanzee ✕ Assay: test ✕ Clear

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

chimpanzee intergenic genome-wide chi-square nucleotide-content
Fast-evolving noncoding sequences in the human genome.

PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

chimpanzee genome hapmap comparative genomic segmental
The evolution and genomic landscape of CGB1 and CGB2 genes.

PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

genomic great cgb1 chimpanzee pcr population hka
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
A genome-wide screen for noncoding elements important in primate evolution.

PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.

phastcons global genome accelerated comparative targeted fisher's
Pseudofam: the pseudogene families database.

PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

eukaryotic over pseudogenes pseudogene blast family sequence
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
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
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
Recurring genomic breaks in independent lineages support genomic fragility.

PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

hg17 genome computationally comparative marker segmental
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

3'-utr mirbase hapmap comparative snp mirna
Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic
Absence of the TAP2 human recombination hotspot in chimpanzees.

PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

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The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

western haplotype males simulated resequencing ld-based sperm
Inconsistencies in Neanderthal genomic DNA sequences.

PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

Fast-evolving noncoding sequences in the human genome.

The evolution and genomic landscape of CGB1 and CGB2 genes.

Heterogeneous genomic molecular clocks in primates.

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

A genome-wide screen for noncoding elements important in primate evolution.

Pseudofam: the pseudogene families database.

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

Variation resources at UC Santa Cruz.

Getting positive about selection.

Recurring genomic breaks in independent lineages support genomic fragility.

Gene losses during human origins.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

The role of positive selection in determining the molecular cause of species differences in disease.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

Absence of the TAP2 human recombination hotspot in chimpanzees.

Inconsistencies in Neanderthal genomic DNA sequences.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.