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 28

System / cell line: comparative ✕ Assay: codon ✕ Clear

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

igvh germline non-igv immunogenetics flow cdna bioinformatic
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 96

gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

avian comparative correlation robustness
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

influenzae novel reference codon phylogenetic comparative
Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

autosomal intronic chimpanzee genes comparative human-chimpanzee background
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Oncogenic mutations in GNAQ occur early in uveal melanoma.

PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

uveal peripheral normal well-characterized pcr sequencing array-based
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

bifidobacterium longum xbai-digested whole-genome base codon
Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

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Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

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CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

genome sequence drosophila novo gene coding
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

anopheles gambiae reanocds05 initio full-length rt-pcr
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp

Experiments

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

Empirical codon substitution matrix.

Evidence for a novel gene associated with human influenza A viruses.

Comparative genomics and understanding of microbial biology.

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

Oncogenic mutations in GNAQ occur early in uveal melanoma.

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

Comparative genomics search for losses of long-established genes on the human lineage.

The gentle art of gene arrangement: the meaning of gene clusters.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.