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 123

System / cell line: analysis ✕ Assay: substitution ✕ Clear

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
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

atm hybridized probe oligonucleotide transcription microarray
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

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MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

trachomatis pneumoniae chlamydiales mlst eburst upgma
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
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
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
Evolution of genomic sequence inhomogeneity at mid-range scales.

PMID 19891785 · PMC2779198 · BMC genomics · 2009 · 7 claims · 3 setups

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MRI regions have comparable levels of de novo mutations to control genomic sequences with average base composition.

chimpanzee population genome whole-genome snp indel
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
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
Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

PMID 17653048 · PMC2776539 · Molecular vision · 2007 · 8 claims · 4 setups

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No RP patient among 68 Japanese subjects carried a RHO mutation causing an amino acid substitution

blood-derived genomic chromosomes rho whole-locus pcr haplotype
Physiology engages with functional genomics - at last.

PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

wild-type caenorhabditis kidney pcr qtl enu copas
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
The role of genomics in tracking the evolution of influenza A virus.

PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

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Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome
A novel HRAS substitution (c.266C>G; p.S89C) resulting in decreased downstream signaling suggests a new dimension of RAS pathway dysregulation in human development.

PMID 22821884 · PMC4166655 · American journal of medical genetics. Part A · 2012 · 8 claims · 6 setups

Has reproduction · 88

A novel heterozygous HRAS c.266C>G (p.S89C) germline mutation was identified in two siblings with severe fetal hydrops/pleural effusion (Patient 1) and polyhydramnios/Dandy-Walker malformation (Patient 2).

cos-7 parental hras genomic ras immunoblotting egf
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups

Has reproduction · 84

The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus

mamiellales ostreococcus tauri shared comparative orthology synteny
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

tuberculosis putative orthologous genomewide blastp clustal nei-gojobori
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

Experiments

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

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

Heterotachy in mammalian promoter evolution.

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

Evolution of genomic sequence inhomogeneity at mid-range scales.

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

Heterogeneous genomic molecular clocks in primates.

Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

Physiology engages with functional genomics - at last.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

Mutation analysis of the MDM4 gene in German breast cancer patients.

The role of genomics in tracking the evolution of influenza A virus.

A novel HRAS substitution (c.266C>G; p.S89C) resulting in decreased downstream signaling suggests a new dimension of RAS pathway dysregulation in human development.

Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.