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 70

System / cell line: sequences ✕ Assay: statistical ✕ Clear

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

simulated same repeat whole-genome genome
Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

cerevisiae genome chimpanzee hot computational microarray comparative
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

paired lung tissue-pair pooled hiv-1 maximum statistical
CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

expressed representative random genes computational orf statistical
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

PMID 15610565 · PMC544599 · BMC genomics · 2004 · 6 claims · 4 setups

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Alu repeats are a source of AREs at 3' UTRs of human mRNA, via poly-A regions of Alu generating complementary poly-T/poly-U regions that acquire regular adenine insertions to form ARE motifs.

utr computationally are repeat positional
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Global distribution of rubella virus genotypes.

PMID 14720390 · PMC3034328 · Emerging infectious diseases · 2003 · 8 claims · 6 setups

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Phylogenetic analysis of 103 E1 gene sequences from 17 countries confirms at least two rubella virus genotypes, RGI and RGII

rubella same phylogenetic genetic virus
Global genetic diversity of human metapneumovirus fusion gene.

PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

hmpv llc-mk2 clinical rt-pcr sequence phylogenetic
Ab initio identification of putative human transcription factor binding sites by comparative genomics.

PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

human-mouse conserved gene consensus comparative statistical gene
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

PMID 18215327 · PMC2265691 · Virology journal · 2008 · 8 claims · 6 setups

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N-linked glycosylation of HIV-1 gp120 differs between plasma and leukocyte compartments

plasma hiv-1 nlg presence env phylogenetic signature
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

dbsnp gpcr transmembrane sequence six-frame sift logistic
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
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
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational

Experiments

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

CRSD: a comprehensive web server for composite regulatory signature discovery.

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Aggregation propensity of the human proteome.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Global distribution of rubella virus genotypes.

Global genetic diversity of human metapneumovirus fusion gene.

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

The distribution of SNPs in human gene regulatory regions.

Empirical codon substitution matrix.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.