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 807

System / cell line: sequences ✕ Clear

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

hg16 genomic individuals element computational pcr pcr-based
Structural organization and interactions of transmembrane domains in tetraspanin proteins.

PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

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TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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202 novel box H/ACA RNA-related sequences were identified in the human genome

genome chimpanzee aca flanking megablast comparative sequence
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
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
The HIV positive selection mutation database.

PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

hiv-1 stanford codon-specific selection conditional
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

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HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

proteome homo domains hmm-hmm hmm subtractive
In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

hmlh1 same cos-7 hela ese splice minigene
First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

PMID 16959032 · PMC1570496 · Retrovirology · 2006 · 8 claims · 6 setups

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Nearly full-length sequencing of 10 HIV-1 seroincident MSM samples revealed 6 subtype B, 3 unique BF recombinants, and 1 novel B/C/F triple recombinant

pbmcs assembled hiv-1 triple nearly phylogenetic bootscan
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

genome tissues novo pairwise rt-pcr
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
MACSIMS: multiple alignment of complete sequences information management system.

PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

balibase-derived sequences same query automatic database initio
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
ChimerDB--a knowledgebase for fusion sequences.

PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

genome candidate pubmed omim blat splice-site ecgene
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
Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

unique hmpv sequence neighbor-joining codon
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
External contamination in single cell mtDNA analysis.

PMID 17668059 · PMC1930155 · PloS one · 2007 · 8 claims · 6 setups

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External DNA contamination is a real and non-negligible problem in single-cell mtDNA sequence analysis

single current laboratory reagent mtdna two-step nested
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

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

Structural organization and interactions of transmembrane domains in tetraspanin proteins.

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

Phylogenetic analysis of RhoGAP domain-containing proteins.

Genome assembly comparison identifies structural variants in the human genome.

The HIV positive selection mutation database.

Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

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

MACSIMS: multiple alignment of complete sequences information management system.

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

ChimerDB--a knowledgebase for fusion sequences.

Inconsistencies in Neanderthal genomic DNA sequences.

Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

External contamination in single cell mtDNA analysis.

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