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).

• A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

  PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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  A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

  coli hela filamentous scfv gfp sds-page fluorescence

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

  PMID 15479470 · PMC526369 · BMC genomics · 2004 · 8 claims · 4 setups

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  65 ePK sequences were identified in the P. falciparum genome and classified via phylogenetic analysis relative to the seven established ePK groups

  falciparum individual recombinant cmgc-group genome-wide blastp kinase

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

  PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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  Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

  genome genomic chromosome randomization

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

  PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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  More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

  dbest liver cultures refseq est oligoarray polymerase

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

  PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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  P. falciparum encodes substantially more membrane transport proteins than originally annotated

  falciparum genome-wide bioinformatic quantification

• Molecular genetics and structural genomics of the human protein kinase C gene module.

  PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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  The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

  metaphase genome pkc genomic fluorescence bioinformatic snp

• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

  PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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  PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

  subset drosophila ensembl lc-ms icat peptide-to-genome

• Spontaneous symmetry breaking in genome evolution.

  PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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  Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

  animal homo model genome-wide alternatively computational

• SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

  PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

  randomly heirs seattlesnps african resequencing genome-wide tag

• 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

• Large-scale and high-confidence proteomic analysis of human seminal plasma.

  PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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  923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

  seminal same list combined sds-page database decoy

• Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

  PMID 19000305 · PMC2586028 · BMC cancer · 2008 · 7 claims · 6 setups

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  16 PTP candidate genes containing coding mononucleotide repeats (cMNR) of at least 7 units were identified via bioinformatic analysis and screened in MSI-H cell lines, cancers, and adenomas

  msi-h genome colorectal fragment bioinformatic sequencing

• Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

  PMID 16945957 · PMC1636363 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SILAC can be used for miRNA target identification

  hela 3'-utr silac microarray dual-luciferase

• Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

  PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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  Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

  genomic maternal 22qtdr chromosome semi-quantitative pcr fish