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).

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.

  PMID 17517762 · PMC1933116 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  Pair-wise sequence alignment-based indel identification lacks discrimination of species specificity and cannot distinguish insertions from deletions.

  chromosomes hg18 ucsc sequence pair-wise

• The UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

  PMID 17981843 · PMC2238977 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  CTCF is the only identified trans-acting factor in vertebrates that confers enhancer-blocking insulator activity

  ohlsson ren zhao tissues chip-chip massive motif

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• Widely variable endogenous retroviral methylation levels in human placenta.

  PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

  term placenta genome bisulfite rt-pcr genome-wide

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

  PMID 18522722 · PMC2447851 · BMC genomics · 2008 · 8 claims · 4 setups

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  A consensus Reference Human NumtS compilation (RHNumtS) was produced by comparing Blastn, MegaBlast and BLAT results with previously published compilations.

  genome genomic blastn megablast blat

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat