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).

• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

  PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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  miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

  conserved putative mirna-target normal comparative machine mirna

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• Evolution of motif variants and positional bias of the cyclic-AMP response element.

  PMID 17288573 · PMC1796609 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  Canonical CRE positional bias toward the -1 to -150 bp TSS region is present in vertebrates (human, mouse, rat, chicken, frog, zebrafish) but absent in sea squirt, fruit fly and worm.

  tss-spanning cres genome known genome-wide comparative cpg

• Structure of protein interaction networks and their implications on drug design.

  PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

  budding pin yeast protein-protein graph-theoretic gene

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal

• Update of the G2D tool for prioritization of gene candidates to inherited diseases.

  PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

  genome genomic etrb computational literature go-similarity

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• miRGen: a database for the study of animal microRNA genomic organization and function.

  PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

  animal genome mouse-human mirna genomic mirna cross-species

• Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

  PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups

  Has reproduction · 89

  The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.

  genomic adapted aligned pcr amplicon multiplex qpcr

• Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

  PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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  CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

  cerevisiae cycle reanalysis statistical optimal

• Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

  PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups

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  An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations

  serum hbv nested pcr oligonucleotide pcr restriction

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• 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

• Determination of point mutational spectra of benzo[a]pyrene-diol epoxide in human cells.

  PMID 1486852 · PMC1519600 · Environmental health perspectives · 1992 · 5 claims · 4 setups

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  A new protocol combining en masse 6-thioguanine-resistant mutant selection, high-fidelity PCR amplification, and DGGE separation can determine point mutational spectra in human cells with high precision and reproducibility

  tk6 184-bp reconstruction point melting

• Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

  PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

  normal aneuploid same genomiphi-amplified array-cgh

• X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

  PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

  ensembl breast mcf7 25-mer probe-to-transcript microarray