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).

• The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

  PMID 14519199 · PMC328453 · Genome biology · 2003 · 8 claims · 5 setups

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  Sequence-profile (PSI-BLAST) searches unify archaeal Alba with eukaryotic RNase P/MRP subunits Rpp20/Pop7 and Rpp25, and with the ciliate macronuclear-development protein Mdp2, into a single Alba superfamily.

  archaeal eukaryotic alba sulfolobus psi-blast sequence phylogenetic

• A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

  PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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  A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

  genomic genome pcr real-time fluorescence sequence

• Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

  PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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  Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

  a549 nsclc expansion wst-1 flow

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

  PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

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  A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

  t-47d agarose chromatin cloning

• Inferring combinatorial regulation of transcription in silico.

  PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

  upstream monocytes same tfbs microarray permutation

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

  PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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  FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

  armd dutch fibulin pef6-ssflag mutation computational site-directed

• Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

  PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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  Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

  swissprot nssnp-containing nssnps machine single-attribute sequence

• Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

  PMID 16432256 · PMC1345699 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  A 17mer PNA spanning K-ras codons 12/13 can serve as both PCR clamp and sensor probe in a single-tube reaction, differentiating all 12 possible point mutations from wild-type by melting temperature shift

  wild-type mixture mutant serial melting real-time limit-of-detection

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• 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

• Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

  PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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  A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

  drosophila genome melanogaster real-time comparative gfp

• MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

  PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

  pooled genomic aneuploid dog mlga

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• SePaCS--a web-based application for classification of seroreactivity profiles.

  PMID 17478503 · PMC1933220 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  SePaCS is a freely available web-based tool that trains and applies multiple classification methods (4 Naive Bayes variants, SVM with RBF kernel, LDA, DLDA) to seroreactivity profiles and outputs results as a summary table plus a detailed PDF report

  blood computational seroreactivity supervised mutual

• INTERFEROME: the database of interferon regulated genes.

  PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

  chimp ifn-treated tissues irg microarray in-house basal

• Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

  PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

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  The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

  brain exon targeted principal

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease

• Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

  PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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  Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

  csf brain normal 2d-dige label-free isotopic