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).

• PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

  PMID 19906711 · PMC2808952 · Nucleic acids research · 2010 · 6 claims · 4 setups

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  PLANdbAffy is a database of Affymetrix probe alignments to the human genome for five widely used arrays (HG-U133A, HG-U133B, HG-U133 Plus 2.0, Human Exon 1.0, Human Gene 1.0)

  hg-u133a ucsc dbsnp probe blat est snp

• PigGIS: Pig Genomic Informatics System.

  PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

  million pig matched wgs blastx repeat sequence

• PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

  PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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  PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

  hpv clinical biotinylated pcr mip molecular microarray

• 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

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• 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

• 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

• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

  PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups

  Has reproduction · 78

  GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.

  clinical tuberculosis registered whole-genome targeted retraining

• 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

• Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

  PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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  125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

  ag09319 gm05388 nhfk whole-genome quantitative dna-associated

• Comparing whole genomes using DNA microarrays.

  PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

  genome saccharomyces mitochondrial sars array comparative resequencing

• 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

• Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

  PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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  Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

  blood pooled gene chip-chip conventional quantitative

• Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

  PMID 18366709 · PMC2323391 · BMC genomics · 2008 · 8 claims · 5 setups

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  Genome diversity among M. avium subspecies is mediated by large sequence polymorphisms (LSPs) commonly associated with mobile genetic elements.

  avium microarray map selected microarray blastn sequencing

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

  Has reproduction · 91

  175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

  one sinensis small-molecular-weight leaves small genome mirna

• Towards reliable whole genome sequencing for outbreak preparedness and response.

  PMID 35945497 · PMC9361258 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 84

  Amplicon-based Nanopore sequencing can rapidly generate whole genome sequences in samples with viral load up to Ct 33.

  culture aligned amplicon-based metagenomic capture-based

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real