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).

• In silico discovery of transcription regulatory elements in Plasmodium falciparum.

  PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

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  GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

  falciparum plasmodium invasion invasion-related microarray motif comparative

• Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

  PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

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  Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

  mcf7 promoter cdna quantitative computational

• SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

  PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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  SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

  cancer lung breast array medip segmentation

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

  PMID 19906696 · PMC2811030 · Nucleic acids research · 2010 · 6 claims · 4 setups

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  MiGS combines MBD2 MBD-domain precipitation of methylated DNA with massively parallel sequencing to enable unbiased, high-throughput genome-wide DNA methylation profiling

  hct116 migs mbd-isolated bisulfite gene

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

  PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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  Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

  gria2 drosophila nova1 cd45 splicing sirna hits-clip

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

  triticum taiqd wheat promoter genome-wide phylogenetic synteny

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

  PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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  Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

  salmonella sequenced typhi whole-genome snp-based selection

• Splicing bioinformatics to biology.

  PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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  Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

  dscam alternative heterologous expressing comparative dicodon reporter

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• ENCODE whole-genome data in the UCSC Genome Browser.

  PMID 19920125 · PMC2808953 · Nucleic acids research · 2010 · 7 claims · 8 setups

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  The UCSC ENCODE Data Coordination Center serves as the primary repository for ENCODE experimental results, providing access via Genome Browser, Table Browser, and FTP download.

  lines chip-seq dnase-seq rna-seq