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).

• Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

  PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

  genomic hek293 m17 south sscp dual-luciferase pcr-rflp

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• Negotiating the boundary between medicine and consumer culture: online marketing of nutrigenetic tests.

  PMID 20022680 · PMC2824846 · Social science & medicine (1982) · 2010 · 8 claims · 3 setups

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  Nutrigenetic testing companies create a new social/marketing space for their products positioned between medicine and consumer culture, rather than being simply delegitimized by boundary work.

  webpages same fda qualitative framing document

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage

• Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.

  PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)

  wandering feeding stage type single scenic immunolabeling

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• 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

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• Finding signals that regulate alternative splicing in the post-genomic era.

  PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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  Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

  intron-containing genome brain-specific cell-free computational comparative selex

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

  PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

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  P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

  vivax genome comparative microsatellite

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun