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).

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

  PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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  A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

  upstream co-expression pre-b microarray-based motif gene

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time

• The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

  PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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  P. falciparum encodes substantially more membrane transport proteins than originally annotated

  falciparum genome-wide bioinformatic quantification

• Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

  PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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  Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

  liver genomic tissues embryos rt-pcr genomic secondary

• BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.

  PMID 15653630 · PMC546182 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  BiSearch is a new web-available primer-design software for bisulfite-treated genomes that also analyzes primer pairs for mispriming sites via a novel search algorithm.

  tyrosine homo hek primer post-design pcr

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

  PMID 17130153 · PMC1702505 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A single Y80A alanine substitution switches Tma endo V from purine-preferring to essentially C-specific mismatch cleavage, including the previously refractory C/C mismatch.

  synthetic k-ras endo pcr restriction

• 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

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual

• Antibody binding loop insertions as diversity elements.

  PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

  gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• CRSD: a comprehensive web server for composite regulatory signature discovery.

  PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

  gene 3'-utr promoter user-submitted genome-wide microrna binding

• Application of ecotoxicogenomics for studying endocrine disruption in vertebrates and invertebrates.

  PMID 16818254 · PMC1874166 · Environmental health perspectives · 2006 · 8 claims · 8 setups

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  Estrogen-responsive genes in mouse uterus are induced in a dose-dependent, ER-α-dependent manner, as shown by loss of induction in ER-α knockout mice.

  reproductive american xenopus fundulus cdna receptor developmental

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

  PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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  A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

  bovine pcr-based comparative rt-pcr

• Heterotachy in mammalian promoter evolution.

  PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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  The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

  promoter ancient chimpanzee comparative ancient micro-indel

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional