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).

• Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

  PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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  Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

  ptk2 t84 escherichia computational expression immunofluorescence immunoblotting

• Absence of somatic alterations of the EB1 gene adenomatous polyposis coli-associated protein in human sporadic colorectal cancers.

  PMID 9823979 · PMC2063196 · British journal of cancer · 1998 · 6 claims · 4 setups

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  No somatic point mutations were found in the entire EB1 coding sequence in sporadic colorectal cancers or adenomas

  sporadic pcr colorectal rt-pcr direct microsatellite

• Detection of germline BRCA1 mutations by Multiple-Dye Cleavase Fragment Length Polymorphism (MD-CFLP) method.

  PMID 11556835 · PMC2375072 · British journal of cancer · 2001 · 6 claims · 4 setups

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  MD-CFLP can detect DNA sequence alterations (single-base substitutions, small insertions/deletions) in BRCA1 fragments longer than 1 kb

  brca1 direct pcr multiple-dye

• Integration of cytogenetic landmarks into the draft sequence of the human genome.

  PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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  7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

  large-insert bac ml-2 dgap012 fluorescence sts array

• Environmental genome project: a positive sequence of events.

  PMID 11171540 · PMC1242069 · Environmental health perspectives · 2001 · 8 claims · 5 setups

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  Exposure to alkylating agents evokes at least threefold expression changes in about one-third of the yeast genome (~2,000 genes), far beyond DNA repair genes alone

  yeast genes population microarray time-course resequencing

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes.

  PMID 12225591 · PMC139409 · Genome biology · 2002 · 8 claims · 7 setups

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  The Fugu rubripes draft genome sequence was generated by whole-genome shotgun sequencing assembled to ~5.6x coverage using the JAZZ pipeline.

  fugu assembled whole-genome computational comparative

• Bench-to-bedside review: fulfilling promises of the Human Genome Project.

  PMID 12133180 · PMC137447 · Critical care (London, England) · 2002 · 8 claims · 4 setups

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  Most common diseases and many drug responses are influenced by inherited genetic variation

  haemophilus genome septic genomic whole-genome snp large-scale

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

  PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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  APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

  apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

  PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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  A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

  pre-mirnas test conserved-hairpin cross-species secondary svm cross-species

• 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

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.

  PMID 16280053 · PMC1410737 · Breast cancer research : BCR · 2005 · 8 claims · 8 setups

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  There is no evidence that highly penetrant exonic or splice site mutations in FANCD2, BRIP1/BACH1, LMO4 or SFN contribute to familial breast cancer

  germline lymphoblastoid dhplc sequencing rt-pcr

• Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

  PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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  HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

  genomic genotype 293t pcr-amplified pcr haplotype cell-cell

• High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

  PMID 16086836 · PMC1190179 · BMC medical genetics · 2005 · 8 claims · 6 setups

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  IVS2-2A>G allele frequency does not differ significantly between hearing-impaired cases and controls among Hispanics and Caucasians (p=0.45)

  genomic mitochondrial slc26a5 pcr sequence splice

• Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

  PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

  tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane

• The impact of low-cost, genome-wide resequencing on association studies.

  PMID 16004723 · PMC3525269 · Human genomics · 2005 · 8 claims · 4 setups

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  The HapMap project provides more than 500,000 SNPs across three major human populations, enabling genome-wide association studies via linkage disequilibrium tagging.

  bacterial phi-x case genome massively genome snp

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window