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).

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• Novel mutations in TARDBP (TDP-43) in patients with familial amyotrophic lateral sclerosis.

  PMID 18802454 · PMC2527686 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Three heterozygous missense mutations (p.M337V, p.N345K, p.I383V) in exon 6 of TARDBP were identified in familial ALS patients

  patients nd10588 lymphoblastoid neuroglioma sanger taqman copy-number

• Ensembl 2009.

  PMID 19033362 · PMC2686571 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  Ensembl provides comprehensive, consistently annotated genome information for chordate genomes with automatically generated genesets and comparative genomics data

  horse mammalian chromosome ensembl post-gene-build genome gerp

• Inverse symmetry in complete genomes and whole-genome inverse duplication.

  PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups

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  Reverse and complement symmetries are essentially absent in genomic sequences at all scales.

  complete coli individual coding k-mer comparison segmental

• Comparative genomic analysis of prion genes.

  PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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  SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

  vertebrate multi-tissue aligned sprn comparative gene cdna

• Mutations in PIK3CA are infrequent in neuroblastoma.

  PMID 16822308 · PMC1533846 · BMC cancer · 2006 · 8 claims · 6 setups

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  PIK3CA activating mutations are infrequent in human neuroblastoma (2.9%, 2/69 tumors)

  neuroblastoma neuroblastoma-derived patients th-mycn targeted sanger rt-pcr

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

  PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

  ncbi genes zebrafish comparative annotation gfp

• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

  PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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  There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

  genomic pcr large outbred comparative denaturing pcr

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• Dcode.org anthology of comparative genomic tools.

  PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

  dlx1 hoxa prothrombin gene comparative multi-species phylogenetic

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• 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

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• The DNA sequence of the human X chromosome.

  PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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  The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

  pac selected chromosome clone-based shotgun comparative

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

  PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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  The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

  coli se11 rapd whole-genome gene

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

  PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

  msi-h aggregated genome mnr sigmoid genome-wide