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).

• Genome comparison without alignment using shortest unique substrings.

  PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

  caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local

• 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

• Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

  PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

  full-length alternative refseq genome pairwise mitochondrial signal

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• 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 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

• Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

  PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

  genome chimpanzee sult1a3 est blast-like comparative pairwise

• Linking disease-associated genes to regulatory networks via promoter organization.

  PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

  orthologous eukaryotic genomatix pubmed promoter model additional

• Bioinformatic mapping of AlkB homology domains in viruses.

  PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

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  AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

  ncbi 146-sequence representative hel psi-blast pfam profile

• DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

  PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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  Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

  identified cst csts comparative coding exon

• 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

• Thirty years into the genomics era: tumor viruses led the way.

  PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups

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  Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes

  sv40 bacteriophage epstein-barr aids-associated restriction recombinant sequencing

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier

• Genomic view of the evolution of the complement system.

  PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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  Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

  chicken complement sponge shark comparative phylogenetic reverse