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).

• G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

  PMID 19846439 · PMC2788932 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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  G-compass is a web-based tool that displays two corresponding genomic regions from human and another vertebrate species simultaneously in parallel, without requiring client installation.

  genome hg18 blastz comparison

• Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

  PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

  wallaby squirrel deer clouded overgo bac comparative

• Identifying synonymous regulatory elements in vertebrate genomes.

  PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

  genome genes genome-wide gene tissue-specificity

• Developments in CORG: a gene-centric comparative genomics resource.

  PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

  upstream gene overlapping c-fos pairwise sequence comparative

• Narcisse: a mirror view of conserved syntenies.

  PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

  annotated genome pairwise pairs sequence nucleic-level conserved

• A genome-wide screen for noncoding elements important in primate evolution.

  PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.

  phastcons global genome accelerated comparative targeted fisher's

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

  PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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  PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

  natural aligned ns3 denv sequence pcp-consensus physicochemical

• Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

  PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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  MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

  macrorna sequence comparative mouse-human population

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• 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

• Getting positive about selection.

  PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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  Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

  genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood

• A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

  PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups

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  A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches

  genome boreoeutherian ferungulate marker-presence whole-genome ancestral combinatorial

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• 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

• Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

  PMID 18304319 · PMC2268676 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  Comparative synteny conservation around a horizontally transferred gene (HTgene) can distinguish single versus multiple independent HGT events even without a robust phylogenetic tree.

  poxvirus core psi-blast comparative molecular

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species