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).

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

  PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

  Has reproduction · 79

  RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

  wgs single whole-genome nested capillary

• Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

  PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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  The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

  genomic electronic pcr pcr-restriction

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

  PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups

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  Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.

  hoxd genomic pcr pcr-amplified comparative pcr southern

• 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

• Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

  PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

  orthologous diverse tissues gene comparative est microarray

• 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

• 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

• 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

• 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

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• 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

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• 'Chumanzee' evolution: the urge to diverge and merge.

  PMID 17129363 · PMC1794591 · Genome biology · 2006 · 8 claims · 3 setups

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  Human-chimpanzee divergence was not a simple clean split; evidence suggests hybridization continued after an initial split.

  chimpanzee rheboon comparative artificial cytogenetic

• Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

  PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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  The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

  bac heart ccs genomic genomic rt-pcr transcription

• Pegasys: software for executing and integrating analyses of biological sequences.

  PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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  Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

  eukaryotic formatted genomic input initio sequence gene

• Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

  PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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  Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

  refseq macaca genomic rhesus exon pcr molecular