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 sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• 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

• Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

  PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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  MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

  genomic domestic pooled colorectal snp pooling microsatellite

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.

  dysgalactiae sdse sdsd isolates genome multilocus pangenome

• snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

  PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs

  whole-genome genome computational gene northern

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• 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

• 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

• 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

• Better smelling through genetics: mammalian odor perception.

  PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

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  Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

  mammals subjects v1r trpc2 comparative genetic targeted

• 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

• Tandem repeats modify the structure of human genes hosted in segmental duplications.

  PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

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  Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

  genome genomic est paired genome-wide comparative cnv

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

  PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

  genome animal aligned est genome-wide comparative est

• 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

• 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

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based