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).

• Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

  PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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  The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

  dog hamster pcr primer pcr blast sequence

• 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

• 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

• 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

• Pseudofam: the pseudogene families database.

  PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

  eukaryotic over pseudogenes pseudogene blast family sequence

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• ECgene: an alternative splicing database update.

  PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

  nine genome sage cdna genome-based chi-squared sage

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• Recurring genomic breaks in independent lineages support genomic fragility.

  PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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  The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

  hg17 genome computationally comparative marker segmental

• 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

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• The role of positive selection in determining the molecular cause of species differences in disease.

  PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

  orthologous omim meta-database panther comparative disease protein-protein

• BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

  PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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  BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

  peripheral blood-derived folliculin chest direct subcloning sequence

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• 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