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

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• Integrating alternative splicing detection into gene prediction.

  PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

  arabidopsis araset thaliana transcript-to-genome initio comparative

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

  PMID 41490125 · PMC12768360 · PloS one · 2026 · 7 claims · 7 setups

  Has reproduction · 69

  Manual curation of RNA-seq-derived de novo transcripts increased the number of functional genes in the NWR annotation by 81% (from 8,701 to 15,738).

  southern granulosa nwr novo bulk isolation read

• 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

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

  PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

  mitochondrial aligned compilation sequence multi-locus

• A third approach to gene prediction suggests thousands of additional human transcribed regions.

  PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

  genome 4.4-mb known nucleotide repeat polyadenylation

• U7 snRNAs: a computational survey.

  PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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  A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

  mammalian drosophilid aligned basal blast sequence consensus

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.

  PMID 17881367 · PMC2238943 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  piRNABank is a web-accessible database storing empirically known piRNA sequences and annotations for human, mouse and rat.

  pirna mapped sequence genome sliding-window

• Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

  PMID 18654618 · PMC2442658 · PLoS genetics · 2008 · 8 claims · 5 setups

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  Loss of AGG interruptions in CGG repeat tracts predisposes FMR1 alleles to instability and faster progression toward premutation/disease state

  fmr1 xq28 genome agg fluorescence genome-wide

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• BIPASS: BioInformatics Pipeline Alternative Splicing Services.

  PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

  transcript aligned pre-computed user-submitted sequence alternative database

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 8 claims · 7 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are diverse and abundant in the halite endolithic microbial community, with 1,538 total ncRNAs discovered across Archaea and Bacteria.

  halite discovered conserved itsrnas strand-specific genome-resolved srna

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed