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).

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• 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 analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

  PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

  matched bone leukemia diagnosis snp flow quantitative

• Genome comparison without alignment using shortest unique substrings.

  PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

  caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual

• Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

  PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

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  NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

  glioblastoma gbm matched sequenced copy gene methylation

• Genetics of bipolar disorder.

  PMID 18689285 · PMC3181866 · Dialogues in clinical neuroscience · 2008 · 8 claims · 6 setups

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  BP-I has a strong genetic component supported by segregation, adoption, and twin studies across populations

  multiplex pooled bp-affected monozygotic genome-wide genome candidate

• The formation of avian montane diversity across barriers and along elevational gradients.

  PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.

  forest population individuals single whole-genome f_st principal

• The truth about mouse, human, worms and yeast.

  PMID 15601543 · PMC3525071 · Human genomics · 2004 · 8 claims · 8 setups

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  Comparing genomes in pairs or larger sets (mouse-human, C. elegans-C. briggsae, multiple Saccharomyces, human-pufferfish, etc.) reveals unsuspected genes and helps eliminate false-positive gene predictions

  mouse-human homo tetraodon region comparative est cross-species

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• A critical reassessment of the role of mitochondria in tumorigenesis.

  PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups

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  A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.

  hepatocellular papillary prostate tissues mtdna mutational

• Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

  PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

  simulated real apoe igf2 cubic pairwise haplotype

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• Comparing time series transcriptome data between plants using a network module finding algorithm.

  PMID 31164912 · PMC6544932 · Plant methods · 2019 · 8 claims · 6 setups

  Has reproduction · 59

  Converting gene expression patterns into co-expression networks and applying a cross-species network module finding algorithm (OrthoClust with simulated annealing) solves the problem of matching developmental stages between two species without requiring one-to-one stage mapping.

  soybean arabidopsis cross-species module reciprocal bulk co-expression

• Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

  PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

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  BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

  genomic pedigrees first-degree study pcr pedigree-based age

• Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

  PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

  human-mouse model genome-wide comparative computational

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

  PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.

  top100h decoys i-tasser non-homologous statistical rdcc comparative