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).

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction

  Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

  tcga same metastatic tumor-only whole-exome wes copy-number

• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

  PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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  Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

  lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl

• Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

  PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 53

  Current (recent) effective population size is equal to or less than 50 fish in all analysed farmed populations

  turbot gilthead european common rad genotype decay

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 5 claims · 6 setups

  Has reproduction

  SLDP selects a subset of WGS variants using GWAS prior information (P-value threshold) combined with LD pruning (r2) to improve genomic prediction accuracy.

  duroc discovery training real low-coverage genome-wide genomic

• Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

  PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

  Has reproduction · 75

  rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

  saccharomyces model ribose-seq emriboseq rhii-hyden-seq

• Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

  PMID 34576874 · PMC8467633 · Microorganisms · 2021 · 7 claims · 7 setups

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  Amitosis causes random assortment of somatic alleles (IESs) in the highly polyploid Paramecium macronucleus, which can be tracked without phenotypic markers using scDNA-seq.

  paramecium tetraurelia telomere-capped simulated single-cell bulk bias

• Ecotype diversity and conversion in Photobacterium profundum strains.

  PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

  photobacterium profundum predicted orthologous whole-genome pulsed-field comparative

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

  Has reproduction · 68

  Siphonophorae is the first diverging clade within Hydroidolina.

  hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq

• The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

  PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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  5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

  extracts pooled same non-assigned pcr parallel conventional

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

  PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

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  A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

  brain peripheral sk-nsh-n genomic rt-pcr direct snp

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

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  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• Microarray-based DNA methylation profiling: technology and applications.

  PMID 16428248 · PMC1345696 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  A microarray-based method enriching unmethylated and methylated DNA fractions via methylation-sensitive restriction enzymes followed by hybridization enables high-throughput DNA methylation profiling of large genomic regions.

  genomic postmortem ligated custom cpg tiling

• Pathways to injury in chronic pancreatitis: decoding the role of the high-risk SPINK1 N34S haplotype using meta-analysis.

  PMID 18414673 · PMC2289874 · PloS one · 2008 · 6 claims · 7 setups

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  SPINK1 N34S is strongly associated with chronic pancreatitis overall

  chronic alcoholic idiopathic tropical meta-analysis genotyping publication

• Risk of pancreatic cancer in families with Lynch syndrome.

  PMID 19861671 · PMC4091624 · JAMA · 2009 · 7 claims · 3 setups

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  Families with germline MMR gene mutations (Lynch Syndrome) have an 8.6-fold increased risk of pancreatic cancer compared to the general U.S. population.

  individuals extracted same modified germline proportional

• Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

  PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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  Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

  peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning

• Primase-based whole genome amplification.

  PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

  genomic plasmids circular agarose picogreen dye-terminator