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).

• Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

  PMID 35073255 · PMC8828049 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 57

  Prokaryotic community similarity follows a significant U-shape relationship over geographic distance up to 4000 km, decreasing within biotas but increasing across biotas after a tipping point of 1760-1920 km

  soil grassland 16s plant soil

• Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

  PMID 35320603 · PMC9323552 · Global change biology · 2022 · 8 claims · 7 setups

  Has reproduction · 39

  Glacier shrinkage (decreasing glacier influence) accelerates downstream organic matter decomposition rates in glacier-fed streams

  benthic sediment subset stream extracellular chlorophyll-a 16s

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.

  PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups

  Has reproduction · 71

  1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)

  lung left blood heart sequencing functional quantitative

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.

  PMID 33772001 · PMC7998036 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  AAMDC is an amplified/overexpressed oncogene in a subgroup of ER-positive breast cancers (IntClust2) associated with poor prognosis

  breast luminal sum52pe t-47d immunohistochemistry fluorescence qrt-pcr

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

  PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.

  pearl old oxford bionano illumina

• 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

  Full-text index only

  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

• Hobbes: optimized gram-based methods for efficient read alignment.

  PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups

  Has reproduction · 83

  Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.

  genome hg18 example reference read-mapping character-substitution algorithmic

• Predominance of CIN versus MSI in the development of rectal cancer at young age.

  PMID 12379157 · PMC130963 · BMC cancer · 2002 · 6 claims · 5 setups

  Full-text index only

  MSI occurs in only a small fraction of rectal cancers in young patients (3/30), far below rates reported in mixed young-onset colorectal cancer series

  paraffin-embedded flow microsatellite sequencing

• ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

  PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

  Full-text index only

  A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

  genomic red computational abo sequencing blood

• Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

  PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

  Full-text index only

  A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

  oocytes genomic fbhm population rt-pcr est direct

• Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

  PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

  genomic genotype 293t pcr-amplified pcr haplotype cell-cell

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• Haplotype analysis suggest common founders in carriers of the recurrent BRCA2 mutation, 3398delAAAAG, in French Canadian hereditary breast and/ovarian cancer families.

  PMID 16539696 · PMC1464093 · BMC medical genetics · 2006 · 7 claims · 6 setups

  Full-text index only

  Carriers of the 3398delAAAAG BRCA2 mutation share one of two closely related haplotypes (7-3-9-3-[3/4]-7), consistent with a common ancestral origin.

  french index unaffected mutation-carrier mutation microsatellite haplotype

• Genetic requirement for pneumococcal ear infection.

  PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

  Full-text index only

  STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

  pneumoniae bioluminescent balb signature-tagged bioluminescent transmission

• X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

  PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

  Full-text index only

  X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

  ensembl breast mcf7 25-mer probe-to-transcript microarray

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac