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).

• The Neandertal genome and ancient DNA authenticity.

  PMID 19661919 · PMC2725275 · The EMBO journal · 2009 · 8 claims · 6 setups

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  Only direct assays of DNA sequence positions where Neandertals differ from all contemporary humans can reliably estimate human contamination.

  neandertal pcr high-throughput genome

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

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  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern

• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

  edna khumbu genome metabarcoding satellite

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

  camellia sinensis small genome mirna

• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

  PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups

  Has reproduction · 89

  SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.

  nasopharyngeal airway patient-matched swab shotgun bulk rt-pcr

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

  PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

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  PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

  trypsin-digested mix serum same shotgun sequest lc-ms

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Report of the 9th HLPP Workshop October 2007, Seoul, Korea.

  PMID 18683817 · PMC4601560 · Proteomics · 2008 · 8 claims · 8 setups

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  An integrated separating-identifying platform identified 6788 proteins (≥2 peptides, 95% confidence) in Chinese human liver samples, including 3721 new to liver and 977 hypothetical proteins

  chinese liver hbv-related mammalian shotgun transcriptome yeast

• Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity.

  PMID 37107373 · PMC10137368 · Foods (Basel, Switzerland) · 2023 · 6 claims · 6 setups

  Has reproduction

  SRP intervention reduces obesity, serum lipid levels, hepatic lipid accumulation, and adipocyte hypertrophy in high-fat-diet rats, especially at high dose.

  rats liver fecal srp body serum histology

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups

  Has reproduction · 66

  Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.

  prostate pca bulk reverse ssgsea

• Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium.

  PMID 19746165 · PMC2736619 · PloS one · 2009 · 7 claims · 4 setups

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  Comparative HPLC-MS/MS proteomic analysis, using phoP-/Q- mutants as controls, identifies PhoP-regulated proteins in S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2

  typhimurium typhi genomic hplc-ms phon microarray

• Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

  PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

  Has reproduction · 90

  Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

  cephalopholis analysis next-generation pacbio ont

• Science star over Asia.

  PMID 16149850 · PMC1201306 · PLoS biology · 2005 · 8 claims · 7 setups

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  Ariff Bongso and associates at Singapore's National University Hospital were the first to derive human embryonic stem cells, from a five-day-old discarded human embryo in 1994, and showed the cells were pluripotent with therapeutic transplant potential.

  blastocyst embryonic fugu rice embryo culture whole-genome

• Rats go genomic.

  PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

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  A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

  recombinant genes serotonin adenomatous genome-wide targeted knockout

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional