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).

• In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

  PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups

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  The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India

  mtdna mitochondrial partial hvs1

• Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

  PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

  genomic anonymized dried pcr-restriction direct molecular

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• 11q13 amplification status and human papillomavirus in relation to p16 expression defines two distinct etiologies of head and neck tumours.

  PMID 17003776 · PMC2360598 · British journal of cancer · 2006 · 8 claims · 7 setups

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  HPV-positive HNSCC tumours are significantly less likely to carry 11q13 amplification than HPV-negative tumours

  hnscc paraffin nested hpv pyrosequencing

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

• Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

  PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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  TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

  pooled hcec-dm corneal 2-d western real-time

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• Malaria genomics meets drug-resistance phenotyping in the field.

  PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups

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  Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.

  falciparum plasmodium drug clinical high-throughput

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

  triticum taiqd wheat rice genome-wide phylogenetic gene

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

  PMID 36451166 · PMC9710047 · Genome biology · 2022 · 7 claims · 6 setups

  Has reproduction · 50

  MoDLE is a high-performance stochastic model that simulates DNA-DNA contacts from loop extrusion genome-wide in minutes using less than 1 GB of RAM

  genome synthetic h1-hesc stochastic molecular ctcf

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

  PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

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  The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

  plasmodium pvama-1 vivax pcr molecular merozoite

• Updated three-stage model for the peopling of the Americas.

  PMID 18797500 · PMC2527656 · PloS one · 2008 · 8 claims · 3 setups

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  Removing nine non-Native American mtDNA sequences eliminates the previously reported early (~40 kya) expansion signal for the proto-Amerind population

  native mitochondrial new bayesian mtdna molecular

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.

  PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups

  Has reproduction · 77

  spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.

  coli simulated net-seq ribosome stochastic