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).

• Genetic variation in Pneumocystis carinii isolates from different geographic regions: implications for transmission.

  PMID 10827116 · PMC2640877 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Genotype frequency distribution patterns varied significantly by patient's place of diagnosis but not by place of birth

  pneumocystis ethanol-preserved genotype pcr nested purification

• Tipping the balance in autoimmune disease.

  PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

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  Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

  patients congenic nzm2410 mrl-lpr snp induced genetic

• Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

  PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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  TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence

  hep-2 archival pneumoniae immunohistochemistry western gel

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.

  hct116 crc huvecs chip-seq bulk single-cell

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest type I interferon (IFN-I) activity among PD midbrain cell types, with microglia showing markedly higher activity in PD.

  midbrain microglia substantia mptp-induced single-cell gene bulk

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

• FAM3C/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice.

  PMID 37226685 · PMC10331587 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  ILEI protein, but not mRNA, is elevated in psoriatic skin and correlates with disease severity

  skin full-thickness normal k5-ileiind immunohistochemistry scrna-seq bulk

• In B-CLL, the codon 72 polymorphic variants of p53 are not related to drug resistance and disease prognosis.

  PMID 16109171 · PMC1208864 · BMC cancer · 2005 · 7 claims · 5 setups

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  The p53 codon 72 polymorphism is not associated with drug resistance or overall survival in B-CLL

  peripheral fresh b-cll sscp-pcr disc kaplan-meier

• 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

• Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

  PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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  wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

  serum colon glioblastoma synthetic seldi-tof gene computational

• Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis.

  PMID 18635889 · PMC2556453 · American journal of respiratory and critical care medicine · 2008 · 7 claims · 5 setups

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  The TLR1 −7202A/G (rs5743551) G allele is associated with elevated TLR1-mediated cytokine production ex vivo

  blood expressing intensive patients tlr-agonist nf-κb surface

• Adapting to a changing world: RAG genomics and evolution.

  PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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  RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

  rag-1 patients zebrafish vertebrate comparative site-directed clinical

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced