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).

• PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

  PMID 18371219 · PMC2397526 · Breast cancer research : BCR · 2008 · 7 claims · 4 setups

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  PIK3CA mutations are not associated with altered sensitivity to preoperative anthracycline-based or taxane-based chemotherapy in ER-positive and ER-negative breast tumors

  tumor breast stage direct immunohistochemistry fluorescence

• Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

  PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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  Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

  genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

  PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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  The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

  aureus 2-d 1-d gelc-ms

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

  PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

  bombyx whole-genome snp novo

• Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

  PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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  Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

  lncap androgen prostate itraq mudpit immunoblot

• Building exposure biology centers to put the E into "G x E" interaction studies.

  PMID 19672377 · PMC2721881 · Environmental health perspectives · 2009 · 8 claims · 4 setups

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  Nongenetic factors account for high attributable risk (often 80-90%) across many chronic diseases, underscoring the importance of environmental exposure.

  mars water archived dried capillary surface adductomics

• Applying proteomics to the diagnosis and treatment of ALS and related diseases.

  PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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  Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

  csf spinal biofluid muscle 2d-dige antibody luminex

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• The process chain for peptidomic biomarker discovery.

  PMID 16410650 · PMC3850862 · Disease markers · 2006 · 8 claims · 3 setups

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  Peptidomics (comprehensive analysis of peptides and small proteins <20 kDa) fills a methodological gap left by standard proteomics, which mainly addresses proteins in the ~10-200 kDa range.

  general body patients 2d-gel peptidomics peptidomic

• Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

  PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

  Has reproduction · 68

  Arg1 is highly and specifically induced in lung CD4+ T cells during in vivo influenza infection

  flow-sort-purified lung cd4+ congenically rna-seq flow expression

• Macrel: antimicrobial peptide screening in genomes and metagenomes.

  PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups

  Has reproduction · 83

  Macrel introduces a novel set of 22 peptide features (6 local, 16 global), including a new Free Energy Transition (FET) feature group, for AMP and hemolytic activity classification

  curated hemopi-1 xiao peptide random benchmark homology-aware

• The use of neuroproteomics in drug abuse research.

  PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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  Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

  rodent brain postmortem sectioned 2d-dige itraq heat

• Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins.

  PMID 32773039 · PMC7438113 · eLife · 2020 · 8 claims · 2 setups

  Has reproduction · 87

  Germline stem cells (GSCs) have a non-canonical PRC2 distribution and lack silenced chromatin, resembling early embryonic progenitors

  drosophila facs-purified hsgfp chipseq

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative