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).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: patients ✕ Assay: shotgun ✕ Clear

Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups

Has reproduction · 89

High pretreatment gut abundance of Lactobacillus (and Bifidobacterium) is strongly associated with the absence of ACRIII in rectal cancer patients undergoing neoadjuvant chemoradiotherapy.

baseline model mice intestinal shotgun fecal intestinal
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups

Has reproduction · 75

geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data

stool deduplicated reference whole-genome taxonomic functional
PCR-free method detects high frequency of genomic instability in prostate cancer.

PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

blood normal prostate matched pcr-free degenerate-pcr blastn
Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

pooled computational identified additional label-free lspad pathway-associated
Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

PMID 15312778 · PMC7127270 · Journal of molecular biology · 2004 · 8 claims · 7 setups

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ORF3a of SARS-CoV encodes an actual 31 kDa, 274-residue protein detected in infected cells and virions

vero crude sera sars-cov 2d-lc-ms sds-page western
A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion
Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional protein-protein
Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

Has reproduction · 79

TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

cecum fecal shotgun humann
The role of proteomics in depression research.

PMID 19997739 · PMC2940035 · European archives of psychiatry and clinical neuroscience · 2010 · 8 claims · 8 setups

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Proteomics offers a complementary, functional-endpoint approach that can elucidate MDD pathophysiological mechanisms and biomarkers beyond transcriptomic/targeted studies

postmortem schizophrenia frontal hypothalamus gel shotgun proteome
Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

PMID 19748658 · PMC8648281 · The Journal of allergy and clinical immunology · 2009 · 8 claims · 3 setups

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Noninvasive D-Squame tape stripping coupled with MS proteomics can profile the AD skin proteome

skin extracted lesion skin lc-ms statistical
Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

hla-b44 plasma macrophages complement proteomics shotgun cap
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
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
Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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VLU infections are polymicrobial with no single bacterium colonizing the wounds

individual pooled second btefap quantitative bulk

Experiments

Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

PCR-free method detects high frequency of genomic instability in prostate cancer.

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

Of mice and men: comparative proteomics of bronchoalveolar fluid.

Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

The role of proteomics in depression research.

Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

Defining the proteome.

Science star over Asia.

Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.