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 23

System / cell line: surface ✕ Assay: comparison ✕ Clear

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry
The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.

PMID 15258332 · PMC3850593 · Disease markers · 2003 · 6 claims · 2 setups

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Urine MS and 1H-NMR spectral patterns can be used to discriminate IC-affected, BC-affected, and unaffected individuals with approximately 84% success rate.

urine surface-binding high-resolution
SELDI-TOF proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18644101 · PMC2481502 · Breast cancer research : BCR · 2008 · 7 claims · 3 setups

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SELDI-TOF MS proteomic profiling of breast carcinomas identifies patient subgroups with differential co-expression of protein peaks that are analogous to gene-expression-based classifications (luminal, basal, HER2 subtypes)

breast seldi-tof hierarchical biomarker
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.

PMID 19689818 · PMC2743709 · BMC cancer · 2009 · 7 claims · 3 setups

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The previously reported classifier (m/z 8,132 and 4,002) failed to discriminate CRC patients from healthy volunteers in this independent validation cohort

serum pooled seldi-tof comparative decision
The use of proteomics in biomarker discovery in neurodegenerative diseases.

PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups

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A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis

csf serum two-dimensional seldi liquid-phase
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

PMID 19888473 · PMC2768585 · PLoS computational biology · 2009 · 8 claims · 5 setups

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Translocation-related human proteins are significantly enriched in intrinsic structural disorder compared to all human proteins

translocation-related translocation cyclin-dependent intrinsic pfam randomized
Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.

PMID 38901430 · PMC11293351 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

Has reproduction · 58

rs56258221 (BACH2/MIR4464) associates with a distinct peripheral blood T cell immunophenotype in people with PSC

peripheral liver facs-sorted cd4+ flow bulk cite-seq
Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

Has reproduction · 85

AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical
Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups

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MLF accumulation more closely reflects the onset of AMD than LF accumulation

donor arpe-19 mlf sucrose phototoxicity fluorescence
Cellular proteins in influenza virus particles.

PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

influenza deglycosylated sucrose lc-ms mudpit electron
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

env u373 mt4-r5 u373-r5 phylogenetic infectivity flow
Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

PMID 20003452 · PMC2801500 · BMC medical genetics · 2009 · 8 claims · 5 setups

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TCOF1 transcript levels are significantly reduced (~18%) in leucocytes of TCS patients compared to controls

leucocytes mesenchymal leucocyte real-time direct flow
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
Next-generation high-density self-assembling functional protein arrays.

PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

test high-density amine-coated array picogreen anti-gst fluorescently
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
High-throughput crystallography for structural genomics.

PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

recombinant recalcitrant hundred family hydrogen situ site-directed
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

Experiments

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.

SELDI-TOF proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

Toward the use of genomics to study microevolutionary change in bacteria.

Oligomeric protein structure networks: insights into protein-protein interactions.

Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.

The use of proteomics in biomarker discovery in neurodegenerative diseases.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.

Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

Cellular proteins in influenza virus particles.

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

Molecular analysis of Plasmodium ovale variants.

Next-generation high-density self-assembling functional protein arrays.

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

High-throughput crystallography for structural genomics.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.