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 89

Assay: purification ✕ Clear

Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques.

PMID 19743430 · PMC2892724 · Proteomics · 2009 · 8 claims · 8 setups

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Lack of efficient enrichment procedures for PTM peptides is a major bottleneck in PTM proteomic research

cytosolic cellular unspecified yeast immunoaffinity azide chemical
Proteomic revelation: SUMO changes partners when the heat is on.

PMID 19638612 · PMC2825085 · Science signaling · 2009 · 8 claims · 4 setups

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A quantitative, system-wide MS approach combining TAP-SUMO-2 purification and triple-SILAC labeling reveals dynamic changes in SUMO-2 modification during heat shock and recovery

hela affinity western sirna
Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

PMID 39300486 · PMC11414060 · Genome biology · 2024 · 8 claims · 8 setups

Has reproduction · 78

ZBTB48 physically interacts with the m6A/m6Am demethylase FTO

hek293 inducible polyadenylated ap-ms co-immunoprecipitation clip
The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 7 claims · 7 setups

Has reproduction · 90

Phage Mimer is the first described single-stranded DNA phage targeting Pectobacterium and belongs to the family Microviridae, subfamily Bullavirinae.

pectobacterium phage cscl-purified pbr phage whole-genome genome
Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

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OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

thp-1 hek293 tandem co-immunoprecipitation oas2
Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

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A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

α5+ computational k562 embryonic ligand tandem hierarchical
Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

PMID 17537823 · PMC1919476 · Nucleic acids research · 2007 · 6 claims · 8 setups

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Endogenous nuclear pre-mRNA processing complexes (supraspliceosomes) were purified at preparative scale from human HeLa cells and chicken DT40 pre-B cells for compositional analysis

hela chicken supraspliceosome extracts glycerol tandem mass
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

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The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
A catalog of human cDNA expression clones and its application to structural genomics.

PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

hex1 ensembl coli recombinant small-scale tag-sequencing blastp
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
From genomes to systems.

PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr
The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.

interaction yeast edge-betweenness chi-squared robustness
Interactome networks: the state of the science.

PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

genes tnfα orf proteins yeast tandem interference
Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

Has reproduction · 78

The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.

leishmania orientalis culture extraction short-read
Large-scale analysis of mutations in RET exon 16 in sporadic medullary thyroid carcinomas in Japan.

PMID 11429053 · PMC5926749 · Japanese journal of cancer research : Gann · 2001 · 5 claims · 4 setups

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RET exon 16 (codon 918) somatic mutations are rare in sporadic MTC among Japanese patients

paraffin-embedded genomic direct pcr-rflp nested
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide
Preclinical and post-treatment changes in the HCC-associated serum proteome.

PMID 17060939 · PMC2360589 · British journal of cancer · 2006 · 7 claims · 6 setups

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SELDI proteomic profiling of serum reveals consistent, statistically significant changes associated with the development of HCC in hepatitis C patients

serum pooled excised seldi-tof anion lc-ms
Antibody binding loop insertions as diversity elements.

PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface
Structural genomics and drug discovery.

PMID 17488474 · PMC3822824 · Journal of cellular and molecular medicine · 2007 · 8 claims · 8 setups

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Membrane proteins represent ~70% of current drug targets but only just over 100 high-resolution structures exist for them, versus >30,000 total structures in public databases dominated by soluble proteins.

coli emre pichia sf9 cell-free bacterial inclusion
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification

Experiments

Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques.

Proteomic revelation: SUMO changes partners when the heat is on.

Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

Proteomics of the lysosome.

A catalog of human cDNA expression clones and its application to structural genomics.

The nuclear pore complex.

From genomes to systems.

The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

Interactome networks: the state of the science.

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

Large-scale analysis of mutations in RET exon 16 in sporadic medullary thyroid carcinomas in Japan.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

Preclinical and post-treatment changes in the HCC-associated serum proteome.

Antibody binding loop insertions as diversity elements.

Structural genomics and drug discovery.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.