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 9

System / cell line: spectra ✕ Assay: prediction ✕ Clear

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

Full-text index only

Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

breast commercial vertebrate genes cdna activity computational
Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

Full-text index only

SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

serum seldi dlbcl pooled seldi-tof-ms proteinchip decision
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

Full-text index only

The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

Has reproduction · 64

The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

caecilian caecilia archival lws pcr eye histology
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

Has reproduction · 93

Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

huvecs huvec long-read bottom-up offline
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

Full-text index only

High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

tuberculosis sanger spectra lc-ms sds-page signal
In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

Full-text index only

This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

vastus skeletal spectra identified phosphopeptide in-solution strong
Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

PMID 19709643 · PMC3159575 · Journal of proteomics · 2009 · 7 claims · 5 setups

Full-text index only

Methanol-based solubilization, alone or combined with PPS, yields significantly higher membrane protein identification/enrichment than PPS alone in monocyte membrane proteomics

bacteriorhodopsin crude immuno-affinity lc-ms sds-page shotgun facs
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

Full-text index only

Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational

Experiments

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.