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: spectra ✕ Assay: gene ✕ Clear

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

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

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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
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
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups

Has reproduction · 53

spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.

two-gene three-gene emt circuit simulation grn scrna-seq
Application of proteomics in the study of tumor metastasis.

PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

young metastatic hepatocellular lines microarray 2de cdna
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

pcr-amplified same sequence luciferase bioluminometric bati comparison
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

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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
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

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Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

ensembl genomic simulation pcr maldi-tof
Large-scale and high-confidence proteomic analysis of human seminal plasma.

PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

seminal same list combined sds-page database decoy
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

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

vastus skeletal spectra identified phosphopeptide in-solution strong
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups

Has reproduction · 63

Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA

clinical nicu genomic maldi-tof pbp2a cefoxitin
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

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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
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

PMID 15905472 · PMC1131937 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Introducing streptavidin-coated magnetic microparticles (MMPs) into a sandwich-type CP-based DNA sensor significantly improves selectivity against non-cognate DNA compared with previously reported CP-amplified sensors.

cell-free synthetic brca1-related artificial fluorescence magnetically salt-stringency
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

Experiments

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

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

spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

Application of proteomics in the study of tumor metastasis.

A mouse plasma peptide atlas as a resource for disease proteomics.

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

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

Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

Large-scale and high-confidence proteomic analysis of human seminal plasma.

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

Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

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

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

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.