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).

• 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

• Comparison of multidimensional shotgun technologies targeting tissue proteomics.

  PMID 19960471 · PMC3465977 · Electrophoresis · 2009 · 6 claims · 4 setups

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  CITP-based multidimensional separation achieves superior overall proteome performance (more total peptide, distinct peptide, and distinct protein identifications) than SCX/MuDPIT under matched conditions

  glioblastoma peptide shotgun spectral database

• Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

  PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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  BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

  serum-derived tumour serum ht29 arms sanger topo

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes.

  PMID 19833877 · PMC2797941 · Diabetes · 2010 · 7 claims · 5 setups

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  Mitochondrial protein abundance is decreased in insulin-resistant (obese and type 2 diabetic) skeletal muscle

  skeletal volunteers bsa shotgun euglycemic-hyperinsulinemic immunoblot

• Perspectives of targeted mass spectrometry for protein biomarker verification.

  PMID 19818677 · PMC2795387 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  SRM/MRM mass spectrometry can quantify targeted proteotypic peptides as surrogates for candidate biomarker proteins in complex plasma samples

  proteins standard plasma sera srm multiplexed immunoaffinity-srm

• Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

  PMID 41826793 · PMC13020910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Pre-generated Blacklist exclusion sets were difficult to reproduce due to sensitivity to input BAM data, aligner choice, and read length

  hg38 gm12878 gse235167 syo-1 chip-seq rna-seq atac-seq

• Development of proteomic patterns for detecting lung cancer.

  PMID 14757945 · PMC3851077 · Disease markers · 2003 · 8 claims · 3 setups

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  A decision tree classification algorithm built on three serum protein mass peaks (8122Da, 1452Da, 1610Da) can discriminate lung cancer patients from healthy controls

  serum pooled seldi-tof-ms decision reproducibility

• Design considerations for workflow management systems use in production genomics research and the clinic.

  PMID 34737383 · PMC8569008 · Scientific reports · 2021 · 8 claims · 2 setups

  Has reproduction · 57

  The choice of WfMS depends both on intrinsic language/engine features and on adoption, collaboration, and technical support within bioinformatics consortia.

  local variant-calling scalability-testing

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

  PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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  Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

  genomic huvec microarray solid-phase real-time

• 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

• The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

  PMID 15748282 · PMC555539 · Nutrition journal · 2005 · 8 claims · 4 setups

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  20 μM quercetin treatment of SW480 cells for 48 h consistently decreased expression of three proteins and increased expression of one protein across four independent experiments.

  sw480 excised two-dimensional quantitative mass

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

  PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups

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  Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

  jurkat silac-based sds-page database

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

  PMID 18615428 · PMC2855839 · Proteomics · 2008 · 6 claims · 4 setups

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  Noise in SELDI-TOF/MALDI-TOF mass spectrometry data is heteroscedastic across the m/z range, with larger variance at lower m/z values, contrary to the homogeneous noise assumption of existing wavelet denoising methods.

  serum raw denoised simulated seldi-tof wavelet-based peak

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry