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 694

Assay: profiling ✕ Clear

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

universal same lim erythrocyte genome-wide cross-platform rt-pcr
Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms
Glycomics and disease markers.

PMID 19775929 · PMC2788081 · Current opinion in chemical biology · 2009 · 8 claims · 7 setups

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Over 70% of all human proteins are glycosylated

serum glycoprotein-derived sera maldi-fticr glycan nanoflow
Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium.

PMID 19746165 · PMC2736619 · PloS one · 2009 · 7 claims · 4 setups

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Comparative HPLC-MS/MS proteomic analysis, using phoP-/Q- mutants as controls, identifies PhoP-regulated proteins in S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2

typhimurium typhi genomic hplc-ms phon microarray
Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

blood baseline-corrected 953-dimensional training seldi-tof wavelet ant
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson
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
Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

Has reproduction · 90

Weak selection conferred by HSC variation created before birth can reliably yield clonal hematopoiesis later in life, demonstrated via shared prenatal circulation of monozygotic (MZ) twins.

blood simulated fluctuating single-cell
Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods.

PMID 34307679 · PMC8272456 · BioMed research international · 2021 · 7 claims · 2 setups

Has reproduction · 32

A pipeline combining Boruta and mRMR feature selection with incremental feature selection (IFS) was used to identify COVID-19-specific transcriptomic biomarkers from blood gene expression data.

blood bulk kegg
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups

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Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression

fibroblast background high-density
Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

cervical cdna microarray combinatorial
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 3 setups

Has reproduction

sRNAtoolbox 2019 adds all major small RNA library preparation protocols (including UMI-based) to sRNAbench with automatic protocol-specific preprocessing.

biological srp046046 ensembl small consensus genome
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

Has reproduction · 94

HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

pbmc cord melanoma lung scrna-seq computational
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

PMID 34772928 · PMC8590018 · Nature communications · 2021 · 8 claims · 5 setups

Has reproduction · 92

PISA-Express is a method that simultaneously measures protein expression and thermal stability (solubility) changes using only two samples per replicate per cell type

hi12 ipsc ht29 foreskin pisa expression cellular
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

Has reproduction · 95

Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

solar saltern combined individual metagenomic taxonomic functional
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

major tissues conserved predicted quantitative bead-based microarray
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups

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Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence

albicans hep-2 rhe blood phenotypic growth adhesion
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based

Experiments

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

Glycomics and disease markers.

Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium.

Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

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

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods.

Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

Phenotypic variation meets systems biology.

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.