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).

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• BTW: a web server for Boltzmann time warping of gene expression time series.

  PMID 16845055 · PMC1538860 · Nucleic acids research · 2006 · 5 claims · 4 setups

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  Symmetric time warping distance is more flexible than Euclidean distance or correlation coefficient for identifying genes with similar temporal expression profiles, especially across sequences of different length.

  cerevisiae homologous yeast boltzmann histogram time

• Predicting position along a looping immune response trajectory.

  PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 5 setups

  Has reproduction · 98

  Looper is an automated computational method that identifies gene pairs that trace looping trajectories when plotted against each other in longitudinally sampled data

  monocytes blood pbmcs montreal microarray qrt-pcr topological

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

  PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

  urothelial clustered genome-wide confocal k-means

• Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

  PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups

  Has reproduction · 75

  Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.

  ascending aortic clinical bulk bulk single-cell western

• Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

  PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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  Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

  european african individuals nondiabetic snp variant direct

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups

  Has reproduction · 59

  An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.

  cd8+ tce activated manual gene principal

• Reconstructing transcriptional regulatory networks through genomics data.

  PMID 20048387 · PMC3666560 · Statistical methods in medical research · 2009 · 7 claims · 5 setups

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  Location data (ChIP-chip/ChIP-seq) alone is insufficient for TRN inference because binding does not imply regulation, TF binding is dynamic across conditions/time, and TRNs involve combinatorial effects of multiple TFs not captured by single-TF ChIP experiments.

  yeast generic perturbations followed chip-chip chip-seq gene

• Core transcriptional signatures of phase change in the migratory locust.

  PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups

  Has reproduction · 60

  PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy

  locusta integrated bulk rnai computational

• Toward stem cell systems biology: from molecules to networks and landscapes.

  PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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  Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

  stem embryonic promyelocytic genome-wide serial chip-chip

• Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.

  PMID 35931118 · PMC9418907 · The Journal of biological chemistry · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  TCDD dose-dependently decreases cobalamin (Cbl) levels, compromising MUT activity and redirecting propionyl-CoA metabolism from the canonical Cbl-dependent carboxylation pathway to the alternate Cbl-independent β-oxidation-like pathway.

  liver hepatic intestinal serum targeted untargeted chip-seq

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 6 claims · 3 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification

  five gene microarray time

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups

  Has reproduction · 32

  A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).

  tcga-luad geo bulk expression methylation

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• Novel insights into adipogenesis from omics data.

  PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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  Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

  3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

• Current and future directions in genomics of amyotrophic lateral sclerosis.

  PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression