A Direct Approach to False Discovery Rates

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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An Introduction to the Bootstrap

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An Introduction to the Bootstrap

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In silico prediction of protein-protein interactions in human macrophages

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Significance analysis of microarrays applied to the ionizing radiation response

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The positive false discovery rate: a Bayesian interpretation and the q-value

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Empirical Bayes analysis of a microarray experiment

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On the adaptive control of the false discovery rate in multiple testing with independent statistics

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Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics

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A step-down multiple hypotheses testing procedure that controls the false discovery rate under independence

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The role of statistics in the data revolution?

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Responses to Ionizing Radiation

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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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MEME SUITE: tools for motif discovery and searching

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PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

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Statistical significance for genomewide studies

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome

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An integrated catalog of reference genes in the human gut microbiome

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The positive false discovery rate: a Bayesian interpretation and the q-value

Storey, J. D. (2003) · The Annals of Statistics · doi:10.1214/aos/1074290335 · Cited by 2,204 · see citing works

Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

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Evolution of genes and genomes on the Drosophila phylogeny

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The gut microbiome in atherosclerotic cardiovascular disease

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Distinct soil microbial diversity under long-term organic and conventional farming

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Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

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Multiple Comparisons Using R

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Activation of proto-oncogenes by disruption of chromosome neighborhoods

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Fat, fibre and cancer risk in African Americans and rural Africans

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Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

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Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs

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Funnel plots for comparing institutional performance

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Interplay between the human gut microbiome and host metabolism

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How does multiple testing correction work?

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Comparison and evaluation of statistical error models for scRNA-seq

Choudhary, S., & Satija, R. (2022) · Genome Biology · doi:10.1186/s13059-021-02584-9 · Cited by 634 · see citing works

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

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A survey on filter techniques for feature selection in gene expression microarray analysis

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Fine-mapping inflammatory bowel disease loci to single-variant resolution

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Impact of regulatory variation from RNA to protein

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Effects of Experimental Sleep Restriction on Weight Gain, Caloric Intake, and Meal Timing in Healthy Adults

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Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

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Multi-tissue DNA methylation age predictor in mouse

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Correlation and Large-Scale Simultaneous Significance Testing

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Normalization, testing, and false discovery rate estimation for RNA-sequencing data

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Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention

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DNA extracted from saliva for methylation studies of psychiatric traits: evidence tissue specificity and relatedness to brain

Smith, A. K., Kilaru, V., Klengel, T., Mercer, K. B., Bradley, B., Conneely, K. N., Ressler, K. J., & Binder, E. B. (2015) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32278 · Cited by 355 · see citing works

NUFIP1 is a ribosome receptor for starvation-induced ribophagy

Wyant, G. A., Abu-Remaileh, M., Frenkel, E. M., Laqtom, N. N., Dharamdasani, V., Lewis, C. A., Chan, S. H., Heinze, I., Ori, A., & Sabatini, D. M. (2018) · Science · doi:10.1126/science.aar2663 · Cited by 363 · see citing works

Differential immune system DNA methylation and cytokine regulation in post-traumatic stress disorder

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When is hub gene selection better than standard meta-analysis?

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Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

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Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

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An exploration of aspects of Bayesian multiple testing

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Genetic structure is influenced by landscape features: empirical evidence from a roe deer population

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Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases

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Technical trading revisited: False discoveries, persistence tests, and transaction costs

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Growth control of the eukaryote cell: a systems biology study in yeast

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Imaging Patterns of Brain Development and their Relationship to Cognition

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Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of <i>Drosophila melanogaster</i>

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HIV infection is associated with compositional and functional shifts in the rectal mucosal microbiota

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Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus

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Estimating False Discovery Proportion Under Arbitrary Covariance Dependence

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Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept

Schizophrenia Working Group of the Psychiatric Genomics Consortium, Franke, B., Enigma Consortium, Stein, J. L., Ripke, S., Anttila, V., Hibar, D. P., van Hulzen, K. J. E., Arias-Vasquez, A., Smoller, J. W., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4228 · Cited by 216 · see citing works

Sex and age differences in atrophic rates: an ADNI study with n=1368 MRI scans

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Genetic variation in the CHRNA5 gene affects mRNA levels and is associated with risk for alcohol dependence

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A statin-dependent QTL for GATM expression is associated with statin-induced myopathy

Mangravite, L. M., Engelhardt, B. E., Medina, M. W., Smith, J. D., Brown, C. D., Chasman, D. I., Mecham, B. H., Howie, B., Shim, H., Naidoo, D., et al. (2013) · Nature · doi:10.1038/nature12508 · Cited by 224 · see citing works

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

Wang, H.-Q., Tuominen, L. K., & Tsai, C.-J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq650 · Cited by 223 · see citing works

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation

Ishimura, R., Nagy, G., Dotu, I., Chuang, J. H., & Ackerman, S. L. (2016) · eLife · doi:10.7554/elife.14295 · Cited by 221 · see citing works

Effects of dependence in high-dimensional multiple testing problems

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The effect of psyllium husk on intestinal microbiota in constipated patients and healthy controls

Jalanka, J., Major, G., Murray, K., Singh, G., Nowak, A., Kurtz, C., Silos-Santiago, I., Johnston, J. M., de Vos, W. M., & Spiller, R. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20020433 · Cited by 219 · see citing works

Multiple testing corrections in quantitative proteomics: A useful but blunt tool

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MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction

Menyhart, O., Weltz, B., & Győrffy, B. (2021) · PLOS ONE · doi:10.1371/journal.pone.0245824 · Cited by 216 · see citing works

Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites

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Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder

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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Kennedy, J. J., Abbatiello, S. E., Kim, K., Yan, P., Whiteaker, J. R., Lin, C., Kim, J. S., Zhang, Y., Wang, X., Ivey, R. G., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2763 · Cited by 184 · see citing works

High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

Labbé, D. P., Zadra, G., Yang, M., Reyes, J. M., Lin, C. Y., Cacciatore, S., Ebot, E. M., Creech, A. L., Giunchi, F., Fiorentino, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12298-z · Cited by 174 · see citing works

Characterization of Distinct Subpopulations of Hepatic Macrophages in HFD/Obese Mice

Morinaga, H., Mayoral, R., Heinrichsdorff, J., Osborn, O., Franck, N., Hah, N., Walenta, E., Bandyopadhyay, G., Pessentheiner, A. R., Chi, T. J., et al. (2015) · Diabetes · doi:10.2337/db14-1238 · Cited by 175 · see citing works

A statistical framework for protein quantitation in bottom-up MS-based proteomics

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Hundreds of genes experienced convergent shifts in selective pressure in marine mammals

Chikina, M., Robinson, J. D., & Clark, N. L. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw112 · Cited by 171 · see citing works

Widespread Cortical Thinning Is a Robust Anatomical Marker for Attention-Deficit/Hyperactivity Disorder

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Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Viñuela, A., Varshney, A., van de Bunt, M., Prasad, R. B., Asplund, O., Bennett, A., Boehnke, M., Brown, A. A., Erdos, M. R., Fadista, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18581-8 · Cited by 152 · see citing works

Causal associations between modifiable risk factors and the Alzheimer's phenome

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Regression-based identification of behavior-encoding neurons during large-scale optical imaging of neural activity at cellular resolution

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Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids

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Candidate gene analysis suggests a role for fatty acid biosynthesis and regulation of the complement system in the etiology of age-related maculopathy

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In touch with your emotions: Oxytocin and touch change social impressions while others’ facial expressions can alter touch

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Complex‐centric proteome profiling by SEC‐SWATH‐MS

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Genetic and clinical factors predict lithium’s effects on PER2 gene expression rhythms in cells from bipolar disorder patients

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Impairments in Cognitive Function and Brain Connectivity in Severe Asymptomatic Carotid Stenosis

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Dynamic contrast‐enhanced MRI texture analysis for pretreatment prediction of clinical and pathological response to neoadjuvant chemotherapy in patients with locally advanced breast cancer

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Transcriptome alterations of prefrontal cortical parvalbumin neurons in schizophrenia

Enwright III, J. F., Huo, Z., Arion, D., Corradi, J. P., Tseng, G., & Lewis, D. A. (2018) · Molecular Psychiatry · doi:10.1038/mp.2017.216 · Cited by 109 · see citing works

Sex and race differences in caloric intake during sleep restriction in healthy adults

Spaeth, A. M., Dinges, D. F., & Goel, N. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.114.086579 · Cited by 118 · see citing works

Modulation of mitochondrial proteome and improved mitochondrial function by biventricular pacing of dyssynchronous failing hearts

Agnetti, G., Kaludercic, N., Kane, L. A., Elliott, S. T., Guo, Y., Chakir, K., Samantapudi, D., Paolocci, N., Tomaselli, G. F., Kass, D. A., et al. (2010) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.109.871236 · Cited by 117 · see citing works

A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology

Adams, S. E., Arnold, D., Murphy, B., Carroll, P., Green, A. K., Smith, A. M., Marsh, P. D., Chen, T., Marriott, R. E., & Brading, M. G. (2017) · Scientific Reports · doi:10.1038/srep43344 · Cited by 111 · see citing works

Organizing Heterogeneous Samples Using Community Detection of GIMME-Derived Resting State Functional Networks

Gates, K. M., Molenaar, P. C. M., Iyer, S. P., Nigg, J. T., & Fair, D. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091322 · Cited by 107 · see citing works

Joint analysis of SNP and gene expression data in genetic association studies of complex diseases

Huang, Y.-T., VanderWeele, T. J., & Lin, X. (2014) · The Annals of Applied Statistics · doi:10.1214/13-aoas690 · Cited by 88 · see citing works

Cortico-cortical feedback engages active dendrites in visual cortex

Fişek, M., Herrmann, D., Egea-Weiss, A., Cloves, M., Bauer, L., Lee, T.-Y., Russell, L. E., & Häusser, M. (2023) · Nature · doi:10.1038/s41586-023-06007-6 · Cited by 80 · see citing works

Comparing connectomes across subjects and populations at different scales

Meskaldji, D. E., Fischi-Gomez, E., Griffa, A., Hagmann, P., Morgenthaler, S., & Thiran, J.-P. (2013) · NeuroImage · doi:10.1016/j.neuroimage.2013.04.084 · Cited by 77 · see citing works

Differences in muscle and adipose tissue gene expression and cardio-metabolic risk factors in the members of physical activity discordant twin pairs.

Leskinen, T., Rinnankoski-Tuikka, R., Rintala, M., Seppänen-Laakso, T., Pöllänen, E., Alen, M., Sipilä, S., Kaprio, J., Kovanen, V., Rahkila, P., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012609 · Cited by 75 · see citing works

Profiling bacterial community in upper respiratory tracts

Yi, H., Yong, D., Lee, K., Cho, Y.-J., & Chun, J. (2014) · BMC Infectious Diseases · doi:10.1186/s12879-014-0583-3 · Cited by 75 · see citing works

Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging

Heinze, I., Bens, M., Calzia, E., Holtze, S., Dakhovnik, O., Sahm, A., Kirkpatrick, J. M., Szafranski, K., Romanov, N., Sama, S. N., et al. (2018) · BMC Biology · doi:10.1186/s12915-018-0547-y · Cited by 65 · see citing works

Combining CRISPRi and metabolomics for functional annotation of compound libraries

Anglada-Girotto, M., Handschin, G., Ortmayr, K., Campos, A. I., Gillet, L., Manfredi, P., Mulholland, C. V., Berney, M., Jenal, U., Picotti, P., et al. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-00970-3 · Cited by 60 · see citing works

Variability in phase and amplitude of diurnal rhythms is related to variation of mood in bipolar and borderline personality disorder

Carr, O., Saunders, K. E. A., Tsanas, A., Bilderbeck, A. C., Palmius, N., Geddes, J. R., Foster, R., Goodwin, G. M., & De Vos, M. (2018) · Scientific Reports · doi:10.1038/s41598-018-19888-9 · Cited by 57 · see citing works

Genetic association analyses of PDYN polymorphisms with heroin and cocaine addiction

Clarke, T. ‐., Ambrose‐Lanci, L., Ferraro, T. N., Berrettini, W. H., Kampman, K. M., Dackis, C. A., Pettinati, H. M., O’Brien, C. P., Oslin, D. W., & Lohoff, F. W. (2012) · Genes, Brain and Behavior · doi:10.1111/j.1601-183x.2012.00785.x · Cited by 55 · see citing works

Eating patterns and food intake of persons with type 1 diabetes within the T1D Exchange

Powers, M. A., Gal, R. L., Connor, C. G., Mangan, M., Maahs, D. M., Clements, M. A., & Mayer-Davis, E. J. (2018) · Diabetes Research and Clinical Practice · doi:10.1016/j.diabres.2018.05.011 · Cited by 53 · see citing works

Transcriptomic analysis of genetically defined autism candidate genes reveals common mechanisms of action

Lanz, T. A., Guilmette, E., Gosink, M. M., Fischer, J. E., Fitzgerald, L. W., Stephenson, D. T., & Pletcher, M. T. (2013) · Molecular Autism · doi:10.1186/2040-2392-4-45 · Cited by 52 · see citing works

Selective Interference with Syntactic Encoding during Sentence Production by Direct Electrocortical Stimulation of the Inferior Frontal Gyrus

Chang, E. F., Kurteff, G., & Wilson, S. M. (2018) · Journal of Cognitive Neuroscience · doi:10.1162/jocn_a_01215 · Cited by 52 · see citing works

Comparison of gene expression and DNA copy number changes in a murine model of lung cancer

Sweet‐Cordero, A., Tseng, G. C., You, H., Douglass, M., Huey, B., Albertson, D., & Jacks, T. (2006) · Genes, Chromosomes and Cancer · doi:10.1002/gcc.20296 · Cited by 45 · see citing works

Toll-like receptor gene polymorphisms are associated with allergic rhinitis: a case control study

Nilsson, D., Andiappan, A. K., Halldén, C., De Yun, W., Säll, T., Tim, C. F., & Cardell, L.-O. (2012) · BMC Medical Genetics · doi:10.1186/1471-2350-13-66 · Cited by 43 · see citing works

Loss of hepatocyte cell division leads to liver inflammation and fibrosis

Dewhurst, M. R., Ow, J. R., Zafer, G., van Hul, N. K. M., Wollmann, H., Bisteau, X., Brough, D., Choi, H., & Kaldis, P. (2020) · PLOS Genetics · doi:10.1371/journal.pgen.1009084 · Cited by 42 · see citing works

Voluntary exercise followed by chronic stress strikingly increases mature adult-born hippocampal neurons and prevents stress-induced deficits in’ what-when-where’ memory

Castilla-Ortega, E., Rosell-Valle, C., Pedraza, C., Rodríguez de Fonseca, F., Estivill-Torrús, G., & Santín, L. J. (2014) · Neurobiology of Learning and Memory · doi:10.1016/j.nlm.2013.12.001 · Cited by 41 · see citing works

Quantitative measurement of allele‐specific protein expression in a diploid yeast hybrid by LC‐MS

Khan, Z., Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., & Kruglyak, L. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.34 · Cited by 37 · see citing works

β‐catenin deficiency in hepatocytes aggravates hepatocarcinogenesis driven by oncogenic β‐catenin and MET

Liang, Y., Feng, Y., Zong, M., Wei, X., Lee, J., Feng, Y., Li, H., Yang, G., Wu, Z., Fu, X., et al. (2018) · Hepatology · doi:10.1002/hep.29661 · Cited by 36 · see citing works

Maternal aggression: New insights from Egr-1

Hasen, N. S., & Gammie, S. C. (2006) · Brain Research · doi:10.1016/j.brainres.2006.06.007 · Cited by 37 · see citing works

A modified Benjamini–Hochberg multiple comparisons procedure for controlling the false discovery rate

Kwong, K. S., Holland, B., & Cheung, S. H. (2002) · Journal of Statistical Planning and Inference · doi:10.1016/s0378-3758(01)00252-x · Cited by 54 · see citing works

Accurate error control in high dimensional association testing using conditional false discovery ratesPreprint

Liley, J., & Wallace, C. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/414318 · Cited by 8 · see citing works

Controlling Error Rates with Multiple Positively-Dependent Tests

Masud, A. A. (2021) · Digital Commons - USU (Utah State University) · doi:10.26076/78d1-9f57

Implementing false discovery rate control: increasing your power

Verhoeven, K. J. F., Simonsen, K. L., & McIntyre, L. M. (2005) · Oikos · doi:10.1111/j.0030-1299.2005.13727.x · Cited by 964 · see citing works

Simultaneous testing of multiple hypotheses using generalized p-values

Tsui, K., & Tang, S. (2007) · Statistics & Probability Letters · doi:10.1016/j.spl.2007.03.022 · Cited by 2 · see citing works