IDEAS home Printed from https://ideas.repec.org/r/bpj/sagmbi/v3y2004i1n3.html
   My bibliography  Save this item

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Citations

Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
as


Cited by:

  1. Arsheed H. Sheikh & Iosif Zacharia & Alonso J. Pardal & Ana Dominguez-Ferreras & Daniela J. Sueldo & Jung-Gun Kim & Alexi Balmuth & Jose R. Gutierrez & Brendon F. Conlan & Najeeb Ullah & Olivia M. Nip, 2023. "Dynamic changes of the Prf/Pto tomato resistance complex following effector recognition," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  2. Nicola J. Armstrong, 2008. "The changing focus of microarray analysis," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 62(3), pages 364-373, August.
  3. Ila Pant & Neeraj Kumar & Imran Khan & Somanahalli Girish Rao & Paturu Kondaiah, 2015. "Role of Areca Nut Induced TGF-β and Epithelial-Mesenchymal Interaction in the Pathogenesis of Oral Submucous Fibrosis," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-19, June.
  4. Dazard, Jean-Eudes & Sunil Rao, J., 2012. "Joint adaptive mean–variance regularization and variance stabilization of high dimensional data," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2317-2333.
  5. Montazeri Zahra & Yanofsky Corey M. & Bickel David R., 2010. "Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-33, June.
  6. Aaron C Ericsson & J Wade Davis & William Spollen & Nathan Bivens & Scott Givan & Catherine E Hagan & Mark McIntosh & Craig L Franklin, 2015. "Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-19, February.
  7. Ricardo C Gehrau & Kellie J Archer & Valeria R Mas & Daniel G Maluf, 2012. "Molecular Profiles of HCV Cirrhotic Tissues Derived in a Panel of Markers with Clinical Utility for Hepatocellular Carcinoma Surveillance," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-12, July.
  8. Chaofeng Yuan & Wensheng Zhu & Xuming He & Jianhua Guo, 2019. "A mixture factor model with applications to microarray data," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(1), pages 60-76, March.
  9. Ming Yuan & Christina Kendziorski, 2006. "A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification," Biometrics, The International Biometric Society, vol. 62(4), pages 1089-1098, December.
  10. Debajyoti Ghosh & Lili Ding & Umasundari Sivaprasad & Esmond Geh & Jocelyn Biagini Myers & Jonathan A Bernstein & Gurjit K Khurana Hershey & Tesfaye B Mersha, 2015. "Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-23, December.
  11. Olivia Prazeres da Costa & Arthur Hoffman & Johannes W Rey & Ulrich Mansmann & Thorsten Buch & Achim Tresch, 2014. "Selection of Higher Order Regression Models in the Analysis of Multi-Factorial Transcription Data," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-8, March.
  12. Tony Marion & Husni Elbahesh & Paul G Thomas & John P DeVincenzo & Richard Webby & Klaus Schughart, 2016. "Respiratory Mucosal Proteome Quantification in Human Influenza Infections," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-16, April.
  13. Jianhua Hu & Fred A. Wright, 2007. "Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean-Variance Model," Biometrics, The International Biometric Society, vol. 63(1), pages 41-49, March.
  14. Nan Li & Matthew N. McCall & Zhijin Wu, 2017. "Establishing Informative Prior for Gene Expression Variance from Public Databases," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 160-177, June.
  15. Theresa Niederberger & Stefanie Etzold & Michael Lidschreiber & Kerstin C Maier & Dietmar E Martin & Holger Fröhlich & Patrick Cramer & Achim Tresch, 2012. "MC EMiNEM Maps the Interaction Landscape of the Mediator," PLOS Computational Biology, Public Library of Science, vol. 8(6), pages 1-10, June.
  16. Brian Caffo & Liu Dongmei & Giovanni Parmigiani, 2004. "Power Conjugate Multilevel Models with Applications to Genomics," Johns Hopkins University Dept. of Biostatistics Working Paper Series 1062, Berkeley Electronic Press.
  17. Daniel J. Fazakerley & Julian van Gerwen & Kristen C. Cooke & Xiaowen Duan & Elise J. Needham & Alexis Díaz-Vegas & Søren Madsen & Dougall M. Norris & Amber S. Shun-Shion & James R. Krycer & James G. , 2023. "Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  18. Alastair G. Kerr & Zuoneng Wang & Na Wang & Kelvin H. M. Kwok & Jutta Jalkanen & Alison Ludzki & Simon Lecoutre & Dominique Langin & Martin O. Bergo & Ingrid Dahlman & Carsten Mim & Peter Arner & Hui , 2022. "The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  19. Simina M. Boca & Héctor Céorrada Bravo & Brian Caffo & Jeffrey T. Leek & Giovanni Parmigiani, 2013. "A Decision-Theory Approach to Interpretable Set Analysis for High-Dimensional Data," Biometrics, The International Biometric Society, vol. 69(3), pages 614-623, September.
  20. Morten Tulstrup & Mette Soerensen & Jakob Werner Hansen & Linn Gillberg & Maria Needhamsen & Katja Kaastrup & Kristian Helin & Kaare Christensen & Joachim Weischenfeldt & Kirsten Grønbæk, 2021. "TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
  21. Asta Laiho & Laura L Elo, 2014. "A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-12, December.
  22. Madsen Tobias & Świtnicki Michał & Juul Malene & Pedersen Jakob Skou, 2019. "EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(6), pages 1-23, December.
  23. Kerr Kathleen F., 2012. "Optimality Criteria for the Design of 2-Color Microarray Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-9, January.
  24. Xin Victoria Wang & Roel G W Verhaak & Elizabeth Purdom & Paul T Spellman & Terence P Speed, 2011. "Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-14, March.
  25. Mark Pinese & Christopher J Scarlett & James G Kench & Emily K Colvin & Davendra Segara & Susan M Henshall & Robert L Sutherland & Andrew V Biankin, 2009. "Messina: A Novel Analysis Tool to Identify Biologically Relevant Molecules in Disease," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-7, April.
  26. Sayantee Jana & Narayanaswamy Balakrishnan & Dietrich Rosen & Jemila Seid Hamid, 2017. "High dimensional extension of the growth curve model and its application in genetics," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 26(2), pages 273-292, June.
  27. Cherif Ben Hamda & Raphael Sangeda & Liberata Mwita & Ayton Meintjes & Siana Nkya & Sumir Panji & Nicola Mulder & Lamia Guizani-Tabbane & Alia Benkahla & Julie Makani & Kais Ghedira & H3ABioNet Consor, 2018. "A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study," PLOS ONE, Public Library of Science, vol. 13(7), pages 1-21, July.
  28. Way-Champ Mah & Thomas Thurnherr & Pierce K H Chow & Alexander Y F Chung & London L P J Ooi & Han Chong Toh & Bin Tean Teh & Yogen Saunthararajah & Caroline G L Lee, 2014. "Methylation Profiles Reveal Distinct Subgroup of Hepatocellular Carcinoma Patients with Poor Prognosis," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-10, August.
  29. Ambroise Jérôme & Bearzatto Bertrand & Robert Annie & Macq Benoit & Gala Jean-Luc, 2012. "Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-20, February.
  30. Cecilia Patitucci & Juan Diego Hernández-Camacho & Elodie Vimont & Sonny Yde & Thomas Cokelaer & Thibault Chaze & Quentin Giai Gianetto & Mariette Matondo & Anastasia Gazi & Ivan Nemazanyy & David A. , 2023. "Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  31. N. Bochkina & S. Richardson, 2007. "Tail Posterior Probability for Inference in Pairwise and Multiclass Gene Expression Data," Biometrics, The International Biometric Society, vol. 63(4), pages 1117-1125, December.
  32. J. McClatchy & R. Strogantsev & E. Wolfe & H. Y. Lin & M. Mohammadhosseini & B. A. Davis & C. Eden & D. Goldman & W. H. Fleming & P. Conley & G. Wu & L. Cimmino & H. Mohammed & A. Agarwal, 2023. "Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  33. Nott, David J. & Yu, Zeming & Chan, Eva & Cotsapas, Chris & Cowley, Mark J. & Pulvers, Jeremy & Williams, Rohan & Little, Peter, 2007. "Hierarchical Bayes variable selection and microarray experiments," Journal of Multivariate Analysis, Elsevier, vol. 98(4), pages 852-872, April.
  34. Wen Yalu & Li Ming & Fu Wenjiang J, 2011. "MA-SNP -- A New Genotype Calling Method for Oligonucleotide SNP Arrays Modeling the Batch Effect with a Normal Mixture Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-23, August.
  35. Marot, Guillemette & Foulley, Jean-Louis & Jaffrzic, Florence, 2009. "A structural mixed model to shrink covariance matrices for time-course differential gene expression studies," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1630-1638, March.
  36. Elizabeth A Osterndorff-Kahanek & Gayatri R Tiwari & Marcelo F Lopez & Howard C Becker & R Adron Harris & R Dayne Mayfield, 2018. "Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain," PLOS ONE, Public Library of Science, vol. 13(1), pages 1-25, January.
  37. Ji Tieming & Liu Peng & Nettleton Dan, 2012. "Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-29, May.
  38. Alexandra Gyurdieva & Stefan Zajic & Ya-Fang Chang & E. Andres Houseman & Shan Zhong & Jaegil Kim & Michael Nathenson & Thomas Faitg & Mary Woessner & David C. Turner & Aisha N. Hasan & John Glod & Ro, 2022. "Biomarker correlates with response to NY-ESO-1 TCR T cells in patients with synovial sarcoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  39. Gallopin Mélina & Celeux Gilles & Jaffrézic Florence & Rau Andrea, 2015. "A model selection criterion for model-based clustering of annotated gene expression data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(5), pages 413-428, November.
  40. Rowena Y Kelley & W Paul Williams & J Erik Mylroie & Deborah L Boykin & Jonathan W Harper & Gary L Windham & Arunkanth Ankala & Xueyan Shan, 2012. "Identification of Maize Genes Associated with Host Plant Resistance or Susceptibility to Aspergillus flavus Infection and Aflatoxin Accumulation," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-12, May.
  41. Rossell David & Guerra Rudy & Scott Clayton, 2008. "Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-29, April.
  42. Luis E. Nieto-Barajas & Peter Müller & Yuan Ji & Yiling Lu & Gordon B. Mills, 2012. "A Time-Series DDP for Functional Proteomics Profiles," Biometrics, The International Biometric Society, vol. 68(3), pages 859-868, September.
  43. Hui Jiang & Tianyu Zhan, 2017. "Unit-Free and Robust Detection of Differential Expression from RNA-Seq Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 178-199, June.
  44. Huiping Zhang & Fan Wang & Henry R Kranzler & Hongyu Zhao & Joel Gelernter, 2013. "Profiling of Childhood Adversity-Associated DNA Methylation Changes in Alcoholic Patients and Healthy Controls," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-9, June.
  45. María Pérez-Burgos & Marco Herfurth & Andreas Kaczmarczyk & Andrea Harms & Katrin Huber & Urs Jenal & Timo Glatter & Lotte Søgaard-Andersen, 2024. "A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  46. Bommert, Andrea & Sun, Xudong & Bischl, Bernd & Rahnenführer, Jörg & Lang, Michel, 2020. "Benchmark for filter methods for feature selection in high-dimensional classification data," Computational Statistics & Data Analysis, Elsevier, vol. 143(C).
  47. Fresno, Cristóbal & Balzarini, Mónica & Fernández, Elmer, 2014. "lmdme: Linear Models on Designed Multivariate Experiments in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 56(i07).
  48. Irati Macaya & Marta Roman & Connor Welch & Rodrigo Entrialgo-Cadierno & Marina Salmon & Alba Santos & Iker Feliu & Joanna Kovalski & Ines Lopez & Maria Rodriguez-Remirez & Sara Palomino-Echeverria & , 2023. "Signature-driven repurposing of Midostaurin for combination with MEK1/2 and KRASG12C inhibitors in lung cancer," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  49. Sophie Depiereux & Florence Le Gac & Bertrand De Meulder & Michael Pierre & Raphaël Helaers & Yann Guiguen & Patrick Kestemont & Eric Depiereux, 2015. "Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-27, September.
  50. Hong, Zhaoping & Lian, Heng, 2012. "BOPA: A Bayesian hierarchical model for outlier expression detection," Computational Statistics & Data Analysis, Elsevier, vol. 56(12), pages 4146-4156.
  51. Yexuan Deng & Sarah T. Diepstraten & Margaret A. Potts & Göknur Giner & Stephanie Trezise & Ashley P. Ng & Gerry Healey & Serena R. Kane & Amali Cooray & Kira Behrens & Amy Heidersbach & Andrew J. Kue, 2022. "Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  52. Marot Guillemette & Mayer Claus-Dieter, 2009. "Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-35, January.
  53. Sébastien L Floor & Aline Hebrant & Jaime M Pita & Manuel Saiselet & Christophe Trésallet & Frederick Libert & Guy Andry & Jacques E Dumont & Wilma C van Staveren & Carine Maenhaut, 2014. "MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
  54. J. T. Gene Hwang & Jing Qiu & Zhigen Zhao, 2009. "Empirical Bayes confidence intervals shrinking both means and variances," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(1), pages 265-285, January.
  55. Tresch Achim & Markowetz Florian, 2008. "Structure Learning in Nested Effects Models," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-28, March.
  56. Caffo Brian S & Liu Dongmei & Scharpf Robert B. & Parmigiani Giovanni, 2009. "Likelihood Estimation of Conjugacy Relationships in Linear Models with Applications to High-Throughput Genomics," The International Journal of Biostatistics, De Gruyter, vol. 5(1), pages 1-25, May.
  57. Rodolfo A. Maniero & Cristiana Picco & Anja Hartmann & Felipe Engelberger & Antonella Gradogna & Joachim Scholz-Starke & Michael Melzer & Georg Künze & Armando Carpaneto & Nicolaus Wirén & Ricardo F. , 2024. "Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  58. Nyangoma Stephen O. & Collins Stuart I. & Altman Douglas G. & Johnson Philip & Billingham Lucinda J., 2012. "Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-42, February.
  59. Sora Yoon & Seon-Young Kim & Dougu Nam, 2016. "Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates," PLOS ONE, Public Library of Science, vol. 11(11), pages 1-16, November.
  60. Tong, Tiejun & Jang, Homin & Wang, Yuedong, 2012. "James–Stein type estimators of variances," Journal of Multivariate Analysis, Elsevier, vol. 107(C), pages 232-243.
  61. Bar Haim Y. & Booth James G. & Wells Martin T., 2012. "A Mixture-Model Approach for Parallel Testing for Unequal Variances," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-21, January.
  62. Marine Jeanmougin & Aurelien de Reynies & Laetitia Marisa & Caroline Paccard & Gregory Nuel & Mickael Guedj, 2010. "Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-9, September.
  63. Elisa Salviato & Vera Djordjilović & Monica Chiogna & Chiara Romualdi, 2019. "SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways," PLOS Computational Biology, Public Library of Science, vol. 15(10), pages 1-28, October.
  64. Feng-Hsiang Chung & Zhen-Hua Jin & Tzu-Ting Hsu & Chueh-Lin Hsu & Hsueh-Chuan Liu & Hoong-Chien Lee, 2015. "Gene-Set Local Hierarchical Clustering (GSLHC)—A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-23, October.
  65. Joao A. Ascensao & Kelly M. Wetmore & Benjamin H. Good & Adam P. Arkin & Oskar Hallatschek, 2023. "Quantifying the local adaptive landscape of a nascent bacterial community," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  66. Atle van Beelen Granlund & Arnar Flatberg & Ann E Østvik & Ignat Drozdov & Bjørn I Gustafsson & Mark Kidd & Vidar Beisvag & Sverre H Torp & Helge L Waldum & Tom Christian Martinsen & Jan Kristian Damå, 2013. "Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-14, February.
  67. Victoria Menzies & Debra E. Lyon & Kellie J. Archer & Qing Zhou & Jenni Brumelle & Kimberly H. Jones & G. Gao & Timothy P. York & Colleen Jackson-Cook, 2013. "Epigenetic Alterations and an Increased Frequency of Micronuclei in Women with Fibromyalgia," Nursing Research and Practice, Hindawi, vol. 2013, pages 1-12, August.
  68. Anke Van den broeck & Hugo Vankelecom & Wouter Van Delm & Lies Gremeaux & Jasper Wouters & Joke Allemeersch & Olivier Govaere & Tania Roskams & Baki Topal, 2013. "Human Pancreatic Cancer Contains a Side Population Expressing Cancer Stem Cell-Associated and Prognostic Genes," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-7, September.
  69. Mohammad Ohid ULLAH, 2013. "Improving The Output Of Signaling Pathway Impact Analysis," Romanian Statistical Review, Romanian Statistical Review, vol. 61(3), pages 38-43, April.
  70. Aaron Wing Cheung Kwok & Chen Qiao & Rongting Huang & Mai-Har Sham & Joshua W. K. Ho & Yuanhua Huang, 2022. "MQuad enables clonal substructure discovery using single cell mitochondrial variants," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  71. Mariel C. Paul & Christian Schneeweis & Chiara Falcomatà & Chuan Shan & Daniel Rossmeisl & Stella Koutsouli & Christine Klement & Magdalena Zukowska & Sebastian A. Widholz & Moritz Jesinghaus & Konsta, 2023. "Non-canonical functions of SNAIL drive context-specific cancer progression," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  72. Leek Jeffrey T & Storey John D., 2011. "The Joint Null Criterion for Multiple Hypothesis Tests," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, June.
  73. Herman M J Sontrop & Wim F J Verhaegh & Marcel J T Reinders & Perry D Moerland, 2011. "An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-12, July.
  74. Yi-Cheng Chang & Jan Manent & Jan Schroeder & Siew Fen Lisa Wong & Gabriel M. Hauswirth & Natalia A. Shylo & Emma L. Moore & Annita Achilleos & Victoria Garside & Jose M. Polo & Paul Trainor & Edwina , 2022. "Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  75. Lund Steven P. & Nettleton Dan & McCarthy Davis J. & Smyth Gordon K., 2012. "Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-44, October.
  76. John S Hall & Rohan Iype & Joana Senra & Janet Taylor & Lucile Armenoult & Kenneth Oguejiofor & Yaoyong Li & Ian Stratford & Peter L Stern & Mark J O’Connor & Crispin J Miller & Catharine M L West, 2014. "Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-14, January.
  77. Saori Kashima & Masatoshi Matsumoto & Takahiko Ogawa & Akira Eboshida & Keisuke Takeuchi, 2012. "The Impact of Travel Time on Geographic Distribution of Dialysis Patients," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-8, October.
  78. Ben Li & Yunxiao Li & Zhaohui S. Qin, 2017. "Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 73-90, June.
  79. Qin, Huaizhen & Ouyang, Weiwei, 2015. "Statistical properties of gene–gene correlations in omics experiments," Statistics & Probability Letters, Elsevier, vol. 97(C), pages 206-211.
  80. Xu, Ping & Brock, Guy N. & Parrish, Rudolph S., 2009. "Modified linear discriminant analysis approaches for classification of high-dimensional microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1674-1687, March.
  81. Bilgrau, Anders Ellern & Eriksen, Poul Svante & Rasmussen, Jakob Gulddahl & Johnsen, Hans Erik & Dybkaer, Karen & Boegsted, Martin, 2016. "GMCM: Unsupervised Clustering and Meta-Analysis Using Gaussian Mixture Copula Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 70(i02).
  82. Xiao Min & Chen Ting & Huang Kunpeng & Ming Ruixing, 2020. "Optimal Estimation for Power of Variance with Application to Gene-Set Testing," Journal of Systems Science and Information, De Gruyter, vol. 8(6), pages 549-564, December.
  83. Dominic Coey & Kenneth Hung, 2022. "Empirical Bayes Selection for Value Maximization," Papers 2210.03905, arXiv.org, revised Jan 2023.
  84. Yu Lianbo & Gulati Parul & Fernandez Soledad & Pennell Michael & Kirschner Lawrence & Jarjoura David, 2011. "Fully Moderated T-statistic for Small Sample Size Gene Expression Arrays," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, September.
  85. Hossain, Ahmed & Beyene, Joseph & Willan, Andrew R. & Hu, Pingzhao, 2009. "A flexible approximate likelihood ratio test for detecting differential expression in microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(10), pages 3685-3695, August.
  86. Yeil Kwon & Zhigen Zhao, 2023. "On F-modelling-based empirical Bayes estimation of variances," Biometrika, Biometrika Trust, vol. 110(1), pages 69-81.
  87. Bernie J Daigle Jr & Alicia Deng & Tracey McLaughlin & Samuel W Cushman & Margaret C Cam & Gerald Reaven & Philip S Tsao & Russ B Altman, 2010. "Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-15, March.
  88. Ju Han & Hang Chang & Orsi Giricz & Genee Y Lee & Frederick L Baehner & Joe W Gray & Mina J Bissell & Paraic A Kenny & Bahram Parvin, 2010. "Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture," PLOS Computational Biology, Public Library of Science, vol. 6(2), pages 1-12, February.
  89. Andres Tapia del Fierro & Bianca den Hamer & Natalia Benetti & Natasha Jansz & Kelan Chen & Tamara Beck & Hannah Vanyai & Alexandra D. Gurzau & Lucia Daxinger & Shifeng Xue & Thanh Thao Nguyen Ly & Ir, 2023. "SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  90. Yan Geng & Lin Li & Jie Yan & Kevin Liu & Aizhen Yang & Lin Zhang & Yingzhi Shen & Han Gao & Xuefeng Wu & Imre Noth & Yong Huang & Junling Liu & Xuemei Fan, 2022. "PEAR1 regulates expansion of activated fibroblasts and deposition of extracellular matrix in pulmonary fibrosis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  91. Francesca Cordero & Marco Beccuti & Maddalena Arigoni & Susanna Donatelli & Raffaele A Calogero, 2012. "Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-10, February.
  92. Soneson, Charlotte & Fontes, Magnus, 2014. "Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 588-598.
  93. Santu Ghosh & Alan M. Polansky, 2022. "Large-Scale Simultaneous Testing Using Kernel Density Estimation," Sankhya A: The Indian Journal of Statistics, Springer;Indian Statistical Institute, vol. 84(2), pages 808-843, August.
  94. Nicholas C. Henderson & Michael A. Newton, 2016. "Making the cut: improved ranking and selection for large-scale inference," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 78(4), pages 781-804, September.
  95. Alin Tomoiaga & Peter Westfall & Michele Donato & Sorin Draghici & Sonia Hassan & Roberto Romero & Paola Tellaroli, 2016. "Pathway crosstalk effects: shrinkage and disentanglement using a Bayesian hierarchical model," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(2), pages 374-394, October.
  96. Chee Ho H’ng & Shanika L. Amarasinghe & Boya Zhang & Hojin Chang & Xinli Qu & David R. Powell & Alberto Rosello-Diez, 2024. "Compensatory growth and recovery of cartilage cytoarchitecture after transient cell death in fetal mouse limbs," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  97. Qianxing Mo & Faming Liang, 2010. "Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model," Biometrics, The International Biometric Society, vol. 66(4), pages 1284-1294, December.
  98. Suraj Peri & Karthik Devarajan & Dong-Hua Yang & Alfred G Knudson & Siddharth Balachandran, 2013. "Meta-Analysis Identifies NF-κB as a Therapeutic Target in Renal Cancer," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-1, October.
  99. Marko Sysi-Aho & Andrey Ermolov & Peddinti V Gopalacharyulu & Abhishek Tripathi & Tuulikki Seppänen-Laakso & Johanna Maukonen & Ismo Mattila & Suvi T Ruohonen & Laura Vähätalo & Laxman Yetukuri & Tain, 2011. "Metabolic Regulation in Progression to Autoimmune Diabetes," PLOS Computational Biology, Public Library of Science, vol. 7(10), pages 1-16, October.
  100. Youngjo Lee & Jan F. Bjørnstad, 2013. "Extended likelihood approach to large-scale multiple testing," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 75(3), pages 553-575, June.
  101. Robin, Stephane & Bar-Hen, Avner & Daudin, Jean-Jacques & Pierre, Laurent, 2007. "A semi-parametric approach for mixture models: Application to local false discovery rate estimation," Computational Statistics & Data Analysis, Elsevier, vol. 51(12), pages 5483-5493, August.
  102. Hongkai Ji & Wing Hung Wong, 2006. "Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes," Biometrics, The International Biometric Society, vol. 62(3), pages 645-663, September.
  103. Bickel David R., 2008. "Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-27, March.
  104. Stephen M Christensen & Laura A L Dillon & Lucas P Carvalho & Sara Passos & Fernanda O Novais & V Keith Hughitt & Daniel P Beiting & Edgar M Carvalho & Phillip Scott & Najib M El-Sayed & David M Mosse, 2016. "Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion," PLOS Neglected Tropical Diseases, Public Library of Science, vol. 10(9), pages 1-17, September.
  105. Asomaning, N. & Archer, K.J., 2012. "High-throughput DNA methylation datasets for evaluating false discovery rate methodologies," Computational Statistics & Data Analysis, Elsevier, vol. 56(6), pages 1748-1756.
  106. Kai Kammers & Margaret A Taub & Ingo Ruczinski & Joshua Martin & Lisa R Yanek & Alyssa Frazee & Yongxing Gao & Dixie Hoyle & Nauder Faraday & Diane M Becker & Linzhao Cheng & Zack Z Wang & Jeff T Leek, 2017. "Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-16, January.
  107. Ahmed Hossain & Hafiz T.A. Khan, 2016. "Identification of genomic markers correlated with sensitivity in solid tumors to Dasatinib using sparse principal components," Journal of Applied Statistics, Taylor & Francis Journals, vol. 43(14), pages 2538-2549, October.
  108. Qiu Jing & Qi Yue & Cui Xiangqin, 2014. "Applying shrinkage variance estimators to the TOST test in high dimensional settings," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(3), pages 323-341, June.
  109. Mark A. van de Wiel & Kyung In Kim, 2007. "Estimating the False Discovery Rate Using Nonparametric Deconvolution," Biometrics, The International Biometric Society, vol. 63(3), pages 806-815, September.
  110. Sisi Ma & Patrick Kemmeren & David Gresham & Alexander Statnikov, 2014. "De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-20, September.
  111. Sinan Xiong & Jianbiao Zhou & Tze King Tan & Tae-Hoon Chung & Tuan Zea Tan & Sabrina Hui-Min Toh & Nicole Xin Ning Tang & Yunlu Jia & Yi Xiang See & Melissa Jane Fullwood & Takaomi Sanda & Wee-Joo Chn, 2024. "Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  112. Mary-Huard Tristan & Jaffrezic Florence & Robin Stéphane, 2012. "ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-22, November.
  113. Hirakawa, Akihiro & Hamada, Chikuma & Yoshimura, Isao, 2011. "Sample size calculation for a regularized t-statistic in microarray experiments," Statistics & Probability Letters, Elsevier, vol. 81(7), pages 870-875, July.
  114. Long Qu & Dan Nettleton & Jack C. M. Dekkers, 2012. "Improved Estimation of the Noncentrality Parameter Distribution from a Large Number of t-Statistics, with Applications to False Discovery Rate Estimation in Microarray Data Analysis," Biometrics, The International Biometric Society, vol. 68(4), pages 1178-1187, December.
  115. Pingzhao Hu & Celia M. T. Greenwood & Joseph Beyene, 2006. "Statistical Methods for Meta-Analysis of Microarray Data: A Comparative Study," Information Systems Frontiers, Springer, vol. 8(1), pages 9-20, February.
  116. Angela L. Riffo-Campos & Guillermo Ayala & Juan Domingo, 2021. "Ordering of Omics Features Using Beta Distributions on Montecarlo p -Values," Mathematics, MDPI, vol. 9(11), pages 1-18, June.
  117. Caroline E. Dewar & Silke Oeljeklaus & Jan Mani & Wignand W. D. Mühlhäuser & Corinne Känel & Johannes Zimmermann & Torsten Ochsenreiter & Bettina Warscheid & André Schneider, 2022. "Mistargeting of aggregation prone mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  118. Hwang J.T. Gene & Liu Peng, 2010. "Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-35, October.
  119. Alexander Kaever & Manuel Landesfeind & Kirstin Feussner & Burkhard Morgenstern & Ivo Feussner & Peter Meinicke, 2014. "Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-12, February.
  120. Jow Howsun & Boys Richard J. & Wilkinson Darren J., 2014. "Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(5), pages 531-551, October.
  121. Gabriela V Cohen Freue & Anna Meredith & Derek Smith & Axel Bergman & Mayu Sasaki & Karen K Y Lam & Zsuzsanna Hollander & Nina Opushneva & Mandeep Takhar & David Lin & Janet Wilson-McManus & Robert Ba, 2013. "Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation," PLOS Computational Biology, Public Library of Science, vol. 9(4), pages 1-15, April.
  122. Perualila-Tan Nolen & Kasim Adetayo & Talloen Willem & Verbist Bie & Göhlmann Hinrich W.H. & QSTAR Consortium & Shkedy Ziv, 2016. "A joint modeling approach for uncovering associations between gene expression, bioactivity and chemical structure in early drug discovery to guide lead selection and genomic biomarker development," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(4), pages 291-304, August.
  123. Hai-Bo Zhang & Xiao-Bao Ding & Jie Jin & Wen-Ping Guo & Qiao-Lei Yang & Peng-Cheng Chen & Heng Yao & Li Ruan & Yu-Tian Tao & Xin Chen, 2022. "Predicted mouse interactome and network-based interpretation of differentially expressed genes," PLOS ONE, Public Library of Science, vol. 17(4), pages 1-16, April.
  124. Erminia Donnarumma & Michael Kohlhaas & Elodie Vimont & Etienne Kornobis & Thibault Chaze & Quentin Giai Gianetto & Mariette Matondo & Maryse Moya-Nilges & Christoph Maack & Timothy Wai, 2022. "Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure," Nature Communications, Nature, vol. 13(1), pages 1-24, December.
  125. Kiiveri, Harri & de Hoog, Frank, 2012. "Fitting very large sparse Gaussian graphical models," Computational Statistics & Data Analysis, Elsevier, vol. 56(9), pages 2626-2636.
  126. Tomi Suomi & Fatemeh Seyednasrollah & Maria K Jaakkola & Thomas Faux & Laura L Elo, 2017. "ROTS: An R package for reproducibility-optimized statistical testing," PLOS Computational Biology, Public Library of Science, vol. 13(5), pages 1-10, May.
  127. Petra Massoner & Karl G Kugler & Karin Unterberger & Ruprecht Kuner & Laurin A J Mueller & Maria Fälth & Georg Schäfer & Christof Seifarth & Simone Ecker & Irmgard Verdorfer & Armin Graber & Holger Sü, 2013. "Characterization of Transcriptional Changes in ERG Rearrangement-Positive Prostate Cancer Identifies the Regulation of Metabolic Sensors Such as Neuropeptide Y," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-11, February.
  128. Oliver J. Ziff & Jacob Neeves & Jamie Mitchell & Giulia Tyzack & Carlos Martinez-Ruiz & Raphaelle Luisier & Anob M. Chakrabarti & Nicholas McGranahan & Kevin Litchfield & Simon J. Boulton & Ammar Al-C, 2023. "Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  129. Dørum Guro & Snipen Lars & Solheim Margrete & Sæbø Solve, 2009. "Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-26, July.
  130. Cornelis J Vermeulen & Kamilla S Pedersen & Hans C Beck & Jørgen Petersen & Kristina Kirilova Gagalova & Volker Loeschcke, 2013. "Proteomic Characterization of Inbreeding-Related Cold Sensitivity in Drosophila melanogaster," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
  131. Kelmansky Diana M. & Martínez Elena J. & Leiva Víctor, 2013. "A new variance stabilizing transformation for gene expression data analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(6), pages 653-666, December.
  132. Xiaohong Li & Guy N Brock & Eric C Rouchka & Nigel G F Cooper & Dongfeng Wu & Timothy E O’Toole & Ryan S Gill & Abdallah M Eteleeb & Liz O’Brien & Shesh N Rai, 2017. "A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-22, May.
  133. Natasha Chandiramani & Xianhong Wang & Marta Margeta, 2011. "Molecular Basis for Vulnerability to Mitochondrial and Oxidative Stress in a Neuroendocrine CRI-G1 Cell Line," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-18, January.
  134. Di Yanming & Schafer Daniel W & Cumbie Jason S & Chang Jeff H, 2011. "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-28, May.
  135. Stephen Salerno Jr. & Mahya Mehrmohamadi & Maria V Liberti & Muting Wan & Martin T Wells & James G Booth & Jason W Locasale, 2017. "RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards," PLOS ONE, Public Library of Science, vol. 12(6), pages 1-19, June.
  136. Miyako Kusano & Henning Redestig & Tadayoshi Hirai & Akira Oikawa & Fumio Matsuda & Atsushi Fukushima & Masanori Arita & Shin Watanabe & Megumu Yano & Kyoko Hiwasa-Tanase & Hiroshi Ezura & Kazuki Sait, 2011. "Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-11, February.
  137. Tommi Välikangas & Tomi Suomi & Courtney E. Chandler & Alison J. Scott & Bao Q. Tran & Robert K. Ernst & David R. Goodlett & Laura L. Elo, 2022. "Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  138. Peter Hall & D. M. Titterington & Jing‐Hao Xue, 2009. "Tilting methods for assessing the influence of components in a classifier," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(4), pages 783-803, September.
  139. Kynon J. M. Benjamin & Ria Arora & Arthur S. Feltrin & Geo Pertea & Hunter H. Giles & Joshua M. Stolz & Laura D’Ignazio & Leonardo Collado-Torres & Joo Heon Shin & William S. Ulrich & Thomas M. Hyde &, 2024. "Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  140. Long Qu & Dan Nettleton & Jack C. M. Dekkers, 2012. "A Hierarchical Semiparametric Model for Incorporating Intergene Information for Analysis of Genomic Data," Biometrics, The International Biometric Society, vol. 68(4), pages 1168-1177, December.
  141. Raihan K Uddin & Shiva M Singh, 2013. "Hippocampal Gene Expression Meta-Analysis Identifies Aging and Age-Associated Spatial Learning Impairment (ASLI) Genes and Pathways," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-16, July.
  142. Iqbal Mahmud & Guimei Tian & Jia Wang & Tarun E. Hutchinson & Brandon J. Kim & Nikee Awasthee & Seth Hale & Chengcheng Meng & Allison Moore & Liming Zhao & Jessica E. Lewis & Aaron Waddell & Shangtao , 2023. "DAXX drives de novo lipogenesis and contributes to tumorigenesis," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  143. Omar Sandoval-Ibáñez & David Rolo & Rabea Ghandour & Alexander P. Hertle & Tegan Armarego-Marriott & Arun Sampathkumar & Reimo Zoschke & Ralph Bock, 2022. "De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b6f complex in Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  144. Peng, Liuhua & Qu, Long & Nettleton, Dan, 2021. "Variable importance assessments and backward variable selection for multi-sample problems," Journal of Multivariate Analysis, Elsevier, vol. 186(C).
  145. Sahra Uygun & Cheng Peng & Melissa D Lehti-Shiu & Robert L Last & Shin-Han Shiu, 2016. "Utility and Limitations of Using Gene Expression Data to Identify Functional Associations," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-27, December.
IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.