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Statistical Applications in Genetics and Molecular Biology

Short Title: Stat. Appl. Genet. Mol. Biol.
Publisher: De Gruyter, Berlin
ISSN: 2194-6302; 1544-6115/e
Online: http://www.degruyter.com/view/j/sagmb
Comments: Published electronic only from 1 (2002) - 11 (2012).
Documents Indexed: 546 Publications (since 2002)
References Indexed: 193 Publications with 6,819 References.
all top 5

Authors

19 Van der Laan, Mark Johannes
7 Bickel, David R.
7 Wu, Rongling
7 Zhao, Hongyu
6 Beyene, Joseph
6 Burzykowski, Tomasz
6 Dudoit, Sandrine
6 Husmeier, Dirk
6 Segal, Mark Robert
5 Cui, Yuehua
5 Hubbard, Alan E.
5 Keles, Sunduz
5 Pollard, Katherine S.
5 Shkedy, Ziv
5 Tritchler, David L.
4 Beerenwinkel, Niko
4 Doerge, Rebecca W.
4 Elston, Robert Claude
4 Finch, Stephen J.
4 Gilks, Walter R.
4 Goeman, Jelle J.
4 Gordon, Derek
4 Joyce, Paul
4 Marjoram, Paul
4 Mertens, Bart J. A.
4 Miecznikowski, Jeffrey C.
4 Sinisi, Sandra E.
4 Smyth, Gordon K.
4 Tibshirani, Robert John
4 Wilson, Susan R.
3 Arribas-Gil, Ana
3 Bagos, Pantelis G.
3 Birkner, Merrill D.
3 Burden, Conrad John
3 Casella, George
3 Corander, Jukka
3 Degruttola, Victor G.
3 Dickhaus, Thorsten
3 Futschik, Andreas
3 Gaile, Daniel P.
3 Gentleman, Robert
3 Graham, Jinko
3 Grzegorczyk, Marco
3 Gu, Hong
3 Hobolth, Asger
3 Hössjer, Ola G.
3 Jaffrézic, Florence
3 Ji, Tieming
3 Kechris, Katherina J.
3 Kelemen, Arpad G.
3 Kirk, Paul D. W.
3 Kubatko, Laura Salter
3 Labbe, Aurelie
3 Laird, Nan McKenzie
3 Lengauer, Thomas
3 Liang, Yulan
3 Lim, Johan
3 Lin, Dan
3 Lin, Shili
3 Lucas, Joseph Edward
3 McNeney, Brad
3 Mitra, Nandita
3 Nerman, Olle
3 Nuel, Gregory
3 Nye, Tom M. W.
3 Pachter, Lior
3 Parmigiani, Giovanni
3 Pawitan, Yudi
3 Polley, Eric C.
3 Rattray, Magnus
3 Robin, Stéphane
3 Rudemo, Mats
3 Shin, Ji-Hyung
3 Sun, Jiehuan
3 Sun, Shuying
3 van Sanden, Suzy
3 van Wieringen, Wessel N.
3 Vingron, Martin
3 Wilkinson, Darren James
3 Yang, Yaning
3 Yu, Xiaoqing
2 Aderhold, Andrej
2 Ahn, Kwangmi
2 Almudevar, Anthony
2 Balding, David Joseph
2 Berg, Arthur
2 Berkhof, Johannes
2 Besse, Philippe C.
2 Bijnens, Luc
2 Billingham, Lucinda J.
2 Binder, Harald
2 Bogdan, Małgorzata
2 Booth, James G.
2 Boulesteix, Anne-Laure Isabeau
2 Boys, Richard J.
2 Bureau, Alexandre
2 Cao, Kim-Anh Lê
2 Chang, Myron N.
2 Chen, Sining
2 Chen, Zhongxue
...and 1,222 more Authors

Publications by Year

Citations contained in zbMATH Open

246 Publications have been cited 1,059 times in 836 Documents Cited by Year
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Zbl 1038.62110
Smyth, Gordon K.
79
2004
Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Zbl 1166.62379
Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S.
44
2004
Super learner. Zbl 1166.62387
Van der Laan, Mark J.; Polley, Eric C.; Hubbard, Alan E.
39
2007
A general framework for weighted gene co-expression network analysis. Zbl 1077.92042
Zhang, Bin; Horvath, Steve
30
2005
Error distribution for gene expression data. Zbl 1083.62114
Purdom, Elizabeth; Holmes, Susan P.
27
2005
Multiple testing. I: Single-step procedures for control of general type I error rates. Zbl 1166.62338
Dudoit, Sandrine; Van der Laan, Mark J.; Pollard, Katherine S.
24
2004
Sparse canonical correlation analysis with application to genomic data integration. Zbl 1276.92071
Parkhomenko, Elena; Tritchler, David; Beyene, Joseph
24
2009
Approximately sufficient statistics and Bayesian computation. Zbl 1276.62077
Joyce, Paul; Marjoram, Paul
22
2008
FADO: a statistical method to detect favored or avoided distances between occurrences of motifs using the Hawkes’ model. Zbl 1095.62126
Gusto, Gaelle; Schbath, Sophie
16
2005
A generalized Sidak-Holm procedure and control of generalized error rates under independence. Zbl 1166.62316
Guo, Wenge; Romano, Joseph
16
2007
A sparse PLS for variable selection when integrating omics data. Zbl 1276.62061
Cao, Kim-Anh Lê; Rossouw, Debra; Robert-Granié, Christèle; Besse, Philippe
16
2008
Extensions of sparse canonical correlation analysis with applications to genomic data. Zbl 1276.62099
Witten, Daniela M.; Tibshirani, Robert J.
16
2009
Permutation \(p\)-values should never be zero: calculating exact \(p\)-values when permutations are randomly drawn. Zbl 1304.92098
Phipson, Belinda; Smyth, Gordon K.
15
2010
Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis. Zbl 1276.92077
Waaijenborg, Sandra; Verselewel de Witt Hamer, Philip C.; Zwinderman, Aeilko H.
14
2008
Univariate shrinkage in the Cox model for high dimensional data. Zbl 1276.62096
Tibshirani, Robert J.
14
2009
On optimal selection of summary statistics for approximate Bayesian computation. Zbl 1304.92047
Nunes, Matthew A.; Balding, David J.
14
2010
Low-order conditional independence graphs for inferring genetic networks. Zbl 1166.62374
Wille, Anja; Bühlmann, Peter
13
2006
Combining results of microarray experiments: A rank aggregation approach. Zbl 1166.92306
Deconde, Robert P.; Hawley, Sarah; Falcon, Seth; Clegg, Nigel; Knudsen, Beatrice; Etzioni, Ruth
13
2006
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Zbl 1166.62361
Opgen-Rhein, Rainer; Strimmer, Korbinian
13
2007
Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge. Zbl 1166.62373
Werhli, Adriano V.; Husmeier, Dirk
13
2007
Asymptotic optimality of likelihood-based cross-validation. Zbl 1038.62040
Van der Laan, Mark J.; Dudoit, Sandrine; Keles, Sunduz
13
2004
Classifying gene expression profiles from pairwise m{RNA} comparisons. Zbl 1072.62107
Geman, Donald; d’Avignon, Christian; Naiman, Daniel Q.; Winslow, Raimond L.
12
2004
A method to increase the power of multiple testing procedures through sample splitting. Zbl 1166.62318
Rubin, Daniel; Dudoit, Sandrine; Van der Laan, Mark
12
2006
Adapting prediction error estimates for biased complexity selection in high-dimensional bootstrap samples. Zbl 1276.62060
Binder, Harald; Schumacher, Martin
12
2008
Importance sampling for the infinite sites model. Zbl 1276.62074
Hobolth, Asger; Uyenoyama, Marcy K.; Wiuf, Carsten
11
2008
Graph selection with GGMselect. Zbl 1296.92110
Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
9
2012
How to analyze many contingency tables simultaneously in genetic association studies. Zbl 1296.92027
Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi
9
2012
Multiple testing. II: Step-down procedures for control of the family-wise error rate. Zbl 1166.62378
Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S.
8
2004
P{LS} dimension reduction for classification with microarray data. Zbl 1086.62119
Boulesteix, Anne-Laure
8
2004
Statistical inference in evolutionary models of DNA sequences via the EM algorithm. Zbl 1081.62094
Hobolth, Asger; Jensen, Jens Ledet
8
2005
Score statistics for mapping quantitative trait loci. Zbl 1276.62062
Chang, Myron N.; Wu, Rongling; Wu, Samuel S.; Casella, George
8
2009
Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065
Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P.
7
2014
A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Zbl 1296.92039
Grzegorczyk, Marco; Husmeier, Dirk
7
2012
Deletion/substitution/addition algorithm in learning with applications in genomics. Zbl 1166.62368
Sinisi, Sandra E.; Van der Laan, Mark J.
7
2004
Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives. Zbl 1108.62303
Van der Laan, Mark J.; Birkner, Merrill D.; Hubbard, Alan E.
7
2005
Transformations for cDNA microarray data. Zbl 1038.92015
Cui, Xiangqin; Kathleen, M.; Kerr, Churchill; Gary, A.
7
2003
Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380
Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon
7
2016
Space oriented rank-based data integration. Zbl 1304.92094
Lin, Shili
7
2010
Optimal tests shrinking both means and variances applicable to microarray data analysis. Zbl 1304.92044
Hwang, J. T. Gene; Liu, Peng
7
2010
Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045
Lee, Woojoo; Lee, Donghwan; Lee, Youngjo; Pawitan, Yudi
6
2011
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Zbl 1296.92187
Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.; Smyth, Gordon K.
6
2012
Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011
Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco
6
2014
Dimension reduction for classification with gene expression microarray data. Zbl 1166.62337
Dai, Jian J.; Lieu, Linh; Rocke, David
6
2006
Numerical solutions for patterns statistics on Markov chains. Zbl 1166.62324
Nuel, Gregory
6
2006
Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods. Zbl 1276.92033
Zucknick, Manuela; Richardson, Sylvia; Stronach, Euan A.
6
2008
Survival analysis with high-dimensional covariates: an application in microarray studies. Zbl 1276.62067
Engler, David; Li, Yi
6
2009
Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089
Golightly, Andrew; Wilkinson, Darren J.
5
2015
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085
Charmpi, Konstantina; Ycart, Bernard
5
2015
TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008
Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili
5
2015
Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043
Jung, Hsuan; Marjoram, Paul
5
2011
The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Zbl 1296.92026
Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; Chang, Jeff H.
5
2011
Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018
Bickel, David R.
5
2012
Empirical Bayes estimation of a sparse vector of gene expression changes. Zbl 1081.62093
Erickson, Stephen; Sabatti, Chiara
5
2005
Hypothesis tests for point-mass mixture data with application to ’omics data with many zero values. Zbl 1276.92074
Taylor, Sandra; Pollard, Katherine
5
2009
Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079
Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S.
4
2015
High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082
Zuber, Verena; Strimmer, Korbinian
4
2011
Stopping-time resampling and population genetic inference under coalescent models. Zbl 1296.92158
Jenkins, Paul A.
4
2012
The beta-binomial SGoF method for multiple dependent tests. Zbl 1296.92084
de Uña-Alvarez, Jacobo
4
2012
Statistical significance threshold criteria for analysis of microarray gene expression data. Zbl 1166.62335
Cheng, Cheng; Pounds, Stanley B.; Boyett, James M.; Pei, Deqing; Kuo, Mei-Ling; Roussel, Martine F.
4
2004
A new type of stochastic dependence revealed in gene expression data. Zbl 1166.92309
Klebanov, Lev; Jordan, Craig; Yakovlev, Andrei
4
2006
Sparse logistic regression with \(L_p\) penalty for biomarker identification. Zbl 1166.62314
Liu, Zhenqiu; Jiang, Feng; Tian, Guoliang; Wang, Suna; Sato, Fumiaki; Meltzer, Stephen J.; Tan, Ming
4
2007
A Bayesian approach to estimation and testing in time-course microarray experiments. Zbl 1166.62327
Angelini, Claudia; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna
4
2007
Drifting Markov models with polynomial drift and applications to DNA sequences. Zbl 1276.92095
Vergne, Nicolas
4
2008
Structure learning in nested effects models. Zbl 1276.92075
Tresch, Achim; Markowetz, Florian
4
2008
Adaptive choice of the number of bootstrap samples in large scale multiple testing. Zbl 1276.62072
Guo, Wenge; Peddada, Shyamal
4
2008
Modeling DNA methylation in a population of cancer cells. Zbl 1276.92092
Siegmund, Kimberly D.; Marjoram, Paul; Shibata, Darryl
4
2008
Weighted multiple hypothesis testing procedures. Zbl 1276.62078
Kang, Guolian; Ye, Keying; Liu, Nianjun; Allison, David B.; Gao, Guimin
4
2009
Estimation of selection intensity under overdominance by Bayesian methods. Zbl 1276.92050
Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid
4
2009
A random coefficients model for regional co-expression associated with DNA copy number. Zbl 1304.92064
van Wieringen, Wessel N.; Berkhof, Johannes; van de Wiel, Mark A.
4
2010
A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007
Meijer, Rosa J.; Krebs, Thijmen J. P.; Goeman, Jelle J.
3
2015
Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure. Zbl 1311.92077
Zhang, Runchu; Mukerjee, Rahul
3
2013
Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions. Zbl 1311.62109
Bickel, David R.
3
2013
Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017
Ji, Tieming; Chen, Jie
3
2015
Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Zbl 1296.92032
Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes
3
2014
Unsupervised classification for tiling arrays: chip-chip and transcriptome. Zbl 1296.92105
Bérard, Caroline; Martin-Magniette, Marie-Laure; Brunaud, Véronique; Aubourg, Sébastien; Robin, Stéphane
3
2011
Weighted lasso with data integration. Zbl 1296.92017
Bergersen, Linn Cecilie; Glad, Ingrid K.; Lyng, Heidi
3
2011
Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034
Francois, Olivier; Laval, Guillaume
3
2011
On the statistical properties of SGoF multitesting method. Zbl 1296.92083
de Uña-Alvarez, Jacobo
3
2011
A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139
Auer, Paul L.; Doerge, Rebecca W.
3
2011
An integrated hierarchical Bayesian model for multivariate eQTL mapping. Zbl 1296.92071
Scott-Boyer, Marie Pier; Imholte, Gregory C.; Tayeb, Arafat; Labbe, Aurelie; Deschepper, Christian F.; Gottardo, Raphael
3
2012
Combining nearest neighbor classifiers versus cross-validation selection. Zbl 1072.62111
Paik, Minhui; Yang, Yuhong
3
2004
BayesMendel: an R environment for Mendelian risk prediction. Zbl 1077.92029
Chen, Sining; Wang, Wenyi; Broman, Karl W.; Katki, Hormuzd A.; Parmigiani, Giovanni
3
2004
A compendium to ensure computational reproducibility in high-dimensional classification tasks. Zbl 1082.92025
Ruschhaupt, Markus; Huber, Wolfgang; Poustka, Annemarie; Mansmann, Ulrich
3
2004
Reproducible research: a bioinformatics case study. Zbl 1138.92300
Gentleman, Robert
3
2005
Empirical Bayes microarray {ANOVA} and grouping cell lines by equal expression levels. Zbl 1086.62124
Lönnstedt, Ingrid; Rimini, Rebecca; Nilsson, Peter
3
2005
A generalized clustering problem, with application to DNA microarrays. Zbl 1166.62331
Belitskaya-Levy, Ilana
3
2006
Cross-validated bagged prediction of survival. Zbl 1166.62326
Sinisi, Sandra E.; Neugebauer, Romain; Van der Laan, Mark J.
3
2006
Quantile-function based null distribution in resampling based multiple testing. Zbl 1166.62302
Van der Laan, Mark J.; Hubbard, Alan E.
3
2006
Detecting local high-scoring segments: a first-stage approach for genome-wide association studies. Zbl 1166.62341
Guedj, Mickael; Robelin, David; Hoebeke, Mark; Lamarine, Marc; Wojcik, Jérôme; Nuel, Gregory
3
2006
Approximate sample size calculations with microarray data: an illustration. Zbl 1166.62339
Ferreira, José A.; Zwinderman, Aeilko
3
2006
An improved nonparametric approach for detecting differentially expressed genes with replicated microarray data. Zbl 1166.62376
Zhang, Shunpu
3
2006
Testing for trends in dose-response microarray experiments: A comparison of several testing procedures, multiplicity and resampling-based inference. Zbl 1166.62353
Lin, Dan; Shkedy, Ziv; Yekutieli, Dani; Burzykowski, Tomasz; Göhlmann, Hinrich W. H.; De Bondt, An; Perera, Tim; Geerts, Tamara; Bijnens, Luc
3
2007
Pre-validation and inference in microarrays. Zbl 1037.62116
Tibshirani, Robert J.; Efron, Brad
3
2002
Fully Bayesian mixture model for differential gene expression: simulations and model checks. Zbl 1276.92090
Lewin, Alex; Bochkina, Natalia; Richardson, Sylvia
3
2007
Multiple testing for SNP-SNP interactions. Zbl 1276.92083
Boulesteix, Anne-Laure; Strobl, Carolin; Weidinger, Stefan; Wichmann, H.-Erich; Wagenpfeil, Stefan
3
2007
A Bayesian analysis strategy for cross-study translation of gene expression biomarkers. Zbl 1276.92066
Lucas, Joseph; Carvalho, Carlos; West, Mike
3
2009
Detecting outlier samples in microarray data. Zbl 1276.62092
Shieh, Albert D.; Hung, Yeung Sam
3
2009
Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207
Koskela, Jere
3
2018
Network enrichment analysis in complex experiments. Zbl 1304.92067
Shojaie, Ali; Michailidis, George
3
2010
Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression. Zbl 1304.92046
Montazeri, Zahra; Yanofsky, Corey M.; Bickel, David R.
3
2010
Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model. Zbl 1420.92087
Li, Xiaohong; Wu, Dongfeng; Cooper, Nigel G. F.; Rai, Shesh N.
1
2019
A penalized regression approach for DNA copy number study using the sequencing data. Zbl 1420.92085
Lee, Jaeeun; Chen, Jie
1
2019
Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207
Koskela, Jere
3
2018
Additive varying-coefficient model for nonlinear gene-environment interactions. Zbl 1398.92163
Wu, Cen; Zhong, Ping-Shou; Cui, Yuehua
1
2018
A statistical method for measuring activation of gene regulatory networks. Zbl 1398.92088
Esteves, Gustavo H.; Reis, Luiz F. L.
1
2018
Non-parametric estimation of population size changes from the site frequency spectrum. Zbl 1398.92191
Waltoft, Berit Lindum; Hobolth, Asger
1
2018
Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization. Zbl 1398.92011
Huang, Hsin-Hsiung; Hao, Shuai; Alarcon, Saul; Yang, Jie
1
2018
Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study. Zbl 1371.92014
Zhang, Haixiang; Zheng, Yinan; Yoon, Grace; Zhang, Zhou; Gao, Tao; Joyce, Brian; Zhang, Wei; Schwartz, Joel; Vokonas, Pantel; Colicino, Elena; Baccarelli, Andrea; Hou, Lifang; Liu, Lei
1
2017
Binary Markov random fields and interpretable mass spectra discrimination. Zbl 1360.92065
Kong, Ao; Azencott, Robert
1
2017
A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type. Zbl 1396.92060
Lakhal-Chaieb, Lajmi; Greenwood, Celia M. T.; Ouhourane, Mohamed; Zhao, Kaiqiong; Abdous, Belkacem; Oualkacha, Karim
1
2017
Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380
Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon
7
2016
HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test. Zbl 1343.92173
Sun, Shuying; Yu, Xiaoqing
2
2016
HMM-DM: identifying differentially methylated regions using a hidden Markov model. Zbl 1343.92180
Yu, Xiaoqing; Sun, Shuying
2
2016
Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Zbl 1343.92028
Yu, Xiaoqing; Sun, Shuying
2
2016
A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments. Zbl 1359.92034
Kruppa, Jochen; Kramer, Frank; Beißbarth, Tim; Jung, Klaus
1
2016
Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies. Zbl 1359.92004
Kakourou, Alexia; Vach, Werner; Nicolardi, Simone; van der Burgt, Yuri; Mertens, Bart
1
2016
Identification of consistent functional genetic modules. Zbl 1343.92017
Miecznikowski, Jeffrey C.; Gaile, Daniel P.; Chen, Xiwei; Tritchler, David L.
1
2016
Bayesian state space models for dynamic genetic network construction across multiple tissues. Zbl 1344.92012
Liang, Yulan; Kelemen, Arpad
1
2016
Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089
Golightly, Andrew; Wilkinson, Darren J.
5
2015
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085
Charmpi, Konstantina; Ycart, Bernard
5
2015
TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008
Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili
5
2015
Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079
Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S.
4
2015
A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007
Meijer, Rosa J.; Krebs, Thijmen J. P.; Goeman, Jelle J.
3
2015
Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017
Ji, Tieming; Chen, Jie
3
2015
Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Zbl 1329.60246
Muchmore, Patrick; Marjoram, Paul
2
2015
A Bayesian mixture model for chromatin interaction data. Zbl 1306.92018
Niu, Liang; Lin, Shili
1
2015
Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles. Zbl 1311.92082
Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk
1
2015
A mutual information estimator with exponentially decaying bias. Zbl 1329.62107
Zhang, Zhiyi; Zheng, Lukun
1
2015
Sample size reassessment for a two-stage design controlling the false discovery rate. Zbl 1330.92014
Zehetmayer, Sonja; Graf, Alexandra C.; Posch, Martin
1
2015
A robust distribution-free test for genetic association studies of quantitative traits. Zbl 1330.92011
Kozlitina, Julia; Schucany, William R.
1
2015
On an extended interpretation of linkage disequilibrium in genetic case-control association studies. Zbl 1330.92078
Dickhaus, Thorsten; Stange, Jens; Demirhan, Haydar
1
2015
On the validity of within-nuclear-family genetic association analysis in samples of extended families. Zbl 1330.92076
Bureau, Alexandre; Duchesne, Thierry
1
2015
An empirical Bayes risk prediction model using multiple traits for sequencing data. Zbl 1330.92097
Li, Gengxin; Cui, Yuehua; Zhao, Hongyu
1
2015
Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065
Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P.
7
2014
Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011
Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco
6
2014
Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Zbl 1296.92032
Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes
3
2014
Combining dependent \(F\)-tests for robust association of quantitative traits under genetic model uncertainty. Zbl 1296.92067
Qu, Long
2
2014
Penalized differential pathway analysis of integrative oncogenomics studies. Zbl 1296.92194
van Wieringen, Wessel N.; van de Wiel, Mark A.
2
2014
Scan statistics analysis for detection of introns in time-course tiling array data. Zbl 1296.92068
Reiner-Benaim, Anat; Davis, Ronald W.; Juneau, Kara
2
2014
Efficient parametric inference for stochastic biological systems with measured variability. Zbl 1296.92042
Johnston, Iain G.
2
2014
Quantifying the multi-scale performance of network inference algorithms. Zbl 1298.92043
Oates, Chris J.; Amos, Richard; Spencer, Simon E. F.
2
2014
Improved variational Bayes inference for transcript expression estimation. Zbl 1296.92064
Papastamoulis, Panagiotis; Hensman, James; Glaus, Peter; Rattray, Magnus
1
2014
Multiple comparisons in genetic association studies: a hierarchical modeling approach. Zbl 1296.92178
Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel
1
2014
Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model. Zbl 1296.92157
Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka
1
2014
A novel characterization of the generalized family wise error rate using empirical null distributions. Zbl 1296.92054
Miecznikowski, Jeffrey C.; Gaile, Daniel P.
1
2014
Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data. Zbl 1298.92041
Jow, Howsun; Boys, Richard J.; Wilkinson, Darren J.
1
2014
Bayesian modelling of compositional heterogeneity in molecular phylogenetics. Zbl 1298.92071
Heaps, Sarah E.; Nye, Tom M. W.; Boys, Richard J.; Williams, Tom A.; Embley, T. Martin
1
2014
Robust methods to detect disease-genotype association in genetic association studies: calculate \(p\)-values using exact conditional enumeration instead of simulated permutations or asymptotic approximations. Zbl 1302.92074
Langaas, Mette; Bakke, Øyvind
1
2014
Markovianness and conditional independence in annotated bacterial DNA. Zbl 1302.92069
Hart, Andrew; Martínez, Servet
1
2014
Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure. Zbl 1311.92077
Zhang, Runchu; Mukerjee, Rahul
3
2013
Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions. Zbl 1311.62109
Bickel, David R.
3
2013
Improving the efficiency of genomic selection. Zbl 1311.92126
Scutari, Marco; Mackay, Ian; Balding, David
2
2013
The mid \(p\)-value in exact tests for Hardy-Weinberg equilibrium. Zbl 1311.92014
Graffelman, Jan; Moreno, Victor
1
2013
General power and sample size calculations for high-dimensional genomic data. Zbl 1311.92015
van Iterson, Maarten; van de Wiel, Mark A.; Boer, Judith M.; de Menezes, Renée X.
1
2013
Graph selection with GGMselect. Zbl 1296.92110
Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
9
2012
How to analyze many contingency tables simultaneously in genetic association studies. Zbl 1296.92027
Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi
9
2012
A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Zbl 1296.92039
Grzegorczyk, Marco; Husmeier, Dirk
7
2012
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Zbl 1296.92187
Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.; Smyth, Gordon K.
6
2012
Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018
Bickel, David R.
5
2012
Stopping-time resampling and population genetic inference under coalescent models. Zbl 1296.92158
Jenkins, Paul A.
4
2012
The beta-binomial SGoF method for multiple dependent tests. Zbl 1296.92084
de Uña-Alvarez, Jacobo
4
2012
An integrated hierarchical Bayesian model for multivariate eQTL mapping. Zbl 1296.92071
Scott-Boyer, Marie Pier; Imholte, Gregory C.; Tayeb, Arafat; Labbe, Aurelie; Deschepper, Christian F.; Gottardo, Raphael
3
2012
A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in microarray time course data. Zbl 1296.92029
Farcomeni, Alessio; Arima, Serena
2
2012
Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Zbl 1296.92035
Ghosh, Debashis
2
2012
Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063
Padilla, Marta; Bickel, David R.
2
2012
Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Zbl 1296.92072
Silver, Matt; Montana, Giovanni; Alzheimer’s Disease Neuroimaging Initiative
1
2012
Fast wavelet based functional models for transcriptome analysis with tiling arrays. Zbl 1296.92024
Clement, Lieven; De Beuf, Kristof; Thas, Olivier; Vuylsteke, Marnik; Irizarry, Rafael A.; Crainiceanu, Ciprian M.
1
2012
A mixture-model approach for parallel testing for unequal variances. Zbl 1296.92015
Bar, Haim Y.; Booth, James G.; Wells, Martin T.
1
2012
A model-based analysis to infer the functional content of a gene list. Zbl 1296.92059
Newton, Michael A.; He, Qiuling; Kendziorski, Christina
1
2012
Adjusting for spurious gene-by-environment interaction using case-parent triads. Zbl 1296.92167
Shin, Ji-Hyung; Infante-Rivard, Claire; Graham, Jinko; McNeney, Brad
1
2012
Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044
Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris
1
2012
Detection of differentially expressed gene sets in a partially paired microarray data set. Zbl 1296.92047
Lim, Johan; Kim, Jayoun; Kim, Sang-cheol; Yu, Donghyeon; Kim, Kyunga; Kim, Byung Soo
1
2012
Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications. Zbl 1296.92159
Kenney, Toby; Gu, Hong
1
2012
Performance of MAX test and degree of dominance index in predicting the mode of inheritance. Zbl 1296.92180
Zintzaras, Elias; Santos, Mauro
1
2012
Analyzing genetic association studies with an extended propensity score approach. Zbl 1296.92179
Zhao, Huaqing; Rebbeck, Timothy R.; Mitra, Nandita
1
2012
Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045
Lee, Woojoo; Lee, Donghwan; Lee, Youngjo; Pawitan, Yudi
6
2011
Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043
Jung, Hsuan; Marjoram, Paul
5
2011
The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Zbl 1296.92026
Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; Chang, Jeff H.
5
2011
High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082
Zuber, Verena; Strimmer, Korbinian
4
2011
Unsupervised classification for tiling arrays: chip-chip and transcriptome. Zbl 1296.92105
Bérard, Caroline; Martin-Magniette, Marie-Laure; Brunaud, Véronique; Aubourg, Sébastien; Robin, Stéphane
3
2011
Weighted lasso with data integration. Zbl 1296.92017
Bergersen, Linn Cecilie; Glad, Ingrid K.; Lyng, Heidi
3
2011
Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034
Francois, Olivier; Laval, Guillaume
3
2011
On the statistical properties of SGoF multitesting method. Zbl 1296.92083
de Uña-Alvarez, Jacobo
3
2011
A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139
Auer, Paul L.; Doerge, Rebecca W.
3
2011
Smoothing gene expression data with network information improves consistency of regulated genes. Zbl 1296.92147
Dørum, Guro; Snipen, Lars; Solheim, Margrete; Saebo, Solve
2
2011
Analyzing time-course microarray data using functional data analysis – a review. Zbl 1296.92025
Coffey, Norma; Hinde, John
2
2011
Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Zbl 1296.92053
Mayer, Claus-Dieter; Lorent, Julie; Horgan, Graham W.
2
2011
Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Zbl 1296.92190
Neuwald, Andrew F.
1
2011
The joint null criterion for multiple hypothesis tests. Zbl 1296.92046
Leek, Jeffrey T.; Storey, John D.
1
2011
Learning monotonic genotype-phenotype maps. Zbl 1296.92016
Beerenwinkel, Niko; Knupfer, Patrick; Tresch, Achim
1
2011
Large sample approximations of probabilities of correct evolutionary tree estimation and biases of maximum likelihood estimation. Zbl 1296.92185
Susko, Edward
1
2011
Permutation \(p\)-values should never be zero: calculating exact \(p\)-values when permutations are randomly drawn. Zbl 1304.92098
Phipson, Belinda; Smyth, Gordon K.
15
2010
On optimal selection of summary statistics for approximate Bayesian computation. Zbl 1304.92047
Nunes, Matthew A.; Balding, David J.
14
2010
Space oriented rank-based data integration. Zbl 1304.92094
Lin, Shili
7
2010
Optimal tests shrinking both means and variances applicable to microarray data analysis. Zbl 1304.92044
Hwang, J. T. Gene; Liu, Peng
7
2010
A random coefficients model for regional co-expression associated with DNA copy number. Zbl 1304.92064
van Wieringen, Wessel N.; Berkhof, Johannes; van de Wiel, Mark A.
4
2010
Network enrichment analysis in complex experiments. Zbl 1304.92067
Shojaie, Ali; Michailidis, George
3
2010
Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression. Zbl 1304.92046
Montazeri, Zahra; Yanofsky, Corey M.; Bickel, David R.
3
2010
An empirical Bayesian method for estimating biological networks from temporal microarray data. Zbl 1304.92066
Rau, Andrea; Jaffrézic, Florence; Foulley, Jean-Louis; Doerge, Rebecca W.
3
2010
Weighted-LASSO for structured network inference from time course data. Zbl 1304.92085
Charbonnier, Camille; Chiquet, Julien; Ambroise, Christophe
3
2010
...and 146 more Documents
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Cited by 1,718 Authors

17 Van der Laan, Mark Johannes
10 Bickel, David R.
9 Farcomeni, Alessio
8 Goeman, Jelle J.
8 Nettleton, Dan
8 Sarkar, Sanat Kumar
7 Boulesteix, Anne-Laure Isabeau
7 Guillot, Dominique
7 Rabier, Charles-Elie
6 Dickhaus, Thorsten
6 Grzegorczyk, Marco
6 Husmeier, Dirk
6 Jenkins, Paul A.
6 Robin, Stéphane
6 Romano, Joseph P.
6 Roquain, Étienne
5 Binder, Harald
5 Bubenik, Peter
5 Drovandi, Christopher C.
5 Guo, Wenge
5 Habiger, Joshua D.
5 Hahn, Georg
5 Khare, Apoorva
5 Rajaratnam, Bala
4 Aderhold, Andrej
4 Buzbas, Erkan Ozge
4 Carone, Marco
4 Golightly, Andrew
4 Hobolth, Asger
4 Hossain, Ahmed
4 Koskela, Jere
4 Li, Hongzhe
4 Miecznikowski, Jeffrey C.
4 Nuel, Gregory
4 Peña, Edsel A.
4 Pettitt, Anthony N.
4 Reynaud-Bouret, Patricia
4 Rosenberg, Noah A.
4 Schifano, Elizabeth D.
4 Tibshirani, Robert John
4 van Wieringen, Wessel N.
4 Verzelen, Nicolas
3 Alquier, Pierre
3 Arslan, Olcay
3 Bar, Haim Y.
3 Benner, Axel
3 Beyene, Joseph
3 Biau, Gérard
3 Blath, Jochen
3 Bogdan, Małgorzata
3 Caffo, Brian S.
3 Chakraborty, Sounak
3 Cheng, Cheng
3 Chiquet, Julien
3 Cui, Yuehua
3 de Menezes, Renée X.
3 Díaz, Iván
3 Dudoit, Sandrine
3 Efron, Bradley
3 Fan, Jianqing
3 Galimberti, Giuliano
3 Gandy, Axel
3 Gillespie, Colin S.
3 Gordon, Alexander Ya.
3 Hall, Peter Gavin
3 Hemerik, Jesse
3 Huang, Haiyan
3 Jaffrézic, Florence
3 Lee, Youngjo
3 Liang, Kun
3 Lim, Johan
3 Liquet, Benoit
3 Liu, Peng
3 Liu, Yufeng
3 Marron, James Stephen
3 Mertens, Bart J. A.
3 Neuvial, Pierre
3 Novikov, Aleksandr Aleksandrovich
3 Parmigiani, Giovanni
3 Porzelius, Christine
3 Pudlo, Pierre
3 Qiu, Jing
3 Rahnenführer, Jörg
3 Ruli, Erlis
3 Sansonnet, Laure
3 Schumacher, Martin
3 Smyth, Gordon K.
3 Soffritti, Gabriele
3 Solari, Aldo
3 Stumpf, Michael P. H.
3 Sun, Qiang
3 Sun, Shuying
3 Tong, Tiejun
3 Tutz, Gerhard E.
3 Villers, Fanny
3 Wang, Ying Xiang Rachel
3 West, Mike
3 Wolf, Michael
3 Wu, Baolin
3 Wu, Rongling
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Cited in 144 Journals

77 Computational Statistics and Data Analysis
64 Statistical Applications in Genetics and Molecular Biology
56 The Annals of Applied Statistics
47 Biometrics
39 The Annals of Statistics
26 Statistics and Computing
25 Electronic Journal of Statistics
22 Journal of the American Statistical Association
22 Journal of Statistical Planning and Inference
20 Biometrical Journal
20 Journal of Multivariate Analysis
20 Computational Statistics
18 Theoretical Population Biology
18 Statistics & Probability Letters
16 Journal of Theoretical Biology
15 Statistical Science
14 Journal of Applied Statistics
12 Scandinavian Journal of Statistics
11 Journal of Statistical Computation and Simulation
9 Journal of Applied Probability
8 Test
8 Biostatistics
8 Computational & Mathematical Methods in Medicine
7 The Canadian Journal of Statistics
7 Journal of the Royal Statistical Society. Series B. Statistical Methodology
6 Bernoulli
6 Advances in Data Analysis and Classification. ADAC
6 Journal of Agricultural, Biological, and Environmental Statistics
6 Bayesian Analysis
5 Journal of Mathematical Biology
5 International Journal of Approximate Reasoning
5 Machine Learning
5 Statistical Papers
5 Statistical Methods and Applications
5 Statistical Analysis and Data Mining
5 Journal of Probability and Statistics
4 Mathematical Biosciences
4 Communications in Statistics. Simulation and Computation
4 Methodology and Computing in Applied Probability
4 Journal of Machine Learning Research (JMLR)
4 Computational Biology and Chemistry
4 Statistical Methodology
4 Statistics Surveys
4 Epidemiologic Methods
3 Bulletin of Mathematical Biology
3 Annals of the Institute of Statistical Mathematics
3 Statistics
3 Communications in Statistics. Theory and Methods
3 Annales de l’Institut Henri Poincaré. Probabilités et Statistiques
3 European Series in Applied and Industrial Mathematics (ESAIM): Probability and Statistics
3 Australian & New Zealand Journal of Statistics
3 Statistical Modelling
3 Statistical Methods in Medical Research
2 Journal of Statistical Physics
2 Physica A
2 Applied Mathematics and Computation
2 Theoretical Computer Science
2 Transactions of the American Mathematical Society
2 Neural Networks
2 Neural Computation
2 European Journal of Operational Research
2 Stochastic Processes and their Applications
2 Applied Mathematics. Series B (English Edition)
2 Applied and Computational Harmonic Analysis
2 Statistica Sinica
2 Lifetime Data Analysis
2 Journal of Nonparametric Statistics
2 Comptes Rendus. Mathématique. Académie des Sciences, Paris
2 Mathematical Biosciences and Engineering
2 Journal of the Korean Statistical Society
2 AStA. Advances in Statistical Analysis
2 Science China. Mathematics
2 Sankhyā. Series A
2 Sankhyā. Series B
2 Journal of Applied and Computational Topology
1 Advances in Applied Probability
1 Computer Methods in Applied Mechanics and Engineering
1 Discrete Applied Mathematics
1 Inverse Problems
1 Information Processing Letters
1 Journal of Computational Physics
1 Journal of Mathematical Analysis and Applications
1 Metrika
1 Advances in Mathematics
1 Information Sciences
1 Journal of Combinatorial Theory. Series A
1 Journal of Computational and Applied Mathematics
1 Journal of Computer and System Sciences
1 Metron
1 Statistica Neerlandica
1 Acta Applicandae Mathematicae
1 Journal of Symbolic Computation
1 Computers & Operations Research
1 SIAM Journal on Matrix Analysis and Applications
1 Queueing Systems
1 The Annals of Applied Probability
1 Linear Algebra and its Applications
1 Pattern Recognition
1 Annales de la Faculté des Sciences de Toulouse. Mathématiques. Série VI
1 Journal of Algebraic Combinatorics
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Cited in 38 Fields

711 Statistics (62-XX)
280 Biology and other natural sciences (92-XX)
146 Numerical analysis (65-XX)
88 Probability theory and stochastic processes (60-XX)
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10 Game theory, economics, finance, and other social and behavioral sciences (91-XX)
7 Algebraic topology (55-XX)
6 Information and communication theory, circuits (94-XX)
5 Systems theory; control (93-XX)
4 Partial differential equations (35-XX)
4 Harmonic analysis on Euclidean spaces (42-XX)
4 Functional analysis (46-XX)
3 Operator theory (47-XX)
3 Quantum theory (81-XX)
2 Algebraic geometry (14-XX)
2 Integral equations (45-XX)
2 Calculus of variations and optimal control; optimization (49-XX)
2 Manifolds and cell complexes (57-XX)
2 Global analysis, analysis on manifolds (58-XX)
2 Statistical mechanics, structure of matter (82-XX)
1 Number theory (11-XX)
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