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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: 561 Publications (since 2002)
References Indexed: 208 Publications with 7,462 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 Koestler, Devin C.
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 Wiuf, Carsten
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.
...and 1,257 more Authors

Publications by Year

Citations contained in zbMATH Open

259 Publications have been cited 1,189 times in 944 Documents Cited by Year
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Zbl 1038.62110
Smyth, Gordon K.
85
2004
Super learner. Zbl 1166.62387
Van der Laan, Mark J.; Polley, Eric C.; Hubbard, Alan E.
46
2007
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.
45
2004
A general framework for weighted gene co-expression network analysis. Zbl 1077.92042
Zhang, Bin; Horvath, Steve
35
2005
Error distribution for gene expression data. Zbl 1083.62114
Purdom, Elizabeth; Holmes, Susan P.
31
2005
Approximately sufficient statistics and Bayesian computation. Zbl 1276.62077
Joyce, Paul; Marjoram, Paul
28
2008
Sparse canonical correlation analysis with application to genomic data integration. Zbl 1276.92071
Parkhomenko, Elena; Tritchler, David; Beyene, Joseph
28
2009
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.
25
2004
On optimal selection of summary statistics for approximate Bayesian computation. Zbl 1304.92047
Nunes, Matthew A.; Balding, David J.
18
2010
Permutation \(p\)-values should never be zero: calculating exact \(p\)-values when permutations are randomly drawn. Zbl 1304.92098
Phipson, Belinda; Smyth, Gordon K.
18
2010
Univariate shrinkage in the Cox model for high dimensional data. Zbl 1276.62096
Tibshirani, Robert J.
18
2009
A generalized Sidak-Holm procedure and control of generalized error rates under independence. Zbl 1166.62316
Guo, Wenge; Romano, Joseph
17
2007
Extensions of sparse canonical correlation analysis with applications to genomic data. Zbl 1276.62099
Witten, Daniela M.; Tibshirani, Robert J.
17
2009
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Zbl 1166.62361
Opgen-Rhein, Rainer; Strimmer, Korbinian
16
2007
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
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.
16
2008
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
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
15
2007
Asymptotic optimality of likelihood-based cross-validation. Zbl 1038.62040
Van der Laan, Mark J.; Dudoit, Sandrine; Keles, Sunduz
14
2004
Low-order conditional independence graphs for inferring genetic networks. Zbl 1166.62374
Wille, Anja; Bühlmann, Peter
14
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
14
2006
Classifying gene expression profiles from pairwise m{RNA} comparisons. Zbl 1072.62107
Geman, Donald; d’Avignon, Christian; Naiman, Daniel Q.; Winslow, Raimond L.
13
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
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
12
2012
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
12
2008
Deletion/substitution/addition algorithm in learning with applications in genomics. Zbl 1166.62368
Sinisi, Sandra E.; Van der Laan, Mark J.
11
2004
Graph selection with GGMselect. Zbl 1296.92110
Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
10
2012
Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380
Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon
10
2016
Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089
Golightly, Andrew; Wilkinson, Darren J.
8
2015
Dimension reduction for classification with gene expression microarray data. Zbl 1166.62337
Dai, Jian J.; Lieu, Linh; Rocke, David
8
2006
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
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.
8
2014
Score statistics for mapping quantitative trait loci. Zbl 1276.62062
Chang, Myron N.; Wu, Rongling; Wu, Samuel S.; Casella, George
8
2009
Transformations for cDNA microarray data. Zbl 1038.92015
Cui, Xiangqin; Kathleen, M.; Kerr, Churchill; Gary, A.
7
2003
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
Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045
Lee, Woojoo; Lee, Donghwan; Lee, Youngjo; Pawitan, Yudi
7
2011
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
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
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.
6
2013
Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079
Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S.
6
2015
Numerical solutions for patterns statistics on Markov chains. Zbl 1166.62324
Nuel, Gregory
6
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
6
2007
Empirical Bayes estimation of a sparse vector of gene expression changes. Zbl 1081.62093
Erickson, Stephen; Sabatti, Chiara
6
2005
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
6
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
6
2014
Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018
Bickel, David R.
6
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
Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011
Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco
6
2014
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
Hypothesis tests for point-mass mixture data with application to ’omics data with many zero values. Zbl 1276.92074
Taylor, Sandra; Pollard, Katherine
6
2009
Survival analysis with high-dimensional covariates: an application in microarray studies. Zbl 1276.62067
Engler, David; Li, Yi
6
2009
BayesMendel: an R environment for Mendelian risk prediction. Zbl 1077.92029
Chen, Sining; Wang, Wenyi; Broman, Karl W.; Katki, Hormuzd A.; Parmigiani, Giovanni
5
2004
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085
Charmpi, Konstantina; Ycart, Bernard
5
2015
Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043
Jung, Hsuan; Marjoram, Paul
5
2011
High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082
Zuber, Verena; Strimmer, Korbinian
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
Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063
Padilla, Marta; Bickel, David R.
5
2012
A new type of stochastic dependence revealed in gene expression data. Zbl 1166.92309
Klebanov, Lev; Jordan, Craig; Yakovlev, Andrei
4
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
4
2006
Super learning: an application to the prediction of HIV-1 drug resistance. Zbl 1166.92315
Sinisi, Sandra E.; Polley, Eric C.; Petersen, Maya L.; Rhee, Soo-Yon; Van der Laan, Mark J.
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
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
Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034
Francois, Olivier; Laval, Guillaume
4
2011
A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139
Auer, Paul L.; Doerge, Rebecca W.
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
Weighted-LASSO for structured network inference from time course data. Zbl 1304.92085
Charbonnier, Camille; Chiquet, Julien; Ambroise, Christophe
4
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
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
Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207
Koskela, Jere
4
2018
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
Pre-validation and inference in microarrays. Zbl 1037.62116
Tibshirani, Robert J.; Efron, Brad
3
2002
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
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
Combining nearest neighbor classifiers versus cross-validation selection. Zbl 1072.62111
Paik, Minhui; Yang, Yuhong
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
Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017
Ji, Tieming; Chen, Jie
3
2015
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
On the statistical properties of SGoF multitesting method. Zbl 1296.92083
de Uña-Alvarez, Jacobo
3
2011
Analyzing time-course microarray data using functional data analysis – a review. Zbl 1296.92025
Coffey, Norma; Hinde, John
3
2011
Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Zbl 1296.92053
Mayer, Claus-Dieter; Lorent, Julie; Horgan, Graham W.
3
2011
Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044
Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris
3
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
3
2012
Stability selection for Lasso, ridge and elastic net implemented with AFT models. Zbl 1445.92142
Khan, Md Hasinur Rahaman; Bhadra, Anamika; Howlader, Tamanna
1
2019
Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics. Zbl 1445.92105
Crook, Oliver M.; Gatto, Laurent; Kirk, Paul D. W.
1
2019
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
4
2018
Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting. Zbl 1398.92010
Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter
1
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
Binary Markov random fields and interpretable mass spectra discrimination. Zbl 1360.92065
Kong, Ao; Azencott, Robert
1
2017
Missing value imputation for gene expression data by tailored nearest neighbors. Zbl 1371.92048
Faisal, Shahla; Tutz, Gerhard
1
2017
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
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
10
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
Differential methylation tests of regulatory regions. Zbl 1343.92019
Ryu, Duchwan; Xu, Hongyan; George, Varghese; Su, Shaoyong; Wang, Xiaoling; Shi, Huidong; Podolsky, Robert H.
1
2016
Identification of consistent functional genetic modules. Zbl 1343.92017
Miecznikowski, Jeffrey C.; Gaile, Daniel P.; Chen, Xiwei; Tritchler, David L.
1
2016
What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment. Zbl 1343.92009
Cui, Shiqi; Ji, Tieming; Li, Jilong; Cheng, Jianlin; Qiu, Jing
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.
8
2015
Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079
Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S.
6
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
6
2015
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085
Charmpi, Konstantina; Ycart, Bernard
5
2015
Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017
Ji, Tieming; Chen, Jie
3
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
Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Zbl 1329.60246
Muchmore, Patrick; Marjoram, Paul
2
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
Corrigendum to: “Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions”. Zbl 1311.62110
Bickel, David R.
1
2015
A mutual information estimator with exponentially decaying bias. Zbl 1329.62107
Zhang, Zhiyi; Zheng, Lukun
1
2015
Application of the fractional-stable distributions for approximation of the gene expression profiles. Zbl 1329.92090
Saenko, Viacheslav; Saenko, Yury
1
2015
A Bayesian mixture model for chromatin interaction data. Zbl 1306.92018
Niu, Liang; Lin, Shili
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.
8
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
6
2014
Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011
Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco
6
2014
Quantifying the multi-scale performance of network inference algorithms. Zbl 1298.92043
Oates, Chris J.; Amos, Richard; Spencer, Simon E. F.
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
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
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 Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments. Zbl 1296.92038
Gómez-Villegas, Miguel A.; Salazar, Isabel; Sanz, Luis
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
Gene set analysis for GWAS: assessing the use of modified Kolmogorov-Smirnov statistics. Zbl 1298.92063
Debrabant, Birgit; Soerensen, Mette
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
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.
6
2013
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
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
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
12
2012
Graph selection with GGMselect. Zbl 1296.92110
Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
10
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
Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018
Bickel, David R.
6
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
Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063
Padilla, Marta; 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
Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044
Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris
3
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
3
2012
Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Zbl 1296.92035
Ghosh, Debashis
3
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
2
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.
2
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
2
2012
A context dependent pair hidden Markov model for statistical alignment. Zbl 1296.92014
Arribas-Gil, Ana; Matias, Catherine
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
Computing posterior probabilities for score-based alignments using ppALIGN. Zbl 1296.92192
Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory
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
7
2011
Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043
Jung, Hsuan; Marjoram, Paul
5
2011
High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082
Zuber, Verena; Strimmer, Korbinian
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
Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034
Francois, Olivier; Laval, Guillaume
4
2011
A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139
Auer, Paul L.; Doerge, Rebecca W.
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
On the statistical properties of SGoF multitesting method. Zbl 1296.92083
de Uña-Alvarez, Jacobo
3
2011
Analyzing time-course microarray data using functional data analysis – a review. Zbl 1296.92025
Coffey, Norma; Hinde, John
3
2011
Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Zbl 1296.92053
Mayer, Claus-Dieter; Lorent, Julie; Horgan, Graham 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
Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Zbl 1296.92190
Neuwald, Andrew F.
1
2011
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Cited by 1,987 Authors

19 Van der Laan, Mark Johannes
13 Bickel, David R.
9 Farcomeni, Alessio
9 Nettleton, Dan
8 Boulesteix, Anne-Laure Isabeau
8 Goeman, Jelle J.
8 Sarkar, Sanat Kumar
7 Dickhaus, Thorsten
7 Grzegorczyk, Marco
7 Guillot, Dominique
7 Husmeier, Dirk
7 Rabier, Charles-Elie
7 Roquain, Étienne
6 Jenkins, Paul A.
6 Robin, Stéphane
6 Romano, Joseph P.
5 Binder, Harald
5 Bubenik, Peter
5 Drovandi, Christopher C.
5 Guo, Wenge
5 Habiger, Joshua D.
5 Hahn, Georg
5 Hobolth, Asger
5 Khare, Apoorva
5 Liu, Yanyan
5 Nuel, Gregory
5 Parmigiani, Giovanni
5 Rajaratnam, Bala
5 Stumpf, Michael P. H.
5 Tibshirani, Robert John
5 Verzelen, Nicolas
4 Aderhold, Andrej
4 Arslan, Olcay
4 Buzbas, Erkan Ozge
4 Carone, Marco
4 Gandy, Axel
4 Golightly, Andrew
4 Hossain, Ahmed
4 Koskela, Jere
4 Lee, Youngjo
4 Li, Hongzhe
4 Miecznikowski, Jeffrey C.
4 Peña, Edsel A.
4 Pettitt, Anthony N.
4 Reynaud-Bouret, Patricia
4 Rosenberg, Noah A.
4 Schifano, Elizabeth D.
4 van Wieringen, Wessel N.
4 Zhou, Wen-Xin
3 Alquier, Pierre
3 Ambroise, Christophe
3 Balakrishnan, Narayanaswamy
3 Bar, Haim Y.
3 Benner, Axel
3 Beyene, Joseph
3 Biau, Gérard
3 Blath, Jochen
3 Bogdan, Małgorzata
3 Braun, Danielle
3 Cabras, Stefano
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 Gillespie, Colin S.
3 Gordon, Alexander Ya.
3 Hall, Peter Gavin
3 Hamid, Jemila Seid
3 Hemerik, Jesse
3 Huang, Haiyan
3 Jaffrézic, Florence
3 Jana, Sayantee
3 Jose, Kanichukattu Korakutty
3 Kim, Sungsu
3 Liang, Kun
3 Lim, Johan
3 Liquet, Benoit
3 Liu, Yufeng
3 Marron, James Stephen
3 Mercier, Sabine
3 Mertens, Bart J. A.
3 Neuvial, Pierre
3 Nott, David John
3 Novikov, Aleksandr Aleksandrovich
3 Porzelius, Christine
3 Pudlo, Pierre
3 Qiu, Jing
3 Qu, Long
3 Rahnenführer, Jörg
3 Robert, Christian P. Robert
3 Ruli, Erlis
3 Sansonnet, Laure
3 Schumacher, Martin
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Cited in 161 Journals

81 Computational Statistics and Data Analysis
66 Statistical Applications in Genetics and Molecular Biology
65 The Annals of Applied Statistics
47 Biometrics
41 The Annals of Statistics
32 Journal of Applied Statistics
27 Statistics and Computing
25 Electronic Journal of Statistics
23 Journal of Multivariate Analysis
23 Journal of Statistical Planning and Inference
22 Journal of the American Statistical Association
22 Computational Statistics
20 Biometrical Journal
19 Statistics & Probability Letters
18 Theoretical Population Biology
18 Statistical Science
17 Journal of Theoretical Biology
16 Journal of Statistical Computation and Simulation
12 Scandinavian Journal of Statistics
12 Communications in Statistics. Simulation and Computation
10 Test
9 Journal of Applied Probability
8 Communications in Statistics. Theory and Methods
8 Biostatistics
8 Computational & Mathematical Methods in Medicine
8 Bayesian Analysis
7 The Canadian Journal of Statistics
7 Machine Learning
7 Statistical Papers
7 Journal of the Royal Statistical Society. Series B. Statistical Methodology
6 Journal of Mathematical Biology
6 Bernoulli
6 Statistical Methods and Applications
6 Advances in Data Analysis and Classification. ADAC
6 Journal of Agricultural, Biological, and Environmental Statistics
5 Mathematical Biosciences
5 International Journal of Approximate Reasoning
5 Methodology and Computing in Applied Probability
5 Statistical Analysis and Data Mining
5 Journal of Probability and Statistics
4 Annals of the Institute of Statistical Mathematics
4 Statistica Sinica
4 Lifetime Data Analysis
4 Statistical Modelling
4 Journal of Machine Learning Research (JMLR)
4 Computational Biology and Chemistry
4 Statistical Methodology
4 Statistics Surveys
4 Journal of Computational and Graphical Statistics
4 Epidemiologic Methods
3 Physica A
3 Bulletin of Mathematical Biology
3 Theoretical Computer Science
3 Statistics
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 Methods in Medical Research
3 Journal of the Korean Statistical Society
2 Advances in Applied Probability
2 Journal of Statistical Physics
2 Applied Mathematics and Computation
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 Journal of Nonparametric Statistics
2 Comptes Rendus. Mathématique. Académie des Sciences, Paris
2 Mathematical Biosciences and Engineering
2 Optimization Letters
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 The American Statistician
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 the Franklin Institute
1 Journal of Mathematical Analysis and Applications
1 Metrika
1 Psychometrika
1 Advances in Mathematics
1 Demonstratio Mathematica
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 Journal of Econometrics
1 Metron
1 Statistica
1 Statistica Neerlandica
1 Insurance Mathematics & Economics
1 Acta Applicandae Mathematicae
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Cited in 40 Fields

800 Statistics (62-XX)
292 Biology and other natural sciences (92-XX)
151 Numerical analysis (65-XX)
95 Probability theory and stochastic processes (60-XX)
57 Computer science (68-XX)
20 Combinatorics (05-XX)
18 Operations research, mathematical programming (90-XX)
15 Game theory, economics, finance, and other social and behavioral sciences (91-XX)
12 Linear and multilinear algebra; matrix theory (15-XX)
10 Algebraic topology (55-XX)
7 Systems theory; control (93-XX)
7 Information and communication theory, circuits (94-XX)
5 Functional analysis (46-XX)
4 Harmonic analysis on Euclidean spaces (42-XX)
4 Operator theory (47-XX)
3 Partial differential equations (35-XX)
3 Quantum theory (81-XX)
3 Statistical mechanics, structure of matter (82-XX)
2 Algebraic geometry (14-XX)
2 Special functions (33-XX)
2 Dynamical systems and ergodic theory (37-XX)
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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)
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