Statistical Applications in Genetics and Molecular Biology

2002 - 2024

Current editor(s): Michael P. H. Stumpf

From De Gruyter
Bibliographic data for series maintained by Peter Golla ().

Access Statistics for this journal.
Is something missing from the series or not right? See the RePEc data check for the archive and series.

Volume 9, issue 1, 2010

An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes pp. 12

Lim Johan, Kim Jayeon and Kim Byung Soo

The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies pp. 14

Zintzaras Elias

Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA pp. 14

Jach Agnieszka E and Marín Juan M

On Optimal Selection of Summary Statistics for Approximate Bayesian Computation pp. 16

Nunes Matthew A and Balding David J

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn pp. 16

Phipson Belinda and Smyth Gordon K

On the Optimal Design of Genetic Variant Discovery Studies pp. 17

Ionita-Laza Iuliana and Laird Nan M

Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium pp. 17

Attia John, Thakkinstian Ammarin, McElduff Patrick, Milne Elizabeth, Dawson Somer, Scott Rodney J, Klerk Nicholas de, Armstrong Bruce and Thompson John

The Detection of Blur in Affymetrix GeneChips pp. 19

Upton Graham J. G. and Harrison Andrew P

A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data pp. 21

Follestad Turid, Jørstad Tommy S, Erlandsen Sten E, Sandvik Arne K, Bones Atle M and Langaas Mette

Mapping Quantitative Trait Loci in a Non-Equilibrium Population pp. 21

Wu Song, Yang Jie and Wu Rongling

Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis pp. 22

Wang Chaolong, Szpiech Zachary A, Degnan James H, Jakobsson Mattias, Pemberton Trevor J, Hardy John A, Singleton Andrew B and Rosenberg Noah A

Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies pp. 22

Lebrec Jeremie J, Stijnen Theo and C van Houwelingen Hans

An Internal Calibration Method for Protein-Array Studies pp. 23

Daly Don Simone, Anderson Kevin K, Seurynck-Servoss Shannon L, Gonzalez Rachel M, White Amanda M and Zangar Richard C

Confidently Estimating the Number of DNA Replication Origins pp. 23

Bhaskar Anand and Keich Uri

Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model pp. 23

Mi Xiaojuan, Eskridge Kent, Wang Dong, Baenziger P. Stephen, Campbell B. Todd, Gill Kulvinder S., Dweikat Ismail and Bovaird James

Predicting Patient Survival from Longitudinal Gene Expression pp. 23

Zhang Yuping, Tibshirani Robert J. and Davis Ronald W.

Epistatic Interactions pp. 24

VanderWeele Tyler J

Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations pp. 24

Berg Arthur, He Qiuling, Shen Ye, Chen Ying, Huang Minren and Wu Rongling

Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles pp. 24

Nagarajan Radhakrishnan and Upreti Meenakshi

Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula pp. 25

Boitard Simon, Mangin Brigitte and Azaïs Jean-Marc

Space Oriented Rank-Based Data Integration pp. 25

Lin Shili

Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing pp. 25

Kim Kyung In, Roquain Etienne and A van de Wiel Mark

Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression pp. 25

Liu Xuejun and Rattray Magnus

Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases pp. 27

Shervais Stephen, Kramer Patricia L, Westaway Shawn K., Cox Nancy J and Zwick Martin

Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression pp. 27

Erhardt Vinzenz, Bogdan Malgorzata and Czado Claudia

Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling pp. 27

Friedrich Torben, Koetschan Christian and Müller Tobias

An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data pp. 28

Rau Andrea, Jaffrézic Florence, Foulley Jean-Louis and Doerge Rebecca W

Weighted-LASSO for Structured Network Inference from Time Course Data pp. 29

Charbonnier Camille, Chiquet Julien and Ambroise Christophe

Testing for Gene-Gene Interaction with AMMI Models pp. 29

Barhdadi Amina and Dubé Marie-Pierre

A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number pp. 30

N van Wieringen Wessel, Berkhof Johannes and A van de Wiel Mark

Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data pp. 30

Garcia-Magariños Manuel, Antoniadis Anestis, Cao Ricardo and González-Manteiga Wenceslao

Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics pp. 31

Kechris Katerina J, Biehs Brian and Kornberg Thomas B

Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach pp. 31

Kasim Adetayo, Lin Dan, Suzy Van Sanden, Clevert Djork-Arné, Bijnens Luc, Göhlmann Hinrich, Amaratunga Dhammika, Hochreiter Sepp, Shkedy Ziv and Talloen Willem

Sparse Partial Least Squares Classification for High Dimensional Data pp. 32

Chung Dongjun and Keles Sunduz

Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression pp. 33

Montazeri Zahra, Yanofsky Corey M. and Bickel David R.

Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data pp. 33

Wang Zhu and Wang C.Y.

The Apportionment of Total Genetic Variation by Categorical Analysis of Variance pp. 34

Khang Tsung Fei and Yap Von Bing

Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis pp. 35

Hwang J.T. Gene and Liu Peng

Network Enrichment Analysis in Complex Experiments pp. 36

Shojaie Ali and Michailidis George

Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment pp. 37

Arribas-Gil Ana

Sub-Modular Resolution Analysis by Network Mixture Models pp. 43

Marras Elisabetta, Travaglione Antonella and Capobianco Enrico

Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association pp. 46

Crosslin David R., Qin Xuejun and Hauser Elizabeth R.

Volume 8, issue 1, 2009

Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates pp. 11

Ahn Kwangmi, Gordon Derek and Finch Stephen J

A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families pp. 13

Larsen Klaus, Petersen Janne, Bernstein Inge and Nilbert Mef

Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications pp. 16

Podani János, Engloner Attila and Major Agnes

Modified FDR Controlling Procedure for Multi-Stage Analyses pp. 17

Tuglus Catherine and J. van der Laan Mark

Transmission Disequilibrium Test Power and Sample Size in the Presence of Locus Heterogeneity pp. 18

Chen Chuanwen, Yang Guang, Buyske Steven, Matise Tara, Finch Stephen J and Gordon Derek

Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements pp. 19

Ding Xiao, Weiss Scott, Raby Benjamin, Lange Christoph and Laird Nan M

Univariate Shrinkage in the Cox Model for High Dimensional Data pp. 20

Tibshirani Robert J.

A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments pp. 20

Wang Lily, Chen Xi, Wolfinger Russell D, Franklin Jeffrey L, Coffey Robert J and Zhang Bing

Balanced Gradient Boosting from Imbalanced Data for Clinical Outcome Prediction pp. 21

Teramoto Reiji

Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness pp. 22

Borchers Bryce, Brown Marshall, McLellan Brian, Bekmetjev Airat and Tintle Nathan L

Adaptive Transmission Disequilibrium Test for Family Trio Design pp. 22

Yuan Min, Tian Xin, Zheng Gang and Yang Yaning

Model Selection Based on FDR-Thresholding Optimizing the Area under the ROC-Curve pp. 22

Graf Alexandra C. and Bauer Peter

M-quantile Regression Analysis of Temporal Gene Expression Data pp. 22

Vinciotti Veronica and Yu Keming

Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates pp. 22

Deng Ling and Moore Dirk F.

Characterizing the D2 Statistic: Word Matches in Biological Sequences pp. 23

Forêt Sylvain, Wilson Susan R and Burden Conrad J

Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study pp. 23

Sato Yasunori, Laird Nan, Suganami Hideki, Hamada Chikuma, Niki Naoto, Yoshimura Isao and Yoshida Teruhiko

Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies pp. 24

Engler David and Li Yi

Weighted Multiple Hypothesis Testing Procedures pp. 24

Kang Guolian, Ye Keying, Liu Nianjun, Allison David B. and Gao Guimin

Estimation of Selection Intensity under Overdominance by Bayesian Methods pp. 24

Buzbas Erkan Ozge, Joyce Paul and Abdo Zaid

A Statistical Model for Genetic Mapping of Viral Infection by Integrating Epidemiological Behavior pp. 24

Li Yao, Berg Arthur, Chang Myron N, Du Ping, Ahn Kwangmi, Mauger David, Liao Duanping and Wu Rongling

Normalization Method for Transcriptional Studies of Heterogeneous Samples - Simultaneous Array Normalization and Identification of Equivalent Expression pp. 25

Qin Li-Xuan and Satagopan Jaya M

Detecting Outlier Samples in Microarray Data pp. 26

Shieh Albert D and Hung Yeung Sam

Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments pp. 26

Dørum Guro, Snipen Lars, Solheim Margrete and Sæbø Solve

A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations pp. 27

Li Qin and Wu Rongling

A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins pp. 27

Thilakarathne Pushpike J, Verbeke Geert, Engelen Kristof and Marchal Kathleen

A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers pp. 28

Lucas Joseph, Carvalho Carlos and West Mike

A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data pp. 28

Hamid Jemila S and Beyene Joseph

Testing of Chromosomal Clumping of Gene Properties pp. 29

Fernandez-Ricaud Luciano, Dalevi Daniel, Blomberg Anders and Nerman Olle

Bayesian Unsupervised Learning with Multiple Data Types pp. 29

Agius Phaedra, Ying Yiming and Campbell Colin

Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data pp. 29

Witten Daniela M and Tibshirani Robert J.

Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry pp. 29

Sampson Joshua and Zhao Hongyu

Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas pp. 29

Lacey Michelle R and Ehrlich Melanie

MC-Normalization: A Novel Method for Dye-Normalization of Two-Channel Microarray Data pp. 30

Landfors Mattias, Fahlén Jessica and Rydén Patrik

A Regularized Regression Approach for Dissecting Genetic Conflicts that Increase Disease Risk in Pregnancy pp. 30

Li Shaoyu, Lu Qing, Fu Wenjiang, Romero Roberto and Cui Yuehua

Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis pp. 34

Morris Nathan J, Elston Robert and Stein Catherine M

Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis pp. 35

Marot Guillemette and Mayer Claus-Dieter

Sparse Canonical Correlation Analysis with Application to Genomic Data Integration pp. 36

Parkhomenko Elena, Tritchler David and Beyene Joseph

Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis pp. 36

?uksza Marta, Kluge Bogus?aw, Ostrowski Jerzy, Karczmarski Jakub and Gambin Anna

Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data pp. 36

Siewert Elizabeth A and Kechris Katerina J

Score Statistics for Mapping Quantitative Trait Loci pp. 37

Chang Myron N, Wu Rongling, Wu Samuel S and Casella George

Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study pp. 40

Nguyen Tuan S and Rojo Javier

Inferring Dynamic Genetic Networks with Low Order Independencies pp. 40

Lèbre Sophie

Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values pp. 45

Taylor Sandra and Pollard Katherine

Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping pp. 46

Hössjer Ola, Hartman Linda and Humphreys Keith

A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions pp. 47

Kuan Pei Fen, Huebert Dana, Gasch Audrey and Keles Sunduz

Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs pp. 49

Ogorek Benjamin A and Stefanski Leonard A

A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms pp. 58

Ferreira José A., Berkhof Johannes, Souverein Olga and Zwinderman Koos