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August 2014, Volume 13, Issue 4
- 1-17 Investigating the performance of AIC in selecting phylogenetic models
by Jhwueng Dwueng-Chwuan & Huzurbazar Snehalata & O’Meara Brian C. & Liu Liang - 1-20 Comparison of statistical methods for finding network motifs
by Albieri Vanna & Didelez Vanessa - 1-20 Multiclass cancer classification based on gene expression comparison
by Yang Sitan & Naiman Daniel Q. - 1-21 Protein domain hierarchy Gibbs sampling strategies
by Neuwald Andrew F. - 1-23 Biological pathway selection through Bayesian integrative modeling
by Zheng Lingling & Yan Xiao & Suchindran Sunil & Dressman Holly & Chute John P. & Lucas Joseph
June 2014, Volume 13, Issue 3
- 1-12 Efficient parametric inference for stochastic biological systems with measured variability
by Johnston Iain G. - 1-15 A boosting approach for adapting the sparsity of risk prediction signatures based on different molecular levels
by Sariyar Murat & Schumacher Martin & Binder Harald - 1-19 Applying shrinkage variance estimators to the TOST test in high dimensional settings
by Qiu Jing & Qi Yue & Cui Xiangqin - 1-20 Using the theory of added-variable plot for linear mixed models to decompose genetic effects in family data
by Duarte Nubia E. & Giolo Suely R. & Pereira Alexandre C. & de Andrade Mariza & Soler Júlia P. - 1-23 A Bayesian clustering approach for detecting gene-gene interactions in high-dimensional genotype data
by Chen Sui-Pi & Huang Guan-Hua - 1-24 A novel characterization of the generalized family wise error rate using empirical null distributions
by Miecznikowski Jeffrey C. & Gaile Daniel P. - 1-47 Statistical inference of regulatory networks for circadian regulation
by Aderhold Andrej & Husmeier Dirk & Grzegorczyk Marco
April 2014, Volume 13, Issue 2
- 123-139 Combining dependent F-tests for robust association of quantitative traits under genetic model uncertainty
by Qu Long - 141-158 Penalized differential pathway analysis of integrative oncogenomics studies
by van Wieringen Wessel N. & van de Wiel Mark A. - 159-171 A data-smoothing approach to explore and test gene-environment interaction in case-parent trios
by Shin Ji-Hyung & McNeney Brad & Graham Jinko & Infante-Rivard Claire - 173-190 Scan statistics analysis for detection of introns in time-course tiling array data
by Reiner-Benaim Anat & Davis Ronald W. & Juneau Kara - 191-201 Variance and covariance heterogeneity analysis for detection of metabolites associated with cadmium exposure
by Salamanca Beatriz Valcarcel & Ebbels Timothy M.D. & Iorio Maria De - 203-216 Improved variational Bayes inference for transcript expression estimation
by Papastamoulis Panagiotis & Glaus Peter & Rattray Magnus & Hensman James - 217-226 Efficient identification of context dependent subgroups of risk from genome-wide association studies
by Dyson Greg & Sing Charles F.
February 2014, Volume 13, Issue 1
- 1-18 Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums
by Fernández-Durán Juan José & Gregorio-Domínguez MarÍa Mercedes - 19-33 Second order optimization for the inference of gene regulatory pathways
by Das Mouli & Murthy Chivukula A. & De Rajat K. - 35-48 Multiple comparisons in genetic association studies: a hierarchical modeling approach
by Yi Nengjun & Lou Xiang-Yang & Mallick Himel & Xu Shizhong - 49-65 A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments
by Gómez-Villegas Miguel A. & Sanz Luis & Salazar Isabel - 67-82 Semi-automatic selection of summary statistics for ABC model choice
by Prangle Dennis & Fearnhead Paul & Cox Murray P. & Biggs Patrick J. & French Nigel P. - 83-104 Detection of epistatic effects with logic regression and a classical linear regression model
by Malina Magdalena & Posch Martin & Ickstadt Katja & Schwender Holger & Bogdan Małgorzata - 105-121 Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model
by Jääskinen Väinö & Parkkinen Ville & Cheng Lu & Corander Jukka
December 2013, Volume 12, Issue 6
- 653-666 A new variance stabilizing transformation for gene expression data analysis
by Kelmansky Diana M. & Martínez Elena J. & Leiva Víctor - 667-678 Kernel approximate Bayesian computation in population genetic inferences
by Nakagome Shigeki & Fukumizu Kenji & Mano Shuhei - 679-701 Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology
by Mramba Lazarus K. & Barber Stuart & Hommola Kerstin & Dyer Lee A. & Wilson Joseph S. & Forister Matthew L. & Gilks Walter R. - 703-722 Accounting for undetected compounds in statistical analyses of mass spectrometry ‘omic studies
by Taylor Sandra L. & Kim Kyoungmi & Leiserowitz Gary S. - 723-742 Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments
by Lacey Michelle R. & Baribault Carl & Ehrlich Melanie - 743-755 Estimation of weighted log partial area under the ROC curve and its application to MicroRNA expression data
by Hossain Ahmed & Beyene Joseph - 757-786 Random forests on distance matrices for imaging genetics studies
by Sim Aaron & Tsagkrasoulis Dimosthenis & Montana Giovanni
October 2013, Volume 12, Issue 5
- 545-557 Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks
by Asif H.M. Shahzad & Sanguinetti Guido - 559-581 Markov chain Monte Carlo sampling of gene genealogies conditional on unphased SNP genotype data
by Burkett Kelly M. & McNeney Brad & Graham Jinko - 583-602 Performance and estimation of the true error rate of classification rules built with additional information. An application to a cancer trial
by Conde David & Salvador Bonifacio & Rueda Cristina & Fernández Miguel A. - 603-618 Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems
by Silk Daniel & Filippi Sarah & Stumpf Michael P. H. - 619-635 Model selection for prognostic time-to-event gene signature discovery with applications in early breast cancer data
by Ahdesmäki Miika & Lancashire Lee & Proutski Vitali & Wilson Claire & Davison Timothy S. & Harkin D. Paul & Kennedy Richard D. - 637-652 Identifying clusters in genomics data by recursive partitioning
by Nilsen Gro & LiestØl Knut & Borgan Ørnulf & Lingjærde Ole Christian
August 2013, Volume 12, Issue 4
- 413-431 Genome-wide association studies with high-dimensional phenotypes
by Marttinen Pekka & Gillberg Jussi & Havulinna Aki & Corander Jukka & Kaski Samuel - 433-448 The mid p-value in exact tests for Hardy-Weinberg equilibrium
by Graffelman Jan & Moreno Victor - 449-467 General power and sample size calculations for high-dimensional genomic data
by van Iterson Maarten & van de Wiel Mark A. & Boer Judith M. & de Menezes Renée X. - 469-487 A graphical model method for integrating multiple sources of genome-scale data
by Dvorkin Daniel & Biehs Brian & Kechris Katerina - 489-503 Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure
by Zhang Runchu & Mukerjee Rahul - 505-516 Bayseian genomic models for the incorporation of pathway topology knowledge into association studies
by Brisbin Abra & Fridley Brooke L. - 517-527 Improving the efficiency of genomic selection
by Scutari Marco & Balding David & Mackay Ian - 529-543 Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions
by Bickel David R.
May 2013, Volume 12, Issue 2
- 129-141 Approximate Bayesian computation (ABC) gives exact results under the assumption of model error
by Wilkinson Richard David
March 2013, Volume 12, Issue 1
- 1-15 Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data
by Zheng Wei & Zhao Hongyu - 17-37 Approximate Bayesian computation with functional statistics
by Soubeyrand Samuel & Guiton François & Klein Etienne K. & Carpentier Florence - 39-48 Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics
by Herbei Radu & Kubatko Laura - 49-70 Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data
by Di Yanming & Emerson Sarah C. & Schafer Daniel W. & Kimbrel Jeffrey A. & Chang Jeff H. - 71-86 Flexible pooling in gene expression profiles: design and statistical modeling of experiments for unbiased contrasts
by Rudolf Henrik & Pricop-Jeckstadt Mihaela & Reinsch Norbert - 87-107 On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
by Filippi Sarah & Barnes Chris P. & Stumpf Michael P.H. & Cornebise Julien - 109-127 Inferring latent gene regulatory network kinetics
by González Javier & Vujačić Ivan & Wit Ernst
December 2012, Volume 11, Issue 6
- 1-34 An Order Estimation Based Approach to Identify Response Genes for Microarray Time Course Data
by Lu Zhiheng K. & O. Brian Allen & Desmond Anthony F.
November 2012, Volume 11, Issue 6
- 1-22 Time Dependent ROC Curves for the Estimation of True Prognostic Capacity of Microarray Data
by Foucher Yohann & Danger Richard - 1-25 A maximum likelihood approach to functional mapping of longitudinal binary traits
by Wang Chenguang & Li Hongying & Wang Zhong & Wang Yaqun & Wang Ningtao & Wang Zuoheng & Wu Rongling - 1-25 Hierarchical Shrinkage Priors and Model Fitting for High-dimensional Generalized Linear Models
by Yi Nengjun & Ma Shuangge
October 2012, Volume 11, Issue 5
- 1-21 Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data
by Hayashi Takeshi - 1-24 Analyzing Genetic Association Studies with an Extended Propensity Score Approach
by Zhao Huaqing & Rebbeck Timothy R. & Mitra Nandita - 1-26 Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms
by Lin Chang-Yun & Lo Yungtai & Ye Kenny Q. - 1-26 A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection
by Schmid Matthias & Hothorn Torsten & Krause Friedemann & Rabe Christina - 1-32 Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data
by Pounds Stanley B. & Gao Cuilan L. & Zhang Hui - 1-42 Estimators of the local false discovery rate designed for small numbers of tests
by Padilla Marta & Bickel David R. - 1-44 Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates
by Lund Steven P. & Nettleton Dan & McCarthy Davis J. & Smyth Gordon K.
September 2012, Volume 11, Issue 5
- 1-29 Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks
by Geeven Geert & van der Laan Mark J. & de Gunst Mathisca C.M. - 1-34 DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms
by Ramsey David M. & Futschik Andreas
November 2012, Volume 11, Issue 5
- 1-22 ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments
by Mary-Huard Tristan & Jaffrezic Florence & Robin Stéphane - 1-28 Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations
by Anderson Eric C. - 1-37 Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data
by Olbricht Gayla R. & Craig Bruce A. & Doerge Rebecca W.
June 2012, Volume 11, Issue 4
- 1-17 Performance of MAX Test and Degree of Dominance Index in Predicting the Mode of Inheritance
by Zintzaras Elias & Santos Mauro - 1-31 A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in Microarray time course data
by Farcomeni Alessio & Arima Serena
May 2012, Volume 11, Issue 4
- 1-26 QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function
by Frommlet Florian & Ljubic Ivana & Arnardóttir Helga Björk & Bogdan Malgorzata - 1-37 Computing Posterior Probabilities for Score-based Alignments Using ppALIGN
by Wolfsheimer Stefan & Hartmann Alexander & Rabus Ralf & Nuel Gregory
July 2012, Volume 11, Issue 4
- 1-17 Correction for Founder Effects in Host-Viral Association Studies via Principal Components
by Reeves Karyn L. & McKinnon Elizabeth J. & James Ian R. - 1-21 Incorporating the Empirical Null Hypothesis into the Benjamini-Hochberg Procedure
by Ghosh Debashis - 1-28 Estimating the Number of One-step Beneficial Mutations
by Wojtowicz Andrzej J. & Miller Craig R. & Joyce Paul - 1-30 Testing clonality of three and more tumors using their loss of heterozygosity profiles
by Ostrovnaya Irina - 1-30 An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping
by Scott-Boyer Marie Pier & Imholte Gregory C. & Tayeb Arafat & Labbe Aurelie & Deschepper Christian F. & Gottardo Raphael - 1-31 A Novel and Fast Normalization Method for High-Density Arrays
by van Iterson Maarten & Duijkers Floor A.M. & Meijerink Jules P.P. & Admiraal Pieter & van Ommen Gert-Jan B. & Boer Judith M. & van Noesel Max M. & Menezes Renee X. - 1-33 How to analyze many contingency tables simultaneously in genetic association studies
by Dickhaus Thorsten & Straßburger Klaus & Schunk Daniel & Morcillo-Suarez Carlos & Illig Thomas & Navarro Arcadi - 1-62 A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology
by Grzegorczyk Marco & Husmeier Dirk
September 2012, Volume 11, Issue 4
- 1-46 Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications
by Kenney Toby & Gu Hong - 1-56 A New Explained-Variance Based Genetic Risk Score for Predictive Modeling of Disease Risk
by Che Ronglin & Motsinger-Reif Alison A.
August 2012, Volume 11, Issue 4
- 1-31 Cluster-Localized Sparse Logistic Regression for SNP Data
by Binder Harald & Müller Tina & Schwender Holger & Golka Klaus & Steffens Michael & Hengstler Jan G. & Ickstadt Katja & Schumacher Martin
March 2012, Volume 11, Issue 3
- 1-31 Normalization, bias correction, and peak calling for ChIP-seq
by Diaz Aaron & Park Kiyoub & Lim Daniel A. & Song Jun S.
May 2012, Volume 11, Issue 3
- 1-19 Detecting Sample Misidentifications in Genetic Association Studies
by Ekstrøm Claus T. & Feenstra Bjarke - 1-29 Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis
by Ji Tieming & Liu Peng & Nettleton Dan - 1-32 The Beta-Binomial SGoF method for multiple dependent tests
by de Uña-Alvarez Jacobo - 1-35 Exploring Multicollinearity Using a Random Matrix Theory Approach
by Feher Kristen & Whelan James & Müller Samuel
April 2012, Volume 11, Issue 3
- 1-21 Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies
by Bogojeska Jasmina & Lengauer Thomas - 1-22 The practical effect of batch on genomic prediction
by Parker Hilary S. & Leek Jeffrey T.
February 2012, Volume 11, Issue 3
- 1-15 GENOVA: Gene Overlap Analysis of GWAS Results
by Tang Clara S. & Ferreira Manuel A. R. - 1-20 Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model
by Ambroise Jérôme & Bearzatto Bertrand & Robert Annie & Macq Benoit & Gala Jean-Luc - 1-21 A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification
by Ferguson John P. & Cho Judy H. & Zhao Hongyu - 1-24 Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes
by French Benjamin & Lumley Thomas & Cappola Thomas P. & Mitra Nandita - 1-30 Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set
by Lim Johan & Kim Jayoun & Kim Sang-cheol & Yu Donghyeon & Kim Kyunga & Kim Byung Soo - 1-34 Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals
by Bickel David R. - 1-42 Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry
by Nyangoma Stephen O. & Collins Stuart I. & Altman Douglas G. & Johnson Philip & Billingham Lucinda J. - 1-52 Graph Selection with GGMselect
by Giraud Christophe & Huet Sylvie & Verzelen Nicolas
January 2012, Volume 11, Issue 2
- 1-5 Special Issue on Computational Statistical Methods for Genomics and Systems Biology
by Labbe Aurélie & Dudoit Sandrine - 1-18 Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
by Glazner Chris & Thompson Elizabeth Alison - 1-19 Gene Filtering in the Analysis of Illumina Microarray Experiments
by Forcheh Anyiawung Chiara & Verbeke Geert & Kasim Adetayo & Lin Dan & Shkedy Ziv & Talloen Willem & Göhlmann Hinrich WH & Clement Lieven - 1-21 Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate
by Zhang Tian-Xiao & Beaty Terri H. & Ruczinski Ingo - 1-23 A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
by Moser Carlee & Gupta Mayetri - 1-23 Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads
by Shin Ji-Hyung & Infante-Rivard Claire & Graham Jinko & McNeney Brad - 1-27 Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees
by Oualkacha Karim & Labbe Aurelie & Ciampi Antonio & Roy Marc-Andre & Maziade Michel - 1-27 A Model-Based Analysis to Infer the Functional Content of a Gene List
by Newton Michael A. & He Qiuling & Kendziorski Christina - 1-31 Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
by Lee Anthony & Caron Francois & Doucet Arnaud & Holmes Chris - 1-32 A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
by Cartwright Reed A. & Hussin Julie & Keebler Jonathan E. M. & Stone Eric A. & Awadalla Philip - 1-37 Querying Genomic Databases: Refining the Connectivity Map
by Segal Mark R. & Xiong Hao & Bengtsson Henrik & Bourgon Richard & Gentleman Robert
January 2012, Volume 11, Issue 1
- 1-9 Optimality Criteria for the Design of 2-Color Microarray Studies
by Kerr Kathleen F. - 1-18 The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses
by Goeman Jelle J. & Finos Livio - 1-20 Stopping-Time Resampling and Population Genetic Inference under Coalescent Models
by Jenkins Paul A. - 1-21 A Mixture-Model Approach for Parallel Testing for Unequal Variances
by Bar Haim Y. & Booth James G. & Wells Martin T. - 1-24 Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach
by Ambroise Jérôme & Robert Annie & Macq Benoit & Gala Jean-Luc - 1-25 MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
by Bhattacharyya Malay & Feuerbach Lars & Bhadra Tapas & Lengauer Thomas & Bandyopadhyay Sanghamitra - 1-27 Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning
by Bulla Ingo & Schultz Anne-Kathrin & Meinicke Peter - 1-29 A Context Dependent Pair Hidden Markov Model for Statistical Alignment
by Arribas-Gil Ana & Matias Catherine - 1-36 Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays
by Clement Lieven & De Beuf Kristof & Thas Olivier & Vuylsteke Marnik & Irizarry Rafael A. & Crainiceanu Ciprian M. - 1-43 Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps
by Silver Matt & Montana Giovanni & Alzheimer's Disease Neuroimaging Initiative
December 2011, Volume 11, Issue 1
- 1-28 Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length
by Burden Conrad J. & Jing Junmei & Wilson Susan R.
May 2011, Volume 10, Issue 1
- 1-19 Quantifying the Relative Contribution of the Heterozygous Class to QTL Detection Power
by McClosky Benjamin & Ma Xiwen & Tanksley Steven D. - 1-22 Disequilibrium Coefficient: A Bayesian Perspective
by Brentani Helena & Nakano Eduardo Y & Martins Camila B & Izbicki Rafael & Pereira Carlos Alberto - 1-26 A Two-Stage Poisson Model for Testing RNA-Seq Data
by Auer Paul L. & Doerge Rebecca W - 1-28 The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq
by Di Yanming & Schafer Daniel W & Cumbie Jason S & Chang Jeff H - 1-30 Inferring Gene Networks using Robust Statistical Techniques
by Nadadoor Venkat R. & Ben-Zvi Amos & Shah Sirish L. - 1-32 Analyzing Time-Course Microarray Data Using Functional Data Analysis - A Review
by Coffey Norma & Hinde John - 1-39 Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees
by Wang Yuancheng & Degnan James H
April 2011, Volume 10, Issue 1
- 1-24 Imputation Estimators Partially Correct for Model Misspecification
by Minin Vladimir N. & O'Brien John D. & Seregin Arseni - 1-30 On the Statistical Properties of SGoF Multitesting Method
by de Uña-Alvarez Jacobo - 1-31 A Non-Parametric Method for Detecting Specificity Determining Sites in Protein Sequence Alignments
by Gilks Walter R & Wang Chinying - 1-41 Meta-Analysis of Family-Based and Case-Control Genetic Association Studies that Use the Same Cases
by Bagos Pantelis G & Dimou Niki L & Liakopoulos Theodore D & Nikolopoulos Georgios K
February 2011, Volume 10, Issue 1
- 1-10 A Robust Statistical Method to Detect Null Alleles in Microsatellite and SNP Datasets in Both Panmictic and Inbred Populations
by Girard Philippe - 1-20 Information Metrics in Genetic Epidemiology
by Tritchler David L & Sucheston Lara & Chanda Pritam & Ramanathan Murali - 1-24 Large Sample Approximations of Probabilities of Correct Evolutionary Tree Estimation and Biases of Maximum Likelihood Estimation
by Susko Edward - 1-29 Interval Estimation of Familial Correlations from Pedigrees
by Mathew George & Song Yeunjoo & Elston Robert
March 2011, Volume 10, Issue 1
- 1-18 Linear Combination Test for Hierarchical Gene Set Analysis
by Wang Xiaoming & Dinu Irina & Liu Wei & Yasui Yutaka - 1-27 Exploratory Analysis of Multiple Omics Datasets Using the Adjusted RV Coefficient
by Mayer Claus-Dieter & Lorent Julie & Horgan Graham W - 1-35 Application of the Lasso to Expression Quantitative Trait Loci Mapping
by Brown Andrew Anand & Richardson Sylvia & Whittaker John - 1-36 A Variance-Components Model for Distance-Matrix Phylogenetic Reconstruction
by Gilks Walter R & Nye Tom M.W. & Lio Pietro
September 2011, Volume 10, Issue 1
- 1-22 Fully Moderated T-statistic for Small Sample Size Gene Expression Arrays
by Yu Lianbo & Gulati Parul & Fernandez Soledad & Pennell Michael & Kirschner Lawrence & Jarjoura David - 1-23 Choice of Summary Statistic Weights in Approximate Bayesian Computation
by Jung Hsuan & Marjoram Paul - 1-25 A Modified Maximum Contrast Method for Unequal Sample Sizes in Pharmacogenomic Studies
by Nagashima Kengo & Sato Yasunori & Hamada Chikuma - 1-27 Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains
by Singer Meromit & Engström Alexander & Schönhuth Alexander & Pachter Lior - 1-34 Assessing Modularity Using a Random Matrix Theory Approach
by Feher Kristen & Whelan James & Müller Samuel
August 2011, Volume 10, Issue 1
- 1-21 Entropy Based Genetic Association Tests and Gene-Gene Interaction Tests
by de Andrade Mariza & Wang Xin - 1-23 MA-SNP -- A New Genotype Calling Method for Oligonucleotide SNP Arrays Modeling the Batch Effect with a Normal Mixture Model
by Wen Yalu & Li Ming & Fu Wenjiang J - 1-26 Smoothing Gene Expression Data with Network Information Improves Consistency of Regulated Genes
by Dørum Guro & Snipen Lars & Solheim Margrete & Saebo Solve - 1-29 Weighted Lasso with Data Integration
by Bergersen Linn Cecilie & Glad Ingrid K. & Lyng Heidi - 1-30 Surveying the Manifold Divergence of an Entire Protein Class for Statistical Clues to Underlying Biochemical Mechanisms
by Neuwald Andrew F.
June 2011, Volume 10, Issue 1
- 1-22 The Joint Null Criterion for Multiple Hypothesis Tests
by Leek Jeffrey T & Storey John D. - 1-27 Multiple Imputation of Missing Phenotype Data for QTL Mapping
by Bobb Jennifer F & Scharfstein Daniel O. & Daniels Michael J. & Collins Francis S & Kelada Samir
October 2011, Volume 10, Issue 1
- 1-21 Adaptive Elastic-Net Sparse Principal Component Analysis for Pathway Association Testing
by Chen Xi - 1-26 Genetic Linkage Analysis in the Presence of Germline Mosaicism
by Weissbrod Omer & Geiger Dan - 1-27 Bayesian Learning from Marginal Data in Bionetwork Models
by Bonassi Fernando V. & You Lingchong & West Mike - 1-40 Fitting Boolean Networks from Steady State Perturbation Data
by Almudevar Anthony & McCall Matthew N. & McMurray Helene & Land Hartmut
November 2011, Volume 10, Issue 1
- 1-20 False Discovery Rate Estimation for Stability Selection: Application to Genome-Wide Association Studies
by Ahmed Ismaïl & Hartikainen Anna-Liisa & Järvelin Marjo-Riitta & Richardson Sylvia - 1-21 Multiple Testing in Candidate Gene Situations: A Comparison of Classical, Discrete, and Resampling-Based Procedures
by Elsäßer Amelie & Victor Anja & Hommel Gerhard - 1-22 Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome
by Bérard Caroline & Martin-Magniette Marie-Laure & Brunaud Véronique & Aubourg Sébastien & Robin Stéphane - 1-24 A Calibrated Multiclass Extension of AdaBoost
by Rubin Daniel B. - 1-30 Modeling Read Counts for CNV Detection in Exome Sequencing Data
by Love Michael I. & Myšičková Alena & Sun Ruping & Kalscheuer Vera & Vingron Martin & Haas Stefan A. - 1-32 Multiscale Characterization of Signaling Network Dynamics through Features
by Capobianco Enrico & Marras Elisabetta & Travaglione Antonella
July 2011, Volume 10, Issue 1
- 1-11 Measurement of Evidence and Evidence of Measurement
by Vieland Veronica J & Hodge Susan E - 1-23 Comparison of Clinical Subgroup aCGH Profiles through Pseudolikelihood Ratio Tests
by Engler David & Shen Yiping & Gusella James & Betensky Rebecca A. - 1-24 Sparse Canonical Covariance Analysis for High-throughput Data
by Lee Woojoo & Lee Donghwan & Lee Youngjo & Pawitan Yudi - 1-25 Deviance Information Criteria for Model Selection in Approximate Bayesian Computation
by Francois Olivier & Laval Guillaume - 1-27 High-Dimensional Regression and Variable Selection Using CAR Scores
by Zuber Verena & Strimmer Korbinian - 1-34 Random Forests for Genetic Association Studies
by Goldstein Benjamin A & Polley Eric C & Briggs Farren B. S.
January 2011, Volume 10, Issue 1
- 1-15 Accuracy and Computational Efficiency of a Graphical Modeling Approach to Linkage Disequilibrium Estimation
by Abel Haley J & Thomas Alun - 1-19 A Three Component Latent Class Model for Robust Semiparametric Gene Discovery
by Alfo' Marco & Farcomeni Alessio & Tardella Luca - 1-23 A Comparison of Multifactor Dimensionality Reduction and L1-Penalized Regression to Identify Gene-Gene Interactions in Genetic Association Studies
by Winham Stacey & Wang Chong & Motsinger-Reif Alison A - 1-27 Log-Linear Modelling of Protein Dipeptide Structure Reveals Interesting Patterns of Side-Chain-Backbone Interactions
by Hommola Kerstin & Gilks Walter R. & Mardia Kanti V. - 1-27 Learning Monotonic Genotype-Phenotype Maps
by Beerenwinkel Niko & Knupfer Patrick & Tresch Achim - 1-31 Repeated Measures Semiparametric Regression Using Targeted Maximum Likelihood Methodology with Application to Transcription Factor Activity Discovery
by Tuglus Catherine & van der Laan Mark J. - 1-32 Learning from Past Treatments and Their Outcome Improves Prediction of In Vivo Response to Anti-HIV Therapy
by Saigo Hiroto & Altmann Andre & Bogojeska Jasmina & Müller Fabian & Nowozin Sebastian & Lengauer Thomas - 1-37 A Markov-Chain Model for the Analysis of High-Resolution Enzymatically 18O-Labeled Mass Spectra
by Valkenborg Dirk & Burzykowski Tomasz
October 2010, Volume 9, Issue 1
- 1-16 Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
by Phipson Belinda & Smyth Gordon K - 1-19 The Detection of Blur in Affymetrix GeneChips
by Upton Graham J. G. & Harrison Andrew P - 1-23 Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
by Mi Xiaojuan & Eskridge Kent & Wang Dong & Baenziger P. Stephen & Campbell B. Todd & Gill Kulvinder S. & Dweikat Ismail & Bovaird James - 1-35 Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
by Hwang J.T. Gene & Liu Peng - 1-46 Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association
by Crosslin David R. & Qin Xuejun & Hauser Elizabeth R.
May 2010, Volume 9, Issue 1
- 1-14 The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies
by Zintzaras Elias - 1-36 Network Enrichment Analysis in Complex Experiments
by Shojaie Ali & Michailidis George
September 2010, Volume 9, Issue 1
- 1-16 On Optimal Selection of Summary Statistics for Approximate Bayesian Computation
by Nunes Matthew A & Balding David J
June 2010, Volume 9, Issue 1
- 1-27 Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression
by Erhardt Vinzenz & Bogdan Malgorzata & Czado Claudia - 1-30 A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number
by van Wieringen Wessel N & Berkhof Johannes & van de Wiel Mark A - 1-33 Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression
by Montazeri Zahra & Yanofsky Corey M. & Bickel David R. - 1-33 Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data
by Wang Zhu & Wang C.Y.
December 2010, Volume 9, Issue 1
- 1-25 Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression
by Liu Xuejun & Rattray Magnus
January 2010, Volume 9, Issue 1
- 1-12 An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
by Lim Johan & Kim Jayeon & Kim Byung Soo - 1-17 Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
by Attia John & Thakkinstian Ammarin & McElduff Patrick & Milne Elizabeth & Dawson Somer & Scott Rodney J & Klerk Nicholas de & Armstrong Bruce & Thompson John - 1-21 A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
by Follestad Turid & Jørstad Tommy S & Erlandsen Sten E & Sandvik Arne K & Bones Atle M & Langaas Mette - 1-22 Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
by Wang Chaolong & Szpiech Zachary A & Degnan James H & Jakobsson Mattias & Pemberton Trevor J & Hardy John A & Singleton Andrew B & Rosenberg Noah A - 1-22 Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
by Lebrec Jeremie J & Stijnen Theo & van Houwelingen Hans C - 1-23 An Internal Calibration Method for Protein-Array Studies
by Daly Don Simone & Anderson Kevin K & Seurynck-Servoss Shannon L & Gonzalez Rachel M & White Amanda M & Zangar Richard C - 1-24 Epistatic Interactions
by VanderWeele Tyler J