Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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

From De Gruyter
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Volume 7, issue 2, 2008

International Competition on Mass Spectrometry Proteomic Diagnosis pp. 4

Mertens Bart

Principal Component Discriminant Analysis pp. 6

Fearn Tom

Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples pp. 11

Pham Thang V, A van de Wiel Mark and Jimenez Connie R

Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach pp. 11

Heidema A. Geert and Nagelkerke Nico

A Classification Model for the Leiden Proteomics Competition pp. 11

Hoefsloot Huub C. J., Smit Suzanne and Smilde Age K.

Autocorrelated Logistic Ridge Regression for Prediction Based on Proteomics Spectra pp. 12

Goeman Jelle J

Clinical Mass Spectrometry Proteomic Diagnosis by Conformal Predictors pp. 12

Gammerman Alex, Nouretdinov Ilia, Burford Brian, Chervonenkis Alexey, Vovk Vladimir and Luo Zhiyuan

Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples pp. 14

J. van der Werff Martijn P., Mertens Bart, E de Noo Mirre, Bladergroen Marco R, Dalebout Hans C, Tollenaar Rob A. E. M. and Deelder Andre M

Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest pp. 14

Datta Somnath

Empirical Bayes Logistic Regression pp. 16

Strimenopoulou Foteini and Brown Philip J

Organizing a Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis pp. 20

Mertens Bart

A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry pp. 22

Valkenborg Dirk, Suzy Van Sanden, Lin Dan, Kasim Adetayo, Zhu Qi, Haldermans Philippe, Jansen Ivy, Shkedy Ziv and Burzykowski Tomasz

Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls pp. 22

Barrett Jennifer H and Cairns David A

Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation pp. 23

Hand David J

Assessing the Validity Domains of Graphical Gaussian Models in Order to Infer Relationships among Components of Complex Biological Systems pp. 37

Villers Fanny, Schaeffer Brigitte, Bertin Caroline and Huet Sylvie

Volume 7, issue 1, 2008

TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background pp. 11

Parmigiani Giovanni, Chen Sining and Velculescu Victor E.

Detecting Two-Locus Gene-Gene Effects Using Monotonisation of the Penetrance Matrix pp. 16

Henningsson Susanne and Nilsson Staffan I

Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power pp. 17

Matthews Abigail G, Haynes Chad, Liu Chang and Ott Jurg

Approximately Sufficient Statistics and Bayesian Computation pp. 18

Joyce Paul and Marjoram Paul

A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent pp. 19

Leibon Gregory, Rockmore Daniel N and Pollak Martin R

Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information pp. 19

Arteaga-Salas Jose Manuel, Harrison Andrew P and Upton Graham J. G.

Accommodating Uncertainty in a Tree Set for Function Estimation pp. 19

Healy Brian C, DeGruttola Victor G and Hu Chengcheng

Phenotyping Genetic Diseases Using an Extension of µ-Scores for Multivariate Data pp. 20

Morales José F., Song Tingting, Auerbach Arleen D. and Knut Wittkowski

A Comparison of Normalization Techniques for MicroRNA Microarray Data pp. 20

Rao Youlan, Lee Yoonkyung, Jarjoura David, Ruppert Amy S, Liu Chang-gong, Hsu Jason C and Hagan John P

Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing pp. 21

Guo Wenge and Peddada Shyamal

Predicting Protein Concentrations with ELISA Microarray Assays, Monotonic Splines and Monte Carlo Simulation pp. 21

Daly Don Simone, Anderson Kevin K, White Amanda M, Gonzalez Rachel M, Varnum Susan M and Zangar Richard C

Pattern Classification of Phylogeny Signals pp. 22

Shi Xiaofei, Gu Hong and Field Chris

Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling pp. 22

Jiang Wenyu, Varma Sudhir and Simon Richard

Modeling DNA Methylation in a Population of Cancer Cells pp. 23

Siegmund Kimberly D., Marjoram Paul and Shibata Darryl

Statistical Methods in Integrative Analysis for Gene Regulatory Modules pp. 23

Zeng Lingmin, Wu Jing and Xie Jun

Re-Cracking the Nucleosome Positioning Code pp. 24

Segal Mark R

Data Distribution of Short Oligonucleotide Expression Arrays and Its Application to the Construction of a Generalized Intellectual Framework pp. 24

Konishi Tomokazu

The Estimator of the Optimal Measure of Allelic Association: Mean, Variance and Probability Distribution When the Sample Size Tends to Infinity pp. 25

Mangin Brigitte, Garnier-Géré Pauline and Cierco-Ayrolles Christine

Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data pp. 25

Fallah Shafagh, Tritchler David and Beyene Joseph

Importance Sampling for the Infinite Sites Model pp. 26

Hobolth Asger, Uyenoyama Marcy K and Wiuf Carsten

Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study pp. 27

Bickel David R.

Adapting Prediction Error Estimates for Biased Complexity Selection in High-Dimensional Bootstrap Samples pp. 28

Binder Harald and Schumacher Martin

Structure Learning in Nested Effects Models pp. 28

Tresch Achim and Markowetz Florian

Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation pp. 29

David Rossell, Guerra Rudy and Scott Clayton

Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis pp. 29

Waaijenborg Sandra, Verselewel de Witt Hamer Philip C. and Zwinderman Aeilko H

Coalescent Time Distributions in Trees of Arbitrary Size pp. 30

Efromovich Sam and Salter Kubatko Laura

Supervised Distance Matrices pp. 30

Pollard Katherine S. and J. van der Laan Mark

A Sparse PLS for Variable Selection when Integrating Omics Data pp. 32

Lê Cao Kim-Anh, Rossouw Debra, Robert-Granié Christèle and Besse Philippe

Nonparametric Functional Mapping of Quantitative Trait Loci Underlying Programmed Cell Death pp. 32

Cui Yuehua, Wu Rongling, Casella George and Zhu Jun

A Composite-Conditional-Likelihood Approach for Gene Mapping Based on Linkage Disequilibrium in Windows of Marker Loci pp. 33

Larribe Fabrice and Lessard Sabin

Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data pp. 34

Kim Chang Sik

Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods pp. 34

Zucknick Manuela, Richardson Sylvia and Stronach Euan A

A Unification of Multivariate Methods for Meta-Analysis of Genetic Association Studies pp. 35

Pantelis Bagos

Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments pp. 41

Husmeier Dirk and Mantzaris Alexander V.

Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences pp. 45

Vergne Nicolas