CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits

Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions ...

Authors: Laurence D Parnell, Britt A Blokker, Hassan S Dashti, Paula-Dene Nesbeth, Brittany Elle Cooper, Yiyi Ma, Yu-Chi Lee, Ruixue Hou, Chao-Qiang Lai, Kris Richardson and José M Ordovás

The genetic interacting landscape of 63 candidate genes in Major Depressive Disorder: an explorative study

Genetic contributions to major depressive disorder (MDD) are thought to result from multiple genes interacting with each other. Different procedures have been proposed to detect such interactions. Which approa...

Authors: Magnus Lekman, Ola Hössjer, Peter Andrews, Henrik Källberg, Daniel Uvehag, Dennis Charney, Husseini Manji, John A Rush, Francis J McMahon, Jason H Moore and Ingrid Kockum

Knowledge-driven genomic interactions: an application in ovarian cancer

Effective cancer clinical outcome prediction for understanding of the mechanism of various types of cancer has been pursued using molecular-based data such as gene expression profiles, an approach that has pro...

Authors: Dokyoon Kim, Ruowang Li, Scott M Dudek, Alex T Frase, Sarah A Pendergrass and Marylyn D Ritchie

ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions

Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they co...

Authors: Philip Zimmermann, Stefan Bleuler, Oliver Laule, Florian Martin, Nikolai V Ivanov, Prisca Campanoni, Karen Oishi, Nicolas Lugon-Moulin, Markus Wyss, Tomas Hruz and Wilhelm Gruissem

Computational genetics analysis of grey matter density in Alzheimer’s disease

Alzheimer’s disease is the most common form of progressive dementia and there is currently no known cure. The cause of onset is not fully understood but genetic factors are expected to play a significant role....

Authors: Amanda L Zieselman, Jonathan M Fisher, Ting Hu, Peter C Andrews, Casey S Greene, Li Shen, Andrew J Saykin and Jason H Moore

Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets

Advances in genomic technologies have enabled the accumulation of vast amount of genomic data, including gene expression data for multiple species under various biological and environmental conditions. Integra...

Authors: Saeed Salem and Cagri Ozcaglar

An iteration normalization and test method for differential expression analysis of RNA-seq data

Next generation sequencing technologies are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key to analyzing massive and complex...

Authors: Yan Zhou, Nan Lin and Baoxue Zhang

A simple structure-based model for the prediction of HIV-1 co-receptor tropism

Human Immunodeficiency Virus 1 enters host cells through interaction of its V3 loop (which is part of the gp120 protein) with the host cell receptor CD4 and one of two co-receptors, namely CCR5 or CXCR4. Entry...

Authors: Dominik Heider, Jan Nikolaj Dybowski, Christoph Wilms and Daniel Hoffmann

First complex, then simple

Authors: James D Malley and Jason H Moore

Innovation is often unnerving: the door into summer

Authors: James D Malley and Jason H Moore

Hypothesis exploration with visualization of variance

The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to synd...

Authors: Douglass Stott Parker, Eliza Congdon and Robert M Bilder

Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors

In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true assoc...

Authors: Timothy H Ciesielski, Sarah A Pendergrass, Marquitta J White, Nuri Kodaman, Rafal S Sobota, Minjun Huang, Jacquelaine Bartlett, Jing Li, Qinxin Pan, Jiang Gui, Scott B Selleck, Christopher I Amos, Marylyn D Ritchie, Jason H Moore and Scott M Williams

An adaptive permutation approach for genome-wide association study: evaluation and recommendations for use

Permutation testing is a robust and popular approach for significance testing in genomic research, which has the broad advantage of estimating significance non-parametrically, thereby safe guarding against inf...

Authors: Ronglin Che, John R Jack, Alison A Motsinger-Reif and Chad C Brown

A classification and characterization of two-locus, pure, strict, epistatic models for simulation and detection

The statistical genetics phenomenon of epistasis is widely acknowledged to confound disease etiology. In order to evaluate strategies for detecting these complex multi-locus disease associations, simulation st...

Authors: Ryan J Urbanowicz, Ambrose LS Granizo-Mackenzie, Jeff Kiralis and Jason H Moore

Semi-supervised consensus clustering for gene expression data analysis

Simple clustering methods such as hierarchical clustering and k-means are widely used for gene expression data analysis; but they are unable to deal with noise and high dimensionality associated with the microarr...

Authors: Yunli Wang and Youlian Pan

Mycoplasma contamination in the 1000 Genomes Project

In silco Biology is increasingly important and is often based on public data. While the problem of contamination is well recognised in microbiology labs the corresponding problem of database corruption has recei...

Authors: William B Langdon

Investigating the relationship between mitochondrial genetic variation and cardiovascular-related traits to develop a framework for mitochondrial phenome-wide association studies

Mitochondria play a critical role in the cell and have DNA independent of the nuclear genome. There is much evidence that mitochondrial DNA (mtDNA) variation plays a role in human health and disease, however, ...

Authors: Sabrina L Mitchell, Jacob B Hall, Robert J Goodloe, Jonathan Boston, Eric Farber-Eger, Sarah A Pendergrass, William S Bush and Dana C Crawford

Supervised DNA Barcodes species classification: analysis, comparisons and results

Specific fragments, coming from short portions of DNA (e.g., mitochondrial, nuclear, and plastid sequences), have been defined as DNA Barcode and can be used as markers for organisms of the main life kingdoms....

Authors: Emanuel Weitschek, Giulia Fiscon and Giovanni Felici

Functional genomics annotation of a statistical epistasis network associated with bladder cancer susceptibility

Several different genetic and environmental factors have been identified as independent risk factors for bladder cancer in population-based studies. Recent studies have turned to understanding the role of gene...

Authors: Ting Hu, Qinxin Pan, Angeline S Andrew, Jillian M Langer, Michael D Cole, Craig R Tomlinson, Margaret R Karagas and Jason H Moore

Risk estimation using probability machines

Logistic regression has been the de facto, and often the only, model used in the description and analysis of relationships between a binary outcome and observed features. It is widely used to obtain the condition...

Authors: Abhijit Dasgupta, Silke Szymczak, Jason H Moore, Joan E Bailey-Wilson and James D Malley

The multiscale backbone of the human phenotype network based on biological pathways

Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic back...

Authors: Christian Darabos, Marquitta J White, Britney E Graham, Derek N Leung, Scott M Williams and Jason H Moore

Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development

The ever-growing wealth of biological information available through multiple comprehensive database repositories can be leveraged for advanced analysis of data. We have now extensively revised and updated the ...

Authors: Sarah A Pendergrass, Alex Frase, John Wallace, Daniel Wolfe, Neerja Katiyar, Carrie Moore and Marylyn D Ritchie

An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation

Personal genome analysis is now being considered for evaluation of disease risk in healthy individuals, utilizing both rare and common variants. Multiple scores have been developed to predict the deleteriousne...

Authors: Thanawadee Preeprem and Greg Gibson

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network

Gene expression profiles have been broadly used in cancer research as a diagnostic or prognostic signature for the clinical outcome prediction such as stage, grade, metastatic status, recurrence, and patient s...

Authors: Dokyoon Kim, Ruowang Li, Scott M Dudek and Marylyn D Ritchie

Big Data analysis on autopilot?

Authors: Scott M Williams and Jason H Moore