QuantGen Group at Michigan State University

About

Our group is interested in the analysis and prediction of complex traits and diseases using genetic (integrating pedigrees, genomics, and other omics) and environmental information. Our research involves methods, software development, and applications in human health, plant and animal breeding. Most of us are affiliated with the Department of Epidemiology and Biostatistics at Michigan State University.

Projects

Genomic Analysis and Prediction of Complex Traits. Development and evaluation of methods and software for analysis and prediction of complex traits using high-dimensional genomic data (e.g., SNPs, genotyping by sequencing, and other types of sequence data). Our research in this area has focused on the use of shrinkage and variable selection in parametric models, as well as on the use of some semi-parametric methods (e.g., RKHS).

Genomics x Environment. Development of methods for integrating high-dimensional genomic and environmental data in a unified framework. We have developed methods that can model interactions between high-dimensional marker panels and high-dimensional environmental covariates. These methods were originally developed and tested with data from wheat trails. We are currently extending some of these methods for analysis of complex human traits and diseases.

Integration of Data from Multiple Omics Layers. Development of models and software for integrating high-dimensional multi-layer omics data. Our focus is on methods that can integrate whole-omics profiles and can model interactions between two or more high-dimensional predictor sets (e.g., genome-by-methylome interactions). We are currently working on using these methods for prediction of breast cancer outcomes and in plant omics applications.

Software development for analysis of big omics data. We have developed several R packages for genetic analysis using pedigrees, genomes and other omics (see software below for further details).

Genomic Analysis of Obesity and Response to Exercise. We maintain an active collaboration with researchers from the TIGER (Training Interventions and Genetics of Exercise Response) study, developing and implementing methods for the identification of genetic factors influencing Body Composition and Response to Exercise Intervention.

Software

BGLR. The Bayesian Generalized Linear Regression R package implements a variety of shrinkage and variable selection methods. The package can be used with whole-genome data (e.g., SNPs, gene expression or other omics), pedigrees and non-genetic covariates, including high-dimensional environmental data. Article CRAN Source Code

BGData. A suite of R packages to enable analysis of extremely large genomic data sets (potentially millions of individuals and millions of molecular markers). Article CRAN Source Code

pedigreemm. An R package for analysis of complex traits and diseases using generalized linear mixed models using likelihood methods. Article Documentation CRAN

pedigreeR. R functions related to pedigrees. Source Code

MTM. Implements a Bayesian Multi-Trait Gaussian models with user defined-(co)variance structures. Documentation Source Code

Activities

People

Agustín González Reymúndez
Agustín González Reymúndez Postdoc

agugonrey@gmail.com

  • Areas of Interest: Genomic tools for QTL mapping and genomic prediction, with applications in human genetics and plant breeding
Alexa Lupi
Alexa Lupi PhD Student

lupialex@msu.edu

  • Areas of Interest: Biostatistics, Statistical Genetics, Epidemiology
Alexander Grueneberg
Alexander Grueneberg Programmer

gruenebe@msu.edu

Ana I. Vazquez
Ana I. Vazquez Assistant Professor

avazquez@msu.edu

Anirban Samaddar
Anirban Samaddar PhD Student

samadda1@msu.edu

  • Areas of Interest: Bayesian Statistics, Time Series, Statistical Genetics
Guanqi Lu
Guanqi Lu PhD Student

luguanqi@msu.edu

  • Areas of Interest: Statistical Genetics, Biostatistics
Gustavo de los Campos
Gustavo de los Campos Associate Professor

gdeloscampos@gmail.com

Harold Wu
Harold Wu PhD Student

wuhao12@msu.edu

  • Areas of Interest: Statistical Genetics, Statistical Modeling, Clinical Trials
Marco López-Cruz
Marco López-Cruz Postdoc

malctony@hotmail.com

Paulino Pérez
Paulino Pérez Associate Professor

perpdgo@gmail.com

Wesley Bird
Wesley Bird Undergraduate Student

birdwes1@msu.edu

  • Areas of Interest: Medical Laboratory Science and Human Biology
  • REPID Scholar
Xuemeng Wang
Xuemeng Wang Master Student

wangxu35@msu.edu

  • Areas of Interest: Biostatistics, Statistical Modeling

Past Members

C. Austin Pickens
C. Austin Pickens Doctoral Candidate

picken21@anr.msu.edu

  • Areas of Interest: Novel biomarker discovery using mass spectrometry-based lipidomics and disease prediction
  • Links: GitHub, ResearchGate
Deniz Akdemir
Deniz Akdemir Postdoc

deniz.akdemir.work@gmail.com

  • Areas of Interest: Data Mining, Multivariate Statistics, Statistical Genetics, Animal and Plant Breeding
Felix Enciso
Felix Enciso PhD Candidate

encisofe@msu.edu

  • Areas of Interest: Genome-wide association and genome selection studies for complex traits in potato, genetic engineering in potato using CRIPRS/Cas9 technology
  • Links: GitHub, Publications
Fernando Aguate
Fernando Aguate Postdoc

fmaguate@gmail.com

  • Areas of Interest: Biostatistics, Statistical Genetics, Plant Breeding, Software Development
  • Links: Website, GitHub, Google Scholar
  • Also joined us as a visitor in 2016 while at Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba (Argentina)
Filipe Couto
Filipe Couto Postdoc

coutoal1@msu.edu

  • Areas of Interest: Biostatistics, plant Breeding, genome-wide association studies and prediction of complex traits in plants
Gabriel Rovere
Gabriel Rovere Postdoc

roverega@msu.edu

  • Areas of Interest: Animal Breeding. Livestock Genetic Evaluations, Horse Breeding, Breeding Goals.
Hank Wu
Hank Wu Master Student

wukuanha@msu.edu

  • Areas of Interest: Biostatistics
Hwasoon Kim
Hwasoon Kim Postdoc

kimhwaso@msu.edu

  • Areas of Interest: Biostatistics, Clinical Trials
  • Links: Website, GitHub
Lian Lian
Lian Lian Postdoc

lianl0501@gmail.com

  • Areas of Interest: Statistical Genetics, Plant Breeding
Mengying Sun
Mengying Sun Research Assistant

msun@epi.msu.edu

  • Areas of Interest: Statistical Modeling
  • Links: GitHub
Michael P. Behring
Michael P. Behring PhD Candidate

behringm@uab.edu

  • Areas of Interest: Epidemiology, Genetics of Cancer
Paige Duren
Paige Duren

durenpai@msu.edu

  • Areas of Interest: Nursing
Raka Mandal
Raka Mandal PhD Student

mandalr1@msu.edu

  • Areas of Interest: Biostatistics, Statistical Learning, Bayesian Statistics
Scott Funkhouser
Scott Funkhouser PhD Student

sfunkhouser@gmail.com

  • Areas of Interest: Software development for multiple omics layers, genomic prediction
  • Links: Website, GitHub
  • Software: editTools
Shyamali Mukerjee
Shyamali Mukerjee Master Student

smukerjee@epi.msu.edu

  • Areas of Interest: Statistical Genetics, Application of Statistical Methods to Public Health Issues
Siddharth Avadhanam
Siddharth Avadhanam Master Student

avadhana@msu.edu

  • Areas of Interest: Statistical Genetics, Biostatistics, Bioinformatics
Yeni Liliana Bernal Rubio
Yeni Liliana Bernal Rubio Postdoc

ylbernal@msu.edu

Yogasudha Veturi
Yogasudha Veturi PhD Candidate

sudhaveturi@gmail.com

  • Areas of Interest: Biostatistics, Statistical Genetics, Plant Breeding

Visitors

2018

Cecilia Salvoro
Cecilia Salvoro

cecilia.salvoro@gmail.com

  • Affiliation: Department of Biology, University of Padova, Padova, Italy
  • Areas of Interest: Human Genetics, Next-generation Sequencing, Genetic Mapping of Diseases, Prediction of Eye Color
  • Links: ResearchGate
Maria Martinez Castillero
Maria Martinez Castillero

mmartinezcastillero@gmail.com

  • Affiliation: University of Padova (Italy)
  • Areas of Interest: Quantitative genetics, programming, animal science
  • Links: LinkedIn
Pernille Bjarup Hansen
Pernille Bjarup Hansen

pernille.bjarup@mbg.au.dk

  • Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, Denmark
  • Areas of interest: Plant genetics, quantitative genetics, abiotic stress and plant breeding

2017

Muhammad Yasir Nawaz
Muhammad Yasir Nawaz

nawazmuh@msu.edu

  • Areas of Interest: Genomic prediction, Livestock breeding, Application of statistical methods to public and animal health issues

2016

Hugo O. Toledo Alvarado
Hugo O. Toledo Alvarado

h.toledo.a@gmail.com

  • Affiliation: Università degli studi di Padova (Italy)
  • Project: The use of Fourier-Transform Infrared (FTIR) Spectra as an innovative tool for predicting fertility traits in dairy cattle
M. Angeles Pérez-Cabal
M. Angeles Pérez-Cabal

mapcabal@vet.ucm.es

  • Affiliation: Complutense of University of Madrid (Spain)
  • Areas of Interest: Animal Breeding

2015

Juan Pablo Gutierrez Garcia
Juan Pablo Gutierrez Garcia

gutgar@ucm.es

  • Affiliation: Complutense of University of Madrid (Spain)
  • Areas of Interest: Animal Breeding and Conservation Genetics
  • Links: Website

2014

Christina Lehermeier
Christina Lehermeier

christina.lehermeier@tum.de

  • Affiliation: Plant Breeding, Technische Universität München (Germany)
  • Areas of Interest: Statistics, Quantitative Genetics, Plant Breeding
  • Links: Google Scholar, TUM Plant Breeding
Swetlana Berger
Swetlana Berger

swmiller@gwdg.de

  • Affiliation: Georg-August-Universität Göttingen (Germany)
  • Areas of Interest: Scale effects in genomic modelling and prediction