Publications

Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls

Published in Heredity, 2020

This study evaluated the use of multiomics data for classification accuracy of rheumatoid arthritis (RA). Three approaches were used and compared in terms of prediction accuracy:(1) whole-genome prediction (WGP) using SNP marker information only,(2) whole-methylome prediction (WMP) using methylation profiles only, and (3) whole-genome/methylome prediction (WGMP) with combining both omics layers.

Recommended citation: Roudbar, Mahmoud Amiri, Mohammad Reza Mohammadabadi, Ahmad Ayatollahi Mehrgardi, Rostam Abdollahi-Arpanahi, Mehdi Momen, Gota Morota, Fernando Brito Lopes, Daniel Gianola, and Guilherme JM Rosa. "Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls." Heredity (2020): 1-17. https://www.nature.com/articles/s41437-020-0301-4

Multi-trait random regression models increase genomic prediction accuracy for a temporal physiological trait derived from high-throughput phenotyping

Published in PLOS ONE , 2020

However, given the capability of HTP to collect multiple temporal phenotypes, one unresolved question in plant breeding is how to jointly model multiple temporal phenotypes. To address this, we aimed to integrate the RRM framework for temporal traits into a MT model.

Recommended citation: Momen M., Campbell T.M., Walia H., Morota G. (2019) Predicting longitudinal traits derived from high-throughput phenomics in contrasting environments using genomic Legendre polynomials and B-splines https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0228118&type=printable

Performance of pedigree and various forms of marker‐derived relationship coefficients in genomic prediction and their correlations

Published in Journal of Animal Breeding and Genetics, 2020

The objective of this work was to compare estimates of genetic and genomic parameters between several types of similarity matrices as well as their predictive performance under a Bayesian multiple‐trait genomic prediction context.

Recommended citation: Solaymani, Samaneh, Ahmad Ayatollahi Mehrgardi, Ali Esmailizadeh, Llibertat Tusell, and Mehdi Momen. "Performance of pedigree and various forms of marker‐derived relationship coefficients in genomic prediction and their correlations." Journal of Animal Breeding and Genetics (2020). https://www.g3journal.org/content/9/10/3369

Predicting longitudinal traits derived from high-throughput phenomics in contrasting environments using genomic Legendre polynomials and B-splines

Published in G3: Genes, Genomes, Genetics, 2019

Here, we sought to apply random regression model(RRM) to forecast the rice projected shoot erea(PSA) in control and water-limited conditions under various longitudinal cross-validation scenarios. To this end, genomic Legendre polynomials and B-spline basis functions were used to capture PSA trajectories.

Utilizing trait networks and structural equation models as tools to interpret multi-trait genome-wide association studies

Published in Plant methods, 2019

We extended the scope of MTM-GWAS by incorporating phenotypic network structures into GWAS using structural equation models (SEM-GWAS). In this network GWAS model, one or more phenotypes appear in the equations for other phenotypes as explanatory variables. A salient feature of SEM-GWAS is that it can partition the total single nucleotide polymorphism (SNP) effects into direct and indirect effects.

Recommended citation: Momen, Mehdi and Campbell, Malachy T. and Walia, Harkamal and Morota, Gota. 2019. Harnessing phenotypic networks and structural equation models to improve genome-wide association analysis.bioRxiv. https://link.springer.com/article/10.1186/s13007-019-0493-x

Leveraging breeding values obtained from random regression models for genetic inference of longitudinal traits

Published in The Plant Genome, 2019

This study builds on the random regression genomic prediction approach described in Campbell et al 2018, and used the derived breeding values for genomic inferenece across time points.

Recommended citation: Campbell M.T., Momen M., Walia H., Morota G. (2019) Leveraging breeding values obtained from random regression models for genetic inference of longitudinal traits. The Plant Genome. https://www.ncbi.nlm.nih.gov/pubmed/31290928

Importance of genotype by environment interaction on genetic analysis of milk yield in Iranian Holstein cows using random regression model.

Published in Animal Production Science, 2018

Changes in the relative performance of genotypes (sires) across different environments, which are referred to as genotype–environment interactions, play an important role in dairy production systems, especially in countries that rely on imported genetic material. Importance of genotype by environment interaction on genetic analysis of milk yield was investigated in Holstein cows by using random regression model.

Recommended citation: Fazel Y., Esmailizadeh A., Momen M., Fozi M. Asadi (2018) Importance of genotype by environment interaction on genetic analysis of milk yield in Iranian Holstein cows using a random regression model. http://www.publish.csiro.au/AN/AN17714

Including Phenotypic Causal Networks in Genome-Wide Association Studies Using Mixed Effects Structural Equation Models

Published in Frontiers in Genetics, 2018

Network based statistical models accounting for putative causal relationships among multiple phenotypes can be used to infer single-nucleotide polymorphism (SNP) effect which transmitting through a given causal path in genome-wide association studies (GWAS). In GWAS with multiple phenotypes, reconstructing underlying causal structures among traits and SNPs using a single statistical framework is essential for understanding the entirety of genotype-phenotype maps.

Recommended citation: Momen Mehdi, Ayatollahi Mehrgardi Ahmad, Amiri Roudbar Mahmoud, Kranis Andreas, Mercuri Pinto Renan, Valente Bruno D., Morota Gota, Rosa Guilherme J. M., Gianola Daniel 2018.Including Phenotypic Causal Networks in Genome-Wide Association Studies Using Mixed Effects Structural Equation Models. https://www.frontiersin.org/articles/10.3389/fgene.2018.00455/full

Quantifying genomic connectedness and prediction accuracy from additive and non-additive gene actions

Published in Genetics Selection Evolution, 2018

We investigated the relationship between the estimated level of connectedness and prediction accuracy in the presence of non-additive genetic variation.

Recommended citation: Momen, Mehdi, and Gota Morota. "Quantifying genomic connectedness and prediction accuracy from additive and non-additive gene actions." Genetics Selection Evolution 50, no. 1 (2018): 45. https://gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0415-9

Predictive ability of genome-assisted statistical models under various forms of gene action

Published in Scientific Reports, 2018

Recent work has suggested that the performance of prediction models for complex traits may depend on the architecture of the target traits. Here we compared several prediction models with respect to their ability of predicting phenotypes under various statistical architectures of gene action.

Recommended citation: Momen M , Ayatollahi Mehrgardi A, Kranis A, Tusell L, Morota G, Rosa G J M, Gianola D. (2018). Predictive ability of genome-assisted predic-tion machines under various statistical genetic architectures.Scientific Reports.8:12309. https://www.nature.com/articles/s41598-018-30089-2

A predictive assessment of genetic correlations between traits in chickens using markers

Published in Genetics Selection Evolution, 2017

Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness. A predictive assessment was used to gauge genetic correlations.

Recommended citation: Momen M.,Mehrgardi, Mehrgardi A. A., Sheikhy A., Esmailizadeh A., Fozi M. A.,Kranis A., Valente B. D.,Rosa, Rosa G. J. M., Gianola D. (2017) A predictive assessment of genetic correlations between traits in chickens using markers https://www.ncbi.nlm.nih.gov/pubmed/28148241

Predictive Ability of Statistical Genomic Prediction Methods When Underlying Genetic Architecture of Trait Is Purely Additive

Published in Iranian Journal of Applied Animal Science, 2016

The objective of this study was to compare different genomic prediction models includes parametric and non-parametric, and assess their abilities toward a specific trait with only additive architecture. We hypothesize that with further exploration of predictive ability of GS models toward the purely genomic architectures, we will clearly find the true accuracy of genomic prediction models under a simple genetic architecture.

Recommended citation: Momen, M., A. Ayatollahi Mehrgardi, A. Sheikhy, A. K. Esmailizadeh, and M. Assadi Foozi. "Predictive Ability of Statistical Genomic Prediction Methods When Underlying Genetic Architecture of Trait Is Purely Additive." Iranian Journal of Applied Animal Science 6, no. 4 (2016): 815-822. http://ijas.iaurasht.ac.ir/article_526626.html