New Faculty for the BCB Program

June 26, 2017

BCB has admitted several new faculty to BCB faculty membership in the recent past. Find all faculty for the BCB program on the people page.  These three faculty were most recently admitted to BCB faculty membership:

Nick V.L. Serão, Ph.D.

Assistant Professor, Animal Breeding & Genetics

Research Interests:

Quantitative genetics and genomics of disease/stress response and fertility in livestock animals; QTL mapping; Genomic prediction/selection; Gene expression analysis; Statistical methods for genomic analyses; Big Data; Modeling of immune response, and infectious diseases

Description of current and future research:

In my current research program, my group makes use of phenotypic and genomic data in order to improve the understanding of complex traits in animals and plants. Phenotypic traits use in my research follow a variety of distributions (quantitative/categorical), sources (e.g. performance, gene expression, metabolomics, proteomics, etc), and patterns (e.g. longitudinal). Genomic data used in my research include high-density genotypes and gene expression. With these types of data, in my group we perform QTL and eQTL mapping, genomic prediction, network and enrichment analyses, and more.

In addition to the use of real data, in my group we make use of simulation in order to evaluate the use of new/alternative methods that can improve the accuracy of QTL mapping and genomic prediction. Moreover, we use simulated data to evaluate alternative breeding strategies with the objective of improving response to selection for novel traits (e.g. disease resitance in pigs).

With the advances in –omics technologies and generation of multiple sources of information, in my future research I would like to work with DNA sequence for fine mapping of previously QTL identified in my work, as well as epigenomic data. Moreover, I want to evaluate and develop statistical methodologies that can make simultaneous use of different sources of information (e.g. DNA, RNA, metabolomics, performance, etc) in order to improve QTL mapping and genomic prediction. In other words, continue doing work on machine learning/big data, including several sources of information.

Address:           239B Kildee Hall, Department of Animal Science

                        Iowa State University, Ames, IA 50014

                        Tel: (515) 294-3435; Fax: (515) 294-6994

                        e-mail: serao@iastate.edu

Education:        Ph.D. (Animal Science), University of Illinois at Urbana-Champaign, 2012

                        M.S. (Animal Breeding and Genetics), Federal University of Viçosa, Brazil, 2009

                        B.S. (Animal Science), Federal University of Viçosa, Brazil, 2007

Position and Experience:

2017 – Present           Assistant Professor, Iowa State University

2015 – 2017               Assistant Professor, North Carolina State University

2013-2015                 Postdoctoral Research Associate, Iowa State University

Recent Publications (underlined students/visiting scientists under my mentoring):

  • Nascimento M, FF Silva, T Sáfadi, ACC Nascimento, TEM Ferreira, LMA Barroso, CF Azevedo, SEF Guimarães, NVL Serão (2017) ICAclust: a tool for clustering of temporal RNA-Seq data. PLOS One (in press).
  • Bueno R, C Campos, R Veroneze, W Silva, LMP Sanglard, NVL Serão, G Hausman, M Dodson, MS Duarte (2017) Technical Note: A comparison among adipogenic induction protocols for dedifferentiated fat (DFAT) cells obtained from subcutaneous fat of pigs. Livestock Science (in press).
  • Dunkelberger JR, NVL Serão, NC Niederwerder, MA Kerrigan, JK Lunney, RRR Rowland, JCM Dekkers (2017) Effect of a major QTL for PRRS-resistance on response to co-infection with PRRS virus and PCV2b in commercial pigs, with or without prior vaccination for PRRS. Journal of Animal Science, 95(2):584-98.
  • Waide EH, CK Tuggle, M. Schroyen, NVL Serão, A Hess, RRR Rowland, JK Lunney, GS Plastow, JCM Dekkers (2017) Genomewide association of piglet responses to infection with one of two isolates of the porcine reproductive and respiratory syndrome virus. Journal of Animal Science, 95(1):16.
  • Benedeti PBB, BC Silva, MVC Pacheco, IC Filho, MM Lopes, W Silva, NVL Serão, E Detmann, SC Valadares Filho, MS Duarte (2017) Grain Processing Effects on Expression of Genes Involved in Volatile Fatty Acid Transport in Rumen Epithelium of Beef Cattle. ASAS-CSAS Annual Meeting & Trade Show, Baltimore, MD, USA, 2017. (accepted - abstract)
  • Benedeti PBB, MM Lopes, SFM Bonilha, NVL Serão, DRG Lopes, W Silva, HC Mantovani, CJ Newbold, ED, MS Duarte (2017) Expression of Genes Involved in Metabolism and Volatile Fatty Acids and Urea Transport in Rumen Epithelium of Bulls Identified for High, Medium, and Low Residual Feed Intake. ASAS-CSAS Annual Meeting & Trade Show, Baltimore, MD, USA, 2017. (accepted - abstract)
  • Sanglard LMP*, M Nascimento*, P Moriel, M Ashwell, MH Poore, MS Duarte, NVL Serão (2017) Effect of maternal nutrition and sex on skeletal muscle gene expression in Angus cattle during immune challenge. ASAS-CSAS Annual Meeting & Trade Show, Baltimore, MD, USA, 2017. (accepted - abstract)
  • Dunkelberger JR, NVL Serão, Z Weng, MC Niederwerder, EH Waide, MA Kerrigan, JK Lunney, RRR Rowland, JCM Dekkers (2017) Biological evidence for genomic regions associated with host response to co-infection with PRRS virus and PCV2b in commercial nursery pigs. In: Journal of Animal Sciences, 95(Suppl. 5):16. ADSA®-ASAS Joint Midwest Meeting, Omaha, NL, USA, 2017 (abstract).
  • See G, NVL Serão, M Knauer (2017) Genetic parameters for age at puberty in sows. In: Journal of Animal Sciences, 95(Suppl. 5):20. ADSA®-ASAS Joint Midwest Meeting, Omaha, NL, USA, 2017 (abstract).
  • Ferring CL*, KA Gray, NVL Serão (2017) Reaction norms for reproductive performance during PRRS and PED outbreaks. In: Journal of Animal Sciences, 95(Suppl. 5):16-17. ADSA®-ASAS Joint Midwest Meeting, Omaha, NL, USA, 2017 (abstract).
  • Barroso LMA*, F Morgante, TFC Mackay, ACC Nascimento*, M Nascimento*, NVL Serão (2017) Genomic prediction accuracies using regularized quantile regression (RQR) methodology. In: Journal of Animal Sciences, 95(Suppl. 5):14-15. ADSA®-ASAS Joint Midwest Meeting, Omaha, NL, USA, 2017 (abstract).
  • Nascimento M*, ACC Nascimento*, W Cai, JCM Dekkers, NVL Serão (2017) Genetic parameters and trends for residual feed intake (RFI), performance traits, and growth curve parameters in pigs selected for low RFI with contrasting growth trajectories. In: Journal of Animal Sciences, 95(Suppl. 5):15. ADSA®-ASAS Joint Midwest Meeting, Omaha, NL, USA, 2017 (abstract).
  • Mayberry KJ, TL Devine, MH Poore, NVL Serão, DH Poole (2017) Evaluation of Angus Cattle Hair Coat Length and its effect on Tolerance to Fescue Toxicity. In: Journal of Animal Sciences, 95(Suppl. 1):40. ASAS Southern Section Meeting, Franklin, TN, USA, 2017 (abstract).
  • Khanal P*, KJ Mayberry, MH Poore, DH Poole, NVL Serão (2017) Effect of genetic response to fescue toxicity on body weight, body temperature, hair coat, hair shed and body condition score in Angus cows. In: Journal of Animal Sciences, 95(Suppl. 1):18-19. ASAS Southern Section Meeting, Franklin, TN, USA, 2017 (abstract).
  • Galliou JM*, P Khanal, KJ Mayberry, MH Poore, DH Poole, NVL Serão (2017) Evaluating the accuracy of a new commercial genetic test for response to fescue toxicosis in cattle. In: Journal of Animal Sciences, 95(Suppl. 1):55-56. ASAS Southern Section Meeting, Franklin, TN, USA, 2017 (abstract).

Lizhi Wang

Associate Professor

Industrial and Manufacturing Systems Engineering

Research Interests: mathematical modeling and computational optimization, with applications in energy, transportation, manufacturing, and agriculture systems. A significant part of the agriculture-related application is plant breeding. In particular, applying operations research methods to improve the efficiency of trait introgression and genomic selection.

Professional Preparation

  • B.E., Automation, University of Science and Technology of China, 2003
  • B.S., Management Science, University of Science and Technology of China, 2003
  • Ph.D., Industrial Engineering, University of Pittsburgh, 2007

Appointments

  • Associate Professor, Industrial and Manufacturing Systems Engineering, Iowa State
  • University, 2013{present
  • Assistant Professor, Industrial and Manufacturing Systems Engineering, Iowa State
  • University, 2007{2013

I have published two journal articles on gene stacking and trait introgression, and three more articles are currently under review.

  • Pan Xu, Lizhi Wang, and William Beavis, “An optimization approach to gene stacking,” European Journal of Operational Research, vol. 214(1), p. 168-178, 2011.
  • Ye Han, John Cameron, Lizhi Wang, and William Beavis, “The predicted cross value for genetic introgression of multiple alleles,” to appear in Genetics, 2017.
  • Matthew Goiffon, Aaron Kusmec, Lizhi Wang, Guiping Hu, and Patrick S. Schnable “Optimal Population Value Selection: A Population-Based Selection Strategy for Improving Response in Genomic Selection,” under review.
  • John Cameron, Ye Han, William Beavis and Lizhi Wang “Trait Introgression as an Operations Research Challenge,” under review.
  • Maryam Nikouei-Mehr and Lizhi Wang, "An Optimization Approach to Detecting Epistatic Effects," under review.

Projects related to plant breeding:

  • PI: William Beavis. Co-PI: Lizhi Wang. “Backcross breeding optimizer,” Syngenta, 8/2012 –12/2013.
  • PI: Walter P Suza. Co-PI: Jessica Barb, William Beavis, Ana Correia, Shuizhang Fei, Thomas Lubberstedt, Michael Retallick, Asheesh Singh, Lizhi Wang, Jianming Yu. “Plant breeding master of science programs for Africa,” Bill and Melinda Gates Foundation. 01/2014 – 12/2016.
  • PI: Lizhi Wang. “Designed adaptation from natural genetic variants,” Plant Science Institute, 1/2015 – 1/2018.
  • PI: Patrick Schnable. Co-PI: Lizhi Wang and Guiping Hu. “Development and Evaluation of Improved Strategies for Genomic Selection via Simulations and Empirical Testing,” USDA, 2/2017 – 2/2020.

Related Publications

  • Lizhi Wang and Pan Xu, \The watermelon algorithm for the bilevel integer linear programming problem," to appear in SIAM Journal on Optimization, 2017.
  • Ye Han, John Cameron, Lizhi Wang, and William Beavis, \The predicted cross value for genetic introgression of multiple alleles," to appear in Genetics, 2017.
  • Mohammad Rahdar, Lizhi Wang, and Guiping Hu, \Potential competition for biomass between biopower and biofuel under RPS and RFS2," Applied Energy, vol.
  • 119, p. 10-20, 2014.
  • Leilei Zhang, Guiping Hu, Lizhi Wang, and Yihsu Chen, \A bottom-up biofuel market equilibrium model for policy analysis," Annals of Operations Research, p.
  • 1-27, 2013.
  • Pan Xu, Lizhi Wang, and William Beavis, \An optimization approach to gene  stacking," European Journal of Operational Research, vol. 214(1), p. 168-178, 2011.

John Nason, Professor

Department of Ecology, Evolution and Organismal Biology (EEOB)

Research Interests:

Specializing in the ecological and evolutionary genetics of plants and their associated insect mutualists (pollinators) and antagonists (e.g., gallers and seed predators). My work has long employed population genetic and phylogenetic approaches using simple genetic markers or Sanger sequence data. In recent years, my lab has increasingly been employing genomic methods, including SNP genotyping  using RAD sequencing, comparative transcriptomics, and phylogenomics based on sequencing of Ultra Conserved Elements (UCEs).

All of these approaches are being employed in a current NSF-supported project on which I am lead PI, titled Multilocus Analyses of Co-Diversification and Phylogenetic Incongruence Between Highly Coevolved Figs and Fig Wasps. In support of this work we have also established a working group to sequence the genomes of a set of interacting plant and insect species central to the NSF project.

Dept. of Ecology, Evolution, and Organismal Biology Phone: (515) 294-2268
Iowa State University
Email: jnason@iastate.edu
Ames, IA 50011
Webpage: jnason.eeob.iastate.edu

Professional Preparation

University of California at Davis Biological Sciences B.S., 1985
University of California at Riverside Botany/Plant Genetics Ph.D., 1991
University of Georgia Botany/Population Genetics Postdoc, 1991-1994

Appointments

  • Professor (2008-present), Dept. of Ecology, Evolution, & Organismal Biology, Iowa State
  • University
  • Assoc. Professor (2003-2008), Dept. of Ecology, Evolution, & Organismal Biology, Iowa State
  • University
  • Assistant Professor (2000-2003), Dept. of Botany, Iowa State University
  • Assistant Professor (1996-2000), Dept. of Biological Sciences, University of Iowa
  • Assistant Research Scientist (1994-1996), Dept. of Botany, University of Georgia

Current Grants

  • The Smithsonian Institution. $50,000. 2017-2018. Title: Genomic and Chemical Consequences of Different Levels of Gene Flow in The Fig-Wasp Pollination Mutualism: A Proposal for Scholarly Studies. PI E. A. Herre (The Smithsonian), Co-PIs T. Heath (ISU), C. Machado (U. Maryland), C. Jander (Harvard U.), J. Nason (ISU), and R. Raguso (Cornell U.).
  • National Science Foundation. $987,767. 2016-2020. Title: Multilocus Analyses of Co-Diversification and Phylogenetic Incongruence Between Highly Coevolved Figs and Fig Wasps. PI J. Nason, Co-PIs T. Heath (ISU) and E. A. Herre (The Smithsonian). ($863,688 to ISU).
  • National Science Foundation. $425,000. 2012-2017. Title: Understanding the Geographical and Community Context of Mutualism Dynamics: Fig-Pollinator-Parasite Interactions in the Sonoran Desert. PI J. Nason.

Products

(i) Five publications most closely related to current NSF-supported research

  • Yu, H., J. D. Nason, L. Zhang, L. Zheng, W. Wu, X. Ge. 2015. De novo transcriptome sequencing in Ficus hirta Vahl. (Moraceae) to investigate gene regulation involved in the biosynthesis of pollinator attracting volatiles. Tree Genetics & Genomes 11:91.
  • Davis, D., D. D. Houston, and J. D. Nason. 2015. Transcriptome facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Gunneridae: Moraceae). Applications in Plant Sciences 3(7):1500028.
  • Tian, W., J. D. Nason, C. A. Machado, L. Zheng, H. Yu, and F. Kjellberg. 2015. Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a figpollinating wasp mutualism. Molecular Ecology 24: 5976-5991.
  • Yu, H., and J. D. Nason. 2013. Nuclear and chloroplast DNA phylogeography of Ficus hirta: obligate pollination mutualism and constraints on range expansion in response to climate change. New Phytologist 197:276-289.
  • Yu, H., J. D. Nason, X. Ge, and J. Zeng. 2010. Slatkin’s Paradox: when direct observation and realized gene flow disagree – a case study in Ficus. Molecular Ecology 19:4441-4453.

(ii) Five additional significant publications

  • Duthie, A. B., K. C. Abbott, and J. D. Nason. 2014. Trade-offs and coexistence: a lottery model applied to fig wasp communities. American Naturalist 183:826-841.
  • Dyer, R. J., J. D. Nason, and R. C. Garrick. 2010. Landscape modeling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology 19:3748-3759.
  • Dyer, R. J., and J. D. Nason. 2004. Population graphs: the graph theoretic shape of genetic structure. Molecular Ecology 13:1713-1727.
  • Sork, V. L., J. D. Nason, D. R. Campbell, and J. F. Fernandez. 1999. Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology and Evolution 6:219-224.
  • Nason, J. D., E. A. Herre, and J. L. Hamrick. 1998. The breeding structure of a tropical keystone plant resource. Nature 391:685-687.

 

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