Genetics and Biochemistry

Dr. Alex Feltus

Alex Feltus

Associate Professor

Ph.D. Cell Biology
2000, Vanderbilt University

Contact Information
Office: 302 Biosystems Research Complex
Phone: (864) 656-3231
Email: ffeltus@clemson.edu
Web: Gene Network Browser

Research Focus Areas
Plant Genetics and Biochemistry
Genomics, Bioinformatics, and Population Genetics

 

Research Activities

Systems Genetics. Network biology techniques (Barabasi AL et al Nature Reviews Genetics (5):101-113, 2004) allow for the measurement, modeling and interpretation of gene expression relationships and gene product physical interactions on a global scale. The Feltus lab focuses on gene co-expression networks which have the power to reveal functionally-related genes based upon the simultaneous co-expression of gene pairs across hundreds to thousands of expression profiling experiments (microarray, RNAseq). By combining high-throughput construction of co-expression networks with additional biological data (Gibson 2013; Feltus 2013), we are discovering and validating genetic subsystems controlling specific biochemical pathways and quantitative phenotypes. Our lab has been especially interested in advancing the field of systems genetics centered on rice (Ficklin 2010). We are also exploring how networks have been modified to meet the physiological requirements of a particular species through comparative network analysis between two grasses: maize and rice (Ficklin 2011). We have created a tripal-based System Genetics module explorer (Gene Net Engine) for the biological networks located at http://sysbio.genome.clemson.edu/.

Paleogenomics. The Feltus lab is studying conserved non-coding sequences (CNS), conserved DNA motifs retained after a whole genome duplication (WGD) event that occurred in the Arabidopsis lineage around 20 million years ago. We have found evidence for a putative cis-regulatory function of the CNSs via expression analysis across nine curated tissue-enriched expression datasets: aerial tissue, flowers, leaves, roots, rosettes, seedlings, seeds, shoots, and whole plants (Spangler 2012). We have constructed co-expression networks from these partitioned datasets and assigned CNSs to gene co-expression modules and gene regulatory networks (Spangler 2012B). Mechanistically, we suspect that some of regulatory control encoded in CNS elements is post0transcriptional at the level of mRNA decay (Spangler 2013). These results provide evidence that CNS molecular footprints are real and have implications in understanding the functional effects of duplicating regulatory machinery after ancient polyploidy events.

Bioenergy Feedstock Development. The Feltus lab has made significant strides in the analysis of sorghum as a bioenergy feedstock. We have screened sorghum varieties for high hydrolysis yield potential (HYP), the maximal enzymatic conversion of biomass to sugar (Vandenbrink 2010). Using biomass conversion variability in these genetic backgrounds as a guide, we have identified secondary traits (e.g. composition, crystallinity; Vandenbrink 2011). While our interests revolve around basic research objectives, we hope that our work will lead to new crop options for marginal lands in South Carolina and beyond.

Plant Genomics. The Feltus lab has a long standing interest in the broad field of plant genomics. We have been an active participant in a T. cacao genome sequencing consortium in collaboration with the Clemson University Genomics Institute (CUGI; http://www.genome.clemson.edu; Feltus 2011, Kuhn 2012, Saski 2011, Haimenen 2011). Another plant genomics collaboration has focused on the sex determination region in the papaya and the full genome assembly (Ming 2008, Yu 2008, Wang 2012, and Na 2012). In addition, we heavily collaborate in grass genomics projects such as the sorghum genome assembly (Paterson 2009) and switchgrass sequencing (Saski 2011). We strive to make significant advances in plant and crop research to help improve agriculture worldwide.

 
 

Courses Taught

BCHM 4400/6400/4400H
Bioinformatics

GEN/BCHM 4930
Senior Seminar

GEN/BCHM 8900
Computational Genomics

BCHM 3050
Essential Elements of Biochemistry

Resources

 

Recent Publications

Joshua P. Vandenbrink, Andrew H. Paterson, Lori Goff, Wenqian Kong, Huizhe Jin and F. Alex Feltus. Identification of Bioconversion Quantitative Trait Loci in the Interspecific Bioenergy Grass Cross Sorghum bicolor x Sorghum propinquum. Theoretical and Applied Genetics (in press), 2013.

Stephen P. Ficklin and F. Alex Feltus. A Systems-Genetics Approach and Data Mining Tool For the Discovery of Genes Underlying Complex Traits in Oryza Sativa. PloS ONE (in press), 2013.

F. Alex Feltus, Stephen P. Ficklin, Scott M Gibson, and Melissa C. Smith. Maximizing Capture of Gene Co-expression Relationships Through Pre-Clustering of Input Expression Samples: An Arabidopsis Case Study. BMC Systems Biology (in press), 2013.

Jacob B Spangler and F. Alex Feltus. Conserved Noncoding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. Frontiers in Plant Science. doi:10.3389/fpls.2013.00129, 2013.

Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida and David N Kuhn. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology 14:R53 doi:10.1186/gb-2013-14-6-r532013, 2013.

Joshua P. Vandenbrink, Andrew H. Paterson, KC Das, Roger N. Hilten, and F. Alex Feltus. Quantitative Models of Hydrolysis Conversion Efficiency and Biomass Crystallinity Index for Plant Breeding. Plant Breeding, (in press; online) DOI: 10.1111/pbr.12066,2013.

Scott M Gibson, Stephen P. Ficklin, Sven Isaacson, Feng Luo, F Alex Feltus, Melissa C Smith. Massive-Scale Gene Co-expression Network Construction and Robustness Testing using Random Matrix Theory. PLoS ONE 8(2): e55871. doi:10.1371/journal.pone.0055871, 2013.

F. Alex Feltus and Joshua P. Vandenbrink. Bioenergy Grass Feedstock: Current options and prospects for improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnology for Biofuels Nov 2;5(1):80, 2012.

Jacob B Spangler, Stephen P. Ficklin, Feng Luo, Michae Freeling and F. Alex Feltus. Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-expressed Gene Modules. PLoS ONE 7(9): e45041. doi:10.1371/journal.pone.0045041, 2012B.

Jacob B Spangler; Sabarinath Subramaniam, Michael Freeling, and F. Alex Feltus. Evidence of Function for Conserved Non-coding Sequence in Arabidopsis thaliana. New Phytologist, 193(1):241-252, 2012A.

Wang J, Jong-Kuk Na, Qingyi Yu, Andrea Gschwend, Jennifer Han, Fanchang Zeng, Rishi Aryal, Robert VanBuren, Jan E. Murray, Wenli Zhang, Rafael Navajas PĀ»rez, F. Alex Feltus, Cornelia Lemke, Eric J. Tong, Cuixia Chen, Ching Man Wai, Ratnesh Singh, Ming-Li Wang, Xiangjia Min, Maqsudul Alam, Deborah Charlesworth, Paul H. Moore, Jiming Jiang, Andrew H. Paterson, Ray Ming. Dynamic rearrangements and gene trafficking in nascent Yh chromosome of papaya. Proceedings of the National Academy of Sciences USA, Aug 21;109(34):13710-5, 2012.

Joshua P. Vandenbrink, Roger N. Hilten, K.C. Das, Andrew H. Paterson, and F. Alex Feltus. Analysis of Crystallinity Index and Hydrolysis Rates in the Bioenergy Crop Sorghum bicolor. BioEnergy Research, DOI: 10.1007/s12155-011-9146-2, 2011.

Stephen P. Ficklin and F. Alex Feltus. Gene Co-Expression Network Alignment and Conservation of Gene Modules Between Two Grass Species: Maize (Zea mays) and Rice (Oryza sativa). Plant Physiology 156(3):1244-56, 2011.

Frank A. Feltus, Chris A. Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E. Staton, Stephen P. Ficklin, Barbara P. Blackmon, Ray J. Schnell, David N. Kuhn, Juan-Carlos Motamayor. Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes. BMC Genomics, 12(1):379, 2011.

Yupeng Wang, Xiyin Wang, Haibao Tang, Xu Tan, Stephen Ficklin, F. Alex Feltus and Andrew H Paterson. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS ONE, 6(12): e28150, 2011.

Christopher A. Saski, Zhigang Li, Frank A. Feltus, Hong Luo. New genomic resources for switchgrass: a bacterial artificial chromosome library (BAC) and comparative analysis of a homoeologous genomic region harboring bioenergy traits. BMC Genomics, 12:369, 2011.

Xumeng Li, F. Alex Feltus, Xiaoqian Sun, Zijun Wang and Feng Luo. Identifying Differentially Expressed Genes in Cancer Patients using A Non-parameter Ising Model. Proteomics, 11(19):3845-52, 2011.

Niina Haiminen, F. Alex Feltus, Laxmi Parida. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Assembly of Complex Genomes. BMC Genomics 12:194, 2011.

Stephen P. Ficklin, Feng Luo, and F. Alex Feltus. The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks. Plant Physiology 154(1):13-24, 2010.

Joshua P. Vandenbrink, Maria P. Delgado, Jim R. Frederick, and F. Alex Feltus. A Sorghum Diversity Panel Biofuel Feedstock Screen for Genotypes with High Hydrolysis Yield Potential. Industrial Crops and Products 31(3):444-448, 2010.