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Song Li

Associate Professor
Dr. Song Li
School of Plant and Environmental Sciences
Room 1120A,
1880 Pratt Drive
Blacksburg, VA 24061-0493


My research, teaching, and outreach are focused on the interface of agriculture and data science. My team develops computational tools and machine learning methods to integrate and interpret large scale data generated by advanced genomics and sensor technologies in agricultural research. More specifically, my research program includes two broad themes. First, we use machine learning to identify gene regulatory networks in plant abiotic stress responses. Second, we develop sensing technology and computational tools for early detection of plant diseases and to collect plant phenotype data at field scale to improve crop breeding programs.


  • Plant genomics and bioinformatics
  • Machine learning
  • High throughput phenotyping


  • Ph.D. Genomics and Bioinformatics, Penn State University, 2010
  • B.S. Biotechnology, Peking University, 2002

To address these emerging data analytic challenges in agriculture, my research program has been focused on developing machine learning and other computational tools to integrate and analyze data from diverse research domains. The long-term goal of my team is to apply artificial intelligence in basic plant research and in modern data-driven agriculture production systems. Projects in our group include the development of:

  1. Field-scale phenotyping capacity using drones
  2. Culture-free disease diagnostic methods using Nanopore sequencing devices
  3. Machine learning tools to predict gene regulatory networks and to identify target genes for breeding and engineering stress resilient crops.
  • ALS 5224: Introduction to Genomic Data Sciences
  • GBCB 5874: Problem Solving in Genetics, Bioinformatics and Computational Biology
  • CSES 5844: Plant Genomics

Assistant Professor | 2014-2019
School of Plant and Environmental Sciences
Virginia Tech. Blacksburg, VA.

Postdoc Associate | 2010-2014
Institute of Genome Science and Policy
Duke University, Durham, NC.

  1. Jun Qin, Ainong Shi, Qijian Song, Song Li, Fengmin Wang, Yinghao Cao, Waltram Ravelombola, Qi Song, Chunyan Yang, Mengchen Zhang. (2019) Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds, Frontiers in Plant Science 10, 1445.
  2. Jiyoung Lee, Ruth Grene, Lenwood Heath, and Song Li. (2019) Comparing time series transcriptome data between plants using a network module finding algorithm, Plant Methods 15(1), 61.
  3. Mimosa Sarma, Jiyoung Lee, Sai Ma, Song Li, and Chang Lu. (2019) A diffusion-based microfluidic device for single-cell RNA-seq. Lab on a Chip 19 (7), 1247-1256.
  4. Boris Vinatzer, Lenwood Heath, Hussain Almohri, Michael Stulberg, Christopher Lowe and Song Li. (2019) Cyberbiosecurity Challenges of Pathogen Genome Databases, Frontiers in Bioengineering. Biotechnology 7:106.
  5. International Arabidopsis Informatics Consortium, Colleen Doherty, Joanna Friesner, Brian Gregory, Ann Loraine, Molly Megraw, Nicholas Provart, R Keith Slotkin, Chris Town, Sarah M Assmann, Michael Axtell, Tanya Berardini, Sixue Chen, Malia Gehan, Eva Huala, Pankaj Jaiswal, Stephen Larson, Song Li, Sean May, Todd Michael, Chris Pires, Chris Topp, Justin Walley, Eve Wurtele. (2019) Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future, Plant Direct 3(1):e00109.
  6. Qi Song, Nathan Catlin, Brad Barbazukb, Song Li. (2018) Computational analysis of alternative splicing in plant genomes. Gene 685 (186-195).
  7. Qi Song, Ruth Grene, Lenwood Heath, Song Li. (2017) Identification of regulatory modules in genome scale transcription regulatory networks. BMC Systems Biology 11:140.
  8. Neelam Redekar, Guillaume Pilot, Victor Raboy, Song Li and M. A. Saghai Maroof. (2017) Inference of transcription regulatory network in low phytic acid soybean seeds. Frontier in Plant Science 8:2029.
  9. Qinghui Mu, Vincent J. Tavella, Jay L. Kirby, Thomas E. Cecere, Matthias Chung, Jiyoung Lee, Song Li, Ansar S. Ahmed, Kristin Eden, Irving Coy Allen, Christopher M. Reilly and Xin M. Luo. (2017) Antibiotics ameliorate lupus-like symptoms in mice. Scientific Reports 7:13675.
  10. Haitham Elmarakeby, Mostafa Arefiyan, Elijah Myers, Song Li, Ruth Grene, and Lenwood S. Heath. (2017) Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. Journal of Computational Biology. 24(12):1226.
  11. Jos R. Wendrich, Barbara K. Möller, Song Li, Shunsuke Saiga, Rosangela Sozzanid, Philip N. Benfey, Bert De Rybel and Dolf Weijersa. (2017) Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. PNAS vol. 114 no. 42. E8922.
  12. Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Song Li. (2017) Multilevel Regulation of Abiotic Stress Responses in Plants. Frontier in Plant Science 8:1564.
  13. Jun Qin, Qijian Song, Ainong Shi, Song Li, Mengchen Zhang and Bo Zhang. (2017) Genome-wide Association Mapping of Resistance to Phytophthora sojae in a Soybean Germplasm Panel from Maturity Groups IV and V. PLoS One 12(9):e0184613.
  14. Sun Shan, Song Li, Avera BN, Strahm BD, Badgley BD. (2017) Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration. Applied Environmental Microbiology 83(14): e00966-17.
  15. Song Li, Masashi Yamada, Xinwei Han, Uwe Ohler, Philip Benfey. (2016) High resolution RNA expression map of the root reveals alternative splicing regulation. Developmental Cell 39:1-15.
  16. Ying Ni, Delasa Aghamirzaie, Haitham Elmarakeby, Eva Collakova, Song Li, Ruth Grene, and Lenwood S. Heath. (2016) A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis. Frontier in Plant Science 7:1936.
  17. Delasa Aghamirzaie, Eva Collakova, Song Li and Ruth Grene. (2016) CoSpliceNet: A framework for co-splicing network inference from transcriptomics data. BMC Genomics 17:845.
  18. Erin E. Sparks, Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H. Hennacy, Jingyuan Zhang, Gina Turco, Jalean J. Petricka, Jessica Foret, Alexander J. Hartemink, Raluca Gordân, Molly Megraw, Siobhan M. Brady, and Philip N. Benfey. (2016) Establishment of expression in the SHORTROOT-SCARECROW transcriptional cascade is through opposing activities of both activators and repressors. Developmental Cell 39(5):585-596.
  19. Miranda D Vieson, Xin M Luo, Song Li, Alexander M Gojmerac, Adrian Castaneda and Christopher M Reilly. (2016) Selective HDAC6 Inhibition Corrects Aberrant B Cell Development in the Bone Marrow of NZB/W F1 Mice. Cell Mol Med., 2:3.
  20. Xiaofeng Liao, Song Li, Robert E. Settlage, Sha Sun, Jingjing Ren, Alec M. Reihl, Husen Zhang, Saikumar V. Karyala, Christopher M. Reilly, S. Ansar Ahmed and Xin M. Luo. (2015) Plasmacytoid Dendritic Cells in Late-Stage Lupus Mice Defective in Producing IFN The Journal of Immunology 195:4578-4582.
  21. Jing Li, Carl Zipper, Song Li, Patricia F. Donovan, Randolph Wynne, Adam Oliphant, Qing Xia. (2015) Character analysis of mining disturbance and reclamation trajectory in surface coal-mine area by time-series NDVI. Transactions of the Chinese Society of Agricultural Engineering 31(16): 251-257.