Selected Publications
Haidong Yan, Qi Song, Jiyoung Lee, John Schiefelbein, Song Li. Identification of cell-type marker genes from plant single-cell RNA-seq data using machine learning. (2020) [biorxiv], [link to code]
Qi Song, Jiyoung Lee, Shamima Akter, Matthew Rogers, Ruth Grene, Song Li. Prediction of condition-specific regulatory genes using machine learning. (2020) Nucleic Acids Research [link to paper], [link to code]
Lindsay C DeMers, Neelam R Redekar, Aardra Kachroo, Sue A Tolin, Song Li, MA Saghai Maroof. A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus. (2020) PloS one [link to paper] [link to code]
Marco E Mechan Llontop, Parul Sharma, Marcela Aguilera Flores, Shu Yang, Jill Pollok, Long Tian, Chenjie Huang, Steve Rideout, Lenwood S Heath, Song Li, Boris A Vinatzer. Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences. (2020) Phytopathology. [link to paper]
Leila Abdelhamid, Xavier Cabana-Puig, Brianna Swartwout, Jiyoung Lee, Song Li, Sha Sun, Yaqi Li, A Catharine Ross, Thomas E Cecere, Tanya LeRoith, Stephen R Werre, Haifeng Wang, Christopher M Reilly, Xin M Luo. Retinoic Acid Exerts Disease Stage-Dependent Effects on Pristane-Induced Lupus. (2020) Frontiers in immunology. [link to paper]
Haidong Yan, Aureliano Bombarely, Song Li. DeepTE: a computational method for de novo classification of transposons with convolu-tional neural network. (2020) Bioinformatics. [link to paper] [link to code]
Jiyoung Lee, Lenwood S Heath, Ruth Grene, Song Li. Comparing time series transcriptome data between plants using a network module finding algorithm. (2019) Plant methods. [link to paper] [link to code]
Jun Qin, Ainong Shi, Qijian Song, Song Li, Fengmin Wang, Yinghao Cao, Waltram Ravelombola, Qi Song, Chunyan Yang, Mengchen Zhang. Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds. (2019) Frontiers in Plant Science. [link to paper]
Boris A Vinatzer, Lenwood S Heath, Hussain MJ Almohri, Michael J Stulberg, Christopher Lowe, Song Li. Cyberbiosecurity Challenges of Pathogen Genome Databases. (2019) Frontiers in bioengineering and biotechnology. [link to paper]
Qi A Song, Nathan S Catlin, W Brad Barbazuk, Song Li. Computational analysis of alternative splicing in plant genomes. (2019) Gene. [link to paper]
Mimosa Sarma, Jiyoung Lee, Sai Ma, Song Li, Chang Lu. A diffusion-based microfluidic device for single-cell RNA-seq. (2019) Lab on a Chip. [link to paper]
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. Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. (2019) Plant direct. [link to paper]
Qi Song, Ruth Grene, Lenwood S Heath, Song Li. Identification of regulatory modules in genome scale transcription regulatory networks. (2017) BMC systems biology. [link to paper]
Neelam Redekar, Guillaume Pilot, Victor Raboy, Song Li, Saghai Maroof. Inference of transcription regulatory network in low phytic acid soybean seeds. (2017) Frontiers in plant science. [link to paper]
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. Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. (2019) Plant direct. [link to paper]
Qi Song, Ruth Grene, Lenwood S Heath, Song Li. Identification of regulatory modules in genome scale transcription regulatory networks. (2017) BMC systems biology. [link to paper]
Neelam Redekar, Guillaume Pilot, Victor Raboy, Song Li, Saghai Maroof. Inference of transcription regulatory network in low phytic acid soybean seeds. (2017) Frontiers in plant science. [link to paper]
Qinghui Mu, Vincent J Tavella, Jay L Kirby, Thomas E Cecere, Matthias Chung, Jiyoung Lee, Song Li, S Ansar Ahmed, Kristin Eden, Irving Coy Allen, Christopher M Reilly, Xin M Luo. Antibiotics ameliorate lupus-like symptoms in mice. (2017) Scientific reports. [link to paper]
Jos R Wendrich, Barbara K Möller, Song Li, Shunsuke Saiga, Rosangela Sozzani, Philip N Benfey, Bert De Rybel, Dolf Weijers. Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. (2017) Proceedings of the National Academy of Sciences. [link to paper]
David C Haak, Takeshi Fukao, Ruth Grene, Zhihua Hua, Rumen Ivanov, Giorgio Perrella, Song Li. Multilevel regulation of abiotic stress responses in plants. (2017) Frontiers in plant science. [link to paper]
Shan Sun, Song Li, Bethany N Avera, Brian D Strahm, Brian D Badgley. Soil bacterial and fungal communities show distinct recovery patterns during forest ecosystem restoration. (2017) Applied and Environmental Microbiology. [link to paper]
Ying Ni, Delasa Aghamirzaie, Haitham Elmarakeby, Eva Collakova, Song Li, Ruth Grene, Lenwood S Heath. A machine learning approach to predict gene regulatory networks in seed development in Arabidopsis. (2016) Frontiers in plant science. [link to paper]
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, Philip N Benfey. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. (2016) Developmental cell. [link to paper]
Delasa Aghamirzaie, Eva Collakova, Song Li, Ruth Grene. CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. (2016) BMC genomics. [link to paper]