学术发表

1. Baoxing Song*, Edward S. Buckler, Michelle C. Stitzer*. New whole-genome alignment tools are needed for tapping into plant diversity.Trends in Plant Science. 2023

2. Baoxing Song*, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler*, Michelle C. Stitzer*. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. PNAS.2022

3. Baoxing Song*, Edward S. Buckler, Hai Wang, Yaoyao Wu, Evan Rees, Elizabeth A. Kellogg, Daniel J. Gates, Merritt Khaipho-Burch, Peter J. Bradbury, Jeffrey Ross-Ibarra, Matthew B. Hufford and M. CintaRomay*. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research. 2021

4. Guang Yang^#, Yan Pan^#, Wenqiu Pan^#, Qingting Song, Ruoyu Zhang, Wei Tong, Licao Cui, Wanquan Ji, Weining Song, Baoxing Song*, Pingchuan Deng*, XiaojunNie*. Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.). New Phytologist. 2024

5. Baoxing Song, Richard Mott, Xiangchao Gan*. Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test. PLoS Genetics. 2018

6. Baoxing Song^*#, Qing Sang^#, Hai Wang, Huimin Pei, XiangChao Gan* and Fen Wang*. Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy. Frontiers in Genetics. 2019

7. Fen Wang^*#, Baohui Zhang^#, Di Wen^#, Rong Liu, Xinzhuan Yao, Zhi Chen, Ren Mu, Huimin Pei, Min Liu, Baoxing Song* and Litang Lu*. Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers. Frontiers in Plant Science. 2022

8. Fen Wang, Zhi Chen, Huimin Pei, Zhiyou Guo, Di Wen, Rong Liu, Baoxing Song*. Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology. Gene. 2021

9. Fen Wang^#, Baoxing Song^#, Xing Zhao, Yaotian Miao, Dengyun Li, Na Zhou, Pengfei Jiang, Qing Sang, Jingfei Huang, Deli Zhang*. Prediction and analysis of the protein-protein interaction networks for chickens, cattle, dogs, horses and rabbits. Current bioinformatics. 2016

10. Baoxing Song^#, Fen Wang^#, Yang Guo, Qing Sang, Min Liu, Dengyun Li, Wei Fang, Deli Zhang. Protein–protein interaction network‐based detection of functionally similar proteins within species. Proteins: Structure, Function, and Bioinformatics. 2012

11. Baoxing Song, XiaoquanSu, Jian Xu, Kang Ning*. MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison. PLoS One. 2012

12. Shuai Wang, Qinlin Xu, Baoxing Song*. Applying AnchorWave to Address Plant Genome Alignment. Bio-protocol. 2023

13. Manisha Munasinghe*, Andrew Read, Michelle C. Stitzer, Baoxing Song, Claire C. Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N. Hirsch, Nathan Springer. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genetics. 2023

14. Hongna Li^#, Lei Hua^#, Shuqing Zhao^#, Hao Ming, Rui Song, Shuyong Pang, Yanna Liu, Hong Chen, Wenjun Zhang, Tao Shen, JinYing Gou, Hailiang Mao, Guiping Wang, Xiaohua Hao, Jian Li, Baoxing Song, Caixia Lan, Zaifeng Li , Xingwang Deng, Jorge Dubcovsky, Xiaodong Wang*, shisheng Chen*. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nature communications. 2023

15. Lukas Baumgarten, Bjorn Pieper, Baoxing Song, Sébastien Mane, JanneLempe, Jonathan Lamb, Elizabeth L Cooke, Rachita Srivastava, Stefan Strütt, Danijela Žanko , Pedro GpCasimiro, Asis Hallab, Maria Cartolano, Alexander D Tattersall, Bruno Huettel, Dmitry AFilatov, PavlosPavlidis, Barbara Neuffer, Christos Bazakos, Hanno Schaefer, Richard Mott,  Xiangchao Gan, Carlos AlonsoBlanco, Stefan Laurent, MiltosTsiantis*. Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns. PLoS biology. 2023

16. Yaoyao Wu, Dawei Li, Yong Hu, Hongbo Li, Guillaume P Ramstein, Shaoqun Zhou, Xinyan Zhang, Zhigui Bao, Yu Zhang, Song Baoxing, Yao Zhou, Yongfeng Zhou, Edeline Gagnon, TiinaSärkinen, Sandra Knapp, Chunzhi Zhang, Thomas Städler, Edward S Buckler, Sanwen Huang*. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell. 2023

17. Guangchao Sun^#, Huihui Yu^#, Peng Wang, Martha LopezGuerrero, Ravi V Mural, Olivier N Mizero, Marcin Grzybowski, Baoxing Song, Karin van Dijk, Daniel P Schachtman, Chi Zhang, James C Schnable*. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome biology. 2023

18. Peter J. Bradbury*, Terry Casstevens, Sara E. Jensen, Lynn Johnson, Zack R. Miller, B Monier, M. CintaRomayBaoxing Song, Edward S Buckler. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 2022

19. Yaoyao Wu, Lynn Johnson, Song Baoxing,CintaRomay, Stitzer Michelle, Adam Siepel, Edward Buckler, Armin Scheben*. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The plant genome. 2022

20. Elad Oren, Galil Tzuri, Asaf Dafna, Evan R Rees, Baoxing Song, Shiri Freilich, Yonatan Elkind, Tal Isaacson, Arthur A Schaffer, Yaakov Tadmor, Joseph Burger, Edward S Buckler, Amit Gur*. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes. Horticulture research. 2022

21. Xi Wu^#, Hui Feng^#, Di Wu, Shijuan Yan, Pei Zhang, Wenbin Wang, Jun Zhang, Junli Ye, Guoxin Dai, Yuan Fan, Weikun Li, Baoxing Song, Zedong Geng, Wanli Yang, Guoxin Chen, Feng Qin, William Terzaghi, Michelle Stitzer, Lin Li, LizhongXiong, Jianbing Yan, Edward Buckler, Wannen Yang*, Mingqiu Dai*. Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance. Genome Biology. 2021

22. Thomas M Winkelmüller^#, Frederickson Entila^#, ShajahanAnver^#, Anna Piasecka, Baoxing Song, EikDahms, Hitoshi Sakakibara, Xiangchao Gan, Karolina Kułak, AnetaSawikowska, PawełKrajewski, MiltosTsiantis, Ruben GarridoOter, Kenji Fukushima, Paul SchulzeLefert, Stefan Laurent, PawełBednarek, Kenichi Tsuda*. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. The Plant cell. 2021

23. Qing Sang*, Alice Pajoro, Hequan Sun, Baoxing Song, Xia Yang, Sara C Stolze, Fernando Andrés, KorbinianSchneeberger, Hirofumi Nakagami, George Coupland. Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition. The Plant Cell. 2020

24. Xiangchao Gan^#, Angela Hay^#, MichielKwantes^#, Georg Haberer, Asis Hallab, Raffaele DelloIoio, Hugo Hofhuis, Bjorn Pieper, Maria Cartolano, Ulla Neumann, Lachezar A Nikolov, Baoxing Song, Mohsen Hajheidari, Roman Briskine, Evangelia Kougioumoutzi, Daniela Vlad, SuviBroholm, Jotun Hein, Khalid Meksem, David Lightfoot, Kentaro K Shimizu, Rie Shimizu-Inatsugi, Martha Imprialou, David Kudrna, Rod Wing, Shusei Sato, Peter Huijser, Dmitry Filatov, Klaus FX Mayer, Richard Mott, MiltosTsiantis*. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature plants. 2016

25. XiaoquanSu^#Weihua Pan^#, Baoxing Song, Jian Xu, Kang Ning*. Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization.  PLoS One. 2014

26. Yong Xiang, Baoxing Song, Guillaume Née, Katharina Kramer, Iris Finkemeier, Wim J.J. Soppe*. Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy. Plant physiology. 2016

27. Fen Wang, Min Liu, Baoxing Song, Dengyun Li, Huimin Pei, Yang Guo, Jingfei Huang*, Deli Zhang*. Prediction and characterization of protein-protein interaction networks in swine. Proteome science. 2012

28. Fen Wang, Baoxing Song, Dengyun Li, Xing Zhao, Yaotian Miao, Pengfei Jiang, Deli Zhang. PPIPP: an online protein-protein interaction network prediction and analysis platform. International Journal of Data Mining and Bioinformatics. 2016

29. XiaoquanSu, Baoxing Song, Xuetao Wang, Xinle Ma, Jian Xu, Kang Ning. Meta-Mesh: metagenomic data analysis system. Chinese Journal of Biotechnology. 2014

30. Manisha Munasinghe*, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N Hirsch, Nathan Springer. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PloS Genetics. 2023