Profiles

Junfeng Xia, PhD

Professor, Institutes of Physical Science and Information Technology

Anhui University, Hefei, Anhui 230601, China

Tel: 86-551-63861990

E-mail: jfxia@ahu.edu.cn; junfeng.xia@foxmail.com

Personal Profile

Junfeng Xia was born in Anhui Province, China. He received his BS degree in Biotechnology in 2005 from Anhui University and PhD degree in Bioinformatics from University of Science and Technology of China in 2010. From 2010 to 2013 he was postdoctoral research fellow at Department of Biomedical Informatics, Vanderbilt University. Since 2013, he has been a professor of bioinformatics at Institutes of Physical Science and Information Technology, Anhui University.

Professional Services

  • Associate Editor, BMC Genomics, 2018-present
  • Associate Editor, BMC Medical Genomics, 2019-present
  • Program Committee Member, International Conference on Intelligent Computing, 2011-2019
  • Program Committee Member, International Conference on Intelligent Biology and Medicine, 2015-2019
  • Program Committee Member, IEEE International Conference on Bioinformatics and Biomedicine, 2018-2019

Selected Publications (*corresponding author)

  1. Yannan Bin, Xiaojuan Wang, Le Zhao, Pengbo Wen and Junfeng Xia *, An analysis of mutational signatures of synonymous mutations across 15 cancer types. BMC Medical Genetics 2019, 20(Suppl 2):190
  2. Na Cheng, Menglu Li, Le Zhao, Bo Zhang, Yuhua Yang, Chun-Hou Zheng and Junfeng Xia *, Comparison and integration of computational methods for deleterious synonymous mutation prediction. Briefings in Bioinformatics, 2019, doi:10.1093/bib/bbz047 (accepted)
  3. Sijia Zhang, Le Zhao, Chun-Hou Zheng and Junfeng Xia *, A feature-based approach to predict hot spots in protein-DNA binding interfaces. Briefings in Bioinformatics, 2019, doi:10.1093/bib/bbz037 (accepted)
  4. Fang Shi, Yao Yao, Yannan Bin, Chun-Hou Zheng and Junfeng Xia *, Computational identification of deleterious synonymous variants in human genomes using a feature-based approach. BMC Medical Genomics 2019, 12 (S1):12
  5. Zhenyu Yue, Le Zhao, Na Cheng and Junfeng Xia *, dbCID: a manually curated resource for exploring the driver indels in human cancer. Briefings in Bioinformatics, 2018, doi:10.1093/bib/bby059
  6. Zhenyu Yue, Le Zhao and Junfeng Xia *, dbCPM: a manually curated database for exploring the cancer passenger mutations. Briefings in Bioinformatics, 2018, doi:10.1093/bib/bby105
  7. Pengbo Wen, Junfeng Xia * , Xianbin Cao, Bin Chen, Yinping Tao, Lijun Wu, An Xu and Guoping Zhao *, dbCRSR: a manually curated database for regulation of cancer radiosensitivity. Database, 2018, 2018: bay049
  8. Shu-Guang Ge, Junfeng Xia, Wen Sha and Chun-Hou Zheng, Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(5): 1115-1121
  9. Pi-Jing Wei, Di Zhang, Hai-Tao Li, Junfeng Xia and Chun-Hou Zheng, DriverFinder: A Gene Length-Based Network Method to Identify Cancer Driver Genes. Complexity, 2017, 2017: 4826206
  10. Pengbo Wen, Peng Xiao, and Junfeng Xia *, dbDSM: a manually curated database for deleterious synonymous mutations. Bioinformatics, 2016, 32(12): 1914-1916
  11. Junfeng Xia, Zhenyu Yue, Yunqiang Di, Xiaolei Zhu, Chun-Hou Zheng, Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features. Oncotarget, 2016, 7(14): 18065-18075
  12. Peng Chen, Shanshan Hu, Jun Zhang, Xin Gao, Jinyan Li, Junfeng Xia * and Bing Wang*, A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016, 13(5): 901-912
  13. Ran Wei, Ming Zhao, Chun-Hou Zheng, Min Zhao * and Junfeng Xia *, Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes. Scientific Reports, 2016, 6: 37358
  14. Chun-Hou Zheng, Wu Yang, Yan-Wen Chong and Junfeng Xia *, Identification of mutated driver pathways in cancer using a multi-objective optimization model. Computers in Biology and Medicine, 2016,72:22-29
  15. Haitao Li, Jun Zhang, Junfeng Xia * and Chun-Hou Zheng *, Identifiation of driver pathways in cancer based on combinatorial patterns of somatic gene mutations. Neoplasma 2016, 63(1):57-63
  16. Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang and Chun-Hou Zheng, CINOEDV: a co-information based method for detecting and visualizing n-order epistatic interactions. BMC Bioinformatics, 2016, 17:214
  17. Rebecca S. Heist, Hyo Sup Shim, Shalini Gingipally, Mari Mino-Kenudson, Long Le, Justin F. Gainor, Zongli Zheng, Martin Aryee, Junfeng Xia, Peilin Jia, Hailing Jin, Zhongming Zhao, William Pao, Jeffrey A. Engelman and A. John Iafrate, MET Exon 14 Skipping in Non-Small Cell Lung Cancer. The Oncologist, 2016, 21(4): 481-486
  18. Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng and Junfeng Xia *, MGDB: a comprehensive database of genes involved in melanoma. Database, 2015, 2015: bav097
  19. Zhenyu Yue, Wenna Zhang, Yongming Lu, Qiaoyue Yang, Qiuying Ding, Junfeng Xia * and Yan Chen *, Prediction of cancer cell sensitivity to natural products based on genomic and chemical properties. PeerJ, 2015, 3:e1425
  20. Chengjun Xie *, Jie Zhang, Rui Li, Jinyan Li, Peilin Hong, Junfeng Xia * and Peng Chen *, Automatic classification for field crop insects via multiple-task sparse representation and multiple-kernel learning. Computers and Electronics in Agriculture, 2015, 119:123-132
  21. Timothy D O’Brien, Peilin Jia, Junfeng Xia, Uma Saxena, Hailing Jin, Huy Vuong, Pora Kim, Qingguo Wang, Martin J Aryee, Mari Mino-Kenudson, Jeffrey A Engelman, Long P Le, A John Iafrate, Rebecca S Heist, William Pao and Zhongming Zhao, Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer. Methods, 2015, 83:118-127
  22. Junfeng Xia, Peilin Jia, Katie Hutchinson, Kimberly B Dahlman, Douglas B Johnson, Jeffrey A Sosman, William Pao and Zhongming Zhao, A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance. Molecular Cancer Therapeutics, 2014,13(7): 1918-1928
  23. Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao and Zhongming Zhao, Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Briefings in Bioinformatics, 2013, 14(4):506-519
  24. Peilin Jia, Hailing Jin, Catherine B, Junfeng Xia, Kadoaki Ohashi, Lin Liu, Valentina Pirazzoli, Kimberly B Dahlman, KaterinaPoliti, Franziska Michor, Zhongming Zhao and William Pao, Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFRmutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Research, 2013, 23 (9):1434-1445
  25. Zhu-Hong You, Ying-Ke Lei, Lin Zhu, Junfeng Xia and Bing Wang, Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. BMC Bioinformatics, 2013, 14(S8): S10
  26. Kimberly B Dahlman #, Junfeng Xia #, Katie Hutchinson #, Charles Ng, Donald Hucks, Peilin Jia, Mohammad Atefi, Zengliu Su, Suzanne Branch, Pamela Lyle, Donna J Hicks, Viviana Bozon, John A Glaspy, Neal Rosen, David B Solit, James L Netterville, Cindy L Vnencak-Jones, Jeffrey A Sosman, Antoni Ribas, Zhongming Zhao and William Pao, BRAF L597 mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer Discovery, 2012, 2:791-797 (cover story)
  27. Junfeng Xia #, Qingguo Wang #, Peilin Jia, Bing Wang, William Pao and Zhongming Zhao, NGS Catalog: A Database of Next Generation Sequencing Studies in Humans. Human Mutation, 2012, 33: E2341-2355
  28. Junfeng Xia #, Leng Han #, Zhongming Zhao，Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics, 2012, 13(S8): S7
  29. Zhixi Su #, Junfeng Xia #, Zhongming Zhao, Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics, 2011, 12(S5): S15
  30. Junfeng Xia, Jingchun Sun, Peilin Jia and Zhongming Zhao, Do cancer proteins really interact strongly in the human protein-protein interaction network? Computational Biology and Chemistry, 2011, 35:121-125
  31. Junfeng Xia, Xing-Ming Zhao, Jiangning Song and De-Shuang Huang, APIS: Accurate prediction of hot spots in protein interfaces by combining protrusion Index with solvent accessibility. BMC Bioinformatics, 2010, 11:174
  32. Junfeng Xia, Xing-Ming Zhao, De-Shuang Huang, Predicting protein-protein interactions from protein sequences using meta predictor. Amino Acids, 2010, 39(5):1595-1599
  33. Junfeng Xia, Kyungsook Han, De-Shuang Huang, Sequence-based prediction of protein-protein interactions by means of rotation forest and autocorrelation descriptor. Protein and Peptide Letters, 2010,17(1): 137-145
  34. Lei Yang, Junfeng Xia *, Jie Gui, Prediction of protein-protein interactions from protein sequence using local descriptors. Protein and Peptide Letters, 2010, 17(9):1085-1090
  35. Ming-Guang Shi, Junfeng Xia, Xue-Ling Li and De-Shuang Huang, Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids, 2010, 38(3):891-899