Basic Information

Personal Information

Name: Ye Kai
Gender:Male
Nationality:Chinese
Birth Date:1977-06-19
Current Position:Professor of Xi’an Jiaotong University
Current Research Fields:Large data mining, pattern recognition, computer algorithms, machine learning, bioinformatics, genomic  variation

Contact

Email:kaiye@xjtu.edu.cn

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Education and Working Experience

 

1995-09~1999-06 -Wuhan University, China, Bachelor

2000-09~2003-06 -Wuhan University, China, Master

2003-07~2003-12 -Wuhan University, China, lecturer

2004-01~2008-12 -Leiden University, The Netherlands, PhD

2008-07~2009-06 -European Bioinformatics Institute, UK, Postdoctoral

2009-07~2012-11 -Leiden University, The Netherlands, Assistant Professor

2012-12~2016-02 -Washington University in St. Louis, US, Assistant Professor

2016-02~now –Xi’an Jiaotong University, China, Professor

Members

 

Member- The 1000 Genomes Project(1000 GP)
Member- The Cancer Genome Atlas(TCGA)
Member- International Cancer Genome Consortium(ICGC)
Member- GoNL
Member- LLS

Awards

 

•BBMRI-NL rainbow grant, euro 105k, PI, 2011-2014
•VENI grant from Dutch research organization, euro 250k, PI, 2011-2014
•BBMRI-NL complementation grant, euro 100k, PI, 2011-2014
•NIH U41, co-PI, 2013-2015
•NIH U01, co-PI, 2012-2015
•June 2009: ‘best paper’ (on Pindel) presented at the Short-SIG on Next-Generation Sequence and Algorithms for Short Read Analysis, ISMB/ECCB 2009 at Stockholm, Sweden. 500 GBP
•‘Researcher of 2008’, Faculty of Science, Leiden University.
•2008 C. J. Kok prize, Leiden University, the Netherlands. 2,500 EURO
•2008 PhD Cum Laude, Leiden University, Leiden, the Netherlands
•NGI/EBI fellowship, The Netherlands. 36,000 euro per year.    
•‘Top Outstanding PhD students abroad’ Award, China. 5,000 USD

Paper publications (within recent five years)

 

20168
1. Computational Pan-Genomics Consortium,“Computational pan-genomics: status, promises and challenges”,Briefings in bioinformatics, 2016, IF 2015:8.399
2. Kai Ye, Jiayin Wang, Reyka Jayasinghe, Eric-Wubbo Lameijer, Joshua F. McMichael, Jie Ning, Michael D. McLellan, Mingchao Xie, Song Cao, Venkata Yellapantula, Kuan-lin Huang, Adam Scott, Steven Foltz, Beifang Niu, Kimberly J. Johnson, Matthijs Moed, P. Eline Slagboom, Feng Chen, Michael C. Wendl, Li Ding, “Systematic discovery of complex insertions and deletions in human cancers”, Nature Medicine, 2016, WOS:000367590700021 IF 2015: 30.357
3. Mark Kroon, Eric Wubbo Lameijer, Nicko Lakenberg, Jayne Hehire-Kwa, Djie Tjwan Thung, P Slagboom, Joost n Kok, Kai Ye#, “Detecting dispersed duplications in high-throughput sequencing data using a database-free approach”, Bioinformatics, 2016, WOS:000371693700004 IF 2015: 5.766
4. Song Cao, Michael C Wendl, Matthew A Wyczalkowski, Kristine Wylie, Kai Ye, Reyka Jayasinghe, Mingchao Xie, Song Wu, Beifang Niu, Robert Grubb III, Kimberly J Johnson, Hiram Gay, Ken Chen, Janet S Rader, John F Dipersio, Feng Chen, Li Ding, “Divergent viral presentation among human tumors and adjacent normal tissues”, Scientific Reports, 2016
5. Beifang Niu, Adam D Scott, Sohini Sengupta, Matthew H Bailey, Prag Batra, Jie Ning, Matthew A Wyczalkowski, Wen-Wei Liang, Qunyuan Zhang, Michael D McLellan, Sam Q Sun, Piyush Tripathi, Carolyn Lou, Kai Ye, R Jay Mashl, John Wallis, Michael C Wendl, Feng Chen, Li Ding, Protein-structure-guided discovery of functional mutations across 19 cancer types, Nature Genetics, 2016
6. Jayne Y Hehir-Kwa, Tobias Marschall, Wigard P Kloosterman, Laurent C Francioli, Jasmijn A Baaijens, Louis J Dijkstra, Abdel Abdellaoui, Vyacheslav Koval, Djie Tjwan Thung, René Wardenaar, Ivo Renkens, Bradley P Coe, Patrick Deelen, Joep De Ligt, Eric-Wubbo Lameijer, Freerk Van Dijk, Fereydoun Hormozdiari, André G Uitterlinden, Cornelia M Van Duijn, Evan E Eichler, Paul IW De Bakker, Morris A Swertz, Cisca Wijmenga, Gert-Jan B van Ommen, P Eline Slagboom, Dorret I Boomsma, Alexander Schönhuth, Kai Ye#, Victor Guryev, Genome of the Netherlands Consortium, A high-quality human reference panel reveals the complexity and distribution of genomic structural variants, Nature Communications, 2016
7. Kai Ye, George Hall, Zemin NingStructural variation detection from next generation sequencingJournal of Next Generation Sequencing & Applications, 2016
8.Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu, Precision Medicine: What Challenges Are We Facing?, Genomics, Proteomics & Bioinformatics, 2016
2015 (7)
9. Wigard P. Kloosterman*, Laurent C. Francioli*, Fereydoun Hormozdiari, Tobias Marschall, Jayne Y. Hehir-Kwa, Abdel Abdellaoui, Eric-Wubbo Lameijer, Matthijs H. Moed, Vyacheslav Koval, Ivo Renkens, Markus J. van Roosmalen, Pascal Arp, Lennart C. Karssen, Bradley P. Coe, Robert E. Handsaker, Eka D. Suchiman, Edwin Cuppen, Djie Tjwan Thung, Mitch McVey, Michael C. Wendl, Genome of the Netherlands Consortium, André Uitterlinden, Cornelia M. van Duijn, Morris A. Swertz, Cisca Wijmenga, GertJan B. van Ommen, P. Eline Slagboom, Dorret I. Boomsma, Alexander Schönhuth, Evan E. Eichler, Paul I.W. de Bakker, Kai Ye#, Victor Guryev#, “Characteristics of de novo structural changes in the human genome”, Genome Research, 2015, WOS:000355565900002 IF 2015: 11.351
10. Peter H. Sudmant*, Tobias Rausch*, Eugene J. Gardner*, Robert E. Handsaker*, Alexej Abyzov*, John Huddleston8, Yan Zhang*, Kai Ye*, Goo Jun, Markus Hsi-Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stu¨tz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J. P. Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y. K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M. Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A. Gibbs, Gabor Marth, Christopher E. Mason, Androniki Menelaou, Donna M. Muzny, Bradley J. Nelson, Amina Noor, Nicholas F. Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E. Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A. Shabalin, Andreas Untergasser, Jerilyn A. Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner , Jonathan Sebat, Mark A. Batzer, Steven A. McCarroll, The 1000 Genomes Project Consortium, Ryan E. Mills, Mark B. Gerstein, Ali Bashir, Oliver Stegle, Scott E. Devine, Charles Lee, Evan E. Eichler, Jan O. Korbel, “An integrated map of structural variation in 2,504 human genomes”, Nature, 526, 75-81, 2015, WOS:000362095100037 IF 2015: 38.138
11. 1000 Genomes Project Consortium, “A global reference for human genetic variation”, Nature, 526, 68-74, 2015, WOS:000362095100036 IF 2015: 38.138 Highly cited Top 1% Hot paper top 0.1%
12. Francioli, Laurent C.; Polak, Paz P; Koren, Amnon; Menelaou, Androniki; Chun, Sung; Renkens, Ivo; van Duijn, Cornelia M.; Swertz, Morris; Wijmenga, Cisca; van Ommen, Gertjan; Slagboom, P. Eline; Boomsma, Dorret I.; Ye, Kai; Guryev, Victor; Arndt, Peter F.; Kloosterman, Wigard P.; de Bakker, Paul I. W.; Sunyaev, Shamil R., “Genome-wide patterns and properties of de novo mutations in humans”, Nature Genetics, 47, 7, 822+, 2015, WOS:000357090300023 IF 2015: 31.616
13. Ramos, Yolande F. M.; Bos, Steffan D.; van der Breggen, Ruud; Kloppenburg, Margreet; Ye, Kai; Lameijer, Eric-Wubbo E. M. W.; Nelissen, Rob G. H. H.; Slagboom, P. Eline; Meulenbelt, Ingrid, “A gain of function mutation in TNFRSF11B encoding osteoprotegerin causes osteoarthritis with chondrocalcinosis”, Annals of the Rheumatic Diseases, 74, 9, 1756-1762, 2015, WOS:000359378100026 IF 2015: 12.384
14. Lu, Charles; Xie, Mingchao; Wendl, Michael C.; Wang, Jiayin; McLellan, Michael D.; Leiserson, Mark D. M.; Huang, Kuan-lin; Wyczalkowski, Matthew A.; Jayasinghe, Reyka; Banerjee, Tapahsama ; Ning, Jie; Tripathi, Piyush; Zhang, Qunyuan; Niu, Beifang; Ye, Kai; Schmidt, Heather K.; et.al, “Patterns and functional implications of rare germline variants across 12 cancer types”, Nature Communications, 6, 2015, WOS:000367569400006 IF 2015: 11.329
15. Ye, Kai; Beekman, Marian; Lameijer, Eric-Wubbo; Zhang, Yanju; Moed, Matthijs H; van den Akker, Erik B; Deelen, Joris; Houwing-Duistermaat, Jeanine J; Kremer, Dennis; Anvar, Seyed Yahya, “Aging as Accelerated Accumulation of Somatic Variants: Whole-Genome Sequencing of Centenarian and Middle-Aged Monozygotic Twin Pairs”, Twin Research and Human Genetics, 16, 6, 1026-1032, 2015, WOS:000328546200002 IF 2015: 2.339
2014 (6)
16. Cancer Genome Atlas Research Network, “Comprehensive molecular profiling of lung adenocarcinoma”, Nature, 511, 7511, 543-550, 2014, WOS:000339566300025 IF 2015: 38.138 Highly cited Top 1% Hot paper top 0.1%
17. Genome of the Netherlands Consortium, “Whole-genome sequence variation, population structure and demographic history of the Dutch population”, Nature genetics, 46, 8, 818-25, 2014, WOS:000339704400009 IF 2015: 31.616 Highly cited Top 1%
18. Djie Tjwan Thung; de Ligt, Joep; Vissers, Lisenka E. M.; Steehouwer, Marloes; Kroon, Mark; de Vries, Petra; Slagboom, Eline P.; Ye, Kai; Veltman, Joris A. ; Hehir-Kwa, Jayne Y., “Mobster: accurate detection of mobile element insertions in next generation sequencing data”, Genome Biology, 15, 10, 2014, WOS:000346605500013 IF 2015: 11.313
19. Boomsma, Dorret I; Wijmenga, Cisca; Slagboom, Eline P; Swertz, Morris A; Karssen, Lennart C; Abdellaoui, Abdel; Ye, Kai; Guryev, Victor; Vermaat, Martijn; van Dijk, Freerk, “The Genome of the Netherlands: design, and project goals”, European Journal of Human Genetics, 22, 2, 221-227, 2014, WOS:000330415800014 IF 2015: 4.580
20. Genome Netherlands Consortium, “Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of the Netherlands’”, European Journal of Human Genetics, 22, 11, 1321-1326, 2014, WOS:000343850200014 IF 2015: 4.580
21. Ramos, Y. F.; Bos, S. D.; van der Breggen, R.; Deelen, J.; Kloppenburg, M.; Ye, K.; Beekman, M.; Lameijer, E-W E.; Nelissen, R. G.; Slagboom, P. E.; Meulenbelt, I., “A Gain of Function Mutation in TNFRSF11B Causes Osteoarthritis with Chondrocalcinosis”, Osteoarthritis and Cartilage, 22, S226-S226, 2014, WOS:000335424800422 IF 2015: 4.535
2013 (6)
22. Kandoth, Cyriac; McLellan, Michael D; Vandin, Fabio; Ye, Kai; Niu, Beifang; Lu, Charles; Xie, Mingchao; Zhang, Qunyuan; McMichael, Joshua F; Wyczalkowski, Matthew A, “Mutational landscape and significance across 12 major cancer types”, Nature, 502, 7471, 333-339, 2013, WOS:000325706300045 IF 2015: 38.138 Highly cited Top 1%
23. Cancer Genome Atlas Research Network, “Integrated genomic characterization of endometrial carcinoma”, Nature, 497, 7447, 67-73, 2013, WOS:000318221500035 IF 2015: 38.138 Highly cited top 1%
24. Khurana. Ekta et. al., “Integrative annotation of variants from 1092 humans: Application to cancer genomics”, Science, 342, 6154, 1235587, 2013, WOS:000325126100049 IF 2015: 33.611
25. Kiezun, Adam et. al., “Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency”,PLoS genetics, 9, 2, e1003301, 2013, WOS:000315638300051 IF 2015: 6.661
26. Niu, Beifang*; Ye, Kai*#; Zhang, Qunyuan; Lu, Charles; Xie, Mingchao; McLellan, Michael D; Wendl, Michael C; Ding, Li#, “MSIsensor: microsatellite instability detection using paired tumor-normal sequence data”, Bioinformatics, 30, 1015-1016, 2013, WOS:000334078300021 IF 2015: 5.766
27. Jia, Zhenyu; Wang, Yipeng; Hu, Yuanjie; McLaren, Christine; Yu, Yingyan; Ye, Kai; Xia, Xiao-Qin; Koziol, James A; Lernhardt, Waldemar; McClelland, Michael, “A Sample Selection Strategy to Boost the Statistical Power of Signature Detection in Cancer Expression Profile Studies”, Anti-cancer agents in medicinal chemistry, 13, 2, 203, 2013, WOS:000317848800004 IF 2015: 2.722
2012 (4)
28. 1000 Genomes Project Consortium, “An integrated map of genetic variation from 1,092 human genomes”, Nature, 491, 7422, 56-65, 2012, WOS:000310434500030 IF 2015: 38.138Highly cited top1%
29. MacArthur et. al., “A systematic survey of loss-of-function variants in human protein-coding genes”, Science, 335, 6070, 823-828, 2012, WOS:000300356400036 IF 2015: 33.611 Highly cited top1%
30. 1000 Genomes Project Consortium, “The 1000 Genomes project: data management and community access”, Nature Methods, 9, 5, 1-4, 2012, WOS:000303544800021 IF 2015: 25.328
31. Zhang, Yanju; Lameijer, Eric-Wubbo; AC't Hoen, Peter; Ning, Zemin; Slagboom, P Eline; Ye, Kai*, “PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data”, Bioinformatics, 28, 4, 479-486, 2012, WOS:000300490500005 IF 2015: 5.766
2011 (5)
32. Mills, Ryan E*; Walter, Klaudia*; Stewart, Chip*; Handsaker, Robert E*; Chen, Ken*; Alkan, Can*; Abyzov, Alexej*; Yoon, Seungtai Chris*; Ye, Kai*; Cheetham, R Keira et al., “Mapping copy number variation by population-scale genome sequencing”, Nature, 470, 7332, 59-65, 2011, WOS:000286886400033 IF 2015: 38.138 Highly cited top1%
33. Gao, Zhan-Guo; Verzijl, Dennis; Zweemer, Annelien; Ye, Kai; IJzerman, Adriaan P; Jacobson, Kenneth A, “Functionally biased modulation of A3 adenosine receptor agonist efficacy and potency by imidazoquinolinamine allosteric enhancers”, Biochemical pharmacology, 82, 6, 658-668, 2011, WOS:000294103900008 IF 2015: 5.091
34. Gomes, Ivone; IJzerman, Adriaan P; Ye, Kai; Maillet, Emeline L; Devi, Lakshmi A, “G protein-coupled receptor heteromerization: a role in allosteric modulation of ligand binding”, Molecular pharmacology, 79, 6, 1044-1052, 2011, WOS:000290673800015 IF 2015: 3.931
35. Long, Quan; Jeffares, Daniel C; Zhang, Qingrun; Ye, Kai; Nizhynska, Viktoria; Ning, Zemin; Tyler-Smith, Chris; Nordborg, Magnus, “PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing”, PloS one, 6, 1, e15292, 2011, WOS:000286511200006 IF 2015: 3.057
36. 1000 Genomes Project, “Demographic history and rare allele sharing among human populations”, Proceedings of the National Academy of Science of the United States of America, 108, 29, 11983-11988, 2011, WOS:000292876900056 IF 2015: 9.423