Publication List of Chuming Chen

Computer Science and Engineering

2013

• Update on activities at the U niversal Protein Resource (UniProt) in 2013

  The UniProt Consortium
  Nucl. Acids Res. 41 (D1): D43-D47 (2013)

2012

• Aberrant iron homeostasis, oxidative fiber enrichment, and activation of ketogenesis i n muscle tissue of ISCU Myopathy patients

  Crooks, Daniel R.; Natarajan, Thanemozhi G.; Chuming Chen; Hongzhan Huang; Ghosh, Manik C.; Wing-Hang Tong; Haller, Ronald G.; Wu, Cathy; Ro Rouault, Tracey A.
  BMC Proceedings, 6(Suppl 3):P58 doi:10.1186/1753-6561-6-S3-P58 (2012)

• Community annotation and bioinformatics workforce development in concert - Little skate genome annotation workshops and jamborees

  Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Sha llee T. Page, Marc Farnum Rendino, W. Kelley Thomas, Daniel W. Udwary, Cathy H. Wu and the North East Bioinformatics Collaborative Curation Team
  Database, doi: 10.1093/database/bar064 (2012)

• Representative Proteomes and Genomes: A standardized, stable and unbiased set of proteomes/genomes ideal for use in genome annotation, metagenom ic efforts and analyzing taxonomic nomenclature biases.

  Mona Motwani, Chuming Chen, Hongzhan Huang, Darren Natale, Jamal Theodore, Cathy H. Wu, Raja Mazumder International Biocuration Conference 2012,April 2-4, 2012.

• Community annotation and bioinformatics workforce development in concert - Little skate genome annotation workshops and jamborees

  Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Sha llee T. Page, Marc Farnum Rendino, W. Kelley Thomas, Daniel W. Udwary, Cathy H. Wu and the North East Bioinformatics Collaborative Curation Team
  International Biocuration Conference 2012,April 2-4, 2012.

2011

• Reorganizing the protein space at the Universal Protein Resource (UniProt)

  The UniProt Consortium
  Nucl. Acids Res. first published online November 18, 2011 doi:10.1093/nar/gkr98

• UniProt Knowledgebase: a hub of integrated protein data

  Michele Magrane and UniProt Consortium
  Database, Vol. 2011 published online March 29, 2011, doi:10.1093/database/bar009 (2011)

• Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

  Chuming Chen, Darren A Natale, Robert D Finn, Hongzhan Huang, Jian Zhang, Cathy H Wu, Raja Mazumder
  PLoS ONE, 6(4): e18910. doi:10.1371/journal.pone.0018910 (2011)

• Bioinformatics for Comparative Proteomics

  Cathy H. Wu and Chuming Chen (Editors)
  Methods in Molecular Biology, Vol. 694. John M. Walker (Series Editor). Humana Press. ISBN: 978-1-60761-976-5 (2011)

• Protein Bioinformatics Databases and Resources

  Chuming Chen, Hongzhan Huang and Cathy H. Wu
  In Methods in Molecular Biology, Vol. 694. Cathy H. Wu and Chuming Chen (Editors), John M. Walker (Series Editor). Humana Press. (2011)

• Ongoing and future developments at the Universal Protein Resource

  The UniProt Consortium
  Nucl. Acids R es. 39(Database issue):D214-9. Epub 2010 Nov 4 (2011).

2010

• From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase

  Ursula Hinz and The UniProt Consortium
  Cell Mol Life Sci. April, 67(7): 1049-1064. (2010)

• Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-throughput "omics" Data

  Chuming Chen, Peter B. McGarvey, Hongzhan Huang and Cathy H. Wu
  Advances in Bioinformatics. Volume 2010, Article ID 423589, 19 pages. doi:10.1155/2010/423589. (2010)

2009

• The Universal Protein Resource (UniProt) in 2010

  The UniProt Consortium
  Nucleic Acids Res. 2009, Oct 20 [Epub ahead of print] (2009)

2008

• Scalable and Efficient Management Framework for Large-scale OWL Ontologies

  Chuming Chen
  Ph.D. Dissertation, Department of Computer Science and Engineering, University of South Carolina. (2008)

• A New Approach to Managing the Evolution of OWL Ontologies

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p. 57-63. (2008)

• Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p. 76-82. (2008)

2007

• Extending Description Logic for Reasoning about Ontology Evolution

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2007 IEEE/WIC/ACM International Conference on Web Intelligence. Silicon Valley, California, USA, p. 452-456. (2007)

• Efficient and Secure Multicast in WirelessMAN: A Cross-layer Design

  Chin-Tser Huang, Manton M. Matthews, M. Ginley, Xinliang Zheng, Chuming Chen, Morris Chang
  Journal of Communications Software and Systems. Vol. 3, No. 3, p. 199-206. (2007)

• Extending Description Logic for Reasoning about Ontology Evolution

  Chuming Chen and Manton M. Matthews
  Technical Report (USC CSE TR-2007-012). (2007)

2006

• Data integration gets 'Sloppy'

  Jonas S. Almeida, Chuming Chen, Robert Gorlitsky, Romesh Stanislaus, Marta Aires-de-Sousa, Pedro Eleuterio, Joao. Carrico, Antonio Maretzek, Andreas Bohn, Allen Chang, Fan Zhang, Rahul Mitra, Gordon B. Mills, Xiaoshu Wang, Helena F. Deus
  Nature Biotechnology, (9):1070-1071. (2006)

2005

• AGML Central: web based gel proteomic infrastructure

  Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, and Jonas S. Almeida
  Bioinformatics, Vol. 21, 1754-1757. (2005)

• Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

  David J. McKillen, Yian A. Chen, Chuming Chen, Matthew J. Jenny, Harold F. Trent III, Javier Robalino, David C. McLean Jr., Paul S. Gross, Robert W. Chapman, Gregory W. Warr and Jonas S. Almeida
  BMC Genomics, 6:34. (2005)

• A Dual Authentication Protocol for IEEE 802.11 Wireless LANs

  Xinliang Zheng, Chuming Chen, Chin-Tser Huang, Manton M. Matthews, Naveen Santhapuri
  In Proceedings of the 2nd International Symposium on Wireless Communication Systems. p. 565-569. (2005)

2004

• A Web Interface for Nessus Network Security Scanner

  Chuming Chen and Manton M. Matthews
  In Proceedings of the International Conference on Internet Computing, Hamid R. Arabnia and Olaf Droegehorn (editors), Las Vegas, Nevada, USA, p. 383-389. (2004)

• A Dual Authentication Protocol for Wireless LANs

  Chuming Chen, Xinliang Zheng, Chin-Tser Huang, and Manton M. Matthews
  Technical Report (USC CSE TR-2004-006). (2004)

2003

• A Web Interface for Nessus Network Security Scanner

  Chuming Chen
  M.S. Thesis, Department of Computer Science and Engineering, University of South Carolina. (2003)

Earth Science

2002

• The Crustal Shortening and Its Timing of Kuqa Rejuvenation Foreland Deformation Belt and its Implication on the Coupling Mechanism of the Basin Depression and Mountains Building in North Flank of Tarim Basin and south foothill of Tianshan Mountains, China

  Lu Huafu, Jia Dong, Jia Chengzao, Wang Shenli, Yin Donghao, Liu Zhihong, Chen Chuming, J. Suppe, A. Hubert Ferarri
  In Proceedings of International symposium on Chinese petroleum exploration in 21st centrury, Hanzhou. (2002)

2001

• Features of the thrust wedge of deformation belt in Kuqa rejuvenation foreland basin

  Lu Huafu, Jia Chenzhao, Jia Dong, Chen Chuming, Liu Zhihong, Wang Guoqiang and Wang Shengli.
  Geological Journal of China Universities, Vol. 7, No. 3, p. 257 - 271. (in Chinese with English abstract). (2001)

2000

• Tectonic Evolutin of Kuqa Rejuventated Foreland Basin

  Liu Zhihong, Lu Huafu, Li Xijian, Jia Chengzao, Lei Ganglin, Chen Chuming, Wang Guoqiang, Fan Xiangtao
  Chinese Journal of Geology, Vol. 35, No. 4, p. 482-492. (in Chinese with English abstract). (2000)

• Structural characteristics and genesis of thrust belt of Kuqa rejuvenation foreland basin

  Lu Huafu, Chen Chuming, Liu Zhihong, Jia Dong, Wang Guoqiang and Jia Chengzhao
  Acta Petrolei Sinica, Vol. 21, No. 3, p. 18 -24. (in Chinese with English abstract). (2000)

• Geometry, Kinematics and Origin of Kuche Rejuvenated Foreland Thrust Belt on the Northern Flank of Tarim Basin

  Chuming Chen
  Ph.D. Dissertation, Department of Earth Sciences, Nanjing University, P. R. China. (in Chinese with English abstract). (2000)

1999

• Nature and timing of the Kuqa Cenozoic structures

  Lu Huafu, Jia Dong, Chen Chuming, Liu Zhihong, Wang Guoqiang and Jia Chenzhao
  Earth Science Frontiers, Vol. 6, No. 4, p. 215 - 221. (in Chinese with English abstract). (1999)

• Closing history of the southern TianShan oceanic basin, Western China: an oblique collisional orogeny

  Chuming Chen, Huafu Lu, Dong Jia, Dongsheng Cai and Shimin Wu
  Tectonophysics, Vol. 302, No. 1-2, p. 23-40. (1999).

• Structures and petroleum accumulation in the Qiulitage thrust front of the Kuqa rejuvenated foreland fold thrust belt on the northern margin of the Tarim basin

  Chen Chuming, Lu Huafu, Jia Dong, Jia Chengzao
  Geological Review, Vol.45, No. 4, p. 423-433. (in Chinese with English abstract) (1999)

1998

• Neogene-Quaternary sedimentary features,structural deformation of the Tarim basin and its petroleum geological significance

  Chen Chuming, Lu Huafu, Jia Dong and Xie Xiaoan
  Acta Sedimentologica Sinica, Vol.16, No.2, p. 113-116. (in Chinese with English abstract)(1998)

• Analyses of superimposed structures in the north Tarim uplift, Tarim basin

  Chen Chuming, Lu Huafu, Wang Guoqiang, Jia Dong and Cai Dongsheng
  Geological Journal of China Universities, Vol. 4, No. 3, p. 294-302. (in Chinese with English abstract)(1998)

• Structural features of northern Tarim basin: implications for regional tectonics and petroleum traps

  Jia Dong, Lu Huafu, Cai Dongsheng, Wu Shimin, Shi Yangshen, Chen Chuming
  AAPG Bulletin, Vol. 82, No. 1, p. 147-159. (1998).

1997

• Arithmetic method in polar stereograhoc projection

  Qian Hui, Dong Huogeng and Chen Chuming
  Geological Journal of China Universities, Vol. 3, No. 3, p. 328-337. (in Chinese with English abstract). (1997)

• Evidence for growth fault-bend folds in the Tarim basin and its implication for fault-slip rates in the Mesozoic and Cenozoic

  Huafu Lu, Dong Jia, Chuming Chen, Dongsheng Cai, Guoqiang Wang, LinZhi Guo and Yangshen Shi
  In Proceedings of 30th International Geological Congress, Vol. 14, p. 253-262. (1997)

• A new model deduced from Kalpin transpression tectonics and its implications to the Tarim basin

  Huafu Lu, Dong Jia, Chuming Chen, Dongsheng Cai, Shimin Wu, Guoqiang Wang, Linzhi Guo, Yangshen Shi, David Gardiner Howell
  In Proceedings of 30th International Geological Congress, Vol. 14, p. 196-202. (1997)

1996

• Origin and evolution of tectonics in central Asia

  Shi Yangshen, Lu Huafu, Jia Dong, Chen Chuming, Cai Dongsheng and Wu Shimin
  Geological Journal of Universities, Vol. 2, No. 2, p. 134-145. (in Chinese with English abstract). (1996)

• 40Ar/39Ar dating of the ophilite melange in Southern Tianshan the the Mylonite in the Southern rim of center Tianshan and their tectonic significance

  Cai Dongsheng, Lu Huafu, Jia Dong, Wu Shimin and Chen Chuming
  Scientia Geologica Sinica, Vol. 34, No. 4, 384-390. (in Chinese with English abstract). (1996)

1995

• Paleozoic plate-tectonic evolution of the Tarim and western Tianshn regions, western China

  Shi Yangshen, Lu Huafu, Jia Dong, Cai Dongsheng, Wu Shimin, Chen Chuming, Howell G. David, Valin C. Zenon
  International Geology Review, Vol. 36, No. 11, p. 1058-1066. (1995).

1994

• Rejuvenation of the Kuqa foreland basin, Northern flank of the Tarim basin, Northwestern China

  Lu Huafu, David G. Howell, Jia Dong, Cai Dongsheng, Wu Shiming, Chen Chuming, Shi Yangshen, Zenon C. Valin
  International Geology Review, Vol. 36, No. 10, p. 1151-1158. (1994).

• Kalpin transpression tectonics, northwestern Tarim basin, western China

  Lu Huafu, Howell G. David, Jia Dong, Cai Dongsheng, Wu Shimin, Chen Chuming, Shi Yangshen, Valin C. Zenon, Guo LinZhi
  International Geology Review, Vol. 36, No. 10, p. 975-981. (1994).

• Structural and Petroleum Geology of Kepin, Kuche and Yinmaili on the Northern Flank of Tarim Basin

  Chuming Chen
  B.S. Thesis, Department of Earth Sciences, Nanjing University, P. R. China. (in Chinese). (1994)