Publication List of Chuming Chen

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Bioinformatics and Computational Biology

  1. KSFinder—a knowledge graph model for link prediction of novel phosphorylated substrates of kinases

    Manju Anandakrishnan, Karen E. Ross, Chuming Chen, Vijay Shanker, Julie Cowart, Cathy H. Wu
    PeerJ, 2023, 11:e16164, DOI:https://doi.org/10.7717/peerj.16164

  2. UniProt: the Universal Protein Knowledgebase in 2023

    UniProt consortium
    Nucleic Acid Research Volume 51, Issue D, https://doi.org/10.1093/nar/gkac1052

  3. A knowledge graph representation learning approach to predict novel kinase–substrate interactions

    Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart and Cathy H. Wu
    Molecular Omics, 2022, DOI: 10.1039/D1MO00521A

  4. iPTMnet RESTful API for Post-translational Modification Network Analysis

    Sachin Gavali, Karen E. Ross, Julie Cowart, Chuming Chen & Cathy H. Wu
    In: KC, D.B. (eds) Computational Methods for Predicting Post-Translational Modification Sites. Methods in Molecular Biology, vol 2499. Humana, New York, NY. (2022) DOI: https://doi.org/10.1007/978-1-0716-2317-6_10

  5. COVID-19 knowledge graph from semantic integration of biomedical literature and databases

    Chuming Chen, Karen E Ross, Sachin Gavali, Julie E Cowart, Cathy H Wu
    Bioinformatics, btab694, Published: 06 October 2021

  6. UniProt: the universal protein knowledgebase in 2021

    UniProt consortium
    Nucleic Acid Research Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100

  7. Protein ontology on the semantic web for knowledge discovery

    Chuming Chen, Hongzhan Huang, Karen E. Ross, Julie E. Cowart, Cecilia N. Arighi, Cathy H. Wu & Darren A. Natale
    Scientific Data volume 7, Article number: 337 (2020)

  8. Understanding ER+ Breast Cancer Dormancy Using Bioinspired Synthetic Matrices for Long‐Term 3D Culture and Insights into Late Recurrence

    Elisa M. Ovadia, Lina Pradhan, Lisa A. Sawicki, Julie E. Cowart, Rebecca E. Huber, Shawn W. Polson, Chuming Chen, Kenneth L. van Golen, Karen E. Ross, Cathy H. Wu, April M. Kloxin
    Advanced Biosystems, First published:30 June 2020 https://doi.org/10.1002/adbi.202000119

  9. piNET: a versatile web platform for downstream analysis and visualization of proteomics data

    Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Wen Niu, Chuming Chen,Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dušica Vidović, Jake Jaffe, Michael MacCoss, Cathy Wu, Ajay Pillai, Avi Ma’ayan, Stephan Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
    Nucleic Acids Research, gkaa436, https://doi.org/10.1093/nar/gkaa436. Published: 29 May 2020

  10. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

    Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra Orchard, Andrea H Auchincloss, Delphine Baratin, Jerven Bolleman, Elisabeth Coudert, Edouard de Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C R Vinayaka, Lai-Su Yeh, Darren A Natale, Kati Laiho, Maria Martin, UniProt Consortium
    Bioinformatics, btaa485, https://doi.org/10.1093/bioinformatics/btaa485

  11. RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

    Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross, Cecilia Arighi, Cathy H Wu
    Database, Volume 2020, 2020, baz157, https://doi.org/10.1093/database/baz157. Published: 12 May 2020

  12. FAIR adoption, assessment and challenges at UniProt

    Leyla Garcia, Jerven Bolleman, Sebastien Gehant, Nicole Redaschi, Maria Martin & UniProt Consortium
    Scientific Data, volume 6, Article number: 175 (2019), PMCID: PMC6754384

  13. Genome sequencing and transcript a nalysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility

    Brenda Neves Porto, Eveline Teixeira Caixeta , Sandra Marisa Mathioni, Pedro Marcus Pereira Vidigal, Laércio Zambolim, Eunize Maciel Zambolim, Nicole Donofrio, Shawn W. Polson, Thiago Andrade Maia, Chuming Chen, Modupe Adetunji, Brewster Kingham, Ronaldo José Durigan Dalio, Mário Lúcio Vilela de Resende
    PLoS One. 2019 Apr 18;14(4):e0215598. doi: 10.1371/journal.pone.0215598. eCollection 2019. PMID: 30998802

  14. PIRSitePredict for protein functional site prediction using position-specific rules

    Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R Vinayaka, John S Garavelli, Cecilia N Arighi, Darren A Natale, Cathy H Wu
    Database, Volume 2019, 1 January 2019, baz026, https://doi.org/10.1093/database/baz026.

  15. UniProt: a worldwide hub of protein knowledge

    UniProt Consortium
    Nucleic Acides Res. 2018, Nov 5. doi: 10.1093/nar/gky1049.

  16. Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

    Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang and Haro ld B. White III
    BMC Genomics 2018, 19:695. https://doi.org/10.1186/s12864-018-5080-4.

  17. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

    Liang-Chin Huang, Karen E. Ross, Timothy R. Baffi, Harold Drabkin, Krzysztof J. Kochut, Zheng Ruan, Peter D’Eustachio , Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A. Natale, Cynthia Smith, Pascale Gaudet, Alexandra C. Newton, Cathy Wu & Natarajan Kannan
    Scientific Reports volume 8, Article number: 6518 (2018) doi:10.1038/s41598-018-24457-1

  18. Protein Bioinformatics Databases and Resources

    Chuming Chen, Hongzhan Huang, Cathy H. Wu
    Methods in Molecular Biology Voulme: 1558, pp. 3-39. doi: 10.1007/978-1-4939-6783-4_1 published February 02, 2017

  19. UniProt: the universal protein knowledgebase

    The UniProt Consortium
    Nucl. Acids Res. doi: 10.1093/nar/gkw1099 First published online: November 29, 2016

  20. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

    Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH
    Nucleic Acids Res 2016 Nov 28. pii: gkw1075. [Epub ahead of print]

  21. Computational Clus tering for Viral Reference Proteomes

    Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu and UniProt Consortium
    Bioinformatics 2016. doi: 10.1093/bioinformatics/btw110

  22. RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

    Christopher W. Resnyk, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Jean Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos and Larry A. Cogburn
    PLoS ONE 2015. 10(10): e0139549. doi:10.1371/journal.pone.0139549

  23. An Integrated Approach for Analyzing Clinical Genomi c Variant Data from Next-Generation Sequencing

    Erin L. Crowgey, Deborah L. Stabley, Chuming Chen, Hongzhan Huang, Katherine M. Robbins, Shawn W. Polson, Katia Sol-Church, Cathy H. Wu
    J Biomol Tech. 2015 Apr : jbt.15-2601-002. Published online 2015 Jan 29. doi: 10.7171/jbt.15-2601-002, PMCID: PMC4310222

  24. UniProt: a hub for protein information

    The UniProt Consortium
    Nucl. Acids Res. doi: 10.1093/nar/gku989 First published online: October 27, 2014

  25. SkateBase, an elasmobranch genome project and collection of mol ecular resources for chondrichthyan fishes

    Jennifer Wyffels, Benjamin L. King, James Vincent, Chuming Chen, Cathy H. Wu, Shawn W. Polson
    F1000Research 2014, 3:191 (doi: 10.12688/f1000research.4996.1)

  26. Software for pre-processing Illumina next-generation sequencing short read sequences

    Chuming Chen, Sari S Khaleel, Hongzhan Huang and Cathy H Wu
    Source Code for Biology and Medicine 2014, 9:8, doi:10.1186/1751-0473-9-8

  27. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

    Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K; UniProt Consortium
    Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016

  28. Activities at the Universal Protein Resource (UniProt)

    The UniProt Consortium
    Nucl. Acids Res. first published online November 18, 2013 doi:10.1093/nar/gkt1140

  29. A fast Peptide Match Service for UniProt Knowledgebase

    Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu, and UniProt Consortium
    Bioinformatics, first published online August 19, 2013 doi:10.1093/bioinformatics/btt484 (2013)

  30. Elevated FGF21 secretion, PGC-1α and ketogenic enzyme expression are hallmarks of iron-sulfur cluster depletion in human skeletal muscle

    Daniel R. Crooks, Thanemozhi G. Natarajan, Suh Young Jeong, Chuming Chen, Sun Young Park, Hongzhan Huang, Manik C. Ghosh, Wing-Hang Tong, Ronald G. Haller, Cathy Wu, and Tracey A. Rouault
    Hum. Mol. Genet. first published online August 13, 2013 doi:10.1093/hmg/ddt393 (2013)

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

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

  32. Community annotation and bioinformatics workforce development in concert - Little skate genome ann otation workshops and jamborees

    Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnu m 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)

  33. 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

  34. 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)

  35. 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)

  36. 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)

  37. 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)

  38. 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).

  39. 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)

  40. 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)

  41. The Universal Protein Resource (UniProt) in 2010

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

  42. 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)

  43. 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)

  44. 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)


Semantic Web, Description Logics, Ontology Engineering

  1. 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)

  2. 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)

  3. 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)

  4. 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)

  5. Extending Description Logic for Reasoning about Ontology Evolution

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


Network Security

  1. 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)

  2. 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)

  3. 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)

  4. 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)

  5. A Web Interface for Nessus Network Security Scanner

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


Petroleum Geology, Structural Geology, Geophysics

  1. 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)

  2. 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)

  3. 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)

  4. 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)

  5. 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)

  6. 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)

  7. 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).

  8. 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)

  9. 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)

  10. 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)

  11. 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).

  12. 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)

  13. 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)

  14. 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)

  15. 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)

  16. 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)

  17. 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).

  18. 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).

  19. 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).

  20. 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)