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Faculty
Philip E. Bourne
Stephenson Dean
School of Data Science
Additional Roles
Professor
Department of Biomedical Engineering
Email: peb6a@virginia.edu
Phone: (434) 924-6867
Additional Contact Information
Website: pebourne.wordpress.com/
Office: 1919 Ivy Rd., Rm. 233
Philip E. Bourne is the founding dean of the School of Data Science, the newest and 12th School to be formed in the University’s 200 year history. He is a world renowned biomedical and data science researcher who has published over 300 papers and five books, launched four companies, received numerous awards, and been elected as fellow to multiple scientific societies. He was the first Associate Vice Chancellor for Innovation and Industrial Alliances at the University of California San Diego and the first Associate Director for Data Science at the National Institutes of Health.
As Dean of the School of Data Science, Bourne is leading an effort to create a new kind of school—a school without walls—guided by common goals: to further discovery, share knowledge, and make a positive impact on society through collaborative, open, and responsible data science research and education. Founded in 2019 through a $120 million gift, the largest in UVA history, the School is positioned to play an integral leadership role in the global digital future. Focusing on interdisciplinary, collaborative research and education, the School joins other departments across UVA, the community, industry, government, and non-profit organizations to use data science to further discovery and make a positive impact on society.
Showing 3 of 3 results
Deep learning meets biology
MSDS student project applies data science tools and techniques to understand 3D protein structures
Analyzing social media to assess extremist group threats
MSDS 2018 Cohort students Kia Duan, Nitesh Prakash, Duncan Rule and Ni Zhuang worked to create a program that could more accurately assess threat levels from rallies and protests led by extremist groups.
How Can Societies Cope in Water-Scarce Environments?
Analyzing how the global trade of food makes societies less reliant on locally available water resources
Selected Publications
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. doi:10.1093/nar/28.1.235
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1), 160018. doi:10.1038/sdata.2016.18
Shindyalov, I. N., & Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering, 11(9), 739–747. doi:10.1093/protein/11.9.739
Ponomarenko, J., Bui, H.-H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1), 514. doi:10.1186/1471-2105-9-514
Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., … Bourne, P. E. (2011). The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database issue), D392-401. doi:10.1093/nar/gkq1021
Günther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., … Preissner, R. (2008). SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research, 36(Database issue), D919-22. doi:10.1093/nar/gkm862
Bourne, Philip E., & Weissig, H. (2003). Structural Bioinformatics (Philip E. Bourne & H. Weissig, Reds). doi:10.1002/0471721204
Rose, P. W., Prlić, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., … Burley, S. K. (2015). The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Research, 43(Database issue), D345-56. doi:10.1093/nar/gku1214
Rose, P. W., Bi, C., Bluhm, W. F., Christie, C. H., Dimitropoulos, D., Dutta, S., … Bourne, P. E. (2013). The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Research, 41(Database issue), D475-82. doi:10.1093/nar/gks1200
Deshpande, N., Addess, K. J., Bluhm, W. F., Merino-Ott, J. C., Townsend-Merino, W., Zhang, Q., … Bourne, P. E. (2005). The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Research, 33(Database issue), D233-7. doi:10.1093/nar/gki057
Kim, Y., Ponomarenko, J., Zhu, Z., Tamang, D., Wang, P., Greenbaum, J., … Peters, B. (2012). Immune epitope database analysis resource. Nucleic Acids Research, 40(Web Server issue), W525-30. doi:10.1093/nar/gks438
Moreland, J. L., Gramada, A., Buzko, O. V., Zhang, Q., & Bourne, P. E. (2005). The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics, 6, 21. doi:10.1186/1471-2105-6-21
Kinnings, S. L., Liu, N., Buchmeier, N., Tonge, P. J., Xie, L., & Bourne, P. E. (2009). Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Computational Biology, 5(7), e1000423. doi:10.1371/journal.pcbi.1000423
Kouranov, A., Xie, L., de la Cruz, J., Chen, L., Westbrook, J., Bourne, P. E., & Berman, H. M. (2006). The RCSB PDB information portal for structural genomics. Nucleic Acids Research, 34(Database issue), D302-5. doi:10.1093/nar/gkj120
Westbrook, J., Feng, Z., Jain, S., Bhat, T. N., Thanki, N., Ravichandran, V., … Berman, H. M. (2002). The Protein Data Bank: unifying the archive. Nucleic Acids Research, 30(1), 245–248. doi:10.1093/nar/30.1.245
Scheeff, E. D., & Bourne, P. E. (2005). Structural evolution of the protein kinase-like superfamily. PLoS Computational Biology, 1(5), e49. doi:10.1371/journal.pcbi.0010049
Zhang, Q., Wang, P., Kim, Y., Haste-Andersen, P., Beaver, J., Bourne, P. E., … Peters, B. (2008). Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Research, 36(Web Server issue), W513-8. doi:10.1093/nar/gkn254
Xie, Li, Li, J., Xie, L., & Bourne, P. E. (2009). Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Computational Biology, 5(5), e1000387. doi:10.1371/journal.pcbi.1000387
Dupont, C. L., Butcher, A., Valas, R. E., Bourne, P. E., & Caetano-Anollés, G. (2010). History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proceedings of the National Academy of Sciences of the United States of America, 107(23), 10567–10572. doi:10.1073/pnas.0912491107
Xie, Lei, & Bourne, P. E. (2008). Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proceedings of the National Academy of Sciences of the United States of America, 105(14), 5441–5446. doi:10.1073/pnas.0704422105
Ponomarenko, J. V., & Bourne, P. E. (2007). Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Structural Biology, 7(1), 64. doi:10.1186/1472-6807-7-64
Yang, S., Doolittle, R. F., & Bourne, P. E. (2005). Phylogeny determined by protein domain content. Proceedings of the National Academy of Sciences of the United States of America, 102(2), 373–378. doi:10.1073/pnas.0408810102
Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D., & Fitzgerald, P. M. (1997). Macromolecular crystallographic information file. Methods in Enzymology, 277, 571–590. doi:10.1016/s0076-6879(97)77032-0
Dupont, C. L., Yang, S., Palenik, B., & Bourne, P. E. (2006). Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proceedings of the National Academy of Sciences of the United States of America, 103(47), 17822–17827. doi:10.1073/pnas.0605798103
Costello, M. J., Michener, W. K., Gahegan, M., Zhang, Z.-Q., & Bourne, P. E. (2013). Biodiversity data should be published, cited, and peer reviewed. Trends in Ecology & Evolution, 28(8), 454–461. doi:10.1016/j.tree.2013.05.002
von Eichborn, J., Murgueitio, M. S., Dunkel, M., Koerner, S., Bourne, P. E., & Preissner, R. (2011). PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Research, 39(Database issue), D1060-6. doi:10.1093/nar/gkq1037
Chang, R. L., Xie, L., Xie, L., Bourne, P. E., & Palsson, B. Ø. (2010). Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Computational Biology, 6(9), e1000938. doi:10.1371/journal.pcbi.1000938
Prlić, A., Yates, A., Bliven, S. E., Rose, P. W., Jacobsen, J., Troshin, P. V., … Willis, S. (2012). BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (Oxford, England), 28(20), 2693–2695. doi:10.1093/bioinformatics/bts494
Prlic, A., Bliven, S., Rose, P. W., Bluhm, W. F., Bizon, C., Godzik, A., & Bourne, P. E. (2010). Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (Oxford, England), 26(23), 2983–2985. doi:10.1093/bioinformatics/btq572
Xie, Lei, Xie, L., Kinnings, S. L., & Bourne, P. E. (2012). Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annual Review of Pharmacology and Toxicology, 52(1), 361–379. doi:10.1146/annurev-pharmtox-010611-134630
Hecker, N., Ahmed, J., von Eichborn, J., Dunkel, M., Macha, K., Eckert, A., … Preissner, R. (2012). SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Research, 40(Database issue), D1113-7. doi:10.1093/nar/gkr912
Xie, Li, Evangelidis, T., Xie, L., & Bourne, P. E. (2011). Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Computational Biology, 7(4), e1002037. doi:10.1371/journal.pcbi.1002037
Kinnings, S. L., Liu, N., Tonge, P. J., Jackson, R. M., Xie, L., & Bourne, P. E. (2011). A machine learning-based method to improve docking scoring functions and its application to drug repurposing. Journal of Chemical Information and Modeling, 51(2), 408–419. doi:10.1021/ci100369f
Xie, Lei, & Bourne, P. E. (2007). A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics, 8 Suppl 4(S4), S9. doi:10.1186/1471-2105-8-S4-S9
Reference Genome Group of the Gene Ontology Consortium. (2009). The Gene Ontology’s Reference Genome Project: a unified framework for functional annotation across species. PLoS Computational Biology, 5(7), e1000431. doi:10.1371/journal.pcbi.1000431
Bourne, Philip E., Addess, K. J., Bluhm, W. F., Chen, L., Deshpande, N., Feng, Z., … Berman, H. M. (2004). The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Research, 32(Database issue), D223-5. doi:10.1093/nar/gkh096
Xie, Lei, Xie, L., & Bourne, P. E. (2011). Structure-based systems biology for analyzing off-target binding. Current Opinion in Structural Biology, 21(2), 189–199. doi:10.1016/j.sbi.2011.01.004
Guda, Chittibabu, Lu, S., Scheeff, E. D., Bourne, P. E., & Shindyalov, I. N. (2004). CE-MC: a multiple protein structure alignment server. Nucleic Acids Research, 32(Web Server issue), W100-3. doi:10.1093/nar/gkh464
Zhang, P., Schon, E. A., Fischer, S. G., Cayanis, E., Weiss, J., Kistler, S., & Bourne, P. E. (1994). An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Computer Applications in the Biosciences : CABIOS, 10(3), 309–317. doi:10.1093/bioinformatics/10.3.309
Bourne, Philip. (2005). Will a biological database be different from a biological journal? PLoS Computational Biology, 1(3), 179–181. doi:10.1371/journal.pcbi.0010034
Bhat, T. N., Bourne, P., Feng, Z., Gilliland, G., Jain, S., Ravichandran, V., … Berman, H. M. (2001). The PDB data uniformity project. Nucleic Acids Research, 29(1), 214–218. doi:10.1093/nar/29.1.214
Berg, J. M., Bhalla, N., Bourne, P. E., Chalfie, M., Drubin, D. G., Fraser, J. S., … Wolberger, C. (2016). Preprints for the life sciences. Science (New York, N.Y.), 352(6288), 899–901. doi:10.1126/science.aaf9133
Ullmann, G. Matthias, Hauswald, M., Jensen, A., & Knapp, E.-W. (2000). Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem I and ferredoxin‐NADP reductase. Proteins, 38(3), 301–309. doi:10.1002/(sici)1097-0134(20000215)38:3<301::aid-prot6>3.3.co;2-p
Pandya, M. J., Sessions, R. B., Williams, P. B., Dempsey, C. E., Tatham, A. S., Shewry, P. R., & Clarke, A. R. (2000). Structural characterization of a methionine-rich, emulsifying protein from sunflower seed. Proteins, 38(3), 341–349. doi:10.1002/(sici)1097-0134(20000215)38:3<341::aid-prot9>3.0.co;2-d
Pandya, Maya J., Sessions, R. B., Williams, P. B., Dempsey, C. E., Tatham, A. S., Shewry, P. R., & Clarke, A. R. (2000). Structural characterization of a methionine‐rich, emulsifying protein from sunflower seed. Proteins, 38(3), 341–349. doi:10.1002/(sici)1097-0134(20000215)38:3<341::aid-prot9>3.3.co;2-4
Ullmann, G. M., Hauswald, M., Jensen, A., & Knapp, E. W. (2000). Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: implications for their interactions with photosystem I and ferredoxin-NADP reductase. Proteins, 38(3), 301–309. doi:10.1002/(sici)1097-0134(20000215)38:3<301::aid-prot6>3.0.co;2-y
García, Angel E., & Hummer, G. (2000). Water penetration and escape in proteins. Proteins, 38(3), 261–272. doi:10.1002/(sici)1097-0134(20000215)38:3<261::aid-prot3>3.3.co;2-h
Parchment, Oswald G., & Essex, J. W. (2000). Molecular dynamics of mouse and Syrian hamster PrP: Implications for activity. Proteins, 38(3), 327–340. doi:10.1002/(sici)1097-0134(20000215)38:3<327::aid-prot8>3.3.co;2-7
Shindyalov, I. N., & Bourne, P. E. (2000). An alternative view of protein fold space. Proteins, 38(3), 247–260. doi:10.1002/(sici)1097-0134(20000215)38:3<247::aid-prot2>3.0.co;2-t
Shindyalov, Ilya N., & Bourne, P. E. (2000). An alternative view of protein fold space. Proteins, 38(3), 247–260. doi:10.1002/(sici)1097-0134(20000215)38:3<247::aid-prot2>3.3.co;2-k
García, A. E., & Hummer, G. (2000). Water penetration and escape in proteins. Proteins, 38(3), 261–272. doi:10.1002/(sici)1097-0134(20000215)38:3<261::aid-prot3>3.0.co;2-q
Glick, M., & Goldblum, A. (2000). A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays. Proteins, 38(3), 273–287. doi:10.1002/(sici)1097-0134(20000215)38:3<273::aid-prot4>3.0.co;2-i
Samanta, Uttamkumar, Pal, D., & Chakrabarti, P. (2000). Environment of tryptophan side chains in proteins. Proteins, 38(3), 288–300. doi:10.1002/(sici)1097-0134(20000215)38:3<288::aid-prot5>3.3.co;2-z
Denessiouk, Konstantin A., & Johnson, M. S. (2000). When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins, 38(3), 310–326. doi:10.1002/(sici)1097-0134(20000215)38:3<310::aid-prot7>3.3.co;2-k
Parchment, O. G., & Essex, J. W. (2000). Molecular dynamics of mouse and Syrian hamster PrP: implications for activity. Proteins, 38(3), 327–340. doi:10.1002/(sici)1097-0134(20000215)38:3<327::aid-prot8>3.0.co;2-g
Denessiouk, K. A., & Johnson, M. S. (2000). When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins, 38(3), 310–326. doi:10.1002/(sici)1097-0134(20000215)38:3<310::aid-prot7>3.0.co;2-t
Gatto, G. J., Jr, Geisbrecht, B. V., Gould, S. J., & Berg, J. M. (2000). A proposed model for the PEX5-peroxisomal targeting signal-1 recognition complex. Proteins, 38(3), 241–246. doi:10.1002/(sici)1097-0134(20000215)38:3<241::aid-prot1>3.0.co;2-1
Glick, Meir, & Goldblum, A. (2000). A novel energy‐based stochastic method for positioning polar protons in protein structures from X‐rays. Proteins, 38(3), 273–287. doi:10.1002/(sici)1097-0134(20000215)38:3<273::aid-prot4>3.3.co;2-9
Samanta, U., Pal, D., & Chakrabarti, P. (2000). Environment of tryptophan side chains in proteins. Proteins, 38(3), 288–300. doi:10.1002/(sici)1097-0134(20000215)38:3<288::aid-prot5>3.0.co;2-7
Meng, G. U. O., 天津工业大学 生命科学学院，天津 300387, School of Life Sciences, Tianjin Polytechnic University, Tianjin 300387, China, Xinming, D., Guang, H. A. N., Huiquan, W., … ECHOEY Technology (Tianjin) Co., Ltd., Tianjin 300308, China. (2021). Research on accurate detection method of egg embryo activity based on convolutional neural network. Yingyong Guangxue (Journal of Applied Optics), 42(2), 268–275. doi:10.5768/jao202142.0202003
Yiqing, C. A. O., 莆田学院 机电工程学院，福建 莆田 351100, School of Mechanical and Electrical Engineering, Putian University, Putian 351100, 福建省激光精密加工工程技术研究中心，福建 莆田 351100, & Fujian Laser Precision Machining Engineering Technology Research Center, Putian 351100, China. (2021). Design of catadioptric panoramic optical imaging system with ultra-large field of view. Yingyong Guangxue (Journal of Applied Optics), 42(4), 608–613. doi:10.5768/jao202142.0401006
Quidu, M. (2023). Hadjeras, Stéphane (2021). Georges Carpentier : l’incroyable destin d’un boxeur devenu star. Préface de Georges Vigarello. Paris, Nouveau Monde, 344 p. Staps, Prépublication(0), I41-8. doi:10.3917/sta.pr1.0041
Philippe, M. (2023). Laurence Munoz, Yves Morales et Yohann Fortune (dir.), L’implication sociale du mouvement sportif associatif : la FSCF entre permanence et mutations. Lille : Septentrion, 2021, 300 p. Staps, Prépublication(0), I46-3. doi:10.3917/sta.pr1.0046
Desfontaine, P. (2023). Ludovic Tenèze, VAR ? Le miroir aux alouettes. Préface de Clément Turpin. Paris : Les Éditions du Panthéon, 2021, 306 p. Staps, Prépublication(0), I42-4. doi:10.3917/sta.pr1.0042
Árpádffy-Lovas, T., Naveed, M., Mohammed, A. S. A., Virág, L., Baczkó, I., & Varró, A. (2022). Species dependent cardiac electrophysiological effects elicited by various potassium channel blocking drugs. The Journal of General Physiology, 154(9). doi:10.1085/jgp.2021ecc2
Falcón, D., Mayoral, I., Ordóñez, A., & Smani, T. (2022). Implication of CREB in the calcium regulation by ischemia/reperfusion in cardiomyocytes. The Journal of General Physiology, 154(9). doi:10.1085/jgp.2021ecc7
Harraz, O. F., Klug, N. R., Senatore, A., Koide, M., & Nelson, M. T. (2022). Piezo1 is a mechanosensor channel in CNS capillaries. The Journal of General Physiology, 154(9). doi:10.1085/jgp.2021ecc12
Idoux, R., Berthier, C., Jacquemond, V., & Allard, B. (2022). Recordings of action potentials, charge movements, and sarcoplasmic reticulum Ca2+ release in isolated adult zebrafish fast skeletal muscle fibers reveals very fast kinetics of excitation-contraction coupling. The Journal of General Physiology, 154(9). doi:10.1085/jgp.2021ecc14
Ma, R., Haji-Ghassemi, O., Ma, D., Jiang, H., Lin, L., Xu, T., … Yuchi, Z. (2022). Structural basis for diamide modulation of ryanodine receptor. The Journal of General Physiology, 154(9). doi:10.1085/jgp.2021ecc17
LG Wiesbaden, Urt. v. 11.7.2019 – 2 O 247/18. (2021). Verstoß gegen die ärztliche Schweigepflicht: Versendung einer Rechnung über Behandlung mit Botox-Spritzen über Arbeitgeber der Behandelten. Medizinrecht: MedR, 39(5), 474–477. doi:10.1007/s00350-021-5888-9
Jamali, M. M., School of Agricultural Sciences, Glocal University, Saharanpur 247121, Uttar Pradesh, India, Zeya, S. B., & Department of Zoology, Aligarh Muslim University, Aligarh 202 002, Uttar Pradesh, India. (2021). First record of the genus Zaommomentedon Girault, 1915 (Hymenoptera: Eulophidae) from India, with description of a new species. Far Eastern entomologist, 428, 1–7. doi:10.25221/fee.428.1
Soni, Y. P., Electrical Engineering Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India., & Fernandez, E. (2021). DC Motor Load performance in DC system with reconfiguration of PV Array. Indian journal of science and technology, 14(11), 964–970. doi:10.17485/ijst/v14i11.2197
Majeed, M., Jamali, M. M., Jabbar Mir, S., School of Agricultural Sciences, Glocal University, Saharanpur 247 121, Uttar Pradesh, India., School of Agricultural Sciences, Glocal University, Saharanpur 247 121, Uttar Pradesh, India., & School of Agricultural Sciences, Glocal University, Saharanpur 247 121, Uttar Pradesh, India. (2021). Taxonomic study of Indian species of the genus Entedon Dalman (Hymenoptera: Chalcidoidea: Eulophidae), with description of two new species. Journal of Insect Biodiversity and Systematics, 7(1), 75–93. doi:10.52547/jibs.7.1.75
Khatri, D. R., Senior ENT & Head Neck Oncologist, YPV Trainer & Healer 247, Vikram Tower Sapna Sangeeta Rd, Indore(M.P.), India.-452007, Bembalkar, M. S., Nanduri, D. V. S., Technical officer(B) ICMR National AIDS Research Institute, Pune, India., & Research & Publications, Yoga Prana Vidya ashram, Sri Ramana Trust, Thally PIN 635118, Tamilnadu, India. (2021). A Pilot Study of the effects of Yoga Prana Vidya (YPV) protocols on social behaviour, cognitive abilities and IQ of mentally challenged children. Pediatric Review International Journal of Pediatric Research, 8(1), 7–15. doi:10.17511/ijpr.2021.i01.02
Raghuvanshi, S., Department of Paper Technology, Indian Institute of Technology, Roorkee, 247667, Uttarakhand, India, Khan, H., Saroha, V., Kadam, A., Dutt, D., … Department of Paper Technology, Indian Institute of Technology, Roorkee, 247667, Uttarakhand, India. (2021). Chemical and structural changes in poplar wood upon steam treatment at constant temperature and pressure conditions for different time intervals. Cellulose Chemistry and Technology, 55(9–10), 961–969. doi:10.35812/cellulosechemtechnol.2021.55.82
Ailing, B. A. N., 池州学院 大数据与人工智能学院， 安徽 池州 247000, School of Big Data and Artificial Intelligence, Chizhou University, ChiZhou, Anhui 247000, P.R.China, & Kai, Z. (2021). Kolmogorov entropy of random attractors for stochastic lattice systems with white noise. 应用数学和力学, 42(7), 735–740. doi:10.21656/1000-0887.410360
Mandal, B., ,CARAMBA, INRIA Nancy-Grand Est., 54600, France, Kar Gangopadhyay, A., & ,Department of Mathematics, Indian Institute of Technology Roorkee, 247667, India. (2021). A note on generalization of bent boolean functions. Advances in Mathematics of Communications, 15(2), 329–346. doi:10.3934/amc.2020069
Gangopadhyay, S., ,Department of Computer Science and Engineering, Indian Institute of Technology Roorkee, Roorkee 247667, India, Riera, C., Stănică, P., ,Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, 5020 Bergen, Norway, & ,Department of Applied Mathematics, Naval Postgraduate School, Monterey, CA 93943, USA. (2021). Gowers U_2 norm as a measure of nonlinearity for Boolean functions and their generalizations. Advances in Mathematics of Communications, 15(2), 241–256. doi:10.3934/amc.2020056
Zhang, Y., School of Big Data and Artificial Intelligence, Chizhou University, Chizhou, Anhui 247000, China, Bao, X., Liu, L.-B., Liang, Z., & School of Mathematics and Statistics, Nanning Normal University, Nanning 530029, China. (2021). Analysis of a finite difference scheme for a nonlinear Caputo fractional differential equation on an adaptive grid. AIMS mathematics, 6(8), 8611–8624. doi:10.3934/math.2021500
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Zikouli, A., School of Forestry and Natural Environment, Aristotle University of Thessaloniki, Box 247, 54124 Thessaloniki, Greece, Andreopoulou, Z., & School of Forestry and Natural Environment, Aristotle University of Thessaloniki, Box 247, 54124 Thessaloniki, Greece; (2020). Environmental policy and legislation in national parks the case of parnassos, Greece. International Journal of Ecosystems and Ecology Science (IJEES), 10(3), 463–468. doi:10.31407/ijees10.305
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Dreisbach, C., Koleck, T. A., Bourne, P. E., & Bakken, S. (2019). A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data. International Journal of Medical Informatics, 125, 37–46. doi:10.1016/j.ijmedinf.2019.02.008
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Xie, Lei, Ge, X., Tan, H., Xie, L., Zhang, Y., Hart, T., … Bourne, P. E. (2014). Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Computational Biology, 10(5), e1003554. doi:10.1371/journal.pcbi.1003554
Caporaso, J. G., Deshpande, N., Fink, J. L., Bourne, P. E., Cohen, K. B., & Hunter, L. (2007, Desember). Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Biocomputing 2008. Presented at the Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA. doi:10.1142/9789812776136_0061
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Perduca, M., Mancia, F., Del Giorgio, R., & Monaco, H. L. (2001). Crystal structure of a truncated form of porcine odorant-binding protein. Proteins, 42(2), 201–209. doi:10.1002/1097-0134(20010201)42:2<201::aid-prot70>3.0.co;2-7
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Reddy, B. V., Li, W. W., Shindyalov, I. N., & Bourne, P. E. (2001). Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins, 42(2), 148–163. doi:10.1002/1097-0134(20010201)42:2<148::aid-prot20>3.0.co;2-
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Perduca, Massimiliano, Mancia, F., Del Giorgio, R., & Monaco, H. L. (2001). Crystal structure of a truncated form of porcine odorant‐binding protein. Proteins, 42(2), 201–209. doi:10.1002/1097-0134(20010201)42:2<201::aid-prot70>3.3.co;2-z
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Zhang, T., & Deng, C. (2024). Technical repair method of Poyang bodiless lacquerware based on scale-invariant feature transform algorithm for healthcare vision. Journal of Testing and Evaluation, 52(1), 20210460. doi:10.1520/jte20210460
Zhao, N. (2024). Improvement of cloud computing medical data protection technology based on symmetric encryption algorithm. Journal of Testing and Evaluation, 52(1), 20210456. doi:10.1520/jte20210456
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Deng, L., Wheeler, W., & Yu, K. (2024). Mendelian randomization test of causal effect using high-dimensional summary data. Statistica sinica. doi:10.5705/ss.202021.0164
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Faiz, H., Khan, O., Ali, I., Hussain, T., Haider, S. T., Siddique, T., … Anjum, Q. S. (2024). Foliar application of triacontanol ameliorates heat stress through regulation of the antioxidant defense system and improves yield of eggplant. Brazilian Journal of Biology, 84. doi:10.1590/1519-6984.253696
Amazonas, M. G., Olentino, D., Lubich, C., Duncan, W. P., & Yamamoto, K. C. (2024). Length-weight relationship for Potamotrygon wallacei (Carvalho, Rosa and Araújo, 2016) caught in the middle Negro River, Barcelos, Brazilian Amazon. Brazilian Journal of Biology, 84. doi:10.1590/1519-6984.253497
Salomon, G. R., Gaglioti, A. L., Machado, L. P. B., Carrasco, A. O. T., & Mateus, R. P. (2024). Note on the phylogenetic position of Eptesicus species in the Vespertilionidae family (Chiroptera) using Brazilian bats and RAG2 sequences. Brazilian Journal of Biology, 84. doi:10.1590/1519-6984.258210
Nunes, Y. B. S., Milke, R., Silva, L. R., França, C. L., Costa, C. E. S. S., Nunes, J. L. S., & Figueiredo, M. B. (2024). Length at first sexual maturity of the freshwater fish fauna of the Baixada Maranhense Environmental Protection Area. Brazilian Journal of Biology, 84. doi:10.1590/1519-6984.256697
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Lupu, M. I., & Department of Engineering and Management in Food and Tourism, Transilvania University of Brasov, Castle Street no. 148, Brasov 500014, Romania. (2022). Evaluation o Different Starter Cultures in Dry Salami. Bulletin of the Transilvania University of Braşov, 14(63)(2), 129–136. doi:10.31926/but.fwiafe.2021.14.63.2.12
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Renesto, D. M., & São Paulo State University, Department of Animal Science, FCAV-Unesp, 14884-900 Jaboticabal, SP, Brazil. (2021). Supplement levels and functional oils to replace virginiamycin for young bulls during early dry season on grasslands and finishing phase in feedlot systems. Revista de investigacion agraria [Spanish journal of agricultural research], 19(3), e0609–e0609. doi:10.5424/sjar/2021193-15795
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Garg, A., Department of Computer Science and Engineering, Sant Longowal Institute of Engineering and Technology, Longowal, Punjab, 148106, India., Kaur, G., & Department of Computer Science and Engineering, Sant Longowal Institute of Engineering and Technology, Longowal, Punjab, 148106, India. (2021). Fuzzy logic based zone head selection algorithm for wireless sensor networks. Journal of University of Shanghai for Science and Technology/Shanghai Ligong Daxue Xuebao, 23(07), 1210–1215. doi:10.51201/jusst/21/07294
Masih, Z. N., & College Of Arts & Sciences, Cornell University, Ithaca Ny 14850, USA And Us Metric Association, Windsor Co 80550, USA. (2021). Some shocking stories: The behavioral response of cancer mortality to spikes in alcohol and tobacco consumption. The American Journal of Applied Sciences, 03(02), 6–14. doi:10.37547/tajas/volume03issue02-02
Bharti, A., Kaur, J., Kumar, A., Singh, S., Kumar, D., & Department of Pharmacology, Akal College of Pharmacy & Technical Education, Mastuana Sahib, Sangrur - 148 001, Punjab, India. (2021). Efficacy of p-coumaric acid in chronic constriction injury induced neuropathic pain in rats. Indian Drugs, 58(09), 52–58. doi:10.53879/id.58.09.12733
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Bhagat, S., Assistant Professor, Department of Chemical Engineering, SLIET-Longowal, 148106, India., Prakash, N., & Assistant Professor, Department of Chemical Engineering, SLIET-Longowal, 148106, India. (2021). Comparative study of Metallocene catalyst propylene polymerization with different iteration rates. Ymer, 20(12), 562–568. doi:10.37896/ymer20.12/53
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Beaver, J. E., Bourne, P. E., & Ponomarenko, J. V. (2007). EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Research, 3(1), 3. doi:10.1186/1745-7580-3-3
Zhang, H., Wang, P., Papangelopoulos, N., Xu, Y., Sette, A., Bourne, P. E., … Peters, B. (2010). Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PloS One, 5(2), e9272. doi:10.1371/journal.pone.0009272
Bauer, R. A., Bourne, P. E., Formella, A., Frömmel, C., Gille, C., Goede, A., … Preissner, R. (2008). Superimpose: a 3D structural superposition server. Nucleic Acids Research, 36(Web Server issue), W47-54. doi:10.1093/nar/gkn285
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic detection of internal symmetry in proteins using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. doi:10.1016/j.jmb.2014.03.010
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Fink, J. L., Kushch, S., Williams, P. R., & Bourne, P. E. (2008). BioLit: integrating biological literature with databases. Nucleic Acids Research, 36(Web Server issue), W385-9. doi:10.1093/nar/gkn317
Vita, R., Vaughan, K., Zarebski, L., Salimi, N., Fleri, W., Grey, H., … Sette, A. (2006). Curation of complex, context-dependent immunological data. BMC Bioinformatics, 7(1), 341. doi:10.1186/1471-2105-7-341
Chang, W., Shindyalov, I. N., Pu, C., & Bourne, P. E. (1994). Design and application of PDBlib, a C++ macromolecular class library. Computer Applications in the Biosciences : CABIOS, 10(6), 575–586. doi:10.1093/bioinformatics/10.6.575
Zhao, Z., Martin, C., Fan, R., Bourne, P. E., & Xie, L. (2016). Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics, 17(1), 90. doi:10.1186/s12859-016-0941-9
Bourne, Philip E., & McEntyre, J. (2006). [Review of Biocurators: contributors to the world of science]. PLoS computational biology, 2(10), e142. doi:10.1371/journal.pcbi.0020142
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Sathiamurthy, M., Peters, B., Bui, H.-H., Sidney, J., Mokili, J., Wilson, S. S., … Sette, A. (2005). An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Research, 1(1), 2. doi:10.1186/1745-7580-1-2
Wang, J., Bourne, P. E., & Bandeira, N. (2011). Peptide identification by database search of mixture tandem mass spectra. Molecular & Cellular Proteomics: MCP, 10(12), M111.010017. doi:10.1074/mcp.M111.010017
Jia, Y., Dewey, T. G., Shindyalov, I. N., & Bourne, P. E. (2004). A new scoring function and associated statistical significance for structure alignment by CE. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 11(5), 787–799. doi:10.1089/cmb.2004.11.787
Xie, Lei, & Bourne, P. E. (2015). Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Frontiers in Pharmacology, 6, 209. doi:10.3389/fphar.2015.00209
Valas, R. E., & Bourne, P. E. (2011). The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biology Direct, 6(1), 16. doi:10.1186/1745-6150-6-16
Valas, R. E., & Bourne, P. E. (2009). Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biology Direct, 4(1), 30. doi:10.1186/1745-6150-4-30
Berman, H., Bourne, P., & Westbrook, J. (2004). The protein data bank: A case study in management of community data. Current proteomics, 1(1), 49–57. doi:10.2174/1570164043488252
Zhao, Z., Xie, L., Xie, L., & Bourne, P. E. (2016). Delineation of polypharmacology across the human structural kinome using a functional site interaction fingerprint approach. Journal of Medicinal Chemistry, 59(9), 4326–4341. doi:10.1021/acs.jmedchem.5b02041
Doctor, K. S., Reed, J. C., Godzik, A., & Bourne, P. E. (2003). The apoptosis database. Cell Death and Differentiation, 10(6), 621–633. doi:10.1038/sj.cdd.4401230
Li, Wilfred W., Quinn, G. B., Alexandrov, N. N., Bourne, P. E., & Shindyalov, I. N. (2003). A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biology, 4(8), R51. doi:10.1186/gb-2003-4-8-r51
Samish, I., Bourne, P. E., & Najmanovich, R. J. (2015). Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics (Oxford, England), 31(1), 146–150. doi:10.1093/bioinformatics/btu769
Ponomarenko, J. V., Bourne, P. E., & Shindyalov, I. N. (2005). Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins, 58(4), 855–865. doi:10.1002/prot.20355
Bourne, Philip E., & Shindyalov, I. N. (2003). Structure comparison and alignment. Methods of Biochemical Analysis, 44, 321–337. Opgehaal van https://www.ncbi.nlm.nih.gov/pubmed/12647393
Weissig, Helge, & Bourne, P. E. (2002). Protein structure resources. Acta Crystallographica. Section D, Biological Crystallography, 58(Pt 61), 908–915. doi:10.1107/s0907444902003906
Tsai, L.-C. L., Xie, L., Dore, K., Xie, L., Del Rio, J. C., King, C. C., … Newton, A. C. (2015). Zeta inhibitory peptide disrupts electrostatic interactions that maintain atypical protein kinase C in its active conformation on the scaffold p62. The Journal of Biological Chemistry, 290(36), 21845–21856. doi:10.1074/jbc.M115.676221
Chang, R. L., Xie, L., Bourne, P. E., & Palsson, B. O. (2013). Antibacterial mechanisms identified through structural systems pharmacology. BMC Systems Biology, 7(1), 102. doi:10.1186/1752-0509-7-102
Bourne, Philip E., Fink, J. L., & Gerstein, M. (2008). Open access: taking full advantage of the content. PLoS Computational Biology, 4(3), e1000037. doi:10.1371/journal.pcbi.1000037
Greer, D. S., Westbrook, J. D., & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (Oxford, England), 18(9), 1280–1281. doi:10.1093/bioinformatics/18.9.1280
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Zhao, Z., Xie, L., & Bourne, P. E. (2017). Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PloS One, 12(6), e0179936. doi:10.1371/journal.pone.0179936
Fink, J. L., Fernicola, P., Chandran, R., Parastatidis, S., Wade, A., Naim, O., … Bourne, P. E. (2010). Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics, 11(1), 103. doi:10.1186/1471-2105-11-103
Bourne, Philip E., Westbrook, J., & Berman, H. M. (2004). The Protein Data Bank and lessons in data management. Briefings in Bioinformatics, 5(1), 23–30. doi:10.1093/bib/5.1.23
Ponomarenko, J. V., Bourne, P. E., & Shindyalov, I. N. (2002). Building an automated classification of DNA-binding protein domains. Bioinformatics (Oxford, England), 18 Suppl 2, S192-201. doi:10.1093/bioinformatics/18.suppl_2.s192
Lewitter, F., & Bourne, P. E. (2011). Teaching bioinformatics at the secondary school level. PLoS Computational Biology, 7(10), e1002242. doi:10.1371/journal.pcbi.1002242
Dunn, M. C., & Bourne, P. E. (2017). Building the biomedical data science workforce. PLoS Biology, 15(7), e2003082. doi:10.1371/journal.pbio.2003082
Bourne, Philip E. (2014b). What Big Data means to me. Journal of the American Medical Informatics Association: JAMIA, 21(2), 194. doi:10.1136/amiajnl-2014-002651
Wodak, S. J., Mietchen, D., Collings, A. M., Russell, R. B., & Bourne, P. E. (2012). Topic pages: PLoS Computational Biology meets Wikipedia. PLoS Computational Biology, 8(3), e1002446. doi:10.1371/journal.pcbi.1002446
Kuo, G. M., Ma, J. D., Lee, K. C., Halpert, J. R., Bourne, P. E., Ganiats, T. G., & Taylor, P. (2011). Institutional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEdTM): bridging the gap between science and practice. Pharmacogenomics, 12(2), 149–153. doi:10.2217/pgs.10.213
Chung, J.-L., Wang, W., & Bourne, P. E. (2007). High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics, 8(1), 223. doi:10.1186/1471-2105-8-223
Berman, Helen M., Henrick, K., Nakamura, H., Markley, J., Bourne, P. E., & Westbrook, J. (2007). [Review of Realism about PDB]. Nature biotechnology, 25(8), 845–846; author reply 846. doi:10.1038/nbt0807-845
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Bernstein, H. J., Bernstein, F. C., & Bourne, P. E. (1998). CIF Applications. VIII. pdb2cif: translating PDB entries into mmCIF format. Journal of applied crystallography, 31(2), 282–295. doi:10.1107/s0021889897007309
Berman, F. D., & Bourne, P. E. (2015). Let’s make gender diversity in data science a priority right from the start. PLoS Biology, 13(7), e1002206. doi:10.1371/journal.pbio.1002206
Gramada, A., & Bourne, P. E. (2006). Multipolar representation of protein structure. BMC Bioinformatics, 7(1), 242. doi:10.1186/1471-2105-7-242
Wang, J., Anania, V. G., Knott, J., Rush, J., Lill, J. R., Bourne, P. E., & Bandeira, N. (2014b). Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Molecular & Cellular Proteomics: MCP, 13(4), 1128–1136. doi:10.1074/mcp.M113.035758
Ng, C., Hauptman, R., Zhang, Y., Bourne, P. E., & Xie, L. (2013, November). Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Biocomputing 2014. Presented at the Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA. doi:10.1142/9789814583220_0014
Bourne, Philip E., Clark, T. W., Dale, R., de Waard, A., Herman, I., Hovy, E. H., & Shotton, D. (2012). Improving the future of research communications and e-scholarship (dagstuhl perspectives workshop 11331). doi:10.4230/DagMan.1.1.41
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Pekurovsky, D., Shindyalov, I. N., & Bourne, P. E. (2004). A case study of high-throughput biological data processing on parallel platforms. Bioinformatics (Oxford, England), 20(12), 1940–1947. doi:10.1093/bioinformatics/bth184
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Youkharibache, P., Veretnik, S., Li, Q., Stanek, K. A., Mura, C., & Bourne, P. E. (2019). The small β-barrel domain: A survey-based structural analysis. Structure (London, England: 1993), 27(1), 6–26. doi:10.1016/j.str.2018.09.012
Guda, P., Bourne, P. E., & Guda, C. (2007). Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins. Biochemical and Biophysical Research Communications, 352(2), 292–298. doi:10.1016/j.bbrc.2006.10.190
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Tate, J. G., Moreland, J. L., & Bourne, P. E. (2001). Design and implementation of a collaborative molecular graphics environment. Journal of Molecular Graphics & Modelling, 19(3–4), 280–287, 369–373. doi:10.1016/s1093-3263(00)00055-3
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Alden, K., Veretnik, S., & Bourne, P. E. (2010). dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics, 11(1), 310. doi:10.1186/1471-2105-11-310
Scheeff, E. D., & Bourne, P. E. (2006a). Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics, 7(1), 410. doi:10.1186/1471-2105-7-410
Birnbaum, A., Hayes, J., Li, W. W., Miller, M. A., Arzberger, P. W., Bourne, P. E., & Casanova, H. (2005). Grid workflow software for a high-throughput proteome annotation pipeline. In Lecture notes in computer science. Grid Computing in Life Science (bll 68–81). doi:10.1007/978-3-540-32251-1_7
Krebs, W. G., & Bourne, P. E. (2004). Statistically rigorous automated protein annotation. Bioinformatics (Oxford, England), 20(7), 1066–1073. doi:10.1093/bioinformatics/bth039
Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB ’04. (2004). Presented at the the eighth annual international conference, San Diego, California, USA. doi:10.1145/974614
Yang, P., Craig, P. A., Goodsell, D., & Bourne, P. E. (2003). BioEditor-simplifying macromolecular structure annotation. Bioinformatics (Oxford, England), 19(7), 897–898. doi:10.1093/bioinformatics/btg103
Shindyalov, I. N., & Bourne, P. E. (1995). WPDB– PC Windows-based interrogation of macromolecular structure. Journal of applied crystallography, 28(6), 847–852. doi:10.1107/s0021889895005723
Bourne, P. E., & Taylor, M. R. (1983). Dicytosinium tetrachlorozincate, [C4H6N3O]2[ZnCl4]. Acta crystallographica. Section C, Crystal structure communications, 39(4), 430–432. doi:10.1107/s0108270183005004
Breen, N., Berrigan, D., Jackson, J. S., Wong, D. W. S., Wood, F. B., Denny, J. C., … Bourne, P. E. (2019). Translational Health Disparities research in a data-rich world. Health Equity, 3(1), 588–600. doi:10.1089/heq.2019.0042
Bliven, S. E., Lafita, A., Rose, P. W., Capitani, G., Prlić, A., & Bourne, P. E. (2019). Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Computational Biology, 15(4), e1006842. doi:10.1371/journal.pcbi.1006842
Bourne, Philip E. (2015). [Review of Confronting the ethical challenges of big data in public health]. PLoS computational biology, 11(2), e1004073. doi:10.1371/journal.pcbi.1004073
Watenpaugh, K. D., Berman, H. M., Bourne, P. E., & Fitzgerald, P. M. D. (1993). The macromolecular CIF dicitionary. Acta crystallographica. Section A, Foundations of crystallography, 49(s1), c412–c413. doi:10.1107/s0108767378088364
Quinn, G. B., Bi, C., Christie, C. H., Pang, K., Prlić, A., Nakane, T., … Rose, P. W. (2015). RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinformatics (Oxford, England), 31(1), 126–127. doi:10.1093/bioinformatics/btu596
Bluhm, W. F., Beran, B., Bi, C., Dimitropoulos, D., Prlic, A., Quinn, G. B., … Bourne, P. E. (2011). Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database: The Journal of Biological Databases and Curation, 2011(0), bar003. doi:10.1093/database/bar003
Chang, W., & Bourne, P. E. (1998). CIF Applications. IX. A new approach for representing and manipulating STAR files. Journal of applied crystallography, 31(3), 505–509. doi:10.1107/s0021889897017019
Bourne, P. E., & Taylor, M. R. (1980). The structure of aqua[3-ethoxy-2-oxobutyraldehyde bis(thiosemicarbazonato)]zinc(II). Acta crystallographica. Section B: Structural crystallography and crystal chemistry, 36(9), 2143–2145. doi:10.1107/s0567740880008151
Donlan, A. N., Sutherland, T. E., Marie, C., Preissner, S., Bradley, B. T., Carpenter, R. M., … Petri, W. A., Jr. (2021). IL-13 is a driver of COVID-19 severity. MedRxiv : The Preprint Server for Health Sciences. doi:10.1101/2020.06.18.20134353
Kolker, E., Altintas, I., Bourne, P., Faris, J., Fox, G., Frishman, D., … Wilmes, P. (2013). Reproducibility: In praise of open research measures. Nature, 498(7453), 170. doi:10.1038/498170b
von Eichborn, J., Bourne, P. E., & Preissner, R. (2011). Cobweb: a Java applet for network exploration and visualisation. Bioinformatics (Oxford, England), 27(12), 1725–1726. doi:10.1093/bioinformatics/btr195
Valas, R. E., & Bourne, P. E. (2010). Save the tree of life or get lost in the woods. Biology Direct, 5(1), 44. doi:10.1186/1745-6150-5-44
Briedis, K. M., Starr, A., & Bourne, P. E. (2008). Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PloS One, 3(2), e1597. doi:10.1371/journal.pone.0001597
Cohen, K. B., Yu, H., Bourne, P. E., & Hirschman, L. (2008). Translating biology: Text mining tools that work. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 13, 551–555. Opgehaal van https://www.ncbi.nlm.nih.gov/pubmed/20827444
Baldridge, K., & Bourne, P. E. (2003). The new biology and the grid. In Wiley Series in Communications Networking & Distributed Systems (bll 907–922). doi:10.1002/0470867167.ch40
Li, Wilfred W., Reddy, B. V. B., Tate, J. G., Shindyalov, I. N., & Bourne, P. E. (2002). CKAAPs DB: A Conserved Key Amino Acid Positions DataBase. Nucleic Acids Research, 30(1), 409–411. doi:10.1093/nar/30.1.409
Bourne, Philip, Holstein, R., & McMullen, J. (2003). UNIX for OpenVMS Users (3rd ed). doi:10.1016/b978-1-55558-276-0.x5000-6
Abel, R., Paredes Ramos, M., Chen, Q., Pérez-Sánchez, H., Coluzzi, F., Rocco, M., … Banerjee, P. (2020). Computational prediction of potential inhibitors of the main protease of SARS-CoV-2. Frontiers in Chemistry, 8, 590263. doi:10.3389/fchem.2020.590263
Zhao, Z., & Bourne, P. E. (2020b). Structural insights into the binding modes of viral RNA-dependent RNA polymerases using a function-site interaction fingerprint method for RNA virus drug discovery. Journal of Proteome Research, 19(11), 4698–4705. doi:10.1021/acs.jproteome.0c00623
Prlić, A., Martinez, M. A., Dimitropoulos, D., Beran, B., Yukich, B. T., Rose, P. W., … Fink, J. L. (2010). Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics, 11(1), 220. doi:10.1186/1471-2105-11-220
Scheeff, E. D., & Bourne, P. E. (2006b). Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics, 7(1), 410. doi:10.1186/1471-2105-7-410
Shindyalov, I. N., Chang, W., Pu, C., & Bourne, P. E. (1994). Macromolecular query language (MMQL): prototype data model and implementation. Protein engineering, design & selection: PEDS, 7(11), 1311–1322. doi:10.1093/protein/7.11.1311
Zhao, Z., & Bourne, P. E. (2020a). Overview of current type I/II kinase inhibitors. In Next Generation Kinase Inhibitors (bll 13–28). doi:10.1007/978-3-030-48283-1_2
Zhao, Z., Xie, L., & Bourne, P. E. (2019). Structural insights into characterizing binding sites in epidermal growth factor receptor kinase mutants. Journal of Chemical Information and Modeling, 59(1), 453–462. doi:10.1021/acs.jcim.8b00458
Mura, C., Draizen, E. J., & Bourne, P. E. (2018). Structural biology meets data science: does anything change? Current Opinion in Structural Biology, 52, 95–102. doi:10.1016/j.sbi.2018.09.003
Gao, J., Prlić, A., Bi, C., Bluhm, W. F., Dimitropoulos, D., Xu, D., … Rose, P. W. (2017). BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinformatics, 33(13), 2047–2049. doi:10.1093/bioinformatics/btx101
Bliven, S. E., Bourne, P. E., & Prlić, A. (2015). Detection of circular permutations within protein structures using CE-CP. Bioinformatics (Oxford, England), 31(8), 1316–1318. doi:10.1093/bioinformatics/btu823
Bourne, Philip E., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Feng, Z., … Berman, H. M. (2011). The evolution of the RCSB Protein Data Bank website. Wiley Interdisciplinary Reviews. Computational Molecular Science, 1(5), 782–789. doi:10.1002/wcms.57
Bourne, Philip E., Briedis, K., Dupont, C., Valas, R., & Yang, S. (2010). Genome evolution studied through protein structure. In Evolutionary Genomics and Systems Biology (bll 153–164). doi:10.1002/9780470570418.ch8
Kuller, A., Fleri, W., Bluhm, W. F., Smith, J. L., Westbrook, J., & Bourne, P. E. (2002). A biologist’s guide to synchrotron facilities: the BioSync web resource. Trends in Biochemical Sciences, 27(4), 213–215. doi:10.1016/s0968-0004(02)02056-x
Weissig, Helge, Shindyalov, I. N., & Bourne, P. E. (1998). Macromolecular structure databases: Past progress and future challenges. Acta crystallographica. Section D, Biological crystallography, 54(6), 1085–1094. doi:10.1107/s0907444998009846
Gramada, A., & Bourne, P. E. (2011). Coarse-graining the electrostatic potential via distributed multipole expansions. Computer Physics Communications, 182(7), 1455–1462. doi:10.1016/j.cpc.2011.03.014
Zhang, Q., Veretnik, S., & Bourne, P. E. (2005). Overview of Structural Bioinformatics. In Bioinformatics Technologies (bll 15–44). doi:10.1007/3-540-26888-x_2
Shahab, A., Chuon, D., Suzumua, T., Li, W. W., Byrnes, R. W., Tanaka, K., … Arzberger, P. W. (2005). Grid portal interface for interactive use and monitoring of high-throughput proteome annotation. In Lecture notes in computer science. Grid Computing in Life Science (bll 53–67). doi:10.1007/978-3-540-32251-1_6
Reddy, B. V. B., & Bourne, P. E. (2005). Protein structure evolution and the scop database. In Methods of biochemical analysis. Structural Bioinformatics (bll 237–248). doi:10.1002/0471721204.ch12
Helliwell, J. R., Achari, A., Bloomer, A. C., Bourne, P. E., Carr, P., Clegg, G. A., … Machin, P. A. (1981). Protein crystal oscillation film data processing: a comparative study. Acta crystallographica. Section A, Foundations of crystallography, 37(a1), C311–C312. doi:10.1107/s0108767381090338
Xie, Li, Ng, C., Ali, T., Valencia, R., Ferreira, B. L., Xue, V., … Xie, L. (2013). Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics, 14 Suppl 3(S3), S9. doi:10.1186/1471-2164-14-S3-S9
Rana, B. K., Bourne, P. E., & Insel, P. A. (2012). Receptor databases and computational websites for ligand binding. Methods in Molecular Biology (Clifton, N.J.), 897, 1–13. doi:10.1007/978-1-61779-909-9_1
Bourne, Philip E., Brenner, S. E., & Eisen, M. B. (2005). PLoS Computational Biology: a new community journal. PLoS Computational Biology, 1(1), e4. doi:10.1371/journal.pcbi.0010004
Bourne, P. E. (2000). Bioinformatics meets data mining: time to dance? Trends in Biotechnology, 18(6), 228–230. doi:10.1016/s0167-7799(00)01430-x
Wang, J., Anania, V. G., Knott, J., Rush, J., Lill, J. R., Bourne, P. E., & Bandeira, N. (2014a). A turn-key approach for large-scale identification of complex posttranslational modifications. Journal of Proteome Research, 13(3), 1190–1199. doi:10.1021/pr400368u
Xie, Li, Kinnings, S. L., Xie, L., & Bourne, P. E. (2012). Predicting the polypharmacology of drugs: Identifying new uses through chemoinformatics, structural informatics, and molecular modeling-based approaches. In Drug Repositioning (bll 163–205). doi:10.1002/9781118274408.ch7
Bourne, Philip E., Beran, B., Bi, C., Bluhm, W., Dunbrack, R., Prlić, A., … Yukich, B. (2010). Will widgets and semantic tagging change computational biology? PLoS Computational Biology, 6(2), e1000673. doi:10.1371/journal.pcbi.1000673
Gramada, A., & Bourne, P. E. (2008). Resolving a distribution of charge into intrinsic multipole moments: a rankwise distributed multipole analysis. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 78(6 Pt 2), 066601. doi:10.1103/PhysRevE.78.066601
Li, W. W., Reddy, B. V., Shindyalov, I. N., & Bourne, P. E. (2001). CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Research, 29(1), 329–331. doi:10.1093/nar/29.1.329
Biggs, J., Pu, C., Groeninger, A., & Bourne, P. E. (1996). PDBtool: An interactive browser and geometry checker for protein structures. Journal of applied crystallography, 29(4), 484–490. doi:10.1107/s002188989600026x
Kittrie, E., Atienza, A. A., Kiley, R., Carr, D., MacFarlane, A., Pai, V., … Bourne, P. E. (2017). Developing international open science collaborations: Funder reflections on the Open Science Prize. PLoS Biology, 15(8), e2002617. doi:10.1371/journal.pbio.2002617
Erren, T. C., & Bourne, P. E. (2007). Ten simple rules for a good poster presentation. PLoS Computational Biology, 3(5), e102. doi:10.1371/journal.pcbi.0030102
Bourne, Philip E., Polka, J. K., Vale, R. D., & Kiley, R. (2017). Ten simple rules to consider regarding preprint submission. PLoS Computational Biology, 13(5), e1005473. doi:10.1371/journal.pcbi.1005473
Rougier, N. P., Droettboom, M., & Bourne, P. E. (2014). Ten simple rules for better figures. PLoS Computational Biology, 10(9), e1003833. doi:10.1371/journal.pcbi.1003833
Bourne, Philip E. (2005b). Ten simple rules for getting published. PLoS Computational Biology, 1(5), e57. doi:10.1371/journal.pcbi.0010057
Bourne, Philip E. (2007). Ten simple rules for making good oral presentations. PLoS Computational Biology, 3(4), e77. doi:10.1371/journal.pcbi.0030077
Vicens, Q., & Bourne, P. E. (2007). Ten simple rules for a successful collaboration. PLoS Computational Biology, 3(3), e44. doi:10.1371/journal.pcbi.0030044
Bourne, Philip E., & Korngreen, A. (2006). Ten simple rules for reviewers. PLoS Computational Biology, 2(9), e110. doi:10.1371/journal.pcbi.0020110
Ekins, S., & Perlstein, E. O. (2014). Ten simple rules of live tweeting at scientific conferences. PLoS Computational Biology, 10(8), e1003789. doi:10.1371/journal.pcbi.1003789
Bourne, Philip E., & Chalupa, L. M. (2006). Ten simple rules for getting grants. PLoS Computational Biology, 2(2), e12. doi:10.1371/journal.pcbi.0020012
Budd, A., Dinkel, H., Corpas, M., Fuller, J. C., Rubinat, L., Devos, D. P., … Wood, N. T. (2015). Ten simple rules for organizing an unconference. PLoS Computational Biology, 11(1), e1003905. doi:10.1371/journal.pcbi.1003905
Masum, H., Rao, A., Good, B. M., Todd, M. H., Edwards, A. M., Chan, L., … Bourne, P. E. (2013). Ten simple rules for cultivating open science and collaborative R&D. PLoS Computational Biology, 9(9), e1003244. doi:10.1371/journal.pcbi.1003244
Bourne, Philip E., & Barbour, V. (2011). Ten simple rules for building and maintaining a scientific reputation. PLoS Computational Biology, 7(6), e1002108. doi:10.1371/journal.pcbi.1002108
Bourne, Philip E., & Friedberg, I. (2006). Ten simple rules for selecting a postdoctoral position. PLoS Computational Biology, 2(11), e121. doi:10.1371/journal.pcbi.0020121
Corpas, M., Gehlenborg, N., Janga, S. C., & Bourne, P. E. (2008). Ten simple rules for organizing a scientific meeting. PLoS Computational Biology, 4(6), e1000080. doi:10.1371/journal.pcbi.1000080
Erren, T. C., Cullen, P., Erren, M., & Bourne, P. E. (2007). Ten simple rules for doing your best research, according to Hamming. PLoS Computational Biology, 3(10), 1839–1840. doi:10.1371/journal.pcbi.0030213
Fletcher, A. C., & Bourne, P. E. (2012b). Ten simple rules to commercialize scientific research. PLoS Computational Biology, 8(9), e1002712. doi:10.1371/journal.pcbi.1002712
Vicens, Q., & Bourne, P. E. (2009). Ten simple rules to combine teaching and research. PLoS Computational Biology, 5(4), e1000358. doi:10.1371/journal.pcbi.1000358
Dashnow, H., Lonsdale, A., & Bourne, P. E. (2014). Ten simple rules for writing a PLOS ten simple rules article. PLoS Computational Biology, 10(10), e1003858. doi:10.1371/journal.pcbi.1003858
Gu, J., & Bourne, P. E. (2007b). Ten simple rules for graduate students. PLoS Computational Biology, 3(11), e229. doi:10.1371/journal.pcbi.0030229
Jolly, M., Fletcher, A. C., & Bourne, P. E. (2012). Ten simple rules to protect your intellectual property. PLoS Computational Biology, 8(11), e1002766. doi:10.1371/journal.pcbi.1002766
Schultheiss, S. J. (2011). Ten simple rules for providing a scientific Web resource. PLoS Computational Biology, 7(5), e1001126. doi:10.1371/journal.pcbi.1001126
Bourne, Philip E. (2011). Ten simple rules for getting ahead as a computational biologist in Academia. PLoS Computational Biology, 7(1), e1002001. doi:10.1371/journal.pcbi.1002001
Goh, H.-H., & Bourne, P. E. (2020b). Ten simple rules for researchers while in isolation from a pandemic. PLoS Computational Biology, 16(6), e1007946. doi:10.1371/journal.pcbi.1007946
Lewitter, F., Bourne, P. E., & Attwood, T. K. (2019). Ten Simple Rules for avoiding and resolving conflicts with your colleagues. PLoS Computational Biology, 15(1), e1006708. doi:10.1371/journal.pcbi.1006708
Bourne, Philip E. (2014a). Ten simple rules for approaching a new job. PLoS Computational Biology, 10(6), e1003660. doi:10.1371/journal.pcbi.1003660
Bateman, A., & Bourne, P. E. (2009). Ten simple rules for chairing a scientific session. PLoS Computational Biology, 5(9), e1000517. doi:10.1371/journal.pcbi.1000517
Parker, M. S., Burgess, A. E., & Bourne, P. E. (2021). Ten simple rules for starting (and sustaining) an academic data science initiative. PLoS Computational Biology, 17(2), e1008628. doi:10.1371/journal.pcbi.1008628
Erren, T. C., Slanger, T. E., Groß, J. V., Bourne, P. E., & Cullen, P. (2015). Ten simple rules for lifelong learning, according to Hamming. PLoS Computational Biology, 11(2), e1004020. doi:10.1371/journal.pcbi.1004020
Fletcher, A. C., & Bourne, P. E. (2012a). Ten simple rules for starting a company. PLoS Computational Biology, 8(3), e1002439. doi:10.1371/journal.pcbi.1002439
Goh, H.-H., & Bourne, P. (2020a). Ten simple rules for writing scientific op-ed articles. PLoS Computational Biology, 16(9), e1008187. doi:10.1371/journal.pcbi.1008187
Bourne, Philip E. (2017). Ten simple rules in considering a career in academia versus government. PLoS Computational Biology, 13(10), e1005729. doi:10.1371/journal.pcbi.1005729
Bourne, Philip E., Polka, J. K., Vale, R. D., & Kiley, R. (2016). Ten simple rules for considering preprints. doi:10.7287/peerj.preprints.2669v1
Fletcher, A. C., Wagner, G. A., & Bourne, P. E. (2020). Ten simple rules for more objective decision-making. PLoS Computational Biology, 16(4), e1007706. doi:10.1371/journal.pcbi.1007706
Bourne, Philip E., Lewitter, F., Markel, S., & Papin, J. A. (2018). One thousand simple rules. PLoS Computational Biology, 14(12), e1006670. doi:10.1371/journal.pcbi.1006670