Gary B. Fogel

Gary Bryce Fogel
Born	1968
Education	University of California, Santa Cruz (B.A. in Biology, minor in Earth Sciences), University of California, Los Angeles (Ph.D. in Biology)
Known for	Computational intelligence, machine learning in bioinformatics and computational biology
Notable work	Applications in viral evolution, drug discovery, cancer research, RNA structure
Awards	Fellow, Institute of Electrical and Electronics Engineers (2012); Fellow, Asia-Pacific Artificial Intelligence Association (2022); Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section (2019, 2023); Meritorious Service Award, IEEE Computational Intelligence Society (2016)
Scientific career
Fields	Biology, computer science, artificial intelligence
Institutions	Natural Selection, Inc., San Diego State University

Gary Bryce Fogel (born 1968) is an American biologist and computer scientist. He is the Chief Executive Officer of Natural Selection, Inc.[1] He is most known for his applications of computational intelligence and machine learning to bioinformatics, computational biology, and industrial optimization.

Education and Research

Fogel was born and raised in La Jolla, California, graduating from La Jolla High School. He received a B.A. in biology with a minor in earth sciences from the University of California, Santa Cruz in 1991 and a Ph.D. in biology from the University of California, Los Angeles in 1998. Fogel has published over 150 peer-reviewed publications in conferences and journals,[2] 2 edited books,[3][4] and 11 patents. As CEO of Natural Selection, Inc., his research focuses on the application of computational intelligence, machine learning, and predictive analytics in areas not limited to: Viral evolution,[5][6][7][8] cellular differentiation,[9][10][11] drug discovery,[12][13][14] RNA structure,[15][16] cis-regulatory elements,[17][18] cancer,[19] and evolutionary game theory[20][21][22] as well as the development of evolutionary algorithms and other approaches.[23][24][25][26][27]

Service

Between 2008–2018 Gary Fogel was editor-in-chief of the Elsevier journal BioSystems.[28] He has served previously as an associate editor for IEEE Transactions on Artificial Intelligence, IEEE Computational Intelligence Magazine (2005–2010), IEEE Transactions on Evolutionary Computation (2001–2013), IEEE Transactions on Emerging Topics in Computational Intelligence (2016–2018), IEEE/ACM Transactions on Computational Biology and Bioinformatics (2004–2008), International Journal of Bioinformatics Research and Applications (2004–2007), International Journal of Data Mining and Bioinformatics (2005–2007), as a consulting editor for the Journal of Computational Intelligence in Bioinformatics (2006–2007), and as an editorial board member of Ecological Informatics (2005–2009) and BMC Big Data Analytics (2015–2020).

Within the IEEE Computational Intelligence Society, Fogel founded the Bioinformatics and Bioengineering Technical Committee and established the IEEE Computational Intelligence in Bioinformatics and Computational Biology conference series, chairing the first two meetings in 2004 and 2005 in San Diego.[29] He served on the IEEE Computational Intelligence Society Administrative Committee (2004–2009, 2014–2022)[30] and served as IEEE CIS Vice President of Conferences (2010–2013, 2019).

Teaching

Gary Fogel also serves as adjunct faculty at San Diego State University in the department of aerospace engineering[31] as well as in the Computational Science Research Center.[32] He has authored four books[33][34][35][36] and numerous articles on the history of early aviation focusing on motorless flight. He is an associate fellow of the American Institute of Aeronautics and Astronautics[37] and serves on the AIAA History Committee.[38]

Awards

• 2023 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section
• 2022 – Elected Fellow of the Asia-Pacific Artificial Intelligence Association
• 2019 – Top 100 AI Leaders in Drug Discovery and Advanced Healthcare by Deep Knowledge Analytics[39]
• 2019 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section
• 2016 – Meritorious Service Award, IEEE Computational Intelligence Society[40]
• 2016 – Outstanding Contribution to the Community Award, AIAA San Diego Section[41]
• 2015 – Outstanding Enhancement of the Image of the Aerospace Profession Award, AIAA San Diego Section
• 2012 – Medal for Significant Achievement, San Diego Chapter of Sigma Xi
• 2012 – Fellow of the Institute of Electrical and Electronics Engineers[42] for contributions to computational intelligence and its application to biology, chemistry, and medicine.

Aeromodeling

Gary Fogel has established national and world records for model aircraft.[43] He helped establish the National Model Aviation Heritage program[44] for the Academy of Model Aeronautics. He is a leader member, contest director, and elected fellow of the Academy of Model Aeronautics.

References

1. "Corporate Management".
2. "Gary Fogel".
3. Fogel, Gary B.; Corne, David W. (2003). Evolutionary Computation in Bioinformatics. ISBN 1558607978.
4. Computational Intelligence in Bioinformatics. 2010. ASIN B0017T76EG.
5. Lamers, Susanna L.; Fogel, Gary B.; Nolan, David J.; Barbier, Andrew E.; Rose, Rebecca; Singer, Elyse J.; Gonzalez-Perez, Maria Paz; McGrath, Michael S. (June 2019). "Emerging Patterns in HIV-1 gp120 Variable Domains in Anatomical Tissues in the Absence of a Plasma Viral Load". AIDS Research and Human Retroviruses. 35 (6): 588–596. doi:10.1089/aid.2018.0267. PMC 6588100. PMID 30793919.
6. Lamers, Susanna L.; Fogel, Gary B.; Liu, Enoch S.; Barbier, Andrew E.; Rodriguez, Christopher W.; Singer, Elyse J.; Nolan, David J.; Rose, Rebecca; McGrath, Michael S. (2018). "Brain-specific HIV Nef identified in multiple patients with neurological disease". Journal of Neurovirology. 24 (1): 1–15. doi:10.1007/s13365-017-0586-0. PMC 5792318. PMID 29063512.
7. Maguire, Alanna; Fogel, Gary B; Kendrick, Samantha L.; Liu, Enoch S; Wisner, Lee; Ramsower, Colleen; Glinsmann-Gibson, Betty; Lamers, Susanna L; McGrath, Michael S.; Rimsza, Lisa M. (2017-12-07). "Human Immunodeficiency Virus (HIV) Status Drives Diffuse Large B Cell Lymphoma through Oncogenic Signaling Pathways". Blood. 130 (Supplement 1): 5128. doi:10.1182/blood.V130.Suppl_1.5128.5128. S2CID 251171043.
8. Lamers, Susanna L.; Rose, Rebecca; Maidji, Ekaterina; Agsalda-Garcia, Melissa; Nolan, David J.; Fogel, Gary B.; Salemi, Marco; Garcia, Debra L.; Bracci, Paige; Yong, William; Commins, Deborah; Said, Jonathan; Khanlou, Negar; Hinkin, Charles H.; Sueiras, Miguel Valdes; Mathisen, Glenn; Donovan, Suzanne; Shiramizu, Bruce; Stoddart, Cheryl A.; McGrath, Michael S.; Singer, Elyse J. (2016-10-15). "HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads". Journal of Virology. 90 (20): 8968–8983. doi:10.1128/JVI.00674-16. PMC 5044815. PMID 27466426.
9. Fogel, Gary B.; Kai, Zoya S.; Zargar, Sahar; Hinton, Andrew; Jones, G. Adam; Wong, Augusta S.; Ficici, Sevan G.; Lopez, Ana D.; King, Charles C. (December 2015). "MicroRNA dynamics during human embryonic stem cell differentiation to pancreatic endoderm". Gene. 574 (2): 359–370. doi:10.1016/j.gene.2015.08.027. PMID 26297998.
10. Hinton, Andrew; Hunter, Shaun E.; Afrikanova, Ivka; Jones, G. Adam; Lopez, Ana D.; Fogel, Gary B.; Hayek, Alberto; King, Charles C. (September 2014). "sRNA-seq Analysis of Human Embryonic Stem Cells and Definitive Endoderm Reveals Differentially Expressed MicroRNAs and Novel IsomiRs with Distinct Targets: sRNA-seq Analysis of Human Embryonic Stem Cells". Stem Cells. 32 (9): 2360–2372. doi:10.1002/stem.1739. PMID 24805944. S2CID 9725569.
11. Hinton, Andrew; Hunter, Shaun; Reyes, Gloria; Fogel, Gary B.; King, Charles C. (2012). "From Pluripotency to Islets". Advances in Genetics Volume 79. Vol. 79. pp. 1–34. doi:10.1016/B978-0-12-394395-8.00001-3. ISBN 978-0-12-394395-8. PMID 22989764.
12. Hecht, David; Fogel, Gary B. (2012). "Modeling the evolution of drug resistance in malaria". Journal of Computer-Aided Molecular Design. 26 (12): 1343–1353. Bibcode:2012JCAMD..26.1343H. doi:10.1007/s10822-012-9618-2. PMC 3535480. PMID 23179493.
13. Hecht, David; Tran, Jonathan; Fogel, Gary B. (October 2011). "Structural-based analysis of dihydrofolate reductase evolution". Molecular Phylogenetics and Evolution. 61 (1): 212–230. Bibcode:2011MolPE..61..212H. doi:10.1016/j.ympev.2011.06.005. PMID 21704717.
14. Hecht, David; Fogel, Gary B. (2009-04-27). "A Novel In Silico Approach to Drug Discovery via Computational Intelligence". Journal of Chemical Information and Modeling. 49 (4): 1105–1121. doi:10.1021/ci9000647. PMID 19348414.
15. Lamers, Susanna L.; Fogel, Gary B.; McGrath, Michael S. (2010). "HIV-miR-H1 evolvability during HIV pathogenesis". Biosystems. 101 (2): 88–96. Bibcode:2010BiSys.101...88L. doi:10.1016/j.biosystems.2010.05.001. PMC 3478900. PMID 20546828.
16. Fogel, G. B. (December 2002). "Discovery of RNA structural elements using evolutionary computation". Nucleic Acids Research. 30 (23): 5310–5317. doi:10.1093/nar/gkf653. PMC 137967. PMID 12466557.
17. Fogel, G. B. (16 July 2004). "Discovery of sequence motifs related to coexpression of genes using evolutionary computation". Nucleic Acids Research. 32 (13): 3826–3835. doi:10.1093/nar/gkh713. PMC 506801. PMID 15266008.
18. Fogel, Gary B.; Weekes, Dana G.; Varga, Gabor; Dow, Ernst R.; Craven, Andrew M.; Harlow, Harry B.; Su, Eric W.; Onyia, Jude E.; Su, Chen (August 2005). "A statistical analysis of the TRANSFAC database". Biosystems. 81 (2): 137–154. Bibcode:2005BiSys..81..137F. doi:10.1016/j.biosystems.2005.03.003. PMID 15941617.
19. Cornforth, Andrew N.; Fogel, Gary; Carbonell, Denysha; Dillman, Robert O. (2015-08-01). "Abstract 4845: Microarray analysis of melanoma autologous tumor cell lines used as the source of tumor associated antigens in patient-specific dendritic cell immunotherapy phase II trial in patients with metastatic melanoma". Cancer Research. 75 (15_Supplement): 4845. doi:10.1158/1538-7445.AM2015-4845.
20. Fogel, David B; Fogel, Gary B; Andrews, Peter C (November 1997). "On the instability of evolutionary stable strategies". Biosystems. 44 (2): 135–152. Bibcode:1997BiSys..44..135F. doi:10.1016/S0303-2647(97)00050-6. PMID 9429748.
21. Fogel, Gary B.; Andrews, Peter C.; Fogel, David B. (June 1998). "On the instability of evolutionary stable strategies in small populations". Ecological Modelling. 109 (3): 283–294. Bibcode:1998EcMod.109..283F. doi:10.1016/S0304-3800(98)00068-4.
22. Fogel, Gary B.; Fogel, David B. (April 2011). "Simulating natural selection as a culling mechanism on finite populations with the hawk–dove game". Biosystems. 104 (1): 57–62. Bibcode:2011BiSys.104...57F. doi:10.1016/j.biosystems.2011.01.002. PMID 21219966.
23. Fogel, David B; Fogel, Gary B; Ohkura, Kazuhiro (July 2001). "Multiple-vector self-adaptation in evolutionary algorithms". Biosystems. 61 (2–3): 155–162. Bibcode:2001BiSys..61..155F. doi:10.1016/S0303-2647(01)00167-8. PMID 11716975.
24. Fogel, G.B.; Greenwood, G.W.; Chellapilla, K. (2000). "Evolutionary computation with extinction: Experiments and analysis". Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512). Vol. 2. pp. 1415–1420. doi:10.1109/CEC.2000.870818. ISBN 0-7803-6375-2. S2CID 14051394.
25. Ashlock, Daniel; Krsic, Nikola; Fogel, Gary B. (2013). "Functions for the analysis of exploration and exploitation". 2013 IEEE Congress on Evolutionary Computation. pp. 2020–2027. doi:10.1109/CEC.2013.6557807. ISBN 978-1-4799-0454-9. S2CID 12294772.
26. Krink, T.; Filipic, B.; Fogel, G.B. (2004). "Noisy optimization problems - a particular challenge for differential evolution?". Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753). pp. 332–339. doi:10.1109/CEC.2004.1330876. ISBN 0-7803-8515-2. S2CID 6842873.
27. Fogel, Gary B.; Fogel, David B. (January 1995). "Continuous Evolutionary Programming: Analysis and Experiments". Cybernetics and Systems. 26 (1): 79–90. doi:10.1080/01969729508927488.
28. "BioSystems".
29. "Dr. Gary Fogel Chairs the Inaugural 2004 IEEE Symposium on Computational Intelligence in". Archived from the original on 2016-12-20.
30. "ADCOM-Administrative Committee - IEEE Computational Intelligence Society". Archived from the original on August 22, 2019.
31. "Faculty, Lecturers and Staff".
32. "CSRC :: Governance".
33. Fogel, Gary (July 2021). Sky Rider: Park Van Tassel and the Rise of Ballooning in the West. ISBN 978-0826362827.
34. Fogel, Gary (July 2000). Wind and Wings: The History of Soaring in San Diego. ISBN 0967033950.
35. Quest for Flight: John J. Montgomery and the Dawn of Aviation in the West. 17 October 2012. ASIN B009W1J8M4.
36. Fogel, Gary B. (7 April 2014). Torrey Pines Gliderport. ISBN 978-1531676087.
37. "AIAA Associate Fellows" (PDF). AIAA. Jan 2022.
38. "About Us".
39. "Top 100 AI Leaders in Drug Discovery and Advanced Healthcare" (PDF). dkaGlobal. Deep Knowledge Analytics.
40. Yen, Gary G. (2016). "2016 IEEE CIS Awards [Society Briefs]". IEEE Computational Intelligence Magazine. 11: 4–7. doi:10.1109/MCI.2015.2502123.
41. "Untitled Page" (PDF).
42. "2012 elevated fellow" (PDF). IEEE Fellows Directory. Archived from the original (PDF) on February 15, 2012.
43. "Aeromodelling and Spacemodelling Records". August 2017.
44. "Academy of Model Aeronautics".