User:V M Reyes

_______________________________________________________________________________________________                         VICENTE  MENDOZA  REYES, Ph.D.

770 West Main Street, Apt. 326                               Tel:  (585) 654-1847 Rochester                                                    Cell:  (585) 287-1531 New York 14611                                      Email:  Vicente.Reyes@ronininstitute.org U.S.A.                                               or:    vicentemreyes@gmail.com or:   vmrsbi.RIT.biology@gmail.com

Scientific & Academic Profile:  http://ronininstitute.org/research-scholars/vicente-reyes/ Scientific Research Activities:  https://www.researchgate.net/profile/Vicente_Reyes/contributions

_______________________________________________________________ FIELDS OF INTEREST:

• Computational Biology & General Bioinformatics • Structural Bioinformatics, Biological Data Mining • Mathematical Biology (Biomathematics), Theoretical Biology • Pedagogy in Quantitative, Computational & Mathematical Life Sciences

_______________________________________________________________ EDUCATION:

Degrees:

Ph.D. Chemistry, California Institute of Technology, Pasadena, California, USA (conc. in molecular biology & biochemistry) B. S. Mathematics (magna cum laude) Univ. of the Philippines, Diliman, Philippines (conc. in pure mathematics & operations research) B. S. Chemistry (magna cum laude) Univ. of the Philippines, Diliman, Philippines (conc. in organic chemistry & biochemistry)

Certificates / Diplomas:

Spec. Cert. in Data Mining, UCSD School of Extended Studies, Winter 2007 Prof. Cert. in Bioinformatics, UCSD School of Extended Studies, Spring 2004 Spec. Cert. In Bioinformatics, UCSD School of Extended Studies, Spring 2002

________________________________________________________________ CAREER HISTORY:

Research Scholar, The Ronin Institute                                        12/2016 -- present Email: Vicente.Reyes@ronininstitute.org http://ronininstitute.org/research-scholars/vicente-reyes/

Research Scholar, Complex Biological Systems Alliance                         12/2016 -- present Email: Vicente.M.Reyes@cbsaimtt.com http://www.cbsaimtt.com/l---z.html#Reyes

Personal Independent Study Mid-Career Sabbatical:                             08/2012 – 02/2017

a.) Mathematical / Theoretical Biology (theory and applications)

Graph/Network Theory, Dynamical Systems Theory, Statistical Mechanics/Thermodynamics; Quaternion Theory; Mathematical Structures & Morphisms;  Category Theory;  Eigenvalue/ Eigenfunction Theory; Vector Calculus; Lebesgue Measure & Integration; Density Functional Theory; Countability & Denumerability Theory; Topology;  Naïve and Axiomatic Set Theory; Fractional Calculus; Spectral Theory; Sigma Algebra; Group Theory for Chemistry & Biology; Potential Theory; Harmonic Analysis; Fourier Theory; Game Theory; Mathematical Physics; Ordinary, Partial & Numerical Differential Equations; Differential Geometry; etc.]

b.) Computer Science (theory and applications)

Automata Theory & Turing Machines; Computability Theory; Computational Complexity; Theory & Analysis of Algorithms; Theory of Data Types and Structures; Boolean Algebra and Logic; Mathematical Logic; Complex Adaptive Systems; Machine Learning & Artificial Intelligence; Quantum Computation; Information Entropy Theory; Relational Algebra; Finite State Machines; Curve (2D and 3D) and Surface Fitting; NP-Hard and NP-Complete Problems;  Graph Algorithms; Linear Programming; Dynamic Programming; DNA & Membrane Computing; Cellular Automata; Cryptography & Cyber-security; Computer Graphics; Computer Languages; Emerging Technologies (most fields); etc.] c.) Biophysics / Biophysical chemistry

Macromolecular x-ray crystallography; protein (multidimensional) NMR; mass spectroscopy;  atomic force microscopy;  electron/cryoelectron microcopy;  dynamic light scattering (DLS); fluorescence resonance energy transfer (FRET); bioenergetics;  radioisotope dating technologies;  biomolecular hydrodynamics (biology at low Reynolds numbers);  quantum biology; organismal magnetoreception;  orchestrated objective reduction (OrchOR); electron paramagnetic (spin) resonance (EPR/ESR);  membrane biophysics;  macromolecular simulation; microscale thermophoresis (MST); cytological patch clamping; light-activated drugs; biomembrane electrostatics, etc.

d.) Biomaterials / Materials Science:

biomaterials (BMs) for drug delivery, gene therapy, scaffolds in tissue engineering, regenerative medicine, autograft, allograft or xenograft as transplant materials; biologically inspired & biomimetic materials; host responses to biomaterials; biocompatibility; therapeutic and diagnostic colloids; biosensor materials & mechanisms; sol-gel materials for bioceramic applications; titanium in medicine; chitin- and chitosan-based BMs; foreign body reaction to BMs; biophotonics; label-free technologies; bioactive glasses; MXenes; nano-geno-toxicology; synthetic & self-assembling nanococoons; structural hierarchy of BMs; photopolymerizable hydrogels; Biomaterials Properties Database (Univ. of Michigan);

e.)  Pharmacoinformatics / Pharmacology / Pharmaceutical Science:

principles of drug discovery and development; L-ADME; pharmacokinetics & pharmacodynamics; pharmacogenetics & pharmacogenomics; Click2Drug: Directory of Computer-Aided Drug Design Tools; CSA & DEA Schedules I-V controlled substances; WHO Model List of Essential Medicines; Anatomical Therapeutic Chemical Classification System (ATCCS); Top 200 Drugs (2015); RxMed;  RxList; Hopkins ABX (Antibiotics) Database;  The Vaccines Database;  Drugs in Clinical Trials Database (DCTDB); USP-NF (United States Pharmacopeia–National Formulary) Online; The NLM Drug Information Portal;  Drugs@FDA; ToxNet (Toxicology Database); New Medicines in Development Database (NMDDB); etc.

f.)  Medical Informatics / Fundamental Principles of Medicine:

Human anatomy & physiology; Personalized medicine; Medical Informatics Tools & Resources: International Statistical Classification of Diseases and Related Health Problems (ICD-10), International Classification of diseases, Diagnosis Codes/Clinical Modification (ICD-10-CM); International Classification of Diseases Procedure Coding System (ICD-10-PCS); Automated Diagnosis; Systematized Nomenclature of Medicine (SNOMED); International Classification of Primary Care (ICPC); International Classification of Diseases for Oncology (ICD-O); Morphology Codes (ICD-O-3-MC); NCI SEER Program;  Undiagnosed Diseases Program Database @ Office of Rare Diseases, NIH; Medscape/WebMD; MedicineNet; EMedicine, MedSeq, etc.

Assistant Professor, Dept. of Biological Sciences, SBMS, COS, R.I.T.            10/2008- 07/2012 (computational biology/bioinformatics)

IRACDA Postdoctoral Fellow & Assistant Project Scientist, UC San Diego School of Medicine, Dept. of Pharmacology,                                      02/2004 – 08/2008 (computational biology/structural bioinformatics)

Structural Bioinformatics Researcher, San Diego Supercomputer Center,           10/2002- 01/2004 (structural bioinformatics)

Bioinformatics studies, UCSD School of Extended Studies, La Jolla, CA,           06/2000 – 09/2002 (general bioinformatics)

Senior Research Associate, The Scripps Research Institute, La Jolla, CA,         04/1995 – 05/2000 (protein x-ray crystallography; structure-based drug design)

Postdoctoral Biochemist, Dept. of Chem. & Biochem., UCSD, La Jolla, CA,          02/1992 - 03/1995 (protein x-ray crystallography; structural enzymology)

Postdoctoral Biologist, Dept’s. of Biol. & Med., UCSD, La Jolla, CA              01/1990 – 07/1991 (HIV/AIDS molecular biology)

Postdoctoral Research Fellow, Lab.Tum. Cell Biol., NCI/NIH, Bethesda, MD        03/1988 – 12/1989 (HIV/AIDS molecular biology)

Graduate Student & Teaching Assistant, Dept. of Biol., CIT, Pasadena, CA         10/1983 – 02/1988 (gene expression molecular biology)

Instructor in Mathematics, Dept. of Math., Univ. of the Philippines, Diliman, Quezon City, PHILIPPINES                                                06/1980 - 08/1982 (differential and integral calculus I, II, and III; statistics & probability)

_______________________________________________________________ AWARDS:

• Nominated:  Eisenhart Outstanding Teaching Award, SY 2011-12, R.I.T. •  IRACDA Postdoctoral Scholars Program, NIGMS, NIH,  2004-‘07 • Bioinformatics Career Development WIA Award, State of California, 2002-‘03 • Postdoctoral Research Fellowship, NIGMS, NIH, 1992-‘95 • John E. Fogarty International Postdoctoral Research Fellowship, NCI, NIH, 1988-‘89 • Laszlo Zechmeister Graduate Fellowship in Chemistry, Caltech, 1983-‘85 • Nat’l. Undergrad. Science & Mathematics Scholarships, NSDB, Philippines, 1976-‘80

_______________________________________________________________ FORMAL GRANTSMANSHIP TRAINING:

•  NIGMS/UoK Internet Grant Writing Workshop (http://www.uky.edu/Projects/GrantWriting), University of Kentucky, Lexington KY, Prof. Donald Frazier, UoK Sch. of Med., Director, May, 2005 •  NIGMS/UoK Internet Grant Writing Workshop (http://www.uky.edu/Projects/GrantWriting), University of Kentucky, Lexington KY,  Prof. Donald Frazier, UoK Sch. of Med., Director, May, 2006 •  NIGMS/UoK Internet Grant Writing Workshop (http://www.uky.edu/Projects/GrantWriting),  University of Kentucky, Lexington KY,  Prof. Donald Frazier, UoK Sch. of Med., Director, May, 2007 •  Grant Writing Workshop-Seminar, Grant Writers’ Seminars and Workshops, LLC (http://www.grantcentral.com), Drs. Stephen W. Russell & David C. Morrison, Lecturers, Pasadena Civic Auditorium, Pasadena, CA Sept., 2005 •  Grant Writing Boot Camp, RIT SRS, sponsor, Rochester, NY, Nov. 22-23, 2010 •  NIH New Investigators Conference (The Sloane Foundation, sponsor), Cold Spring Harbor Laboratories, Cold Spring Harbor, Long Island, NY, March 14, 2011

_______________________________________________________________ SCIENTIFIC EDITORIAL REVIEW BOARD GUEST MEMBER FOR:

• Frontiers in Bioinformatics and Computational Biology • Journal of Computational Biology and Bioinformatics Research • Journal of Bioinformatics in Nutrition (Signpost Open Access) • Journal of Computational Biology and Bioinformatics Research (guest, 2014)

_______________________________________________________________ MOST RECENT PUBLICATIONS:

35. Priya P.* and Reyes, V.M.   “A Cancer Biotherapy Resource” (2015) [e-pub of *M.S. thesis: arxiv.org/abs/1602.08111  ;   Quantitative Biology: Biomolecules ]. Full article: arxiv.org/ftp/arxiv/papers/1602/1602.08111.pdf

34. DeFelice, J.* and Reyes, V.M., "Spherical Distance Metrics Applied to Protein Structure Classification" (2015)  [e-pub of *M.S. thesis:  arxiv.org/abs/1602.08079  ;  Quantitative Biology: Biomolecules]. Full article: arXiv.org/ftp/arXiv/papers/1602/1602.08079.pdf

33. Cheguri, S.* and Reyes, V.M. "Size-Independent Quantification of Ligand Binding Site Depth in Receptor Proteins" (2015) [e-pub of *M.S. thesis, part 1: arxiv.org/abs/1602.08115 ;  Quantitative Biology: Biomolecules ]. Full article: arxiv.org/ftp/arxiv/papers/1602/1602.08115.pdf

32. Cheguri, S.* and Reyes, V.M. " Representing Rod-Shaped Protein 3D Structures in Cylindrical Coordinates"  (2015) [e-pub of *M.S. thesis, part 2: arxiv.org/abs/1602.08113  ;  Quantitative Biology: Biomolecules ]. Full article: arxiv.org/ftp/arxiv/papers/1602/1602.08113.pdf

31. Banerjee A.* and Reyes, V.M.  "Prediction  of  Flavin  Mononucleotide  (FMN)  Binding Sites  in  Proteins  Using  the  3D Search  Motif  Method  and  Double-Centroid Reduced Representation of Protein 3D Structures" (2015) [e-pub of *M.S. thesis:  arxiv.org/abs/1602.08119  ;  Quantitative Biology: Biomolecules]. Full article: arxiv.org/ftp/arxiv/papers/1602/1602.08119.pdf

30. Sheth, V.N.* and Reyes, V.M.   “Visualization of Protein 3D Structures in Reduced Representation with Simultaneous Display of Intra- and Inter-Molecular Interactions” (2015) [e-pub of *M.S. thesis: arxiv.org/abs/1602.08117  ;  Quantitative Biology: Biomolecules ]. Full article: arxiv.org/ftp/arxiv/papers/1602/1602.08117.pdf

29. Reyes, V.M.  “Implementation of the Spherical Coordinate Representation of Protein 3D Structures and its Applications Using FORTRAN 77/90 Language.” (2015)  [e-pub ahead of publication:  arXiv.org/abs/1512.00424   [Quantitative Biology: Biomolecules]] (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1512/1512.00424.pdf

28. Reyes, V.M.  “Implementation of the Tangent Sphere and Cutting Plane Methods in the Quantitative Determination of Ligand Binding Site Burial Depths in Proteins Using FORTRAN 77/90 Language.” (2015) [e-pub ahead of publication: arXiv.org/abs/1512.00423  [Quantitative Biology: Biomolecules]]  (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1512/1512.00423.pdf

27. Reyes, V.M.  “Implementation of The Double-Centroid Reduced Representation of Proteins and its Application to the Prediction of Ligand Binding Sites and Protein-Protein Interaction Partners Using FORTRAN 77/90 Language.” (2015) [e-pub ahead of publication: arXiv.org/abs/1512.00003  [Quantitative Biology: Biomolecules]]   (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1512/1512.00003.pdf

26. Reyes, V.M.  “A Global and Local Structure-Based Method for Predicting Binary Protein-Protein Interaction Partners: Proof of Principle and Feasibility.” (2015) [e-pub ahead of publication: arXiv.org/abs/1505.01144  [Quantitative Biology: Biomolecules]]  (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1505/1505.01144.pdf

25. Reyes, V.M.  “Structure-Based Function Prediction of Functionally Unannotated Structures in the PDB:  Prediction of ATP, GTP, Sialic Acid, Retinoic Acid and Heme-bound and -Unbound (Free) Nitric Oxide Protein Binding Sites.”  (2015) [e-pub ahead of publication: arXiv.org/abs/1505.01143  [Quantitative Biology: Biomolecules]]  (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1505/1505.01143.pdf

24. Reyes, V.M.  “An Automatable Analytical Algorithm for Structure-Based Protein Functional Annotation via Detection of Specific Ligand 3D Binding Sites: Application to ATP (ser/thr Protein Kinases) and GTP (Small Ras–type G-Proteins) Binding Sites” (2015) [e-pub ahead of publication: arXiv.org/abs/1505.01141   [Quantitative Biology: Biomolecules]]  (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arXiv/papers/1505/1505.01141.pdf (submitted Jan. 2017 for publication in “Math.for Applic’s.”)

23.  Reyes, V.M.  "Two Complementary Methods for Relative Quantification of Ligand Binding Site Burial Depth in Proteins: The ‘Cutting Plane’ and ‘Tangent Sphere’ Methods" (2015) [e-pub ahead of publication: arXiv.org/abs/1505.01142 [Quantitative Biology: Biomolecules]]  (to be submitted to a peer- reviewed journal for publication in 2016/2017). Full article: arXiv.org/ftp/arxiv/papers/1505/1505.01142.pdf

22.  Cheguri, S. and Reyes, V.M., “A Database/Webserver for Size-Independent Quantification of Ligand Binding Site Burial Depth in Receptor Proteins: Implications on Protein Dynamics”, J. Biomol. Struct. & Dyn., Book of Abstracts, Albany 2011: The 17th Conversation, June 14-18, 2011, Vol. 28 (6) June 2011, p. 1013

21.  Cheguri, S. and Reyes, V.M., “Using Cylindrical Coordinates to Represent Rod-Shaped and Other Fibrous Protein 3D Structures: Potential Advantages and Applications”, J. Biomol. Struct. & Dyn., Book of Abstracts, Albany 2011: The 17th Conversation, June 14-18, 2011, Vol. 28 (6) June 2011, p. 1014

20.  DeFelice and Reyes, V.M., “Towards a Spherical Coordinate System Metric for Quantitative Comparison of Protein 3D Structures”, J. Biomol. Struct. & Dyn., Book of Abstracts, Albany 2011: The 17th Conversation, June 14-18, 2011, Vol. 28 (6) June 2011, p. 1015

19.  Priya, P. and Reyes, V.M., “Cancer Meets the “Omics”:  A Comprehensive Cancer Biotherapy Database with Links to Multiple Bioinformatics Websites/WebServers - Facilitating the Search for Anticancer Biological Agents”, J. Biomol. Struct. & Dyn., Book of Abstracts, Albany 2011: The 17th Conversation, June 14-18, 2011, Vol. 28 (6) June 2011, p. 1016

18.  Reyes, V.M., “Using Cartographic Techniques to Project Protein 3D Surfaces onto the 2D Plane:  Potential Applications and Implications”, J. Biomol. Struct. & Dyn., Book of Abstracts, Albany 2011: The 17th Conversation, June 14-18, 2011, Vol. 28 (6) June 2011, p. 1017

17.  Reyes, V.M., "Representation of Protein 3D Structures in Spherical (ρ,φ,θ) Coordinates and Two of Its Potential Applications", Interdiscip. Sci.: Comp. Life Sci., Sept. 2011, Vol. 3, No. 3, pp. 161-174.

16. Reyes, V.M*. & Sheth, V.N., "Visualization of Protein 3D Structures in 'Double-Centroid' Reduced Representation: Application to Ligand Binding Site Modeling and Screening" (March 2013) Essential Reference: Bioinformatics - Concepts, Methodologies, Tools, and Applications; Information Resources Management Association, ed.;  Ch. 59, Vol. 2, Sect. 4: Cases and Applications, pp. 1158-1173.

15. Reyes, V.M*. & Sheth, V.N., "Visualization of Protein 3D Structures in 'Double-Centroid' Reduced Representation: Application to Ligand Binding Site Modeling and Screening" (March 2011), Handbook of Research in Computational and Systems Biology: Interdisciplinary Approaches, IGI-Global/Springer, Ch. 26, pp. 583-598;

_______________________________________________________________ PRESENTATIONS (since January 2009):

• Sixth Annual Joint Conference of the Upstate Chapters of the American Statistical Association (UP-STAT 2017), Canisius College, Buffalo, NY, April 2st-22nd, 2017

• Fifth Annual Joint Conference of the Upstate Chapters of the American Statistical Association (UP-STAT 2016), Canisius College, Buffalo, NY, April 22nd-23rd, 2016

• Fourth Annual Joint Conference of the Upstate Chapters of the American Statistical Association (UP-STAT 2015), SUNY Geneseo, NY, April 10th-11th, 2015

• Jackson State University, Department of Biology, College of Science, Engineering and Technology, Jackson, MS 39217,  June 19, 2014

• New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083 March 6, 2014

• New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083 March 6, 2014

• University of Maryland - University Center, Bioinformatics Division, Department of Information Systems & Technology, Adelphi, MD, 20783,  January 18, 2013

• Kazakhstan Embassy, Washington D.C., U.S.A., for Dept. of Computational Sciences, School of Science and Technology, Nazarbayev University, Astana, Kazakhstan, November 15, 2012

• Ph.D. Colloquium Series, Golisano College of Computational & Information Sciences, RIT campus, March 16, 2012,

• Open Forum with the Upstate New York Translational Research Network August 11, 2011, Idea Factory, Wallace Library, RIT campus

• 17th Conversation on BSDIE (Biological Structure, Dynamics, Interaction and Expression), SUNY-Albany, Albany, NY, June 14-18, 2011

• The Bioinformatics Cluster Seminar Series, University of Rochester Medical Center, Rochester, NY, March 10, 2011

• Invited Plenary Speaker, ICCSB (Int'l. Conference on Computational and Systems Biology) 2010, Hangzhou/Shanghai, China, Oct. 21-23, 2010:  Research paper submitted 7/14/2010

• Gordon Research Conference on IDRs (Intrinsically Disordered Regions) and Unfoldomics, Davidson, NC (Davidson College), 07/11-07/16/2010; presented one poster; actively participated in post-talk discussions

• Gordon Research Conference on Biopolymers, Newport, RI (Salve Regina University), 6/06-6/11/2010; presented two posters; actively participated in post-talk discussions

• Gordon Research Conference on Proteins, Holderness, NH (Holderness School), 06/21-06/26/2009; presented two posters; actively participated in post-talk discussions

• 16th Conversation on BSDIE (Biological Structure, Dynamics, Interaction and Expression, SUNY-Albany, Albany, NY, June 16-20, 2009

• Pacific Symposium on Biocomputing, Jan. 5-9, 2009, Big Island, Hawaii

• ISBRA 2009  (5th International Symposium on Bioinformatics Research and Applications), May 13 -16, 2009, Nova Southeastern University, Ft. Lauderdale, FL (with bioinformatics graduate student, Vrunda Sheth)

• RIT's  I.T. Collaboratory Access Grid Seminar Series,  "Visualization of Protein 3D Structures in Double-Centroid Reduced Representation" Vicente Reyes, and Vrunda Sheth, Dept. of Biological Sciences, Bioinformatics Program, R.I.T. (broadcast over the Access Grid from RIT's  I.T. Collaboratory), Jan. 22, 2009.

• R.I.T. Mathematics Dept. Colloquium Series, "Two Structural Proteomics Algorithms and Their Applications", Feb. 4, 2009

______________________________________________________________ COURSES TAUGHT at R.I.T. (since March 2009):

Perl for Bioinformatics, Spring 2009, 2010 and 2011; UNIX Under the Hood, Fall 2010; Bioinformatics, Winter 2010, 2011 and 2012; Bioinformatics Seminar: “Protein-Protein Interactions,” Fall 2009; “Cancer Biotherapy from the Informatics Perspective,“ Fall 2010; “The Protein Folding Problem,“ Fall 2011; Proteomics & Molecular Modeling, Spring 2009, 2010, 2011 and 2012

COURSES TAUGHT before joining R.I.T. in Fall 2008:

Calculus with Analytic Geometry I (Univ. of the Philippines,  1980’s); Calculus with Analytic Geometry II (Univ. of the Philippines, 1980’s); Calculus with Analytic Geometry III    (Univ. of the Philippines, 1980’s); Fundamentals of Probability and Statistics   (Univ. of the Philippines, 1980’s); Calculus for Pre-Medicine Students   (Univ. of the Philippines, 1980’s); Macromolecular X-Ray Crystallography (a segment of) (Univ. of Calif., San Diego, 1990’s); Biochemistry (San Diego State Univ., 1990’s); Biology 101 (San Diego State Univ., 2000’s)

____________________________________________________________________ RELEVANT SKILLS:

• Managerial / Management skills (large and small groups) • Mentoring & Advising skills (on-on-one) • Classroom teaching / lecturing skills • Scientific Research Article and Review Writing • Scientific Journalism / Editing skills • Course / Curriculum development • Program (undergraduate and graduate) initiation & development • Grant-writing / Grant application and follow-up • Business Plan Writing • Research Program Management & Supervision (incl. Project Management) • Symposium /Conference / Workshop organization and management • Scientific Research Article Review, Analysis and Critique • Workplace Conflict Mediation, • Programming Language Skills: Fortran 77/90; UNIX; C-Shell Programming; Sed & Awk; Perl; C; C++; R; Weka Data Mining; Python; MatLab; Mathematica; Microsoft Office Suite, etc., Biocomputing software skills: (too many to enumerate here)

