RYSZARD CZERMINSKI, PhD

adfu3o@r.postjobfree.com 508-***-****

linkedin.com/in/RyszardCzerminski

SUMMARY

Scientific and technical expert with a strong background in computational science, mathematics, physics, chemistry, biology, data analysis, and scientific software development. Extensive pharmaceutical, life science, business, and soft- ware industry experience with hands-on drug discovery project support, application development in diverse domains and building computational strategies and capabilities. Enjoys and excels at applying multidisciplinary experience to problem-solving through identifying and implementing innovative solutions. CORE COMPETENCIES

• Cheminformatics • QSAR • Combinatorial Chemistry • De Novo, Structure and Ligand Based Drug Design • Molec- ular Dynamics • Homology Modeling and Sequence Analysis • Multiple sequence alignment • Mechanistic and Population PK/PD Modeling • Stochastic Processes • In Silico ADMET • Modeling and Simulation • Machine Learning • Statistics • Optimization Algorithms • Multi-Objective Optimization and Decision Making • Genetic and Evolutionary Algorithms • Exploratory Data Analysis and Visualization • Algorithm Design and Implementa- tion • Scientific Software Development • Broad Range of Computer Languages (R, Python, Bash, and others) • High Performance Computing

PROFESSIONAL EXPERIENCE

Lead Data Scientist: Renaissance Alliance, Wellesley, MA December 2018 – July 2020

• Insurance, Data analysis, reporting and visualization

• R, Python, Julia, SQL, Azure Data Studio, Bitbucket, Asana, SiSense Adjunct Faculty: Merrimack College, North Andover, MA Spring 2019

• “Machine Learning” Course

Adjunct Faculty: Northeastern University, Boston, MA 2015 – 2018

• “Intro to Computational Statistics” Course

Senior Data Scientist: CiBO, Cambridge, MA March 2018 – June 2018

• Computational Agronomy

• Crop model (SALUS) testing, validation and development

• Scala

Senior Data Engineer: Agero, Medford, MA October 2016 – March 2018

• Digital Signal Processing, Time Series analysis, and Transport Mode classification

• Call volume analysis and forecasting (Prophet)

• Optimization of service area assignment (Linear Programming / COIN-OR)

• Python (Numpy/SciPy/scikit-learn), H2O

• AWS (Lambda/EC2/S3/Redshift), DataBricks, Spark, HDF5, Atlassian Tools & Git Senior Data Scientist: Altman Vilandrie & Company, Boston, MA January 2016 – July 2016

• Marketing Mix Modeling (MMM)

• Ridge Regression, Lasso, Baysian Linear Regression, Shapely Value

• Python (Numpy/SciPy/scikit-learn), R

• Member of Agile Software Development Team (GitHub, Atlassian Tools) 1 adfu3o@r.postjobfree.com 508-***-****

Principal Data Scientist: Next Step Living, Boston, MA September 2013 – April 2015

• Predictive models development for micro-targeting of prospective customers

• Established and managed partnerships with external data vendors

• Data management, analysis and visualization

• Logistics, route optimization, scheduling

• Python, R, Salesforce CRM, PostgresSQL/PostGIS

Director of Modeling: Parilogix, Woburn, MA November 2012 – June 2013

• Chronic Disease Management System design

• Development of ODE based models for blood glucose level

• Managment: CRO, Contractors, External Partners

Principal Scientist: AstraZeneca, Waltham, MA July 2007 – April 2012

• prioritized compounds for screening and synthesis using QSAR & machine learning methods

• designed compounds for supported projects using structure and ligand based methods

• developed reaction-based de novo drug design method; application was used for compound library enrichment

• population PK/PD and mechanistic PD models for compound assessment

• developed bacterial population growth models to optimize dosing regimens through time-kill study

• coach and mentor for junior members of the group

• led a small team of PhD computational chemists

Principal Scientist: TransTech Pharma, High Point, NC February 2007 - June 2007

• CNS disease area project support – lead discovery and optimization

• utilized de novo drug design methods (EA-Inventor) to propose new synthetic targets Research Investigator II: Novartis, Cambridge, MA June 2003 - October 2006

• supported projects in cardiovascular, metabolic disorder and infectious disease areas

• discovered new scaffolds using 3D ligand similarity methods

• organized training sessions for the CADD group with software vendors and external experts

• organized visits at Novartis by leading scientists in computational chemistry field Staff Investigator: ArQule Inc., Woburn, MA September 1999 - March 2003

• developed combinatorial library optimization methods used in MapMaker(TM):

• developed and implemented diverse subset selection algorithms

• developed multiobjective scoring methods based on Borda Count approach

• introduced Support Vector Machine (SVM) technique to the QSAR classification problems: thorough compari- son between SVM and Neural Networks classification methods

• combinatorial library enumeration (using Daylight’s Reaction Toolkit)

• applied graph-theoretical methods for exhaustive enumeration of molecular fragments

• fragment-based 2D/3D de novo drug design approaches Senior Principal Investigator: Moldyn Inc., Cambridge, MA April 1997 - August 1999

• lead GUI development and validation for InsightII, CHARMm and MBO(N)D

• developed biopolymer partitioning method based on clique finding graph algorithms

• developed wavelet based approaches for MALDI-TOF signal denoising

• developed GA-based algorithm for Mass Spectra peak assignment Senior Computational Chemist: MSI (now BIOVIA), Burlington, MA February 1991 – March 1997

• principal contact with academic groups developing new computational chemistry methods

• expert on molecular simulations and analysis for customer support and internal projects

• development and applications of Molecular Dynamics, Genetic Algorithms and clustering methods

• software support for CHARMm and CHARMm/Quanta integration 2 adfu3o@r.postjobfree.com 508-***-****

PREVIOUS PROFESSIONAL EXPERIENCE: Department of Chemistry, University of Illinois at Chicago, Chicago, IL - Postdoctoral Research Associate (with Professor R. Elber); Institute of Physics, Polish Academy of Sciences, War- saw, Poland - Assistant, Senior Assistant and Research Associate. EDUCATION

• Ph.D. in Biophysics, Institute of Physics, Polish Academy of Sciences, Warsaw, POLAND

• M.Sc. in Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, POLAND

• Deep Learning Specialization (Coursera) - Fall 2017

• Functional Programming Principles in Scala by École Polytechnique Fédérale de Lausanne on Coursera. Certificate earned at Friday, August 17, 2018 8:16 PM GMT

• Advanced Machine Learning with TensorFlow on Google Cloud Platform Specialization (Coursera) - July 2020

AWARDS

• Scientific Scholarship for Distinguished Students

• Award of the Scientific Secretary of the Polish Academy of Sciences

• Award of the Scientific Secretary of the Polish Academy of Sciences for the participation in the work "Tau- tomerism of nucleic acid bases - investigations in low temperature matrices and in the gas phase"

• Award of the Scientific Secretary of the Polish Academy of Sciences for the participation in the work “Investi- gations of structure and intermolecular interactions of analogs of nucleic acid bases with anticancer and antiviral activity”

COMPUTER/SOFTWARE SKILLS

Packages and Libraries: MOE, OpenEye Tools, PipeLine Pilot, Spotfire, KNIME, Daylight Toolkits, CHARMM, GAUSSIAN, GAMESS, GNU Tools, Glide, GOLD, AutoDock, BLAST, CLUSTAL, LaTeX Programming: R, Python: Numpy/SciPy/Pandas, Bash, SVL, Matlab, C, FORTRAN. Systems: UNIX/Linux, Windows/DOS. Mid- dleware: CORBA, SOAP, RESTful APIs. Databases: MySQL, Oracle, PostgreSQL. Distributed Computing: SGE, MPI, some experience with Spark.

OTHER

• Communications Director for Boston Area Group for Informatics for 2006

• Reviewer for Current Computer-Aided Drug Design, Chemical Biology & Drug Design

• Reviewer for Journal of Computer-Aided Molecular Design and for NIH Study Section 3 adfu3o@r.postjobfree.com 508-***-****

PUBLICATIONS

1. R. Czermin ski,B. Lesyng, A. Pohorille "Tautomerism of Oxopyridines and Oxopyrimidines - Theoretical Study with Complete Optimization of Geometry" Int. J. Quant. Chem. 16, 1141 (1979) 2. R. Czermin ski, B. Lesyng, A. Pohorille "Tautomerism of Pyrimidine Bases - Uracil, Cytosine and Isocytosine: Theoretical Study with Complete Optimization of Geometry" Int. J. Quant. Chem. 16, 605 (1979) 3. A.L. Sobolewski, R. Czermin ski, K. Kuczera "On the Nature of the Background Absorption in Vibrational Overtone Spectroscopy" Mol. Phys. 50, 971 (1983)

4. K. Kuczera, R. Czermin ski "Properties of Quadratic Force Field in Redundant Coordinates" J. Mol. Struct. 105, 269 (1983)

5. R. Czermin ski, K. Kuczera, H. Rostkowska, M. Nowak and K. Szczepaniak "Autoassociates and Tautomerism of 2-oxo-5-halogeno-pyrimidines: Theoretical and Experimental Investigations" J. Mol. Struct. 140, 235 (1986) 6. R. Czermin ski"Intermolecular Interactions: Reliability of Results Obtained for Small Hydrogen Bonded Dimers by Claverie’s Method" Int. J. Quant. Chem. 31, 649 (1987) 7. R. Czermin ski "Reparametrization of Claverie’s Method for Intermolecular Energy Calculation" J. Mol. Struct. 170, 245 (1988)

8. A. Sobolewski, R. Czermin ski"The Potential Energy Surfaces and the Radiationless Dynamics of Excited States of Benzene and Pyridazine" Chem. Phys. 130, 123 (1989) 9. W.B. Person, K. Szczepaniak, M. Szczesniak, J.S. Kwiatkowski, L. Hernandez and R. Czermin ski"Tautomerism of Nucleic Acid Bases and the Effect of Molecular Interactions on Tautomeric Equilibria" J. Mol. Struct. 194, 239 (1989)

10. R. Czermin ski, J.S. Kwiatkowski, W.B. Person and K. Szczepaniak - "Quantum-Mechanical Studies of the Structures of Cytosine Dimers and Guanine-Cytosine Pairs" J. Mol. Struct. 198, 297 (1989) 11. R. Czermin ski,R. Elber "Reaction Path Study of Conformational Transitions and Helix Formation in a Tetrapep- tide" Proc. Nat. Acad. Sci. 86, 6963 (1989)

12. R. Czermin ski,R. Elber "Reaction Path Study of Conformational Transitions in Flexible Systems: Applications to Peptides" J. Chem. Phys. 92, 5580 (1990)

13. L. Lapin ski, R. Czermin ski, M. Nowak, J. Fulara "Ab initio, CNDO/2 and Matrix Isolation Studies of 2- Hydroxy-Pyrimidine Infrared Absorption Spectra" J. Mol. Struct. 220, 147 (1990) 14. R. Czermin ski, V. Yip, W. Nowak and R. Elber "Molecular Dynamics Simulation of Ligand Diffusion in Globins" June 1990, ACS meeting, Dekalb, IL, USA. - invited paper 15. R. Czermin ski, K. Szczepaniak, W.B. Person, J.S. Kwiatkowski "Intermolecular Interactions and Tautomerism of Nucleic Acid Bases and their Analogues" J. Mol. Struct. 237, 151 (1990) 16. R. Elber, R. Czermin ski, W. Nowak, C. Choi and A. Ulitsky "Dynamics of Conformational Transitions in Peptides and Ligand Diffusion in Proteins" - a mini-review for "Chemical Design Automation News" December 1990, Vol. 5 (12)

17. R. Czermin ski, R. Elber "Self Avoiding Walk Between Two Fixed Points as a Tool to Calculate Reaction Paths in Large Molecular Systems" Int. J. Quant. Chem. 24, 167 (1990) 18. R. Czermin ski, R. Elber "Computational Studies of Ligand Diffusion in Globins: I. Leghemoglobin" Proteins 10, 70 (1991)

19. W. Nowak, R. Czermin ski and R. Elber "Reaction Path Study of Ligand Diffusion in Proteins: Application of the Self Penalty Walk (SPW) Method to Calculate Reaction Coordinates for the Motion of CO Through Leghemoglobin" J. Am. Chem. Soc. 113, 5627 (1991)

20. V. Buch, R. Czermin ski "Eigenstates of a quantum-mechanical particle on a topologically disordered surface: H(D) atom physisorbed on an amorphous ice cluster (H2O)115" J. Chem. Phys. 95(8), 6026 (1991) 21. R. Czermin ski,A. Roitberg, C. Choi, A.Ulistsky and R. Elber "Conformational Transitions". AIP 239. Advances in Biomolecular Simulations 135. (1991)

22. R. Czermin ski,A. Yasri and D. Hartsough "Use of Support Vector Machine in Pattern Classification: Application to QSAR Studies" Quantitative Structure-Activity Relationships, 20(3), 227-240 (2001) 23. Yasunobu Takano, Masahiro Koizumi, Takayuki Hara, Tomohisa Nakada, Satoshi Sugiura, Reiko Takarada, Yasuharu Nakai, Yoshiharu Takazawa, Midori Takimoto-Kamimura, Ryszard Czermin ski "Design of Novel Factor Xa inhibitors: Using MCSS functionality maps" Journal of Molecular Graphics and Modeling, 22(2), 4 adfu3o@r.postjobfree.com 508-***-****

1005-114 (2003)

24. John Manchester and Ryszard Czermin ski“SAMFA:Simplifying Molecular Description for 3D-QSAR” Journal of Chemical Information and Modeling, 48(6) 1167-1173 (2008) 25. John Manchester and Ryszard Czermin ski "CAUTION: Popular ’Benchmark’ Data Sets Do Not Distinguish the Merits of 3D QSAR Methods"

Journal of Chemical Information and Modeling, 49(6) 1449-1454 (2009) 26. Sameer Kawatkar, Hongming Wang, Ryszard Czermin ski,Diane Joseph-Mccarthy "Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide" Journal of Computer-Aided Molecular Design, 23(8) 527-539 (2009)

PRESENTATIONS

1. February 1, 1988, Department of Chemistry, University of Illinois at Chicago - "Theoretical Studies of Cytosine and Guanine: Formation of Alternative Tautomeric Pairs" (departmental seminar); 2. May 13-14, 1988, 21 Annual Midwest Theoretical Chemistry Conference, Argonne National Laboratory -

"Molecular Dynamics Study of CO Diffusion in Leghemoglobin" (poster with R. Elber); 3. June 15, 1988, Mount Sinai School of Medicine in New York "Theoretical Studies of Cytosine and Guanine: Formation of Alternative Tautomeric Pairs" (invited lecture); 4. August 30, 1989, Polygen Corporation, "Reaction Path Study of Helix Formation in a Tetrapeptide" (invited lecture);

5. October 12, 1989, Department of Chemistry, University of Illinois at Chicago - "Reaction Path Study of Helix Formation in a Tetrapeptide" (departmental seminar); 6. March 20, 1990, Sanibel Symposium - "Self Avoiding Walk Between Two Fixed Points as a Tool to Calculate Reaction Paths in Large Molecular Systems" (poster with R. Elber); 7. May 17-19, 1990, XXIII Midwest Theoretical Chemistry Conference - "Self Avoiding Walk Between Two Fixed Points as a Tool to Calculate Reaction Paths in Large Molecular Systems" (poster with R. Elber); "Reaction Path Study of Ligand Diffusion in Leghemoglobin" (poster with W. Nowak and R. Elber); 8. October 20, 1991, NIH, Bethesda - "Reaction Paths Algorithms. Application to Helix Formation in Tetrapeptide and B-Z transition in DNA" (invited lecture);

9. November 8, 1991, Polygen/MSI, Waltham - "Reaction Paths Algorithms. Application to Helix Formation in Tetrapeptide and B-Z transition in DNA" (company seminar); 10. June 23-26, 1994, Computers in Chemistry’ 94, Wroclaw, Poland - "Salt effects in B/Z DNA transition: feasi- bility study of linearized Poisson-Boltzmann equation" (invited lecture) 11. July 3-8, 1994, Gordon Conference on Computational Chemistry New Hampton School, New Hampton, NH, USA - "Reaction Path Study of the B to Z Transition in a Six Base Pair DNA" (poster) 12. June 30 - July 5, 1996, Gordon Conference on Computational Chemistry, New Hampton School, New Hampton, NH, USA - "Is it feasible to calculate dynamic trajectory directly from principle of stationary action ?" (poster) 13. September 7-11, 1997, 214th American Chemical Society National Meeting, Las Vegas, NV, D. Chin, C. Padilla, K. Delak, R. Czermin ski, H. Alper, M. Watanabe, V. Karlov, R. Nagle, H. Chun, V. Mohan, and D. Haney.

“Application of a Fast Computational Method for Studying Rupture Forces: HIV Ligand Interactions, and DNA Stretching"

14. September 7-11, 1997, 214th American Chemical Society National Meeting, Las Vegas, NV, D. Chin, C. Padilla, K. Delak, R. Czermin ski, H. Alper, M. Watanabe, V. Karlov, R. Nagle, H. Chun, V. Mohan, and D. Haney.

"Application of a Fast Computational Method for Studying Rupture Forces: HIV Ligand Interactions, and DNA Stretching,"

15. September 7-11, 1997, 214th American Chemical Society National Meeting, Las Vegas, NV, D. Chin, H., C. Padilla, K. Delak, R. Czermin ski, H. Alper, M. Watanabe, V. Karlov, R. Nagle, H. Chun, V. Mohan, and D. Haney. "Studying Rupture Forces of HIV-Ligand Interactions, and DNA Stretching Using a Fast Computational Method" (poster)

16. September 11-12, 1997. NMHCC Conference, Washington, D.C., D. Chin, C. Padilla, H. Alper, M. Watanabe, V. Karlov, R. Czermin ski, and H. Chun. "New Fast and Efficient Molecular Modeling Methods for Rational Drug Design: Structure-Based Design & Information Systems to Enhance Discovery Productivity" 5 adfu3o@r.postjobfree.com 508-***-****

17. June 28 - July 2, 1998, Gordon Conference on Computational Chemistry, Tilton School, Tilton, NH, USA -

"Automated body definition for multibody dynamics: graph-theoretical clique cover approach" (poster) 18. April 1-5, 2001, 221st National Meeting, San Diego, CA, J. I. Manchester, R. Czermin ski, J. Patterson, D. S. Hartsough "MapMaker: A tool for product-based library optimization" 19. February 20-22, 2005, CUP VI, OpenEye Users Meeting, Santa Fe, NM, R. Czermin ski, J, Jenkins "Using ROCS, EON, FEPOPS and 2D methods for prospective and retrospective similarity searching: experiences and results" (poster)

20. July 1, 2005, Nicolaus Copernicus University, Torun, Poland "Critical assessment of generalizing power of QSAR regression models" (invited presentation)

21. June 28, 2006, Computational Chemistry Group Users Group Meeting, Montreal, Canada R. Czermin ski "Crit- ical assessment of generalizing power of QSAR regression models" (invited presentation) 22. July 24-27, 2006, Novartis Institutes for Biomedical Research Conference, Venice, Italy R. Czermin ski "Multi- Objective Optimization (MOO) Primer" (poster)

23. June 22-25, 2008, Strasbourg Summer School on Cheminformatics: CheminfoS3, Obernai, France R. Czer- min ski and John Manchester "SAMFA: how much can we simplify molecular description without sacrificing predictive ability of 3D-QSAR models?" (poster)

24. June 23-26, 2009, Computational Chemistry Group Users Group Meeting, Montreal, Canada R. Czermin ski and John Manchester “CAUTION: Popular ’Benchmark’ Data Sets Do Not Distinguish the Merits of 3D QSAR Methods” (invited presentation)

25. August 16-20, 2009, ACS National Meeting in Washington, DC “Computational Chemistry in the Discovery

& Development of Novel Anti-Infective Agents (CINF)” symposium co-chair (together with G.S. Weston and John Manchester)

26. March 8-10, 2010, OpenEyes CUP XI Meeting: The Eldorado Hotel Santa Fe, New Mexico Ryszard Czermin ski

“QSAR’s null hypothesis“ (invited presentation)

27. June 20-23, 2011, Computational Chemistry Group Users Group Meeting, Montreal, Canada R. Czermin skiand Greg Bisacchi “Bacterial GyrB ATPase: Phylogenetic and Pocket Similarity Based Neighborhoods” (invited presentation)

28. June 5-9 2011, 9th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands Ulf Norinder, Sarah Aaron, David Buttar, Lars Carlsson, Hongming Chen, Ryszard Czermin ski,Andy Davis, Johan Ulander, Dan Warner and David Wood “Large-Scale in silico Model Building” (poster) 29. November 15-16, 2011, Predictive Sciences AstraZeneca Conference (internal) Virna Schuck, Ryszard Cz- ermin ski, Joseph Newman, Richard Alm “Application of Mathematical Models to Optimize In Vitro PKPD Studies in Infection” (poster)

30. September 27-28, 2012, BIT12 - Bioinformatics in Torun, Torun, Poland Ryszard Czermin ski “Computational Drug Design and Bioinformatics” (invited presentation) 31. November 5, 2012, University of Texas at Austin, The Institute for Computational Engineering and Sciences

(ICES) Ryszard Czermin ski “De Novo Drug Design” (invited presentation) 6 adfu3o@r.postjobfree.com 508-***-****

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