ANTON FILIKOV

94 Center St., Burlington, MA 01803, (781) 258-6569, [email protected]

LINKEDIN

https://www.linkedin.com/in/anton-filikov-156b9714

PROFESSIONAL SUMMARY

 Computational drug design - structural modeling, virtual ligand screening, binding scoring,
pharmacophores, receptor- and ligand-based design, homology modeling, toxicity and specificity
prediction and optimization
 Bioinformatics – sequences, pathways, expression, omics, biomarkers, targets, MoA
 Cheminformatics - QSAR, QSPR, fragment-based design, combinatorial libraries, fingerprints

 AI. Machine learning. Deep learning. Predictive modeling. NLP. Statistics. Advanced analytics
 Data science – web interfaces, databases, data processing/analytics – design, implementation,
coding, mining, analysis, integration, modeling, visualization 
 Cloud computing, Python, Spark, PySpark, SQL, MongoDB, Hadoop, Cloudera, CDSW, AWS, S3,
EC2; R, Perl, C++, Java, Unix, Biovia Pipeline Pilot
 Diverse data experience – clinical, claims, EHR, SNOMED, ICD-10, LOINC, IBM Truven,
biosensor, drug discovery, translational, toxicology, pharmacology, physical, chemical, molecular
structure, genomics, proteomics, microarray, business, financial, economic, manufacturing, sales,
big data, terabyte datasets 

 Support of applied projects and method development/programming 

 Broad knowledge of healthcare domain and drug development 
 Management: agile project matrix and line management experience
 Business development experience 
 Excellent communication, presentation and people skills 
 Creativity and sense of innovation 
 Extensive patent and publication lists in top journals

SKILLS

 AI: machine learning, deep  Python, PySpark, R, Perl, C++,  Computational toxicology and
learning, NLP Unix, Biovia Pipeline Pilot pharmacology
 Predictive and prescriptive  RDKit. Numpy, Pandas, Sklearn,  Molecular, pharmacophore,
modeling, statistics, advanced Matplotlib, Seaborn, ADMET, QSAR, QSPR
analytics TensorFlow, Statsmodels, Boto3 modeling
 Cloud computing, AWS, S3,  Computational drug design,  Line and matrix management
DynamoDB, Big Data, SQL, bioinformatics, cheminformatics
MongoDB
EXPERIENCE

Associate Director, Computational Drug Discovery Aug 2021 - Current

Arrakis Therapeutics | Waltham, MA
 Developed predictive solubility model with performance in line with the best literature examples
 Developed and optimized machine learning workflows and AI models, data integration/processing and
advanced cheminformatics tools for chemical library expansion
 Supported multiple drug discovery projects and designed several SAR efforts

Principal Data Scientist Jul 2020 - Jul 2021

Lexagene | Beverly, MA
 Uncovered and developed critical insights using the following techniques and technologies: Predictive
modeling, deep learning, data wrangling, data integration, optimization of technology parameters, Python,
SQL, AWS, DynamoDB, S3

Adjunct Professor Feb 2020 - Dec 2020

Northeastern University | Boston, MA
 Part time lecturer: Enterprise Analytics.
 Statistics, simulation, forecasting, risk analysis, advanced optimization, decision models with uncertainty and
risk.

Senior Data Scientist Jan 2019 - Mar 2020

Bose Corporation | Framingham, MA
 Generated actionable insights for design, manufacturing and marketing using prediction modeling and
advanced analytics
 Optimization of supply chain and manufacturing/testing processes
 Customer segmentation, Customer engagement
 Voice of customer
 NLP: Document classification, Sentiment extraction
 Machine learning including advanced methods, e.g. deep learning
 Descriptive, diagnostic, predictive and prescriptive analytics
 Natural language processing and understanding
 Apache Spark, PySpark, CDSW, Python, TensorFlow, SQL, NLP, NLU, BERT, ELMo

Science Computing Contractor Aug 2018 - Dec 2018

Merck | Boston, MA
 Designed, developed and optimized pipelines of advanced cheminformatics tools
 Visualization tools and relational databases.
 Coding of front- and back-end.
 Pipeline Pilot, PilotScript, SQL.

Watson Health Data Scientist Oct 2015 - Aug 2018

IBM | Cambridge, MA
 Developed a novel machine learning algorithm - Stratified Cascade Learning
 Developed and re-engineered algorithms for dimensionality reduction and model-based feature selection on
binary, continuous and categorical data
 Statistics, predictive and prescriptive modeling - institutional readmissions, risk of hospitalization, social
determinants of health
 Prediction of hypoglycemic events from time-series data - artificial pancreas project 
 Real world healthcare data - claims, EHR/EMR, SNOMED, ICD-10, medical devices, IBM Truven data.
 Coding (SQL, Python, Java, R and SPL) of software modules for ETL,
  Calculation of features and modeling algorithms 
 Agile project management 
 Evaluation of effectiveness of healthcare payment models alternative to fee-for-service model.

Principal Research Investigator Apr 2014 – Jul 2015

Sanofi-Genzyme | Waltham, MA
 Supported drug discovery through development of web interfaces, data processing pipelines and visualization
tools for uploading diverse assay data into relational and NoSQL databases
 Designed and implemented a data warehouse for mass spectra-based metabolomics and biomarker research
 Built a web interface for software for large-scale population genetic analyses (Hardy-Weinberg, directional
selection, haplotype frequencies, linkage disequilibrium)
 Pipeline Pilot, PilotScript, SQL, NoSQL, MongoDB, HTML, Javascript, MATLAB, R, Python, Java, TIBCO
Spotfire

Technical Lead Contractor Sep 2013 - Apr 2014

AbbVie | Chicago, IL
 Designed twelve web applications (web interface plus data extraction and processing pipeline) for regulatory
submission to the FDA of clinical data
 Relational databases: design of queries and architecture, maintenance.
 Coding of both front- and back-end.
 Pipeline Pilot, PilotScript, SQL, Oracle, Javascript, Tibco Spotfire.

Scientific Computing Contractor May 2011 - Jun 2013

National Cancer Institute | Bethesda, MD
 Provided statistical and modeling support for several drug discovery projects using gene expression analysis,
biomarker identification, mechanism of action, analysis of genomic databases, data mining, lead generation
by VLS
 Developed a structural bioinformatic tool for searching PDB for particular 3D features
 Designed a fragment-like library and implemented ~700 drug/fragment-likeness filters.
 Machine learning modeling (PCA, PLS, neural networks) of gene expression and QSAR - insights into MOA,
putative targets and biomarkers
 Implemented web interface for compound design and a web-based visualizer of activity cliffs
 Molecular modeling - Androgen receptor, Nrf2-Keap1 (IVR domain and of its Zn-mediated dimer), C-Myc,
Mnk, Akt, EGFR, BRAF

Bioinformatics Contractor Dec 2010 - Feb 2011

Cubist Pharmaceuticals | Lexington, MA
 Developed a web-based application for integration of pre-clinical data into company database using PipeLine
Pilot, PilotScript, Perl, UNIX

Principal Investigator May 2002 - Dec 2010

ArQule | Woburn, MA
 Supported numerous drug discovery and development projects using molecular modeling, computational
chemistry, bioinformatics, cheminformatics and machine learning
 Extensive experience on all stages from hit discovery to IND
 Co-developed ArQule technology platform for fragment-based discovery of allosteric kinase inhibitors
 Designed hundreds of combinatorial libraries for Pfizer and internal use
 Developed a novel ultra-fast “surrogate” docking algorithm
 Developed ADMET, serum binding and bioavailability models 
 Developed several cheminformatic applications (Daylight, PipeLine Pilot)
 Refined reagent-level and product-level diversity management methods.
 Augmented reactivity and toxicity filters for design of compound libraries.
 Developed a model for prediction of reagent reactivity
 Developed QSAR, COMFA/COMSIA and pharmacophore models - inhibitors of proteases and kinases
 Hit discovery: Developed VLS protocol with 15% to 25% experimental hit rate (low µM IC50)
  Lead optimization: Drove affinity of several compound series (kinase targets) down to sub-nM range
 Developed structural model of hERG 
 Developed ML-based onco- and kinase-likeness scoring methods
 Developed a method for identification of proteins for selectivity assays
 Experimental: Developed a thermal shift fluorimetry assay for binding 
 Line management: one Ph.D report
 

EDUCATION

Ph.D
Kurchatov Institute of Atomic Energy, Moscow, Russia
Chemical Physics and Mathematics
http://eng.nrcki.ru, http://en.wikipedia.org/wiki/Kurchatov_Institute

M.Sc.
Moscow Institute of Physics and Technology, Moscow, Russia
Molecular Biophysics and Chemical Physics
http://en.wikipedia.org/wiki/Moscow_Institute_of_Physics_and_Technology

Certificate, MongoDB for Developers

MongoDB University

Certificate, R Programming
Coursera

TensorFlow for Artificial Intelligence and Deep Learning

Cloudera

Natural Language Processing

Cloudera

Statistical Analysis of Microarray Data

NIH

Introduction to Microarray Databases

NIH

Multivariate Data Analysis and Statistical Design

Umetrics
 

HONORS AND AWARDS

 2010, “Best Team of the Year”, ArQule, as member of Hit Generation Team that delivered 2 chemotypes in
lead optimization in 9 months for Daiichi-Sankyo collaboration
 2009, “Best Team of the Year”, ArQule, as member of team that developed a suite of biophysical assays
 1992, NATO grant for the project: "Labeling of Proteins using Solid State Catalytic Hydrogen Isotope
Exchange"
 

EDITORIAL

 Editor: Current Proteomics, MedCrave Online Journal of Proteomics & Bioinformatics

  Reviewer: Proteins: Structure, Function, and Bioinformatics, Current Computer-Aided Drug Design, Journal
of Chemical Information and Modeling, Journal of Molecular Graphics and Modelling, European Journal of
Medicinal Chemistry, Bioorganic & Medicinal Chemistry, Expert Opinion on Drug Metabolism and
Toxicology, Mini Reviews in Medicinal Chemistry, The 5th International Symposium on Management,
Engineering and Informatics: MEI 2009.
 Organizing Committees:
 2005-2009, Annual Congress of International Drug Discovery Science and Technology (IDDST), SAB
member
 2007-2008, Communications Director, BAGIM (Boston Area Group for Informatics and Modeling),
www.bagim.org
 2005, 230th ACS National Meeting, Symposium on Visualization and Interpretation of Computational
Models
 

PATENT APPLICATIONS

 Filikov A, System and method for automated prediction of event probabilities with model based filtering. US
62/980,938, 2020.
 

PATENTS

 Ashwell; Mark A. Brassard; Chris, Filikov; Anton, Hill; Jason, Koerner; Steffi, Lapierre; Jean-Marc, Liu;
Yanbin, Namdev; Nivedita, Nicewonger; Robert, Palma; Rocio, Tandon; Manish, Vensel; David, Matsuda;
Akihisa, Iimura; Shin, Yamamoto; Yuko Substituted imidazopyridinyl-aminopyridine compounds, US
8,501,770, 2013
 Ali; Syed M., Ashwell; Mark A., Brassard; Chris, Dalton; Audra, Filikov; Anton, Hill; Jason, Namdev;
Nivedita, Palma; Rocio, Tandon; Manish, Vensel; David, Wang; Jianqiang, Westlund; Neil Substituted
imidazolyl-5,6-dihydrobenzo[N]isoquinoline compounds US 8,263,610, 2012
 Desjarlais JR, Filikov A, Steed PM, Zalevsky J, Szymkowski DE Treatment of TNF-alpha related disorders
with TNF-alpha variant proteins. US 7,687,461, 2010
 Lapierre JM, Namdev ND, Ashwell MA, France DS, Wu H, Hutchins PM, Tandon M, Liu Y, Link JS, Ali
AM, Brassard CJ, Nicewonger RB, Filikov A, Carazza RJ, RAF inhibitors and their uses. US 7,501,430, 2009
 Dahiyat, Bassil I; Desjarlais, John R; Filikov, Anton; Muchhal, Umesh; Tansey, Malu; Zalevsky, Jonathan
Protein based TNF-alpha variants for the treatment of TNF-alpha related disorders WO-03033720,
AU2002334766, 2007.
 Dahiyat, Bassil, I., Desjarlais, John, R.; Filikov, Anton; Muchhal, Umesh; Tansey, Malu; Zalevsky, Jonathan.
TNF-alpha variants proteins for the treatment of TNF-alpha related disorders. US 7,244,823 B2. 2007.
 Filikov AV, Method of Prediction of Solubility of Chemical Compounds. US 7,117,102 B2, 2006.
 Dahiyat, Bassil, I., Filikov, Anton Tnf-alpha variants. US 7,056,695 B2, 2006.
 Dahiyat, Bassil, I., Filikov, Anton Tnf- variants. US 7,101,974 B2, 2006.
 Filikov, Anton, Dahiyat, Bassil, I. Nucleic acids and proteins with growth hormone activity. US 6,946,265,
2005.

PUBLICATIONS

 Filikov A, Pethe S., Fischer A., Kelley R., Ozminkowski R., Use of Stratified Cascade Learning to Predict
Hospitalization Risk with only Socioeconomic Factors. J. Biomed. Inform. 2020 Apr 104:103393
https://doi.org/10.1016/j.jbi.2020.103393
 Pepe A, Pamment M, Kim YS, Lee S, Lee M-J, Trepel J, Filikov A, Malhotra S, Synthesis and structure–
activity relationship studies of novel dihydropyridones as androgen receptor modulators, J. Med. Chem. 2013
Nov 14;56(21):8280-97.
  Vélez C, Cox O, Rosado-Berrios C, Molina D, Arroyo L,Carro S, Filikov A, Kumar V, Malhotra S,Cordero
M, Zayas B, Novel Nitrobenzazolo[3,2-a]quinolinium Salts Induce Cell Death through a Mechanism
Involving DNA Damage, Cell Cycle Changes, and Mitochondrial Permeabilization. Open Journal of
Apoptosis, 2013 Apr 29;2(2):13-22.
 Yoon S Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S., Optimization of high
throughput virtual screening by combining shape-matching and docking methods. J. Chem. Info. Model.,
2008, Feb 27.
 Yoon S, Smellie A, Hartsough D, Filikov A, Surrogate Docking: Structure-Based Virtual Screening at High
Throughput Speed. J. Comput. Aided. Mol. Des., 2005, 19(7):483-97.
 Yoon S, Smellie A, Hartsough D, Filikov A, Computational identification of proteins for selectivity assays.
Proteins: Structure, Function, and Bioinformatics, 2005 Mar 15;59(3):434-443.
 Steed PM, Tansey MG, Zalevsky J, Zhukovsky EA, Desjarlais JR, Szymkowski DE, Abbott C, Carmichael
D, Chan C, Cherry L, Cheung P, Chirino AJ, Chung HH, Doberstein SK, Eivazi A, Filikov AV, Gao SX,
Hubert RS, Hwang M, Hyun L, Kashi S, Kim A, Kim E, Kung J, Martinez SP, Muchhal US, Nguyen DH,
O'Brien C, O'Keefe D, Singer K, Vafa O, Vielmetter J, Yoder SC, Dahiyat BI., Inactivation of TNF signaling
by rationally designed dominant-negative TNF variants. Science. 2003 Sep 26;301(5641):1895-8.
 Filikov AV, Hayes RJ, Luo P, Stark DM, Chan C, Kundu A, Dahiyat BI., Computational Stabilization of
Human Growth Hormone. Protein Sci. 2002 Jun;11(6):1452-61.
 Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL , Identification of ligands
for RNA targets via structure-based virtual screening: HIV-1 TAR. J. Comput. Aided. Mol. Des. 2000
14(6):593-610.
 James TL, Lind KE, Filikov AV, Mujeeb A, Three-Dimensional RNA Structure-Based Drug Discovery. J.
Biomol. Struct. Dynam., 11(1), 1-5 (1999).
 Bell TW, Khasanov AB, Drew MG, Filikov A, James TL, A Small-Molecule Guanidinium Receptor: The
Arginine Cork. Angew. Chem. Int. Ed. Engl. 1999 Sep;38(17):2543-2547.
 Filikov AV, James TL, Structure-based design of ligands for protein basic domains: application to the HIV-1
Tat protein. J. Comput. Aided Mol. Des., 1998 May;12(3):229-40.
 

RECENT PRESENTATIONS

 A. Filikov, M. Athi, M. Orescanin, Segmentation of Home Speaker 500 Users Based on Feature Usage. Bose
Lab Expo, 2019, Boston
 D. Bondarev, A. Filikov, J. Patterson, C. Wang, O. Stradella, Flexible Solution and Integrated Web Interface
for Processing and Uploading of Diverse Bioassay Data, BioIT-2015, Boston
 Anton Filikov, Antonella Pepe, Vineet Kumar, Sanjay V Malhotra, Design of antiandrogens: Challenge of
receptor modeling, Fall ACS National Meeting, Indianapolis, September 2013.
 Anton Filikov, Structural and Property Profile Analysis of the CBC Diversity Screening Library Collection,
Chemical Biology Consortium Steering Committee Meeting, Bethesda, May 8, 2013.
 Anton Filikov, Antagonistic androgen receptor structure: Useful models despite low homology, ICM User
Group Meeting, San Diego, March 30-31, 2012.
 Anton Filikov and Mark A. Ashwell, R-group virtual screening with guided docking, 239th ACS National
Meeting, San Francisco, March 21–25, 2010.
 

LANGUAGES

Fluent in Russian
 

OTHER SKILLS

 Diplomas in Jazz Improvisation, Jazz Studio Moskvorechie (Moscow), San Francisco City College, Pasadena
City College
 Pianist in The NIH Jazz Band (2011-2013)
 Recent music videos:
 https://www.youtube.com/watch?v=uxJyScNj23w
 https://www.youtube.com/watch?v=uxJyScNj23w
 https://www.youtube.com/watch?v=Fi9_GJfGbiA
 https://www.youtube.com/watch?v=K8y9bXu-zJo