Principal – Computational Biology

• May 2022 - Present

Computational Biologist

• Jun 2020 - May 2022

Machine learning driven Drug Discovery

Computational Biology Data Scientist

• Aug 2019 - Jun 2020

Developing and optimizing a sensitive experimental protocol and computational methods for early detection of cancer in cell-free DNA in blood plasma samples. Creating R and Python packages powered by ML for epigenetic analysis of sequencing and Illumina methylation array data Developing and optimizing a sensitive experimental protocol and computational methods for early detection of cancer in cell-free DNA in blood plasma samples. Creating R and Python packages powered by ML for epigenetic analysis of sequencing and Illumina methylation array data

Research Fellow in Computational Biology

• Jul 2016 - Aug 2019

• Designed methods and developed server for analysis of mutational signatures in tumors and prediction of cancer driver mutations outperforming other methods (MutaGene) • Quantified the effects of epigenetic factors linked to cancer mutagenesis • Derived statistical potentials and developed AI approaches for scoring protein interfaces and inferring structural interactomes with applications to drug repurposing (IBIS)

Postdoctoral Fellow in Computational Biology

• Aug 2013 - Jul 2016

• Studied evolution of protein binding sites and applied this knowledge to prediction of specificity in protein interfaces at residue-level resolution • Developed novel methods for building structural protein-protein interactomes on a large scale • Designed algorithms and methods for integrative analysis of cancer genomics data

Instructor in Applied Machine Learning

• Oct 2016 - May 2019

• Designed and taught the course covering Machine and Deep Learning with Python • Communicated Machine Learning concepts and best practices to non-experts • Designed and taught the course covering Machine and Deep Learning with Python • Communicated Machine Learning concepts and best practices to non-experts

Postdoctoral Research Scientist

• Apr 2011 - Jun 2013

• Developed the server for analysis of allosteric regulation in protein function (SPACER) • Discovered and characterized building blocks of enzymatic functions; developed probabilistic models for application to protein design; this approach has been experimentally verified in collaboration with Dan Tawfik and David Baker labs • Identified and annotated the descriptors/structure-sequence motifs of nucleotide ligand binding (NBDB database) • Characterized the determinants of thermophilic… Show more • Developed the server for analysis of allosteric regulation in protein function (SPACER) • Discovered and characterized building blocks of enzymatic functions; developed probabilistic models for application to protein design; this approach has been experimentally verified in collaboration with Dan Tawfik and David Baker labs • Identified and annotated the descriptors/structure-sequence motifs of nucleotide ligand binding (NBDB database) • Characterized the determinants of thermophilic and aerobic adaptation in prokaryotes on DNA, RNA, protein and protein interactions levels

Research Assistant

• Nov 2007 - Jun 2011

Guest Researcher

• Apr 2010 - Jul 2010

In close collaboration with Dan Tawfik lab working on directed protein evolution reconstructed ancestral prototypes of nucleotide and dinucleotide bonding and hydrolysis functions in ancient protein folds, such as Rossmann fold and P-loop hydrolase. This work lead to a PNAS publication in collaboration with David Baker lab. In close collaboration with Dan Tawfik lab working on directed protein evolution reconstructed ancestral prototypes of nucleotide and dinucleotide bonding and hydrolysis functions in ancient protein folds, such as Rossmann fold and P-loop hydrolase. This work lead to a PNAS publication in collaboration with David Baker lab.

Google Summer of Code Program

• Apr 2007 - Sep 2007

Implementing support for chemical data formats in Strigi search engine for the KDE project Implementing support for chemical data formats in Strigi search engine for the KDE project

Computer-Aided Drug Design (now merged with Abbott Labs)

• Oct 2006 - Jul 2007

Built a high quality homology model of a human potassium channel Kv7.1 for cardio toxicity screening (Long QT Syndrome) of drugs. The model was validated with KCNQ1 mutagenesis and patch clamping Built a high quality homology model of a human potassium channel Kv7.1 for cardio toxicity screening (Long QT Syndrome) of drugs. The model was validated with KCNQ1 mutagenesis and patch clamping

Systems Analyst

• 2004 - 2006

Software Developer / Systems Analyst

• 2001 - 2003

Systems and Network Engineer

• 1999 - 2000