Resume-Kamalika Ray
Personal Data
Address: F-403, F�rsterstra�e,70, 66111 Saarbr�cken, Saarland, Germany Phone: ------------5 email: ------------ Alternate email: ------------ Work Experience
Dec�16�Jan�19 Associate Scientist II at D.E.Shaw/Schrodinger.Inc Role: Responsible for providing scientific solutions and in-depth analysis of the user issues related to different modules of Schrodinger Suite and PyMOL. Other duties were writing Python scripts using Schrodinger APIs to meet user needs and maintenance of existing scripts of the Suite.
Summer 2016 Bioinformatics Research Assistant, Repository of Tomato Genomic Resources (RTGR), University of Hyderabad. Advisor: Dr. Rameshwar Sharma. Description: The central idea of the project was to do networking, using Cytoscape, of profiles of metabolites and hormones isolated from tomato roots and also from tomato fruits at different stages of ripening. Work also involved using CAMBA software to detect mutation after Next Generation Sequencing of PCR products in 48/64 fold pooled DNA samples.
Monsoon 2015 TeachingAssistant,AdvancedBiomolecularArchitecture,Prof. AbhijitMitra (IIIT Hyderabad) Role: The duties involved taking tutorials, grading exams and homeworks, and occasionally, preparing questions for practical exams.
Education
2019-2021 Master of Science in Bio-informatics (expected) Saarland University, Saarbr�cken, Germany
2014-2016 Master of Technology in Bio-Informatics International Institute of Information Technology, Hyderabad, India CGPA: 9.11/10, Rank: 1 out of 13
2010-2014 Bachelor of Technology in Bio-Technology West Bengal University of Technology, Kolkata, India CGPA: 8.52/10, Rank: 4 out of 26
2010 Class XII Kendriya Vidyalaya, Kolkata, India Percentage: 76.6%
Selected Coursework
NGS data analysis, Advanced Bioinformatics, Artificial Intelligence, Algorithms in Sequence Analysis, Single-Cell Genomics, Computer Aided Drug Design
Publications
Alka Kumari, Kamalika Ray, Sadhna Sadhna, Arun Pandey, Yellamaraju Sreelakshmi, Rameshwar Sharma. (2017). Metabolomic homeostasis shifts after callus formation and shoot regeneration in tomato. PLoS ONE. 12. 10.1371/journal.pone.0176978.
Computational Proficiency
Programming Python, C++, R (basic) , C(basic) Scripting Bash Web Related HTML, CSS OS Linux, Windows DBMS MySQL Computational Biology Schrodinger Maestro Suite Cytoscape, PyMol, Autodock Vina, CHARMM Others GIT, JIRA, NetSuite Projects
Dec�15-May�16 Structural and dynamical properties of chiral peptide nucleic acids, IIIT Hyderabad. Advisor: Dr. U Deva Priyakumar. Description: This project was aimed to study the structural and dynamic properties of chiral pepetide nucleic acids. The study is carried out by creating simulations of chiral peptide nucleic acids using CHARMM36 force field. Our experimental results discuss about the stability of pna complexes.
May�15-Dec�15 Benchmark study of various geometry based protein pocket detection algorithms, IIIT Hyderabad. Advisor: Dr. U Deva Priyakumar. Desription: The importance of protein 3D structures to the field of motivated our study of a dozen geometry-based algorithms for binding site detection in proteins. Our main result is ranking these algorithms based on their suitability for this purpose.
Summer�13 Identification of eukaryotic-like serine/ threonine and tyrosine kinase inhibitor in human pathogenic bacteria Enterobacteriacea, National Institute of Cholera and Enteric Diseases (ICMR). Advisor(s): Dr. Santasabuj Das and Dr. Rahul Shubhra Mandal. Description: The eukaryotic type serine-threonine protein kinases (STPKs) found in normal human microbiote and in pathogenic bacteria play a key role in regulation of pathogenicity. Our aim was to find out novel eukaryotic type kinases in pathogenic bacteria and screening the bacterial genome sequences using serine/threonine and tyrosine kinase signatures available in PROSITE database. We could predict two novel serine/threonine kinases and their functions.
Recognition and Awards
� Received Gold Medal for ranking 1st in M.Tech in Bioinformatics of batch 2014-16 at IIIT Hyderabad. � Dean�s Merit List (M.Tech in Bioinformatics) at IIIT Hyderabad for the academic years 2014-15 and 2015-16. � Awarded a certificate for participation in the workshop �LIMS based portal for plant Metabolomics� organized by Computational Core for Plant Metabolomics (CCPM6), February 2016. � Awarded a certificate for participation in the American Chemical Society (ACS) on Campus event at University of Hyderabad on January 29, 2016. � Awarded a Merit Certificate for securing 3rd Rank in third year B.Tech. � Participation in a seminar on Networking Drug Discovery and Pharm Innovation on 6th February, 2012. � Received certificates for completion of Python and Linux workshops conducted remotely by IIT Bombay.
Languages
Native Bengali Full Working Proficiency English (IELTS certified - 7.5 score) Working Proficiency Hindi
Personal Data
Address: F-403, F�rsterstra�e,70, 66111 Saarbr�cken, Saarland, Germany Phone: ------------5 email: ------------ Alternate email: ------------ Work Experience
Dec�16�Jan�19 Associate Scientist II at D.E.Shaw/Schrodinger.Inc Role: Responsible for providing scientific solutions and in-depth analysis of the user issues related to different modules of Schrodinger Suite and PyMOL. Other duties were writing Python scripts using Schrodinger APIs to meet user needs and maintenance of existing scripts of the Suite.
Summer 2016 Bioinformatics Research Assistant, Repository of Tomato Genomic Resources (RTGR), University of Hyderabad. Advisor: Dr. Rameshwar Sharma. Description: The central idea of the project was to do networking, using Cytoscape, of profiles of metabolites and hormones isolated from tomato roots and also from tomato fruits at different stages of ripening. Work also involved using CAMBA software to detect mutation after Next Generation Sequencing of PCR products in 48/64 fold pooled DNA samples.
Monsoon 2015 TeachingAssistant,AdvancedBiomolecularArchitecture,Prof. AbhijitMitra (IIIT Hyderabad) Role: The duties involved taking tutorials, grading exams and homeworks, and occasionally, preparing questions for practical exams.
Education
2019-2021 Master of Science in Bio-informatics (expected) Saarland University, Saarbr�cken, Germany
2014-2016 Master of Technology in Bio-Informatics International Institute of Information Technology, Hyderabad, India CGPA: 9.11/10, Rank: 1 out of 13
2010-2014 Bachelor of Technology in Bio-Technology West Bengal University of Technology, Kolkata, India CGPA: 8.52/10, Rank: 4 out of 26
2010 Class XII Kendriya Vidyalaya, Kolkata, India Percentage: 76.6%
Selected Coursework
NGS data analysis, Advanced Bioinformatics, Artificial Intelligence, Algorithms in Sequence Analysis, Single-Cell Genomics, Computer Aided Drug Design
Publications
Alka Kumari, Kamalika Ray, Sadhna Sadhna, Arun Pandey, Yellamaraju Sreelakshmi, Rameshwar Sharma. (2017). Metabolomic homeostasis shifts after callus formation and shoot regeneration in tomato. PLoS ONE. 12. 10.1371/journal.pone.0176978.
Computational Proficiency
Programming Python, C++, R (basic) , C(basic) Scripting Bash Web Related HTML, CSS OS Linux, Windows DBMS MySQL Computational Biology Schrodinger Maestro Suite Cytoscape, PyMol, Autodock Vina, CHARMM Others GIT, JIRA, NetSuite Projects
Dec�15-May�16 Structural and dynamical properties of chiral peptide nucleic acids, IIIT Hyderabad. Advisor: Dr. U Deva Priyakumar. Description: This project was aimed to study the structural and dynamic properties of chiral pepetide nucleic acids. The study is carried out by creating simulations of chiral peptide nucleic acids using CHARMM36 force field. Our experimental results discuss about the stability of pna complexes.
May�15-Dec�15 Benchmark study of various geometry based protein pocket detection algorithms, IIIT Hyderabad. Advisor: Dr. U Deva Priyakumar. Desription: The importance of protein 3D structures to the field of motivated our study of a dozen geometry-based algorithms for binding site detection in proteins. Our main result is ranking these algorithms based on their suitability for this purpose.
Summer�13 Identification of eukaryotic-like serine/ threonine and tyrosine kinase inhibitor in human pathogenic bacteria Enterobacteriacea, National Institute of Cholera and Enteric Diseases (ICMR). Advisor(s): Dr. Santasabuj Das and Dr. Rahul Shubhra Mandal. Description: The eukaryotic type serine-threonine protein kinases (STPKs) found in normal human microbiote and in pathogenic bacteria play a key role in regulation of pathogenicity. Our aim was to find out novel eukaryotic type kinases in pathogenic bacteria and screening the bacterial genome sequences using serine/threonine and tyrosine kinase signatures available in PROSITE database. We could predict two novel serine/threonine kinases and their functions.
Recognition and Awards
� Received Gold Medal for ranking 1st in M.Tech in Bioinformatics of batch 2014-16 at IIIT Hyderabad. � Dean�s Merit List (M.Tech in Bioinformatics) at IIIT Hyderabad for the academic years 2014-15 and 2015-16. � Awarded a certificate for participation in the workshop �LIMS based portal for plant Metabolomics� organized by Computational Core for Plant Metabolomics (CCPM6), February 2016. � Awarded a certificate for participation in the American Chemical Society (ACS) on Campus event at University of Hyderabad on January 29, 2016. � Awarded a Merit Certificate for securing 3rd Rank in third year B.Tech. � Participation in a seminar on Networking Drug Discovery and Pharm Innovation on 6th February, 2012. � Received certificates for completion of Python and Linux workshops conducted remotely by IIT Bombay.
Languages
Native Bengali Full Working Proficiency English (IELTS certified - 7.5 score) Working Proficiency Hindi