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Ronak S.
Metropolitan Mobile Home Park, United States
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This represents your current experience. It calculates by analyzing your connected repositories. By measuring your skills by your code, we are creating the ranking, so you can know how good are you comparing to another developers and what you have to improve to be better
Information on how to increase score and ranking details you can find in this blog post.
283.5
CodersRank Rank
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Perl
Developer
United States
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Python
Developer
United States
Highest experience points: 0 points,
0 activities in the last year
Python
159.1
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HTML
26.4
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JavaScript
18.3
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Perl
13.4
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JSON
12.2
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Batchfile
7.3
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List your work history, including any contracts or internships
Memorial Sloan Kettering Cancer Center
6 years 11 months
Manager, Computational Biology
Dec 2020 - Jun 2021 (6 months)
- Design, develop, and implement software tools for processing and analyzing high-throughput next-generation sequencing data, specifically for “liquid biopsy” applications
- Direct and supervise a team responsible for the development, maintenance, and operation of bioinformatics pipelines and the dissemination of results
- Work in concert with CMO teams and group leaders to provide analytical support to collaborative research projects at the Center
- Create databases and informatics systems for data management and pipeline automation
- Coordinate with clinical and research bioinformaticians to develop methods and establish best practices
- Direct and supervise a team responsible for the development, maintenance, and operation of bioinformatics pipelines and the dissemination of results
- Work in concert with CMO teams and group leaders to provide analytical support to collaborative research projects at the Center
- Create databases and informatics systems for data management and pipeline automation
- Coordinate with clinical and research bioinformaticians to develop methods and establish best practices
Principal Computational Biologist
May 2019 - Dec 2020 (1 year 7 months)
- Design, develop, and implement software tools for processing and analyzing high-throughput next-generation sequencing data, specifically for “liquid biopsy” applications
- Direct and supervise a team responsible for the development, maintenance, and operation of bioinformatics pipelines and the dissemination of results
- Work in concert with CMO teams and group leaders to provide analytical support to collaborative research projects at the Center
- Create databases and informatics systems for data management and pipeline automation
- Coordinate with clinical and research bioinformaticians to develop methods and establish best practices
- Direct and supervise a team responsible for the development, maintenance, and operation of bioinformatics pipelines and the dissemination of results
- Work in concert with CMO teams and group leaders to provide analytical support to collaborative research projects at the Center
- Create databases and informatics systems for data management and pipeline automation
- Coordinate with clinical and research bioinformaticians to develop methods and establish best practices
Principal Computational Biologist
Oct 2016 - Sep 2017 (11 months)
- Direct the development of new tools and algorithms for integrative analysis of DNA-seq, RNA-seq, and whole exome sequencing datasets
- Lead efforts in the analysis of large public datasets and databases, such as TCGA, ICGC as well as work with PI and Collabrators in analyzing coustom datasets.
- Explore and implement external methods, technologies, and collaborations of value to the CMO platform
- Leverage public cancer genomic data to support decisions on clinical indications and target populations
- Contribute production-grade code to the clinically regulated pipeline, following industry-standard software development procedures
- Lead a small team that develops, maintains, tests, and deploys the NGS pipeline
- Act as subject matter expert on DNA/RNA sequencing, bioinformatics algorithms, and genomic data
- Lead efforts in the analysis of large public datasets and databases, such as TCGA, ICGC as well as work with PI and Collabrators in analyzing coustom datasets.
- Explore and implement external methods, technologies, and collaborations of value to the CMO platform
- Leverage public cancer genomic data to support decisions on clinical indications and target populations
- Contribute production-grade code to the clinically regulated pipeline, following industry-standard software development procedures
- Lead a small team that develops, maintains, tests, and deploys the NGS pipeline
- Act as subject matter expert on DNA/RNA sequencing, bioinformatics algorithms, and genomic data
Senior Computational Biologist
Mar 2015 - Oct 2016 (1 year 7 months)
- Design, develop, and operate computational pipelines for the analysis of next-generation sequencing data
- Analyze data sets to discover and annotate cancer-causing genetic mutations in tumor specimens
- Evaluate and test third party software packages. Develop, refine, and improve bioinformatics tools for interpretation of large genomic data sets
- Work directly with experimental lab staff to assess and improve assay performance
- Design and develop databases to track specimen information, experimental parameters, performance metrics, and genomic results
- Maintain detailed records of all analyses, draft technical procedures and written summaries pertaining to research work, and present results and progress updates at lab meetings
- Analyze data sets to discover and annotate cancer-causing genetic mutations in tumor specimens
- Evaluate and test third party software packages. Develop, refine, and improve bioinformatics tools for interpretation of large genomic data sets
- Work directly with experimental lab staff to assess and improve assay performance
- Design and develop databases to track specimen information, experimental parameters, performance metrics, and genomic results
- Maintain detailed records of all analyses, draft technical procedures and written summaries pertaining to research work, and present results and progress updates at lab meetings
Bioinformatics Engineer III
Jan 2014 - Mar 2015 (1 year 2 months)
- Developed the framework to detect, filter & annotate structural aberrations from NGS datasets.
- Compared datasets & published w.r.t TCGA & MSK-IMPACT targeted sequencing panel having effusion fluids, FFPE and FROZEN samples for Ovarian Carcinoma.
- Mentored summer student to analyze data from MSK-IMPACT to optimize Indel detection process.
- Worked with the clinical group in updating and optimizing of the clinical ngs pipeline for faster runtime and high quality results.
- Analyzed whole exome sequencing data from Agilent Sure Select, Agilent Haloplex & Nimblegen SeqCap for comparison w.r.t Uniformity, Coverage, GC Bias & Reproducibility features for each assay.
- Compared datasets & published w.r.t TCGA & MSK-IMPACT targeted sequencing panel having effusion fluids, FFPE and FROZEN samples for Ovarian Carcinoma.
- Mentored summer student to analyze data from MSK-IMPACT to optimize Indel detection process.
- Worked with the clinical group in updating and optimizing of the clinical ngs pipeline for faster runtime and high quality results.
- Analyzed whole exome sequencing data from Agilent Sure Select, Agilent Haloplex & Nimblegen SeqCap for comparison w.r.t Uniformity, Coverage, GC Bias & Reproducibility features for each assay.
Bioinformatics Analyst
Oct 2012 - Dec 2013 (1 year 2 months)
- Developed computational framework to analyze next generation sequencing data generated from MSK-IMPACT a targeted next generation sequencing panel for solid tumors.
- Using this framework I processed multiple research project leading to multiple publications.
- Help to transition this research framework to clinical lab, thus it became the basis for all computational pipeline [Raindance & Ion Torrent platform] currently running in clinical lab. The framework was build in modular fashion for plug & play at each processing step and running it again from any-step where it might fail, without the need to rerun whole process.
- Helped clinical lab to validate the computational framework as well as validate the MSK-IMPACT assay to be used in New York State.
- Using this framework I processed multiple research project leading to multiple publications.
- Help to transition this research framework to clinical lab, thus it became the basis for all computational pipeline [Raindance & Ion Torrent platform] currently running in clinical lab. The framework was build in modular fashion for plug & play at each processing step and running it again from any-step where it might fail, without the need to rerun whole process.
- Helped clinical lab to validate the computational framework as well as validate the MSK-IMPACT assay to be used in New York State.
Northwell Health
Oct 2017 - Apr 2019 (1 year 6 months)
Director, Research Informatics
- Leads the design, development, and programs methods, processes, and systems to consolidate and analyze unstructured, diverse “big data” sources to generate actionable insights and solutions for client services and product enhancement.
- Selects, develops, manages and evaluates direct reports and oversees the development, management and evaluation of indirect reports.
- Oversees staff in developing software applications, including web applications, creating registration databases, performing statistical and graphical analysis and report generation and presentation.
- Drive computational biology best practices, including adoption of cloud computing, development of reusable libraries, version control, automated testing, thorough documentation, and reproducible research
- Develops computational tools in biology that use genomic data to generate biological hypotheses.
- Develops and oversees financial management including budget, salary, capital and revenue projections.
- Selects, develops, manages and evaluates direct reports and oversees the development, management and evaluation of indirect reports.
- Oversees staff in developing software applications, including web applications, creating registration databases, performing statistical and graphical analysis and report generation and presentation.
- Drive computational biology best practices, including adoption of cloud computing, development of reusable libraries, version control, automated testing, thorough documentation, and reproducible research
- Develops computational tools in biology that use genomic data to generate biological hypotheses.
- Develops and oversees financial management including budget, salary, capital and revenue projections.
Monsanto
Mar 2011 - Oct 2012 (1 year 7 months)
Bioinformatics Analyst / Application Developer
• Performed primary analysis of sequence data including quality control and handling of multiplexed samples, and provide feedback to experimental biologists.
• Have made `draft' quality plant genome sequences with the help of publicly available and in-house developed software for assembly of next generation sequencing data.
• Made production pipeline script to run on server as well as on Sun Grid Engine in batch format for assessment of the genomes.
• Written scripts to create XML representation of reports using and used XSLT and CSS templates for web representation of the reports. Made Web based User Interface (UI) for in-house software pipeline
• Have made `draft' quality plant genome sequences with the help of publicly available and in-house developed software for assembly of next generation sequencing data.
• Made production pipeline script to run on server as well as on Sun Grid Engine in batch format for assessment of the genomes.
• Written scripts to create XML representation of reports using and used XSLT and CSS templates for web representation of the reports. Made Web based User Interface (UI) for in-house software pipeline
Add some compelling projects here to demonstrate your experience
iAnnotateSV:iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data.
Feb 2015 - Present
iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data. This works for majority is just re-writing of a tool called dRanger_annotate written in matlab by Mike Lawrence at Broad Institue. But it also has some additional functionality and control over the annotation w.r.t the what transcripts to be used for annotation. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina.
Ion-Torrent Data Analysis
Aug 2012 - Present
Analyzing Ion-Torrent data for developing snap-shot genomes for marker-discovery. Process the 200bp reads as well as 400bp reads and made snap-shot assembly using tmap, and produced mutational profile data using GATK.
Web-Portal Development for Genome Assembly SnapShot
Sep 2011 - Present
Developed an Perl, XML-XSLT based Web-Portal to visualize results of Snapshot-Genome Assembly.
This section lets you add any degrees or diplomas you have earned.
George Mason University
Masters, Bioinformatics and Computational Biology
Jan 2008 - Jan 2010
D.Y.Patil University School of Biotechnology and Bioinformatics
B.Tech, Bioinformatics
Jan 2004 - Jan 2008
Worked on Microbes that help in creating natural repellent against pesticides without affecting plant and created a progrma in C++ for survival at diffrent conditions.(All done at BARC)
Institute of Bioinformatics and Applied Biotechnology
Certification in GENES to DRUGS: In-Silico Drug Discovery, Computational Biology
Jan 2006 - Jan 2006