Prasanna Ramachandran
Menlo Park,CA
Summary
Proficient proteomics data scientist with expertise in mass spectrometry data analysis, bioinformatics, and computational biology, driving impactful insights through advanced data-driven methodologies
Overview
15
15
years of professional experience
Work History
Manager, Biostatistics
InterVenn Biosciences
South San Francisco, CA
07.2023 - 09.2024
- Manage the clinical data science team, facilitate inter-departmental collaborations and communications, resource allocation for various projects
- Data analysis of patient data generated from internal or external patient samples in targeted assays for various disease conditions including CRC, ovarian cancer, NASH, HCC, pancreatic cancer, Covid
- Generating machine learning models for predicting diseased states compared to controls
- Software tools used include Python, Scikit-Learn, Numpy, Pandas, Matplotlib, Google Cloud Platform (GCP), git, R (familiarity)
- Building and utilizing data analysis pipelines for converting raw experimental mass spectrometry generated data into to a usable format
- Generating reports for quality checks of experimental runs and exploratory data analysis
- Building and maintaining Google Cloud SQL (MySQL) and Cloud Firestore (no SQL) database on Google Cloud Platform to store data generated from patient samples
- Data analyses of discovery glycoproteomics experiments using Proteome Discoverer/Byonic to find glycopeptides that might be indicative of diseased states
- Writing manuscripts for peer reviewed publications, presenting results at conferences.
Senior Bioinformatician
InterVenn Biosciences
South San Francisco, CA
12.2021 - 07.2023
- Data analysis of patient data generated from internal or external patient samples in targeted assays for various disease conditions including CRC, ovarian cancer, NASH, HCC, pancreatic cancer, Covid
- Generating machine learning models for predicting diseased states compared to controls
- Software tools used include Python, Scikit-Learn, Numpy, Pandas, Matplotlib, Google Cloud Platform (GCP), git, R (familiarity)
- Building and utilizing data analysis pipelines for converting raw experimental mass spectrometry generated data into to a usable format
- Generating reports for quality checks of experimental runs and exploratory data analysis
- Building and maintaining Google Cloud SQL (MySQL) and Cloud Firestore (no SQL) database on Google Cloud Platform to store data generated from patient samples
- Data analyses of discovery glycoproteomics experiments using Proteome Discoverer/Byonic to find glycopeptides that might be indicative of diseased states
- Writing manuscripts for peer reviewed publications, presenting results at conferences.
Senior Scientist
InterVenn Biosciences
South San Francisco, CA
11.2018 - 12.2021
- Data analysis of patient data generated from internal or external patient samples in targeted assays for various disease conditions including CRC, ovarian cancer, NASH, HCC, pancreatic cancer, Covid
- Generating machine learning models for predicting diseased states compared to controls
- Software tools used include Python, Scikit-Learn, Numpy, Pandas, Matplotlib, Google Cloud Platform (GCP), git, R (familiarity)
- Building and utilizing data analysis pipelines for converting raw experimental mass spectrometry generated data into to a usable format
- Generating reports for quality checks of experimental runs and exploratory data analysis
- Building and maintaining Google Cloud SQL (MySQL) and Cloud Firestore (no SQL) database on Google Cloud Platform to store data generated from patient samples
- Data analyses of discovery glycoproteomics experiments using Proteome Discoverer/Byonic to find glycopeptides that might be indicative of diseased states
- Writing manuscripts for peer reviewed publications, presenting results at conferences.
Bioinformatics Scientist
Second Genome
South San Francisco, CA
08.2016 - 05.2018
- Building machine learning models using SVM, Random Forest and Logistic Regression to predict protein behavior in biological assays
- Software tools used include Python, Scikit-Learn, NumPy, Pandas, Matplotlib, AWS EC2, AWS S3
- Built and maintained a MySQL database of environmental genome and metagenomes on AWS Aurora and Athena
- Bioinformatics support for various internal projects.
Scientist
Eurofins Lancaster Laboratory (Genentech)
South San Francisco, CA
05.2013 - 06.2015
- Early stage molecular assessment of therapeutic antibodies to identify spots of potential modifications in the complementarity determining regions (CDRs)
- Used machine learning (ScikitLearn) to predict outcome of experiments based on previous experimental results
- Developed a Python/MySQL based GUI/Database tool to store data generated in the group and retrieve it in a meaningful manner
- Developed a software tool in Python to calculate the mass of CDR containing tryptic fragments containing sites of potential post-translational modifications and generate automated report template
- Peptide mapping to identify spots of potential modifications in the complementarity determining regions (CDRs) using the Orbitrap Elite
- Quantification of modified derivatives within the CDRs using XCalibur
- Intact mass measurement and characterization of therapeutic antibodies using Agilent HPLC-Chip/Q-TOF.
Post-Doctoral Fellow
Stanford University
Palo Alto
08.2011 - 05.2013
Post-Doctoral Fellow
University Of Washington
Seattle, WA
06.2009 - 11.2009
Education
Doctor of Philosophy (Ph.D.) - Biochemistry and Molecular Biology
University of California
Los Angeles, CA01.2009
Bachelor of Pharmacy (B.Pharm.) - Pharmaceutical Sciences
Birla Institute of Technology
Mesra, India01.1999
Skills
- Python, Scikit-Learn, Numpy, Pandas, Matplotlib, Google Cloud Platform (GCP), AWS EC2, AWS S3, MySQL, PostgresSQL, git, R (familiarity), mass spectrometry
Awards
- ASBMB 2012 Graduate/ Postdoctoral Travel Award - American Society for Biochemistry and Molecular Biology 2012
- FDA Commissioner's Fellowship (declined) - Food and Drug Administration 2010
- UCLA Fundamental Clinical Research Training Grant (T32 DE007296) - National Institute of dental and craniofacial Research (NIDCR) 2007
- CMB Training Grant (Ruth L. Kirschstein National Service Award, GM07185) - National Institute of Health
Timeline
Manager, Biostatistics
InterVenn Biosciences
07.2023 - 09.2024
Senior Bioinformatician
InterVenn Biosciences
12.2021 - 07.2023
Senior Scientist
InterVenn Biosciences
11.2018 - 12.2021
Bioinformatics Scientist
Second Genome
08.2016 - 05.2018
Scientist
Eurofins Lancaster Laboratory (Genentech)
05.2013 - 06.2015
Post-Doctoral Fellow
Stanford University
08.2011 - 05.2013
Post-Doctoral Fellow
University Of Washington
06.2009 - 11.2009
Doctor of Philosophy (Ph.D.) - Biochemistry and Molecular Biology
University of California
Bachelor of Pharmacy (B.Pharm.) - Pharmaceutical Sciences
Birla Institute of Technology
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