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Computational Biologist, Discovery Scientist, Bioinformatics Scientist

Woburn, Massachusetts, 01801, United States
February 15, 2018

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Somdutta Saha

Woburn, Massachusetts *****

(501) ***-****


Research scientist with over four years of post-Ph.D. industry experience in analysis, interpretation, and visualization of multi-omics and chemical dataset empowering data-driven decision-making in discovery and pre-clinical research.

Deep scientific knowledge in immunology, molecular biology, microbiology, genetics and novel target identification.

Leading bioinformatician with vast experience in using variety of open source and proprietary bioinformatics and chemical informatics tools and database structures.

Proven expertise in communicating analytical analysis verbally and in writing for scientific and technical audiences.

Track record of solving problems, innovating analysis, presenting and communicating in a matrix environment.

Expertise in curating and annotating data, biomarker development, handling team resources and offering solution.

Demonstrated ability to work collaboratively across multiple therapy areas- oncology, metabolic, rare disease and think creatively.

Recipient of the GSK Silver Impact Award for overall performance in December 2016.

Skills and Techniques

Computational analysis of pre-clinical proteomics data using R and data visualization with ggplots.

Metagenomics/16srRNA sequence analysis and functional analysis with QIIME v 1.9, PICRUST v 1.0.0, STAMP

DNA next-generation sequencing data analysis and RNA-seq data analysis, usearch, uclust, bowtie, bwt, cufflinks

Knowledge of open source dataset and analysis platforms like TCGA LAND, OncoLAND, GTEx, GEO,cbiopotal

Gene Set Enrichment/Pathway analysis tools – MetaCoreTM, KPA, GeneTrail, Reactome, STRING, KEGG, Cytoscape

Application of statistical methods – t-test (parametric/non-parametric), ANOVA, linear and non-linear regression, unsupervised clustering methods – PCA, PCoA

Molecular modeling suites and macromolecule visualization software like Discovery Studio, MOE, PyMOL

NLP-based text mining tools –Linguamatics and Literature mining – GoPubMed, PubMed.

Programming languages: PERL, R, Python

Relational database using MySQL, TIBCOTM Spotfire® for data visualization.

OS working experience -Linux, Windows, and Mac along with experience of working on the Sun Grid Engine; familiarity with creating standardized workflows with cloud computing (DNA Nexus).

Public domain search engines and databases – EBI/NCBI, UniProt, ChEMBL, IMGT, IgBLAST (immuno-genetics and immuno- informatics tools), genome browsers and Broad Institute tools.

Other bioinformatics/metabolite resources - Open Targets, Biocyc, Metacyc, HMDB, ChEBI, PDB, PubChem

Cheminformatics expert and working with predictive models for predicting compound activity.

Familiarity with different machine learning algorithms.

Biological assay management and submission – PerkinElmer E-Notebook for Biology.

Bioinformatics troubleshooting, code writing, knowledge of standard biochemical and biological laboratory techniques.

Work Experience

SOLID BIOSCIENCES, Cambridge, MA 2017 – Present

Research Scientist

Lead investigator in computational proteomic analysis of pre-clinical study with treated animals affected by muscular dystrophy; identified novel biomarkers for tracking clinical endpoints.

Integrated in-house pre-clinical (dosed with an investigational gene therapy drug) transcriptomics, proteomics, and metabolomics dataset with external datasets or natural history dataset to stratify biochemical biomarkers in terms of disease progression and healing.

Key computational scientist overseeing any internal needs in structure-based molecular modeling, protein sequence analysis, and external vendor management.

Identifies the informatics needs of the organizations and established the resources in house.

GLAXOSMITHKLINE, King of Prussia, PA 2014 – 2017

Post-doctoral Researcher – Computational Biology (Microbial Metabolite)

Discovered novel bioactive compounds that regulate immunological or metabolic events in the human host via host-microbe interaction from GSK compound library.

Performed NGS analysis of 16srRNA and further interpretation of microbial ecology in clinical cohorts to help drive critical decision making for investigational drugs; RNA-seq analysis of tissue transciptome and subsequent gene set enrichment and pathway analysis.

Successfully planned hypothesis-driven in vitro phenotypic screens and identified appropriate in vivo models for therapeutic testing.

Assisted in the proper storage and retrieval of information to/from databases; performed meaningful interpretation, visualization, and presentation of scientific results internally and externally.

Coordinated meetings with on- and off-shore interdisciplinary teams that included developing agenda, updating progress, and setting up follow-up action items.

Positively impacted the growth of microbiome-oriented strategies in the organization by partnering with different therapy areas within the company.

Facilitated decision making for active programs across cross-functional teams comprising biologists, chemists, informaticians, and statisticians.

Managed a group of six post-doc scientists for organizing the first global symposium for GSK post-docs in GSK Upper Merion Site in December 2016.

Assisted in early talent acquisition for GSK’s various undergraduate and graduate programs; represented GSK in several hiring events in Penn State University, University of Pennsylvania, and Annual Biomedical Conference for Minority Students (ABRCMS), 2015 and 2016.


ORISE Fellow – Chemical Informatics

Helped with regulatory decision making as well as applied tools for data-mining toxicology and/or clinical adverse effect findings using various computational chemistry tools.

Created and enhanced training databases for modeling.

Developed, validated, and optimized (Q)SAR models using a data set of 900 chemicals and their activities.


Graduate Research Assistant

Discovered the evolution and recognition pattern of antibodies reactive to neo-carbohydrate antigens using structure-based antibody modeling techniques and molecular simulation; immunogenicity prediction, researched antigen-antibody interactions at the binding pocket, epitope recognition, and maturation pathway for T cell independent antigenic recognition of antibodies.

Developed an immunogenic peptide that mimics carbohydrate-carbohydrate interactions after careful consideration of the structural aspects of carbohydrate antigenic recognition.

Maintained cancer cell lines, operated Biacore, performed protein purification and quantification assays, and set up experiments to study antigen-antibody interactions in Biacore 3000.

Led the bioinformatics efforts of the team and continued to work as an external collaborator on projects.


Graduate Research Assistant

Expert in handling the bioinformatics needs of the scientists in the team, group, or university; found solutions to problems and offered solutions, making them easily available to the scientists.

Excellent at maintaining core bioinformatics facility at UALR; provided access to students, faculty members, or researchers in terms of software and tools on a need basis.

GLAXOSMITHKLINE, Durham, NC 2012 – 2013

Scientist Student intern – Computational Biology (2013)

Performed application of human microbiome studies to drug discovery; created a comprehensive microbial metabolite library resource that allowed evaluation of microbial metabolome in various pre-/clinical studies by integration of publicly available metabolome databases to build an in-house resource.

Designed a web portal using different structural parameters with the goal of finding candidate molecules for combating gut-related disorder and to assess changes in metabolome that influence physiological parameters using Pipeline Pilot.

R&D Ph.D. Intern – Computational and Structural Chemistry Division (2012)

Investigated the physical aspects of permeation and identified chemical descriptors and appropriate numerical models (including both novel and traditional) for modeling permeation data.

Helped initiate a new collaboration with experimentalists researching on dermal permeation for treatment and analyzed their in-house data.


Ph.D., Bioinformatics, University of Arkansas at Little Rock, Arkansas, US (2008 – 2013)

Thesis Title: Structural Approaches for Targeted Therapy

M.S., Bioinformatics, West Bengal University of Technology, Kolkata, India (2005 – 2007)

B.Sc., Chemistry (Hons.), St. Xavier’s College, Kolkata India (2001 – 2004)

Selected Peer-reviewed Publications


1.Wang Z, Saha S. (2017). Microbiome Differences Between Metformin and Liraglutide Treated T2DM Subjects. Endocrinology, Diabetes & Metabolism. DOI: 10.1002/edm2.9.

2.Saha S, Rajpal D, Brown J. (2015). “Metabolites from Human Microbiota as a Potential Source of New Drugs”. Drug Discovery Today. Apr; 21(4):692-8.

3.Saha S. (2017). “Perspective: small molecules as players in targeted therapies”. Bioinformatics Review Feb; 3(2):1-3

4.Saha S. (2015). “Commensal Gut Microbes play an important role in shaping host physiology”. Journal of Bacteriology & Mycology: Open Access. Nov 18; 1(2):1-3 (invited mini-review).

5.Saha S. (2016). “The Microbe Story at ASM microbe 2016-Need for Microbiome Research”. Bioinformatics Review. Aug 16;2 (4) (News).

6.Kieber-Emmons T, Monzavi-Karbassi B, Pashov A, Saha S, Murali R. and Kohler H (2012). “The promise of the anti-idiotype concept”. Frontiers in Oncology. Dec 19; 2:196.

7.Saha S, Pashov A. et al. (2014). "Defining the Recognition Elements of Lewis Y-Reactive Antibodies". PLoS One. Aug 12; 9(8).

8.Kieber-Emmons T, Saha S, Pashov A, Monzavi-Karbassi B, Murali R.(2014). “Carbohydrate-mimetic peptides for pan anti-tumor responses”. Frontiers in Immunology. Jun 30; 5:308.

9.Saha S, Murali R, Pashov A, Kieber-Emmons T. (2015). “The Potential Role of Solvation in Antibody Recognition of the Lewis Y Antigen”. Monoclonal Antibodies in Immunodiagnosis and Immunotherapy. Oct 22; 34(5):295-302.

10.Saha S. (2016). “Tumor Associated Carbohydrate Antigens in Targeted Therapy”. Journal of Post-doctoral Research. May; 4(5):1-12 (mini-review)

11.Rao A, and Saha S. (2017). “Developing Antibiotics with “Selfish DNA” Plasmids”. Journal of Post-doctoral Research; July; 5: 5 (Editorial)

12.Murali R, Saha S, Pashov A, Kieber-Emmons T. (2017). “Summarizing Solvation Effects on Antibody Structure and Function”. Journal of Nature and Science. 3(7): e402.

13.Book chapter: Saha S, Pashov A, et al. (2011). "Carbohydrate Mimetic Peptide vaccines" In: Anticarbohydrate Antibodies- From Molecular Basis to Clinical Application (Ed: P Kosma and S. Müller-Loennies). Oct 11; 229-254 (invited review).

14.Book: Saha S. (2016). “Structural Approaches for Targeted Therapy: the complex world of tumor associated carbohydrate antigens in cancer”. Lambert Publishers Oct 19:128.

Selected Oral Presentations

1.Selected judge in the Computational and Systems Biology track. Annual Biomedical Research Conference for Minority Students (ABRCMS) 2017, Phoenix, Arizona, November 2-4, 2017.

2.Invited post-doctoral representative from GSK and selected student poster session judge in the Cancer Biology track: ABRCMS 2016. Tampa, Florida, November 9-12, 2016.

3.Selected speaker and facilitator. Oral presentation category for American Society of Microbiology (ASM) 2016, June16-20, Boston, 2016.

4.Invited post-doctoral representative from GSK and student poster session judge: ABRCMS 2015: Seattle, November 2015.

5.Guest lecturer: Microbiome lecture part 2: Ursinus College, November 2015.

6.Invited speaker at the third ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2012): October, Florida 2012 in their Immunoinformatics workshop.

Selected Awards and Poster Presentations

1.Presented a poster at the Keystone Symposium – Gut Microbiota Modulation of Host Physiology: The Search for Mechanism (C1), Mar 1 - 6, 2015 at Keystone, Colorado, USA. The title for the poster was “Computational Approaches for the Identification of Gut Microbiome Modulators and Immunomodulatory Metabolites”.

2.Presented a poster at the GSK-Duke Statistics workshop in Durham, NC on Sept 30, 2014. Poster title was “Meta-analyses of an integrated microbial- and host-metabolite resource reveal new ways of creating biological knowledge”.

3.Presented a poster titled “Minimal Mutations That Define Lewis Y Reactive Antibodies” at the “International Conference on Open Source for Computer-Aided Translational Medicine” from Feb 22-25, 2012 at Chandigarh, India.

4.Recipient of the NSF-funded female and minority student travel award at the second ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2011) held from Aug 1-3 at Chicago, Illinois, USA and was selected for presenting a poster at their Immunoinformatics workshop.

Selected Membership Affiliations

American Society for Microbiology (July 2015 – Present)

Associate Member of the American Society for Biochemistry and Molecular Biology (February 2016 – Present)

American Peptide Society (May 2017 – Present)

Editorial Board member of PostDoc Journal: Journal of Post-Doctoral Research (September 2015 – Present)

Editorial Board member of Bioinformatics Review (April 2016 – Present)

Invited Reviewer for Manuscript Submissions

Diabetes, Obesity and Metabolism (since October 2017)

ASM Microbe 2017 Conference abstract reviewer in Host Microbe Track

BMC Cancer (since January 2016)

Springer India

Journal of Postdoctoral Research (since October 2015)

Applied Microbiology and Biotechnology (February 2016 – Present) (impact factor: 3.16 in 2014)

SAGE Academica group of journals, including Evolutionary Bioinformatics, Biomarker Insights, Biochemistry Insights, Drug Target Insights, Bioinformatics, and Biology Insights

MCBIOS (MidSouth Computational Biology and Bioinformatics Society) 2016 and 2017 Proceedings

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