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Professional Experience

EMD Serono, Inc (Billerica MA)

Oct 2020 – Present: Associate Scientific Director of Bioinformatics
Nov 2016 – Oct2020: Principal Scientist Bioinformatics

  • Lead data analysis and biomarker strategy for predictive biomarker discovery for avelumab (Bavencio), a PD-L1 inhibitor jointly developed by EMD-Serono and Pfizer

  • Co-ordinate data analysis and biomarker development in collaboration with Pfizer Bioinformatics and Biomarker groups.

  • Understand tumor- tumor microenvironment interactions generated from tumor tissues and liquid biopsies using more than 10 platforms generating epigenomic, genomic, transcriptomic, proteomic, Digital Pathology, Radiomics and other data types. Developing AWS based pipelines

  • Comparison and co-ordination of computational and biomarker technological platforms for Roadmap 2020, Precision Oncology and Bedside2bench initiatives that aims to provide EMD with an edge at the forefront of immuno-oncology.

  • Interviewing candidates for expanding bioinformatics capabilities at EMD Serono, mentoring/supervising of colleagues/contractors/co-op students and oversee analysis at CROs.

Activities with Clinical Biomarker & Companion Diagnostics (including job rotation)

  • Participating in establishment of liquid biopsy, digital pathology/radiomics and lung immunotherapy platforms

  • Lead for development of indication agnostic signature from epigenetic biomarker signature with Oxford Biodynamics (data generation, overseeing analysis and interpretation, report & publications)

  • Lead for NCI collaboration for genomic biomarkers of response that determine immune function and safety signals

  • Part of first in industry collaboration between MD Anderson Apollo platform and EMD Serono that aims to carry out genomics aware, longitudinal data driven clinical trials of various EMD Serono assets.

  • Rotation project: development of Bintranfusp alpha trials in TNBC and Cervical cancers

  • Rotation project: development of a PCR based CDx assay for patient selection for TNBC trial with Qiagen

  • Identification and assessment of vendors/academic collaborators and due diligence

Career development and other activities

  • Editor of department newsletter that communicates TxM contributions and novel research to R&D leaders and beyond, providing branding to TxM (July 2020-Present)

  • Mentored by Global biostatistics and epidemiology group in understanding department processes and setting up trials in immunology (April 2020-Sept 2020)

  • worked with an executive coach to improve leadership and other skills and career development steps (Sep 2020-Feb 2021)

  • Member of Translational medicine extended leadership team and lead for People and Culture initiative (2019-2021)

TRACTION/Institute for Applied Cancer Science (A moonshot platform), The UT MD Anderson Cancer Center (Houston TX)

June 2012 – Aug 2016: Principal Institute Research Scientist for epigenomic drug discovery

  • Supported multiple early-stage small molecule drug discovery programs for targets in Bromodomains, Lysine Demethylases and protein Arginine methyl transferases gene families. Computational work helped in target discovery, validation, generate MOA and responder hypothesis and determining clinical path reach go/no-go decisions at key points.

  • Quantified immune suppressive environment across tumor types and generated responder hypothesis by data mining for the OX40 immunotherapy program, a milestone-based collaboration with IACS and GlaxoSmithKline.

  • Involved in multiple internal and outreach projects/grants targeting activity of mutant KRAS in PDAC.

  • Built IACS pre-clinical model database combining large-scale genomic profiles and other metadata from publicly available genomic profiles and internally generated data.

  • Devised methodology for model-based analysis of in-vivo functional genomic library screens for context based target identification.

  • Set up the IACS NGS RNA-Seq, RPPA and other pipelines.

  • Lead a team of 6 polish scientists (2013-15) in setting up the RNA-Seq and statistical analysis pipeline at the Poznan Supercomputing and networking center of Polish academy of science and data analysis.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute & Harvard School of Public Health (Boston MA)

June 2009-May 2012: Team leader and Research Fellow
Advisors: Cheng Li & Nikhil C. Munshi

Scientific Leadership and tool development

  • As a team leader (3 members) completed development of multiple methodology and platforms for data integration
    - Supervised building of the canEvolve portal for cancer integrative genomics and evolution.
    - Co-supervised the development of dChip-GemiNi method for regulatory network based integration of gene and microRNA expression profiles to identify candidate regulators of oncogenesis across cancer types
    - Lead a study on evolution of methodologies for integrating cancer copy number alterations with gene expression profiles
    - Developed the NetSurv methodology for generating sparse multivariate survival models from ultra-high dimensional oncogenomics data using L1 and L2 penalization. It utilizes gene co-expression networks and allows for better patient stratification.
    - Participated in development of dChIP-Surv module for microarray data

  • Participated in writing ~15 grant proposals with 3 funded grants and 1 received score above cutoff
    - Comparative network analysis of Human cancers to identify conserved and distinct pathway alterations. Role: PI (Won Claudia Adams Barr Award)

  • A Survival model for high-risk Multiple Myeloma patients combining dysregulated Gene Expression and Alternative splicing events. Role: PI (Won a DF/HCC Myeloma SPORE (NIH 5P50 CA100707-0 career development award)

  • Integrative Oncogenomics of Multiple Myeloma. NIH P01 1P01CA155258-01 Role: Named Personnel in B& B Core

Focus on Multiple Myeloma

  • Member of Multiple Myeloma SPORE at DFCI led by Dr. Kenneth C Anderson

  • Closely collaborated with Hematology Laboratory of Prof. Herve Avet-Loiseau at Univ. Nates in France.

  • Studied shaping and functional consequences of the dosage effect landscape in multiple myeloma.

  • Developed a composite survival model integrating gene expression and alternative splicing events for Multiple Myeloma patients identifying prognostic markers.

  • Participated in studies building classifier to identify subtypes of MM based on gene expression profiles and identifying dysregulated pathways in these subtypes.

  • Participated in a study pointing out difficulties in predicting treatment response in MM from gene expression profiles

Institute for Genomics and Systems Biology, The university of Chicago and Argonne National Laboratory, Chicago, IL & Yale University of Medicine, New Haven, CT

Jan 2006-May 2009: Postdoctoral Scholar & Bioinformatics coordinator for the modENCODE project
Advisor: Kevin White

Scientific Leadership and project management

  • I co-wrote the proposal for and worked as the Bioinformatics coordinator for the modENCODE project in the White laboratory. The project aimed to identify DNA sequence based functional elements in Drosophila melanogaster genome

  • Collaborated with Prof. Robert Grossman’s laboratory at UIC and members of Mike Pepka’s group at the Argonne National Laboratory for building cloud based storage, analysis and integration pipelines

  • Communicated with in-house data producers as well as other consortium member laboratories, and timely delivery of data to DCC and writing reports.

  • Studied distribution and functional roles of Drosophila melanogaster insulators and sequence specific transcription factors and participated in multiple studies that illucidated functional elements in Drosophila genome (> 1300 citations)

Tool Development

  • Created pipelines for quality control and primary analysis for gene expression and genome-wide protein-DNA association data generated with microarray and NGS platforms.

  • Lead development of Open Life Science Gateway that provides web-based access to TeraGrid resources. OLSGW was used for high-throughput analysis of 12 Drosophila genomes to Identify all sequence specific transcription factors and DNA associated proteins in the 12 Drosophila species

  • Lead the development of the BEOracle and BROracle SVM classifiers, for identifying B- cell epitopes that could provide highly specific antibodies, from protein sequences

  • Developed an HMM based segmenting procedure for identifying regions in epigenomic marks (Negre et al., 2010)

  • Participated in developing Bionimbus cloud based LIMS for storage and analysis portal

  • Lead the Development of the Flynet genomic resource for storing and visualizing Drosophila melanogaster regulatory networks

Structural and Computational Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany

PhD. Candidate
Advisor: Peer Bork

  • My thesis work provided guidelines to then nascent field of text-mining (4 papers, >350 citations)
    - Identified appropriate full-text article sections to mine for specific information
    - Generate biomedical domain specific PAS frames
    - Automated generation of a database for event of interest.

  • Other work included generating sensitive profiles to identify remote similarities in protein sequences and annotate function of protein families using data mining.

  • Obtained PhD fellowship from the Max Delbrück Centrum für Moleculare Medizin, Berlin- Buch, Germany and additional EMBL funding towards PhD

  • Obtained travel award from the PIA project grant of Dr. Nigel Collier to visit his laboratory in Japan

  • Obtained full funding from Centre De Reserca Matematica, Barcelona, Spain to attend ‘Mathematical Foundation of the Learning Theory’ conference

National Center for biological Sciences, Tata Institute of Fundamental Research, Bangalore, India

Aug 1998-June 2001: Junior Scholar and M.Sc. candidate
Advisor: R. Sowdhamini

  • One of only 5 candidates selected from country wide competition and interview process for a fellowship

  • M.Sc. degree obtained on the basis of research thesis carried out at the “best place to do biological science in India” with 3 publications.
    - Identified remote similarities (8% sequence identity) between structurally characterized bacterial K + channels and Human Insp3R and RyR Ca +2 channels. A homology model for the transmembrane tetramer was built that explained the ion specificity.
    - Identified structural determinants of binding and specificity in TGF-beta ligands – receptor interactions. Built homology models and carried out docking studies on binding mode of type II receptor to the ligand dimer and type I receptor complex.
    - Carried out a study to systematically annotate function of Drosophila melanogaster serine protease gene family (237 domains) using data mining and data integration.