Virendra Chaudhri

Omics and multimodal analysis and integration of datasets with focus around genetic datasets. Expertise in mathematical and computational modeling, quantitative systems pharmacology, data-driven modeling, machine learning, and statistical methods in gene and protein expression.

Experience with metabolomics, RNA-seq, scRNA-seq, ChIP-seq, ATAC-seq, spatial transcriptomics, and Hi-C analysis. Proficient in R, MATLAB, shell, Python, and NextFlow scripting with AWS, Azure, and EC2 cloud computing experience.

Data Scientist III at Sanofi (2025-01 – 2025-04)

Working through Adecco as full-time contract employee

Senior Computational Scientist at Sanofi (2022-07 – 2024-12)

Employed through RCH solutions as full-time contract employee

• Biomarkers, PD/PK/Efficacy modeling dupilumab responses in atopic dermatitis (AD). Application to Sanofi pipelines. AD targetID, proposed new targets.
• Endotyping of AD and Psoriasis, BioMAP consortium efforts, data tracking and internalization.
• AD and asthma patient stratification and developed multiple classifiers of disease endotypes. HCP predictive modeling (Senior Lead)
• Single cell and spatial transcriptomics analysis in AD, CRISPR-screening analyisis.
• AI/ML approaches to identify patient endotypes and delivered ready to use classifier in clinical setting for trials with targeted new therapies.

Computational Biologist/Research Scientist at University of Pittsburgh (2019-03 – 2022-07)

The role involves mentoring younger colleagues, graduate students and undergraduate trainees in computational biology.

• Worked as a full-time computational biologist, with focus on single-cell analysis (scRNA-seq, scATAC-seq), along with skin-immunology of skin resident T cells, skin resident mast cells, and skin innervating different subsets of neurons, memory B cells, lung immunology, and lung fibrosis. (Project Leader)
• Developed an algorithm in R to isolate novel composite elements from DNA-seq or ATAC-seq data without knowledge of TF ChIP-seq data. Available on GitHub as CEseek. (Project Leader)
• CEseek implementation on ImmGen ATAC-seq data: discovered thousands of new novel Composite Elements (CEs) and delivered a software solution in key molecular biology problem (Project Leader)

Research Associate/Computational Biologist at Cincinnati Children's Hospital Medical Center (2017-06 – 2019-02)

Research Associate position (1 year, 8 months) continuing from Post-Doctoral Fellow role

• Designed and performed experiments ChIP-seq, RNA-seq, nascent-RNA-Seq, FAIRE-seq, STARR-seq, HiC, prepared NGS libraries, analyzed output for NGS sequencing datasets using Shell scripting, R, and Homer leading to identification of >10,000 mammalian enhancers with first ever created mammalian cell's cis regulome.
• Integrated all omics datasets to chart the first functionally filtered cis-regulome of a mammalian cell (B cells). Identification of 10,000 functional enhancers and their connectivity to genes using Hi-C. (Project Leader)
• Integrated omics data from disparate sequencing depths ranging from millions of reads to billions of reads using parallel computing.
• B cell immunology but computational biology extended to hematopoietic progenitors and skin resident langerhans cells.

Post-Doctoral Fellow/Computational Biologist at Cincinnati Children's Hospital Medical Center (2013-06 – 2017-06)

Post-Doctoral Fellow position (4 years)

Post-Doctoral Associate/Computational at Weill Cornell Medical College (2011-01 – 2013-06)

• Led project studying the metabolism of cancer-associated fibroblasts (CAFs) isolated from the tumors of NSCLC patients.
• Performed experiments and analyzed mass spectrometry and RNA-seq data in R, MATLAB, and Python.
• Performed linear regression and classification methods (machine learning) of metabolic datasets based on the severity of cancer of donor patients.

Research Scholar, Computational Biology at Memorial Sloan-Kettering Cancer Center (2010-01 – 2011-01)

• Performed T-cell signaling experiments and mathematical modeling. T-cell isolation, FACS and mathematical modeling using R and MATLAB.

Post-Doctoral Fellow at International Centre for Genetic Engineering and Biotechnology (2009-10 – 2009-12)

• Performed analysis of microarray data using MATLAB from the human macrophages infected with various strains of Mycobacterium Tuberculosis by support vector machines (SVM, machine learning kernel methods) to classify the strains based on host gene expression signatures.
• Collaborated with multidisciplinary teams to design innovative experimental protocols.
• Analyzed data using statistical software to interpret research findings effectively.

Graduate Student Researcher at International Centre for Genetic Engineering and Biotechnology (2004-09 – 2009-09)

Advisor: Kanury V.S. Rao

• Designed and performed organic synthesis of small peptides using both solid and solution chemistry.
• Purified synthesized peptides using HPLC, analysis using NMR and mass spectrometry, towards building nanotubes from small peptides. Also synthesized small peptides for biological assays and nanotube formation.
• Performed experimental and mathematical modeling of B cell signaling.
• Performed cell culture assays, western blotting, molecular cloning.
• Modeled B cell receptor signaling using initial value problem described as coupled ordinary differential equations in MATLAB.
• Established and served as administrator for mid-range supercomputing facility (SGI Altix server) running proprietary Susy Linux with SGI-pro-pack.

Ph.D. in Immunology – International Centre for Genetic Engineering and Biotechnology (2009)

M.Sc. in Biotechnology – Kumaun University (2003)

B.Sc. in Biology and Chemistry – Kumaun University (2001)