2021–2022
Data Science Coursework
Dalarna University, Sweden
Training in statistics, programming, machine learning foundations, computational analysis and data visualization.
MOLECULAR BIOLOGIST · BIOINFORMATICIAN
Pradeep Bompada
I am a molecular biologist and bioinformatician whose research integrates molecular biology, functional genomics, genome editing, next-generation sequencing and computational biology to investigate gene regulation, chromatin biology and disease mechanisms.
ABOUT
Research at the intersection of biology and computation
I have developed a research profile that bridges wet-lab molecular biology and bioinformatics. My work spans CRISPR genome editing, next-generation sequencing, epigenetics, cancer biology, metabolism and computational analysis.
I am currently conducting research at the University of Colorado focused on pediatric brain tumors and regulatory mechanisms involving transcription, chromatin accessibility, single-cell genomics and three-dimensional genome organization.
12PubMed-indexed publications
10+Years of research experience
4Research institutions
Wet lab + DataIntegrated expertise
EDUCATION
Academic training
2020
PhD in Molecular Biology
Lund University, Sweden
Research in epigenetic and transcriptomic regulation, pancreatic islet biology, type 2 diabetes and biomarker discovery.
2015
Master’s in Molecular Biology
Lund University, Sweden
Advanced training in molecular genetics, gene regulation, cell biology and experimental research.
2013
Bachelor’s in Biotechnology
GITAM University, India
Foundation in biotechnology, genetics, biochemistry, cell biology and molecular biology.
MAJOR RESEARCH THEMES
Areas of scientific investigation
These themes summarize the major biological questions, disease areas and analytical approaches that have shaped my research career.
Epigenetics and Gene Regulation
Investigating how chromatin modifications and transcriptional programs regulate cellular responses in health and disease.
- Histone acetylation
- Chromatin remodeling
- Transcriptional regulation
- ChIP-seq, ChIP-qPCR and RNA-seq
Type 2 Diabetes and Metabolism
Studying glucose-responsive gene regulation and molecular mechanisms controlling pancreatic β-cell function and diabetic complications.
- TXNIP and hyperglycemia
- Osteopontin regulation
- Pancreatic islets
- Diabetic kidney
Atherosclerosis and Macrophage Biology
Exploring lipid accumulation, ceramides and inflammatory macrophage responses in vascular disease.
- Ceramide accumulation
- Macrophage models
- Patient-derived samples
- Therapeutic-target identification
Cancer Biology
Investigating tumor-regulatory mechanisms and therapeutic vulnerabilities using experimental and computational genomics.
- Pediatric brain tumors
- Medulloblastoma
- Glioma and DIPG
- Ewing sarcoma
Pediatric Brain Tumors
Current research focuses on transcriptional and epigenetic mechanisms in childhood brain tumors.
- DIPG and pediatric high-grade glioma
- Medulloblastoma
- CDK12-mediated transcription
- Therapeutic resistance
Single-cell Genomics
Using high-resolution sequencing to characterize cellular heterogeneity, cell states and regulatory networks.
- scRNA-seq
- scATAC-seq
- RNA+ATAC multiome
- Trajectory and communication analysis
Bioinformatics
Developing reproducible workflows for large-scale sequencing data and publication-ready biological interpretation.
- RNA-seq, ChIP-seq and ATAC-seq
- Hi-C and 3D genome analysis
- Differential analysis
- R, Python and Linux
CRISPR Genome Engineering
Applying genome-editing approaches to functional genomics and disease-mechanism studies.
- CRISPR/Cas9
- Guide RNA design
- Lentiviral delivery
- Functional validation
PROFESSIONAL EXPERIENCE
Research stories across my career
November 2024–Present
University of Colorado Anschutz Medical Campus
Molecular Biology & Bioinformatics Research
My current research focuses on understanding the molecular mechanisms that drive pediatric brain tumors, including diffuse intrinsic pontine glioma, pediatric high-grade glioma and medulloblastoma. By integrating molecular biology with computational genomics, I investigate chromatin organization, transcriptional regulation and cellular heterogeneity using RNA sequencing, single-cell genomics, chromatin accessibility profiling and three-dimensional genome analyses. The goal is to identify mechanisms of tumor progression and therapeutic resistance that may contribute to improved treatment strategies.
Epigenetic regulationCDK12 biologyscRNA-seqscATAC-seqHi-CChromatin organizationTherapeutic resistance
June 2023–October 2024
City of Hope National Medical Center
Postdoctoral Research
During my postdoctoral research at City of Hope, I investigated molecular mechanisms regulating cancer progression using genome engineering, molecular biology and computational genomics. My work combined CRISPR/Cas9 genome editing, lentiviral vector systems, functional genomics, drug-response studies and analysis of public sequencing datasets to identify novel therapeutic targets and improve our understanding of cancer biology. This multidisciplinary approach integrated experimental validation with large-scale genomic analysis to support translational cancer research.
CRISPRLentiviral systemsFunctional genomicsEwing sarcomaDrug responsePublic NGS analysis
November 2022–May 2023
Lund University
Postdoctoral Research
My postdoctoral research investigated how lipid metabolism influences inflammation and cardiovascular disease. I focused on ceramide accumulation in macrophages and its contribution to atherosclerosis by combining molecular biology, cell culture and translational studies using patient-derived samples. This work aimed to identify molecular mechanisms that could support new therapeutic approaches for cardiovascular disease.
Ceramide biologyMacrophagesAtherosclerosisPatient samplesInflammation
Lund University
Doctoral Research
My doctoral research focused on understanding how epigenetic mechanisms regulate gene expression during metabolic disease. Using chromatin immunoprecipitation, RNA sequencing, molecular biology and bioinformatics analyses, I investigated histone acetylation, transcriptional regulation, pancreatic islet biology, diabetic kidney disease and blood-based biomarkers. This work contributed to a better understanding of the molecular pathways underlying type 2 diabetes and related metabolic disorders.
Histone acetylationTXNIPPancreatic isletsDiabetesChIP-seqRNA-seqBiomarkers
Assistant Researcher
Foundational Research Experience
My early research experience established the experimental foundation for my scientific career. During this period, I developed expertise in molecular biology techniques, laboratory organization, experimental design and collaborative biomedical research while gaining extensive hands-on experience in cell and molecular biology.
Cell culturePCRRT-qPCRELISAExperimental optimizationScientific documentation
TECHNICAL EXPERTISE
Methods and analytical platforms
Molecular Biology
Cell culturePrimary cellsPCRRT-qPCRChIPELISASDS-PAGE
Genome Editing
CRISPR/Cas9Guide RNA designLentivirusKnockoutsSNP editing
Sequencing Technologies
RNA-seqChIP-seqATAC-seqHi-CscRNA-seqscATAC-seqMultiome
Bioinformatics
SeuratScanpyHarmonyArchRCellChatTrajectory analysis
Programming
RPythonLinuxSnakemakeHPC
Scientific Communication
Publication figuresManuscriptsPresentationsMentoringCollaboration
CURRENT RESEARCH PROJECTS
University of Colorado
My current research focuses on understanding the molecular and epigenetic mechanisms underlying pediatric brain tumors through the integration of molecular biology, next-generation sequencing and computational genomics.
Epigenetic regulation in pediatric brain tumors
Investigating chromatin and transcriptional mechanisms that shape tumor-cell states and disease progression.
CDK12-mediated transcriptional regulation
Studying how CDK12 affects gene expression in glioma cells and identifying potential therapeutic strategies.
Single-cell transcriptomics
Resolving tumor-cell heterogeneity, immune states and cellular responses using scRNA-seq.
Single-cell chromatin accessibility
Characterizing regulatory elements and transcription-factor programs using scATAC-seq and multiome data.
Hi-C and 3D genome organization
Studying chromatin compartments, domain structure and long-range regulatory organization in brain tumor models.
Therapeutic resistance and tumor ecosystems
Integrating genomic layers to identify mechanisms of resistance and candidate therapeutic vulnerabilities.
PAST RESEARCH PROJECTS
Research programs across previous institutions
These projects summarize the scientific questions and experimental approaches that defined my earlier research at City of Hope and Lund University.
CITY OF HOPE NATIONAL MEDICAL CENTER
Postdoctoral Research
My postdoctoral research at City of Hope combined cancer biology, genome engineering and computational genomics to investigate mechanisms of tumor progression and identify potential therapeutic targets.
CRISPR-based functional genomics
Designed and applied CRISPR/Cas9 strategies to investigate candidate genes, generate edited cell models and evaluate their functional roles in cancer-related pathways.
Lentiviral vector production and delivery
Produced and titrated lentiviral vectors for efficient gene delivery, genome editing and downstream functional studies in mammalian cell systems.
Ewing sarcoma target discovery
Investigated genes and molecular pathways that influence Ewing sarcoma biology and the therapeutic response to candidate inhibitors.
Cancer drug-response studies
Performed drug titration and cell-based assays to characterize treatment responses and identify biologically relevant dose ranges.
Public NGS data mining
Analyzed publicly available sequencing datasets to identify candidate genes, regulatory mechanisms and therapeutic vulnerabilities for experimental follow-up.
Circadian gene regulation in adipogenesis
Investigated the role of a newly identified clock-related gene in adipocyte differentiation and metabolic regulation.
LUND UNIVERSITY
Postdoctoral Research
My postdoctoral work at Lund University focused on the relationship between lipid metabolism, macrophage biology and atherosclerotic disease using experimental models and patient-derived material.
Ceramide accumulation in macrophages
Developed in-vitro models to examine how ceramide accumulation changes macrophage function and contributes to disease-associated cellular states.
Macrophage inflammation and lipid metabolism
Studied the interaction between lipid handling, inflammatory signaling and macrophage biology in the context of vascular disease.
Atherosclerosis mechanisms
Investigated molecular and cellular processes that contribute to plaque development and progression in atherosclerotic disease.
Patient-derived sample studies
Handled and analyzed patient-derived samples to connect experimental observations with clinically relevant cardiovascular disease biology.
Therapeutic target exploration
Worked with clinical collaborators to evaluate molecular pathways that could represent potential intervention points in atherosclerosis.
Translational cardiovascular research
Integrated molecular experiments with clinically informed questions to improve understanding of lipid-driven vascular inflammation.
LUND UNIVERSITY
Doctoral Research
My doctoral research investigated how glucose and metabolic stress alter epigenetic regulation and gene expression in pancreatic islets, kidney tissue and blood cells.
Histone acetylation of TXNIP in pancreatic islets
Studied how glucose-induced histone acetylation regulates thioredoxin-interacting protein expression in pancreatic islets.
Epigenetic regulation of TXNIP in kidney
Investigated how hyperglycemia influences chromatin regulation and TXNIP expression in diabetic kidney tissue.
Osteopontin regulation in pancreatic islets
Examined the biological role of osteopontin and the molecular mechanisms controlling its expression in pancreatic islets.
Osteopontin regulation in diabetic kidney
Characterized glucose-stimulated epigenetic regulation of osteopontin expression in kidney-related diabetes models.
Epigenome-wide histone acetylation profiling
Analyzed histone acetylation changes in peripheral blood mononuclear cells from patients with type 2 diabetes and atherosclerotic disease.
Blood-based epigenetic biomarker discovery
Investigated disease-associated epigenetic signatures with potential relevance as blood-based biomarkers for metabolic disease.
ChIP-seq and RNA-seq method development
Developed cost-efficient chromatin immunoprecipitation and sequencing workflows for diverse cell and tissue systems.
Pancreatic islet transcriptomics
Integrated gene-expression profiling and bioinformatics to understand glucose-responsive transcriptional programs in pancreatic islets.
FOUNDATIONAL RESEARCH EXPERIENCE
Assistant Researcher
My early research experience established the experimental foundation for my later doctoral and postdoctoral work through hands-on molecular and cellular biology.
Mammalian cell culture
Maintained and experimentally manipulated mammalian cell models while developing strong aseptic technique and reproducible culture practices.
PCR and RT-qPCR workflows
Performed nucleic-acid extraction, primer-based amplification and quantitative gene-expression analysis for research projects.
Protein and functional assays
Applied SDS-PAGE, ELISA and related assays to evaluate molecular changes and cellular responses.
Experimental optimization
Improved laboratory protocols by comparing conditions, troubleshooting workflows and documenting reproducible procedures.
Scientific documentation
Maintained organized experimental records, summarized results and supported interpretation of collaborative research findings.
Laboratory organization
Supported project coordination, reagent planning and efficient execution of parallel experimental activities.
PUBLICATIONS
12 PubMed-indexed articles
Grouped by research area and listed with journal, authors, DOI and PMID.
Pediatric Brain Tumors
2025
2025
Diabetes & Epigenetics
2021
2020
2019
2018
2017
2016
2016
2016
Immunology
2019
COVID-19
2020
CURRICULUM VITAE
Academic and professional record
Download the complete CV for education, research experience, technical expertise and scientific contributions.
Download Curriculum VitaeRESEARCH VISION
Integrating experimental and computational biology
My long-term goal is to integrate molecular biology, genomics and computational biology to understand disease mechanisms and translate genomic discoveries into meaningful biological insights. By combining experimental approaches with reproducible computational methods, I aim to contribute to more effective therapeutic strategies for complex human diseases.
CONTACT
Let’s connect and collaborate
Open to scientific collaborations, bioinformatics projects and research opportunities across molecular biology, cancer genomics and computational biology.
✉️ bompadap@gmail.com
📍 Aurora, Colorado, USA
🏛 University of Colorado Anschutz Medical Campus
📄 Download CV📚 PubMed publications