Research Labs
Explore cutting-edge research in the Department of Biochemistry and Molecular Genetics through our state-of-the-art research labs, where innovative investigations and scientific advancements take place.
Research Labs Heading link
| Ackerman Lab | Transcriptional mechanisms regulating hematopoietic (myeloid) development and gene expression. Eosinophil effector functions in asthma and other allergic diseases, tissue remodeling, and fibrosis. Biochemistry, cell and structural biology of eosinophil protein mediators of inflammation. |
| Benevolenskaya Lab | Mechanisms of promotion of differentiation by retinoblastoma protein (pRB), the role of histone demethylases RBP2 and PLU1 in cell fate determination and differentiation in mammalian cells. Global analysis of the transcriptional network regulated by RBP2-related proteins. |
| Caffrey Lab | Biochemical and NMR studies are directed at elucidating the structure and mechanisms of viral proteins, development of novel sensors of viruses, antiviral therapeutics. |
| Chronis Lab | Delineating principles of Stem Cell and iPSC biology and Developmental lineage choice. TF-driven mechanisms that determine cell fate specification during mammalian development, cellular reprogramming, and cancer. |
| Fan Lab | RNA biochemistry in animal development and regeneration. |
| Frolov Lab | Role of RB tumor suppressor pathway in development and cancer. Single-cell genomics. |
| Gaponenko Lab | Biophysical and biochemical characterization of macromolecular interactions with an emphasis on cancer-related proteins, structure based drug discovery and design |
| Hay Lab | Mechanisms of cell survival, cell cycle control, metabolism, and genesis of cancer. The PI3K/PTEN/AKT/mTOR signaling. The function of Akt isoforms at the cellular and organismal levels. |
| Jun Lab | Wound repair and regeneration, immune regulation, inflammation, cell signaling |
| Kuchay Lab | Regulation of proteostasis at cellular membranes by ubiquitin ligases and a newly identified GGTase 3. Functional involvement in diseases including cancer, cardiovascular disease and metabolic disease. |
| Lavie Lab | Structure-based design of novel therapeutic agents by prodrug development and enzyme modifications. X-ray crystallographic structure determination of enzymes involved in prodrug activation. |
| Merrill Lab | Mammalian stem cell and developmental biology, WNT signaling, Genome Editing. |
| Nakamura Lab | Roles of Checkpoint Proteins and Chromatin Modifications in Genome Stability, DNA Repair and Telomere Maintenance. |
| Raychaudhuri Lab | Regulation of mammalian cell cycle, cancer biology, transcription factors |
| Rehman Lab | Cell biology, bioinformatics, Alzheimer’s disease, inflammation and immunity, viral and bacterial infections, metabolism of cancer cells, vascular cells, stem cells and organoids. |
| Salahudeen Lab | Lung Cancer; Head And Neck Cancer; Squamous Cancers; Neoplasia; Progenitor Cell Plasticity, single cell and spatial transcriptomics |
| Segev Lab | From Yeast to Human Cells and Disease: 1) Regulation and Coordination of Trafficking Inside Cells: secretion, endocytosis, and autophagy; 2) Neurological Disorders (neurodevelopmental and neurodegeneration)-associated mutations in highly conserved genes |
| Shikano Lab | Protein interactions direct the selective sorting of membrane proteins, Regulation of GPCRs, cell signaling |
| Tyner Lab | Regulation of epithelial cell differentiation Cell cycle regulation in regenerating tissues. |
Professors/Labs accepting GEMS rotation students Heading link
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PIs accepting rotation students.
Elizaveta Benevolenskaya
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Constantinos Chronis
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Yuhang Fan
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Maxim Frolov
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Vadim Gaponenko
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Joonil Jun
Assistant ProfessorPhone:
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Shafi Kuchay
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Brad Merrill
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Toru M. Nakamura
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Jalees Rehman
Benjamin Goldberg Professor and HeadPhone:
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Ameen Salahudeen
Assistant ProfessorEmail:
Nava Segev
Distinguished ProfessorPhone:
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Rotation Project Description
Lab GEMS Research Concentration Rotation Project Name Project Description Benevolenskaya Molecular Biology and Genetics
Cancer BiologyStudying new mechanisms of drug resistance using single cell RNA sequencing Roles of histone demethylase KDM5A in pRB-mediated differentiation Fan Molecular Biology and Genetics
Cell Biology and Regenerative MedicineRNA biochemistry in animal development and regeneration RNA and its chemical modifications are key regulators of cell fate decisions and represent promising functional targets for regenerative biology. However, their collective roles in animal development and tissue regeneration remain largely unexplored. To address this gap, we will utilize planarians and sea squirts as model organisms to investigate the dynamics and functions of RNA biochemistry. Our study aims to compare RNA biochemistry and RNA-binding landscapes across organisms with varying regenerative capacities. By integrating advanced genomics and biochemistry approaches, we will investigate the non-canonical roles of RNA biochemistry during cell differentiation. This research seeks to uncover evolutionarily novel mechanisms driving regeneration and identify new epigenetic targets for therapeutic intervention. Frolov Molecular Biology and Genetics
Cancer BiologyThe role of Hippo and RB tumor suppressor pathways in control of cell proliferation and differentiation 1) To begin exploring the mechanisms of E2F/Rb-dependent activation of metabolic genes during adult skeletal muscle development.
The expression of metabolic genes is activated by E2F/Rb in differentiating muscle but not in proliferating adult muscle precursors. The goal of the project is to understand the mechanistic basis of these differences. Approaches used: genetics, genomics and biochemistry.
2) Role of Homothorax (Hth) in Hippo pathway in the eye progenitor cells.
The Hippo tumor suppressor pathway controls organ size by regulating the transcriptional co-activator Yki (YAP). Sd is the best known DNA-binding factor that recruits Yki to target genes. Recent data generated in the lab suggest that, in eye progenitor cells Yki is recruited by a different DNA-binding factor called Homothorax (Hth). The goal of this project is to evaluate this hypothesis using single cell genomics, bioinformatics, genetics and cell biology approaches.Jun Molecular Biology and Genetics "1. Intestinal regeneration modeling using organoid.
2. Cellular senescence in mouse model of colitis."1. Intestinal stem cells are vital for regeneration during homeostasis and after injury. Severe injuries often result in stem cell loss, and intestinal regeneration can only resume upon restoring the stem cell pool through reprogramming or dedifferentiation. 3D organoid culture provides a great platform to study molecular mechanisms. However, a suitable organoid model for post-injury stem cell regeneration is not readily available. We are developing a new genetically engineered organoid model.
2. We identified cellular senescence as a wound-healing response critical for injury repair. During chemicals-induced colitis in mice, cellular senescence occurs in mesenchymal cells (fibroblasts). We study the interaction of mesenchymal cells and intestinal epithelial cells for intestinal regeneration and the effect of cellular senescence on stem cells and regeneration. "Kuchay Molecular Biology and Genetics
Cancer Biology
Cell Biology and Regenerative MedicineUnderstanding the role of aberrant protein turnover at cellular membranes in health and disease. We employ interdisciplinary approaches (e.g., Proteomics, CRISPR/CAS9 gene editing, cell and mouse genetics, biochemistry, pharmacology) to investigate the role of membrane bound E3-ubiquitin ligases, enzymes that mark protein targets with ubiquitin polymers, to induce their complete degradation via ubiquitin proteasome system. We are interested in molecular mechanisms, developing new tools and assays for the membrane compartment specific E3-ligases to leverage our expertise for the targeted- protein degradation of disease-causing deregulated protein targets. Merrill Molecular Biology and Genetics
Cell Biology and Regenerative MedicineSynthetic Biology - CRISPR The project is essential the construction of and testing/validation of a new synthetic biology tool using aspects of CRISPR systems to provide mammalian cells with a set of genetic instructions not encoded within their genomes. It will involve some molecular DNA cloning, design of new DNA sequences, and hopefully testing how well the new sequences function in cells. Nakamura Molecular Biology and Genetics
Cancer BiologyRegulation of telomere maintenance. Telomeres are specialized nucleoprotein structures at the end of linear chromosomes, essential for stable maintenance of eukaryotic genomes.
We currently have two possible GEMS student rotation projects. The first project will be based on the characterization of a novel RPA (Replication Protein A) mutant that fails to maintain telomeres and survive by circularizing chromosomes, even though telomerase is robustly recruited to telomeres. The second project will be characterizing various mutants that affect the transcription of long noncoding RNA (lncRNA) known as TERRA and cause telomere elongation.Rehman Molecular Biology and Genetics
Cancer Biology
Cell Biology and Regenerative Medicine
Microbiology, Immunity and Inflammation
NeurobiologyProject 1: Development of human stem cell derived organoids to model lung disease
Project 2: The role of inflammation and infection in promoting Alzheimer's Disease
Project 3: Maternal-fetal inheritance of inflammatory stressProject 1: Working with stem cell derived progenitor cells of the lung epithelium, lung fibroblasts and lung vascular cells to create an organoid platform in which disease mechanisms can be studied. For the rotation, the primary goal will be for students to learn how to generate the organoids and assess the maturation of differentiated cells. Depending on the interest level and time, we can also subject the organoids to stressors and assess whether disease responses can be observed. A senior scientist will assist and guide the student to learn stem cell culture, differentiation and organoid assembly.
Project 2: Do repeated inflammatory stressors and bacterial or viral infections promote neurodegenerative disorders? Students will work with a neurobiologist in our lab and expose mice carrying human Alzheimer's disease mutations to stressors such as bacterial toxins or viral nucleic acid mimics and quantify how such stressors impact the blood brain barrier, premature senescence in certain brain areas and impair regeneration.
Project 3: How does inflammatory stress during pregnancy get transmitted to the next generation. Students will work with an immunologist to expose pregnant mice to bacterial toxins or viral stressors and then assess changes in the immune system, bone marrow and vasculature of the progeny. The assessment will focus on using flow cytometry to quantify changes in the hematopoietic and vascular lineages, as well as isolate cell populations for molecular studies.Salahudeen Cancer Biology
Molecular Biology and Genetics
Cell Biology and Regenerative Medicine
Microbiology, Immunity and InflammationDissecting immune cell populations in tissue homeostasis and cancer We are examining what immune cells infiltrate and promote tissue regeneration and whether these same cells play a role in the initial steps of tumor formation. We are utilizing mouse models, patient samples, and are conducting assays using spatial transcriptomics, single cell RNA-seq, explant cultures, and conventional histology and other cell biology techniques. Segev Molecular Biology and Genetics Project 1: The role of Rab1 GTPase in membrane traffic coordination and neurological disease
Project 2: Aberrant Processing Bodies (PBs) accumulation and clearance in a neurodevelopmental disorderIn both projects we use cutting-edge molecular genetics, biochemistry and microscopy technologies in yeast and human cells, to study cell biological questions related to human disease.
In Project 1, we study the effect of depletion of Rab1 GTPase or its TRAPP activator on secretion, Golgi morphology and autophagy, all of which are associated with neurological disorders.
In Project 2, we study the effect of mutations associated with neurodevelopment in human patients on the formation of aberrant PBs and explore cellular pathways that can clear them.GEMS Information
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Undergraduate Research Opportunities
Many of our faculty members accept undergraduate students to participate in their research projects.