Rothenberg, Ellen V.

Committee Member — 114 thesises

• Chow, Janet — A Pathobiont of the Mammalian Microbiota Balances Intestinal Inflammation and Colonization (2011, Dissertation (Ph.D.))
• Damle, Sagar S. — A Study of Information Processing in the Sea Urchin Embryo by Rewiring Mesodermal Gene Regulatory Networks and cis-Regulatory Analysis of Skeletogenic Regulators (2011, Dissertation (Ph.D.))
• Schwartz, Morgan Sarah — Accelerating Biological Discovery with Deep Learning and Spatial Optical Barcodes (2024, Dissertation (Ph.D.))
• McQueen, Anne T. — Ammonium Ion Effects on Hybridoma Cell Physiology (1989, Dissertation (Ph.D.))
• Del Real, Marissa Morales — Analysis of a Transcriptional Network Involving PU.1, Notch, and Gata3 in the Lymphomyeloid Lineage Decision during Early T-cell Development (2013, Dissertation (Ph.D.))
• Brorson, Kurt Andrew — Analysis of Expression, Structure and Evolution of Non-Classical Class I Major Histocompatibility Complex Genes (1990, Dissertation (Ph.D.))
• Boysen, Anne-Cecilie — Analysis of the Human T Cell Receptor α/δ Locus: New Approaches to Mapping and Sequencing (1996, Dissertation (Ph.D.))
• Fors, Lance — Analysis of the Structure, Expression and Evolution of the Shark Myelin Proteins and Genes (1990, Dissertation (Ph.D.))
• Kim, Stuart Kilsu — Antibody Genes, Oncogenes and Antisense Genes (1985, Dissertation (Ph.D.))
• Chapman, Tara Lynn — Biochemical Characterization of Two Cytomegalovirus MHC Class I Homologs (2000, Dissertation (Ph.D.))
• Hsiao, Elaine Yih-Nien — Brain, Gut and Immune Interactions in Autism Spectrum Disorder (2013, Dissertation (Ph.D.))
• Tan, Frederick Eng How — Brfl Post-Transcriptionally Regulates Pluripotency and Differentiation Responses Downstream of Erk MAP Kinase (2014, Dissertation (Ph.D.))
• Zhang, Mark Guangde — Bridging Sensory Perception to Developmental Decision Making in Caenorhabditis elegans (2024, Dissertation (Ph.D.))
• Sucov, Henry Michael — Characterization and Developmental Regulation of a Gene Expressed Specifically in the Skeletogenic Lineage of the Sea Urchin Embryo (1989, Dissertation (Ph.D.))
• Eakle, Kurt Andrew — Characterization of the SEC18 Gene of S. cerevisiae: Identification of a Protein Involved in Yeast Secretion (1989, Dissertation (Ph.D.))
• Perez, Andrew Alexander — ChIP-DIP: a Multiplexed Method for Mapping Proteins to DNA Uncovers Combinatorics Controlling Gene Expression (2024, Dissertation (Ph.D.))
• Fisher-Aylor, Katherine Irene — Chromatin Topology and Transcription in Myogenesis (2017, Dissertation (Ph.D.))
• Kirouac, Martha — cis-Regulatory Control of Three Cell Fate-Specific Genes in Vulval Organogenesis of C. elegans and C. briggsae (2003, Dissertation (Ph.D.))
• Fisher, Douglas Arthur — Class I Genes of the Major Histocompatibility Complex: Structural Studies on Genes of the Tla Locus (1986, Dissertation (Ph.D.))
• Galton, Riley — Co-Option of the piRNA Pathway to Regulate Neural Crest Specification (2023, Dissertation (Ph.D.))
• Galimidi, Rachel P. — Combating HIV with Novel Antibody Architectures (2016, Dissertation (Ph.D.))
• Brown, Keith B. — Comparative Studies of Vulva Development in C. briggsae (2001, Dissertation (Ph.D.))
• Iverson, Tina Michelle — Crystallographic Investigations of Respiratory Proteins (2000, Dissertation (Ph.D.))
• Hamburger, Zsuzsa Andrea — Crystallographic Studies of Invasin, a Bacterial Adhesion Molecule from Yersinia pseudotuberculosis (2002, Dissertation (Ph.D.))
• Beeler, Suzannah Michelle — Deciphering Regulation in Escherichia coli: From Genes to Genomes (2022, Dissertation (Ph.D.))
• Laubscher, Emily Chiu — Deep Learning-Enabled Integrated Measurements of Immune Signaling in Primary Human Macrophages (2024, Dissertation (Ph.D.))
• Funkhouser, William Keith Jr. — Demyelinating autoimmunity: murine T cell epitopes of MBP and primate T cell receptor Vβ variation (1992, Dissertation (Ph.D.))
• Cohen, Alexander Armand — Developing Multivalent Nanoparticle Vaccines Against Current and Future Viruses (2021, Dissertation (Ph.D.))
• Wang, Jue (Phyllis) — Direct Visualization of Cellular Protein Complexes in situ by Fluorescence-Guided Cryo-FIB-SEM and Cryo-ET (2025, Dissertation (Ph.D.))
• Ho, Margaret Ching Wai (MC) — Discovery of Active Cis-Regulatory Elements and Transcription Factor Footprints in Nematodes Using Functional Genomics Approaches (2015, Dissertation (Ph.D.))
• Fernandes, Jolene Sabrina — Dissection of Gene Regulatory Networks Underlying Patterning and Morphogenesis in the C. elegans Vulva (2007, Dissertation (Ph.D.))
• Banerjee, Abhik Kumar — Diverse Roles of RNA-protein Interactions: From Viral Antagonism to Mammalian Development (2021, Dissertation (Ph.D.))
• Garcia, Mayra — Dorsal-Ventral Patterning and Gene Regulation in the Early Embryo of Drosophila melanogaster (2012, Dissertation (Ph.D.))
• Yong, John — Dynamics and Heterogeneity of Gene Expression and Epigenetic Regulation at the Single-Cell Level (2015, Dissertation (Ph.D.))
• Jensen, Elizabeth Hwang — Elucidating the Role of O-GlcNAc Glycosylation in Neurobiology and Neurodegeneration (2018, Dissertation (Ph.D.))
• Yu, Kenneth Kwok-Chang — Engineering Immunity Against HIV (2012, Dissertation (Ph.D.))
• Caldera, Luis Fernando — Engineering Immunological Solutions for Pandemic-Level Threats (2026, Dissertation (Ph.D.))
• Martin, Christopher Hayes — Evolution and Expression at the 68C Glue Gene Cluster of Drosophila (1988, Dissertation (Ph.D.))
• Erkenbrack, Eric Matthew — Evolution of Developmental Gene Regulatory Networks in Echinoids (2016, Dissertation (Ph.D.))
• Prakash, Sharan Jagdish — Experimental and Neuroinformatic Definition of Neural Circuits in Caenorhabditis elegans (2024, Dissertation (Ph.D.))
• Levy, David E. — Expression of Endogenous Retroviruses in Inbred Mice : Coordinate Regulation and Structure of Multiple Transcription Units (1985, Dissertation (Ph.D.))
• Cohen, Sarah Michelle — Formation and Function of Ascarosides in the Nematodes C. elegans and C. briggsae (2021, Dissertation (Ph.D.))
• Lee, Pei Yun — Function and Regulation of the Strongylocentrotus purpuratus gatae Gene (2007, Dissertation (Ph.D.))
• Hahn, Young Shin Lim — Functional Analysis of Viral Nonstructural and Structural Proteins (1989, Dissertation (Ph.D.))
• Kronenberg, Mitchell — Gene Expression in B and T Lymphocytes: (1) Evolution of Rat Cκ Alleles (2) The T-cell Receptor Problem (1983, Dissertation (Ph.D.))
• Cornelison, Dawn D. W. — Gene expression in wild-type and MyoD-null satellite cells: regulation of activation, proliferation, and myogenesis (1998, Dissertation (Ph.D.))
• Meulemans, Daniel Keith — Genetic Correlates of Neural Crest Evolution (2004, Dissertation (Ph.D.))
• Sandler, Jeremy Edward — Genome Activation and Regulation of Signaling in the Rapidly Dividing Drosophila Embryo (2017, Dissertation (Ph.D.))
• Zhang, Jingli A. — Global Analysis of Dynamic Epigenetic Marking and Transcriptional Regulation Underlying T-Cell Lineage Commitment (2012, Dissertation (Ph.D.))
• Moiseyenko, Anastasiya O. — Gut Microbiota as Modulators and Therapeutic Targets in Parkinson’s Disease (2026, Dissertation (Ph.D.))
• Khosravi, Arya — Gut Microbiota Promote Hematopoiesis to Control Bacterial Infection (2014, Dissertation (Ph.D.))
• Kuntz, Steven Gregory — hlh-1 and the C. elegans Body Wall Muscle Transcriptional Differentiation Network (2011, Dissertation (Ph.D.))
• Gordon, Sean Patrick — Hormone and Gene Feedback during Development and Regeneration in Arabidopsis thaliana (2009, Dissertation (Ph.D.))
• Röschinger, Tom — Illuminating the Regulatory Dark Matter of E. coli with Massively Parallel Reporter Assays (2026, Dissertation (Ph.D.))
• Takei, Yodai — Integrated Spatial Genomics Reveals Organizational Principles of Single-Cell Nuclear Architecture (2021, Dissertation (Ph.D.))
• Shen, Yue — Interkingdom Communication of a Bacterial Mutualist and its Mammalian Host (2012, Dissertation (Ph.D.))
• Nahmad Bensusan, Marcos — Interpretation and Scaling of Positional Information During Development (2011, Dissertation (Ph.D.))
• Zarnegar, Mark Andrew — Investigating the Transcriptional Mechanisms Controlling Sfpi1, a Critical Regulatory Node Within Multiple Lineage Specifying Subcircuits of the Hematopoietic Gene Regulatory Network (2010, Dissertation (Ph.D.))
• Klein, Joshua Simon — Investigations in the Design and Characterization of HIV-1 Neutralizing Molecules (2009, Dissertation (Ph.D.))
• Tesar, Devin Brent — Investigations of the Mechanisms of Receptor-Mediated Immunoglobulin Transport in Mammals and Birds (2009, Dissertation (Ph.D.))
• Smith, Stephen Edward Paucha — Maternal Immune Activation and Abnormal Behavior in the Adult Offspring: Towards a Mechanism (2008, Dissertation (Ph.D.))
• Quintero Cadena, Porfirio — Mechanism and Scaling of Eukaryotic Transcription Activation (2021, Dissertation (Ph.D.))
• Mehta, Arnav — MicroRNA-132 is a Physiological Regulator of Hematopoietic Stem Cell Function and B-cell Development (2015, Dissertation (Ph.D.))
• Anaya, Michael Aurelio — Modernization of Monoclonal Antibody Screening and Protein-interaction Assays (2021, Dissertation (Ph.D.))
• Wang, Kang-Sheng — Molecular characterization of a receptor for the Togavirus Sindbis virus (1991, Dissertation (Ph.D.))
• Liu, Yang — Molecular Mechanism of Sulfated Carbohydrate Recognition: Structural and Biochemical Studies of the Cysteine-Rich Domain of Mannose Receptor (2001, Dissertation (Ph.D.))
• Gandhi, Shashank — Molecular Mechanisms Underlying Cardiac Neural Crest Development in Avian Embryos (2021, Dissertation (Ph.D.))
• Chour, William — Molecular Technologies for Antigen-Based Immunity (2021, Dissertation (Ph.D.))
• Sarma, Anish Anandsai — Multicellular Control (2023, Dissertation (Ph.D.))
• Koontz, Alison Lindsay — Neural Crest and Placodal Cells Contributions to Cranial Sensory Development (2022, Dissertation (Ph.D.))
• Hemmati, Houman David — Neural Stem and Progenitor Cells in Cancer and Development (2006, Dissertation (Ph.D.))
• Green, Harry Miguel — Novel Methods for Studying Ras/Erk MAP Kinase Signaling in Developing T Cells (2006, Dissertation (Ph.D.))
• Sun, Yi Henry — Organization and Evolution of the Class I Genes in the Murine Major Histocompatibility Complex (1986, Dissertation (Ph.D.))
• Wittrup, Karl Dane — Plasmid Propagation in the Yeast Saccharomyces cerevisiae: Flow Cytometry Studies and Segregated Modeling (1989, Dissertation (Ph.D.))
• Martin, Warham Lance — Protein-Protein Recognition: The Neonatal Fc Receptor and Immunoglobulin G (2001, Dissertation (Ph.D.))
• Preugschat, Frank — Proteolytic processing of the nonstructural proteins of dengue 2 virus (1990, Dissertation (Ph.D.))
• Viloria Winnett, Alexander — Quantitative Nucleic Acid Measurements Inform Strategies to Mitigate Viral Outbreaks (2025, Dissertation (Ph.D.))
• Cui, Miao — Refining Sea Urchin Developmental Gene Regulatory Network Models by Incorporating Wnt Signaling and Information Processed at the hox11/13b Locus (2016, Dissertation (Ph.D.))
• Culler, Stephanie June — Reprogramming Alternative Splicing Using Cis-Acting Intronic Control Elements (2009, Dissertation (Ph.D.))
• Tang, Weiyi — Retroviral Lineage Analysis of the Vagal Neural Crest Reveals Multipotency Towards the Cardiac and Enteric Fates (2022, Dissertation (Ph.D.))
• Michelsohn, Arie M. — Sequential Steps in the Determination of Chromaffin Cell Fate by Glucocorticoids (1992, Dissertation (Ph.D.))
• Zhou, Wen — Single-Cell Analysis of Normal and Perturbed Early T-Cell Developmental Processes (2021, Dissertation (Ph.D.))
• Warren, Luigi Andrea — Single-Cell Gene-Expression Analysis by Quantitative RT-PCR (2008, Dissertation (Ph.D.))
• Rao, Dinesh Subba — Small RNAs Play Big Roles in Hematopoietic Development (2010, Dissertation (Ph.D.))
• Leung, Thomas Hin-Chai — Specificity of Transcription Activation by NF-kB Subunits (2005, Dissertation (Ph.D.))
• Yang, Zheng — SpLacZ-MERCS-Coupled CRISPRi Screening Identifies Novel Mitochondria-ER Contact Sites Regulators (2025, Dissertation (Ph.D.))
• Ahmed, Alysia Ashley — Structural Characterization of Pro-inflammatory and Anti-inflammatory Immunoglobulin G Fc Proteins (2015, Dissertation (Ph.D.))
• Benjamin Schooler, Jordan — Structural Studies of Human Immunodeficiency Virus Type I by CryoElectron Tomography (2006, Dissertation (Ph.D.))
• Mortazavi, Ali — Structure and Evolution of Mammalian Gene Networks (2008, Dissertation (Ph.D.))
• Matthews, Beverley Bond — Structure and Expression of the Actin Gene Family of Drosophila melanogaster (1987, Dissertation (Ph.D.))
• Hahn, Chang Soo — Structure-Function Relationships in the Structural Proteins and in the RNAs of Alphaviruses and Flaviviruses (1988, Dissertation (Ph.D.))
• Saxena, Abigail Green — Sulfur-Cycling in Methane-Rich Ecosystems: Uncovering Microbial Processes and Novel Niches (2013, Dissertation (Ph.D.))
• Irizarry, Jihyun — Temporally Changing Roles of Morphogen Dorsal in the Drosophila Early Embryo (2021, Dissertation (Ph.D.))
• Millward, Steven Wesley — The Design, Synthesis, and Evolution of Macrocyclic mRNA Display Libraries Containing Unnatural Amino Acids (2007, Dissertation (Ph.D.))
• Montgomery, Jennifer Pielstick — The Effects of Behavioral Stress and Endothelin Receptor Antagonists on Cancer (2007, Dissertation (Ph.D.))
• Shih, Pei-Yin — The Ethology of Stress in Nematodes (2019, Dissertation (Ph.D.))
• Barbee, Susannah Dale — The Functions of Phosphatidylinositol 3-Kinase in T Lymphocyte Development: Roles in Positive Selection and Thymic Exit (2005, Dissertation (Ph.D.))
• Lee, James Joseph — The Genomic Organization and Expression of the Strongylocentrotus purpuratus Actin Gene Family (1986, Dissertation (Ph.D.))
• Lee, James Siho — The Genomics of Stress-Induced Life Cycle Decisions in Nematodes (2019, Dissertation (Ph.D.))
• Garrity, Paul Allen — The in vivo examination of transcriptional control mechanisms in mammalian cells (1993, Dissertation (Ph.D.))
• Hill, Russell James — The LIN-3 gene of the nematode C. elegans is the vulval-inducing signal (1994, Dissertation (Ph.D.))
• Vernooij, Bernardus Theodorus Maria — The Mouse T Cell Receptor Gamma Genes (1992, Dissertation (Ph.D.))
• Ashby, Meredith Howard — The Sea Urchin Regulome in Development (2007, Dissertation (Ph.D.))
• Gao, Boning — The Structure and Expression of the Gene Coding for Bindin, a Species Specific Sea Urchin Protein (1986, Dissertation (Ph.D.))
• Abedi, Mohamad — Thermal Bioswitches for Non-Invasive Control of Cellular Therapies (2021, Dissertation (Ph.D.))
• Yang, Lili — Towards Engineering Immunity (2004, Dissertation (Ph.D.))
• Kirilusha, Anthony George — Transcription Factor Occupancy in Differentiating Skeletal Muscle (2014, Dissertation (Ph.D.))
• DeSalvo, Gilberto — Transcriptional Enhancer Activity of Biochemically Marked Genomic Elements (2018, Dissertation (Ph.D.))
• Huang, Yuanyun (Rose) — Transcriptional Regulation of Zebrafish Enteric Nervous System Development (2027, Dissertation (Ph.D.))
• Wang, Hai — Transmembrane Ephrin Ligands in Neural and Vascular Development (1999, Dissertation (Ph.D.))
• Piraner, Dan Ilya — Tunable Thermal Bioswitches as a Control Modality for Next Generation Therapeutics (2019, Dissertation (Ph.D.))
• Lee, Justin — Ultrasound Control and Imaging of Cellular Immunotherapy (2024, Dissertation (Ph.D.))
• Adams, Meghan Sara — Uncovering Molecular Properties of Neural Crest Cells (2009, Dissertation (Ph.D.))
• Urrutia, Hugo Alexander — Understanding Cessation of Neural Crest Migration and Onset of Gangliogenesis (2025, Dissertation (Ph.D.))