Elowitz, Michael

Software from CaltechTHESIS committee

• Honson, Drew D. (2025) Development and Application of Proteomic and Genomic Methods in RNA Biology; 10.7907/08dq-1q63
• Jiang, Jialong (2024) Revealing Regulatory Network Organization Through Single-Cell Perturbation Profiling and Maximum Entropy Models; 10.7907/5zta-9818
• Duan, Mengtong (Tom) (2024) Expanding Frontiers in Biomedical Imaging and Synthetic Biology: Dynamic Acoustic Reporter Gene Imaging and Ratio-Tuning of Mammalian mRNA Polycistronic Expression; 10.7907/avgk-yc71
• Bhamidipati, Pranav Subramanyam (2024) Modeling and Design of Synthetic Biochemical Circuits for Biological Phenotypes; 10.7907/gpc6-hb40
• Ivy, Tobin William (2024) Implementing and Modeling Gene Drives for Population Modification and Suppression; 10.7907/10pa-x574
• Goronzy, Isabel Nadine (2024) Higher-Order Chromatin States and Nuclear Structures Regulating Gene Expression; 10.7907/8gm2-jn84
• Mayfield, Acacia Michelle Hori (2024) Customized and Modular Control of Gene Expression for Precision Gene Therapies; 10.7907/d05v-0t68
• Bhat, Prashant (2023) On the Role of Three-Dimensional Genome Organization in Gene Regulation and mRNA Splicing; 10.7907/vg8a-y851
• Marken, John Paul (2023) Experimental and Theoretical Frameworks for Enabling Environmental Synthetic Biology; 10.7907/h50w-p058
• Wang, Sheng (2023) Synthetic Circuits for Multicellular Spatial Patterning; 10.7907/3rbk-g805
• Huang, Jining (2023) Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens; 10.7907/54tw-ym95
• Ma, Yitong (2023) Multicellular Synthetic Biology in Mammalian Systems; 10.7907/w0q1-7s17
• Zhu, Ronghui (2023) Multicellular Circuit Design in Mammalian Cells; 10.7907/p0fn-qa56
• Kuintzle, Rachael Christine (2023) Diversity in Notch Ligand-Receptor Signaling Interactions; 10.7907/w8gj-jb92
• Edmonds, KeHuan Kuo (2022) Imaging Cell Lineage with a Synthetic Digital Recording System; 10.7907/a4m3-m603
• Su, Christina Janet (2022) Principles of Addressing Specificity in Promiscuous Ligand-Receptor Systems; 10.7907/z7dv-m192
• Andrade Meirelles, Lucas (2022) The Nuanced Effects of Redox-Active Metabolites on Bacterial Physiology and Antibiotic Susceptibility; 10.7907/67p2-q992
• Dobreva, Tatyana (2022) Engineering Tools to Probe and Manipulate the Immune System at Single-Cell Resolution; 10.7907/n3rs-ft69
• Shur, Andrey Sergeyvich (2022) Serine Integrase-Based Event Recording in E. coli; 10.7907/x4q0-nx18
• Gong, Mengsha (2022) Remodeling Jellyfish; 10.7907/pfn8-aw15
• Klumpe, Heidi Elizabeth (2021) Context-Dependent, Combinatorial Logic of BMP Signaling; 10.7907/3vv4-bk06
• Takei, Yodai (2021) Integrated Spatial Genomics Reveals Organizational Principles of Single-Cell Nuclear Architecture; 10.7907/4ces-zm75
• Ren, Xinying (Cindy) (2021) Principles for Designing Robust and Stable Synthetic Microbial Consortia; 10.7907/hc8x-3280
• Banerjee, Abhik Kumar (2021) Diverse Roles of RNA-protein Interactions: From Viral Antagonism to Mammalian Development; 10.7907/tfb9-n887
• Chong, Lucy Shin (2021) Engineering and Delivery of Programmable Protein Circuits as Potential Therapeutic Devices; 10.7907/jdhe-by95
• Hanewich-Hollatz, Mikhail Henning (2020) Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology; 10.7907/NS2B-DJ96
• Chure, Griffin Daniel (2020) The Molecular Biophysics of Evolutionary and Physiological Adaptation; 10.7907/q8h6-xr92
• Silverman, Bradley Ross (2020) Protein-Mediated Colloidal Assembly; 10.7907/x3ya-fq67
• Bogatyrev, Said R. (2020) Development of Analytical Tools and Animal Models for Studies of Small-Intestine Dysbiosis; 10.7907/VJDZ-7B52
• Nunns, Harry James Rogan (2019) Linearity in Cell Signaling Pathways; 10.7907/WP0J-E945
• Shih, Pei-Yin (2019) The Ethology of Stress in Nematodes ; 10.7907/1E7G-K373
• Frankiw, Luke Steven (2019) mRNA Splicing-Mediated Gene Expression Regulation in Innate Immunity; 10.7907/NBQG-BS67
• Kim, Kibeom (2019) Memory and Decoding in Signaling Transduction Pathways; 10.7907/BJDQ-JX45
• Frick, Christopher Lee (2019) How Single Cells Sense Smad3 Signal; 10.7907/WNM4-4R58
• Shao, Zixuan (2019) Biological Responses to Therapeutic Treatments of Human Vascular Diseases; 10.7907/P2S4-AY40
• Chen, Chun-Kan (2018) Revealing the Mechanism of Xist-mediated Silencing; 10.7907/Z94J0C9J
• Belliveau, Nathan Maurice (2018) Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli; 10.7907/Z9DN438T
• Park, Jin (2018) Circuits of Dynamically Interacting Sigma Factors in Single Cells; 10.7907/CT0B-Q853
• Nandagopal, Nagarajan (2018) New Capabilities of the Notch Signaling Pathway; 10.7907/Z98050TB
• Swaminathan, Anandh (2018) Application, Computation, and Theory for Synthetic Gene Circuits; 10.7907/Z9833Q67
• Barnes, Stephanie Loos (2018) Decoding the Regulatory Genome: Quantitative Analysis of Transcriptional Regulation in Escherichia coli; 10.7907/D13T-7868
• Shah, Sheel Mukesh (2017) Highly Multiplexed Single Cell In Situ RNA Detection; 10.7907/Z9X63JXH
• Kim, Jinho (2017) Compact Microscope System for Biomedical Applications; 10.7907/Z9H9937R
• Guo, Shaobin (2017) Prototyping Diverse Synthetic Biological Circuits in a Cell-Free Transcription-Translation System; 10.7907/Z9CR5RDK
• Fisher-Aylor, Katherine Irene (2017) Chromatin Topology and Transcription in Myogenesis; 10.7907/Z9K07290
• Acharya, Aneesh (2016) Multiplexed Analysis of Diverse RNA Classes via Hybridization Chain Reaction; 10.7907/Z95M63N0
• Sun, Zachary Zhipeng (2016) An in vitro Biomolecular Breadboard for Prototyping Synthetic Biological Circuits; 10.7907/Z9TB14TW
• Hsiao, Victoria (2016) Synthetic Circuits for Feedback and Detection in Bacteria; 10.7907/Z9WD3XJW
• Rios, Gustavo (2016) Nanofabricated Neural Probe System for Dense 3-D Recordings of Brain Activity; 10.7907/Z9BG2M0B
• Lubeck, Eric (2016) Towards in situ Single Cell Systems Biology; 10.7907/Z9BK1999
• Yong, John (2015) Dynamics and Heterogeneity of Gene Expression and Epigenetic Regulation at the Single-Cell Level; 10.7907/Z9ZC80VX
• Mahdavi, Alborz (2015) Synthetic Biology Tools for Targeted Incorporation of Non-Canonical Amino Acids into Cellular Proteins; 10.7907/Z9W66HS4
• Cornejo de los Santos, Emmanuel Lorenzo (2015) Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits; 10.7907/Z9M61H64
• Hoenselaar, Andreas (2015) The Structure of Hippocampal Activity During REM Sleep; 10.7907/Z98W3B8H
• Singer, Zakary Sean (2015) Metastability and Dynamics of Stem Cells: From Direct Observations to Inference at the Single Cell Level; 10.7907/Z9ST7MS1
• Srinivas, Niranjan (2015) Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement; 10.7907/Z9KD1VVJ
• Goldberg, Mark David (2015) Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers; 10.7907/Z9P848V6
• Tan, Frederick Eng How (2014) Brfl Post-Transcriptionally Regulates Pluripotency and Differentiation Responses Downstream of Erk MAP Kinase; 10.7907/MM53-XC23
• Jones, Daniel Lawson III (2014) Sequence-Function Relationships in E. coli Transcriptional Regulation; 10.7907/4J7V-WD59
• Loson, Oliver Calvin (2014) Regulation of Mitochondrial Division by the Drp1 Receptors; 10.7907/J23G-KQ18
• Inagaki, Hidehiko K. (2014) Neuronal Mechanism of State Control in Drosophila melanogaster; 10.7907/MPZX-TN59
• LeBon, Lauren E. (2014) The Logic of Receptor-Ligand Interactions in the Notch Signaling Pathway; 10.7907/83PA-9833
• Lakhanpal, Amit (2014) Experimental and Theoretical Studies of Notch Signaling-Mediated Spatial Pattern; 10.7907/RGPT-RS80
• Sternberg, Jonathan Ben-Zion (2013) Signal Transduction with Hybridization Chain Reactions; 10.7907/Z90Z719Z
• Venturelli, Ophelia Shalini (2013) Role of Feedback and Dynamics of a Gene Regulatory Network; 10.7907/WGK3-Y839
• Zheng, Guoan (2013) Innovations in Imaging System Design: Gigapixel, Chip-Scale and MultiFunctional Microscopy; 10.7907/SF6E-S775
• Bower, Danielle Vera Brown (2013) Chemical and Neural Regulation of Embryonic Branching Morphogenesis; 10.7907/Z9SX6B6R
• Levine, Joseph H. (2012) Genetic Regulatory Circuit Dynamics: Analysis and Synthesis; 10.7907/35A7-K421
• Ford, William Chastang (2012) I. Quantal Effects in Biochemical Cooperativity and a Proposed Mechanism for the Differentiation of Calcium Signaling in Synaptic Plasticity. II. Evolutionary Algorithms for the Optimization of Methods in Computational Chemistry; 10.7907/Z9HH6H1Z
• Galloway, Kate Elizabeth (2012) The Development of RNA-based Control Systems to Regulate Signaling and Dictate Cell Fate in a Model MAPK Pathway; 10.7907/CBBN-GX03
• Young, Jonathan Wan (2012) Architecture, Dynamics, and Function of the General Stress Response System in B. subtilis; 10.7907/93MF-Q808
• Hariadi, Rizal Fajar (2011) Non-Equilibrium Dynamics of DNA Nanotubes ; 10.7907/6GQW-YG26
• Ward, Catherine Marie (2011) Medea Selfish Genetic Elements as Tools for Altering Traits of Wild Populations: A Theoretical Analysis; 10.7907/T656-ZN91
• Garcia, Hernan G. (2011) Transcriptional Regulation by the Numbers; 10.7907/63RG-8P84
• Sen, Shaunak (2011) Regulatory Consequences of Bandpass Feedback in a Bacterial Phosphorelay; 10.7907/NPZD-G382
• Schaedel, Oren Noah (2011) Dynamic Regulation of the Dauer Decision; 10.7907/JZ9E-AD68
• Kuntz, Steven Gregory (2011) hlh-1 and the C. elegans Body Wall Muscle Transcriptional Differentiation Network; 10.7907/18XS-YM65
• Gu, Ming (2010) Interactions Between Hippocampal Areas CA3 and CA1 During Slow-Wave Sleep ; 10.7907/Z9BV7DMM
• Choi, Harry Ming Tak (2010) Programmable In Situ Amplification for Multiplexed Bioimaging ; 10.7907/K4A3-1K41
• Dalal, Chiraj Kiran (2010) Causes and Consequences of Gene Expression Noise; 10.7907/MHSR-9875
• Ursell, Tristan Scott (2009) Stretching the Definition of a Lipid Bilayer: Elasticity's Role in Protein and Lipid Organization; 10.7907/Q0R5-K353
• Bayer, Travis Scott (2009) Synthetic Regulation and Genetic Control of an Ecological Strategy; 10.7907/3GDB-C409
• Brenner, Sarah Katherine (2009) Engineering Synthetic Biofilm-Forming Microbial Consortia; 10.7907/PMZ3-4Z96
• Axelrod, Blake Waters (2009) Single Cell Pico Force Microscopy: A Novel Tool for High Resolution Measurement of Cell Forces; 10.7907/ESGS-Z942
• Gordon, Sean Patrick (2009) Hormone and Gene Feedback during Development and Regeneration in Arabidopsis thaliana; 10.7907/T3CR-TC54
• Cox, Robert Sidney, III (2008) Transcriptional Regulation and Combinatorial Genetic Logic in Synthetic Bacterial Circuits; 10.7907/KRW6-DH88
• Han, Lin (2008) In vitro DNA Mechanics in Gene Regulation: One Molecule at a Time; 10.7907/7573-A922
• Maerkl, Sebastian Josef (2008) Microfluidic Large Scale Integration and its Application to Systems Biology; 10.7907/5CMX-CV08
• Lee, Wonhee (2008) Microfluidic Chip Calorimeters for Biological Applications; 10.7907/W8E0-4W22
• Mattson, Matthew Sanford (2008) Understanding and Treating Eye Diseases: Mechanical Characterization and Photochemical Modification of the Cornea and Sclera; 10.7907/DXGR-GV57
• Dunlop, Mary Julia (2008) Dynamics and Correlated Noise in Gene Regulation; 10.7907/AC8V-6S05
• Balagaddé, Frederick Kiguli (2007) Microfluidic Technologies for Continuous Culture and Genetic Circuit Characterization; 10.7907/NJ5Z-XV43
• Murphy, Gavin Erick (2007) Cryoelectron Tomography of Bacteria and their Macromolecular Machines; 10.7907/517B-0Z68
• Kim, Jongmin (2007) In Vitro Synthetic Transcriptional Networks; 10.7907/Q9YA-N192
• Bao, Xiaoyan Robert (2007) Lost in a Crowd: Observations of Single DNA Knots and Single Mammalian Cells; 10.7907/F2XV-MC44
• Collins, Cynthia Hollie (2006) Directed Evolution of the Transcriptional Activator LuxR; 10.7907/61qd-8j79
• Lacenere, Christopher J. (2006) Advances in Single Molecule Nucleic Acid Sequencing; 10.7907/CA4B-S389
• Kulkarni, Rajan P. (2006) Mechanics of the Cytoskeleton: Examining the Dynamics of Cytoplasmic Transport through Fluorescence Microscopy; 10.7907/85ea-ed40
• Drummond, David Allan (2006) Misfolding Dominates Protein Evolution; 10.7907/DH8E-2N10
• Vyawahare, Saurabh (2006) Manipulating Fluids: Advances in Micro-Fluidics, Opto-Fluidics and Fluidic Self-Assembly; 10.7907/04XY-C430
• Kartalov, Emil Paskalev (2004) Single-Molecule Detection and DNA Sequencing-by-Synthesis; 10.7907/50YQ-0S81
• Hansen, Carl Lars Genghis (2004) Microfluidic Technologies for Structural Biology; 10.7907/N9T3-7114