Browse by Committee Member

2025

Bhattacharya, Paulomi (2025) RNA-Mediated Toxicity In Neurodegeneration: The Mechanistic Role Of The C9ORF72 Repeat Expansion In ALS Molecular Pathogenesis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2ywx-7a47. https://resolver.caltech.edu/CaltechTHESIS:03182025-023751137

Chakravorty, Arun (2025) Bridging Space and Time: Resolving the Temporal Dynamics of the Seminiferous Epithelial Cycle Using Spatial Transcriptomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2rcd-0v79. https://resolver.caltech.edu/CaltechTHESIS:05112025-035044867

Chen, Xiaoqiao (2025) Active Acquisition Methods for Single Cell Genomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/nsn8-nd79. https://resolver.caltech.edu/CaltechTHESIS:07052024-170119371

Colón, Katsuya Lex (2025) In Situ Signal Amplification for Spatial Transcriptomics Using Programmable DNA Assemblies. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/pp5f-pk64. https://resolver.caltech.edu/CaltechThesis:03312025-203601435

Fang, Meichen (2025) A Biophysical Approach to Normalization and Trajectory Inference in Single-Cell RNA Sequencing Data Analysis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/asek-t904. https://resolver.caltech.edu/CaltechTHESIS:06032025-002120461

Flores-Bautista, Emanuel (2025) The Topology of Cellular Ontogeny. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/t8hc-yq15. https://resolver.caltech.edu/CaltechTHESIS:06022025-234901151

Lourenço, Alexandre Luiz (2025) Building Closed-Loop Frameworks for AI-Guided Protein Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/8can-jz97. https://resolver.caltech.edu/CaltechTHESIS:05312025-073148050

Loving Ngo, Rebekah Kiana (2025) Methods for Long Read RNA-Seq Transcriptomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3nz8-3c83. https://resolver.caltech.edu/CaltechTHESIS:06012025-204136107

McGill, Mason Benjamin (2025) Visual Systems and the Forces That Shape Them. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/y27w-m760. https://resolver.caltech.edu/CaltechTHESIS:06092025-113042101

Schaus, Lucas Jean Nicolas (2025) Studies on Scaling Throughput in Protein Engineering. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/jqng-x012. https://resolver.caltech.edu/CaltechTHESIS:08022024-005547280

Viloria Winnett, Alexander (2025) Quantitative Nucleic Acid Measurements Inform Strategies to Mitigate Viral Outbreaks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/qe3a-a670. https://resolver.caltech.edu/CaltechTHESIS:12092024-223834150

Wang, Zitong (Jerry) (2025) Theoretical and Computational Analysis of Cell Migration in Complex Tissue Environments. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/mj08-b258. https://resolver.caltech.edu/CaltechTHESIS:06152024-132652470

Yang, Yujing (2025) Exploring Cell Diversity in Complex Tissues through Spatial Genomics and Spatial Transcriptomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/r85x-qs80. https://resolver.caltech.edu/CaltechTHESIS:05302025-191432965

2024

Bhamidipati, Pranav Subramanyam (2024) Modeling and Design of Synthetic Biochemical Circuits for Biological Phenotypes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/gpc6-hb40. https://resolver.caltech.edu/CaltechTHESIS:06012024-054725051

Jiang, Jialong (2024) Revealing Regulatory Network Organization Through Single-Cell Perturbation Profiling and Maximum Entropy Models. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/5zta-9818. https://resolver.caltech.edu/CaltechTHESIS:06032024-182223499

Saladi, Shyam Madhukar (2024) Some Computer Studies of Membrane Proteins, Molecular Chaperones, and Color. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/40cw-kn70. https://resolver.caltech.edu/CaltechTHESIS:10232023-184021847

Schwartz, Morgan Sarah (2024) Accelerating Biological Discovery with Deep Learning and Spatial Optical Barcodes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/55c7-8142. https://resolver.caltech.edu/CaltechTHESIS:05282024-221603734

2023

Bernstein, Jeremy David (2023) Optimisation & Generalisation in Networks of Neurons. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/1jz8-5t85. https://resolver.caltech.edu/CaltechTHESIS:10132022-000100592

Gálvez Merchán, Ángel (2023) Studies of mRNA Expression and Degradation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/esxk-ch24. https://resolver.caltech.edu/CaltechTHESIS:06042023-195408313

Hirokawa, Soichi (2023) Dynamics of Protein-Mediated Polymer Coupling and their Implications in Antibody Production and Emergent Patterning. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/fpmm-a552. https://resolver.caltech.edu/CaltechTHESIS:08252022-153300158

Jorgensen, Victoria Lynn (2023) Stem Cell-Derived Embryo Models in Mouse and Human to Illuminate the “Black Box” of Pre- to Post-Implantation Development. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/t1fe-3915. https://resolver.caltech.edu/CaltechTHESIS:06112023-211027828

Kuintzle, Rachael Christine (2023) Diversity in Notch Ligand-Receptor Signaling Interactions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/w8gj-jb92. https://resolver.caltech.edu/CaltechTHESIS:05302023-215054202

Ma, Yitong (2023) Multicellular Synthetic Biology in Mammalian Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/w0q1-7s17. https://resolver.caltech.edu/CaltechTHESIS:04132023-015900885

Moses, Lambda (2023) Computation Foundations of Spatial Transcriptomics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/rt24-pq60. https://resolver.caltech.edu/CaltechTHESIS:05312023-213322223

Raghavan, Guruprasad (2023) Engineering Artificial Systems with Natural Intelligence. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/374f-1202. https://resolver.caltech.edu/CaltechTHESIS:03172023-050019811

Zhu, Ronghui (2023) Multicellular Circuit Design in Mammalian Cells. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/p0fn-qa56. https://resolver.caltech.edu/CaltechTHESIS:07252022-061122576

2022

Banks, Rachel A. (2022) Experimental and Theoretical Studies of Non-Equilibrium Systems: Motor-Microtubule Assemblies and the Human-Earth System. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/5ee6-j454. https://resolver.caltech.edu/CaltechTHESIS:11282021-042001335

Abdel-Haq, Reem (2022) Gut Microbiome Modulates Microglia Physiology in Homeostatic and Disease States. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ht1j-2461. https://resolver.caltech.edu/CaltechTHESIS:03162022-173632582

Barlow, Jacob T. (2022) Quantitative Sequencing and its Application to Studies of the Human Small-Intestine Microbiota. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ca28-fk21. https://resolver.caltech.edu/CaltechTHESIS:10282021-191743624

Beeler, Suzannah Michelle (2022) Deciphering Regulation in Escherichia coli: From Genes to Genomes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/p3rg-m937. https://resolver.caltech.edu/CaltechTHESIS:08182021-053622635

Brown, David (2022) Principles of Massively Parallel Sequencing for Engineering and Characterizing Gene Delivery. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/yqjm-6609. https://resolver.caltech.edu/CaltechTHESIS:02132022-064810187

Dobreva, Tatyana (2022) Engineering Tools to Probe and Manipulate the Immune System at Single-Cell Resolution. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/n3rs-ft69. https://resolver.caltech.edu/CaltechTHESIS:10172021-215439860

Galstyan, Vahe (2022) Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/1fzr-1240. https://resolver.caltech.edu/CaltechTHESIS:08242021-212959886

Poole, William (2022) Compilation and Inference with Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/x3qc-je74. https://resolver.caltech.edu/CaltechTHESIS:11102021-210013472

Razo-Mejia, Manuel (2022) Physical Biology of Cellular Information Processing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/kpc2-b345. https://resolver.caltech.edu/CaltechTHESIS:08242021-212609828

Row, Hyeongjoo (2022) Mechanical Approach to Active Matter: Reverse Osmotic Effect and Motility-Induced Phase Separation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/qef0-e420. https://resolver.caltech.edu/CaltechTHESIS:05252022-172145394

Su, Christina Janet (2022) Principles of Addressing Specificity in Promiscuous Ligand-Receptor Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/z7dv-m192. https://resolver.caltech.edu/CaltechTHESIS:06022022-032024376

Tang, Weiyi (2022) Retroviral Lineage Analysis of the Vagal Neural Crest Reveals Multipotency Towards the Cardiac and Enteric Fates. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/qakz-vm04. https://resolver.caltech.edu/CaltechTHESIS:04162022-233242577

da Veiga Beltrame, Eduardo (2022) Stories in Single Cell RNA Sequencing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4kgh-8420. https://resolver.caltech.edu/CaltechTHESIS:06022022-201232129

2021

Chour, William (2021) Molecular Technologies for Antigen-Based Immunity. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/z20t-nq62. https://resolver.caltech.edu/CaltechTHESIS:02192021-010538691

Eng, Chee Huat (Linus) (2021) Plus Ultra: Genome-Wide Spatial Transcriptomics with RNA seqFISH+. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/nvfe-5j74. https://resolver.caltech.edu/CaltechTHESIS:05302021-051953086

Gandhi, Shashank (2021) Molecular Mechanisms Underlying Cardiac Neural Crest Development in Avian Embryos. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/y1e4-d090. https://resolver.caltech.edu/CaltechTHESIS:06012021-203020365

Morrison, Muir (2021) Statistical Mechanics of Problems in Transcription Regulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/d042-rp26. https://resolver.caltech.edu/CaltechTHESIS:06082021-005042886

Parkin, James Michael (2021) Signal Amplification in Synthetic Bacterial Communication. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/50p8-bd89. https://resolver.caltech.edu/CaltechTHESIS:03262021-160841703

Quintero Cadena, Porfirio (2021) Mechanism and Scaling of Eukaryotic Transcription Activation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/m21w-8461. https://resolver.caltech.edu/CaltechTHESIS:07072020-154545363

Ross, Tyler David (2021) Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/q85h-j730. https://resolver.caltech.edu/CaltechTHESIS:07082020-113341068

2020

Ireland, William Thornton (2020) A Quantitative and High-Throughput Approach to Gene Regulation in Escherichia coli. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/0sk3-hd69. https://resolver.caltech.edu/CaltechTHESIS:03262020-092455420

Kim, Dong-Wook (2020) Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior in Mice. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/RGVK-9962. https://resolver.caltech.edu/CaltechTHESIS:12162019-183140887

Neumann, Adam Patrick (2020) Towards Single Molecule Imaging Using Nanoelectromechanical Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/n4ap-7h91. https://resolver.caltech.edu/CaltechTHESIS:05182020-141933604

2019

Angeles-Albores, David (2019) A Theory of Genetic Analysis Using Transcriptomic Phenotypes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/JRNS-NS05. https://resolver.caltech.edu/CaltechTHESIS:10232018-150005837

He, Peng (2019) The Changing Mouse Embryo Transcriptome at Whole Tissue and Single-Cell Resolution. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/35S4-HG18. https://resolver.caltech.edu/CaltechTHESIS:02192019-004236200

Singhal, Vipul (2019) Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/g31j-ch52. https://resolver.caltech.edu/CaltechTHESIS:08262018-213846283

Yi, Lynn Donglin (2019) Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/0YE6-2217. https://resolver.caltech.edu/CaltechTHESIS:10102018-143313907

2018

Barnes, Stephanie Loos (2018) Decoding the Regulatory Genome: Quantitative Analysis of Transcriptional Regulation in Escherichia coli. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/D13T-7868. https://resolver.caltech.edu/CaltechTHESIS:05292018-133205686

Belliveau, Nathan Maurice (2018) Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9DN438T. https://resolver.caltech.edu/CaltechTHESIS:01052018-221609680