Thomson, Matthew

Committee Member — 74 thesises

• Fang, Meichen — A Biophysical Approach to Normalization and Trajectory Inference in Single-Cell RNA Sequencing Data Analysis (2025, Dissertation (Ph.D.))
• Ireland, William Thornton — A Quantitative and High-Throughput Approach to Gene Regulation in Escherichia coli (2020, Dissertation (Ph.D.))
• Angeles-Albores, David — A Theory of Genetic Analysis Using Transcriptomic Phenotypes (2019, Dissertation (Ph.D.))
• Schwartz, Morgan Sarah — Accelerating Biological Discovery with Deep Learning and Spatial Optical Barcodes (2024, Dissertation (Ph.D.))
• Chen, Xiaoqiao — Active Acquisition Methods for Single Cell Genomics (2025, Dissertation (Ph.D.))
• Wexler, Helen — Algae as a Platform for Sustainable Biocomposites: Process–Structure–Property Relations (2026, Dissertation (Ph.D.))
• Felce, Catherine E. — Biophysical Modeling for Gene Expression and Evolution (2026, Dissertation (Ph.D.))
• Chakravorty, Arun — Bridging Space and Time: Resolving the Temporal Dynamics of the Seminiferous Epithelial Cycle Using Spatial Transcriptomics (2025, Dissertation (Ph.D.))
• Du, Rongrong — Build Synthetic Circuits at Different Scales (2026, Dissertation (Ph.D.))
• Lourenço, Alexandre Luiz — Building Closed-Loop Frameworks for AI-Guided Protein Design (2025, Dissertation (Ph.D.))
• Poole, William — Compilation and Inference with Chemical Reaction Networks (2022, Dissertation (Ph.D.))
• Moses, Lambda — Computation Foundations of Spatial Transcriptomics (2023, Dissertation (Ph.D.))
• Beeler, Suzannah Michelle — Deciphering Regulation in Escherichia coli: From Genes to Genomes (2022, Dissertation (Ph.D.))
• Barnes, Stephanie Loos — Decoding the Regulatory Genome: Quantitative Analysis of Transcriptional Regulation in Escherichia coli (2018, Dissertation (Ph.D.))
• Kapasiawala, Manisha Kaushik — Design Considerations for Synthetic Cells (2026, Dissertation (Ph.D.))
• Amaya Perez, Enrique — Designing Intelligent Agents for Real-Time Experimental Control and Multi-Task Generalization (2026, Dissertation (Ph.D.))
• Kuintzle, Rachael Christine — Diversity in Notch Ligand-Receptor Signaling Interactions (2023, Dissertation (Ph.D.))
• Hirokawa, Soichi — Dynamics of Protein-Mediated Polymer Coupling and their Implications in Antibody Production and Emergent Patterning (2023, Dissertation (Ph.D.))
• Raghavan, Guruprasad — Engineering Artificial Systems with Natural Intelligence (2023, Dissertation (Ph.D.))
• Dev, Ishaan Joshan — Engineering Multi-Protein Assemblies with Machine Learning and Experimental Optimization (2027, Dissertation (Ph.D.))
• Dobreva, Tatyana — Engineering Tools to Probe and Manipulate the Immune System at Single-Cell Resolution (2022, Dissertation (Ph.D.))
• Banks, Rachel A. — Experimental and Theoretical Studies of Non-Equilibrium Systems: Motor-Microtubule Assemblies and the Human-Earth System (2022, Dissertation (Ph.D.))
• Yang, Yujing — Exploring Cell Diversity in Complex Tissues through Spatial Genomics and Spatial Transcriptomics (2025, Dissertation (Ph.D.))
• Ross, Tyler David — Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions (2021, Dissertation (Ph.D.))
• Abdel-Haq, Reem — Gut Microbiome Modulates Microglia Physiology in Homeostatic and Disease States (2022, Dissertation (Ph.D.))
• Chadly, Duncan Matthew — High-Resolution Phylogenetic Lineage Recording with CRISPR Base Editors (2026, Dissertation (Ph.D.))
• Röschinger, Tom — Illuminating the Regulatory Dark Matter of E. coli with Massively Parallel Reporter Assays (2026, Dissertation (Ph.D.))
• Colón, Katsuya Lex — In Situ Signal Amplification for Spatial Transcriptomics Using Programmable DNA Assemblies (2025, Dissertation (Ph.D.))
• Row, Hyeongjoo — Mechanical Approach to Active Matter: Reverse Osmotic Effect and Motility-Induced Phase Separation (2022, Dissertation (Ph.D.))
• Quintero Cadena, Porfirio — Mechanism and Scaling of Eukaryotic Transcription Activation (2021, Dissertation (Ph.D.))
• Loving Ngo, Rebekah Kiana — Methods for Long Read RNA-Seq Transcriptomics (2025, Dissertation (Ph.D.))
• Markarian, Nicholas — Mixtures of Latent Variable Models for Interpreting Gene Expression Covariation from Pathways to Transcriptomes (2026, Dissertation (Ph.D.))
• Bhamidipati, Pranav Subramanyam — Modeling and Design of Synthetic Biochemical Circuits for Biological Phenotypes (2024, Dissertation (Ph.D.))
• Singhal, Vipul — Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts (2019, 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.))
• Zhu, Ronghui — Multicellular Circuit Design in Mammalian Cells (2023, Dissertation (Ph.D.))
• Ma, Yitong — Multicellular Synthetic Biology in Mammalian Systems (2023, Dissertation (Ph.D.))
• Kim, Dong-Wook — Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior in Mice (2020, Dissertation (Ph.D.))
• Zhang, Yameng — Neural Circuits Underlying Salt-Taste Valence (2026, Dissertation (Ph.D.))
• Bernstein, Jeremy David — Optimisation & Generalisation in Networks of Neurons (2023, Dissertation (Ph.D.))
• Razo-Mejia, Manuel — Physical Biology of Cellular Information Processing (2022, Dissertation (Ph.D.))
• Eng, Chee Huat (Linus) — Plus Ultra: Genome-Wide Spatial Transcriptomics with RNA seqFISH+ (2021, Dissertation (Ph.D.))
• Gornet, James Andrew — Predictive Coding for Cognitive Mapping (2027, Dissertation (Ph.D.))
• Su, Christina Janet — Principles of Addressing Specificity in Promiscuous Ligand-Receptor Systems (2022, Dissertation (Ph.D.))
• Brown, David — Principles of Massively Parallel Sequencing for Engineering and Characterizing Gene Delivery (2022, Dissertation (Ph.D.))
• Belliveau, Nathan Maurice — Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli (2018, Dissertation (Ph.D.))
• Viloria Winnett, Alexander — Quantitative Nucleic Acid Measurements Inform Strategies to Mitigate Viral Outbreaks (2025, Dissertation (Ph.D.))
• Barlow, Jacob T. — Quantitative Sequencing and its Application to Studies of the Human Small-Intestine Microbiota (2022, Dissertation (Ph.D.))
• Liu, Shichen — Reconstituting Cellular Intelligence in Nonliving Biomolecular Matter (2026, Dissertation (Ph.D.))
• Duarte, Ana Isabel — Resolving and Mathematizing Energetic Gradients That Facilitate Cytoskeletal Self-Assembly (2026, 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.))
• Jiang, Jialong — Revealing Regulatory Network Organization Through Single-Cell Perturbation Profiling and Maximum Entropy Models (2024, Dissertation (Ph.D.))
• Larios-Colorado, David Antonio — Reverse Engineering the Programming Logic of Cytoskeletal Dynamics (2026, Dissertation (Ph.D.))
• Subramanian, Arjuna Michael — Rewriting the Sequence and Structure Rules of Deep Protein Space (2026, Dissertation (Ph.D.))
• Bhattacharya, Paulomi — RNA-Mediated Toxicity In Neurodegeneration: The Mechanistic Role Of The C9ORF72 Repeat Expansion In ALS Molecular Pathogenesis (2025, Dissertation (Ph.D.))
• Parkin, James Michael — Signal Amplification in Synthetic Bacterial Communication (2021, Dissertation (Ph.D.))
• Saladi, Shyam Madhukar — Some Computer Studies of Membrane Proteins, Molecular Chaperones, and Color (2024, Dissertation (Ph.D.))
• Morrison, Muir — Statistical Mechanics of Problems in Transcription Regulation (2021, Dissertation (Ph.D.))
• Yi, Lynn Donglin — Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing (2019, Dissertation (Ph.D.))
• Jorgensen, Victoria Lynn — Stem Cell-Derived Embryo Models in Mouse and Human to Illuminate the “Black Box” of Pre- to Post-Implantation Development (2023, Dissertation (Ph.D.))
• da Veiga Beltrame, Eduardo — Stories in Single Cell RNA Sequencing (2022, Dissertation (Ph.D.))
• Galstyan, Vahe — Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling (2022, Dissertation (Ph.D.))
• Gálvez Merchán, Ángel — Studies of mRNA Expression and Degradation (2023, Dissertation (Ph.D.))
• Schaus, Lucas Jean Nicolas — Studies on Scaling Throughput in Protein Engineering (2025, Dissertation (Ph.D.))
• Olson, Blade A. — Synthetic Antigen-Presenting Vesicles for Selective Immunomodulation (2026, Dissertation (Ph.D.))
• He, Peng — The Changing Mouse Embryo Transcriptome at Whole Tissue and Single-Cell Resolution (2019, Dissertation (Ph.D.))
• Flores-Bautista, Emanuel — The Topology of Cellular Ontogeny (2025, Dissertation (Ph.D.))
• Wang, Zitong (Jerry) — Theoretical and Computational Analysis of Cell Migration in Complex Tissue Environments (2025, Dissertation (Ph.D.))
• Neumann, Adam Patrick — Towards Single Molecule Imaging Using Nanoelectromechanical Systems (2020, Dissertation (Ph.D.))
• White, Jonathan Alexander — Untangling Overlapping Barcodes in Image-Based Spatial Genomics (2026, Dissertation (Ph.D.))
• McGill, Mason Benjamin — Visual Systems and the Forces That Shape Them (2025, Dissertation (Ph.D.))
• Zellinger, Michael J. — White Elephants and Cash Cows: Economically Wrangling the Zoo of AI Models (2026, Dissertation (Ph.D.))
• Martinez, Zachary A. — Tokens, Topologies, Taxa: Towards Declarative Biology and Bioengineering (2026, Dissertation (Ph.D.))