Research and Thesis

A senior thesis is a year-long research for credit course worth 8 credits and is letter graded. Students must identify a faculty sponsor that is willing to host and mentor them latest by the end of Spring semester of Junior year (students may decide to start earlier) since the thesis proposal is due mid-July before senior year. Faculty sponsors must be a Harvard faculty or an affiliate of Harvard. Once your proposal is accepted, you may enroll in MCB/CPB 99AB. Students enrolled in 99AB are expected to work ~15 hours/week during term time. Research mentors are expected to provide training on both the science and writing. The undergraduate office will provide supplemental support by hosting a number of workshops and exercises aimed at improving the quality of presentation and writing.

• A Characterization of the Chromatin Features of Murine Cardiac Multi-Transcription Factor Regions  Ambroise, Rachelle PI: Pu, William
• Exploring the Structure and Substrate Specificity of Two Insect Gustatory Receptors Baek, Serin PI: Gaudet, Rachelle
• Developing a novel temperature-modulated CRISPR/Cas12 gene editing system for iPSC disease modeling in X-linked Dystonia Parkinsonism Cai, Connie PI: Bragg, Cristopher
• Developing a Metabolic Imaging Protocol for Investigating Aneuploidy Das, Indrani PI: Hekstra, Doeke
• Deep Learning Models for Variant Pathogenicity Prediction Estanboulieh, Ralph PI: Manrai, Arjun
• Exploring the Effects of Raising cAMP on Cellular Ubiquitination Freeman, Stephen PI: Goldberg, Alfred
• A Cellular Heartbeat: Defining the Biophysical Determinants of Global E. coli Nucleoid Dynamics Gould, Samuel PI: Kleckner, Nancy
• Towards Inducing Antineoplastic-vulnerable Cancer Cell States with Small Molecules  Ho, William PI: Schreiber, Stuart
• Are the Even-skipped stripes short-range morphogen gradients?: Quantitative anaylsis of Drosophila segmentation gene regulation via multiplexed imaging of transcripts and proteins  Howard, Mary Kathryn PI: DePace, Angela
• Comparing Drug-induced and Spontaneous Colon Inflammation Using scRNA-seq Kim, Edward PI: Wucherpfennig, Kai
• A Systematic Comparison of Conformational Movements of LeuT-fold Transporters Licht, Jacob PI: Gaudet, Rachelle
• Identifying New Loci Associated with Antibiotic Resistance in Bacterial Genomes Through the Use of Multiple Species in Genome-Wide Association Studies Nakamoto, Carter PI: Farhat, Maha
• A defined region in the interior wall of the assembly protein BamA mediates catalytic folding of B-barrels in the outer membrane of Gram-negative bacteria  Pan, Lydia PI: Kahne, Daniel
• Mechanism of Inhibitor-Induced Degradation of EGFR Siddiqui, Saher PI: Schreiber, Stuart
• The Natural Viral Environment of Caenorhabditis elegans: Interactions between RNA Interference, the Dauer State, and Orsay Virus Infection Stainier, William PI: Hunter, Craig
• Evaluation of Molecular Dynamics-Based Modeling for Electric Field-Stimulated X-Ray Crystallography  Sun, Chris PI: Hekstra, Doeke
• Predicting Electrolyte Viscocity and Conductivity with Applications in Alkaline Aqueous Organic Redox Flow Batteries  Wang, Cliffton PI:Aziz, Michael

• Elucidating the interactions between oncogenic protein inhibitors and PRC2  Araten, Sarah PI: Liau, Brian
• Investigating the role of the G1 phase of the cell cycle in genetic instability in S. cerevisiae  Chen, Yi PI: Murray, Andrew
• Resolving the Molecular Details of a Predicted Interface Between DivIB and DivIC in the Divisome of B. subtilis  Cho, Andrew PI: Garner, Ethan
• Constructing ubiquitin-DNA chimeras to facilitate transition state studies  Gamada, DarartuPI:  Hekstra, Doeke
• Investigating RNA Structure in Translation: A Functional and Biochemical Characterization of the CaMK2a Internal Ribosome Entry Site  Gao, Michael  PI: D’Souza, Victoria
• The Role of FAM55A and FAM55D in Mediating Intestinal Homeostasis and Inflammatory Bowel Disease  Kanneganti, ApurvaPI: Xavier, Ramnik
• Elucidating biomarkers for clinical response to combination anti-PD-1 and anti-CTLA-4 immunotherapy in patients with advanced melanoma Nijim, Sally PI: Hodi, Stephen
• Effects of Size and Motion Parallax on Perceived Depth in Two-Dimensional Virtual Reality Displays  Park, Jungyeon PI: Engert, Florian
• Investigation of the function of MreD, an essential protein in bacterial morphogenesis  Qiu, Jeanna  PI: Bernhardt, Thomas
• Direct or Indirect, That Is The Question: Mechanism of Amphiregulin Induced Modulation of Muscle Stem Cells  Shadpour, Michael  PI: Wagers, Amy
• Determining Changes in TET3 Protein-Protein Interactions Controlled by O-GlcNAcylation  Tang, Stephanie PI: Woo, Christina
• Determining metal selectivity imparted by variations in the metal-binding site of Nramp-family transporters  Yoo, Unice PI: Gaudet, Rachelle
• Developing Molecular Detection Assays for Powassan Virus  Zamirpour, Siavash  PI: Sabeti, Pardis

• Engineering and Evaluating RlmD-conjugated Cytosine Base Editors
  to Enhance the Precision of Cytosine-To-Thymine Editing Eton, Elliot PI: Liu, David
• The role of YAP in intrahepatic cholangiocellular carcinoma using a novel organoid-based model Kim, Daniel PI: Camargo, Fernando
• Nuclear Receptor Regulation of Cardiomyocyte Maturation Lee, Julianna PI: Pu, William
• Quantifying the Approach of Cancer
  Cells Towards the Apoptotic Threshold Li, Willa PI: Letai, Anthony
• Developing a Programmable Editor for Installing N6-Methyladenosine (m6A) RNA Modifications Zhuang, Miao PI: Liu, David
• Towards Engineering an Escherichia coli Nissle 1917 Promoter Library as a Living Diagnostic of Inflammatory Bowel Disease Trivedi, Disha PI: Silver, Pamela
• Investigating the role of trophoblasts in the establishment of pregnancy immune tolerance Xu, Lily PI: Strominger, Jack

• Iron Tetraphenyl Porphyrin as a Formate-Selective CO2 Reduction Catalyst Asimow, Naomi PI: Nocera, Daniel
• Fabrication of Novel Electrodes for Neural-electronic Interfaces Ban, Steven PI: Park, Hongkun
• Capsule remodeling in Klebsiella pneumoniae ST258 Braxton, Julian PI: Hung, Deborah
• Mechanisms of DNA-Protein Crosslink Proteolysis During DNA Replication Gao, Alan PI: Walter, Johannes
• Characterization of TMEM41B and VPS37A in mammalian autophagy Huang, Tina PI: Denic, Vlad
• 2P or Not 2P: Targeted Optogenetic Perturbation at Millisecond Precision and Single-Cell Resolution Kim, Jeonjun PI: Cohen, Adam
• Development of field-deployable diagnostic tools for improved detection of Lassa virus in endemic regions Lachenauer, Anna PI: Sabeti, Pardis
• The effect of modulating tumor cell and T cell metabolism on the PD-1 pathway and immune response to cancer Lane, Jaina PI: Sharpe, Arlene
• Characterizing transcriptional effects of knocking out schizophrenia-associated genes tcf4 and znf804a Li, Eric PI: Schier, Alexander
• Structural Equilibrium of the IBV Pseudoknot and its Role in Ribosomal Frameshifting Lo Bello, Josie PI: D’Souza, Victoria
• Regulation of Intra-myocardial fibrosis by IL-33/ST2 Signaling Malick, Alyyah PI: Lee, Richard
• Exploring the O-GlcNAcylation Status Of Histone 2B Naftaly, Jeff PI: Woo, Christina
• The pursuit of mechanism: Computational approaches to infer the biological basis of differential response to therapeutics treatment in cancer cell lines Petros, Brittany PI: Clemons, Paul
• Engineering an in vivo system to study localization of ancient reconstructed RuBisCO in cyanobacteria Ward, Ryan PI: Kacar, Betul
• An Investigation of the Encoding of Molecular Properties into Odor Perception using Gaussian Processes Zinzuwadia, Aniket PI: Aspuru-Guzik, Alan

• How do you turn this thing on?: Investigating mechanisms of innate immune modulation by pathogens, probiotics, and metabolites. Rubin, Dan, PI: Kagan, Jonathan
• The C. Elegans microRNA miR-70 Plays a Critical Role in Defense Against Starvation. Reece, Akana, PI: Soukas, Alexander
• An Investigation of Cell-Type Specific Degenerative Mechanisms in C9ORF72 ALS. Chowdhary, Kaitavjeet, PI: Eggan, Kevin
• Novel Small-Molecule Fusion Inhibitors Targeting the Membrane Proximal External Region of HIV-1 Envelope. Danis, David, PI: Chen, Bing
• Studies on the induction and mode of action of a novel antimicrobial produced through an actinomycete interspecies interaction. Ndousse-Fetter, Sula, PI: Kolter, Roberto
• Continued genomic surveillance elucidates recent evolutionary behaviors of Lassa virus in West Africa.  Nekoui, Mahan, PI: Sabeti, Pardis
• Investigating the assembly of clustered protocadherins involved in dendrite self-avoidance. Vogt, Bennett, PI: Gaudet, Rachelle
• Structural and Biophysical Studies of Ligand Binding and Cytosolic Interactions in TRPA1. Zurier, Hannah, PI: Gaudet, Rachelle
• Characterizing temperature-sensitive hydrogels and exploring their use as actuators for surgical devices. Dobre, Ioana, PI: Wood, Robert

• Expanding the Genome Editing Toolbox Through Characterization of Orthogonal CRISPR-Cas9 Nucleases Joung, Keith PI: Topkar, Ved
• Social regulation of appetite by the neuropeptide oxytocin Kunes, Samuel PI: Wong, Sandy
• An Investigation on SMG-8 Inhibition on PHA-4 in C. elegans Mango, Susan PI: Zhu, Meng’ou
• Contributions of Qa-1 Restricted CD8+ Tregs to the Immune Response Against Melanoma Dougan, Stephanie PI: Li, Albert

• EXPLORING THE ORIGINS OF LIFE: Enhancing the Permeability of RNA Oligomers through Model Protocells Szostak, Jack PI: Mirza, Fatima (Fatima)
• LIN28A and LIN28B play distinct and significant roles in mouse embryonic fibroblast reprogramming and induced pluripotent stem cell differentiation Daley, George PI: Tintara, Supisara (Supisara)
• The molecular basis of capsaicin sensitivity in the nociceptor TRPV1 Gaudet, Rachelle PI: Zheng, Eric (Eric)
• A Regulatory Model of Heat Shock by Protein Assembly Drummond, Allan PI: Rojek, Alexandra (Alexandra)
• The Role of microRNAs in Regulating Cardiac Exercise Phenotypes Rosenzweig, Anthony PI: Wei, Xin (Paul)
• Developing cyclic peptide inhibitors to target the KRAS-G12V/BRAF protein-protein interaction Verdine, Greg PI: Gong, Jan (Jan)
• Thinking Outside the Cell: Nucleic Acid Content of Exosomes and Extracellular Fluid Church, George PI: Kowal, Emma (Emma)
• Single-Molecule Characterization of Clathrin Coat and Clathrin-Coated Vesicle Disassembly Elucidates Mechanistic Functions of Auxilin Kirchhausen, Tomas PI: Bu, Kevin (Kevin)
• Understanding Microbial Toolkits: Computational and Experimental Study of Microbial Metabolism that Impacts Human Health Balskus, Emily PI: Marks, Jonathan (Jonathan)
• An Investigation into Novel Enhancer Chromatin Readers Shi, Yang PI: Chin, Kuo-Kai (Kuo-Kai)
• Development and Application of Interaction Determination using Unpurified Proteins (IDUP): A Rapid Method of Drug Discovery Liu, David PI: Jain, Tara (Tara)
• Regulation of ADP-activated signaling by hydrogen peroxide and β-arrestin-2 in vascular endothelial cells Michel, Thomas PI: Kramer, Daniel (Danny)
• Combating Prebiotic Replication Obstruction: Design of a Method for the In Vitro Selection of Catalytic RNAs Capable of Removing 2′3′-Cyclic Phosphates Szostak, Jack PI: Pian, Julia (Julia)
• Viral Polyprotein Processing in IMNV: Cleavage Activity of the NGN Motif Nibert, Max PI: Yang, May (May)
• Understanding the Structural and Functional Domains of BCL11A Orkin, Stuart PI: Li, Dan (Dan)
• Identifying New Regulators of Iron Homeostasis Fraenkel, Paula PI: Cheng, Aaron (Aaron)

• Evolving a Direct Inhibitor of MYC Verdine, Greg PI: Jiang, Yanting (Sam)
• Adaptive apoptotic signaling in cancer limits the efficacy of targeted therapies Fisher, David PI: Kim, Daniel (Daniel)
• Computational and experimental investigation of the regulation of the fold change response in TNF-induced NF-kB activation Gaudet, Suzanne PI: Chen, Weilin (Ina)
• Cancer cells dependent on activating mutations in CTNNB1 are co-dependent on the anti-apoptotic protein Bcl-xL and are hypersensitive to the apoptosis inducer navitoclax Schreiber, Stuart PI: Ebright, Richard (Richard)
• Where Heart Disease Meets Cancer: A Novel Role of CDKN2A/p16 in Modulating Cardiomyocyte Senescence and Cardiac Regeneration Rosenzweig, Anthony PI: Kandola, Manjinder (Manjinder)
• Identification of telomere length regulators in Plasmodium falciparum Duraisingh, Manoj PI: Leung, Yvette (Yvette)
• Modeling diffusion through nanoporous structures Aizenburg, Joanna PI: Lin, Kathy (Kathy)
• Examining the Role of the Thermodynamic Driving Force on DNA Polymerase Fidelity Xie, Sunney PI: Lu, Jenny (Jenny)
• PfRACK: A scaffolding protein of unknown function in Plasmodium falciparum Dvorin, Jeffrey PI: Pine, Stewart (Stew)
• Structural study of a novel partial Ca2+-free linker and a positively selected variation in Protocadherin-15: Implications for hearing and cell adhesion Gaudet, Rachelle PI: Powers, Robert (Robert)
• “An in vivo Investigation of the Local and Global Dynamics of the Bacterial
  Chromosome in Escherichia coli Zhuang, Xiaowei PI: Su, David (David)”
• Identification of GW8510 as a Neuroprotective Agent in a Gene-Expression Based Computational Screen for Potential Therapeutics for Parkinson’s Disease Schreiber, Stuart PI: Wimalasena, Nivanthika (Nivanthika)

• Modification of Stress Granule Assembly During Caspase-Mediated Apoptosis Lieberman, Judy PI: Deutsch, Aaron (Aaron)
• Ploidy-Specific Variation of ASYNAPSIS1 in Arabidopsis arenosa Bomblies, Kirsten PI: Xue, Katherine (Katherine)
• Sensory Transient Receptor Potential Channels as Targets of Nature’s Defenses Clapham, David PI: Philipson, Benjamin (Ben)
• Investigating the Binding of Diverse Fragments to NFkB1 (p50) and Biophysical Study of NFkB1 and the NFkB1-DNA Complex Young, Damian PI: Berry, Kayla (Kayla)
• Alternating Antibiotic Therapy Can Slow the Evolution of Resistance Through Negative Cross-Resistance Kishony, Roy PI: Kim, Seungsoo (Seungsoo)
• Guiding Osteogenic Differentiation of Mesenchymal Stem Cells Using a Collagen-I Peptide Mimic Mooney, PI: David Lee, Shimwoo (Shimwoo)
• Investigation of the Biosynthetic Origins of Cremeomycin Balskus, Emily PI: Pechersky, Yakov (Yakov)
• An experimental approach to exploring the relationship between protein stability and evolvability Liu, David PI: Yang, David (David)
• Discovery and Applications of Naturally Supercharged Human Proteins Liu, David PI: Shih, Allen (Allen)
• The Impact of HSP72 and IL-6 on the Regenerative Ability of Skeletal Muscle in Aged Mice Wagers, Amy PI: Wang, Stephanie (Stephanie)
• Investigation of candidate molecular controls over segmental specificity of corticospinal motor neurons during development Macklis, Jeffrey PI: Song, Janet (Janet)
• Mitochondrial and Reactive Oxygen Species Intracellular Asymmetry During Neutrophil Chemotaxis Irimia, Daniel PI: Patel, Sachin (Sachin)
• Genome-wide Characterization of the Regulation of the High-Light Stress Response in the Cyanobacterium Synechococcus elongatus PCC 7942 O’Shea, Erin PI: Kennard, Andrew (Andrew)

• Structural studies of the 3’ terminal stem loop of 7SK snRNA D’Souza, Victoria PI: Gonzalez, Grecia (Grecia)
• The Effect of RNA Structure on Nonenzymatic Template-Directed Polymerization in the RNA World Chen, Irene PI: Ivica, Nikola (Nikola)
• Chromosome Dynamics in Cyanobacteria O’Shea, Erin PI: Jain, Isha (Isha)
• The Mammalian SID-1 RNA Transporter Ortholog SidT2 is Required For Nursing and Neonatal Survival Hunter, Craig PI: Nakatsuka, Nathan (Nathan)
• Structural insights into asymmetric motor domains of the ABC transporter TAP Gaudet, Rachelle PI: Ni, Kevin (Kevin)
• TRANSIENT RECEPTOR POTENTIAL CHANNELS ON INTRACELLULAR MEMBRANES IN Ca2+ SIGNALING AND APOPTOTIC PATHWAYS Clapham, David PI Penumaka, Anirudh (Ani)
• Engineering an Injectable, Macropore-Forming, Biocompatible Scaffold for the Delivery of Cancer Immunotherapies Mooney, David PI: Xu, Maria (Maria)
• Exploring Differences in Carbon Metabolism Between Short-Fat and Long-Skinny Ridgeia piscesae Girguis, Peter PI: Yu, Chung (Tom)
• Finding the Antidote for Fanconi Anemia Deficient Cells D’Andrea, Alan PI: Zhao, John (John)
• The Roles of Rac1, Cdc42, and PACSIN2 in Regulation of Endothelial Nitric Oxide Synthase Michel, Thomas PI: Fryhofer, George (George)

• D. discoideum Integrate Chemical and Mechanical Signals to Achieve Directional Motility Gunawardena, Jeremy PI: Chattopadhyay, Arhana (Arhana)

CPB concentrators are encouraged to do research in any area of the life sciences of interest. Many labs on the Cambridge campus as well as labs at Harvard Medical School or affiliated hospitals host undergraduate researchers. Talk to the ADUS, Dominic Mao,, Concentration Advisor Monique Brewster, or to the Co-Head-Tutors, about how to find a lab that matches your interests. You may also contact the undergraduate science research advisor, Anna Babakhanyan.

Useful links:

• How to get involved with research.
• Open undergraduate research positions
• URAF Independent Research Fellowships