Student Publications

The following is a list of publications our students have co-authored on their work during their time in the SSPB Program.
SSPB student authors are noted in bold.

2026
  • Batra, S. S.; Cabrera, A.; Spence, J. P.; Goell, J.; Anand, S. S.; Hilton, I. B.; Song, Y. S. Predicting the Effect of CRISPR-Cas9-Based Epigenome Editing. eLife 2026, 12, RP92991. [link]
  • Bontapalle, S. A.; Carpenter, M. D.; LaTurner, Z. W.; Stadler, L. B.; Ajo-Franklin, C. M.; Verduzco, R. Real-Time Bioelectronic Sensors Based on Electroactive Bacteria with Organic Electrochemical Transistors. Biosens. Bioelectron. 2026, 309, 118798. [link]
  • Brahmachari, S.; Oliveira Jr., A. B.; Mello, M. F.; Contessoto, V. G.; Onuchic, J.N. Exploring the Energy Landscape of Bacterial Chromosome Segregation. Proc. Natl. Acad. Sci. U.S.A. 2026, 123, e2535321123. [link]
  • Bruncz, A. R.; Chatterjee, A.; Gatica-Gutierrez, H.; Brasel, S.; Belyanin, A.; Gustavsson, A.-K.; Huang, S. Discovery of Crystallized and Weakly Coupled Aggregates of Pseudocyanine Iodide. J. Phys. Chem. B 2026, 130, 1622–1633. [link]
  • Chavez, M. S.; Chen, W.-C.; Li, S.; Ajo-Franklin, C. M. Bioelectrochemical Systems for the Detection and Removal of Environmental Pollutants. Curr. Opin. Biotechnol. 2026, 98, 103456. [link]
  • Dwivedi, S.; Kar, S.; Horton, A. P.; Gollihar, J. D. ViralMap: Predicting Features in Viral Proteins from Primary Sequence. J. Virol. 2026, published July 28, 2026. [link]
  • Jansen, Z.; Le, X.; Wei, Q.; Kulhanek, D. L.; Alperovich, N.; Vasilyeva, O.; Gilmour, A. R.; Ross, D.; Thyer, R. Mapping the Phenotypic Landscape of a Transcriptional Repressor Using Deep Mutational Scanning and Growth-Based Quantitative Sequencing. Nucleic Acids Res. 2026, 54 (5), gkag206. [link]
  • Kulhanek, D. L.; Wei, Q.; Head, J.; Hellinger, J.; Jansen, Z.; Gilmour, A. R.; Segall-Shapiro, T.; Brodbelt, J. S.; Usama, S. M.; Thyer, R. Engineering a Bright Near-Infrared Fluorescent Protein by Screening a Comprehensive Phenotypic Landscape. Protein Sci. 2026, 35 (6), e70610. [link]
  • LaTurner, Z. W.; Dysart, M. J.; Schwartz, S. K.; Zeng, E.; Chappell, J.; Silberg, J. J.; Stadler, L. B. Cross-Order Detection of Bacteriophage Transduction in Microbial Communities Using RNA Barcoding. Nat. Commun. 2026, 17, in press. [link]
  • Lazar, J. T.; Haller, D. J.; Ghaddar, A.; Kim, J. J.; Yang, K.; Castillo-Hair, S. M.; Gilmour, A. R.; Thyer, R.; Tabor, J. J. A Stationary Phase-Specific Bacterial Green Light Sensor for Enhancing Metabolite Production. Nat. Commun. 2026, 17, 1071. [link]
  • Li, S.; Zhu, D.; Saha, K.; Kundu, B. B.; Sonkusale, S.; Britton, R. A.; Ajo-Franklin, C. M. Synthetic Microbial Co-Cultures for Modular Bioelectronic Sensing in Diverse Environments. Nat. Biotechnol. 2026, 42, 1066–1077. [link]
  • Lim, H. E.; Llanos, C. D.; Chappell, J.; Segatori, L. Establishing an RNA Sensor with High Sensitivity and Dynamic Range Utilizing a Signal Amplifier Platform. ACS Synth. Biol. 2026, 15 (4), 1300–1311. [link]
  • Liu, B.; Seet, Z. R. D.; Peng, X.; Bennett, M. R.; Lakin, M. R.; Chappell, J. Engineering Plasmids with Synthetic Origins of Replication. Nat. Commun. 2026. [link]
  • Nguyen, C. H. C.; Suggs, O.; Ajo-Franklin, C. M. Unleashing the Potential of S-Layer Proteins for Engineered Living Materials. Curr. Opin. Microbiol. 2026, 93, 102789. [link]
  • Oliveira Jr., A. B.; Mello, M. F.; Oliveira, R. J.; Dodero-Rojas, E.; Brahmachari, S.; Contessoto, V. G.; Onuchic, J. N. A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization. Proc. Natl. Acad. Sci. U.S.A. 2026, 123 (4), e2530583123. [link]
  • Rai, K.; O’Connell, R. W.; Piepergerdes, T. C.; Wang, Y.; Brown, L. B. C.; Samra, K. D.; Wilson, J. A.; Lin, S.; Zhang, T. H.; Ramos, E. M.; Sun, A.; Kille, B.; Curry, K. D.; Rocks, J. W.; Treangen, T. J.; Mehta, P.; Bashor, C. J. Ultra-High-Throughput Mapping of Genetic Design Space. Nature 2026, 650 (8103), 1035–1044. [link]
  • Sattari Khavas, D.; Schwartz, S. K.; Bird, P.; Truong, A.; Silberg, J. J. Microbial Spies and Bloggers: Programming Cells to Convert Environmental Information into Discernible Signals. Curr. Opin. Biotechnol. 2026, 98, 103436. [link]
  • Tian, X.; Wang, H.; Wang, B.; Zhang, J.; Yan, D.; Ingabire, J.; Coffler, S.; Duret, G.; Pham, Q.-K.; Bao, G.; Wang, J.; Veeraraghavan, A.; Robinson, J. T.; Goetz, S. M.; Peterchev, A. V. High-Power Dual-Channel Chamber for High-Frequency Magnetic Neuromodulation. J. Neural Eng. 2026, 23 (2), 026020. [link]
  • Wang, M.; González, L.; Saha, S.; Josić, K.; Mugler, A.; Bennett, M. R. Fast, Long-Range Intercellular Signal Propagation through Growth-Assisted Positive Feedback. Cell Syst. 2026, 17 (3), 101517. [link]
  • Wang, M.; Bueno, C.; Wolynes, P. G. Aggregation of Huntingtin Exon 1 Proteins at Flat and Curved Membrane Surfaces. J. Phys. Chem. B 2026, 130 (7), 2133–2143. [link]
  • Watanabe, S.; Lee, S.; Harb, M.; Nouraein, S.; Raisley, E.; Li, H.; Buitrago, N.; Pforr, B.; Szablowski, J. O. Monitoring In Vivo Transcription with Synthetic Serum Markers. Nat. Commun. 2026, 17, 6880. [link]
  • Windham, E.; Myerscough, D.; Schwartz, S. K.; Carpenter, M. D.; Ajo-Franklin, C. M.; Silberg, J. J. Using Domain Insertion to Create Sulfite Reductases That Present Chemical-Dependent Activities. ACS Synth. Biol. 2026, 15 (6), 2595–2604. [link]
2025
  • Batts, A. J.; Tsitsos, F. N.; Ingabire, J.; Duret, G.; Gorman, S. L.; Tsakri, D.; Noel, R. L.; Ji, R.; Kwon, N.; Pham, Q.-K.; Zhang, L.; Bao, G.; Robinson, J. T.; Konofagou, E. E. A Multifunctional Theranostic Ultrasound Platform for Remote Magnetogenetics and Expanded Blood–Brain Barrier Opening. Brain Stimul. 2025, 18 (6), 1939–1951. [link]
  • Ekness, F.; Wold, E. A.; Leasure, C. S.; Musteata, E.; Monteith, A. J.; Laut, C.; Rosato, A. E.; Skaar, E. P.; Tabor, J. J. A Staphylococcus aureus Virulence Inhibitor Identified by SaeRS Refactoring and Screening in Bacillus subtilis. ACS Synth. Biol. 2025, 14 (4), 1191–1203. [link]
  • Gillett, D. L.; Selinidis, M.; Seamons, T.; George, D.; Igwe, A. N.; Del Valle, I.; Egbert, R. G.; Hofmockel, K. S.; Johnson, A. L.; Matthews, K. R. W.; Masiello, C. A.; Stadler, L. B.; Chappell, J.; Silberg, J. J. A Roadmap to Understanding and Anticipating Microbial Gene Transfer in Soil Communities. Microbiol. Mol. Biol. Rev. 2025, 89 (2), e00225-24. [link]
  • Grandel, N. E.; Alexander, A. M.; Peng, X.; Palamountain, C.; Alnahhas, R. N.; Hirning, A. J.; Josić, K.; Bennett, M. R. Long-Term Homeostasis in Microbial Consortia via Auxotrophic Cross-Feeding. Nat. Commun. 2025, 16, 8573. [link]
  • Harb, M.; Nouraein, S.; Szablowski, J. O. Site-Specific Noninvasive Delivery of Retrograde Viral Vectors to the Brain. Bioeng. Transl. Med. 2026, 11 (1), e70062. [link]
  • Kalvapalle, P.B.; Staubus, A.; Dysart, M. J.; Gambill, L.; Reyes Gamas, K.; Lu, L. C.; Silberg, J. J.; Stadler, L. B.; Chappell, J. Information Storage across a Microbial Community Using Universal RNA Barcoding. Nat. Biotechnol. 2025, 44 (2), 269–276. [link]
  • Kundu, B. B.; Krishnan, J.; Szubin, R.; Patel, A.; Palsson, B. O.; Zielinski, D. C.; Ajo-Franklin, C. M. Extracellular Respiration Is a Latent Energy Metabolism in Escherichia coli. Cell 2025, 188 (11), 2907–2924.e23. [link]
  • Li, H.; Nouraein, S.; Lee, S.; Link, S. S.; Raisley, E. K.; Szablowski, J. O. Nonsurgical Control of Seizure Threshold with Acoustically Targeted Chemogenetics. ACS Chem. Neurosci. 2025, 16 (22), 4327–4340. [link]
  • Nouraein, S.; Li, H.; Lee, S.; Saenz, V. A.; Raisley, E. K.; Watanabe, S.; Costa, V. D.; Szablowski, J. O. Erasable Serum Markers. Proc. Natl. Acad. Sci. U.S.A. 2025, 122 (49), e2511741122. [link]
  • Palma, C. S. D.; Haller, D. J.; Chatterjee, S.; Tabor, J. J.; Igoshin, O. A. Changes in Spo0A~P Pulsing Frequency Control Biofilm Matrix Deactivation. PLoS Comput. Biol. 2025, 21 (6), e1013263. [link]
  • Reyes Gamas, K.; Seamons, T. R.; Dysart, M. J.; Fang, L.; Chappell, J.; Stadler, L. B.; Silberg, J. J. Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA. ACS Synth. Biol. 2025, 14 (9), 3530–3542. [link]
  • Yang, X.; Rocks, J. W.; Jiang, K.; Walters, A. J.; Rai, K.; Liu, J.; Nguyen, J.; Olson, S. D.; Mehta, P.; Collins, J. J.; Daringer, N. M.; Bashor, C. J. Engineering Synthetic Phosphorylation Signaling Networks in Human Cells. Science 2025, 387 (6729), 74–81. [link]
  • Zhu, D.; Galley, J.; Pizzini, J.; Musteata, E.; Douglas, M. V.; Chazin, W. J.; Skaar, E. P.; Tabor, J. J.; Britton, R. A. Microbial Biosensor for Sensing and Treatment of Intestinal Inflammation. Adv. Sci. 2025, 12 (27), 2504364. [link]
2024
  • Alba, R. A. C.; Li, S.; Kundu, B. B.; Ajo-Franklin, C. M.; Cai, R. Characterizing Mediated Extracellular Electron Transfer in Lactic Acid Bacteria with a Three-Electrode, Two-Chamber Bioelectrochemical System. J. Vis. Exp. 2024, No. 210, 67204. [link]
  • Haller, D. J.; Castillo-Hair, S. M.; Tabor, J. J. Optogenetic Control of B. subtilis Gene Expression Using the CcaSR System. In Optogenetics; Methods in Molecular Biology; Humana Press: New York, NY, 2025; Vol. 2840, pp 1–17. [link]
  • Jansen, Z.; Alameri, A.; Wei, Q.; Kulhanek, D. L.; Gilmour, A. R.; Halper, S.; Schwalm, N. D., III; Thyer, R. A Modular Toolkit for Environmental Rhodococcus, Gordonia, and Nocardia Enables Complex Metabolic Manipulation. Appl. Environ. Microbiol. 2024, 90 (8), e00340-24. [link]
  • Jimenez, E. M.; Nguyen, C.; Shakeel, A.; Tesoriero, R., Jr.; Charrier, M.; Stull, A.; Ajo-Franklin, C. M. Genetically Modifying the Protein Matrix of Macroscopic Living Materials to Control Their Structure and Rheological Properties. ACS Synth. Biol. 2024, 13 (12), 3936–3947. [link]
  • Kalvapalle, P. B.; Sridhar, S.; Silberg, J. J.; Stadler, L. B. Long-Duration Environmental Biosensing by Recording Analyte Detection in DNA Using Recombinase Memory. Appl. Environ. Microbiol. 2024, 90 (4), e02363-23. [link]
  • Lee, S.; Nouraein, S.; Kwon, J. J.; Huang, Z.; Wojick, J. A.; Xia, B.; Corder, G.; Szablowski, J. O. Engineered Serum Markers for Non-Invasive Monitoring of Gene Expression in the Brain. Nat. Biotechnol. 2024, 42, 1717–1725. [link]
  • Li, S.; Zuo, X.; Carpenter, M. D.; Verduzco, R.; Ajo-Franklin, C. M. Microbial Bioelectronic Sensors for Environmental Monitoring. Nat. Rev. Bioeng. 2025, 3, 30–49. [link]
  • Loveless, T. B.; Carlson, C. K.; Dentzel Helmy, C. A.; Hu, V. J.; Ross, S. K.; Demelo, M. C.; Murtaza, A.; Liang, G.; Ficht, M.; Singhai, A.; Pajoh-Casco, M. J.; Liu, C. C. Open-Ended Molecular Recording of Sequential Cellular Events into DNA. Nat. Chem. Biol. 2025, 21 (4), 512–521. [link]
  • Nelson, T.; Vargas-Hernández, S.; Freire, M.; Cheng, S.; Gustavsson, A.-K. Multimodal Illumination Platform for 3D Single-Molecule Super-Resolution Imaging throughout Mammalian Cells. Biomed. Opt. Express 2024, 15 (5), 3050–3063. [link]
  • Rai, K.; Wang, Y.; O'Connell, R. W.; Patel, A.; Bashor, C. J. Using Machine Learning to Enhance and Accelerate Synthetic Biology. Curr. Opin. Biomed. Eng. 2024, 31, 100553. [link]
  • Seo, J. P.; Trippett, J. S.; Huang, Z.; Lee, S.; Nouraein, S.; Wang, R. Z.; Szablowski, J. O. Acoustically Targeted Measurement of Transgene Expression in the Brain. Sci. Adv. 2024, 10 (32), eadj7686. [link]
2023
  • Aghlara-Fotovat, S.; Musteata, E.; Doerfert, M. D.; Baruch, M.; Levitan, M.; Tabor, J. J.; Veiseh, O. Hydrogel-Encapsulation to Enhance Bacterial Diagnosis of Colon Inflammation. Biomaterials 2023, 301, 122246. [link]
  • Bachhav, B.; de Rossi, J.; Llanos, C. D.; Segatori, L. Cell Factory Engineering: Challenges and Opportunities for Synthetic Biology Applications. Biotechnol. Bioeng. 2023, 120 (9), 2441–2459. [link]
  • Brink, K. R.; Hunt, M. G.; Mu, A. M.; Groszman, K.; Hoang, K. V.; Lorch, K. P.; Pogostin, B. H.; Gunn, J. S.; Tabor, J. J. An E. coli Display Method for Characterization of Peptide–Sensor Kinase Interactions. Nat. Chem. Biol. 2023, 19 (4), 451–459. [link]
  • Chen, M.; Kim, B.; Jarvis, M. I.; Fleury, S.; Deng, S.; Nouraein, S.; Butler, S.; Lee, S.; Chambers, C.; Hodges, H. C.; Szablowski, J. O.; Suh, J.; Veiseh, O. Immune Profiling of Adeno-Associated Virus Response Identifies B Cell-Specific Targets That Enable Vector Re-Administration in Mice. Gene Ther. 2023, 30 (5), 429–442. [link]
  • Chen, P. J.; McMullin, A. B.; Visser, B. J.; Mei, Q.; Rosenberg, S. M.; Bates, D. Interdependent Progression of Bidirectional Sister Replisomes in Escherichia coli. eLife 2023, 12, e82241. [link]
  • Chen, Z.; Zarazúa-Osorio, B.; Srivastava, P.; Fujita, M.; Igoshin, O. A. The Slowdown of Growth Rate Controls the Single-Cell Distribution of Biofilm Matrix Production via a SinI-SinR-SlrR Network. mSystems 2023, 8 (2), e00622-22. [link]
  • Dodero-Rojas, E.; Mello, M. F.; Brahmachari, S.; Oliveira Junior, A. B.; Contessoto, V. G.; Onuchic, J. N. PyMEGABASE: Predicting Cell-Type-Specific Structural Annotations of Chromosomes Using the Epigenome. J. Mol. Biol. 2023, 435 (15), 168180. [link]
  • Farahani, P. E.; Yang, X.; Mesev, E. V.; Fomby, K. A.; Brumbaugh-Reed, E. H.; Bashor, C. J.; Nelson, C. M.; Toettcher, J. E. pYtags Enable Spatiotemporal Measurements of Receptor Tyrosine Kinase Signaling in Living Cells. eLife 2023, 12, e82863. [link]
  • Gambill, L.; Staubus, A.; Mo, K. W.; Ameruoso, A.; Chappell, J. A Split Ribozyme That Links Detection of a Native RNA to Orthogonal Protein Outputs. Nat. Commun. 2023, 14, 543. [link]
  • Goike, J.; Hsieh, C.-L.; Horton, A. P.; Gardner, E. C.; Zhou, L.; Bartzoka, F.; Wang, N.; Javanmardi, K.; Herbert, A.; Abbassi, S.; Xie, X.; Xia, H.; Shi, P.-Y.; Renberg, R.; Segall-Shapiro, T. H.; Terrace, C. I.; Wu, W.; et al. SARS-CoV-2 Omicron Variants Conformationally Escape a Rare Quaternary Antibody Binding Mode. Commun. Biol. 2023, 6 (1), 1250. [link]
  • Jansen, Z.; Reilly, S. R.; Lieber-Kotz, M.; Li, A. Z.; Wei, Q.; Kulhanek, D. L.; Gilmour, A. R.; Thyer, R. Interrogating the Function of Bicistronic Translational Control Elements to Improve Consistency of Gene Expression. ACS Synth. Biol. 2023, 12 (6), 1608–1615. [link]
  • Kalvapalle, P. B.; Sun, T.; O'Donnell, M. A.; Stadler, L. B. Snapshot ARG Removal Rates across Wastewater Treatment Plants Are Not Representative Due to Diurnal Variations. ACS ES&T Water 2023, 3 (1), 166–175. [link]
  • Lee, J.; Campillo, B.; Hamidian, S.; Liu, Z.; Shorey, M.; St-Pierre, F. Automating the High-Throughput Screening of Protein-Based Optical Indicators and Actuators. Biochemistry 2023, 62 (2), 169–177. [link]
  • Liu, B.; Cuba Samaniego, C.; Bennett, M. R.; Franco, E.; Chappell, J. A Portable Regulatory RNA Array Design Enables Tunable and Complex Regulation across Diverse Bacteria. Nat. Commun. 2023, 14, 5268. [link]
  • Mukherjee, S.; Kim, B.; Cheng, L. Y.; Doerfert, M.; Li, J.; Zhou, Y.; Vegas, A. J. Screening Hydrogels for Antifibrotic Properties by Implanting Cellularly Barcoded Alginates in Mice and a Non-Human Primate. Nat. Biomed. Eng. 2023, 7 (5), 568–581. [link]
  • Nouraein, S.; Lee, S.; Saenz, V. A.; Del Mundo, H. C.; Yiu, J.; Szablowski, J. O. Acoustically Targeted Noninvasive Gene Therapy in Large Brain Volumes. Gene Ther. 2024, 31 (3–4), 85–94. [link]
  • Tejedor-Sanz, S.; Li, S.; Kundu, B. B.; Ajo-Franklin, C. M. Extracellular Electron Uptake from a Cathode by the Lactic Acid Bacterium Lactiplantibacillus plantarum. Front. Microbiol. 2023, 14, 1298023. [link]
  • Wang, Q.; Nute, M.; Treangen, T. J. Bakdrive: Identifying a Minimum Set of Bacterial Species Driving Interactions across Multiple Microbial Communities. Bioinformatics 2023, 39 (Suppl. 1), i47–i56. [link]
  • Wolken, M.; Sun, T.; McCall, C.; Schneider, R.; Caton, K.; Hundley, C.; Hopkins, L.; Ensor, K.; Domakonda, K.; Kalvapalle, P.; Persse, D.; Williams, S.; Stadler, L. B. Wastewater Surveillance of SARS-CoV-2 and Influenza in PreK–12 Schools Shows School, Community, and Citywide Infections. Water Res. 2023, 231, 119648. [link]
  • Yang, W.; Templeton, C.; Rosenberger, D.; Bittracher, A.; Nüske, F.; Noé, F.; Clementi, C. Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS Cent. Sci. 2023, 9 (2), 186–196. [link]
  • Zhai, Y.; Pribis, J. P.; Dooling, S. W.; Garcia-Villada, L.; Minnick, P. J.; Xia, J.; Liu, J.; Mei, Q.; Fitzgerald, D. M.; Herman, C.; Hastings, P. J.; Costa-Mattioli, M.; Rosenberg, S. M. Drugging Evolution of Antibiotic Resistance at a Regulatory Network Hub. Sci. Adv. 2023, 9 (25), eadg0188. [link]
  • Zong, D. M.; Sadeghpour, M.; Molinari, S.; Alnahhas, R. N.; Hirning, A. J.; Giannitsis, C.; Ott, W.; Josić, K.; Bennett, M. R. Tunable Dynamics in a Multistrain Transcriptional Pulse Generator. ACS Synth. Biol. 2023, 12 (12), 3531–3543. [link]
2022
  • Al-Radhawi, M. A.; Tripathi, S.; Zhang, Y.; Sontag, E. D.; Levine, H. Epigenetic Factor Competition Reshapes the EMT Landscape. Proc. Natl. Acad. Sci. U.S.A. 2022, 119 (42), e2210844119. [link]

  • Balaji, A.; Kille, B.; Kappell, A. D.; Godbold, G. D.; Diep, M.; Elworth, R. A. L.; Qian, Z.; Albin, D.; Nasko, D. J.; Shah, N.; Pop, M.; Segarra, S.; Ternus, K. L.; Treangen, T. J. SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning. Genome Biol. 2022, 23, 133. [link]

  • Behrens, C.; Yadav, S. C.; Korympidou, M. M.; Zhang, Y.; Haverkamp, S.; Irsen, S.; Schaedler, A.; Lu, X.; et al Retinal Horizontal Cells Use Different Synaptic Sites for Global Feedforward and Local Feedback Signaling. Curr. Biol. 2022, 32 (3), 545–558.e5. [link]

  • Bondaruk, J.; Jaksik, R.; Wang, Z.; Cogdell, D.; Lee, S.; Chen, Y.; et al. The Origin of Bladder Cancer from Mucosal Field Effects. iScience 2022, 25 (7), 104551. [link]

  • Bueno, C.; Liman, J.; Schafer, N. P.; Cheung, M. S.; Wolynes, P. G. A Generalized Flory-Stockmayer Kinetic Theory of Connectivity Percolation and Rigidity Percolation of Cytoskeletal Networks. PLoS Comput. Biol. 2022, 18 (5), e1010105. [link]

  • Campbell, I. J.; Atkinson, J. T.; Carpenter, M. D.; Myerscough, D.; Su, L.; Ajo-Franklin, C. M.; Silberg, J. J. Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion. Biochemistry 2022, 61 (13), 1337–1350. [link]

  • Chen, X.; Jin, S.; Chen, M.; Bueno, C.; Wolynes, P. G. The Marionette Mechanism of Domain–Domain Communication in the Antagonist, Agonist, and Coactivator Responses of the Estrogen Receptor. Proc. Natl. Acad. Sci. U.S.A. 2023, 120 (6), e2216906120. [link]

  • Chen, Z.; Srivastava, P.; Zarazúa-Osorio, B.; Marathe, A.; Fujita, M.; Igoshin, O. A. Bacillus subtilis Histidine Kinase KinC Activates Biofilm Formation by Controlling Heterogeneity of Single-Cell Responses. mBio 2022, 13 (1), e01694-21. [link]

  • Curry, K. D.; Wang, Q.; Nute, M. G.; Tyshaieva, A.; Reeves, E.; Soriano, S.; Wu, Q.; Graeber, E.; Finzer, P.; Mendling, W.; Savidge, T.; Villapol, S.; Dilthey, A.; Treangen, T. J. Emu: Species-Level Microbial Community Profiling of Full-Length 16S rRNA Oxford Nanopore Sequencing Data. Nat. Methods 2022, 19 (7), 845–853. [link]

  • de Rossi, J.; Arefeayne, Y.; Robinson, A.; Segatori, L. Emerging Technologies for Genetic Control Systems in Cellular Therapies. Curr. Opin. Biotechnol. 2022, 78, 102833. [link]

  • Del Valle, I.; Gao, X.; Ghezzehei, T. A.; Silberg, J. J.; Masiello, C. A. Artificial Soils Reveal Individual Factor Controls on Microbial Processes. mSystems 2022, 7 (4), e00301-22. [link]

  • Govorunova, E. G.; Gou, Y.; Sineshchekov, O. A.; Li, H.; Lu, X.; Wang, Y.; Brown, L. S.; St-Pierre, F.; Xue, M.; Spudich, J. L. Kalium Channelrhodopsins Are Natural Light-Gated Potassium Channels That Mediate Optogenetic Inhibition. Nat. Neurosci. 2022, 25 (7), 967–974. [link]

  • Gu, X.; Schafer, N. P.; Bueno, C.; Lu, W.; Wolynes, P. G. A Structural Dynamics Model for How CPEB3 Binding to SUMO2 Can Regulate Translational Control in Dendritic Spines. PLoS Comput. Biol. 2022, 18 (11), e1010657. [link]

  • Guerra-Resendez, R. S.; Brenner, D.; Hilton, I. B. Tuning Neurodegeneration-Linked Gene Expression, One (Edited) Base at a Time. Mol. Ther. 2022, 30 (12), 3512–3514. [link]

  • Guerra-Resendez, R. S.; Hilton, I. B. Harnessing CRISPR-Cas9 for Epigenetic Engineering. In Riboregulator Design and Analysis; Chappell, J.; Takahashi, M. K., Eds.; Methods in Molecular Biology; Humana: New York, NY, 2022; Vol. 2518, pp 237–251.[link]

  • Ingabire, J.; McKenney, H.; Sebesta, C.; Badhiwala, K.; Kemere, C.; Kapur, S.; Robinson, J. T. Evaluation of Aerosol Particle Leak and Standard Surgical Mask Fit with 3 Elastomeric Harness Designs. JAMA Netw. Open 2022, 5 (1), e2145811. [link]

  • Jin, S.; Bueno, C.; Lu, W.; Wang, Q.; Chen, M.; Chen, X.; Wolynes, P. G.; Gao, Y. Computationally Exploring the Mechanism of Bacteriophage T7 gp4 Helicase Translocating along ssDNA. Proc. Natl. Acad. Sci. U. S. A. 2022, 119 (32), e2202239119. [link]

  • Lee, J.; St-Pierre, F. A Blueprint for Glow Tag Engineering. Nat. Rev. Chem. 2022, 6 (1), 7–8. [link]

  • Liu, B.; Cuba Samaniego, C.; Bennett, M. R.; Chappell, J.; Franco, E. RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks. ACS Synth. Biol. 2022, 11 (3), 1240–1250. [link]

  • Liu, B.; Chappell, J. Computational Design of Small Transcription Activating RNAs (STARs). In Riboregulator Design and Analysis; Chappell, J.; Takahashi, M. K., Eds.; Methods in Molecular Biology; Humana: New York, NY, 2022; Vol. 2518, pp 87–97. [link]

  • Liu, B.; Samaniego, C. C.; Bennett, M. R.; Franco, E.; Chappell, J. A Portable Regulatory RNA Array Design Enables Tunable and Complex Regulation across Diverse Bacteria. Nat. Commun. 2023, 14, 5268. [link]

  • Liu, L.; Nemashkalo, A.; Rezende, L.; Jung, J. Y.; Chhabra, S.; Guerra, M. C.; Heemskerk, I.; Warmflash, A. Nodal Is a Short-Range Morphogen with Activity That Spreads through a Relay Mechanism in Human Gastruloids. Nat. Commun. 2022, 13, 497. [link]

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2020
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2019
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2018
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2017
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  • Dongya Jia. Operating principles of tristable circuits regulating cellular differentiation. Phys. Biol. 2017, 14(3): 035007. [link]
  • Dongya Jia. Modeling the genetic regulation of cancer metabolism: interplay between glycolysis and oxidative phosphorylation. Cancer Res. 2017; 77(7):1564-1574. [link]
  • Dongya Jia. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017, 13(3): e1005456. [link]
  • Dongya Jia. Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity. PNAS 2017, 114(13): E2644-E2653. [link]
  • Dongya Jia. Distinguishing mechanisms underlying EMT tristability. Cancer Converg. 2017, 1: 2. [link]
  • Prashant Kalvapalle. Using cellular fitness to map the structure and function of a major facilitator superfamily effluxes. Mol. Sys. Biol. 2017; 13(12): 964. [link]
  • Tyler McLaughlin. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks. Biol Open. 2017, 6(6): 785-799. [link]
  • Juexiao Sherry Wang and Yan Helen Yan. Modular probes for enriching and detecting complex nucleic acid sequences. Nat. Chem. 2017, 9:1222-1229. [link]
2016
  • Joshua Atkinson. Cellular assays for ferredoxins: a strategy for understanding electron flow through protein carriers that link metabolic pathways. Biochem. 2016, 55(51): 7047-7064. [link]
  • Joshua Atkinson. The structure of a thermophilic kinase shapes fitness upon random circular permutation. ACS Synth. Biol. 2016, 5(5): 415-425. [link]
  • Ilenne Del Valle. Charcoal disrupts soil microbial communication through a combination of signal sorption and hydrolysis. ACS Omega, 2016 1(2): 226–233. [link]
  • Felix Ekness. An open-hardware platform for optogenetics and photobiology. Sci Rep. 2016; 6: 35363. [link]
  • Dongya Jia. Modeling delayed processes in biological systems. Phys. Rev. E. 2016; 94: 032408. [link]
  • Dongya Jia. Stability of the hybrid epithelial/mesenchymal phenotype. Oncotarget 2016, 7(19): 27067-27084. [link]
  • Dongya Jia. Tumor Budding: The Name is EMT. Partial EMT. J. Clin. Med. 2016; 5(5): 51. [link]
  • Brianna Kuypers. Tolerance of a knotted near-infrared fluorescent protein to random circular permutation. Biochem. 2016, 55(27): 3763-3773. [link]
  • Tyler McLaughlin. Collective dynamics of processive cytoskeletal motors. Soft Matter 2016, 12(1): 14-21. [link]
  • Qian Mei. Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. Sci Adv. 2016, 2(11): e1601605. [link]
  • Yidan Pan. Prediction of influenza B vaccine effectiveness from sequence data. Vaccine 2016, 34(38): 4610-4617. [link]
2015
  • Jia, D.; Jolly, M. K.; Boareto, M.; Parsana, P.; Mooney, S. M.; Pienta, K. J.; Levine, H.; Ben-Jacob, E. OVOL Guides the Epithelial-Hybrid-Mesenchymal Transition. Oncotarget 2015, 6 (17), 15436–15448. [link]
  • Jolly, M. K.; Boareto, M.; Huang, B.; Jia, D.; Lu, M.; Ben-Jacob, E.; Onuchic, J. N.; Levine, H. Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis. Front. Oncol. 2015, 5, 155. [link]
  • Jolly, M. K.; Jia, D.; Boareto, M.; Mani, S. A.; Pienta, K. J.; Ben-Jacob, E.; Levine, H. Coupling the Modules of EMT and Stemness: A Tunable “Stemness Window” Model. Oncotarget 2015, 6 (28), 25161–25174. [link]
  • Takahashi, C. N.; Miller, A. W.; Ekness, F.; Dunham, M. J.; Klavins, E. A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization. ACS Synth. Biol. 2015, 4 (1), 32–38. [link]
  • Wang, J. S.; Zhang, D. Y. Simulation-Guided DNA Probe Design for Consistently Ultraspecific Hybridization. Nat. Chem. 2015, 7 (7), 545–553. [link]
  • Wu, L. R.; Wang, J. S.; Fang, J. Z.; Evans, E. R.; Pinto, A.; Pekker, I.; Boykin, R.; Ngouenet, C.; Webster, P. J.; Beechem, J.; Zhang, D. Y. Continuously Tunable Nucleic Acid Hybridization Probes. Nat. Methods 2015, 12 (12), 1191–1196. [link]
2014
  • Guenther, C. M.; Kuypers, B. E.; Lam, M. T.; Robinson, T. M.; Zhao, J.; Suh, J. Synthetic Virology: Engineering Viruses for Gene Delivery. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 2014, 6 (6), 548–558. [link]
  • Ho, M. L.; Judd, J.; Kuypers, B. E.; Yamagami, M.; Wong, F. F.; Suh, J. Efficiency of Protease-Activatable Virus Nanonodes Tuned through Incorporation of Wild-Type Capsid Subunits. Cell. Mol. Bioeng. 2014, 7 (3), 334–343. [link]