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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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, 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.; 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.; 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 (1), 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]

  • 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]

  • Tripathi, S.; Kessler, D. A.; Levine, H. Minimal Frustration Underlies the Usefulness of Incomplete Regulatory Network Models in Biology. Proc. Natl. Acad. Sci. U.S.A. 2023, 120 (1), e2216109120. [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, 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, 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]

  • Liu, Z.; Lu, X.; Villette, V.; Gou, Y.; Colbert, K. L.; Lai, S.; Guan, S.; Land, M. A.; Lee, J.; et al. Sustained Deep-Tissue Voltage Recording Using a Fast Indicator Evolved for Two-Photon Microscopy. Cell 2022, 185 (18), 3408–3425.e29. [link]

  • Mahadevan, A. S.; Long, B. L.; Hu, C. W.; Ryan, D. T.; Grandel, N. E.; Britton, G. L.; et al. cytoNet: Spatiotemporal Network Analysis of Cell Communities. PLoS Comput. Biol. 2022, 18 (6), e1009846. [link]

  • Markosian, C.; Staquicini, D. I.; Dogra, P.; Dodero-Rojas, E.; Lubin, J. H.; et al. Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection. Mol. Biol. Evol. 2022, 39 (5), msac091. [link]

  • Molinari, S.; Tesoriero, R. F., Jr.; Li, D.; Sridhar, S.; Cai, R.; Soman, J.; Ryan, K. R.; Ashby, P. D.; Ajo-Franklin, C. M. A De Novo Matrix for Macroscopic Living Materials from Bacteria. Nat. Commun. 2022, 13, 5544. [link]

  • Oliveira, A. B., Jr.; Contessoto, V. G.; Hassan, A.; Byju, S.; Wang, A.; Wang, Y.; Dodero-Rojas, E.; Mohanty, U.; Noel, J. K.; Onuchic, J. N.; Whitford, P. C. SMOG 2 and OpenSMOG: Extending the Limits of Structure-Based Models. Protein Sci. 2022, 31 (1), 158–172. [link]

  • Park, S. H.; Cao, M.; Pan, Y.; Davis, T. H.; Saxena, L.; Deshmukh, H.; Fu, Y.; Treangen, T.; Sheehan, V. A.; Bao, G. Comprehensive Analysis and Accurate Quantification of Unintended Large Gene Modifications Induced by CRISPR-Cas9 Gene Editing. Sci. Adv. 2022, 8 (42), eabo7676. [link]

  • Soriano, S.; Curry, K.; Wang, Q.; Chow, E.; Treangen, T. J.; Villapol, S. Fecal Microbiota Transplantation Derived from Alzheimer’s Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls. Int. J. Mol. Sci. 2022, 23 (9), 4476. [link]

  • Sridhar, S.; Ajo-Franklin, C. M.; Masiello, C. A. A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. ACS Synth. Biol. 2022, 11 (9), 2909–2916. [link]

  • Tripathi, S.; Brahmachari, S.; Onuchic, J. N.; Levine, H. DNA Supercoiling-Mediated Collective Behavior of Co-Transcribing RNA Polymerases. Nucleic Acids Res. 2022, 50 (3), 1269–1279. [link]

  • Tripathi, S.; Park, J. H.; Pudakalakatti, S.; Bhattacharya, P. K.; Kaipparettu, B. A.; Levine, H. A Mechanistic Modeling Framework Reveals the Key Principles Underlying Tumor Metabolism. PLoS Comput. Biol. 2022, 18 (2), e1009841. [link]

  • Zhang, K.; Song, P.; Dai, P.; Zhang, J. X.; Wu, L. R.; Cheng, L. Y.; Pinto, A.; Kwong, L.; Cabrera, K.; Wen, R.; Zhang, D. Y. Cost-Efficient Sequence-Based Nonextensible Oligonucleotide in Real-Time PCR and High-Throughput Sequencing. ACS Sens. 2022, 7 (4), 1165–1174.[link]
2021
  • Abhimanyu; Ontiveros, C. O.; Guerra-Resendez, R. S.; Nishiguchi, T.; Ladki, M.; Hilton, I. B.; Schlesinger, L. S.; DiNardo, A. R. Reversing post-infectious epigenetic-mediated immune suppression. Front. Immunol. 2021, 12, 688132. [link]

  • Baig, H.; Fontanarossa, P.; Kulkarni, V.; McLaughlin, J.; Vaidyanathan, P.; Bartley, B.; Bhakta, S.; Bhatia, S.; Bissell, M.; Clancy, K.; Cox, R. S.; Goñi Moreno, A.; Gorochowski, T.; Grunberg, R.; Lee, J.; Luna, A.; Madsen, C.; Misirli, G.; Nguyen, T.; Le Novere, N.; Palchick, Z.; Pocock, M.; Roehner, N.; Sauro, H.; Scott-Brown, J.; Sexton, J. T.; Stan, G.-B.; Tabor, J. J.; Terry, L.; Vazquez Vilar, M.; Voigt, C. A.; Wipat, A.; Zong, D.; Zundel, Z.; Beal, J.; Myers, C. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3. J. Integr. Bioinform. 2021, 18 (3), 20200045. [link]

  • Bird, L. J.; Kundu, B. B.; Tschirhart, T.; Corts, A. D.; Su, L.; Gralnick, J. A.; Ajo-Franklin, C. M.; Glaven, S. M. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth. Biol. 2021, 10 (11), 2808–2823. [link]

  • Britton, G.; Chhabra, S.; Massey, J.; Warmflash, A. Fate-Patterning of 2D Gastruloids and Ectodermal Colonies Using Micropatterned Human Pluripotent Stem Cells. In Programmed Morphogenesis: Methods and Protocols; Ebrahimkhani, M. R.; Hislop, J., Eds.; Methods in Molecular Biology; Humana: New York, 2021; Vol. 2258, pp 119–130. [link]

  • Cartwright, I. M.; Dowdell, A. S.; Lanis, J. M.; Brink, K. R.; Mu, A.; Kostelecky, R. E.; Schaefer, R. E. M.; Welch, N.; Onyiah, J. C.; Hall, C. H. T.; Gerich, M. E.; Tabor, J. J.; Colgan, S. P. Mucosal acidosis elicits a unique molecular signature in epithelia and intestinal tissue mediated by GPR31-induced CREB phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (20), e2023871118. [link]

  • Chen, Y.; Talukder, R.; Merritt, B. Y.; King, K. Y.; Kimmel, M.; Rivero, G.; Sosa, R. Genomic trajectory in leukemogenesis of myeloproliferative neoplasms: A case report. BMC Med. Genomics 2021, 14 (1), 137. [link]

  • Chhabra, S.; Warmflash, A. BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo. Biol. Open 2021, 10 (9), bio058617. [link]

  • Contessoto, V. G.; Cheng, R. R.; Hajitaheri, A.; Dodero-Rojas, E.; Mello, M. F.; Lieberman-Aiden, E.; Wolynes, P. G.; Di Pierro, M.; Onuchic, J. N. The Nucleome Data Bank: Web-Based Resources to Simulate and Analyze the Three-Dimensional Genome. Nucleic Acids Res. 2021, 49 (D1), D172–D182. [link]

  • Dai, Z.; Yang, X.; Wu, F.; Wang, L.; Xiang, K.; Li, P.; Lv, Q.; Tang, J.; Dohlman, A.; Dai, L.; Shen, X.; You, L. Living fabrication of functional semi-interpenetrating polymeric materials. Nat. Commun. 2021, 12, 3422. [link]

  • Del Valle, I.; Fulk, E. M.; Kalvapalle, P.; Silberg, J. J.; Masiello, C. A.; Stadler, L. B. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front. Microbiol. 2021, 11, 618373. [link]

  • Deshmukh, A. P.; Vasaikar, S. V.; Tomczak, K.; Tripathi, S.; den Hollander, P.; Arslan, E.; Chakraborty, P.; Soundararajan, R.; Jolly, M. K.; Rai, K.; Levine, H.; Mani, S. A. Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (19), e2102050118. [link]

  • Dodero-Rojas, E.; Onuchic, J. N.; Whitford, P. C. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021, 10, e70362. [link]

  • Gagliano, G.; Nelson, T.; Saliba, N.; Vargas-Hernández, S.; Gustavsson, A.-K. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front. Synaptic Neurosci. 2021, 13, 761530. [link]

  • Grandel, N. E.; Reyes Gamas, K.; Bennett, M. R. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol. 2021, 29 (12), 1095–1105. [link]

  • Jayanthi, B.; Bachhav, B.; Wan, Z.; Martinez Legaspi, S.; Segatori, L. A platform for post-translational spatiotemporal control of cellular proteins. Synth. Biol. 2021, 6 (1), ysab002. [link]

  • Jia, D.; Park, J. H.; Kaur, H.; Jung, K. H.; Yang, S.; Tripathi, S.; Galbraith, M.; Deng, Y.; Jolly, M. K.; Kaipparettu, B. A.; Onuchic, J. N.; Levine, H. Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. Br. J. Cancer 2021, 124 (12), 1902–1911. [link]

  • Karzbrun, E.; Khankhel, A. H.; Megale, H. C.; Glasauer, S. M. K.; Wyle, Y.; Britton, G.; Warmflash, A.; Kosik, K. S.; Siggia, E. D.; Shraiman, B. I.; Streichan, S. J. Human neural tube morphogenesis in vitro by geometric constraints. Nature 2021, 599 (7884), 268–272. [link]

  • Khodakov, D.; Li, J.; Zhang, J. X.; Zhang, D. Y. Highly multiplexed rapid DNA detection with single-nucleotide specificity via convective PCR in a portable device. Nat. Biomed. Eng. 2021, 5 (7), 702–712. [link]

  • LaTurner, Z. W.; Zong, D. M.; Kalvapalle, P.; Reyes Gamas, K.; Terwilliger, A.; Crosby, T.; Ali, P.; Avadhanula, V.; Hernandez Santos, H.; Weesner, K.; Hopkins, L.; Piedra, P. A.; Maresso, A. W.; Stadler, L. B. Evaluating Recovery, Cost, and Throughput of Different Concentration Methods for SARS-CoV-2 Wastewater-Based Epidemiology. Water Res. 2021, 197, 117043. [link]

  • Liu, J.; Mei, Q.; Nimer, S.; Fitzgerald, D. M.; Rosenberg, S. M. Genomic Mapping of DNA-Repair Reaction Intermediates in Living Cells with Engineered DNA Structure-Trap Proteins. Methods Enzymol. 2021, 661, 155–181. [link]

  • Liu, Z.; Zhao, F.; Zhao, B.; Yang, J.; Ferrara, J.; Sankaran, B.; Venkataram Prasad, B. V.; Kundu, B. B.; Phillips, G. N., Jr.; Gao, Y.; Hu, L.; Zhu, T.; Gao, X. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat. Commun. 2021, 12, 4158. [link]

  • Lu, W.; Bueno, C.; Schafer, N. P.; Moller, J.; Jin, S.; Chen, X.; Chen, M.; Gu, X.; Davtyan, A.; de Pablo, J. J.; Wolynes, P. G. OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS Comput. Biol. 2021, 17 (2), e1008308. [link]

  • Mackelprang, R.; Aurand, E. R.; Bovenberg, R. A. L.; Brink, K. R.; Charo, R. A.; Delborne, J. A.; Diggans, J.; Ellington, A. D.; Fortman, J. L. C.; Isaacs, F. J.; Medford, J. I.; Murray, R. M.; Noireaux, V.; Palmer, M. J.; Zoloth, L.; Friedman, D. C. Guiding Ethical Principles in Engineering Biology Research. ACS Synth. Biol. 2021, 10 (5), 907–910. [link]

  • Mehrabiani, K. M.; Cheng, R. R.; Onuchic, J. N. Expanding direct coupling analysis to identify heterodimeric interfaces from limited protein sequence data. J. Phys. Chem. B 2021, 125 (41), 11408–11417. [link]

  • Mei, Q.; Fitzgerald, D. M.; Liu, J.; Xia, J.; Pribis, J. P.; Zhai, Y.; Nehring, R. B.; Paiano, J.; Li, H.; Nussenzweig, A.; Hastings, P. J.; Rosenberg, S. M. Two mechanisms of chromosome fragility at replication-termination sites in bacteria. Sci. Adv. 2021, 7 (25), eabe2846. [link]

  • Molinari, S.; Tesoriero, R. F.; Ajo-Franklin, C. M. Bottom-up approaches to engineered living materials: Challenges and future directions. Matter 2021, 4 (10), 3095–3120. [link]

  • Oliveira, A. B., Jr.; Contessoto, V. G.; Mello, M. F.; Onuchic, J. N. A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. J. Mol. Biol. 2021, 433 (6), 166700. [link]

  • Orozco-Hidalgo, M. T.; Charrier, M.; Tjahjono, N.; Tesoriero, R. F., Jr.; Li, D.; Molinari, S.; Ryan, K. R.; Ashby, P. D.; Rad, B.; Ajo-Franklin, C. M. Engineering High-Yield Biopolymer Secretion Creates an Extracellular Protein Matrix for Living Materials. mSystems 2021, 6 (2), e00903-20. [link]

  • Sapoval, N.; Mahmoud, M.; Jochum, M. D.; Liu, Y.; Elworth, R. A. L.; Wang, Q.; Albin, D.; Ogilvie, H. A.; Lee, M. D.; Villapol, S.; Hernandez, K. M.; Maljkovic Berry, I.; Foox, J.; Beheshti, A.; Ternus, K.; Aagaard, K. M.; Posada, D.; Mason, C. E.; Sedlazeck, F. J.; Treangen, T. J. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021, 31 (4), 635–644. [link]

  • Sharma, R.; Dever, D. P.; Lee, C. M.; Azizi, A.; Pan, Y.; Camarena, J.; Köhnke, T.; Bao, G.; Porteus, M. H.; Majeti, R. The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells. Nat. Commun. 2021, 12, 472. [link]

  • Song, P.; Chen, S. X.; Yan, Y. H.; Pinto, A.; Cheng, L. Y.; Dai, P.; Patel, A. A.; Zhang, D. Y. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nat. Biomed. Eng. 2021, 5 (7), 690–701.[link]

  • Staquicini, D. I.; Tang, F. H. F.; Markosian, C.; Yao, V. J.; Staquicini, F. I.; Dodero-Rojas, E.; Contessoto, V. G.; Davis, D.; O’Brien, P.; Habib, N.; et al. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (30), e2105739118. [link]

  • Thadani, N. N.; Zhou, Q.; Reyes Gamas, K.; Butler, S.; Bueno, C.; Schafer, N. P.; Morcos, F.; Wolynes, P. G.; Suh, J. Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophys. J. 2021, 120 (3), 489–503. [link]

  • Tripathi, S.; Xing, J.; Levine, H.; Jolly, M. K. Mathematical Modeling of Plasticity and Heterogeneity in EMT. In The Epithelial-to Mesenchymal Transition: Methods and Protocols; Campbell, K.; Theveneau, E., Eds.; Methods in Molecular Biology; Humana: New York, 2021; Vol. 2179, pp 385–413. [link]

  • Wang, Q.; Kille, B.; Liu, T. R.; Elworth, R. A. L.; Treangen, T. J. PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment. Nat. Commun. 2021, 12, 1167. [link]

  • Xia, B.; Sebesta, C.; Lee, S.; Nair, V.; Zhao, X.; Coffler, S.; Robinson, J. T.; Szablowski, J. O. Biohybrid approaches to interface with the nervous system: the best of both worlds. Curr. Opin. Biotechnol. 2021, 72, 86–94. [link]

  • Yang, J.; Lee, J.; Land, M. A.; Lai, S.; Igoshin, O. A.; St-Pierre, F. A synthetic circuit for buffering gene dosage variation between individual mammalian cells. Nat. Commun. 2021, 12, 4132. [link]

  • Zhang, J. X.; Yordanov, B.; Gaunt, A.; Wang, M. X.; Dai, P.; Chen, Y.-J.; Zhang, K.; Fang, J. Z.; Dalchau, N.; Li, J.; Phillips, A.; Zhang, D. Y. A deep learning model for predicting next-generation sequencing depth from DNA sequence. Nat. Commun. 2021, 12, 4387. [link]
2020
  • Baig, H.; Fontanarrosa, P.; Kulkarni, V.; McLaughlin, J.; Vaidyanathan, P.; Bartley, B.; Bhatia, S.; Bhakta, S.; Bissell, M.; Clancy, K.; Cox, R. S.; Goñi Moreno, A.; Gorochowski, T.; Grunberg, R.; Luna, A.; Madsen, C.; Misirli, G.; Nguyen, T.; Le Novere, N.; Palchick, Z.; Pocock, M.; Roehner, N.; Sauro, H.; Scott-Brown, J.; Sexton, J. T.; Stan, G.-B.; Tabor, J. J.; Vazquez Vilar, M.; Voigt, C. A.; Wipat, A.; Zong, D.; et al. Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinformatics 2020, 17 (2–3), 20200014. [link]

  • Bao, X. R.; Pan, Y.; Lee, C. M.; Davis, T. H.; Bao, G. Tools for experimental and computational analyses of off-target editing by programmable nucleases. Nat. Protoc. 2021, 16 (1), 10–26. [link]

  • Campbell, I. J.; Kahanda, D.; Atkinson, J. T.; Sparks, O. N.; Kim, J.; Tseng, C. P.; Verduzco, R.; Bennett, G. N.; Silberg, J. J. Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential. ACS Synth. Biol. 2020, 9 (12), 3245–3253. [link]

  • Campbell, I. J.; Olmos, J. L., Jr.; Xu, W.; Kahanda, D.; Atkinson, J. T.; Sparks, O. N.; Miller, M. D.; Phillips, G. N., Jr.; Bennett, G. N.; Silberg, J. J. Prochlorococcus Phage Ferredoxin: Structural Characterization and Electron Transfer to Cyanobacterial Sulfite Reductases. J. Biol. Chem. 2020, 295 (31), 10610–10623. [link]

  • Chakraborty, P.; George, J. T.; Tripathi, S.; Levine, H.; Jolly, M. K. Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. Front. Bioeng. Biotechnol. 2020, 8, 220. [link]

  • Del Valle, I.; Webster, T. M.; Cheng, H.-Y.; Thies, J. E.; Kessler, A.; Miller, M. K.; Ball, Z. T.; MacKenzie, K. R.; Masiello, C. A.; Silberg, J. J.; Lehmann, J. Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication. Sci. Adv. 2020, 6 (5), eaax8254. [link]

  • Dodero-Rojas, E.; Ferreira, L. G.; Leite, V. B. P.; Onuchic, J. N.; Contessoto, V. G. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. PLoS One 2020, 15 (1), e0222900. [link]

  • Elworth, R. A. L.; Wang, Q.; Kota, P. K.; Barberan, C. J.; Coleman, B.; Balaji, A.; Gupta, G.; Baraniuk, R. G.; Shrivastava, A.; Treangen, T. J. To petabytes and beyond: Recent advances in probabilistic and signal processing algorithms and their application to metagenomics. Nucleic Acids Res. 2020, 48 (10), 5217–5234. [link]

  • Fulk, E. M.; Huh, D.; Atkinson, J. T.; Lie, M.; Masiello, C. A.; Silberg, J. J. A split methyl halide transferase AND gate that reports by synthesizing an indicator gas. ACS Synth. Biol. 2020, 9 (11), 3104–3113.[link]

  • Hamidi, S.; Nakaya, Y.; Nagai, H.; Alev, C.; Kasukawa, T.; Chhabra, S.; Lee, R.; Niwa, H.; Warmflash, A.; Shibata, T.; Sheng, G. Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation. Development 2020, 147 (3), dev184960. [link]

  • Hartsough, L. A.; Park, M.; Kotlajich, M. V.; Lazar, J. T.; Han, B.; Lin, C.-C. J.; Musteata, E.; Gambill, L.; Wang, M. C.; Tabor, J. J. Optogenetic control of gut bacterial metabolism to promote longevity. eLife 2020, 9, e56849. [link]

  • Jia, W.; Tripathi, S.; Chakraborty, P.; Chedere, A.; Rangarajan, A.; Levine, H.; Jolly, M. K. Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. Oncotarget 2020, 11 (27), 2611–2624. [link]

  • Jin, S.; Chen, M.; Chen, X.; Bueno, C.; Lu, W.; Schafer, N. P.; Lin, X.; Onuchic, J. N.; Wolynes, P. G. Protein Structure Prediction in CASP13 Using AWSEM-Suite. J. Chem. Theory Comput. 2020, 16 (6), 3977–3988. [link]

  • Jin, S.; Contessoto, V. G.; Chen, M.; Schafer, N. P.; Lu, W.; Chen, X.; Bueno, C.; Hajitaheri, A.; Sirovetz, B. J.; Davtyan, A.; Papoian, G. A.; Tsai, M.-Y.; Wolynes, P. G. AWSEM-Suite: A protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Res. 2020, 48 (W1), W25–W30. [link]

  • Lee, J.; Liu, Z.; Suzuki, P. H.; Ahrens, J. F.; Lai, S.; Lu, X.; Guan, S.; St-Pierre, F. Versatile phenotype-activated cell sorting. Sci. Adv. 2020, 6 (43), eabb7438. [link]

  • Liman, J.; Bueno, C.; Eliaz, Y.; Schafer, N. P.; Waxham, M. N.; Wolynes, P. G.; Levine, H.; Cheung, M. S. The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks. Proc. Natl. Acad. Sci. U.S.A. 2020, 117 (20), 10825–10831. [link]

  • Mahmoud, M.; Gener, A. R.; Khayat, M. M.; English, A. C.; Balaji, A.; Zhou, A.; Hehn, A.; Fungtammasan, A.; Chrisman, B. S.; Chin, C.-S.; Lin, C.-F.; Lo, C.-H.; Liao, C.; Carvalho, C. M. B.; Diesh, C.; Symer, D. E.; Kalra, D.; Albin, D.; et al. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine. F1000Research 2020, 9, 1141. [link]

  • Ortega-Rodríguez, M.; Solís-Sánchez, H.; Álvarez-García, L.; Dodero-Rojas, E. On twin peak quasi-periodic oscillations resulting from the interaction between discoseismic modes and turbulence in accretion discs around black holes. Mon. Not. R. Astron. Soc. 2020, 492 (2), 1755–1760. [link]

  • Pan, Y.; Tian, R.; Lee, C. M.; Bao, G.; Gibson, G. Fine-mapping within eQTL credible intervals by expression CROP-seq. Biol. Methods Protoc. 2020, 5 (1), bpaa008. [link]

  • Robinson, T. M.; Ho, M. L.; Wahlig, B.; Gough, V.; Banta, A.; Reyes Gamas, K.; Kang, B.; Lee, E.; Chen, W.; Suh, J. An essential N-terminal serine-rich motif in the AAV VP1 and VP2 subunits that may play a role in viral transcription. Virology 2020, 546, 127–132. [link]

  • Sheen, P.; Monsalve, A.; Campos, J.; Huerta, R.; Antiparra, R.; Arteaga, H.; Duran, P.; Bueno, C.; Kirwan, D. E.; Gilman, R. H.; Zimic, M. Metallochaperones Are Needed for Mycobacterium tuberculosis and Escherichia coli Nicotinamidase-Pyrazinamidase Activity. J. Bacteriol. 2020, 202 (2), e00331-19. [link]

  • Tian, R.; Pan, Y.; Etheridge, T. H. A.; Deshmukh, H.; Gulick, D.; Gibson, G.; Bao, G.; Lee, C. M. Pitfalls in single clone CRISPR-Cas9 mutagenesis to fine-map regulatory intervals. Genes 2020, 11 (5), 504. [link]

  • Trenton, N. J.; McLaughlin, R. T.; Bellamkonda, S. K.; Tsao, D. S.; Rodzinski, A.; Mace, E. M.; Orange, J. S.; Schweikhard, V.; Diehl, M. R. Membrane and actin tethering transitions help IQGAP1 coordinate GTPase and lipid messenger signaling. Biophys. J. 2020, 118 (3), 586–599. [link]

  • Tripathi, S.; Chakraborty, P.; Levine, H.; Jolly, M. K. A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. PLoS Comput. Biol. 2020, 16 (2), e1007619. [link]

  • Tripathi, S.; Kessler, D. A.; Levine, H. Biological networks regulating cell fate choice are minimally frustrated. Phys. Rev. Lett. 2020, 125 (8), 088101. [link]

  • Tripathi, S.; Levine, H.; Jolly, M. K. The physics of cellular decision making during epithelial–mesenchymal transition. Annu. Rev. Biophys. 2020, 49, 1–18. [link]

  • Wu, B.; Atkinson, J. T.; Kahanda, D.; Bennett, G. N.; Silberg, J. J. Combinatorial design of chemical-dependent protein switches for controlling intracellular electron transfer. AIChE J. 2020, 66 (3), e16796. [link]

  • Yan, Y. H.; Zhang, D. Y.; Wu, L. R. Encoding multiple digital DNA signals in a single analog channel. Nucleic Acids Res. 2020, 48 (11), e65. [link]

  • Yang, X.; Her, J.; Bashor, C. J. Mammalian signaling circuits from bacterial parts. Nat. Chem. Biol. 2020, 16 (2), 110–111. [link]
2019
  • Ameruoso, A.; Gambill, L.; Liu, B.; Villegas Kcam, M. C.; Chappell, J. Brave new ‘RNA’ world—advances in RNA tools and their application for understanding and engineering biological systems. Curr. Opin. Syst. Biol. 2019, 14, 32–40. [link]

  • Atkinson, J. T. Life simplified: Recompiling a bacterial genome for synonymous codon compression. Synth. Biol. 2019, 4 (1), ysz017. [link]

  • Atkinson, J. T.; Campbell, I. J.; Thomas, E. E.; Bonitatibus, S. C.; Elliott, S. J.; Bennett, G. N.; Silberg, J. J. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat. Chem. Biol. 2019, 15 (2), 189–195. [link]

  • Atkinson, J. T.; Jones, A. M.; Nanda, V. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng., Des. Sel. 2019, 32 (11), 489–501. [link]

  • Atkinson, J. T.; Wu, B.; Segatori, L.; Silberg, J. J. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. In Methods in Enzymology; Shukla, A. K., Ed.; Academic Press: 2019; Vol. 621, pp 191–212. [link]

  • Beal, J.; Nguyen, T.; Gorochowski, T. E.; Goñi-Moreno, A.; Scott-Brown, J.; McLaughlin, J. A.; Madsen, C.; Aleritsch, B.; Bartley, B.; Bhakta, S.; et al. Communicating structure and function in synthetic biology diagrams. ACS Synth. Biol. 2019, 8 (8), 1818–1825. [link]

  • Britton, G.; Heemskerk, I.; Hodge, R.; Qutub, A. A.; Warmflash, A. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. Development 2019, 146 (20): dev179093. [link]

  • Chhabra, S.; Liu, L.; Goh, R.; Kong, X.; Warmflash, A. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. PLoS Biol. 2019, 17 (10), e3000498. [link]

  • Heemskerk, I.; Burt, K.; Miller, M.; Chhabra, S.; Guerra, M. C.; Liu, L.; Warmflash, A. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. eLife 2019, 8, e40526. [link]

  • Jayanthi, B. E. K.; Zhao, W.; Segatori, L. Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. In Methods in Enzymology; Academic Press, 2019; 622, 1–27. [link]

  • Jia, D.; George, J. T.; Tripathi, S. C.; Kundnani, D. L.; Lu, M.; Hanash, S. M.; Onuchic, J. N.; Jolly, M. K.; Levine, H. Testing the gene expression classification of the EMT spectrum. Phys. Biol. 2019, 16 (2), 025002. [link]

  • Jia, D.; Li, X.; Bocci, F.; Tripathi, S.; Deng, Y.; Jolly, M. K.; Onuchic, J. N.; Levine, H. Quantifying cancer epithelial-mesenchymal plasticity and its association with stemness and immune response. J. Clin. Med. 2019, 8 (5), 725. [link]

  • Jia, D.; Lu, M.; Jung, K. H.; Park, J. H.; Yu, L.; Onuchic, J. N.; Kaipparettu, B. A.; Levine, H. Elucidating cancer metabolic plasticity by coupling gene regulation with metabolic pathways. Proc. Natl. Acad. Sci. U.S.A. 2019, 116 (9), 3909–3918. [link]

  • Klein, H. L.; Bačinskaja, G.; Che, J.; Cheblal, A.; Elango, R.; Epshtein, A.; Fitzgerald, D. M.; Gómez-González, B.; Khan, S. R.; Kumar, S.; Leland, B. A.; Marie, L.; Mei, Q.; et al. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb. Cell 2019, 6 (1), 1–64. [link]

  • Madsen, C.; Goñi-Moreno, A.; Palchick, Z.; P, U.; Roehner, N.; Bartley, B.; Bhatia, S.; Bhakta, S.; Bissell, M.; Clancy, K.; Cox, R. S.; et al. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. J. Integr. Bioinform. 2019, 16(2): 20180101. [link]

  • Molinari, S.; Shis, D. L.; Bhakta, S. P.; Chappell, J.; Igoshin, O. A.; Bennett, M. R. A synthetic system for asymmetric cell division in Escherichia coli. Nat. Chem. Biol. 2019, 15, 917-924. [link]

  • Pribis, J. P.; García-Villada, L.; Zhai, Y.; Lewin-Epstein, O.; Wang, A. Z.; Liu, J.; Xia, J.; Mei, Q.; Fitzgerald, D. M.; Bos, J.; Austin, R. H.; Herman, C.; Bates, D.; Hadany, L.; Hastings, P. J.; Rosenberg, S. M. Gamblers: An antibiotic-induced evolvable cell subpopulation differentiated by reactive-oxygen-induced general stress response. Mol. Cell 2019, 74 (4), 785-800.e7. [link]

  • Schmidl, S. R.; Ekness, F.; Sofjan, K.; Daeffler, K. N.-M.; Brink, K. R.; Landry, B. P.; Gerhardt, K. P.; Dyulgyarov, N.; Sheth, R. U.; Tabor, J. J. Rewiring bacterial two-component systems by modular DNA-binding domain swapping. Nat. Chem. Biol. 2019, 15 (7), 690–698. [link]

  • Wang, Q.; Chen, M.; Schafer, N. P.; Bueno, C.; Song, S. S.; Hudmon, A.; Wolynes, P. G.; Waxham, M. N.; Cheung, M. S. Assemblies of calcium/calmodulin-dependent kinase II with actin and their dynamic regulation by calmodulin in dendritic spines. Proc. Natl. Acad. Sci. U.S.A. 2019, 116 (38), 18937–18942. [link]

  • Xia, J.; Chiu, L. Y.; Nehring, R. B.; Bravo Núñez, M. A.; Mei, Q.; Perez, M.; Zhai, Y.; Fitzgerald, D. M.; Pribis, J. P.; Wang, Y.; et al. Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell 2019, 176 (1–2), 127–143.e24. [link]

  • Xia, J.; Mei, Q.; Rosenberg, S. M. Tools to live by: Bacterial DNA structures illuminate cancer. Trends Genet. 2019, 35 (5), 383–395. [link]
2018
  • Atkinson, J. T.; Jones, A. M.; Zhou, Q.; Silberg, J. J. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Res. 2018, 46 (13), e76. [link]

  • Cheng, H.-Y.; Masiello, C. A.; Del Valle, I.; Gao, X.; Bennett, G. N.; Silberg, J. J. Ratiometric gas reporting: A nondisruptive approach to monitor gene expression in soils. ACS Synth. Biol. 2018, 7 (3), 903–911. [link]

  • Huang, B.; Jia, D.; Feng, J.; Levine, H.; Onuchic, J. N.; Lu, M. RACIPE: A computational tool for modeling gene regulatory circuits using randomization. BMC Syst. Biol. 2018, 12 (1), 74. [link]

  • Jia, D.; Park, J. H.; Jung, K. H.; Levine, H.; Kaipparettu, B. A. Elucidating the metabolic plasticity of cancer: Mitochondrial reprogramming and hybrid metabolic states. Cells 2018, 7 (3), 21. [link]

  • Jolly, M. K.; Preca, B.-T.; Tripathi, S. C.; Jia, D.; George, J. T.; Hanash, S. M.; Brabletz, T.; Stemmler, M. P.; Maurer, J.; Levine, H. Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioeng. 2018, 2 (3), 031908. [link]

  • Kotlajich, M. V.; Xia, J.; Zhai, Y.; Lin, H.-Y.; Bradley, C. C.; Shen, X.; Mei, Q.; Wang, A. Z.; Lynn, E. J.; Shee, C.; Chen, L.-T.; Li, L.; Miller, K. M.; Herman, C.; Hastings, P. J.; Rosenberg, S. M. Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells. DNA Repair 2018, 72, 86–92. [link]

  • Lee, C. M.; Davis, T. H.; Bao, G. Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity. Exp. Physiol. 2018, 103 (4), 456–460. [link]

  • Tripathi, S.; Deem, M. W. The standard genetic code facilitates exploration of the space of functional nucleotide sequences. J. Mol. Evol. 2018, 86 (6), 325–339. [link]

  • Tripathi, S.; Jolly, M. K.; Woodward, W. A.; Levine, H.; Deem, M. W. Analysis of hierarchical organization in gene expression networks reveals underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer. Front. Oncol. 2018, 8, 244. [link]

  • Ye, F.; Jia, D.; Lu, M.; Levine, H.; Deem, M. W. Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma. Oncotarget 2018, 9 (19), 15015-15026. [link]

  • Zhang, J. X.; Fang, J.; Duan, W.; Wu, L. R.; Zhang, A. W.; Dalchau, N.; Yordanov, B.; Petersen, R.; Phillips, A.; Zhang, D. Y. Predicting DNA hybridization kinetics from sequence. Nat. Chem. 2018, 10 (1), 91–98. [link]

  • Zong, D. M.; Cinar, S.; Shis, D. L.; Josić, K.; Ott, W.; Bennett, M. R. Predicting transcriptional output of synthetic multi-input promoters. ACS Synth. Biol. 2018, 7 (8), 1834–1843. [link]
2017
  • Joshua Atkinson. PERMutation Using Transposase Engineering (PERMUTE): a simple approach for constructing circularly permuted protein libraries. Methods Mol Biol. 2017; 1498:295-308. [link]
  • Carlos Bueno. Resolving the NFκB heterodimer binding paradox: strain and frustration guide the binding of dimeric transcription factors. J. Am. Chem. Soc. 2017; 139(51): 18558-18566. [link]
  • Timothy Davis. CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies. Blood. 2017, 130(3): 285-296. [link]
  • Timothy Davis. Design and validation of CRISPR/Cas9 systems for targeted gene modification in induced pluripotent stem cells. Methods Mol. Biol. 2017, 1498: 3-21. [link]
  • Dongya Jia. Phenotypic plasticity and cell fate decisions in cancer: insights from dynamical systems theory. Cancers 2017, 9(7): 70. [link]
  • Dongya Jia. The GRHL2/ZEB feedback loop-a key axis in the regulation of EMT in breast cancer. J. Cell. Biochem. 2017, 118(9): 2559-2570. [link]
  • 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]

  • Teimouri, H.; Kolomeisky, A. B.; Mehrabiani, K. Theoretical analysis of dynamic processes for interacting molecular motors. J. Phys. A: Math. Theor. 2015, 48 (6), 065001. [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]