Publications

2026
  • Coming Soon
2025

  • Alnahhas RN, Andreani V, Dunlop MJ. Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival. mSystems. 2025 Jun 17;10(6):e0158824. doi: 10.1128/msystems.01588-24. Read here
  • Baka T, Moore J, Qin F, Yurista SR, Zhang A, He H, Chambers JM, Croteau D, Goel RK, Smith H, Wang MC, Chen CS, Hobai IA, Rombaldova M, Kuda O, Tardiff JC, Balschi JA, Pimentel DR, Seidman CE, Seidman JG, Emili A, Colucci WS, Luptak I. Empagliflozin enhances metabolic efficiency and improves left ventricular hypertrophy in a hypertrophic cardiomyopathy mouse model. Eur Heart J. 2025 Oct 22;46(40):4105-4119. doi: 10.1093/eurheartj/ehaf324. Read here
  • Chen J, Borison A, Densmore D, Wong WW. Cell-free recombinase-integrated Boolean output system. Cell Syst. 2025 Oct 15;16(10):101395. doi: 10.1016/j.cels.2025.101395. Read here
  • Ching T, van Steen ACI, Gray-Scherr D, Teo JL, Vasan A, Jeon J, Shah J, Patel A, Stoddard AE, Bays JL, Eyckmans J, Chen CS. TapeTech microfluidic connectors: adhesive tape-enabled solution for organ-on-a-chip system integration. Lab Chip. 2025 Mar 11;25(6):1474-1488. doi: 10.1039/d4lc00970c. Read here
  • Descoteaux AE, Radulovic M, Alburi D, Bradham CA. CMTM4 is an adhesion modulator that regulates skeletal patterning and primary mesenchyme cell migration in sea urchin embryos. Dev Biol. 2025 May;521:85-95. doi: 10.1016/j.ydbio.2025.02.009. Read here
  • Dukovski I, Golden L, Zhang J, Osborne M, Segrè D, Korolev KS. Biophysical metabolic modeling of complex bacterial colony morphology. Cell Syst. 2025 Aug 20;16(8):101352. doi: 10.1016/j.cels.2025.101352. Read here
  • Ewoldt JK, DePalma SJ, Jewett ME, Karakan MÇ, Lin YM, Mir Hashemian P, Gao X, Lou L, McLellan MA, Tabares J, Ma M, Salazar Coariti AC, He J, Toussaint KC Jr, Bifano TG, Ramaswamy S, White AE, Agarwal A, Lejeune E, Baker BM, Chen CS. Induced pluripotent stem cell-derived cardiomyocyte in vitro models: benchmarking progress and ongoing challenges. Nat Methods. 2025 Jan;22(1):24-40. doi: 10.1038/s41592-024-02480-7. Read here
  • Feng Z, Blumenthal E, Mehta P, Goyal A. A theory of ecological invasions and its implications for eco-evolutionary dynamics. Proc Natl Acad Sci U S A. 2025 Dec 9;122(49):e2505850122. doi: 10.1073/pnas.2505850122. Read here
  • Floros KV, Fairchild CK Jr, Li J, Zhang K, Roberts JL, Kurupi R, Paudel D, Xing Y, Hu B, Kraskauskiene V, Hosseini N, Shen S, Inge MM, Smith-Fry K, Li L, Sotiriou A, Dalton KM, Jose A, Abdelfadiel EI, Hill RD, Slaughter JM, Shende M, Lorenz MR, Tanaka N, Kajino T, Nelson ML, Hinojosa MR, Kehinde VA, Belvin BR, Sugiokto FG, Lai Z, Dimopoulos AC, Boikos SA, Stamatouli AM, Lewis JP, Manjili MH, Ebi H, Valerie K, Li R, Poklepovic A, Koblinski JE, Siggers T, Banito A, Dozmorov MG, Jones KB, Radhakrishnan SK, Faber AC. Targeting SUMOylation promotes cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma. Nat Commun. 2025 Nov 5;16(1):9761. doi: 10.1038/s41467-025-64665-8. Read here
  • Gibbs JR, Mei C, Wunderlich Z. Beyond the heat shock pathway: Heat stress responses in Drosophila development. Dev Biol. 2025Feb;518:53-60. doi: 10.1016/j.ydbio.2024.11.003. Read here
  • Goyal A, Rocks JW, Mehta P. Universal Niche Geometry Governs the Response of Ecosystems to Environmental Perturbations. PRX Life. 2025 Feb-Apr;3(1):10.1103/prxlife.3.013010. doi: 10.1103/prxlife.3.013010. Read here
  • Incandela JT, Hu K, Joshi P, Rosenstein JK, Larkin JW. Non-optical, label-free electrical capacitance imaging of microorganisms. mBio. 2025 Sep 10;16(9):e0167625. doi: 10.1128/mbio.01676-25. Read here
  • Kang NR, Im J, Biondo JR, Sharpes CE, Rhea KA, Garden PM, Jaramillo Montezco JJ, Ringaci A, Grinstaff MW, Phillips DA, Miklos AE, Green AA. A Rapid and Modular Nanobody Assay for Plug-and-Play Antigen Detection. ACS Synth Biol. 2025 Sep 19;14(9):3423-3433. doi: 10.1021/acssynbio.5c00182. Read here
  • Kuffner CJ, Marzilli AM, Ngo JT. RNA-stabilized coat proteins for sensitive and simultaneous imaging of distinct single mRNAs in live cells. Nat Methods. 2025 Sep 22:10.1038/s41592-025-02782-4. doi: 10.1038/s41592-025-02782-4. Read here
  • Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Carroll BS, Plassmeyer SP, Emenecker RJ, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Moyer DC, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Holehouse AS, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Mol Cell. 2025 Apr 3;85(7):1445-1466.e13. doi: 10.1016/j.molcel.2025.03.004. Read here
  • Le Q, Ngo JT. Protease-Containing Nanobodies for Detecting and Manipulating Intracellular Antigens Using Antiviral Drugs. ACS Chem Biol. 2025 Jun 20;20(6):1145-1152. doi: 10.1021/acschembio.5c00176. Read here
  • Li L, Yang J, Perry L, Bays JL, Bhatia SN, Eyckmans J, Chen CS. Engineering a heparin-mimetic biomaterial to promote tissue vascularization. Commun Biol. 2025 Nov 14;8(1):1570. doi: 10.1038/s42003-025-08946-4. Read here
  • Li Z, Fuxman Bass JI. ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets. Front Bioinform. 2025 Jun 19;5:1604418. doi: 10.3389/fbinf.2025.1604418. Read here
  • Lin H, Seitz S, Tan Y, Lugagne JB, Wang L, Ding G, He H, Rauwolf TJ, Dunlop MJ, Connor JH, Porco JA Jr, Tian L, Cheng JX. Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering. Nat Methods. 2025May;22(5):1040-1050. doi: 10.1038/s41592-024-02575-1. Read here
  • Lion AT, Bodine SM, McCutcheon KR, Ghogale M, Chandragiri S, Abayawardena D, Shrestha BD, Descoteaux A, Alvarez K, Balkman JA, Cocke B, Wikramanayake AH, Schlezinger J, Wong JY, Prakash VN, Bradham CA. PFAS compounds PFOA and Gen X are teratogenic to sea urchin embryos. Dev Biol. 2025 Sep;525:139-154. doi: 10.1016/j.ydbio.2025.06.004. Read here
  • Lu C, Li Y, Cummings JR, Banskota S. Delivery of genome editors with engineered virus-like particles. Methods Enzymol. 2025;712:475-516. doi: 10.1016/bs.mie.2025.01.007. Read here
  • McGee JE, Kirsch JR, Kenney D, Cerbo F, Chavez EC, Shih TY, Douam F, Wong WW, Grinstaff MW. Complete substitution with modified nucleotides in self-amplifying RNA suppresses the interferon response and increases potency. Nat Biotechnol. 2025May;43(5):720-726. doi: 10.1038/s41587-024-02306-z. Read here
  • McIntyre D, Arguijo D, Kawata K, Densmore D. Component library creation and pixel array generation with micromilled droplet microfluidics. Microsyst Nanoeng. 2025 Jan 14;11(1):6. doi: 10.1038/s41378-024-00839-6. Read here
  • Moyer DC, Reimertz J, Fuxman Bass JI, Segrè D. Flux sampling and context-specific genome-scale metabolic models for biotechnological applications. Trends Biotechnol. 2025 Aug 7:S0167-7799(25)00271-9. doi: 10.1016/j.tibtech.2025.07.010. Read here
  • Moyer DC, Reimertz J, Segrè D, Fuxman Bass JI. MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models. Genome Biol. 2025 Mar 28;26(1):79. doi: 10.1186/s13059-025-03533-6. Read here
  • Mulder OJ, Peters Kostman M, Almodaimegh A, Edge MD, Larkin JW. An agent-based model of metabolic signaling oscillations in Bacillus subtilis biofilms. PLoS Comput Biol. 2025 Dec 4;21(12):e1013746. doi: 10.1371/journal.pcbi.1013746. Read here
  • O’Connor OM, Dunlop MJ. Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells. PLoS Comput Biol. 2025 May 23;21(5):e1013071. doi: 10.1371/journal.pcbi.1013071. Read here
  • Padmakumar JP, Sun JJ, Cho W, Zhou Y, Krenz C, Han WZ, Densmore D, Sontag ED, Voigt CA. Partitioning of a 2-bit hash function across 66 communicating cells. Nat Chem Biol. 2025 Feb;21(2):268-279. Read here
  • Patalano SD, Fuxman Bass P, Fuxman Bass JI. Transcription factors in the development and treatment of immune disorders. Transcription. 2025 Feb;16(1):118-140. doi: 10.1080/21541264.2023.2294623. Epub 2023 Dec 15. Read here
  • Peng H, Kotelnikov S, Egbert ME, Ofaim S, Stevens GC, Phanse S, Saccon T, Ignatov M, Dutta S, Istace Z, Moutaoufik MT, Aoki H, Kewalramani N, Sun J, Gong Y, Padhorny D, Poda G, Alekseenko A, Porter KA, Jones G, Rodionova I, Guo H, Pogoutse O, Datta S, Saier M, Crovella M, Vajda S, Moreno-Hagelsieb G, Parkinson J, Segre D, Babu M, Kozakov D, Emili A. Ligand interaction landscape of transcription factors and essential enzymes in E. coli. Cell. 2025 Mar 6;188(5):1441-1455.e15. Read here
  • Rijal K, Mehta P. A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits. Elife. 2025 Mar 17;14:RP103877. doi: 10.7554/eLife.103877. Read here
  • Riley AT, Robson JM, Ulanova A, Green AA. Generative and predictive neural networks for the design of functional RNA molecules. Nat Commun. 2025 May 4;16(1):4155. doi: 10.1038/s41467-025-59389-8. Read here
  • Scott H, Segrè D. Metabolic Flux Modeling in Marine Ecosystems. Ann Rev Mar Sci. 2025 Jan;17(1):593-620. doi: 10.1146/annurev-marine-032123-033718. Read here
  • Tous C, Kinstlinger IS, Rice MEL, Deng J, Wong WW. Multiplexing light-inducible recombinases to control cell fate, Boolean logic, and cell patterning in mammalian cells. Sci Adv. 2025 May 9;11(19):eadt1971. doi: 10.1126/sciadv.adt1971. Read here
  • Tran JC, Kuffner CJ, Marzilli AM, Miller RE, Silfen ZE, McMahan JB, Sloas DC, Chen CS, Ngo JT. Fluorescein-based SynNotch adaptors for regulating gene expression responses to diverse extracellular and matrix-based cues. Nat Commun. 2025 Jan 20;16(1):852. doi: 10.1038/s41467-025-56148-7. Read here
  • Vasan A, Kim S, Davis E, Roh DS, Eyckmans J. Advances in Designer Materials for Chronic Wound Healing. Adv Wound Care. 2025 Oct;14(10):552-568. doi: 10.1089/wound.2024.0108. Read here
  • Yan Z, Li Y, Eshed A, Wu K, Ticktin ZM, Murugan V, Lim ES, Hong F, Green AA. Programmable fluorescent aptamer-based RNA switches for rapid identification of point mutations. Nat Chem. 2025 Dec;17(12):1826-1838. doi: 10.1038/s41557-025-01995-6. Read here
  • Yang X, Rocks JW, Jiang K, Walters AJ, Rai K, Liu J, Nguyen J, Olson SD, Mehta P, Collins JJ, Daringer NM, Bashor CJ. Engineering synthetic phosphorylation signaling networks in human cells. Science. 2025 Jan 3;387(6729):74-81. doi: 10.1126/science.adm8485. Read here
  • Yazicigil RT, Bali A, Caygara D, Densmore D. Improving engineered biological systems with electronics and microfluidics. Nat Biotechnol. 2025 Jul;43(7):1067-1083. doi: 10.1038/s41587-025-02709-6. Read here
  • Zhou Y, Voigt CA, Densmore D. Constraint-Based Sub-Graph Partitioning for Multi-Cellular Biological Networks. IEEE Trans Comput Biol Bioinform. 2025 Jul-Aug;22(4):1888-1901. doi: 10.1109/TCBBIO.2025.3575288. Read here

 

2024

  • Coming Soon