Publications

Oliveira, S. M. D., & Densmore, D. (2022, September 2). Hardware, software, and Wetware Codesign environment for Synthetic Biology. BioDesign Research. Retrieved from https://spj.sciencemag.org/journals/bdr/2022/9794510/

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Landaverde L;Turcinovic J;Doucette-Stamm L;Gonzales K;Platt J;Connor JH;Klapperich C; (n.d.). Comparison of binaxnow and SARS-COV-2 qrt-PCR detection of the omicron variant from matched Anterior Nares swabs. Microbiology spectrum. Retrieved from https://pubmed.ncbi.nlm.nih.gov/36255297/

 

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Turcinovic J;Kuhfeldt K;Sullivan M;Landaverde L;Platt JT;Doucette-Stamm L;Hanage WP;Hamer DH;Klapperich C;Landsberg HE;Connor JH; (n.d.). Linking contact tracing with genomic surveillance to deconvolute SARS-COV-2 transmission on a university campus. iScience. Retrieved from https://pubmed.ncbi.nlm.nih.gov/36246573/

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Bouton TC;Atarere J;Turcinovic J;Seitz S;Sher-Jan C;Gilbert M;White L;Zhou Z;Hossain MM;Overbeck V;Doucette-Stamm L;Platt J;Landsberg HE;Hamer DH;Klapperich C;Jacobson KR;Connor JH; (n.d.). Viral Dynamics of Omicron and delta SARS-COV-2 variants with implications for timing of release from isolation: A longitudinal cohort study. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. Retrieved from https://pubmed.ncbi.nlm.nih.gov/35737948/

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Kuhfeldt K;Turcinovic J;Sullivan M;Landaverde L;Doucette-Stamm L;Hamer DH;Platt JT;Klapperich C;Landsberg HE;Connor JH; (n.d.). Examination of SARS-COV-2 in-class transmission at a large urban university with public health mandates using epidemiological and genomic methodology. Retrieved from https://pubmed.ncbi.nlm.nih.gov/35930286/

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Petros BA;Turcinovic J;Welch NL;White LF;Kolaczyk ED;Bauer MR;Cleary M;Dobbins ST;Doucette-Stamm L;Gore M;Nair P;Nguyen TG;Rose S;Taylor BP;Tsang D;Wendlandt E;Hope M;Platt JT;Jacobson KR;Bouton T;Yune S;Auclair JR;Landaverde L;Klapperich CM;Hamer DH;Hana. (n.d.). Early introduction and rise of the omicron sars-COV-2 variant in highly vaccinated university populations. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. Retrieved from https://pubmed.ncbi.nlm.nih.gov/35616119/

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Bouton TC;Atarere J;Turcinovic J;Seitz S;Sher-Jan C;Gilbert M;White L;Zhou Z;Hossain MM;Overbeck V;Doucette-Stamm L;Platt J;Landsberg HE;Hamer DH;Klapperich C;Jacobson KR;Connor JH; (n.d.). Viral Dynamics of Omicron and delta SARS-COV-2 variants with implications for timing of release from isolation: A longitudinal cohort study. medRxiv : the preprint server for health sciences. from https://pubmed.ncbi.nlm.nih.gov/35411341/

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​Landaverde, L., McIntyre, D., Robson, J., Fu, D., Ortiz, L., Chen, R., Oliveira,  S.M.D., [...] (2021) Detailed Overview of the Buildout and Integration of an Automated High-Throughput CLIA Laboratory for SARS-CoV-2 Testing on a Large Urban Campus. medRxiv. doi:10.1101/2021.09.13.21263214.

 

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Hamer, D.H., [...], Densmore, D., Brown, R.A. (2021) Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic. JAMA Netw Open. 2021;4. doi:10.1001/jamanetworkopen.2021.16425

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Chen, R., Emery, N.J., Pavan, M., Oliveira, S.M.D. (2020) Laboratory Protocol Automation: A Modular DNA Assembly and Bacterial Transformation Case Study. In Proceedings of 12th IWBDA (IWBDA2020), Worcester, MA, Aug. 3-5. https://www.iwbdaconf.org/2020/docs/IWBDA2020Proceedings.pdf

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Lashkaripour, A., Rodriguez, C., Ortiz, L., and Densmore, D. (2019). Performance tuning of microfluidic flow-focusing droplet generators. Lab on a Chip, 19(6), 1041-1053. https://pubs.rsc.org/en/content/articlelanding/2019/lc/c8lc01253a/unauth#!divAbstract

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Sanka, R., Lippai, J., Samarasekera, D., Nemsick, D., and Densmore, D. (2019). 3DμF - Interactive Design Environment for Continuous Flow Microfluidic Devices. Scientific Reports 9(1). https://doi.org/10.1038/s41598-019-45623-z

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Hillson, N., Caddick, M., [...], Freemont, P.S. (2019). Building a Global Alliance of Biofoundries. Nature Communications, 10:2040. https://www.nature.com/articles/s41467-019-10079-2

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Walsh III, D.I., Pavan, M., Ortiz, L., Wick, S., Bobrow, J., Guido, N.J., Leinicke, S., Fu, D., Pandit, S., Qin, L., Carr, P.A., Densmore, D. (2019). Standardizing automated DNA assembly: best practices, metrics, and protocols using robots. SLAS TECHNOLOGY: Translating Life Sciences Innovation, 24(3), 282-290.  https://journals.sagepub.com/doi/abs/10.1177/2472630318825335 

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Sanka, R., Crites, B., McDaniel, J., Brisk, P., and Densmore, D. (2019). Specification, Integration, and Benchmarking of Continuous Flow Microfluidic Devices: Invited Paper. In 2019 IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 1–8. https://doi.org/10.1109/ICCAD45719.2019.8942171

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Lashkaripour, A., Silva, R., and Densmore, D. (2018). Desktop micro-milled microfluidics. Microfluidics and Nanofluidics, 22:31. https://link.springer.com/article/10.1007/s10404-018-2048-2

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Ortiz, L., Pavan, M., McCarthy, L., Timmons, J., Densmore, D. (2017). Automated Robotic Liquid Handling Assembly of Modular DNA Devices. J. Vis. Exp. (), e54703. https://www.jove.com/video/54703/automated-robotic-liquid-handling-assembly-of-modular-dna-devices

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Silva, R., Dow, P., Dubay, R., Lissandrello, C., Holder, J., Densmore, D., & Fiering, J. (2017). Rapid prototyping and parametric optimization of plastic acousto-fluidic devices for blood–bacteria separation. Biomedical Microdevices, 19(3), 70. https://link.springer.com/article/10.1007/s10544-017-0210-3

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Silva, R., Bhatia, S., and Densmore, D. (2016). A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive. Lab on a Chip 16.14: 2730-2741. https://pubs.rsc.org/en/content/articlehtml/2016/lc/c6lc00477f

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Huang, H., and Densmore, D. (2014). Fluigi: Microfluidic device synthesis for synthetic biology. ACM Journal on Emerging Technologies in Computing Systems (JETC) 11.3: 26. https://dl.acm.org/doi/abs/10.1145/2660773

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Huang, H., and Densmore, D. (2014). Integration of microfluidics into the synthetic biology design flow. Lab on a Chip 14.18 (2014): 3459-3474. https://pubs.rsc.org/en/content/articlehtml/2014/lc/c4lc00509k