Publications

Papers authored by TeselaGen team

Hillson, Nathan J. “A Procedural Framework for Benchmarking Biofoundry Capabilities.” ACS Synthetic Biology 12.12 (2023): 3778-3782. https://pubs.acs.org/doi/full/10.1021/acssynbio.3c00491
Martin, Hector G., et al. “Perspectives for self-driving labs in synthetic biology.” Current Opinion in Biotechnology 79 (2023): 102881. https://www.sciencedirect.com/science/article/pii/S0958166922002154
Berezin, Casey-Tyler, et al. “Ten simple rules for managing laboratory information.” PLoS computational biology 19.12 (2023): e1011652. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011652
Nava, Alberto A., et al. “Automated platform for the plasmid construction process.” ACS Synthetic Biology 12.12 (2023): 3506-3513. https://pubs.acs.org/doi/full/10.1021/acssynbio.3c00292
Engineering Biology Research Consortium. “Engineering Biology for Climate and Sustainability: A research roadmap for a cleaner future.” (2022). https://par.nsf.gov/servlets/purl/10496223
Mackelprang, Rebecca, et al. “Making security viral: shifting engineering biology culture and publishing.” ACS synthetic biology 11.2 (2022): 522-527. https://pubs.acs.org/doi/full/10.1021/acssynbio.1c00324
Roy, Somtirtha, et al. “Multiomics data collection, visualization, and utilization for guiding metabolic engineering.” Frontiers in bioengineering and biotechnology 9 (2021): 612893. https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2021.612893/full
Plahar, Hector A., et al. “BioParts—a biological parts search portal and updates to the ICE parts registry software platform.” ACS Synthetic Biology 10.10 (2021): 2649-2660. https://pubs.acs.org/doi/10.1021/acssynbio.1c00263
Cable, Jennifer, et al. “Synthetic biology: at the crossroads of genetic engineering and human therapeutics—a Keystone Symposia report.” Annals of the New York Academy of Sciences 1506.1 (2021): 98-117. https://nyaspubs.onlinelibrary.wiley.com/doi/10.1111/nyas.14710
Oberortner, Ernst, et al. An integrated computer-aided design and manufacturing workflow for synthetic biology. Springer US, 2020. https://link.springer.com/protocol/10.1007/978-1-0716-0908-8_1
Zhang, Jie, et al. “Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism.” Nature communications 11.1 (2020): 4880. https://www.nature.com/articles/s41467-020-17910-1
Fero, Michael J., et al. Combinatorial-hierarchical DNA library design using the TeselaGen DESIGN Module with j5. Springer US, 2020. https://link.springer.com/book/10.1007/978-1-0716-0908-8?noAccess=true
Doci, Gledon, et al. “DNA Scanner: a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors.” (2020): ysaa011. https://academic.oup.com/synbio/article/5/1/ysaa011/5892266
Goyal, Garima, et al. “Repurposing a microfluidic formulation device for automated DNA construction.” PloS one 15.11 (2020): e0242157. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0242157
Hillson, Nathan, et al. “Building a global alliance of biofoundries.” Nature communications 10.1 (2019): 2040. https://www.nature.com/articles/s41467-019-10079-2
Quinn, Jacqueline Y., et al. “SBOL visual: a graphical language for genetic designs.” PLoS biology 13.12 (2015): e1002310. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002310
Linshiz, Gregory, et al. “PR-PR: cross-platform laboratory automation system.” ACS synthetic biology 3.8 (2014): 515-524. https://pubs.acs.org/doi/full/10.1021/sb4001728
Galdzicki, Michal, et al. “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.” Nature biotechnology 32.6 (2014): 545-550. https://www.nature.com/articles/nbt.2891
Hillson, Nathan J. “j5 DNA assembly design automation.” DNA cloning and assembly methods (2014): 245-269. https://link.springer.com/protocol/10.1007/978-1-62703-764-8_17
Golberg, Alexander, et al. “Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies.” Biofuels, Bioproducts and Biorefining 8.1 (2014): 67-82. https://scijournals.onlinelibrary.wiley.com/doi/10.1002/bbb.1438
Linshiz, Gregory, et al. “PaR-PaR laboratory automation platform.” ACS synthetic biology 2.5 (2013): 216-222. https://pubs.acs.org/doi/full/10.1021/sb300075t
Quinn, Jacqueline, et al. “Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology.” 5th International Workshop on Bio-Design Automation. 2013. https://jakebeal.github.io/Publications/IWBDA2013-SBOLv.pdf
Galdzicki, Michal, et al. Synthetic biology open language (SBOL) version 1.1. 0. 2012. https://dspace.mit.edu/handle/1721.1/73909

Publications authored by third-parties, citing Teselagen

Berthenet, Kevin, et al. “Atypical contribution of caspase-3 to melanoma cancer cell motility by regulation of coronin 1B activity.” bioRxiv (2024): 2024-06. https://www.biorxiv.org/content/biorxiv/early/2024/07/02/2024.06.27.601010.full.pdf
Vindman, Cindy, et al. “The Convergence of AI and Synthetic Biology: The Looming Deluge.” arXiv preprint arXiv:2404.18973 (2024). https://arxiv.org/abs/2404.18973
Ha, Yuanchi, et al. “Data-driven learning of structure augments quantitative prediction of biological responses.” PLOS Computational Biology 20.6 (2024): e1012185. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012185
Yang, Chunhe, et al. “AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System.” ACS Synthetic Biology (2024). https://pubs.acs.org/doi/full/10.1021/acssynbio.4c00063
Yu, Wenfei, et al. “Designing a synthetic moss genome using GenoDesigner.” Nature plants (2024): 1-9. https://www.nature.com/articles/s41477-024-01693-0
Petersen, Søren D., et al. “teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering.” PLOS Computational Biology 20.3 (2024): e1011929. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011929
Buecherl, Lukas, et al. “Synthetic biology open language (SBOL) version 3.1. 0.” Journal of integrative bioinformatics 20.1 (2023): 20220058. https://www.degruyter.com/document/doi/10.1515/jib-2022-0058/html
Petersen, Søren, et al. “Literate programming for iterative design-build-test-learn cycles in bioengineering.” bioRxiv (2023): 2023-06. https://www.biorxiv.org/content/10.1101/2023.06.18.545451v1.abstract
Zurawski, Jason, et al. “Biological and Environmental Research network requirements review final report.” (2023). https://escholarship.org/uc/item/3mz7h3mm
Kianpour, Neda. “Identification of optimal sgRNA candidates for mutagenesis of the ALS1 gene in Ipomoea batatas using in-vitro cleavage assay and CRISPR/Cas9 technology.” MS thesis. Inland Norway University, 2023. https://brage.inn.no/inn-xmlui/handle/11250/3109914
Kulamikhina, Irina, Natalia Kanunnikova, and Olga Selezneva. “Tracking of plasmodesmata localization with the use of fluorescently labelled VAP27 protein.” BIO Web of Conferences. Vol. 78. EDP Sciences, 2023. https://www.bio-conferences.org/articles/bioconf/pdf/2023/23/bioconf_mtsitvw2023_02004.pdf
Garcia Martin, Hector. “Accelerating engineered microbe optimization through machine learning and multi-omics datasets.” Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Teselagen Biotechnology, San Francisco, CA (United States), 2023. https://www.osti.gov/biblio/2324610
Liew, Fungmin Eric, et al. “Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.” Nature biotechnology 40.3 (2022): 335-344. https://www.nature.com/articles/s41587-021-01195-w
Buecherl, Lukas, and Chris J. Myers. “Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology.” Current opinion in microbiology 68 (2022): 102155. https://www.sciencedirect.com/science/article/pii/S136952742200039X
Dixon, Thomas A., Thomas C. Williams, and Isak S. Pretorius. “Bioinformational trends in grape and wine biotechnology.” Trends in Biotechnology 40.1 (2022): 124-135. https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(21)00113-X
Chilakwad, Shama. “Automation and analysis of high-dimensionality experiments in biocatalytic reaction screening.” Diss. UCL (University College London) (2022). https://discovery.ucl.ac.uk/id/eprint/10156237/
Lv, Xueqin, et al. “New synthetic biology tools for metabolic control.” Current Opinion in Biotechnology 76 (2022): 102724. https://www.sciencedirect.com/science/article/pii/S0958166922000581
Zhang, Mengyan, et al. “Machine learning guided batched design of a bacterial Ribosome Binding Site.” ACS Synthetic Biology 11.7 (2022): 2314-2326. https://pubs.acs.org/doi/full/10.1021/acssynbio.2c00015
Yeoh, Jing Wui, et al. “Genetic Circuit Design Principles.” Handbook of Cell Biosensors (2022): 339-381. https://link.springer.com/referenceworkentry/10.1007/978-3-030-23217-7_171
Bi, Xinyu, et al. “Construction of multiscale genome-scale metabolic models: Frameworks and challenges.” Biomolecules 12.5 (2022): 721. https://www.mdpi.com/2218-273X/12/5/721
Wanner, Nicole, et al. “The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing.” BMC genomics 22 (2021): 1-11. https://link.springer.com/article/10.1186/s12864-021-08046-7
Council, Innovation Policy. “Thailand Synthetic Biology Ecosystem Assessment and Recommendations.” (2021). https://www.nxpo.or.th/th/wp-content/uploads/2021/10/Synthetic-Biology-Ecosystem-29Oct21.pdf
Pavan, Marilene. “Setting up an automated biomanufacturing laboratory.” Synthetic Gene Circuits: Methods and Protocols (2021): 137-155. https://link.springer.com/protocol/10.1007/978-1-0716-1032-9_5
Pellowe, Grant. “Developing Novel Methods for Co-translational Studies of Membrane Protein Folding.” Diss. King’s College London, 2021. https://kclpure.kcl.ac.uk/ws/portalfiles/portal/155491110/2021_Pellowe_Grant_1629641_ethesis_PUREVersion.pdf
Vrana, Justin, et al. “Aquarium: open-source laboratory software for design, execution and data management.” Synthetic Biology 6.1 (2021): ysab006. https://academic.oup.com/synbio/article/6/1/ysab006/6124325
Macdonald, Gareth John. “CDMOs Embrace Industry 4.0 to Satisfy Customer Demand: The digitalization of bioprocessing technology isn’t happening for its own sake, but to ensure that outsourced manufacturing tasks, however diverse, will be part of highly integrated processes.” Genetic Engineering & Biotechnology News 41.4 (2021): 43-45. https://www.liebertpub.com/doi/full/10.1089/gen.41.04.14
Yeoh, Jing Wui, et al. “SynBiopython: an open-source software library for Synthetic Biology.” (2021): ysab001. https://academic.oup.com/synbio/article/6/1/ysab001/6146421
Bahera, Basanta Kumara, Ram Prasad, and Shyambhavee Behera. “Commercial Biomolecules.” Life Sciences Industry: From Laboratories to Commercialization of Research. Singapore: Springer Singapore, 2021. 1-27. https://link.springer.com/chapter/10.1007/978-981-16-2051-5_1
Dixon, Thom. “The grey zone of cyber-biological security.” International Affairs 97.3 (2021): 685-702. https://academic.oup.com/ia/article-abstract/97/3/685/6225366
Baig, Hasan, et al. “Synthetic biology open language (SBOL) version 3.0. 0.” Journal of integrative bioinformatics 17.2-3 (2020): 20200017. https://www.degruyter.com/document/doi/10.1515/jib-2020-0017/html
Bergquist, Peter L., Sana Siddiqui, and Anwar Sunna. “Cell-free biocatalysis for the production of platform chemicals.” Frontiers in Energy Research 8 (2020): 193. https://www.frontiersin.org/journals/energy-research/articles/10.3389/fenrg.2020.00193/full
Marx, Dagan C., et al. “Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA.” Protein Science 29.10 (2020): 2043-2053. https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3924
Dixon, Thomas A., and Isak S. Pretorius. “Drawing on the past to shape the future of synthetic yeast research.” International Journal of Molecular Sciences 21.19 (2020): 7156. https://www.mdpi.com/1422-0067/21/19/7156
Philp, Jim, and David Winickoff. “Innovation ecosystems in the bioeconomy.” (2019). https://www.oecd-ilibrary.org/science-and-technology/innovation-ecosystems-in-the-bioeconomy_e2e3d8a1-en
Urquiza-García, Uriel, Tomasz Zieliński, and Andrew J. Millar. “Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs.” Synthetic Biology 4.1 (2019): ysz016. https://academic.oup.com/synbio/article/4/1/ysz016/5520957
Yee, Aubrey M. “Life Formed: Evolutionary Design and the Futures of a Political Biology.” Diss. University of Hawai’i at Manoa, 2019. https://www.proquest.com/docview/2272720599/fulltextPDF/3CF1A1560704219PQ/1
Jaschke, Paul R., et al. “Definitive demonstration by synthesis of genome annotation completeness.” Proceedings of the National Academy of Sciences 116.48 (2019): 24206-24213. https://www.pnas.org/doi/abs/10.1073/pnas.1905990116
Smalley, Eric. “Microsoft makes splash in AI-enabled lab solutions.” Nature Biotechnology 37.8 (2019): 832-835. https://www.nature.com/articles/d41587-019-00018-3
Szymanski, Erika, and Emily Scher. “Models for DNA design tools: The trouble with metaphors is that they don’t go away.” ACS Synthetic Biology 8.12 (2019): 2635-2641. https://pubs.acs.org/doi/full/10.1021/acssynbio.9b00302
Petersen, Søren Dalsgård. “Methods for predictable and accelerated engineering of metabolism in eukaryotes.” (2019). https://orbit.dtu.dk/en/publications/methods-for-predictable-and-accelerated-engineering-of-metabolism
Mantle, Jennifer L., et al. “Cyberbiosecurity for biopharmaceutical products.” Frontiers in Bioengineering and Biotechnology 7 (2019): 116. https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2019.00116/full
Nowogrodzki, Anna. “Gene design goes automatic.” Nature 564.7735 (2018): 291-292. https://www.nature.com/articles/d41586-018-07662-w
Cannon, Tomas. “Genetics and Genetic Engineering.” Scientific e-Resources, 2018. https://www.google.com/books/edition/Genetics_and_Genetic_Engineering/MePEDwAAQBAJ
Peters, N. Kent. “US Department of Energy Bioenergy Research Centers: 10-Year Retrospective. Breakthroughs and Impacts, 2007-2017.” No. DOE/SC-0193. USDOE Office of Science (SC), Washington, DC (United States). Biological and Environmental Research (BER); Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2018. https://www.osti.gov/biblio/1471705
Myers, Chris J., et al. “A standard-enabled workflow for synthetic biology.” Biochemical Society Transactions 45.3 (2017): 793-803. https://portlandpress.com/biochemsoctrans/article-abstract/45/3/793/66896/A-standard-enabled-workflow-for-synthetic-biology
Samineni, Meher. “Software Compliance Testing For The Synthetic Biology Open Language”. Diss. The University of Utah, 2017. https://geneticlogiclab.org/publication/samineni-software-2017/samineni-software-2017.pdf
Appleton, Evan, et al. “Design automation in synthetic biology.” Cold Spring Harbor perspectives in biology 9.4 (2017): a023978. https://cshperspectives.cshlp.org/content/9/4/a023978.full
Bates, Maxwell, et al. “Genetic constructor: an online DNA design platform.” ACS synthetic biology 6.12 (2017): 2362-2365. https://pubs.acs.org/doi/full/10.1021/acssynbio.7b00236
Sharma, Sunanda. “Design for the modern prometheus: towards an integrated biodesign workflow.” Diss. Massachusetts Institute of Technology, 2016. https://dspace.mit.edu/handle/1721.1/106048
Wilson, Erin H., et al. “Genotype specification language.” ACS Synthetic Biology 5.6 (2016): 471-478. https://pubs.acs.org/doi/full/10.1021/acssynbio.5b00194
Steele, Lindsay M., and Y. O. Agyeman. “An Investigation of Innovative Energy Technologies Entering the Market between 2009-2015, Enabled by EERE-Funded R&D.” No. PNNL-31017. Pacific Northwest National Lab.(PNNL), Richland, WA (United States). https://www.osti.gov/biblio/1832102
Myers, Chris, et al. “The synthetic biology open language.” Computational Methods in Synthetic Biology (2015): 323-336. https://link.springer.com/protocol/10.1007/978-1-4939-1878-2_16
Bomgardner, Melody M. “Seeking Better Biofuels.” Chemical & Engineering News 93.42 (2015): 8-10. https://www.illiumtech.com/Tech_pubs/Seeking_Better_Biofuels%20_%20CEN_October_26_2015.pdf
Baek, Chang-Ho, et al. “DNA assembly tools and strategies for the generation of plasmids.” Plasmids: Biology and Impact in Biotechnology and Discovery (2015): 599-613. https://onlinelibrary.wiley.com/doi/epdf/10.1128/9781555818982.ch30
Jijakli, Kenan, et al. “Molecular genetic techniques for algal bioengineering.” Biomass and Biofuels from Microalgae: Advances in Engineering and Biology (2015): 155-171. https://link.springer.com/chapter/10.1007/978-3-319-16640-7_9
Pauthenier, Cyrille, and Jean-Loup Faulon. “PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.” Nucleic acids research 42.W1 (2014): W205-W209. https://academic.oup.com/nar/article/42/W1/W205/2436901
Myers, Chris J. “Platforms for genetic design automation.” Methods in Microbiology. Vol. 40. Academic Press, (2013). 177-202. https://www.sciencedirect.com/science/article/pii/B9780124170292000078

Patents and patent applications

Abeliuk, Eduardo, et al. “Method, apparatus, and computer-readable medium for optimal pooling of nucleic acid samples for next generation sequencing.” U.S. Patent Application No. 17/219,474. https://patents.google.com/patent/US20210304844A1/en
Abeliuk, Eduardo, et al. “Method, apparatus, and computer-readable medium for efficiently optimizing a phenotype with a specialized prediction model.” U.S. Patent No. 11,620,544. 4 Apr. 2023. https://patents.google.com/patent/US9150916B2/en
Abeliuk, Eduardo, et al. “Method, apparatus, and computer-readable medium for efficiently optimizing a phenotype with a combination of a generative and a predictive model.” U.S. Patent No. 11,574,703. 7 Feb. 2023. https://patents.google.com/patent/US11574703B2/en
Hillson, Nathan J. “Scar-less multi-part DNA assembly design automation.” U.S. Patent No. 9,361,427. 7 Jun. 2016. https://patents.google.com/patent/US9361427B2/en
Christen, Beat, et al. “Compositions and methods for identifying the essential genome of an organism.” U.S. Patent No. 9,150,916. 6 Oct. 2015. https://patents.google.com/patent/US9150916B2/en

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Publications

Papers authored by TeselaGen team

Publications authored by third-parties, citing Teselagen

Patents and patent applications

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