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An integrated engineering worldview of synthetic biology education through the lens of webinar based pedagogy.
Published in:
Frontiers in Bioengineering & Biotechnology, 2024, p. 1, doi. 10.3389/fbioe.2024.1431374
By:
- George, Iain;
- Ross, Paul;
- Yixian Yang;
- Holub, Martin;
- Rajpurohit, Nina;
- Aldulijan, Ibrahim;
- Beal, Jacob;
- Vignoni, Alejandro;
- Mishler, Dennis
Publication type:
Article
SBOL Visual: A Graphical Language for Genetic Designs.
Published in:
PLoS Biology, 2015, v. 13, n. 12, p. 1, doi. 10.1371/journal.pbio.1002310
By:
- Quinn, Jacqueline Y.;
- IIICox, Robert Sidney;
- Adler, Aaron;
- Beal, Jacob;
- Bhatia, Swapnil;
- Cai, Yizhi;
- Chen, Joanna;
- Clancy, Kevin;
- Galdzicki, Michal;
- Hillson, Nathan J.;
- Le Novère, Nicolas;
- Maheshwari, Akshay J.;
- McLaughlin, James Alastair;
- Myers, Chris J.;
- P, Umesh;
- Pocock, Matthew;
- Rodriguez, Cesar;
- Soldatova, Larisa;
- Stan, Guy-Bart V.;
- Swainston, Neil
Publication type:
Article
Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals.
Published in:
Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02325-5
By:
- Kiwimagi, Katherine A.;
- Letendre, Justin H.;
- Weinberg, Benjamin H.;
- Wang, Junmin;
- Chen, Mingzhe;
- Watanabe, Leandro;
- Myers, Chris J.;
- Beal, Jacob;
- Wong, Wilson W.;
- Weiss, Ron
Publication type:
Article
Studying pathogens degrades BLAST-based pathogen identification.
Published in:
Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-32481-z
By:
- Beal, Jacob;
- Clore, Adam;
- Manthey, Jeff
Publication type:
Article
Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24123-7
By:
- Tan, Timothy J. C.;
- Yuan, Meng;
- Kuzelka, Kaylee;
- Padron, Gilberto C.;
- Beal, Jacob R.;
- Chen, Xin;
- Wang, Yiquan;
- Rivera-Cardona, Joel;
- Zhu, Xueyong;
- Stadtmueller, Beth M.;
- Brooke, Christopher B.;
- Wilson, Ian A.;
- Wu, Nicholas C.
Publication type:
Article
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.
Published in:
Nature Biotechnology, 2014, v. 32, n. 6, p. 545, doi. 10.1038/nbt.2891
By:
- Galdzicki, Michal;
- Clancy, Kevin P;
- Oberortner, Ernst;
- Pocock, Matthew;
- Quinn, Jacqueline Y;
- Rodriguez, Cesar A;
- Roehner, Nicholas;
- Wilson, Mandy L;
- Adam, Laura;
- Anderson, J Christopher;
- Bartley, Bryan A;
- Beal, Jacob;
- Chandran, Deepak;
- Chen, Joanna;
- Densmore, Douglas;
- Endy, Drew;
- Grünberg, Raik;
- Hallinan, Jennifer;
- Hillson, Nathan J;
- Johnson, Jeffrey D
Publication type:
Article
Cas9 gRNA engineering for genome editing, activation and repression.
Published in:
Nature Methods, 2015, v. 12, n. 11, p. 1051, doi. 10.1038/nmeth.3580
By:
- Kiani, Samira;
- Chavez, Alejandro;
- Tuttle, Marcelle;
- Hall, Richard N;
- Chari, Raj;
- Ter-Ovanesyan, Dmitry;
- Qian, Jason;
- Pruitt, Benjamin W;
- Beal, Jacob;
- Vora, Suhani;
- Buchthal, Joanna;
- Kowal, Emma J K;
- Ebrahimkhani, Mohammad R;
- Collins, James J;
- Weiss, Ron;
- Church, George
Publication type:
Article
CRISPR transcriptional repression devices and layered circuits in mammalian cells.
Published in:
Nature Methods, 2014, v. 11, n. 7, p. 723, doi. 10.1038/nmeth.2969
By:
- Kiani, Samira;
- Beal, Jacob;
- Ebrahimkhani, Mohammad R;
- Huh, Jin;
- Hall, Richard N;
- Xie, Zhen;
- Li, Yinqing;
- Weiss, Ron
Publication type:
Article
Functional Synthetic Biology.
Published in:
Synthetic Biology (23977000), 2023, v. 8, n. 1, p. 1, doi. 10.1093/synbio/ysad006
By:
- Aldulijan, Ibrahim;
- Beal, Jacob;
- Billerbeck, Sonja;
- Bouffard, Jeff;
- Chambonnier, Gaël;
- Ntelkis, Nikolaos;
- Guerreiro, Isaac;
- Holub, Martin;
- Ross, Paul;
- Selvarajah, Vinoo;
- Sprent, Noah;
- Vidal, Gonzalo;
- Vignoni, Alejandro
Publication type:
Article
Highly-automated, high-throughput replication of yeast-based logic circuit design assessments.
Published in:
Synthetic Biology (23977000), 2022, v. 7, n. 1, p. 1, doi. 10.1093/synbio/ysac018
By:
- Goldman, Robert P;
- Moseley, Robert;
- Roehner, Nicholas;
- Cummins, Breschine;
- Vrana, Justin D;
- Clowers, Katie J;
- Bryce, Daniel;
- Beal, Jacob;
- DeHaven, Matthew;
- Nowak, Joshua;
- Higa, Trissha;
- Biggers, Vanessa;
- Lee, Peter;
- Hunt, Jeremy P;
- Mosqueda, Lorraine;
- Haase, Steven B;
- Weston, Mark;
- Zheng, George;
- Deckard, Anastasia;
- Gopaulakrishnan, Shweta
Publication type:
Article
Multicolor plate reader fluorescence calibration.
Published in:
Synthetic Biology (23977000), 2022, v. 7, n. 1, p. 1, doi. 10.1093/synbio/ysac010
By:
- Beal, Jacob;
- Telmer, Cheryl A;
- Vignoni, Alejandro;
- Boada, Yadira;
- Baldwin, Geoff S;
- Hallett, Liam;
- Lee, Taeyang;
- Selvarajah, Vinoo;
- Billerbeck, Sonja;
- Brown, Bradley;
- Cai, Guo-nan;
- Cai, Liang;
- Eisenstein, Edward;
- Kiga, Daisuke;
- Ross, David;
- Alperovich, Nina;
- Sprent, Noah;
- Thompson, Jaclyn;
- Young, Eric M;
- Endy, Drew
Publication type:
Article
Automatic Compilation from High-Level Biologically- Oriented Programming Language to Genetic Regulatory Networks.
Published in:
PLoS ONE, 2011, v. 6, n. 8, p. 1, doi. 10.1371/journal.pone.0022490
By:
- Beal, Jacob;
- Lu, Ting;
- Weiss, Ron
Publication type:
Article
Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems.
Published in:
PLoS ONE, 2010, v. 5, n. 1, p. 1, doi. 10.1371/journal.pone.0008125
By:
- Indurkhya, Sagar;
- Beal, Jacob
Publication type:
Article
The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?
Published in:
EMBO Reports, 2020, v. 21, n. 5, p. 1, doi. 10.15252/embr.202050521
By:
- Beal, Jacob;
- Goñi‐Moreno, Angel;
- Myers, Chris;
- Hecht, Ariel;
- Vicente, María del Carmen;
- Parco, Maria;
- Schmidt, Markus;
- Timmis, Kenneth;
- Baldwin, Geoff;
- Friedrichs, Steffi;
- Freemont, Paul;
- Kiga, Daisuke;
- Ordozgoiti, Elena;
- Rennig, Maja;
- Rios, Leonardo;
- Tanner, Kristie;
- Lorenzo, Víctor;
- Porcar, Manuel
Publication type:
Article
Progress and Prospects for a Nucleic Acid Screening Test Set.
Published in:
Applied Biosafety: Journal of the American Biological Safety Association, 2024, v. 29, n. 3, p. 133, doi. 10.1089/apb.2023.0033
By:
- Wheeler, Nicole E.;
- Bartling, Craig;
- Carter, Sarah R.;
- Clore, Adam;
- Diggans, James;
- Flyangolts, Kevin;
- Gemler, Bryan T.;
- Rife Magalis, Brittany;
- Beal, Jacob
Publication type:
Article
High-performance chemical- and light-inducible recombinases in mammalian cells and mice.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-12800-7
By:
- Weinberg, Benjamin H.;
- Cho, Jang Hwan;
- Agarwal, Yash;
- Pham, N. T. Hang;
- Caraballo, Leidy D.;
- Walkosz, Maciej;
- Ortega, Charina;
- Trexler, Micaela;
- Tague, Nathan;
- Law, Billy;
- Benman, William K. J.;
- Letendre, Justin;
- Beal, Jacob;
- Wong, Wilson W.
Publication type:
Article
Synthetic biology open language (SBOL) version 3.1.0.
Published in:
Journal of Integrative Bioinformatics, 2023, v. 20, n. 1, p. 1, doi. 10.1515/jib-2022-0058
By:
- Buecherl, Lukas;
- Mitchell, Thomas;
- Scott-Brown, James;
- Vaidyanathan, Prashant;
- Vidal, Gonzalo;
- Baig, Hasan;
- Bartley, Bryan;
- Beal, Jacob;
- Crowther, Matthew;
- Fontanarrosa, Pedro;
- Gorochowski, Thomas;
- Grünberg, Raik;
- Kulkarni, Vishwesh;
- McLaughlin, James;
- Mısırlı, Göksel;
- Oberortner, Ernst;
- Wipat, Anil;
- Myers, Chris
Publication type:
Article
Synthetic biology open language visual (SBOL visual) version 3.0.
Published in:
Journal of Integrative Bioinformatics, 2021, v. 18, n. 3, p. 1, doi. 10.1515/jib-2021-0013
By:
- Baig, Hasan;
- Fontanarossa, Pedro;
- McLaughlin, James;
- Scott-Brown, James;
- Vaidyanathan, Prashant;
- Gorochowski, Thomas;
- Misirli, Goksel;
- Beal, Jacob;
- Myers, Chris
Publication type:
Article
Synthetic biology open language (SBOL) version 3.0.0.
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0017
By:
- Baig, Hasan;
- Fontanarrosa, Pedro;
- Kulkarni, Vishwesh;
- McLaughlin, James Alastair;
- Vaidyanathan, Prashant;
- Bartley, Bryan;
- Beal, Jacob;
- Crowther, Matthew;
- Gorochowski, Thomas E.;
- Grünberg, Raik;
- Misirli, Goksel;
- Scott-Brown, James;
- Oberortner, Ernst;
- Wipat, Anil;
- Myers, Chris J.
Publication type:
Article
Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs.
Published in:
PLoS ONE, 2021, v. 16, n. 6, p. 1, doi. 10.1371/journal.pone.0252263
By:
- Beal, Jacob;
- Baldwin, Geoff S.;
- Farny, Natalie G.;
- Gershater, Markus;
- Haddock-Angelli, Traci;
- Buckley-Taylor, Russell;
- Dwijayanti, Ari;
- Kiga, Daisuke;
- Lizarazo, Meagan;
- Marken, John;
- de Mora, Kim;
- Rettberg, Randy;
- Sanchania, Vishal;
- Selvarajah, Vinoo;
- Sison, Abigail;
- Storch, Marko;
- Workman, Christopher T.
Publication type:
Article
Extracellular Vesicles Secreted by Mouse Decidual Cells Carry Critical Information for the Establishment of Pregnancy.
Published in:
Endocrinology, 2022, v. 163, n. 12, p. 1, doi. 10.1210/endocr/bqac165
By:
- Ma, Qiuyan;
- Beal, Jacob R;
- Song, Xiangning;
- Bhurke, Arpita;
- Bagchi, Indrani C;
- Bagchi, Milan K
Publication type:
Article
Author Correction: Robust estimation of bacterial cell count from optical density.
Published in:
2020
By:
- Beal, Jacob;
- Farny, Natalie G.;
- Haddock-Angelli, Traci;
- Selvarajah, Vinoo;
- Baldwin, Geoff S.;
- Buckley-Taylor, Russell;
- Gershater, Markus;
- Kiga, Daisuke;
- Marken, John;
- Sanchania, Vishal;
- Sison, Abigail;
- Workman, Christopher T.;
- iGEM Interlab Study Contributors;
- Aachen;
- Pehlivan, Meryem;
- Roige, Biel Badia;
- Aalto-Helsinki;
- Aarnio, Tiu;
- Kivisto, Samu;
- Koski, Jessica
Publication type:
Correction Notice
Robust estimation of bacterial cell count from optical density.
Published in:
Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-01371-9
By:
- Beal, Jacob;
- Farny, Natalie G.;
- Haddock-Angelli, Traci;
- Selvarajah, Vinoo;
- Baldwin, Geoff S.;
- Buckley-Taylor, Russell;
- Gershater, Markus;
- Kiga, Daisuke;
- Marken, John;
- Sanchania, Vishal;
- Sison, Abigail;
- Workman, Christopher T.;
- iGEM Interlab Study Contributors;
- Aachen;
- Pehlivan, Meryem;
- Roige, Biel Badia;
- Aalto-Helsinki;
- Aarnio, Tiu;
- Kivisto, Samu;
- Koski, Jessica
Publication type:
Article
Robust estimation of bacterial cell count from optical density.
Published in:
Communications Biology, 2020, v. 3, n. 1, p. N.PAG, doi. 10.1038/s42003-020-01127-5
By:
- Beal, Jacob;
- Farny, Natalie G.;
- Haddock-Angelli, Traci;
- Selvarajah, Vinoo;
- Baldwin, Geoff S.;
- Buckley-Taylor, Russell;
- Gershater, Markus;
- Kiga, Daisuke;
- Marken, John;
- Sanchania, Vishal;
- Sison, Abigail;
- Workman, Christopher T.;
- iGEM Interlab Study Contributors;
- Aachen;
- Pehlivan, Meryem;
- Roige, Biel Badia;
- Aalto-Helsinki;
- Aarnio, Tiu;
- Kivisto, Samu;
- Koski, Jessica
Publication type:
Article
An integrated engineering worldview of synthetic biology education through the lens of webinar based pedagogy.
Published in:
Frontiers in Bioengineering & Biotechnology, 2024, p. 01, doi. 10.3389/fbioe.2024.1431374
By:
- George, Iain;
- Ross, Paul;
- Yixian Yang;
- Holub, Martin;
- Rajpurohit, Nina;
- Aldulijan, Ibrahim;
- Beal, Jacob;
- Vignoni, Alejandro;
- Mishler, Dennis
Publication type:
Article
Levels of autonomy in synthetic biology engineering.
Published in:
Molecular Systems Biology, 2020, v. 16, n. 12, p. 1, doi. 10.15252/msb.202010019
By:
- Beal, Jacob;
- Rogers, Miles
Publication type:
Article
On the Evaluation of Space–Time Functions.
Published in:
Computer Journal, 2013, v. 56, n. 12, p. 1500, doi. 10.1093/comjnl/bxs099
By:
- Beal, Jacob;
- Usbeck, Kyle;
- Benyo, Brett
Publication type:
Article
Editorial.
Published in:
Computer Journal, 2013, v. 56, n. 12, p. 1397, doi. 10.1093/comjnl/bxs160
By:
- Beal, Jacob;
- Dulman, Stefan;
- Michel, Olivier;
- Spicher, Antoine
Publication type:
Article
Correction: Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli.
Published in:
2016
By:
- Beal, Jacob;
- Haddock-Angelli, Traci;
- Gershater, Markus;
- de Mora, Kim;
- Lizarazo, Meagan;
- Hollenhorst, Jim;
- Rettberg, Randy;
- null, null
Publication type:
Correction Notice
Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli.
Published in:
PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150182
By:
- Beal, Jacob;
- Haddock-Angelli, Traci;
- Gershater, Markus;
- de Mora, Kim;
- Lizarazo, Meagan;
- Hollenhorst, Jim;
- Rettberg, Randy;
- null, null
Publication type:
Article
A standard-enabled workflow for synthetic biology.
Published in:
Biochemical Society Transactions, 2017, v. 45, n. 3, p. 793, doi. 10.1042/BST20160347
By:
- Myers, Chris J.;
- Beal, Jacob;
- Gorochowski, Thomas E.;
- Kuwahara, Hiroyuki;
- Madsen, Curtis;
- McLaughlin, James Alastair;
- Mısırlı, Göksel;
- Nguyen, Tramy;
- Oberortner, Ernst;
- Samineni, Meher;
- Wipat, Anil;
- Zhang, Michael;
- Zundel, Zach
Publication type:
Article
Role of Endometrial Extracellular Vesicles in Mediating Cell-to-Cell Communication in the Uterus: A Review.
Published in:
Cells (2073-4409), 2023, v. 12, n. 22, p. 2584, doi. 10.3390/cells12222584
By:
- Beal, Jacob R.;
- Ma, Qiuyan;
- Bagchi, Indrani C.;
- Bagchi, Milan K.
Publication type:
Article
Engineering modular intracellular protein sensoractuator devices.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03984-5
By:
- Siciliano, Velia;
- DiAndreth, Breanna;
- Jin Huh;
- Weiss, Ron;
- Monel, Blandine;
- Clayton, Kiera L.;
- McKeon, AnneMarie;
- Walker, Bruce D.;
- Beal, Jacob;
- Wroblewska, Liliana
Publication type:
Article
Composable continuous-space programs for robotic swarms.
Published in:
Neural Computing & Applications, 2010, v. 19, n. 6, p. 825, doi. 10.1007/s00521-010-0382-8
By:
- Bachrach, Jonathan;
- Beal, Jacob;
- McLurkin, James
Publication type:
Article
Quantification of bacterial fluorescence using independent calibrants.
Published in:
PLoS ONE, 2018, v. 13, n. 6, p. 1, doi. 10.1371/journal.pone.0199432
By:
- Beal, Jacob;
- Haddock-Angelli, Traci;
- Baldwin, Geoff;
- Gershater, Markus;
- Dwijayanti, Ari;
- Storch, Marko;
- de Mora, Kim;
- Lizarazo, Meagan;
- Rettberg, Randy;
- null, null
Publication type:
Article
FIELD-BASED COORDINATION WITH THE SHARE OPERATOR.
Published in:
Logical Methods in Computer Science (LMCS), 2020, v. 16, n. 4, p. 1, doi. 10.23638/LMCS-16(4:1)2020
By:
- AUDRITO, GIORGIO;
- BEAL, JACOB;
- DAMIANI, FERRUCCIO;
- PIANINI, DANILO;
- VIROLI, MIRKO
Publication type:
Article
Trading accuracy for speed in approximate consensus.
Published in:
Knowledge Engineering Review, 2016, v. 31, n. 4, p. 325, doi. 10.1017/S0269888916000175
By:
- Beal, Jacob
Publication type:
Article
Organizing genome engineering for the gigabase scale.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14314-z
By:
- Bartley, Bryan A.;
- Beal, Jacob;
- Karr, Jonathan R.;
- Strychalski, Elizabeth A.
Publication type:
Article
Reducing DNA context dependence in bacterial promoters.
Published in:
PLoS ONE, 2017, v. 12, n. 4, p. 1, doi. 10.1371/journal.pone.0176013
By:
- Carr, Swati B.;
- Beal, Jacob;
- Densmore, Douglas M.
Publication type:
Article

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