Perspectives for self-driving labs in synthetic biology

Authors: Martin, Hector Garcia, Radivojevic, Tijana, Zucker, Jeremy, Bouchard, Kristofer, Sustarich, Jess, Peisert, Sean, Arnold, Dan, Hillson, Nathan, Babnigg, Gyorgy, Marti, Jose Manuel, Mungall, Christopher J., Beckham, Gregg T., Waldburger, Lucas, Carothers, James, Sundaram, ShivShankar, Agarwal, Deb, Simmons, Blake A., Backman, Tyler, Banerjee, Deepanwita, Tanjore, Deepti, Ramakrishnan, Lavanya, Singh, Anup

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2210.09085

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

Authors: Sanders, Lauren M., Yang, Jason H., Scott, Ryan T., Qutub, Amina Ann, Martin, Hector Garcia, Berrios, Daniel C., Hastings, Jaden J. A., Rask, Jon, Mackintosh, Graham, Hoarfrost, Adrienne L., Chalk, Stuart, Kalantari, John, Khezeli, Kia, Antonsen, Erik L., Babdor, Joel, Barker, Richard, Baranzini, Sergio E., Beheshti, Afshin, Delgado-Aparicio, Guillermo M., Glicksberg, Benjamin S., Greene, Casey S., Haendel, Melissa, Hamid, Arif A., Heller, Philip, Jamieson, Daniel, Jarvis, Katelyn J., Komarova, Svetlana V., Komorowski, Matthieu, Kothiyal, Prachi, Mahabal, Ashish, Manor, Uri, Mason, Christopher E., Matar, Mona, Mias, George I., Miller, Jack, Myers Jr., Jerry G., Nelson, Charlotte, Oribello, Jonathan, Park, Seung-min, Parsons-Wingerter, Patricia, Prabhu, R. K., Reynolds, Robert J., Saravia-Butler, Amanda, Saria, Suchi, Sawyer, Aenor, Singh, Nitin Kumar, Soboczenski, Frank, Snyder, Michael, Soman, Karthik, Theriot, Corey A., Van Valen, David, Venkateswaran, Kasthuri, Warren, Liz, Worthey, Liz, Zitnik, Marinka, Costes, Sylvain V.

Subject Terms: Quantitative Biology - Other Quantitative Biology, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2112.12582

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

Authors: Scott, Ryan T., Antonsen, Erik L., Sanders, Lauren M., Hastings, Jaden J. A., Park, Seung-min, Mackintosh, Graham, Reynolds, Robert J., Hoarfrost, Adrienne L., Sawyer, Aenor, Greene, Casey S., Glicksberg, Benjamin S., Theriot, Corey A., Berrios, Daniel C., Miller, Jack, Babdor, Joel, Barker, Richard, Baranzini, Sergio E., Beheshti, Afshin, Chalk, Stuart, Delgado-Aparicio, Guillermo M., Haendel, Melissa, Hamid, Arif A., Heller, Philip, Jamieson, Daniel, Jarvis, Katelyn J., Kalantari, John, Khezeli, Kia, Komarova, Svetlana V., Komorowski, Matthieu, Kothiyal, Prachi, Mahabal, Ashish, Manor, Uri, Martin, Hector Garcia, Mason, Christopher E., Matar, Mona, Mias, George I., Myers, Jr., Jerry G., Nelson, Charlotte, Oribello, Jonathan, Parsons-Wingerter, Patricia, Prabhu, R. K., Qutub, Amina Ann, Rask, Jon, Saravia-Butler, Amanda, Saria, Suchi, Singh, Nitin Kumar, Soboczenski, Frank, Snyder, Michael, Soman, Karthik, Van Valen, David, Venkateswaran, Kasthuri, Warren, Liz, Worthey, Liz, Yang, Jason H., Zitnik, Marinka, Costes, Sylvain V.

Subject Terms: Quantitative Biology - Other Quantitative Biology, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2112.12554

Learning from learning machines: a new generation of AI technology to meet the needs of science

Authors: Pion-Tonachini, Luca, Bouchard, Kristofer, Martin, Hector Garcia, Peisert, Sean, Holtz, W. Bradley, Aswani, Anil, Dwivedi, Dipankar, Wainwright, Haruko, Pilania, Ghanshyam, Nachman, Benjamin, Marrone, Babetta L., Falco, Nicola, Prabhat, Arnold, Daniel, Wolf-Yadlin, Alejandro, Powers, Sarah, Climer, Sharlee, Jackson, Quinn, Carlson, Ty, Sohn, Michael, Zwart, Petrus, Kumar, Neeraj, Justice, Amy, Tomlin, Claire, Jacobson, Daniel, Micklem, Gos, Gkoutos, Georgios V., Bickel, Peter J., Cazier, Jean-Baptiste, Müller, Juliane, Webb-Robertson, Bobbie-Jo, Stevens, Rick, Anderson, Mark, Kreutz-Delgado, Ken, Mahoney, Michael W., Brown, James B.

Subject Terms: Computer Science - Machine Learning, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2111.13786

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Authors: Banerjee, Deepanwita, Yunus, Ian S., Wang, Xi, Kim, Jinho, Srinivasan, Aparajitha, Menchavez, Russel, Chen, Yan, Gin, Jennifer W., Petzold, Christopher J., Martin, Hector Garcia, Magnuson, Jon K., Adams, Paul D., Simmons, Blake A., Mukhopadhyay, Aindrila, Kim, Joonhoon, Lee, Taek Soon

Source: In Metabolic Engineering March 2024 82:157-170

Automated flow-based/digital microfluidic platform integrated with onsite electroporation process for multiplex genetic engineering applications

Authors: Iwai, Kosuke, Ando, David, Kim, Peter W., Gach, Phillip C., Raje, Manasi, Duncomb, Todd A., Heinemann, Joshua V., Northen, Trent R., Martin, Hector Garcia, Hillson, Nathan J., Adams, Paul D., Singh, Anup K.

Source: 2018 IEEE Micro Electro Mechanical Systems (MEMS) Micro Electro Mechanical Systems (MEMS), 2018 IEEE. :1229-1232 Jan, 2018

Relation: 2018 IEEE Micro Electro Mechanical Systems (MEMS)

ART: A machine learning Automated Recommendation Tool for synthetic biology

Authors: Radivojević, Tijana, Costello, Zak, Workman, Kenneth, Martin, Hector Garcia

Subject Terms: Quantitative Biology - Quantitative Methods, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/1911.11091

Workflow Automation in Liquid Chromatography Mass Spectrometry

Authors: Gentz, Reinhard, Martin, Hector Garcia, Baidoo, Edward, Peisert, Sean

Source: 2019 15th International Conference on eScience (eScience) eScience (eScience), 2019 15th International Conference on. :638-639 Sep, 2019

Relation: 2019 15th International Conference on eScience (eScience)

How to Hallucinate Functional Proteins

Authors: Costello, Zak, Martin, Hector Garcia

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1903.00458

Artificial Intelligence for Synthetic Biology.

Authors: ESLAMI, MOHAMMED¹, ADLER, AARON², CACERES, RAJMONDA S.³, DUNN, JOSHUA G.⁴, KELLEY-LOUGHNANE, NANCY⁵, VARALJAY, VANESSA A.⁶, MARTIN, HECTOR GARCIA⁷

Source: Communications of the ACM; May2022, Vol. 65 Issue 5, p88-97, 10p, 1 Color Photograph, 6 Diagrams, 1 Chart, 1 Graph

MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design

Authors: Blay, Vincent, Radivojevic, Tijana, Allen, Jonathan E., Hudson, Corey M., Martin, Hector Garcia

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(15):3551-3564

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632697951&indx=1&recIds=ETOCRN632697951

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Authors: Roell, Garrett W., Carr, Rhiannon R., Campbell, Tayte, Shang, Zeyu, Henson, William R., Czajka, Jeffrey J., Martín, Hector García, Zhang, Fuzhong, Foston, Marcus, Dantas, Gautam, Moon, Tae Seok, Tang, Yinjie J.

Source: In Metabolic Engineering September 2019 55:120-130

Linearity and Scaling of a Statistical Model for the Species Abundance Distribution

Authors: Martin, Hector Garcia, Goldenfeld, Nigel

Subject Terms: Condensed Matter - Statistical Mechanics, Quantitative Biology

Access URL: http://arxiv.org/abs/cond-mat/0107076

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing

Authors: Oyetunde, Tolutola, Bao, Forrest Sheng, Chen, Jiung-Wen, Martin, Hector Garcia, Tang, Yinjie J.

Source: Biotechnology advances. 36(4):1308-1315

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100115277200.0x000001&indx=1&recIds=ETOCvdc_100115277200.0x000001

Two-Scale ^1^3C Metabolic Flux Analysis for Metabolic Engineering

Authors: Ando, David, Martin, Hector Garcia

Source: Methods in molecular biology. 1671:333-342

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN614007060&indx=1&recIds=ETOCRN614007060

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Authors: Brunk, Elizabeth, George, Kevin W., Alonso-Gutierrez, Jorge, Thompson, Mitchell, Baidoo, Edward, Wang, George, Petzold, Christopher J., McCloskey, Douglas, Monk, Jonathan, Yang, Laurence, O’Brien, Edward J., Batth, Tanveer S., Martin, Hector Garcia, Feist, Adam, Adams, Paul D., Keasling, Jay D., Palsson, Bernhard O., Lee, Taek Soon

Source: In Cell Systems 25 May 2016 2(5):335-346

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Authors: Zhang, Jie, Petersen, Søren D., Radivojevic, Tijana, Ramirez, Andrés, Pérez-Manríquez, Andrés, Abeliuk, Eduardo, Sánchez, Benjamín J., Costello, Zak, Chen, Yu, Fero, Michael J., Martin, Hector Garcia, Nielsen, Jens, Keasling, Jay D., Jensen, Michael K.

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174543866.0x000001&indx=1&recIds=ETOCvdc_100174543866.0x000001

Dissecting Biological "Dark Matter" with Single-Cell Genetic Analysis of Rare and Uncultivated TM7 Microbes from the Human Mouth

Authors: Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Lösekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A., Quake, Stephen R.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2007 Jul . 104(29), 11889-11894.

Access URL: https://www.jstor.org/stable/25436219

On the Origin and Robustness of Power-Law Species-Area Relationships in Ecology

Authors: Martín, Héctor García, Goldenfeld, Nigel

Source: Proceedings of the National Academy of Sciences of the United States of America, 2006 Jul 01. 103(27), 10310-10315.

Access URL: https://www.jstor.org/stable/30049620

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design.

Authors: Tao, Xavier B, LaFrance, Sarah, Xing, Yifei, Nava, Alberto A, Martin, Hector Garcia, Keasling, Jay D, Backman, Tyler W H

Source: Nucleic Acids Research; 1/6/2023, Vol. 51 Issue D1, pD532-D538, 7p