Publications

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26 entries « 1 of 2 »
1.

Ross C. Bretherton Rubul Mout, Justin Decarreau; Baker, David

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity Journal Article

In: Proceedings of the National Academy of Sciences, 2024.

Abstract | Links | BibTeX

2.

Davila-Hernandez, Fatima A; Jin, Biao; Pyles, Harley; Zhang, Shuai; Wang, Zheming; Huddy, Timothy F; Bera, Asim K; Kang, Alex; Chen, Chun-Long; Yoreo, James J De; Baker, David

Directing polymorph specific calcium carbonate formation with de novo protein templates Journal Article

In: Nature Communications, vol. 14, no. 1, pp. 8191, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

3.

Li, Zhe; Wang, Shunzhi; Nattermann, Una; Bera, Asim K; Borst, Andrew J; Yaman, Muammer Y; Bick, Matthew J; Yang, Erin C; Sheffler, William; Lee, Byeongdu; Seifert, Soenke; Hura, Greg L; Nguyen, Hannah; Kang, Alex; Dalal, Radhika; Lubner, Joshua M; Hsia, Yang; Haddox, Hugh; Courbet, Alexis; Dowling, Quinton; Miranda, Marcos; Favor, Andrew; Etemadi, Ali; Edman, Natasha I; Yang, Wei; Weidle, Connor; Sankaran, Banumathi; Negahdari, Babak; Ross, Michael B; Ginger, David S; Baker, David

Accurate computational design of three-dimensional protein crystals Journal Article

In: Nature Materials, 2023.

Abstract | Links | BibTeX

4.

Bethel, Neville P.; Borst, Andrew J.; Parmeggiani, Fabio; Bick, Matthew J.; Brunette, TJ; Nguyen, Hannah; Kang, Alex; Bera, Asim K.; Carter, Lauren; Miranda, Marcos C.; Kibler, Ryan D.; Lamb, Mila; Li, Xinting; Sankaran, Banumathi; Baker, David

Precisely patterned nanofibres made from extendable protein multiplexes Journal Article

In: Nature Chemistry, 2023.

Abstract | Links | BibTeX

5.

Alghadeer, Ammar; Hanson-Drury, Sesha; Patni, Anjali P.; Ehnes, Devon D.; Zhao, Yan Ting; Li, Zicong; Phal, Ashish; Vincent, Thomas; Lim, Yen C.; O’Day, Diana; Spurrell, Cailyn H.; Gogate, Aishwarya A.; Zhang, Hai; Devi, Arikketh; Wang, Yuliang; Starita, Lea; Doherty, Dan; Glass, Ian A.; Shendure, Jay; Freedman, Benjamin S.; Baker, David; Regier, Mary C.; Mathieu, Julie; Ruohola-Baker, Hannele

Single-cell census of human tooth development enables generation of human enamel Journal Article

In: Developmental Cell, 2023.

Abstract | Links | BibTeX

6.

Lutz, Isaac D.; Wang, Shunzhi; Norn, Christoffer; Courbet, Alexis; Borst, Andrew J.; Zhao, Yan Ting; Dosey, Annie; Cao, Longxing; Xu, Jinwei; Leaf, Elizabeth M.; Treichel, Catherine; Litvicov, Patrisia; Li, Zhe; Goodson, Alexander D.; Rivera-Sánchez, Paula; Bratovianu, Ana-Maria; Baek, Minkyung; King, Neil P.; Ruohola-Baker, Hannele; Baker, David

Top-down design of protein architectures with reinforcement learning Journal Article

In: Science, 2023.

Abstract | Links | BibTeX

7.

Yang, Huilin; Ulge, Umut Y.; Quijano-Rubio, Alfredo; Bernstein, Zachary J.; Maestas, David R.; Chun, Jung-Ho; Wang, Wentao; Lin, Jian-Xin; Jude, Kevin M.; Singh, Srujan; Orcutt-Jahns, Brian T.; Li, Peng; Mou, Jody; Chung, Liam; Kuo, Yun-Huai; Ali, Yasmin H.; Meyer, Aaron S.; Grayson, Warren L.; Heller, Nicola M.; Garcia, K. Christopher; Leonard, Warren J.; Silva, Daniel-Adriano; Elisseeff, Jennifer H.; Baker, David; Spangler, Jamie B.

Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds Journal Article

In: Nature Chemical Biology, 2023.

Abstract | Links | BibTeX

8.

Said, Meerit Y.; Kang, Christine S.; Wang, Shunzhi; Sheffler, William; Salveson, Patrick J.; Bera, Asim K.; Kang, Alex; Nguyen, Hannah; Ballard, Ryanne; Li, Xinting; Bai, Hua; Stewart, Lance; Levine, Paul; Baker, David

Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks Journal Article

In: Chemistry of Materials, 2022.

Abstract | Links | BibTeX

9.

Wicky, B. I. M.; Milles, L. F.; Courbet, A.; Ragotte, R. J.; Dauparas, J.; Kinfu, E.; Tipps, S.; Kibler, R. D.; Baek, M.; DiMaio, F.; Li, X.; Carter, L.; Kang, A.; Nguyen, H.; Bera, A. K.; Baker, D.

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

10.

Vulovic, Ivan; Yao, Qing; Park, Young-Jun; Courbet, Alexis; Norris, Andrew; Busch, Florian; Sahasrabuddhe, Aniruddha; Merten, Hannes; Sahtoe, Danny D.; Ueda, George; Fallas, Jorge A.; Weaver, Sara J.; Hsia, Yang; Langan, Robert A.; Pl"uckthun, Andreas; Wysocki, Vicki H.; Veesler, David; Jensen, Grant J.; Baker, David

Generation of ordered protein assemblies using rigid three-body fusion Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 23, 2021.

Abstract | Links | BibTeX

11.

Hsia, Yang; Mout, Rubul; Sheffler, William; Edman, Natasha I.; Vulovic, Ivan; Park, Young-Jun; Redler, Rachel L.; Bick, Matthew J.; Bera, Asim K.; Courbet, Alexis; Kang, Alex; Brunette, T. J.; Nattermann, Una; Tsai, Evelyn; Saleem, Ayesha; Chow, Cameron M.; Ekiert, Damian; Bhabha, Gira; Veesler, David; Baker, David

Design of multi-scale protein complexes by hierarchical building block fusion Journal Article

In: Nature Communications, 2021.

Abstract | Links | BibTeX

12.

Ben-Sasson, Ariel J.; Watson, Joseph L.; Sheffler, William; Johnson, Matthew Camp; Bittleston, Alice; Somasundaram, Logeshwaran; Decarreau, Justin; Jiao, Fang; Chen, Jiajun; Mela, Ioanna; Drabek, Andrew A.; Jarrett, Sanchez M.; Blacklow, Stephen C.; Kaminski, Clemens F.; Hura, Greg L.; De Yoreo, James J.; Kollman, Justin M.; Ruohola-Baker, Hannele; Derivery, Emmanuel; Baker, David

Design of biologically active binary protein 2D materials Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

13.

Pyles, Harley; Zhang, Shuai; Yoreo, James J. De; Baker, David

Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article

In: Nature, 2019.

Abstract | Links | BibTeX

14.

Shen, Hao; Fallas, Jorge A.; Lynch, Eric; Sheffler, William; Parry, Bradley; Jannetty, Nicholas; Decarreau, Justin; Wagenbach, Michael; Vicente, Juan Jesus; Chen, Jiajun; Wang, Lei; Dowling, Quinton; Oberdorfer, Gustav; Stewart, Lance; Wordeman, Linda; De Yoreo, James; Jacobs-Wagner, Christine; Kollman, Justin; Baker, David

De novo design of self-assembling helical protein filaments Journal Article

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links | BibTeX

15.

Butterfield, Gabriel L. *; Lajoie, Marc J. *; Gustafson, Heather H.; Sellers, Drew L.; Nattermann, Una; Ellis, Daniel; Bale, Jacob B.; Ke, Sharon; Lenz, Garreck H.; Yehdego, Angelica; Ravichandran, Rashmi; Pun, Suzie H.; King, Neil P.; Baker, David

Evolution of a designed protein assembly encapsulating its own RNA genome Journal Article

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links | BibTeX

16.

Bale, Jacob B.; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O.; Gonen, Tamir; King, Neil P.; Baker, David

Accurate design of megadalton-scale two-component icosahedral protein complexes Journal Article

In: Science, vol. 353, no. 6297, pp. 389-394, 2016.

Abstract | Links | BibTeX

17.

Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason M.; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity Journal Article

In: Science, vol. 352, no. 6286, pp. 680–687, 2016, ISSN: 0036-8075.

Abstract | Links | BibTeX

18.

Garcia, Kristen E; Babanova, Sofia; Scheffler, William; Hans, Mansij; Baker, David; Atanassov, Plamen; Banta, Scott

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction Journal Article

In: Biotechnology and Bioengineering, pp. n/a–n/a, 2016, ISSN: 1097-0290.

Abstract | Links | BibTeX

19.

Doyle, L; Hallinan, J; Bolduc, J; Parmeggiani, F; Baker, D; Stoddard, BL; Bradley, P

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

In: Nature, vol. 528(7583), pp. 585-8, 2015.

Abstract | Links | BibTeX

20.

Bale, Jacob B; Park, Rachel U; Liu, Yuxi; Gonen, Shane; Gonen, Tamir; Cascio, Duilio; King, Neil P.; Yeates, Todd O.; Baker, David

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression Journal Article

In: Protein science : a publication of the Protein Society, 2015, ISSN: 1469-896X.

Abstract | Links | BibTeX

26 entries « 1 of 2 »