JOURNAL ARTICLES

Cerda A.**,  Rivera M.**,  Armijo G.,  Ibarra C,  Reyes J.,  Blazquez-Sanchez P., Aviles J.,  Arce A., Seguel A.,  BrownAJ,  Vasquez Y., Cortez-San Martin M.,  Cubillos F.,  Garcia P.,  Ferres M.,  Ramirez-Sarmiento C*,  Federici F*,  Gutierrez R.* A One-Step open RT-qPCR for SARS-CoV-2 detection (submitted) 2022 Medrxiv preprint 
(*Co-corresponding)

Oróstica B., Núñez I., Matute T., Núñez F., Federici F*. Building an Open-Source DNA Assembler Device. 2022 (enviado, preprint in prep) (*Corresponding authors)

Vidal Gonzalo, Vidal Carlos, Muñoz Macarena, Yañez Guillermo, Federici Fernan, Rudge Timothy*. Accurate Characterization of Dynamic Gene Expression and Growth Rate Profiles. Synthetic Biology, 7 (2) 2022

Guzman-Chavez, F. Arce, A. Adhikari, A. Vadhin, S. Pedroza-Garcia J A. Gandini, Ajioka J. Molloy, J. Sanchez-Nieto, S. Varner, J. Federici, F & Haseloff, J.*. “Constructing cell-free expression systems for low-cost access”. ACS Synthetic Biology 2022 11(3) 1114

Moore, K; Cahill, J; Aidelberg, G; Aronoff, R; Bektaş, A; Bezdan, D; Butler, D; Chittur, S; Codyre, M; Federici, F; Tanner, N; Tighe, S; True, R; Ware, S; Wyllie, A; Afshin, E; Bendesky, A; Chang, C; Dela Rosa, R; Elhaik, E; Erickson, D; Goldsborough, A; Hadasch, K; Hayden, A; Her, S-Y; Karl, J; Kim, C; Kunstman, T; Landau, Z; Land, K; Langhorst, B; Lindner, A; Mayer, B; McLaughlin, L; McLaughlin, M; Molloy, J; Mozsary, C; Nadler, J; Ng, D; O’Connor, D; Ongerth, J; Osuolale, O; Pinharanda, A; Plenker, D; Ranjan, R; Rosbash, M; Rotem, A; Segarra, J; Sherrill-Mix, S; To, S; Vogt, M; Yu, A; The gLAMP Consortium, Mason, C. Loop-Mediated Isothermal Amplification (LAMP) Detection of SARS-CoV-2 and Myriad other applications.  (2021) Journal Biomolecular Techniques. 33 (2) Special issue on LAMP for SARS-CoV-2

Arce, A; Guzman, F; Gandini, C; Puig, J; Matute, T; Haseloff, J; Dalchau, N; Molloy, J; Pardee, K; Federici, F “Decentralizing cell-free RNA sensing with the use of low-cost cell extracts” (2021) Front. Bioeng. Biotechnol. (*Corresponding author)

Matute, T; Isaac, I; Maira, R; Reyes, J; Blazquez-Sanchez, P; Arce, A; Brown, A; Gandini, C; Molloy, J; Ramirez-Sarmiento, C;* and Federici, F*. Homebrew reagents for low cost RT-LAMP. 2021. J. Biomolecular Techniques, Special issue on LAMP for SARS-CoV-2 (*Co-corresponding authors)

Ali Bektaş, Mike F. Covington, Guy Aidelberg, Anibal Arce, Tamara Matute, Isaac Núñez, Julia Walsh, David Boutboul, Ariel B. Lindner, Fernán Federici, Anitha Jayaprakash. Accessible LAMP-Enabled Rapid Test (ALERT) for detecting SARS-CoV-2 2021. Viruses.

Yáñez G., Gómez B., Codoceo V., Muñoz M., Nuñez I., Matute T., Arce A., Vidal G., Vidal C., Dahlin J., Federici F, Timothy J. Rudge*. Flapjack: a data management and analysis tool for genetic circuit characterization. 2021. ACS Synth. Biol., 10, 1, 183–191

asbcd6.2021.10.issue-1.largecover

Pollak B.*, Matute T., Nuňez I., Cerda A., Lopez C., Vargas V., Kan A., Bielinski V., von Dassow P., Dupont C., Federici F.*. Universal Loop assembly (uLoop): open, efficient, and cross-kingdom DNA fabrication. 2020. Synthetic Biology.
(*Co-corresponding authors)

Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares Jr., Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. García, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibañez, Nicholas A.T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastián R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M.G. Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Iñaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne Swart, Anastasios Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukeš.  Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. 2020. Nature Methods 17, 481–494
Highlighted in Science , SpringerNature and GB Moore Foundation
Commented in Nat. Methods editorial 
Featured on Nature Methods News and Views.

Muñoz MA, Matute T, Nuñez I, Valdes A, Ruiz CA, Vidal G, Federici F*, Rudge TJ*. Phase space characterization for gene circuit design (Biorxiv)
(*Co-corresponding authors)

Kan A., Del Valle I., Rudge T., Federici F. Haseloff J. Intercellular adhesion promotes clonal mixing in growing bacterial populations. Journal of The Royal Society Interface 2018 ;15(146). pii: 20180406. doi: 10.1098/rsif.2018.0406
rsif.15.issue-146.cover

Pollak B., Cerda A., Delmans M., Álamos S., Moyano T., West A., Gutiérrez R., Patron N., Federici F.* Haseloff J*. Loop Assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol. 2019 Apr;222(1):628-640. (protocols in protocols.io)
(*Co-corresponding authors)

NewPhyt

Zuniga, A; De la Fuente, F; Federici, F; Lionne, C ; Bonnet, J; de Lorenzo, V; Gonzalez, B. “An engineered device for indoleacetic acid production under quorum sensing signals enables Cupriavidus pinatubonensis JMP134 to stimulate plant growth“.  ACS Synth. Biol., 2018, 7 (6), pp 1519–1527

GOSH communitiy. Global Open Science Hardware Roadmap: Making Open Science Hardware ubiquitous by 2025. (2018)

Nuñez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, Federici F.  Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLoS ONE, 2017, 12(11): e0187163  (preprint at Biorxiv) (all raw data, code, sequence files, protocols and design files at Github, OpenScienceFramework, Docubricks and protocols.io_1, _2, _3)
Featured on University of Cambridge Synthetic biology, OpenPlant
PLoS Open Source Toolkit Editor´s pick
Winner of the PLoS Open Source Toolkit Anniversary Prize
Featured on Sandeep´s Nature article/interview 

Nuñez I., Matute T., Del Valle I., Kan A., Choksi A.,  Endy D., Haseloff J., Rudge T., and  Federici F. Artificial symmetry-breaking for morphogenetic engineering bacterial colonies. ACS Synth. Biol., 2017, 6 (2), pp 256–265 pdf (postprint here)
(all raw data, sequence files, code, and protocols at Github, OpenScienceFramework, and protocols.io) (Cover)

ACS Synthetic Biology

Grant P., Dalchau N., Brown J., Federici F., Rudge T., Yordanov B., Patage O., Phillips A., and Haseloff J. Orthogonal intercellular signaling for programmed spatial behaviour. 2016. Mol Sys Biol. 12 (1):849. pdf

*Rudge T., *Brown J.,*Federici F., Dalchau N., Phillips A., Ajioka J.. and Haseloff J. Characterization of intrinsic properties of promoters. 2015. ACS Synth. Biol., 2016, 5 (1), pp 89–98,
(*joint first author) pdf

Ron M., Kajala K., Pauluzzi G., Wang D., Renoso M., Zumstein K., Garcha J., Winte S., Masson H., Inagaki S, Federici F., Sinha N., Deal R., Bailey-Serres J., Brady S. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. 2014. Plant Physiology 166 (2):455-692

*Rudge T.,*Federici F., *Steiner P.J., Kan A. and Haseloff J. Cell Polarity-Driven Instability Generates Self-Organized, Fractal Patterning of Cell Layers. 2013. ACS Synthetic Biology, 2 (12), pp 705–714. pdf
(*joint first author)

Federici F., Rudge T., Pollak B., Haseloff J., Gutierrez R. Synthetic Biology: opportunities for Chilean bioindustry and education. 2013 Biological Research 46, 383-393. pdf

*Federici F., *Dupuy L., Laplaze L., Heisler M., and Haseloff J. Integrated genetic and computation methods for in planta cytometry. 2012. Nature Methods 9: 483-485. pdf
(*joint first author)

Aquea F., Federici F., Moscoso C., Vega A., Haseloff J. and Arce-Johnson. A molecular framework for the inhibition of Arabidopsis root growth in response to boron toxicity. 2011. Plant Cell and Environment 35:719-34.

Maizel A., Wangenheim D., Federici F., Haseloff J., and Stelzer E., High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy. 2011. Plant Journal 68:377-85.

*Ubeda-Tomás S., *Federici F., Casimiro I., Beemster G., Bhalerao R., Swarup R, Doerner P., Haseloff J., Bennett M. Gibberellin signalling in the endodermis controls Arabidopsis root meristem size. 2009 Current Biology 19:1194-9.
(*joint first author)

*Poupin M., *Federici F., Medina C., Matus J., Timmermann T., Arce-Johnson P. Isolation of the three grape sub-lineages of B-class MADS-box TM6, PISTILLATA and APETALA3 genes, which are differentially expressed during flower and fruit development. 2007 Gene 404:10-24. (*joint first author)

BOOK CHAPTERS

Benjamin D. and Federici F. Bioprocessing. in book “Bio Design: Nature + Science + Creativity” by Myers W. and Antonelli P.. MoMA-NY. Museum of Modern Art, New York editorial. US. (2013)

Benjamin D. and Federici F. Biologic. (2014) in book “Synthetic Aesthetics” by Endy D. Ginsberg D. and Elfick A. MIT press. US (2014).

OTHER PUBLICATIONS

Ochoa A,  Federici F,  Grünberg R,  Nadra A,  Rodríguez P and  Sánchez I. TECNOx: A Latin American Syn Bio (and more) student competition. 2016. Plos SynBio Blog.