96 entries « 1 of 2 »

2022

96.

Matthew Tridgett; Maria Ababi; Alfonso Jaramillo

Lambda red recombineering of bacteriophage in the lysogenic state Journal Article

In: Methods in molecular biology, vol. 2479, pp. (in press), 2022, ISBN: 9781071622322.

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95.

Maria Ababi; Matthew Tridgett; Alexander Osgerby; Alfonso Jaramillo

Scarless ssDNA Recombineering of Phage in the Lysogenic State Journal Article

In: Methods in molecular biology (Clifton, N.J.), vol. 2479, pp. (in press), 2022, ISBN: 9781071622322.

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Scarless ssDNA Recombineering of Phage in the Lysogenic State

2021

94.

Daniel Camsund; Alfonso Jaramillo*; Peter Lindblad*

Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor in Escherichia coli Journal Article

In: BioDesign Research, 2021.

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Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor in Escherichia coli
93.

Satya Prakash; Adrian Racovita; Clenira Varela; Mark Walsh; Roberto Galizi; Mark Isalan; Alfonso Jaramillo

Engineering Adaptive Gene Circuits in Bacteria Mastering Game Playing by Reinforcement Learning Journal Article

In: Biophysical Journal, 2021.

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2020

92.

Roberto Galizi; John N. Duncan; William Rostain; Charlotte M Quinn; Marko Storch; Manish Kushwaha; Alfonso Jaramillo

Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics Journal Article

In: The CRISPR Journal, vol. 3, no. 5, pp. 398–408, 2020.

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Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics
91.

Andreas K. Broedel; Rui Rodrigues; Alfonso Jaramillo; Mark Isalan

Accelerated evolution of a minimal 63-amino acid dual transcription factor Journal Article

In: Science advances, vol. 6, no. 24, pp. eaba2728, 2020, (2 citations (Semantic Scholar/DOI) [2021-05-15]).

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Accelerated evolution of a minimal 63-amino acid dual transcription factor
90.

Aurelija M. Grigonyte; Christian Harrison; Paul R. MacDonald; Ariadna Montero-Blay; Matthew Tridgett; John Duncan; Antonia P. Sagona; Chrystala Constantinidou; Alfonso Jaramillo*; Andrew Millard*

Comparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7 Journal Article

In: Viruses, vol. 12, no. 2, pp. 193, 2020, (5 citations (Semantic Scholar/DOI) [2021-05-15]).

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Comparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7
89.

Matthew Tridgett; Maria Ababi; Alexander Osgerby; Robert Ramirez Garcia; Alfonso Jaramillo

Engineering Bacteria to Produce Pure Phage-like Particles for Gene Delivery Journal Article

In: ACS Synthetic Biology, 2020, (0 citations (Semantic Scholar/DOI) [2021-05-15]).

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Engineering Bacteria to Produce Pure Phage-like Particles for Gene Delivery
88.

Adrian Racovita; Alfonso Jaramillo

Reinforcement learning in synthetic gene circuits Journal Article

In: Biochemical Society transactions, vol. 48, no. 4, pp. 1637–1643, 2020, (1 citations (Semantic Scholar/DOI) [2021-05-15]).

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Reinforcement learning in synthetic gene circuits

2019

87.

Xiaohan Yang; Lei S. Qi; Alfonso Jaramillo; Zong-Ming Max Cheng

Biodesign Research to Advance the Principles and Applications of Biosystems Design Journal Article

In: BioDesign Research, vol. 2019, pp. 1–4, 2019, (3 citations (Semantic Scholar/DOI) [2021-05-15]).

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86.

Roberto Galizi; Alfonso Jaramillo

Engineering CRISPR guide RNA riboswitches for in vivo applications Journal Article

In: Current Opinion in Biotechnology, vol. 55, pp. 103–113, 2019, (9 citations (Semantic Scholar/DOI) [2021-05-15]).

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Engineering CRISPR guide RNA riboswitches for in vivo applications

2018

85.

Teresa Cordero; Arantxa Rosado; Eszter Majer; Alfonso Jaramillo; Guillermo Rodrigo; José-Antonio Daròs

Boolean Computation in Plants Using Post-translational Genetic Control and a Visual Output Signal Journal Article

In: ACS Synthetic Biology, vol. 7, no. 10, pp. 2322–2330, 2018, (3 citations (Semantic Scholar/DOI) [2021-05-15]).

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Boolean Computation in Plants Using Post-translational Genetic Control and a Visual Output Signal
84.

Andreas K. Broedel; Mark Isalan; Alfonso Jaramillo

Engineering of biomolecules by bacteriophage directed evolution Journal Article

In: Current Opinion in Biotechnology, vol. 51, pp. 32–38, 2018, (10 citations (Semantic Scholar/DOI) [2021-05-15]).

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Engineering of biomolecules by bacteriophage directed evolution
83.

Eunice A. Ferreira; Catarina C. Pacheco; Filipe Pinto; José Pereira; Pedro Lamosa; Paulo Oliveira; Boris Kirov; Alfonso Jaramillo; Paula Tamagnini

Expanding the toolbox for Synechocystis sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters Journal Article

In: Synthetic Biology, vol. 3, no. 1, pp. ysy014, 2018, (20 citations (Semantic Scholar/DOI) [2021-05-15]).

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Expanding the toolbox for Synechocystis sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters
82.

Catarina Coutinho Pacheco; Zsófia Büttel; Filipe Pinto; Guillermo Rodrigo; Javier Carrera; Alfonso Jaramillo; Paula Tamagnini

Modulation of intracellular O2 concentration in Escherichia coli strains using Oxygen Consuming Devices (OCDs) Journal Article

In: ACS Synthetic Biology, vol. 7, no. 7, pp. 1742–1752, 2018, (1 citations (Semantic Scholar/DOI) [2021-05-15]).

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Modulation of intracellular O2 concentration in Escherichia coli strains using Oxygen Consuming Devices (OCDs)
81.

Anis Senoussi; Jonathan Lee Tin Wah; Yoshihiro Shimizu; Jerome Robert; Alfonso Jaramillo; Sven Findeiß; Ilka M. Axmann; André Estévez-Torres

Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System Journal Article

In: ACS Synthetic Biology, vol. 7, no. 5, pp. 1269–1278, 2018, (8 citations (Semantic Scholar/DOI) [2021-05-15]).

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Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System
80.

Mark Howarth; Alfonso Jaramillo

ScienceDirect Editorial overview: Nanobiotechnology: Baby steps and giant strides towards molecular mastery Journal Article

In: Current Opinion in Biotechnology, vol. 51, pp. iv–vi, 2018, (0 citations (Semantic Scholar/DOI) [2021-05-15]).

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2017

79.

Alfonso Jaramillo

Engineered stable ecosystems Journal Article

In: Nature microbiology, vol. 2, no. 8, pp. 17119, 2017, (0 citations (Semantic Scholar/DOI) [2021-05-15]).

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Engineered stable ecosystems
78.

Guillermo Rodrigo; Satya Prakash; Shensi Shen; Eszter Majer; José-Antonio Daròs; Alfonso Jaramillo

Model-based design of RNA hybridization networks implemented in living cells Journal Article

In: Nucleic Acids Research, vol. 45, no. 16, pp. 9797–9808, 2017, (8 citations (Semantic Scholar/DOI) [2021-05-15]).

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Model-based design of RNA hybridization networks implemented in living cells
77.

Andreas K. Broedel; Alfonso Jaramillo; Mark Isalan

Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication Journal Article

In: Nature Protocols, vol. 12, no. 9, pp. 1830–1843, 2017, (12 citations (Semantic Scholar/DOI) [2021-05-15]).

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Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication

2016

76.

Andreas K. Brdel; Alfonso Jaramillo; Mark Isalan

Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Journal Article

In: Nature Communications, vol. 7, pp. 13858, 2016.

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Engineering orthogonal dual transcription factors for multi-input synthetic promoters.
75.

Guillermo Rodrigo; Satya Prakash; Teresa Cordero; Manish Kushwaha; Alfonso Jaramillo

Functionalization of an Antisense Small RNA Journal Article

In: Journal of Molecular Biology, vol. 428, no. 5 Pt B, pp. 889–892, 2016, (4 citations (Semantic Scholar/DOI) [2021-05-15]).

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Functionalization of an Antisense Small RNA
74.

Antonia P. Sagona; Aurelija M. Grigonyte; Paul R. MacDonald; Alfonso Jaramillo

Genetically modified bacteriophages Journal Article

In: Integrative biology : quantitative biosciences from nano to macro, vol. 8, no. 4, pp. 465–474, 2016, (17 citations (Semantic Scholar/DOI) [2021-05-15]).

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Genetically modified bacteriophages
73.

Manish Kushwaha; William Rostain; Satya Prakash; John N. Duncan; Alfonso Jaramillo

Using RNA as Molecular Code for Programming Cellular Function Journal Article

In: ACS Synthetic Biology, vol. 5, no. 8, pp. 795–809, 2016, (32 citations (Semantic Scholar/DOI) [2021-05-15]).

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Using RNA as Molecular Code for Programming Cellular Function
72.

Martina Pasini; Alfred Fernández-Castané; Alfonso Jaramillo; Carles Mas; Gloria Caminal; Pau Ferrer

Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli Journal Article

In: New biotechnology, vol. 33, no. 1, pp. 78–90, 2016, (20 citations (Semantic Scholar/DOI) [2021-05-15]).

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Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli

2015

71.

Martyn Amos; Ilka Maria Axmann; Nils Bluthgen; Fernando Cruz; Alfonso Jaramillo; Alfonso Rodriguez-Paton; Friedrich Simmel

Bacterial computing with engineered populations Journal Article

In: vol. 373, no. 2046, pp. 20140218, 2015, (11 citations (Semantic Scholar/DOI) [2021-05-15]).

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70.

Jack Hassall; Paul MacDonald; Teresa Cordero; William Rostain; Alfonso Jaramillo

Design and Characterization of Topological Small RNAs Journal Article

In: Methods in molecular biology (Clifton, N.J.), vol. 1316, no. Chapter 13, pp. 149–167, 2015, ISSN: 978-1-4939-2729-6, (1 citations (Semantic Scholar/DOI) [2021-05-15]).

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Design and Characterization of Topological Small RNAs
69.

Alfonso Jaramillo

Droplet-based method and device for the continuous proliferation of living cells in suspension Miscellaneous

2015.

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68.

Shensi Shen; Guillermo Rodrigo; Satya Prakash; Eszter Majer; Thomas E. Landrain; Boris Kirov; Jos-Antonio Dars; Alfonso Jaramillo

Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Journal Article

In: Nucleic Acids Research, vol. 43, no. 10, pp. 5158–5170, 2015.

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Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.
67.

Guillermo Rodrigo; Eszter Majer; Satya Prakash; Jos-Antonio Dars; Alfonso Jaramillo; Juan F. Poyatos

Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells Journal Article

In: Biophysical Journal, vol. 109, pp. 1070–1076, 2015.

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66.

William Rostain; Thomas E. Landrain; Guillermo Rodrigo; Alfonso Jaramillo

Regulatory RNA design through evolutionary computation and strand displacement Journal Article

In: Methods in molecular biology (Clifton, N.J.), vol. 1244, pp. 63–78, 2015.

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2014

65.

P. Parutto; L. Le Goff; H. Léger; G. Mercy; E. Kouwe; A. Chhun; B. Baudu; G. Guillocheau; F. Amiot; L. Ujéda; W. Rostain; C. Pauthenier; T. Cerisy; N. Pollet; A. Tolonen; Alfonso Jaramillo

Characterization and modeling of an iron-sensitive system in Escherichia coli Inproceedings

In: pp. 107–118, 2014.

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64.

Guillermo Rodrigo; Satya Prakash; Shensi Shen; Eszter Majer; Jos-Antonio Dars; Alfonso Jaramillo

Cooperative riboregulation in living cells through allosteric programming of toehold activation Journal Article

In: BioRxiv, pp. 009688, 2014.

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63.

William Rostain; Shensi Shen; Teresa Cordero; Guillermo Rodrigo; Alfonso Jaramillo

Engineering a circular riboregulator in Escherichia coli Journal Article

In: BioRxiv, pp. 008987, 2014.

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62.

Guillermo Rodrigo; Alfonso Jaramillo

RiboMaker: computational design of conformation-based riboregulation Journal Article

In: Bioinformatics, vol. 30, no. 17, pp. 2508–2510, 2014.

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2013

61.

Guillermo Rodrigo; Thomas E. Landrain; Shensi Shen; Alfonso Jaramillo

A new frontier in synthetic biology: automated design of small RNA devices in bacteria Journal Article

In: Trends in genetics : TIG, vol. 29, no. 9, pp. 529–536, 2013.

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60.

Guillermo Rodrigo; Alfonso Jaramillo

AutoBioCAD: full biodesign automation of genetic circuits Journal Article

In: ACS Synthetic Biology, vol. 2, no. 5, pp. 230–236, 2013.

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59.

Javier Carrera; Alfonso Jaramillo

Automated design of bacterial genome sequences Journal Article

In: BMC systems biology, vol. 7, pp. 108, 2013, (1 citations (Semantic Scholar/DOI) [2021-05-15]).

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58.

Mara Surez Diez; Anas M. Pujol; Manolis Matzapetakis; Alfonso Jaramillo; Olga Iranzo

Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Journal Article

In: Biotechnology Journal, vol. 8, no. 7, pp. 855–864, 2013.

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57.

A. Jaramillo; D. Zeliszewski

Design of the living automates | La conception du vivant s'automatise Journal Article

In: Biofutur, no. 339, pp. 36-39, 2013.

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56.

Guillermo Rodrigo; Thomas E. Landrain; Eszter Majer; Jos-Antonio Dars; Alfonso Jaramillo

Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization Journal Article

In: PLoS Computational Biology, vol. 9, no. 8, pp. e1003172, 2013.

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55.

Alfonso Jaramillo; Alfonso Jaramillo; Dominique Zeliszewski

The idea of automated living Journal Article

In: Biofutur, 2013.

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54.

Guillermo Rodrigo; Boris Kirov; Shensi Shen; Alfonso Jaramillo

Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model Journal Article

In: Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 23, no. 2, pp. 025109, 2013.

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2012

53.

Catalin I. Fetita; Boris Kirov; Alfonso Jaramillo; Christophe Lefevre

An automated approach for single-cell tracking in epifluorescence microscopy applied to E. coli growth analysis on microfluidics biochips Inproceedings

In: Medical Imaging, 2012.

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52.

Javier Carrera; J. Carrera; S. F. Elena; Santiago F. Elena; Alfonso Jaramillo

Computational design of genomic transcriptional networks with adaptation to varying environments. Journal Article

In: Proceedings of the National Academy of Sciences, vol. 109, no. 38, pp. 15277–15282, 2012.

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51.

Guillermo Rodrigo; Thomas E. Landrain; Alfonso Jaramillo

De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 38, pp. 15271–15276, 2012.

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50.

G. Rodrigo; A. Jaramillo; M. A. Blázquez

Erratum: Integral control of plant gravitropism through the interplay of hormone signaling and gene regulation (Biophysical Journal (2011) 101 (757-763)) Journal Article

In: Biophysical Journal, vol. 102, no. 10, 2012.

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49.

Javier Carrera; Asun Fernndez Carmen; Rafael Fernndez-Muoz; Jose Luis Rambla; Clara Pons; Alfonso Jaramillo; Santiago F. Elena; Antonio Granell

Fine-tuning tomato agronomic properties by computational genome redesign. Journal Article

In: PLoS Computational Biology, vol. 8, no. 6, pp. e1002528, 2012.

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48.

Guillermo Rodrigo; Javier Carrera; Thomas E. Landrain; Alfonso Jaramillo

Perspectives on the automatic design of regulatory systems for synthetic biology Journal Article

In: FEBS Lett, vol. 586, no. 15, pp. 2037–2042, 2012.

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2011

47.

Guillermo Rodrigo; Javier Carrera; Alfonso Jaramillo

Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors Journal Article

In: Nucleic Acids Research, vol. 39, no. 20, pp. e138–e138, 2011.

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96 entries « 1 of 2 »