Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Autores: Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano
Publicado en: PLOS ONE, Edición 10/9, 2015, Página(s) e0137354, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0137354

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Autores: Wei-Hua Chen, Vera van Noort, Maria Lluch-Senar, Marco L. Hennrich, Judith A. H. Wodke, Eva Yus, Andreu Alibés, Guglielmo Roma, Daniel R. Mende, Christina Pesavento, Athanasios Typas, Anne-Claude Gavin, Luis Serrano, Peer Bork
Publicado en: Nucleic Acids Research, Edición 44/3, 2016, Página(s) 1192-1202, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkw004

In-Yeast Engineering of a Bacterial Genome Using CRISPR/Cas9

Autores: Iason Tsarmpopoulos, Géraldine Gourgues, Alain Blanchard, Sanjay Vashee, Joerg Jores, Carole Lartigue, Pascal Sirand-Pugnet
Publicado en: ACS Synthetic Biology, Edición 5/1, 2016, Página(s) 104-109, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.5b00196

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

Autores: Ivan Junier, E. Besray Unal, Eva Yus, Verónica Lloréns-Rico, Luis Serrano
Publicado en: Cell Systems, Edición 2/6, 2016, Página(s) 391-401, ISSN 2405-4712
Editor: Elsevier Inc.
DOI: 10.1016/j.cels.2016.04.015

Fast-Growing Engineered Microbes: New Concerns for Gain-of-Function Research?

Autores: Lei Pei, Markus Schmidt
Publicado en: Frontiers in Genetics, Edición 9, 2018, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2018.00207

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Autores: Rienk A. Rienksma, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publicado en: Frontiers in Cellular and Infection Microbiology, Edición 8, 2018, ISSN 2235-2988
Editor: Frontiers Media S. A.
DOI: 10.3389/fcimb.2018.00264

Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story

Autores: Niels Zondervan, Jesse van Dam, Peter Schaap, Vitor Martins dos Santos, Maria Suarez-Diez
Publicado en: International Journal of Molecular Sciences, Edición 19/2, 2018, Página(s) 347, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19020347

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Autores: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos, Christian Fleck
Publicado en: BMC Systems Biology, Edición 12/1, 2018, ISSN 1752-0509
Editor: BioMed Central
DOI: 10.1186/s12918-018-0584-8

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Autores: Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar, Luís Serrano
Publicado en: Nature Communications, Edición 8, 2017, Página(s) 14665, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/ncomms14665

A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants

Autores: Eva Yus, Jae-Seong Yang, Adrià Sogues, Luis Serrano
Publicado en: Nature Communications, Edición 8/1, 2017, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-017-00239-7

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life

Autores: Tjerko Kamminga, Jasper J. Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A. P. Martins dos Santos, Jetta J. E. Bijlsma, Peter J. Schaap
Publicado en: Frontiers in Cellular and Infection Microbiology, Edición 7, 2017, ISSN 2235-2988
Editor: Frontiers Media S. A.
DOI: 10.3389/fcimb.2017.00031

Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome

Autores: Maria Lluch-Senar, Francesco M. Mancuso, Héctor Climente-González, Marcia I. Peña-Paz, Eduard Sabido, Luis Serrano
Publicado en: PROTEOMICS, Edición 16/4, 2016, Página(s) 554-563, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201500187

Synthetic livestock vaccines as risky interference with nature? Lay and expert arguments and understandings of “naturalness”

Autores: Kia Ditlevsen, Cecilie Glerup, Peter Sandøe, Jesper Lassen
Publicado en: Public Understanding of Science, Edición 29/3, 2020, Página(s) 289-305, ISSN 0963-6625
Editor: SAGE Publications
DOI: 10.1177/0963662520906083

Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells

Autores: Ana M. Mariscal, Shigeyuki Kakizawa, Jonathan Y. Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D. Weyman, Kim S. Wise, Chuck Merryman, Gavin Tse, Adam J. Moore, Clyde A. Hutchison, Hamilton O. Smith, Masaru Tomita, J. Craig Venter, John I. Glass, Jaume Piñol, Yo Suzuki
Publicado en: ACS Synthetic Biology, Edición 7/6, 2018, Página(s) 1538-1552, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.8b00028

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Autores: Eva Yus, Verónica Lloréns-Rico, Sira Martínez, Carolina Gallo, Hinnerk Eilers, Cedric Blötz, Jörg Stülke, Maria Lluch-Senar, Luis Serrano
Publicado en: Cell Systems, Edición 9/2, 2019, Página(s) 143-158.e13, ISSN 2405-4712
Editor: Elsevier Inc.
DOI: 10.1016/j.cels.2019.07.001

CReasPy-Cloning: A Method for Simultaneous Cloning and Engineering of Megabase-Sized Genomes in Yeast Using the CRISPR-Cas9 System

Autores: Estelle Ruiz, Vincent Talenton, Marie-Pierre Dubrana, Gabrielle Guesdon, Maria Lluch-Senar, Franck Salin, Pascal Sirand-Pugnet, Yonathan Arfi, Carole Lartigue
Publicado en: ACS Synthetic Biology, Edición 8/11, 2019, Página(s) 2547-2557, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.9b00224

SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes

Autores: Ariadna Montero-Blay, Samuel Miravet-Verde, Maria Lluch-Senar, Carlos Piñero-Lambea, Luis Serrano
Publicado en: DNA Research, Edición 26/4, 2019, Página(s) 327-339, ISSN 1340-2838
Editor: Oxford University Press
DOI: 10.1093/dnares/dsz012

Genetic Safeguards for Safety-by-design: So Close Yet So Far

Autores: Enrique Asin-Garcia, Amalia Kallergi, Laurens Landeweerd, Vitor A.P. Martins dos Santos
Publicado en: Trends in Biotechnology, 2020, ISSN 0167-7799
Editor: Elsevier BV
DOI: 10.1016/j.tibtech.2020.04.005

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

Autores: Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vitor A. P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez
Publicado en: Scientific Data, Edición 6/1, 2019, ISSN 2052-4463
Editor: Nature Publishing Group
DOI: 10.1038/s41597-019-0263-7

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Autores: Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins dos Santos, Maria Suarez-Diez, Peter J Schaap
Publicado en: Bioinformatics, Edición 34/8, 2017, Página(s) 1401-1403, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btx767

Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model

Autores: Erika Gaspari, Annika Franke, Diana Robles-Diaz, Robert Zweigerdt, Ingo Roeder, Thomas Zerjatke, Henning Kempf
Publicado en: Stem Cell Research, Edición 32, 2018, Página(s) 1-7, ISSN 1873-5061
Editor: Elsevier
DOI: 10.1016/j.scr.2018.07.025

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Autores: Tjerko Kamminga, Simen-Jan Slagman, Vitor A.P. Martins dos Santos, Jetta J.E. Bijlsma, Peter J. Schaap
Publicado en: Trends in Biotechnology, Edición 37/8, 2019, Página(s) 805-816, ISSN 0167-7799
Editor: Elsevier BV
DOI: 10.1016/j.tibtech.2019.03.005

SyNDI: synchronous network data integration framework

Autores: Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publicado en: BMC Bioinformatics, Edición 19/1, 2018, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-018-2426-5

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate

Autores: Tjerko Kamminga, Simen-Jan Slagman, Jetta J. E. Bijlsma, Vitor A. P. Martins dos Santos, Maria Suarez-Diez, Peter J. Schaap
Publicado en: Biotechnology and Bioengineering, 2017, ISSN 0006-3592
Editor: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.26347

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining

Autores: Jesse C.J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Peter J. Schaap, Maria Suarez-Diez
Publicado en: bioRXiv, 2017
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/184747

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