Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Autorzy: Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano
Opublikowane w: PLOS ONE, Numer 10/9, 2015, Strona(/y) e0137354, ISSN 1932-6203
Wydawca: 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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 44/3, 2016, Strona(/y) 1192-1202, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkw004

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

Autorzy: Iason Tsarmpopoulos, Géraldine Gourgues, Alain Blanchard, Sanjay Vashee, Joerg Jores, Carole Lartigue, Pascal Sirand-Pugnet
Opublikowane w: ACS Synthetic Biology, Numer 5/1, 2016, Strona(/y) 104-109, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.5b00196

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

Autorzy: Ivan Junier, E. Besray Unal, Eva Yus, Verónica Lloréns-Rico, Luis Serrano
Opublikowane w: Cell Systems, Numer 2/6, 2016, Strona(/y) 391-401, ISSN 2405-4712
Wydawca: Elsevier Inc.
DOI: 10.1016/j.cels.2016.04.015

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

Autorzy: Lei Pei, Markus Schmidt
Opublikowane w: Frontiers in Genetics, Numer 9, 2018, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2018.00207

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Autorzy: Rienk A. Rienksma, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Opublikowane w: Frontiers in Cellular and Infection Microbiology, Numer 8, 2018, ISSN 2235-2988
Wydawca: Frontiers Media S. A.
DOI: 10.3389/fcimb.2018.00264

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

Autorzy: Niels Zondervan, Jesse van Dam, Peter Schaap, Vitor Martins dos Santos, Maria Suarez-Diez
Opublikowane w: International Journal of Molecular Sciences, Numer 19/2, 2018, Strona(/y) 347, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19020347

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

Autorzy: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos, Christian Fleck
Opublikowane w: BMC Systems Biology, Numer 12/1, 2018, ISSN 1752-0509
Wydawca: BioMed Central
DOI: 10.1186/s12918-018-0584-8

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Autorzy: 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
Opublikowane w: Nature Communications, Numer 8, 2017, Strona(/y) 14665, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms14665

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

Autorzy: Eva Yus, Jae-Seong Yang, Adrià Sogues, Luis Serrano
Opublikowane w: Nature Communications, Numer 8/1, 2017, ISSN 2041-1723
Wydawca: 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

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

Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome

Autorzy: Maria Lluch-Senar, Francesco M. Mancuso, Héctor Climente-González, Marcia I. Peña-Paz, Eduard Sabido, Luis Serrano
Opublikowane w: PROTEOMICS, Numer 16/4, 2016, Strona(/y) 554-563, ISSN 1615-9853
Wydawca: 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”

Autorzy: Kia Ditlevsen, Cecilie Glerup, Peter Sandøe, Jesper Lassen
Opublikowane w: Public Understanding of Science, Numer 29/3, 2020, Strona(/y) 289-305, ISSN 0963-6625
Wydawca: SAGE Publications
DOI: 10.1177/0963662520906083

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

Autorzy: 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
Opublikowane w: ACS Synthetic Biology, Numer 7/6, 2018, Strona(/y) 1538-1552, ISSN 2161-5063
Wydawca: 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

Autorzy: Eva Yus, Verónica Lloréns-Rico, Sira Martínez, Carolina Gallo, Hinnerk Eilers, Cedric Blötz, Jörg Stülke, Maria Lluch-Senar, Luis Serrano
Opublikowane w: Cell Systems, Numer 9/2, 2019, Strona(/y) 143-158.e13, ISSN 2405-4712
Wydawca: 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

Autorzy: Estelle Ruiz, Vincent Talenton, Marie-Pierre Dubrana, Gabrielle Guesdon, Maria Lluch-Senar, Franck Salin, Pascal Sirand-Pugnet, Yonathan Arfi, Carole Lartigue
Opublikowane w: ACS Synthetic Biology, Numer 8/11, 2019, Strona(/y) 2547-2557, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.9b00224

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

Autorzy: Ariadna Montero-Blay, Samuel Miravet-Verde, Maria Lluch-Senar, Carlos Piñero-Lambea, Luis Serrano
Opublikowane w: DNA Research, Numer 26/4, 2019, Strona(/y) 327-339, ISSN 1340-2838
Wydawca: Oxford University Press
DOI: 10.1093/dnares/dsz012

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

Autorzy: Enrique Asin-Garcia, Amalia Kallergi, Laurens Landeweerd, Vitor A.P. Martins dos Santos
Opublikowane w: Trends in Biotechnology, 2020, ISSN 0167-7799
Wydawca: 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

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

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

Autorzy: Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins dos Santos, Maria Suarez-Diez, Peter J Schaap
Opublikowane w: Bioinformatics, Numer 34/8, 2017, Strona(/y) 1401-1403, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btx767

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

Autorzy: Erika Gaspari, Annika Franke, Diana Robles-Diaz, Robert Zweigerdt, Ingo Roeder, Thomas Zerjatke, Henning Kempf
Opublikowane w: Stem Cell Research, Numer 32, 2018, Strona(/y) 1-7, ISSN 1873-5061
Wydawca: Elsevier
DOI: 10.1016/j.scr.2018.07.025

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Autorzy: Tjerko Kamminga, Simen-Jan Slagman, Vitor A.P. Martins dos Santos, Jetta J.E. Bijlsma, Peter J. Schaap
Opublikowane w: Trends in Biotechnology, Numer 37/8, 2019, Strona(/y) 805-816, ISSN 0167-7799
Wydawca: Elsevier BV
DOI: 10.1016/j.tibtech.2019.03.005

SyNDI: synchronous network data integration framework

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

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

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

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

Autorzy: Jesse C.J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Peter J. Schaap, Maria Suarez-Diez
Opublikowane w: bioRXiv, 2017
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/184747

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