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Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution.

Schaerli Y, Jiménez A, Duarte JM, Mihajlovic L, Renggli J, Isalan M, Sharpe J, Wagner A.

Mol Syst Biol. 2018 Sep 10;14(9):e8102. doi: 10.15252/msb.20178102.


Commentary: Synthetic Addiction Extends the Productive Life Time of Engineered Escherichia coli Populations.

Enrico Bena C, Grob A, Isalan M, Bosia C, Ceroni F.

Front Bioeng Biotechnol. 2018 Jun 12;6:77. doi: 10.3389/fbioe.2018.00077. eCollection 2018. No abstract available.


Neuro-Cardio Mechanisms in Huntington's Disease and Other Neurodegenerative Disorders.

Critchley BJ, Isalan M, Mielcarek M.

Front Physiol. 2018 May 23;9:559. doi: 10.3389/fphys.2018.00559. eCollection 2018. Review.


Drug-Inducible Control of Lethality Genes: A Low Background Destabilizing Domain Architecture Applied to the Gal4-UAS System in Drosophila.

Kogenaru M, Isalan M.

ACS Synth Biol. 2018 Jun 15;7(6):1496-1506. doi: 10.1021/acssynbio.7b00302. Epub 2018 May 15.


Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR.

Grob A, Marbiah M, Isalan M.

Methods Mol Biol. 2018;1766:285-301. doi: 10.1007/978-1-4939-7768-0_16.


Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.

Perez-Carrasco R, Barnes CP, Schaerli Y, Isalan M, Briscoe J, Page KM.

Cell Syst. 2018 Apr 25;6(4):521-530.e3. doi: 10.1016/j.cels.2018.02.008. Epub 2018 Mar 21.


Trp-ing upon new repressors.

Brödel AK, Isalan M.

Nat Chem Biol. 2018 Apr;14(4):328-329. doi: 10.1038/s41589-018-0012-9. No abstract available.


Engineering of biomolecules by bacteriophage directed evolution.

Brödel AK, Isalan M, Jaramillo A.

Curr Opin Biotechnol. 2018 Jun;51:32-38. doi: 10.1016/j.copbio.2017.11.004. Epub 2017 Nov 22. Review.


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

Brödel AK, Jaramillo A, Isalan M.

Nat Protoc. 2017 Sep;12(9):1830-1843. doi: 10.1038/nprot.2017.084. Epub 2017 Aug 10.


Early transcriptional alteration of histone deacetylases in a murine model of doxorubicin-induced cardiomyopathy.

Piotrowska I, Isalan M, Mielcarek M.

PLoS One. 2017 Jun 29;12(6):e0180571. doi: 10.1371/journal.pone.0180571. eCollection 2017.


A three-step framework for programming pattern formation.

Scholes NS, Isalan M.

Curr Opin Chem Biol. 2017 Oct;40:1-7. doi: 10.1016/j.cbpa.2017.04.008. Epub 2017 May 2. Review.


Transcriptional Signature of an Altered Purine Metabolism in the Skeletal Muscle of a Huntington's Disease Mouse Model.

Mielcarek M, Smolenski RT, Isalan M.

Front Physiol. 2017 Mar 2;8:127. doi: 10.3389/fphys.2017.00127. eCollection 2017.


Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis.

Senthivel VR, Sturrock M, Piedrafita G, Isalan M.

Sci Rep. 2016 Dec 16;6:39178. doi: 10.1038/srep39178.


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

Brödel AK, Jaramillo A, Isalan M.

Nat Commun. 2016 Dec 16;7:13858. doi: 10.1038/ncomms13858.


Changes in cardiac nucleotide metabolism in Huntington's disease.

Toczek M, Kutryb-Zajac B, Zukowska P, Slominska EM, Isalan M, Mielcarek M, Smolenski RT.

Nucleosides Nucleotides Nucleic Acids. 2016 Dec;35(10-12):707-712.


Deimmunization for gene therapy: host matching of synthetic zinc finger constructs enables long-term mutant Huntingtin repression in mice.

Agustín-Pavón C, Mielcarek M, Garriga-Canut M, Isalan M.

Mol Neurodegener. 2016 Sep 6;11(1):64. doi: 10.1186/s13024-016-0128-x.


An impaired metabolism of nucleotides underpins a novel mechanism of cardiac remodeling leading to Huntington's disease related cardiomyopathy.

Toczek M, Zielonka D, Zukowska P, Marcinkowski JT, Slominska E, Isalan M, Smolenski RT, Mielcarek M.

Biochim Biophys Acta. 2016 Nov;1862(11):2147-2157. doi: 10.1016/j.bbadis.2016.08.019. Epub 2016 Aug 26.


From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Ciechonska M, Grob A, Isalan M.

Integr Biol (Camb). 2016 Apr 18;8(4):383-93. doi: 10.1039/c5ib00271k. Epub 2016 Jan 11. Review.


The propagation of perturbations in rewired bacterial gene networks.

Baumstark R, Hänzelmann S, Tsuru S, Schaerli Y, Francesconi M, Mancuso FM, Castelo R, Isalan M.

Nat Commun. 2015 Dec 16;6:10105. doi: 10.1038/ncomms10105.


A shared mechanism of muscle wasting in cancer and Huntington's disease.

Mielcarek M, Isalan M.

Clin Transl Med. 2015 Dec;4(1):34. doi: 10.1186/s40169-015-0076-z. Epub 2015 Dec 14.


Sender-receiver systems and applying information theory for quantitative synthetic biology.

Barcena Menendez D, Senthivel VR, Isalan M.

Curr Opin Biotechnol. 2015 Feb;31:101-7. doi: 10.1016/j.copbio.2014.08.005. Epub 2014 Oct 1. Review.


A split intein T7 RNA polymerase for transcriptional AND-logic.

Schaerli Y, Gili M, Isalan M.

Nucleic Acids Res. 2014 Oct 29;42(19):12322-8. doi: 10.1093/nar/gku884. Epub 2014 Sep 27.


A unified design space of synthetic stripe-forming networks.

Schaerli Y, Munteanu A, Gili M, Cotterell J, Sharpe J, Isalan M.

Nat Commun. 2014 Sep 23;5:4905. doi: 10.1038/ncomms5905.


β-catenin fluctuates in mouse ESCs and is essential for Nanog-mediated reprogramming of somatic cells to pluripotency.

Marucci L, Pedone E, Di Vicino U, Sanuy-Escribano B, Isalan M, Cosma MP.

Cell Rep. 2014 Sep 25;8(6):1686-1696. doi: 10.1016/j.celrep.2014.08.011. Epub 2014 Sep 4.


Cooperativity to increase Turing pattern space for synthetic biology.

Diambra L, Senthivel VR, Menendez DB, Isalan M.

ACS Synth Biol. 2015 Feb 20;4(2):177-86. doi: 10.1021/sb500233u. Epub 2014 Aug 22.


Genetically encoded sender-receiver system in 3D mammalian cell culture.

Carvalho A, Menendez DB, Senthivel VR, Zimmermann T, Diambra L, Isalan M.

ACS Synth Biol. 2014 May 16;3(5):264-72. doi: 10.1021/sb400053b. Epub 2013 Dec 20.


Building synthetic gene circuits from combinatorial libraries: screening and selection strategies.

Schaerli Y, Isalan M.

Mol Biosyst. 2013 Jul;9(7):1559-67. doi: 10.1039/c2mb25483b. Epub 2013 Jan 23. Review.


Transfecting RNA quadruplexes results in few transcriptome perturbations.

Sanders PG, Cotterell J, Sharpe J, Isalan M.

RNA Biol. 2013 Feb;10(2):205-10. doi: 10.4161/rna.22781. Epub 2012 Dec 12.


Synthetic zinc finger repressors reduce mutant huntingtin expression in the brain of R6/2 mice.

Garriga-Canut M, Agustín-Pavón C, Herrmann F, Sánchez A, Dierssen M, Fillat C, Isalan M.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3136-45. doi: 10.1073/pnas.1206506109. Epub 2012 Oct 10.


The PLOS ONE synthetic biology collection: six years and counting.

Peccoud J, Isalan M.

PLoS One. 2012;7(8):e43231. doi: 10.1371/journal.pone.0043231. Epub 2012 Aug 15. Review.


Systems biology: A cell in a computer.

Isalan M.

Nature. 2012 Aug 2;488(7409):40-1. doi: 10.1038/488040a. No abstract available.


Zinc-finger nucleases: how to play two good hands.

Isalan M.

Nat Methods. 2011 Dec 28;9(1):32-4. doi: 10.1038/nmeth.1805. No abstract available.


A biobrick library for cloning custom eukaryotic plasmids.

Constante M, Grünberg R, Isalan M.

PLoS One. 2011;6(8):e23685. doi: 10.1371/journal.pone.0023685. Epub 2011 Aug 25.


p53 Gene repair with zinc finger nucleases optimised by yeast 1-hybrid and validated by Solexa sequencing.

Herrmann F, Garriga-Canut M, Baumstark R, Fajardo-Sanchez E, Cotterell J, Minoche A, Himmelbauer H, Isalan M.

PLoS One. 2011;6(6):e20913. doi: 10.1371/journal.pone.0020913. Epub 2011 Jun 9.


Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation.

Munteanu A, Constante M, Isalan M, Solé RV.

BMC Syst Biol. 2010 May 17;4:66. doi: 10.1186/1752-0509-4-66.


Gene networks and liar paradoxes.

Isalan M.

Bioessays. 2009 Oct;31(10):1110-5. doi: 10.1002/bies.200900072.


This title is false.

Isalan M, Morrison M.

Nature. 2009 Apr 23;458(7241):969. doi: 10.1038/458969a. No abstract available.


Engineering prokaryotic gene circuits.

Michalodimitrakis K, Isalan M.

FEMS Microbiol Rev. 2009 Jan;33(1):27-37. doi: 10.1111/j.1574-6976.2008.00139.x. Epub 2008 Nov 4. Review.


Evolvability and hierarchy in rewired bacterial gene networks.

Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L.

Nature. 2008 Apr 17;452(7189):840-5. doi: 10.1038/nature06847.


Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences.

Fajardo-Sanchez E, Stricher F, Pâques F, Isalan M, Serrano L.

Nucleic Acids Res. 2008 Apr;36(7):2163-73. doi: 10.1093/nar/gkn059. Epub 2008 Feb 14.


Localized transfection with magnetic beads coated with PCR products and other nucleic acids.

Santori MI, Gonzalez C, Serrano L, Isalan M.

Nat Protoc. 2006;1(2):526-31.


Histone acetyltransferase activity of p300 is required for transcriptional repression by the promyelocytic leukemia zinc finger protein.

Guidez F, Howell L, Isalan M, Cebrat M, Alani RM, Ivins S, Hormaeche I, McConnell MJ, Pierce S, Cole PA, Licht J, Zelent A.

Mol Cell Biol. 2005 Jul;25(13):5552-66.


Localized transfection on arrays of magnetic beads coated with PCR products.

Isalan M, Santori MI, Gonzalez C, Serrano L.

Nat Methods. 2005 Feb;2(2):113-8. Epub 2005 Jan 21.


Engineering gene networks to emulate Drosophila embryonic pattern formation.

Isalan M, Lemerle C, Serrano L.

PLoS Biol. 2005 Mar;3(3):e64. Epub 2005 Feb 22.


Inhibition of human telomerase activity by an engineered zinc finger protein that binds G-quadruplexes.

Patel SD, Isalan M, Gavory G, Ladame S, Choo Y, Balasubramanian S.

Biochemistry. 2004 Oct 26;43(42):13452-8.


Zinc-finger protein-targeted gene regulation: genomewide single-gene specificity.

Tan S, Guschin D, Davalos A, Lee YL, Snowden AW, Jouvenot Y, Zhang HS, Howes K, McNamara AR, Lai A, Ullman C, Reynolds L, Moore M, Isalan M, Berg LP, Campos B, Qi H, Spratt SK, Case CC, Pabo CO, Campisi J, Gregory PD.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):11997-2002. Epub 2003 Sep 26.


Repression of the HIV-1 5' LTR promoter and inhibition of HIV-1 replication by using engineered zinc-finger transcription factors.

Reynolds L, Ullman C, Moore M, Isalan M, West MJ, Clapham P, Klug A, Choo Y.

Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1615-20. Epub 2003 Feb 6.


Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors.

Papworth M, Moore M, Isalan M, Minczuk M, Choo Y, Klug A.

Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1621-6. Epub 2003 Feb 6.

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