SAÚL ARES' SCIENTIFIC PAGE

Training some young future scientists at the LoGS lab.

Last Name: Ares First name: Saúl
Birth date : July 17, 1977. Birthplace: Newark, NJ, USA
Gender: male. Marital status: single
Affiliation: Logic of Genomic Systems Laboratory, Centro Nacional de Biotecnología - CSIC
Position: Postdoc Researcher
Address: Saul Ares
Logic of Genomic Systems Laboratory, Centro Nacional de Biotecnología - CSIC
Calle Darwin 3, 28049 Madrid, Spain
Phone: +34 91585 4307
e-mail: saul.aresctp(at)csic.es (remove ctp to send me mail)
URL: http://www.mpipks-dresden.mpg.de/~saul
ResearcherID page: http://www.researcherid.com/rid/B-4082-2008
Google Scholar page: http://scholar.google.com/citations?user=qMPc_JAAAAAJ&hl=en

Also member of the GISC (Grupo Interdisciplinar de Sistemas Complejos).

Degrees

Ph.D. Physics of Complex Systems	Universidad Carlos III de Madrid	2005
M.S. Applied Mathematics	Universidad Carlos III de Madrid	2002
B.S. Theoretical Physics	Universidad Complutense de Madrid	2000

Research interests

• Segmentation and somitogenesis in vertebrates.
• Neurogenesis in the vertebrate retina.
• Synthetic biology: genetic circuits in E. coli.
• Heterocyst differentiation and patterning in cyanobacteria.
• Nonlinear dynamics, coupled oscillators and time delay.
• Gene regulatory networks.
• Statistical physics of extended systems.
• DNA physics: thermal denaturation and hairpin formation.
• Number theory and its relation with statistical mechanics.
• Complex Systems.

Keywords: Systems Biology, Developmental Biology, Biological Clocks, Synthetic Biology, Nonlinear Dynamics, Delay Differential Equations, Statistical Mechanics, Stochastic Processes, Numerical Simulation, DNA, Complex Systems.

Grants as Principal Investigator

Title: Physics of development: pattern formation in embryos and cyanobacteria (PHYSDEV)
Project code: FIS2012-32349
Funding agency: Ministry of Economy and Competitiveness (Spain)
Funding awarded: 18000 euros
Period funded: 2013-2014

Publications in international peer-reviewed journals

Pau Formosa-Jordan, Marta Ibañes, Saúl Ares and José María Frade:
Lateral inhibition and neurogenesis: novel aspects in motion, International Journal of Developmental Biology, in press.

Koichiro Uriu, Saúl Ares, Andrew C. Oates and Luis G. Morelli:
Dynamics of mobile coupled phase oscillators, Physical Review E, 87, 032911 (2013). Link, PDF file.

E. Ullner, S. Ares, L. G. Morelli, A. C. Oates, F. Jülicher, E. Nicola, R. Heussen, D. Whitmore, K. Blyuss, M. Fryett, A. Zakharova, A. Koseska, N. R. Nene, A. Zaikin:
Noise and oscillations in biological systems: multidisciplinary approach between experimental biology, theoretical modelling and synthetic biology, International Journal of Modern Physics B, 26, 1246009 (2012). Link, PDF file.

Christian Schröter, Saúl Ares, Luis G. Morelli, Alina Isakova, Korneel Hens, Daniele Soroldoni, Martin Gajewski, Frank Jülicher, Sebastian J. Maerkl, Bart Deplancke and Andrew C. Oates:
Topology and dynamics of the zebrafish segmentation clock core circuit, PLoS Biology, 10, e1001364 (2012). Link (open access).
Article heading the "Weekly Editor's Picks" at PLoS Biology's homepage. Editorial synopsis.
Nature Reviews Genetics published a Research Highlight.

Pau Formosa-Jordan, Marta Ibañes, Saúl Ares and José María Frade:
Regulation of neuronal differentiation at the neurogenic wavefront, Development, 139, 2321-2329 (2012). Link, PDF file, supplementary material.
Article highlighted in the "In this issue" section of Development: PDF file. SA is a senior and corresponding author of this work.

Saúl Ares, Luis G. Morelli, David J. Jörg, Andrew C. Oates and Frank Jülicher:
Collective Modes of Coupled Phase Oscillators with Delayed Coupling, Physical Review Letters, 108, 204101 (2012). Link, PDF file.

Koichiro Uriu, Saúl Ares, Andrew C. Oates and Luis G. Morelli:
Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions, Physical Biology, 9, 036006 (2012). Link
Main text, PDF file.
Supplementary text, PDF file.

Luis G. Morelli, Koichiro Uriu, Saúl Ares and Andrew C. Oates:
Computational Approaches to Developmental Patterning, Science, 336, 187-191 (2012). Link, Final PDF draft.

Andrew C. Oates, Luis G. Morelli and Saúl Ares:
Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock, Development, 139, 625-639 (2012). Link, PDF file.

Daniela Roellig, Luis G. Morelli, Saúl Ares, Frank Jülicher and Andrew C. Oates:
SnapShot: The Segmentation Clock, Cell, 145, 800 (2011). Link
First Enhanced Snapshot ever to be published by Cell, it includes multimedia features.

Leah Herrgen, Saúl Ares, Luis G. Morelli, Christian Schröter, Frank Jülicher and Andrew C. Oates:
Intercellular coupling regulates the period of the segmentation clock, Current Biology, 20, 1244-1253 (2010). Link
Main text, PDF file.
Supplementary text, PDF file.
Article selected for the cover of the issue of July 27, 2010 of Current Biology.

George Kalosakas and Saúl Ares:
Dependence on temperature and GC content of bubble length distributions in DNA, The Journal of Chemical Physics, 130, 235104 (2009). PDF file.
(Both authors contributed equally to this work.)

Luis G. Morelli, Saúl Ares, Leah Herrgen, Christian Schröter, Frank Jülicher and Andrew C. Oates:
Delayed coupling theory of vertebrate segmentation, The HFSP Journal, 3, 55-66 (2009). PDF file.
(LGM and SA contributed equally to this work.)
Selected in the Virtual Journal of Biological Physics Research.

Saúl Ares and Angel Sánchez:
Modelling Disorder: the Cases of Wetting and DNA Denaturation, The European Physical Journal B 56, 253 (2007). PDF file.

Saúl Ares and George Kalosakas:
Distribution of bubble lengths in DNA, Nano Letters 7, 307 (2007). PDF file.

Saúl Ares and Mario Castro:
Hidden structure in the randomness of the prime number sequence?, Physica A 360, 285 (2006). PDF file.

Saúl Ares, Nikos K. Voulgarakis, Kim Ø. Rasmussen and Alan R. Bishop:
Bubble Nucleation and Cooperativity in DNA Melting, Physical Review Letters 94, 035504 (2005). PDF file.
Selected in the Virtual Journal of Biological Physics Research.

Saúl Ares and Angel Sánchez:
Equilibrium roughening transition in a 1D modified sine-Gordon model, Physical Review E 70, 061607 (2004). PDF file.

Saúl Ares, Angel Sánchez and Alan R. Bishop:
Super-roughening as a disorder-dominated flat phase, Europhysics Letters 66, 552 (2004). PDF file.

Saúl Ares, José A. Cuesta, Angel Sánchez and Raúl Toral:
Apparent phase transitions in finite one-dimensional sine-Gordon lattices, Physical Review E 67, 046108, (2003). PDF file.

PhD Thesis (in spanish)

Modelos de Superficies e Intercaras: Transiciones de Fase, Desorden y Aplicaciones
(S. Ares' PhD Thesis: Surface and Interface Models: Phase Transitions, Disorder and Applications).
PDF file in A4 page format (3.3M).
PDF file in B5 page format (3.4M).
My thesis at the archive of Universidad Carlos III de Madrid: link.

Other publications

Saúl Ares, Luis G. Morelli, Koichiro Uriu and Andrew C. Oates:
Formación de patrones en el desarrollo embrionario, Revista Española de Física, Vol. 26, No. 4, 23-30 (2012). PDF file.
Article selected for the issue's cover.

Research stays longer than a month

Institution: Institut Mediterrani de Estudis Avançats (IMEDEA), CSIC-Universitat de les Illes Balears, Palma de Mallorca, Balearic Islands, Spain.
Date: 10/14/2001 - 11/16/2001
Reaserch subject: study of the sine-Gordon model in one dimension.

Institution: École Normale Superiéure de Lyon, Lyon, France.
Date: 02/23/2004 - 04/25/2004
Research subject: DNA dynamics and statistics: hairpin formation.

Institution: Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
Date: 05/18/2004 - 07/18/2004
Research subject: statistical mechanics of DNA: denaturation transition.

Institution: Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
Date: 09/01/2005 - 09/30/2011
Research subject: theoretical studies of embryonic development

Miscellanea

Teaching experience:
Assistant Teacher: 100 hours of classes of Algebra for Technical Engineers, courses 2003-2004 and 2004-2005, Universidad Carlos III de Madrid.
Design and supervision of the one week project Simulation of the central dogma of molecular biology in the Porto Summer School of Physics 2008.
Design and supervision of five one week PhD practicals of the International Max Planck Research School for Molecular Cell Biology and Bioengineering (2007 - 2009).
Two lectures at the PhD Summer School PHYSBIO: Non-equilibrium in Physics and in Biology (St. Etienne de Tinee, France, 2006).
Certificado de Aptitud Pedagogica (CAP, Certificate of Pedagogical Aptitude, Universidad Complutense de Madrid, 2001).

Habilitation from the Spanish Agency for Evaluation of Quality and Habilitation (ANECA) for the positions of Associate Professor (Profesor Contratado Doctor), Private University Professor (Profesor de Universidad Privada) and Assistant Professor (Profesor Ayudante Doctor).

Member of the Spanish Physical Society (since 2002), the European Physical Society (since 2008), the Spanish Society for Biochemistry and Molecular Biology (since 2010) and the Max Planck LeadNet (Max Planck Network of Research Leaders) (since 2011).

Referee for several scientific journals, among them: Physical Review Letters, Physical Review E, Journal of Biological Physics, Europhysics Letters, New Journal of Physics, Chemical Physics Letters, Journal of Physics: Condensed Matter, Physica A, Physica B.

Fluent in English, Spanish, Portuguese and Galician. German: medium level, French: low level.

Operating systems: Linux, UNIX, MacOS and MS Windows administration.

Programming languages: C and FORTRAN.

Mathematical packages: Matlab, Maple, Mathematica.

Graphics: Xmgrace, Gnuplot, Xfig, GIMP, Adobe Illustrator.

Image processing: ImageJ, FIJI.

Text processing: L^ATEX, OpenOffice, StarOffice, MS Office.