Curriculum Vitae

Nils Giordano, PhD


Computational Systems Biologist
Microbial communitiesMetabolic ModelingData ScienceMetagenomics

Fluent in Biology, Maths, and Computer Sciences
Love smart code, elegant equations, and Life’s fundamental laws


Research experience

Jan. 2018 - present

Postdoctoral Researcher at LS2N CNRS UMR 6004 (Nantes, France)

Close collaborators: Dr. Samuel Chaffron (Computational Biology team, LS2N, CNRS) & Dr. Damien Eveillard (Computation Biology team, LS2N, Université de Nantes)

  • Project: From Environmental Omics to Eco-Systems Metabolic Modeling of Microbial Communities
Sep. 2012 - Mar. 2017

Research and Teaching Assistant (PhD Student) at Université Grenoble Alpes – INRIA (Grenoble, France)

Supervisors: Dr. Hidde de Jong (Project-team Ibis, INRIA) & Pr. Johannes Geiselmann (team BIOP, LIPhy)

  • Led a theoretical and experimental study of resource allocations in bacterium E. coli

  • Used Optimal Control Theory principles to show that unexpected resource allocation behaviors can be predicted by assuming that bacteria optimize growth (published in Plos Comp. Biol.)

  • Engineered and monitored cells with fluorescent ribosomes using a microplate reader, microscope and microfluidic device

Feb.-Jun. 2012

Research Assistant (Intern) at INRIA (Grenoble, France)

Supervisors: Dr. Hidde de Jong & Dr. Delphine Ropers (Project-team Ibis, INRIA)

  • Reviewed and implemented state-of-the-art methods of sensitivity analysis on a complex model of the gene expression machinery in bacterium E. coli

  • Developed a brand-new dynamical method of global sensitivity analysis

  • Helped to identify the key parameters driving the model dynamics and to reduce its complexity

Feb.-Jun. 2011

Research Assistant (Intern) at University of Cambridge – DAMTP (Cambridge, United Kingdom)

Supervisor: Pr. Raymond E. Goldstein (Goldstein lab, University of Cambridge)

  • Led a theoretical study about the evolution towards multicellularity in microalgae (Volvocales)

  • Developed a general model of phosphate uptake and growth in microalgae

  • Explored the role of the extracellular matrix for phosphate storage, especially in changing environments

Jun.-Jul. 2010

Research Assistant (Intern) at École Normale Supérieure (Paris, France)

Supervisor: Dr. Silvia de Monte (Eco-evolutionary Mathematics, IBENS)

  • Analyzed time-series fluorescence data of oscillating yeast cells suspensions subject to periodic forcing

  • Modified an existing mathematical model based on Hopf bifurcation to recreate the observed dynamics

  • Showed that even when an irrational forcing is applied, the biological system does not exhibit any chaotic behavior (published in Journal of Computational Interdisciplinary Sciences)

Teaching experience

Sept. 2013-Aug. 2016

Teaching assistant; Université Grenoble Alpes (Grenoble, France), 229 hours

  • Bioinformatics: from genome analysis to modeling (BSc)
    This introductory course was taught to 2nd-year students in collaboration with Dr. Thierry Gautier. I was in charge of the part about modeling, which means I was responsible for choosing the content, designing and teaching the lectures, tutorials, and practical exercices, but also designing the final exam and grading.

  • Population genetics, conservation biology, biodiversity and evolution (BSc and MSc)
    These different courses were taught from 2nd-year to 4th-year students. I mostly supervized tutorials and helped to design and grade the final exams.

  • Prokaryotic genetics and microbiology (BSc)
    This course was taught to 2nd-year students. I supervized tutorials and practical exercices at the bench.

  • Modeling and simulation of genetic regulatory networks (MSc)
    This course was taught to 5th-year students. It was organized for students of École Normale Supérieure, and taught in collaboration with Dr. Hidde de Jong. I helped to choose the content, teach the lectures and supervize the practical exercices. I also helped to design and grad the final exam.

Education

2017

PhD, Systems Biology – Université Grenoble Alpes (Grenoble, France)

  • Title: Microbial growth control in changing environments: Theoretical and experimental study of resource allocation in Escherichia coli
  • Supervisors: Dr. Hidde de Jong & Pr. Johannes Geiselmann
  • Laboratories: Project-team Ibis (INRIA Grenoble – Rhône-Alpes) and team BIOP (Laboratoire Interdisciplinaire de Physique, Université Grenoble Alpes)
2012

MSc, Cell Systems Biology with honours – École Normale Supérieure & Université Pierre et Marie Curie (Paris, France)

  • 2nd year: Gene regulatory networks, cell ecosystems, cell machinery, microscopy (quantification, image processing), graph theory, comparative genomics, population genetics, structural bioinformatics, modeling of biopolymers

  • 1st year: In silico biology, genes and genomes, from gene to function, ecological systems biology, biophysics, biomathematics

2010

BSc, Life sciences with honours – École Normale Supérieure & Université Pierre et Marie Curie (Paris, France)

  • Experimental practice, ecology, physiology, molecular and cellular biology, genetics and epigenetics, bioinformatics, statistics, biomathematics, statistical and optical physics, weak-bond chemistry, modeling in biology
2009-2013

ENS Diploma – École Normale Supérieure (Paris, France)

  • French leading research school, selected via a national competitive exam

Publications

2017
Mathematical Modeling of Microbes: Metabolism, Gene Expression, and Growth
de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé J-L
Journal of The Royal Society Interface. 14.136 (2017): 20170502.
2016
Dynamical allocation of cellular resources as an optimal control problem: Novel insights into microbial growth strategies.
Giordano N, Mairet F, Gouzé J-L, Geiselmann J, de Jong H.
PLoS Computational Biology. 2016;12(3):e1004802.
2012
Dynamical responses of oscillating yeast cells suspensions to periodic forcing.
Giordano N, D’Ovidio F, Danø S, Sørensen PG, De Monte S.
Journal of Computational Interdisciplinary Sciences. 2012;3(2):77–86.

Technical skills

Computing

  • Daily user of Python, Git, and Unix/shell scripting.

  • Experienced with Matlab/Octave, Scilab, R, PHP, SQL, HTML/CSS.

  • Curious about Julia, Ruby, Rust

Mathematics

  • Proficient in data analysis and modeling, in particular linear and non-linear dynamical systems.

  • Familiar with time-series analysis, image analysis, sensitivity analysis. More recently Kalman filtering, calculus of variations and optimal control theory.

  • Curious of statistics, graph theory, molecular modeling, machine learning (deep-learning).

Biology

Bioinformatics
Metagenomics, next-generation sequencing
Molecular biology
Cloning (molecular design, overlap PCR, Gibson assembly), chromosomic modifications (electroporation, lambda-red recombineering)
Laboratory Robotics
Microplate reader (Perkin Elmer, Tecan), fluorescence microscope (Zeiss), microfluidic device (Mother machine)

Languages

French
Native speaker
English
Fluent
Italian
Basic

Extracurricular activities

  • Outdoor and indoor climbings (~ 6A/B outdoor, 6B/C indoor, french quotations)
  • Contributor on bioinfo-fr.net, a communautary French blog for bioinformaticians
  • Member of RSG France – JeBIF, the French society for young bioinformaticians
  • Advocate for the open-source and libre cultures


Nantes (France)