This page contains links and references to papers I published in international scientific journals. Here below is a list of selected papers published in the field of

  • NGS analysis
  • System Biology
  • Plant Science
  • Gravitational Waves.
A full list of publications from Spires is also available with 70+ papers and proceedings. If you do not have access to the PDF files form the journal sites, you may want to look at some of them in the arXiv. Additionally, I worked in Plant Science and some proceedings and conferences links from the VirtualPlants team are also available.

I'm trying to keep a full list of publications. Finally, my google scholar page and ResearchGate page provide also complete list of publications and proceedings.



Sequana coverage: detection and characterization of genomic variations using running median and mixture models

Figure: coverage (number of reads mapping on the genome; here measles virus) in black. Sequana_coverage extract/detect outliers (above and below the red line) using a running median approach (blue line) combined with gaussian mixture models and clustering. HTML reports are given as a convenient way to explore the events.
Author(s): Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer
Journal reference: GigaScience, Volume 7, Issue 12, December 2018, giy110





Phosphoproteomic analyses reveal novel cross‐modulation mechanisms between two signaling pathways in yeast

Figure: The pheromone and HOG pathways (PW) of Saccharomyces cerevisiae
Author(s): Stefania Vaga, Marti Bernardo‐Faura, Thomas Cokelaer, Alessio Maiolica, Christopher A Barnes, Ludovic C Gillet, Björn Hegemann, Frank van Drogen, Hoda Sharifian, Edda Klipp, Matthias Peter, Julio Saez‐Rodriguez, Ruedi Aebersold
Journal reference: Molecular System Biology 2014, 10:767

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

Figure: MEIGO workflow.
Author(s): Jose A Egea, David Henriques, Thomas Cokelaer, Alejandro F Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R Banga and Julio Saez-Rodriguez
Journal reference: BMC Bioinformatics 2014, 15:136

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

Figure: Strategy used by participants to spend credits on experiments
Author(s): Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M Sauro, Gustavo Stolovitzky and Julio Saez-Rodriguez
Journal reference: BMC Systems Biology 2014, 8:13


Authors: C. Chaouiya et al.
Journal reference: BMC Systems Biology BMC systems Biology 2013, 7:135

BioServices: a common Python package to access biological Web Services programmatically

Author(s):Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach and Julio Saez-Rodriguez
Journal reference: Bioinformatics, 29 (24) 3241-3242 (2013)

Searching for gravitational waves from binary coalescence

Author(s):S.Babak et al
Journal reference: Phys. Rev. D 87, 024033 (2013)

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Figure: Models generated with caspo
Author(s): Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Journal reference: Bioinformatics(2013) 29 (18) 2320-2326
Figure: comparison of algorithm performances by transcription factor

Evaluation of methods for modeling transcription factor sequence specificity.

Author(s): Matthew T Weirauch et al
Journal reference: Nature Biotechnology 31, 126-134 (2013)


Figure: Different formalisms used in CellNOptR

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Author(s): Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel Goncalves, Melody K Morris, Martijn van Iersel, Douglas A Lauffenburger and Julio Saez-Rodriguez
Journal reference: BMC Systems Biology 6 (1), 133
Figure: branching and tree modelisation and visulation using L-systems and Python

L-Py: an L-System simulation framework for modeling plant development based on a dynamic language

Author(s): Boudon F, Pradal C, Cokelaer T, Prusinkiewicz P, Godin, C


Figure: workflow using VisuAlea

VisuAlea: Towards a Scientific Modelling Environment using Visual Programming

Author(s): Christophe Pradal, Daniel Barbeau, Thomas Cokelaer, Eric Moscardi
EuroScipy 2010


Figure: Variation of spin and angular momentum of spinning black holes

Template banks to search for compact binaries with spinning components in gravitational wave data

Author(s): Chris Van Den Broeck, Duncan A. Brown, Thomas Cokelaer, Ian Harry, Gareth Jones, B. S. Sathyaprakash, Hideyuki Tagoshi, Hirotaka Takahashi
Journal reference: Phys. Rev. D 80, 024009 (2009), Citing Articles (8)
Export: Bibtex version , arXiv link: 0904.1715


Parameter Estimation Of Inspiralling Compact Binaries In Ground-Based Detectors: Comparison Between Monte Carlo Simulations And The Fisher Information Matrix

Author(s): T. Cokelaer
Export: Bibtex version
Figure: accidental events and detected simulated injections

Search for gravitational waves from binary inspirals in S3 and S4 LIGO data

Author(s): LIGO Scientific Collaboration, B. Abbott et al., Corresponding author: T. Cokelaer
Journal reference: Phys. Rev. D 77, 062002 (2008), Citing Articles (59)
Export: Bibtex version , arXiv link: 0704.3368

A Template Bank to Search for Gravitational Waves from Inspiralling Compact Binaries: II. Phenomenological Model

Author(s): T. Cokelaer
Export: Bibtex version , arXiv link: 0709.1050
Figure: Hexagonal template bank placement to search for coalescing binaries in LIGO detectors

Gravitational waves from inspiralling compact binaries: Hexagonal template placement and its efficiency in detecting physical signals

Author(s): T. Cokelaer
Journal reference: Phys. Rev. D 76, 102004 (2007), Citing Articles (24)
Export: Bibtex version , arXiv link: 0706.4437

Search for gravitational waves from binary black hole inspirals in LIGO data

Author(s): LIGO Scientific Collaboration, B. Abbott et al.
Journal reference: Phys. Rev. D 73, 062001 (2006), Citing Articles (44)
Export: Bibtex version , arXiv link: 0509129

A template bank to search for gravitational waves from inspiralling compact binaries: I. Physical models

Author(s):S Babak, R Balasubramanian, D Churches, T Cokelaer and B S Sathyaprakash
Class. Quantum Grav. 23 No 18 (21 September 2006) 5477-5504
(include in the Highlights of 2006/2007)
Abstract and download: gr-qc/0604037

GEO600 Online Detector Characterization System

Author(s): R Balasubramanian, S. Babak, D Churches, T Cokelaer
Class. Quantum Grav. 22 (2005) 4973-4986
Abstract and download: gr-qc/0504140v1

Report on the search for binary black holes inspiral in S3 LIGO data.

Author(s): By LIGO Scientific Collaboration (T. Cokelaer for the LIGO collaboration).
Prepared for 6th Edoardo Amaldi Conference on Gravitational Waves (Amaldi6), Kise Nago, Okinawa, Japan, 20-24 Jun 2005. Published in J.Phys.Conf.Ser.32:29-34,2006.
Abstract and download: jpconf6_32_006

Searching for Gravitational Waves from Binary Inspirals with LIGO

Author(s): Duncan A. Brown, Stanislav Babak, Patrick R. Brady, Nelson Christensen, Thomas Cokelaer, Jolien D. E. Creighton, Stephen Fairhurst, Gabriela Gonzalez, Eirini Messaritaki, B. S. Sathyaprakash, Peter Shawhan, Natalia Zotov
Class.Quant.Grav. 21 (2004) S1625-S1633
Abstract and download: gr-qc/0705.1572