Thomas Cokelaer

Thomas Cokelaer
Institut Pasteur · C3BI-HUB bioinformatics and biostatistics

40.83
 · 
PhD
About
213
Research items
39,348
Reads
6,478
Citations
Introduction
Thomas Cokelaer currently works at the C3BI-HUB bioinformatics and biostatistics, Institut Pasteur. Thomas does research in Molecular Biology, Cell Biology and Cancer Research. Their current project is 'DREAMTools: a Python package for scoring collaborative challenges'.
Research Experience
Jan 2016
Institut Pasteur International Network
Position
  • Research Engineer
Oct 2015 - Dec 2015
Wellcome Sanger Institute
Position
  • Bioinformatician
Aug 2011 - Aug 2015
EMBL-EBI
Position
  • Research staff
Network
Cited By
Followers
Following
Research
Research items (213)
Article
Full-text available
We designed a PyQt graphical user interface - Sequanix - aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit confi...
Preprint
Full-text available
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 co...
Article
Genomic features are used as biomarkers of sensitivity to kinase inhibitors used widely to treat human cancer, but effective patient stratification based on these principles remains limited in impact. Insofar as kinase inhibitors interfere with signaling dynamics, and, in turn, signaling dynamics affects inhibitor responses, we investigated associa...
Article
Full-text available
Background Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to map experimental data onto reference biological n...
Article
Therapies targeting specific molecular processes, in particular kinases, are major strategies to treat cancer. Genomic features are commonly used as biomarkers for drug sensitivity, but our ability to stratify patients based on these features is still limited. As response to kinase inhibitors is a dynamic process affecting largely signal transducti...
Article
Full-text available
Background: Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to calibrate experimental data onto reference biolo...
Article
Full-text available
Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancer-driven alterations identified in 11,289 tumors from 29 tissues (integrating somatic mutations, copy numbe...
Article
Full-text available
It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silic...
Article
On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-wave Observatory (LIGO) simultaneously observed the binary black hole merger GW150914. We report the results of a matched-filter search using relativistic models of compact-object binaries that recovered GW150914 as the most significant event during th...
Article
Full-text available
DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational medicine. Each challenge asks participants to develop and apply computational methods to either predict unobserved outcomes or to identify unknown model parameters given a set of training data....
Article
Full-text available
Unlabelled: DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational medicine. Each challenge asks participants to develop and apply computational methods to either predict unobserved outcomes or to identify unknown model parameters given a set of tr...
Article
Full-text available
The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, l...
Article
Full-text available
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional deregulations within human cells (e.g., cancers). In this context, we present several python packages linked t...
Article
Full-text available
Cells respond to environmental stimuli via specialized signaling pathways. Concurrent stimuli trigger multiple pathways that integrate information, predominantly via protein phosphorylation. Budding yeast responds to NaCl and pheromone via two mitogen-activated protein kinase cascades, the high osmolarity, and the mating pathways, respectively. To...
Article
Full-text available
Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dial...
Article
Full-text available
Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present...
Article
Full-text available
Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for accomplishing such tasks. While significant progress has been made, effective experimental strategies for parameter identification and for dist...
Article
Full-text available
Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific c...
Article
Full-text available
Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g.,...
Article
Full-text available
Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima nor to report the complete fam...
Article
Full-text available
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein's DNA-binding specificity, but these methods have not been systematically compared. Here we applied 26 such approaches to in...
Article
Full-text available
This paper reports on an all-sky search for periodic gravitational waves from sources such as deformed isolated rapidly spinning neutron stars. The analysis uses 840 hours of data from 66 days of the fifth LIGO science run (S5). The data were searched for quasimonochromatic waves with frequencies f in the range from 50 to 1500 Hz, with a linear fre...
Article
Full-text available
A stochastic background of gravitational waves is expected to arise from a superposition of a large number of unresolved gravitational-wave sources of astrophysical and cosmological origin. It should carry unique signatures from the earliest epochs in the evolution of the Universe, inaccessible to standard astrophysical observations(1). Direct meas...
Chapter
Full-text available
MAppleT is a functional-structural plant model that has been built for simulating architectural development of apple trees. It has the capability of representing tree growth within a virtual space where the development of individual organs depends on geometrical traits. The purpose of this research is to investigate the influence of apple trees' ar...
Article
Full-text available
Background Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand signaling both in physiological and diseased situations. Context-specific medium/high throughput proteomic data measured upon perturbation is now relatively easy to obtain but formali...
Data
Full-text available
Experimental setting for the HepG2 analysis. HepG2 cells were stimulated with the above stimuli in combination with the above-mentioned inhibitors in different combinations. The 16 species mentioned here were then measured using a luminex assay at 30 minutes and 3 hours post stimulation, leading to a total of 136 samples. All species are mentioned...
Data
Full-text available
Summary of results from 3 independent trainings for the HepG2 example. Frequency of selection of each edge in the scaffold model, across all models with a score within 10% of the best scoring model, summarized across 3 independent training runs. The top panel shows the summary for the edges at time 1and the bottom panel shows the equivalent for tim...
Data
Full-text available
Example of results for the HepG2 real data application. A. Previous knowledge network used for this analysis. B. Example of a trained model obtained in one of the optimization round, with a subset of the simulation results obtained with this network (C). For the networks the color codes are as follows: nodes: green=stimulated, red=inhibited, blue=m...
Data
Full-text available
Exploration of an asynchronous updating scheme for the CNORdt extension. This figure shows the results obtained by training the toy model to data as in Figure 2 but using an asynchronous updating scheme with random firing order of the activation rules, in development for the CNORdt extension. We can see that asynchronous updating adds no new inform...
Data
Full-text available
Technical aspects of the HepG2 analysis. This file provides additional information regarding this analysis, such as the parameters used etc.
Article
Full-text available
We describe the implementation of a search for gravitational waves from compact binary coalescences in LIGO and Virgo data. This all-sky, all-time, multi-detector search for binary coalescence has been used to search data taken in recent LIGO and Virgo runs. The search is built around a matched filter analysis of the data, augmented by numerous sig...
Article
Full-text available
The study of plant development requires increasingly powerful modeling tools to help understand and simulate the growth and functioning of plants. In the last decade, the formalism of L-systems has emerged as a major paradigm for modeling plant development. Previous implementations of this formalism were made based on static languages, i.e., langua...
Article
The efficiency of light interception is a driving factor for plant transpiration and photosynthesis, and contributes greatly to plant growth. For a fruit tree, the efficiency of light interception is also a key factor to improve yield quality. Such efficiency is highly dependent on the tree geometrical and topological organisation which may vary be...
Article
We present a search for gravitational waves from 116 known millisecond and young pulsars using data from the fifth science run of the LIGO detectors. For this search, ephemerides overlapping the run period were obtained for all pulsars using radio and X-ray observations. We demonstrate an updated search method that allows for small uncertainties in...