Positions available
Jan 2024 lab currently full.
Sept-Oct 2023 : 2 postdoc positions available in the lab after PhD : Filled
1-Neuroscience, computer science, statistics and clinic. Signal processing and classification methods in neuroscience requires deep applied mathematics. During anesthesia the electro-encephalogram (EEG) reveals transient events such as alpha spindles or burst suppressions. In the past, we have developed neuronal network modeling to study the transition from one state to another. The models could reproduce in part the dynamics of thalamo-cortical loops [1,2]. The goal of this postdoc is to develop a real-time classification from EEG, respiratory and blood markers a prediction of deep-sedation using classfication approaches.
contact : David Holcman <david.holcman chez ens.fr>
2-Neuroscience, computer science, statistics and clinic. Using exceptional data based on EEG and neuropixel, we aim at studying deep-sedation by analyzing the thalamo-cortical loop. The project consists in developing data analysis of brain signal, modeling and identifying novel pattern. Ideal for somebody passionate about decoding neuronal plasticity.
contact : David Holcman <david.holcman chez ens.fr>
asap.
September 2022 : The Holcman’s group is looking for a CNRS engineer that would like to join the lab [not an external recruitment] to take part of our effort :
– Research and development on real-time algorithm, DL, classification algorithms, developments of general softwares, voice recognition, image segmentation.
– Large databases management of EEG, ECG, Single trajectory, calcium imaging
– software organization,management
– Website administration
– Programing python,matlab,etc...
Applications : cell biology, neuroscience, clinical data.
contact : David Holcman <david.holcman>
November 2021 : 5 Positions available under ERC-Adv to the lab :
contact :
David Holcman <david.holcman chez ens.fr>
Position 1 : Master+PhD FILLED
Title : Extracting patterns to predict the output of coma from EEG
Project : We aim to extract novel features from combining multiple EEGs recording obtained in coma patients receiving auditory inputs. We shall use an existing data basis and our goal is to construct a general decision methodology based on classification approaches, wavelets, to predict the state of a patient in coma.
Working conditions : the research involves The groups S. Jaffard (Creteil U.) and D. Holcman (ENS) dedicated to Wavelets, Applied Mathematics and Computational biology offer a joint training period at a Master level for continuing on a PhD. Fields covered are signal processing of EEG, connecting devices, stochastic processes, classification, ML-methods and large data analysis. The project is in collaboration with Pr. N. Kubis (Lariboisiere Hospital, Paris) and Pr. R. Sonneville (Bichat hospital).
Candidate : The candidate for this position is expected to be strongly motivated by signal processing and medical sciences. He/she should have a background in applied mathematics. The candidate should be passionate by her/his research. Students are encouraged to write a publication at the end of the training period. We strongly encourage student motivated to continue on a PhD thesis. The group has a strong tradition in training students that are joining top international institutions.
Position 2 : Postdoc/PhD
Title : Multiscale modeling and simulations of electro-diffusion, calcium dynamics in mitochondria.
Project : This project concerns the analysis of current and voltage in mitochondria (coll. E. Korkotian W. Institute). We propose to develop a novel model of electro-diffusion using Poisson-Nernst-Planck (PNP). PNP in microdomains can be used to predict the distribution of voltage. The model use PDE. The candidate will use Comsol to generate simulation. We propose to simulate the current flow inside channels account for the geometry and the different ions. The model will be used to better understand the Calcium-Voltage relation and ATP genesis.
Candidate : The candidate for this position is expected to be strongly motivated by numerical simulations, biophysics, analysis and biological sciences. He/she should have a background in simulations, theoretical chemistry, physics or applied mathematics. The candidate should be passionate by her/his research. Students are encouraged to write a publication at the end of the training period. We strongly encourage student motivated to continue on a PhD thesis. The group has a long tradition in training Phds and postdocs.
Position 3 : Postdoc/PhD
Title : Modeling and Analysis of large amount of single particle trajectories of super-resolution images in cellular biology
Project : This project concerns the analysis of hundreds of thousands of single stochastic particle trajectories to extract biophysical parameters of live cell organization in collaboration with the groups of S. Basu, E. Laue (U of Cambridge) and C. Obara from J. Lippincott-Schwartz group (Janilia). Possibility to spend times in Cambridge.
Our aim is to extract novel features in experimental data by developing stochastic analysis in parallel with image processing to correlate the position of trajectories with objects that lie below the diffraction limit. The second step is to compute statistical quantities such as residence times. We will apply this approach to the cell nucleus and the synapse of neurons.
Refs.
– Basu, S., Shukron, O., Hall, D., Parutto, P., Ponjavic, A., Shah, D., ... & Laue, E. D. (2021). Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics. Biorxiv, 2020-04.
– D. Holcman N.Hoze, Statistical methods for large ensemble of super-resolution stochastic single particle trajectories, Annual Review of Statistics and Applications, 2017,4 1-35
Candidate : The candidate for this position is expected to be strongly motivated by mathematical and application to the biological sciences. He/she should have a background in applied mathematics. The candidate should be passionate by her/his research. Students are encouraged to write a publication at the end of the training period. We strongly encourage student motivated to continue on a PhD thesis. The group has a strong tradition in training students that are joining top international institutions.
Position 4 : Msc
Title : Image processing, modeling and data classification to study the spatial organisation and migratory routes of microglial cells in the embryo
Project :
The aim of this project is to use labelled tissues across the entire embryo in the sagittal plane, to provide a spatiotemporal characterisation of migrating versus non-migrating cell distributions within and between different stages. Using Machine-learning and image processing, we will identify the population grows from one stage to the next by looking at proliferation. Because these cells enter the brain from the periphery, we will use the present classification to identify routes of entry into the forebrain, midbrain and hindbrains.
Outcome
This research will clarify the spatiotemporal distributions of the cells using an unbiased mathematical approach. The classification approach will be used result to study how cell destination depends on morphogenic gradients.
Location and Duration : U. of Cambridge, least 3 months.
Candidate : The candidate for this position is expected to be strongly motivated by signal processing and medical sciences. He/she should have a background in applied mathematics. The candidate should be passionate by her/his research. Students are encouraged to write a publication at the end of the training period. We strongly encourage student motivated to continue on a PhD thesis. Both groups have a strong tradition in training students that are joining top international institutions.
Position 5 : Engineer or Postdoc
Development of a SaaS application for EEG analysis
Prerequisites for the job at an engineering level :
The candidate should be highly motivated and interested in scientific computing. They are expected to have a strong background in computer science, in particular being familiar with object-oriented programming, web applications, version control, and software testing. Tasks will be assigned either on backend or frontend development depending on the candidate technical skills.
Preferred skills for the backend include
● Python
● Scipy ecosystem
● Python web frameworks (e.g. django, flask)
● RDBMS (e.g. MariaDB, Postgres)
Preferred skills for the frontend include
● HTML & CSS
● Javascript
● Frontend frameworks (e.g. React, Vue) and the Flux architecture
Ideally, the candidate will have a record of at least one previous project.
Background
A large quantity of medical data is routinely acquired in hospitals, but accurate and patient-tailored analysis of these data by specialists is often impossible due to technical constraints and limited time. We developed mathematical models to automatically analyse physiological data such as electroencephalographic recordings (EEG), extracting information that can help practitioners in the decision making. To deploy this novel approach, we need to provide an easily accessible software as a service (SaaS) application that will allow to load patient data and obtain personalized reports and predictions.
Goal : Developing a SaaS for EEG analysis
The candidate will contribute to the development of a SaaS product addressed to medical doctors. The application will implement models to analyze the brain activity based on EEG and extract variables of interest. A web interface will allow access to the results of mathematical analysis and provide user-friendly visualizations.
contact :
David Holcman <david.holcman chez ens.fr>
October 15 2019 :
Few postdoc positions are now available in
1-Electrodiffusion-Analysis-simulations of nanocompartment (Applied mathematics/physics)
2-Analysis of EEG-simulations network (Applied math./computer-science)
3-Analysis of trajectories
Master positions
1-EEG analysis (Computer science/applied math/physics).
2-Building an operational web platform to analyze EEG (Computer science/applied math/physics).
3-Real time EEG analysis during surgery (Computer science/applied math/physics).
4-Simulation and analysis of Electro-diffusion in neurons.
5-Analysis of super-resolution trajectories.
SEND YOUR CV before Deadline November 15 2019
david.holcman attt ens.fr
Jan 2019 : FILLED
Position available !! URGENT !!
SEND YOUR CV before Deadline Jan 31 2019
The group of D. Holcman (ENS) dedicated to Applied Mathematics and Computational biology offers a postdoc. Fields covered are , modeling polymer, simulation, analysis, chromatin and data analysis.
Title : Analysis, modeling and simulations to reconstruct the cell nucleus organization and the chromatin dynamics from HiC data of cancer cells.
Project :
We recently developed several new methods to reconstruct the chromatin organization from large contact map matrices, using coarse-graining and stochastic polymer models. Our goal is now to develop models of chromatin and representation to study changes of chromatin under stress conditions or across a developing tissue, including immune and cancer cells.
The goal of this postdoc is to develop polymer model, simulations, data in collaboration with experimental groups.
Project is in Collaboration with Daan Noordermeer (Orsay).
Some Refs.
– A.Amitai, D. Holcman, Encounter time of two chromatin loci is governed by polymer de-condensation and modification of local interactions, submitted Phys. Rev.E ;97(3-1):032417. doi : 10.1103/PhysRevE.97.032417. 2018.
– O. Shukron D. Holcman, Polymer model reconstruction from chromosomal capture data and stochastic simulations of transient encounters, PLoS Comput Biol 13 (4), e1005469 2017.
– Shukron M. Hauer, D. Holcman, First passage time statistics in two locus chromatin single trajectories, Scientific Report, 2017.
– A Amitai, D Holcman, Polymer physics of nuclear organization and function Physics Reports 678, 1-83 (2017).
– O. Shukron, V.Piras, D Noorderdaam, D. Holcman, Statistics of cross-linked chromatin organization during cell differentiation reconstructed by heterogeneous polymer models (revision) Nat. Comm 2018.
Duration : at least 2-3 years.
Candidate : The candidate for this position is expected to be strongly motivated by mathematical/physical and biological sciences. He/she should have a background in applied mathematics/stat phys/theoretical physics or compt. biology. The candidate should be passionate by her/his research. Students are encouraged to write publications.
Contact information :
David Holcman,
46, rue d’Ulm, 75005 Paris, France
Email : david.holcman chez ens.fr
webpage : www.biologie.ens.fr/bcsmcbs/