- Comp-neuro - lists.cnsorg.org

Post-doc or Research Engineer position offer: Computational modeling of genetic mutations at cellular level

by Elif Köksal

*Context.* Developmental and epileptic encephalopathies (DEEs) are a group of severe rare diseases where the combined effect of seizures, most often drug resistant, and the non-seizures consequences of the disease etiology, often genetic, entail a debilitating encephalopathy with drastic effects on the neurodevelopmental, psychiatric, and motor abilities of the patients. DEEs due to potassium channel mutations (K-DEEs) are emblematic of this disease presentation. *Rationale.* The mechanisms underlying the relationship between i) the molecular effect of a gene mutation (KCNB1/KCNT1/KCNA2) on specific voltage gated potassium channel function, and ii) the patient-specific phenotypes observed in scalp-recorded EEG signals remain elusive. Computational models inspired from neuronal physiology is now recognized as a most efficient way to bridge the gap between i) changes occurringat the level of neurons and neuronal circuits and ii) electroencephalographic (EEG) signals recorded in patients containing markers of the underlying pathology. *Objective.* The objective of the proposed research position is to design novel neuro-inspired models taking into account the molecular effect of a gene mutation on the specific voltage-gated potassium (K) channel function and the specific phenotypes observed in patients (scalp-recorded EEG signals) and in genetically-modified mice (local field potentials) in which downregulation or upregulation of K channels is induced. *Methods*. Detailed multicompartment models (i.e. including dendrites, soma and axon) will be developed. They will be based on Hodgkin and Huxley's (HH) formalism. They will describe both passive (membrane capacitance, axial resistivity, leakage conductance, and membrane time constant) and active (voltage-gated and ligand-gated ion channels) membrane properties. The channel pathogenic variants of KCNB1/KCNT1/KCNA2 mutations identified in 2 other work packages (1 & 2) will be inserted in the membrane in order to study the impact of the channel mutation on the firing rate curves of considered neuron subtypes, typically pyramidal neurons (PYR), somatostatin (SST-), parvalbumin (PV-), and vasoactive intestinal polypeptide (VIP-) positive interneurons. Optimization methods will be developed for identifying optimal parameters minimizing the distance between real and simulated electrophysiological signals (LFPs). Models will use the Hodgkin & Huxley formalism. They will be developed in Python. They will extend already-existing models at cellular level. Strong background is available ( https://perso.univ-rennes1.fr/fabrice.wendling/) *Scientific domains.* Engineering (computational, biomedical); Neuroscience; Neurology; Computer Science (implementation of Python routines into an existing software application named COALIA). *Scientific environment.* This research will benefit from an outstanding clinical research environment, centeredaround the largest curated K-DEE cohorts, coordinated by the Necker reference center for rare epilepsies (Prof. Rima Nabbout), and assembling an extensive group of experts from various specializations, including clinical,electrophysiological, psychological, computational, translational research, biotechnology and pharma industry. *Candidate profile.* The research project is at the interface between biomathematics (neuro-inspired models) and neuroscience/neurology (epilepsy). The Post-doc/Engineer fellow (PhD level) will preferably have a strong background in computational neuroscience/systems biology or in electrical engineering with experience in bio-signal processing. Knowledge in electrophysiology and/or EEG analysis would be an asset. *Contract *The position will be opened March. 1st, 2024 (flexible). The contract is for 3 years (flexible). The employer is the University of Rennes. The competitive salary will be according to experience (2300 Euros net, minimum). The candidate will also have access to the French system benefits. Location in the city of Rennes, France. LTSI-Inserm laboratory, University of Rennes. In addition, the hired person will have the opportunity to actively collaborate with other groups involved in the innov4epik RHU project (2024-2029), funded by the French National Research Agency (ANR). *Contact (please provide resume, cover letter and email of 2 references)* Pascal Benquet (Prof Univ Rennes, LTSI, France) Email: pascal.benquet(a)univ-rennes.fr Fabrice Wendling (DR Inserm, LTSI, France) Email: fabrice.wendling(a)inserm.fr

Jan. 30, 2024

PLENA 2024 - Pucon Learning and AI Summit

by Prof Sonja Gruen

Dear Colleagues, The Pucón Learning and AI (PLENA) Summit https://plena.cenia.cl is taking place in the South of South America, in Pucon, Chile this April 8 -12, 2024. Check Chile out here https://www.youtube.com/watch?v=RK3Ou8vq84Y and https://www.youtube.com/watch?v=eSYpegYD4jc . We invite you to explore the intersection of neuroscience and AI, with a particular focus on mechanisms of learning. PLENA is a small gathering of experts and trainees that will provide a platform for AI and experimental neuroscience researchers to delve into the mechanisms of learning at the cellular, systems, and behavioral levels. Upon multiple requests we have set up a rolling application extending to March 8th, 2024. Secure your place by applying as soon as possible. We will be selecting on a first-come-first-serve basis until we have reached our capacity of 120 researchers and trainees. Register here: https://plena.cenia.cl/registration/ See our spectacular and diverse lineup of speakers here: https://plena.cenia.cl/speakers/ We have also added a coordinated sequence of three workshops entitled Bridging Scales from Neural Activity to Learning Machines “from the detailed analysis of neuronal activity to the construction and simulation of full-scale models to the application of abstract learning machines”. Access is included with your registration. Access is included with your registration. See you in Chile! PLENA Scientific Committee: Roberto Araya (U. Montreal, Canada) Christopher Pack (McGill University, Canada) Pedro Maldonado (Universidad de Chile, Chile) Markus Diesmann (Jülich Research Center, Germany) We thank our sponsors, partners and affiliated institutions -- Prof. Dr. Sonja Gruen, Director Inst of Neuroscience and Medicine (INM-6/-10) Tel +49-2461-61-4748 (secr) Computational and Systems Neuroscience & tel +49-2461-61-9301 (lab) Institute for Advanced Simulation (IAS-6) Mob +49-175-2972436 Jülich Research Centre and JARA Institute I Jülich, Germany Theoretical Systems Neurobiology RWTH Aachen University, Aachen, Germany www.csn.fz-juelich.de elephant.readthedocs.io

Jan. 30, 2024

Computational neuroscience PhD position in the Mejias lab at Amsterdam

by Jorge Mejias

Dear all, The Mejias lab and the Cognitive and Systems Neuroscience Group at the University of Amsterdam are seeking a highly qualified and motivated candidate for a PhD position in Computational Neuroscience. The position falls under the Horizon Health Europe Consortium grant “Virtual Brain Twins for Personalized Treatment of Psychiatric Disorders”. This Consortium constitutes a large collaboration between different European institutions, aiming to develop personalized brain simulation software (“virtual brain twins”) to improve the diagnosis and treatment of schizophrenia. The main objective of this PhD project is to develop a biologically realistic computational model of the human brain, and use it to study alterations in brain activity associated with schizophrenia. Such model will make use of local neural mass models (developed by our Consortium partners) to simulate multiple brain areas, and will bring them together using structural connectivity data from human subjects. The model will be then used to explore the effects of schizophrenia-related alterations in brain dynamics and function, and to derive patient-specific virtual brain simulations to improve diagnosis and explore treatments in collaboration with clinical Consortium partners. The project will be supervised by Dr. Jorge Mejias, principal investigator in computational neuroscience and leader of the Dutch component of the Consortium, and by Prof. Dr. Cyriel Pennartz, head of the Cognitive and Systems Neuroscience Group. You will closely collaborate with other Consortium members, particularly with the team of Prof. Viktor Jirsa at Aix-Marseille University, and will also benefit from interactions with local colleagues including other theoretical, computational and experimental neuroscientists at the Cognitive and Systems Neuroscience Group. We are looking for candidates with: • a Master's Degree in computational neuroscience or closely related field, with a focus on modeling biological neural systems. Alternatively, a Master Degree in Physics, Mathematics, Computational Science or a closely related field, and a clear background or affinity for brain modeling; • strong quantitative and analytical skills, including calculus, linear algebra, differential equations, dynamical systems, stochastic processes and complex systems; • strong computational/programming skills (preferably with Python), including numerical methods for differential equations, machine learning and data analysis; • a keen, demonstrated interest in neuroscience research; • experience with computational neuroscience modeling projects, with virtual brain simulation engines (e.g. TVB), and/or with high performance computers is considered an advantage; • ability to read and understand relevant neuroscientific, cognitive and clinical literature and use experimental data to build models; • ability to communicate effectively in English, within a multidisciplinary team and in an international context; We offer a temporary contract for 38 hours per week for the duration of 4 years, which will culminate in the defense of your PhD thesis. We will also draft an educational plan that includes attendance of courses and (international) meetings, and you will also assist in teaching and other activities in the lab. The gross monthly salary will range from €2,770 in the first year to €3,539 in the last year, based on a full-time appointment (38 hours per week). Additionally, you will receive every year an 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants, effectively increasing their net salary. The lab is located in the state-of-the-art facilities of the Science Park at the University of Amsterdam, a top research university with a strong focus on cognition and brain research, and it has good communications with other academic and research centers in the city. As one of the most vibrant cities in Europe, Amsterdam has a rich historical and cultural heritage that includes the UNESCO World Heritage city center and canals, dozens of world-class museums and restaurants, and an exciting nightlife. The city promotes a healthy lifestyle with fantastic work-life balance, plenty of outdoor life, parks and recreational areas, an excellent bicycle path networks and an expat-friendly environment. The application deadline is February 25, 2024. Candidates may apply by following this link: https://vacatures.uva.nl/UvA/job/PhD-position-in-Computational-Neuroscience… Best, Jorge Mejias -- Jorge F. Mejias, PhD Assistant Professor Cognitive and Systems Neuroscience Swammerdam Institute for Life Sciences University of Amsterdam, 1098XH Amsterdam The Netherlands www.ugr.es/~jmejias

Jan. 30, 2024

Computational Neuroscience Ph.D. position with FONTOLAN, GUTKIN and KHAZIPOV labs @INMED Marseille

by Lorenzo Fontolan

Ph.D. funding is available through the Alan Turing Centre for Living Systems to work with the *Fontolan* lab in collaboration with the *Khazipov *lab in Marseille and the *Gutkin* lab in Paris. The candidate will develop a *neuronal network model of the early Sharp Waves in the neonatal rodent hippocampus*. More details on the project: https://centuri-livingsystems.org/phd2024-18/ Information about the selection process: https://centuri-livingsystems.org/recruitment/ *Deadline February 15* -- *Desired profile* The Ph.D. student should hold a Master’s degree in *physics/applied mathematics/electrical engineering/computational neuroscience*. Basic skills in modelling of neural/biological systems can be of additional advantage. Of high importance are: i) the ability to work in an interdisciplinary environment, ii) the willingness to dig into the biological intricacies of neural circuits, and iii) to combine analytical and numerical approaches that incorporate experimental data. *Project description* *During development, neuronal networks display peculiar patterns of activity, directly involved in the formation of neuronal circuits. Early Sharp Waves (eSPWs) are the predominant structured activity pattern in the developing entorhinalhippocampal network of neonatal rodents, which is thought to be essential for the formation of the connections between the entorhinal cortex (EC) and the hippocampus. Considerable amount of data on cellular, synaptic and network aspects of EC-driven eSPWs in the neonatal hippocampus has been accumulated recently in the Khazipov team at INMED, yet the generative mechanisms of eSPWs remain elusive. One of the central hypotheses involves the different modes of operation of the early vs late EC-hippocampal network, which is enabled by delated development of GABAergic inhibition and large temporal integration window of excitatory inputs from EC or other hippocampal subnetworks. The aim of this project is to identify the generative mechanism of eSPWs by developing a biologically accurate circuit model of EC-driven eSPWs based on recent data, and formulate specific predictions that will be experimentally tested in the Khazipov lab.* *Objectives* - Construct a comprehensive circuit model of the EC-hippocampal network incorporating cellular, synaptic, and population data to simulate network activity during development, and particularly the genesis of eSPWs. - Identify the key network components of the EC-hippocampal circuit in the generation of eSPW via model predictions. - Test the different hypotheses regarding the generative role of developing EC-hippocampus connectivity in eSPW onset, considering the role of delayed GABAergic inhibition and temporal integration windows of network inputs. *References* - Leinekugel X, Khazipov R, Cannon R, Hirase H, Ben Ari Y, Buzsaki G. (2002) Correlated bursts of activity in the neonatal hippocampus in vivo. Science 296(5575):2049-52 - Valeeva G, Janackova S, Nasretdinov A, Rychkova V, Makarov R, Holmes GL, Khazipov R, Lenck-Santini PP. (2019) Emergence of Coordinated Activity in the Developing Entorhinal-Hippocampal Network. Cereb Cortex 29(2):906-20. - Fontolan L, Hyafil A, Krupa M, Gutkin B. (2013) Analytical insights on theta-gamma coupled neural oscillators. J Math. Neuroscience 3(1):16. - Finkelstein A, Fontolan L, Economo MN, et al. Attractor dynamics gate cortical information flow during decisionmaking. Nat Neurosci 24, 843–850 (2021). https://doi.org/10.1038/s41593-021-00840-6 - Romagnoni A, Colonnese, M, Touboul J and Gutkin B (2020) Progressive Alignment of Inhibitory and Excitatory Delay May Drive a Rapid Developmental Switch in Cortical Network Dynamics, J. Neurophys, 123(5):1583-1599. Doi: 10.1152/jn.00402.2019-- Lorenzo Fontolan -- Group Leader *Turing Centre for Living Systems (CENTURI) Institut de Neurobiologie de la Méditerranée & Centre de Physique Théorique Université Aix-Marseille, France* *https://www.inmed.fr/neural-computation-and-dynamics <https://www.inmed.fr/neural-computation-and-dynamics>* *https://centuri-livingsystems.org/l-fontolan/ <https://centuri-livingsystems.org/l-fontolan/>*

Jan. 30, 2024

Scientist position at the Allen Institute

by Anton Arkhipov

Dear Colleagues, A Scientist position is open at the Allen Institute in the area of biologically realistic modeling. Please see the job description here: https://alleninstitute.org/careers/jobs/?jobId=A95FAC9B-4F0F-044B-5458-CAA4… The Scientist will develop bio-realistic network simulations at the level of a cortical area and the whole cortex, leveraging our multimodal datasets on brain composition and connectivity and training models on in vivo data using AI approaches. The goal is to use modeling together with experiments from our collaborators to understand the mechanisms underlying brain responses to sensory stimulation, including periodic sensory stimuli and the resulting entrainment of neuronal populations. Please consider applying and reach out if you have any questions. We are looking forward to hearing from you. Best wishes, Anton Arkhipov Investigator Allen Institute Seattle, WA antona(a)alleninstitute.org<mailto:antona@alleninstitute.org>

Jan. 30, 2024

Call for abstracts: Mathematics of Neuroscience and AI. Rome, 28-31st May 2024.

by Ruairidh McLennan Battleday

We are delighted to announce our call for abstracts for the 5th International Convention on the Mathematics of Neuroscience and AI, to be held in Rome 28-31st May 2024. In this high-profile convention we examine computational accounts of the brain and mind from the perspectives of biocomputation, neural theory, and cognitive science. We then take findings and theory back into the creation of robust, generalizable, and scalable AI: www.neuromonster.org Keynote Speakers Professor Peter Dayan (Max Planck Institute, Tübingen) Professor Sophie Deneve (ENS, Paris) Professor Wolfgang Maass (TUG) Professor Mackenzie Mathis (EPFL) Professor Anne Collins (UC Berkeley) Dr Feryal Behbahani (Google DeepMind) Dr Giovanni Pezzulo (NRC of Italy, Rome) Session Chairs Biocomputation Yasmine Ayman (Harvard) Professor Dan Nicolau Jr (KCL) Neural theory Dr James Whittington (Stanford / Oxford) Dr Francesca Mastrogiuseppe (Champalimaud) Cognitive science Dr Ruairidh Battleday (Harvard / MIT) Dr Antonella Maselli (NRC Italy) AI Dr Ishita Dasgupta (Google DeepMind) Dr Ilia Sucholutsky (Princeton) Confirmed speakers Biocomputation Professor Andrew Adamatzky (UWE) Professor Panayiota Poirazi (FORTH, Crete) Professor Jason Shepherd (Utah) Professor Christine Grienberger (Brandeis) Neural theory Professor Rafal Bogacz (Oxford) Professor Athena Akrami (UCL) Dr Sophia Sanborn (USB / UBC) Dr Lea Duncker (Stanford) Cognitive science Professor Dagmar Sternad (Northeastern) Professor Bill Thompson (UC Berkeley) Professor Samuel McDougle (Yale) Dr Fred Callaway (NYU / Harvard) AI Professor Kevin Ellis (CMU) Professor Najoung Kim (BU, Google) Dr André Barreto (DeepMind) Dr Maria Eckstein (DeepMind) We invite submissions for each session via this Google form: https://forms.gle/u8tJU4PtkT1EKYte7 These will be accepted for poster, spotlight, or a short talk. The submission format is a single A4 sheet containing (at least) an abstract of 250 words, along with any additional material you think valuable. Submission deadline is 28th February AOE. The convention will be held at the Villa Wolkonsky, in San Giovanni, Rome (10 minutes walk from the Colosseum). A limited number of early-bird registrations have been posted on our website! Normal registration will follow after the submission deadline. We hope that you come and join us! The Organizing Committee. -- Dr Ruairidh McLennan Battleday BMBCh (Oxon) PhD Postdoctoral Research Fellow Center for Brain Science, Harvard University Center for Brains, Minds, and Machines, MIT

Jan. 30, 2024

PhD Position

by Ahmed El Hady

PhD position available : Foraging tasks are emerging as crucial models for naturalistic decision making in rodents . On mechanistic level, those tasks give us the opportunity to understand how individual sensitivities to time and effort drive variability in the strategy of rodents facing an explore vs exploit dilemma. If those questions are of interest to you , there is an opening for a PhD position at the Centuri Turing Center for living systems in Marseille where the project is advised by David Robbe ( INMED, Marseille) , Eloy Christophe ( IRPHE, Marseille) and Ahmed El Hady ( Cluster for Advanced Study of Collective Behavior, Konstanz ). The project will combine theoretical and experimental approaches to understand how foraging strategies vary in terms of their sensitivities to time and effort during a variety of experimental conditions. We are looking for a candidate with a strong quantitative background, capable to developing numerical simulation/model (i.e. strong programing skills) and with a strong taste for animal behavior and cognition For more details and application procedure , please check the website : https://centuri-livingsystems.org/phd2024-19/ Please do not hesitate to get in touch in case you have any questions, Ahmed El hady Dr. Ahmed El Hady Group Leader Cluster for Advanced Study of Collective Behavior Max Planck Institute of Animal Behavior Universitätsstraße 10, 78464 Konstanz Room ZT 907 Postbox 687 Tel.: +49 7531 88-4742

Jan. 29, 2024

Second Call for Papers: RaPID-5@LREC-COLING 2024

by Dim X

************************************************************************************* *Second Call for Papers:* The 5th workshop on: "*Resources and ProcessIng of linguistic, para-linguistic and extra-linguistic Data from * * people with various forms of cognitive/psychiatric/developmental impairments*" *Workshop*: co-located with LREC-COLING 2024 | Turin, Italy | May 21st, 2024 RaPID-5 serves as an interdisciplinary platform for researchers to exchange insights, methods, and experiences related to collecting and processing data from individuals with mental, cognitive, neuropsychiatric, or neurodegenerative impairments. The workshop focuses on creating, processing, and applying such data resources from individuals at different stages and severity levels of these impairments. The ultimate goal of RaPID-5 is to facilitate the study of relationships among linguistic, paralinguistic, and extra-linguistic observations, with applications ranging from aiding diagnosis to enhancing monitoring and predicting individuals at higher risk, ultimately promoting multidisciplinary collaboration across clinical, language technology, computational linguistics, and computer science communities. *Submission deadline*: Sun., 17th of March, 2024 (anywhere on earth - new date!) *Paper submission*: https://softconf.com/lrec-coling2024/rapid2024/ *Website and more details*: https://spraakbanken.gu.se/en/rapid-2024 *Contact*: Dimitrios Kokkinakis *Contact email*: dimitrios.kokkinakis(a)gu.se *Invited Speakers: * - Dr. Alexandra König, BSc MSc PhD, Institut national de recherche en informatique et en automatique (INRIA); Cobtek (Cognition; Behaviour; Technology) Lab; University Côte d'Azur, France - Prof. Maria Liakata, EPSRC/UKRI Turing Institute AI fellow, Queen Mary University of London, UK *Organizing committee*: - Kathleen C. Fraser, National Research Council, Canada; - Dimitrios Kokkinakis, University of Gothenburg, Sweden; - Kristina Lundholm Fors, Lund University, Sweden; - Charalambos K. Themistocleous, University of Oslo, Norway; - Athanasios Tsanas, The University of Edinburgh, UK; - Fredrik Öhman, University of Gothenburg and Sahlgrenska University Hospital, Sweden **************************************************************************************

Jan. 27, 2024

Summer school "Cognitive Foundations of Decision-Making" in Rabat, Marocco

by Rava A. da Silveira

Applications are open for the interdisciplinary summer school “*Cognitive** Foundations of Decision-Making.”* The summer school is aimed at young scholars interested in decision-making in general, and the neural and cognitive foundations of decision-making in particular. The summer school will be held on *July 22–27, 2024*, on the beautiful campus of University Mohammed VI Polytechnic, in Rabat, Morocco. Information, including details on how to apply, can be found at https://www.rislab.net/summerschool. The lecturers will include Larbi Alaoui (Universitat Pompeu Fabra), Rava Azeredo da Silveira (ENS and University of Basel), Peter Bossaerts (University of Cambridge), Joseph Kable (University of Pennsylvania), Rafael Polania (ETH Zurich), Ryan Webb (University of Toronto).

Jan. 27, 2024

Call for Applications & Help Promote: Gatsby Bridging Programme (Maths Summer School)

by Lin, I-Chun

Application deadline: 23 February 2024 (We may need to stop accepting applications before this date if the number received exceeds our capacity to review.) Programme dates: 24 Jun - 9 Aug 2024 (London, UK) Programme details: www.ucl.ac.uk/gatsby/study-and-work/gatsby-bridging-programme The Gatsby Computational Neuroscience Unit at UCL is running the Gatsby Bridging Programme - an intensive, 7-week mathematics summer school. The programme is designed for penultimate/final-year undergraduates and Master’s students (incl. recent graduates) who aspire to pursue a postgraduate research degree in Theoretical Neuroscience or Machine Learning but whose degree course does not have a strong mathematical focus. Participants will attend in-person lectures/tutorials/problem-solving sessions to develop mathematics skills and intuition necessary to enter both fields and have the opportunity to interact with our researchers. We aim to be inclusive and to increase the diversity of students entering both fields. Thus, we strongly encourage applications from students in underrepresented groups in Science, Engineering, Technology and Mathematics. A limited number of bursaries are available to students who may find it difficult to participate for financial reasons. We would also appreciate it if you could help us reach students who may benefit from this programme. Here are some ways you can help us spread the word: * Distributing the Call for Applications email among colleagues and interested students. * Sharing our posts on social media: - X/Twitter: twitter.com/GatsbyUCL/status/1747929384135127272 - Mastodon: neuromatch.social/@GatsbyUCL/111776402260388914 - LinkedIn: www.linkedin.com/posts/i-chun-lin-49270817_mathematics-summerschool-theoret… Thank you for any support you are willing to give us. If you have any questions, please don’t hesitate to get in touch. Best, I-Chun -- I-Chun Lin Scientific Programme Manager Gatsby Computational Neuroscience Unit

Jan. 25, 2024