- Comp-neuro - lists.cnsorg.org

Data Scientist Position in Bioinformatics and Neuroscience at Boston University
by Chen, Jerry Jan. 7, 2021

Jan. 7, 2021

The Lab of Jerry Chen at Boston University is hiring a Staff-Level Data Scientist to be involved in several multi-year BRAIN Initiative related NIH and NSF funded projects. These projects focus on understanding cortical computation during behavior by combining behavior, genomics, spatial transcriptomics, anatomical reconstructions, and large-scale population recordings. This person will be involved in help to analyze experimental data, developing software tools to aid in the data analysis, and helping with data infrastructure and management. Specific Projects include: 1. Analysis of genomic data. 2. Image analysis for in situ sequencing of gene expression (ie. spatial transcriptomics) 3. Automated behavioral training and video analysis. 4. Analysis of dense electron microscope reconstructions of neuronal connectivity (ie. Connectomics). Required Skills: * BA/BS degree (MS/PhD preferred) in Computer Science, Mathematics, Engineering, Bioinformatics, Neuroscience or related technical field. * One to three years of academic or professional experience. * Programming experience in MATLAB, Python, and R is required. * Extensive background in either genomic analysis, image analysis, computer vision, or machine learning is preferred. If interested in applying, please submit a CV along with 3 references to jerry(a)chen-lab.org<https://mail.google.com/mail/?view=cm&fs=1&tf=1&to=jerry@chen-lab.org> Jerry Chen, PhD. Assistant Professor Department of Biology Boston University jerry(a)chen-lab.org<mailto:jerry@chen-lab.org> www.chen-lab.org

1 0

Permanent position in computational modeling of neurostimulation in mental disorders
by Axel Hutt Jan. 6, 2021

Jan. 6, 2021

------------------------------------------------------------------------------------ Permanent position in computational modeling of neurostimulation in mental disorders ------------------------------------------------------------------------------------ The research of the INRIA-team MIMESIS in Strasbourg / France (https://mimesis.inria.fr) aims to create a synergy between clinicians and scientists to develop new healthcare technologies. The team researchers collaborate closely with clinicians and choose their research focus along the clinical applications. Major scientific objectives are the development of advanced online- and offline simulations involving new numerical techniques for real-time computation and data-driven simulation dedicated to patient-specific modelling. One application branch is embedded in neuroscience with a specific focus on general anaesthesia and neurostimulation of patients suffering from mental disorders. For instance, members of MIMESIS work in the recently funded project A/D Drugs (https://www.inria.fr/en/ad-drugs-exploratory-action-aimed-optimising-neuros…) to develop novel neurostimulation techniques in psychosis that may emerge in schizophrenia patients. The team offers the possibility to apply for a permanent position as Chargé de Recherche (CR) or Directeur de Recherche (DR) in the research field of computational neuroscience with a strong focus on linking brain network modelling with experimental data. The new colleague should have a strong expertise in neurostimulation and/or modelling of experimental data observed in mental disorders. Strong programming and mathematical skills are mandatory. INRIA is a French National Institute for Research in Digital Science and Technology (https://www.inria.fr/en) with 8 research centres in France. The team MIMESIS is located in the centre of Strasbourg on the hospital campus as part of the Research Centre Nancy Grand Est. The application deadline will be mid of February 2021, but it is recommended to contact the team (by email: axel.hutt(a)inria.fr) in advance. For more details or sending your application documents (CV including publication list), please contact Dr. Axel Hutt (email: axel.hutt(a)inria.fr) .

1 0

Postdoc in machine learning at EPFL (Lausanne, Switzerland)
by Milekovic Tomislav Jan. 6, 2021

Jan. 6, 2021

Postdoc position in the lab of Prof. Gregoire Courtine at EPFL (Lausanne, Switzerland) Machine learning techniques to develop and enhance clinical treatments based on electrical stimulation of the spinal cord Location: The laboratory of Prof. Gregoire Courtine at the Swiss Federal Institute of Technology (EPFL) in Lausanne, Switzerland, is looking to fill a fully funded postdoc position. The qualified candidate will benefit from joining a very dynamic and multidisciplinary group working at the interface of computational neuroscience, neuroengineering, prosthetics and biology. EPFL provides state-of-the-art facilities and is one of the leading technical universities worldwide. Postdoc salaries at EPFL rank the highest in the world. Opportunity: The offered position will be based at the Defitech Center for interventional Neurotherapies (NeuroRestore) - a research and innovation center joining EPFL’s lab of Prof. Gregoire Courtine and the University Hospital of Lausanne (CHUV) lab of Prof. Jocelyne Bloch. NeuroRestore conceives, develops and applies medical therapies aimed to restore neurological functions. To this end, NeuroRestore integrates implantable neurotechnologies with innovative treatments developed through rigorous preclinical and clinical studies. By working with our network of vibrant high-tech start-ups and established medical technology companies, NeuroRestore is committed to validate our medical therapy concepts. The overarching goal of NeuroRestore is to see our medical therapies used every day in hospitals and rehabilitation clinics worldwide. Description: Therapies based on epidural electrical stimulation (EES) of the spinal cord can restore the ability to walk to people paralyzed by spinal cord injury, and alleviate gait deficits of people with Parkinson’s disease. EES does this by recruiting sensory axons within dorsal spinal roots that enter the spinal cord between the vertebrae to increase the activation of the spinal motor pools that, in turn, move the muscles. Yet, the efficacy of the EES-based therapies relies on synchronizing users’ movement intentions with the spatiotemporal stimulation protocols that reliably and accurately generate paralyzed movements. Due to the large state space of all the stimulation parameters (location, amplitude, frequency, etc.) efficacy of the therapy depends on the fast and accurate initialization of the stimulation protocols. As the patients use the stimulation, small movements of the array, as well as changes in spine position due to users’ posture can reduce the usability of the stimulation. Stimulation efficacy can be enhanced by dynamically adjusting the stimulation protocols to changes to the way how to users’ spinal cord reacts to stimulation. Finally, the functional use of the stimulation largely depends on the accurate timing of stimulation delivery. Machine learning approaches that infer users’ intentions based on behavioral, physiological or neural recordings can vastly improve the synchronization between intended and therapy-supported movements and, therefore, play a critical role in achieving functional recovery of patients. While the current medical devices mostly support block-based stimulation protocols that remain constant for hundreds of milliseconds, upcoming devices will enable changes of stimulation at a millisecond resolution, thus opening a new field for machine learning approaches that exploit these capabilities. The successful candidate will work to develop, implement and apply machine learning algorithms and approaches to enhance EES-based therapies. Specifically, he will: * Design the mapping procedures for the generation of transfer functions that relate the continuously-controlled stimulation to the evoked muscle activity. * Develop algorithms that automatically adjust these transfer functions as the interaction between patients and their EES-based therapy evolves. * Implement machine learning techniques that utilize users’ behavioral, physiological and neural signals to continuously synchronize the delivery of stimulation with the users’ movement intentions. * Lead the team that develops machine learning methods to initialize and adjust block-based EES protocols. * Assist and oversee the development and implementation of machine learning methods that use inference of discrete motor events to synchronize block-based EES protocols with the users’ intentions. By integrating well-equipped and expertly staffed rodent, non-human primate and clinical research facilities, NeuroRestore provides an ideal substrate for rapidly developing, integrating and clinically validating cutting-edge machine learning concepts within medical therapies, with the capacity to push successfully proven concepts into the technology transition phase. The successful candidate will have access to these animal platforms and will work within the framework of multiple NeuroRestore clinical trials with people with spinal cord injury and Parkinson’s disease. They will benefit from the possibility of validating their concepts in animal experiments and implementing them within the therapies being tested in the clinical trials. Prerequisites: · Doctoral degree (PhD) · Proficiency in Python, Matlab and C++ · Strong background in quantitative data analysis · Experience with applying multiple machine learning techniques to behavioral, physiological, biological and/or neural datasets · Good written and verbal skills in English Contact: Applications including a CV and a cover letter describing your background and interest should be sent to tomislav.milekovic(a)epfl.ch<mailto:tomislav.milekovic@epfl.ch>. Informal inquiries are welcome.

1 0

Postdoc opportunity (fully funded): Theories and Models of Behaving Brains
by Ann Kennedy Jan. 5, 2021

Jan. 5, 2021

The Kennedy lab (kennedylab.org<http://kennedylab.org/>) is hiring multiple fully-funded postdoctoral researchers for neural network modeling, data analysis, or deep learning projects. Our research goal is to develop new methods for analyzing and modeling high dimensional data, which we use to understand the structure of behavior, its control by the brain, and the dependence of brain activity and behavior on context, experience, and internal state. We work in close collaboration with experimental groups, with available projects studying neural encoding of state and behavior in basal ganglia, hippocampus, hypothalamus, and cortex. We are also pursuing pure theory projects, studying computation and dynamics in heterogeneous neural networks, inspired by the remarkable cell type diversity that has been uncovered throughout the brain via single-cell RNA sequencing experiments. We are a new theoretical neuroscience laboratory at Northwestern University, in the Physiology department of Feinberg Medical School on Chicago's Miracle Mile. Northwestern's Physiology department is ranked #3 in the US, and has an incredible concentration of expertise in the motor control and reward circuitry of the basal ganglia and cortex. Interested applicants, please email ann.kennedy(a)northwestern.edu<mailto:ann.kennedy@northwestern.edu> with a CV and a comment on your research interests.

1 0

Postdoc Position - Human Intracerebral Speech Perception
by Lori Holt Jan. 5, 2021

Jan. 5, 2021

Interested to join a highly collaborative, vibrant research environment in Pittsburgh? We are seeking to understand how the brain flexibly maps speech input across manipulations in short-term input regularities. The postdoctoral position will be supported by a new NIH-sponsored research project, *Flexible representation of speech in the supratemporal plane*, that weds the joint expertise of Lori Holt (Carnegie Mellon University) and Taylor Abel (Pediatric Neurosurgery, University ofPittsburgh) to advance how dynamic, flexible aspects of the mapping of speech input to phonemes are represented in the intracerebral response of human cortex measured with stereoelectroencephalography. You can find more info here: https://www.cmu.edu/dietrich/psychology/holtlab/PDF/cmupittpostdocad2020.pdf Please feel free to be in touch with questions for Lori (loriholt(a)cmu.edu) or Taylor (abeltj(a)upmc.edu) ______________________________________________________________ loriholt Professor, Department of Psychology | Neuroscience Institute | Center for the Neural Basis of Cognition Carnegie Mellon University loriholt(a)cmu.edu | www.psy.cmu.edu/~holtlab/ pronouns: she, her, hers

1 0

Digital Info Day - International Master & PhD in Computational Neuroscience @ BCCN Berlin - 27.01.21
by Graduate Programs Jan. 5, 2021

Jan. 5, 2021

Dear Computational Neuroscientists, Please share the following event information with anyone who may be interested. We at the Bernstein Center for Computational Neuroscience (BCCN) Berlin will hold a "Digital Info Day" to discuss our International Master & Doctoral Programs in Computational Neuroscience on Wednesday, January 27th, at 3pm (CET). The event will consist of talks by: * Prof. Dr. Klaus Obermayer (head of the programs) * Lisa Velenosi (teaching coordinator) * Current master and doctoral students Attendees will also have the opportunity to meet & discuss with current students and ask any questions or concerns that they may have. See our website <https://www.bccn-berlin.de/events-list/information-day-international-gradua…> for a more detailed schedule and registration link. Best regards and happy new year, Lisa Velenosi -- Lisa Velenosi Teaching Coordinator Bernstein Center for Computational Neuroscience Humboldt-Universität zu Berlin Philippstraße 13, Haus 6; 10115 Berlin; Germany Tel: +49 (0)30 2093 6773 Technische Universität Berlin Marchstraße 23; Raum 5.061; 10587 Berlin; Germany Tel: +49 (0)30 314 72006 SFB1315 - Network Outreach Coordinator PhD & Postdoc Cohort

1 0

Creating a list of important computational predictions
by Yiota Poirazi Jan. 4, 2021

Jan. 4, 2021

Dear all, I believe you would agree that, the greatest recognition of our computational work comes with the experimental verification of our computational predictions. To highlight the most important outcomes of our theoretical work and facilitate a closer interaction with experimental labs so as to increase the chances of our predictions being experimentally tested, I would like to encourage you to nominate your favorite prediction at the following google form: https://docs.google.com/forms/d/e/1FAIpQLSeJZ2RrXJ0nZonIuyNzN0Cl gXDKDb7xTzoJOiqZTGxm9Kh7ow/viewform?c=0&w=1&usp=mail_form_link This effort started during the CNS 2017 meeting in Antwerp with the support of the OCNS Board. The resulting list will be posted on the CNS 2017 web site and disseminated in social media, as a reference for experimentalists. Thank you very much for supporting this important effort! Best wishes, Yiota Poirazi -- Panayiota Poirazi, Ph.D. Research Director Computational Biology Laboratory Institute of Molecular Biology and Biotechnology (IMBB) Foundation of Research and Technology-Hellas (FORTH) Vassilika Vouton, P.O.Box 1385, GR 70013, Heraklion, Crete GREECE Tel: +30 2810 391139 Fax: +30 2810 391101 Εmail: poirazi(a)imbb.forth.gr Lab site: www.dendrites.gr FENS-Kavli Network of Excellence <http://www.fens.org/Outreach/FENS-Kavli-Network-of-Excellence/> -- This message has been scanned for viruses and dangerous content by *E.F.A. Project* <http://www.efa-project.org>, and is believed to be clean. Click here to report this message as spam. <http://mailgate1.imbb.forth.gr/cgi-bin/learn-msg.cgi?id=4BCD7A00A1.A57D7&to…> -- Panayiota Poirazi, Ph.D. Research Director Computational Biology Laboratory Institute of Molecular Biology and Biotechnology (IMBB) Foundation of Research and Technology-Hellas (FORTH) Vassilika Vouton, P.O.Box 1385, GR 70013, Heraklion, Crete GREECE Tel: +30 2810 391139 Fax: +30 2810 391101 Εmail: poirazi(a)imbb.forth.gr Lab site: www.dendrites.gr FENS-Kavli Network of Excellence <http://www.fens.org/Outreach/FENS-Kavli-Network-of-Excellence/>

2 1

WorldWideNeuRise, an online seminar series promoting early-career researchers
by William Podlaski Jan. 4, 2021

Jan. 4, 2021

We are very pleased to announce the new seminar series WWNeuRise that explicitly targets PhD students and postdocs (https://neurise.github.io/) WWNeuRise aims to give early career scientists an opportunity to share their exciting work with a large audience and make connections with people interested in similar questions. The seminar series will be hosted on WWNeuro and sponsored by eLife. The first seminar block, entitled "Neuroscience at the intersection of experiment and theory", will start in January 2021 and features six exciting talks by Nicolas Meirhaeghe (Jazayeri lab, MIT) Federico Stella (Battaglia lab, Donders Institute) Soledad Gonzalo Cogno (Moser lab, NTNU) Zoe Ashwood (Pillow lab, Princeton University) Claire Hales (Robinson lab, University of Bristol) Arseny Finkelstein (Svododa lab, Janelia HHMI) For more information, please visit the WWNeuRise website ( https://neurise.github.io/) or twitter (https://twitter.com/WWNeuRise) We are looking forward to seeing you all in January! The organising committee, Ellen Boven (Apps lab, U Bristol) Christina Buetfering (Häusser lab, U College London) Lucie Descamps (Kentros lab, NTNU) Gily Ginosar (Ulanovsky lab, Weizmann Institute) Loreen Hertäg (Sprekeler lab, TU Berlin) Joram Keijser (Sprekeler lab, TU Berlin) Bill Podlaski (Machens lab, Champalimaud)

1 0

Call for community project proposals and mentors for INCF's participation in GSoC 2021 - expression of interest due January 15
by Malin Sandström Jan. 4, 2021

Jan. 4, 2021

Hello all, ------- Please forward this email to prospective mentors you might have in your network ---- INCF will be applying again to Google Summer of Code, for the 11th time running. Last year was a record year in the number and diversity of projects, we hope to do at least as well this year! A note on scope: we are looking for open source project ideas with some sort of *neuro connection* - fixes or extensions to big/broadly applicable or small/niche tools used by neuroscience researchers, efforts and initiatives in the broad field of computational neuroscience. If your project supports or implements *neuroscience standards or best practices*, we are especially happy (but all projects are treated equally, when it comes to slot assignments). This year, we are *also looking for mentors who come without their own projects *and are willing to take on student-proposed projects that fit their interests. As you may have seen earlier this year, Google has announced some changes to the program <https://opensource.googleblog.com/2020/10/google-summer-of-code-2021-is-bri…>. Projects will now be SHORTER (10 weeks instead of 12) and entry thresholds for students will be diversified, which will allow more varied student backgrounds. In compensation, there will be more projects. This means, if you have a running project from previous years that you want to continue, you may need to *re-scope* its contents and aims a bit, maybe even split it in two (independent) parts. With a shorter time span and a more varied student body, where not all students will be as near to full-fledged computer scientists, we will need to put a bit more effort into *introductions, support *and *confidence-building*. INCF will help with this, please refer interested students to us at an early stage so we can onboard them into our 'potential students' community. Another important change: this time (and in years forward), we aim to *keep all prospective students in the INCF community*, regardless of if they are accepted to a project or not. They may well be candidates for next year, and also, since you will be putting actual effort into project discussions, we want to make sure it is useful. Also, the usual reminder: there is no guarantee that INCF is accepted this year until we hear from Google on *March 9*. Please be clear with this in your communication with students. The* timeline <https://summerofcode.withgoogle.com/how-it-works/>* is similar to the years before: Applications open near the *end of January (29th)*, they close near *mid February (19th)*. We aim to have a live project ideas list in mid January. Orgs are announced on *March 9*, and student applications are open *March 21 - April 19*. *Important*: last year we were near peak capacity in the number of project ideas on our final list, with a flurry of last-minute activity. We therefore want interested mentors to contact us (gsoc(a)incf.org or malin(a)incf.org) *early* with a declaration of interest and a short summary of the intended project, latest *January 15*. If you want to mentor but don't have a project idea, you are still welcome to join our list of potential mentors for ideas that originate with students. Actual project descriptions should ideally come by *January 22*, a week before we officially go live with the project list on *January 29*, but we will take on late requests from *previous mentors only* (including mentors of previous non-accepted projects) on a case-by-case basis if they are well described and properly scoped. Project template: Each submission should come *by email* and contain: 1) An *informative title* with relevant keywords (good-to-have: name of tool/project, name of programming language) 2) A *project description* including a brief general intro, motivation, aims, scope and skills/skill level needed. Please indicate 2-5 tech keywords (Python, C++, Java, SQL, REST, CUDA, ...) 3) Name of *lead mentor* + a *named co-mentor or backup mentor* who would be able and willing to back the main/contact mentor up in mentoring in case something unforeseen happens (can be more than one, as long as you are internally clear on who does what) 4) Any planned *longer absences* during the lead up/student interaction period (*February 1 - April 19*, especially the last week) or the project period (May 17 - *August 30*), and the plan for covering them. 5)* Format*: your choice - txt, doc, docx, pdf or a link to a webpage with the full description(s). Anything that can be copied and pasted. NB: Project ideas will be posted on *Neurostars.org* after the ideas list goes live, and prospective mentors are expected to *join the forum and be available* for questions from students during the run up to the announcement (late Jan - early March) and the student interactions period (March-April). This can be handled by email, mostly, if you prefer, once you have set your NeuroStars account up. Questions and project submissions: please email *malin(a)incf.org <malin(a)incf.org>* AND cc *gsoc(a)incf.org <gsoc(a)incf.org>*. Happy new year of coding! /Malin -- Malin Sandström, PhD Community Engagement Officer malin.sandstrom(a)incf.org International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org

1 0

Postdoctoral fellow – Systems Neuroscience of Alzheimer’s Disease
by Williamson, Ross S Dec. 29, 2020

Dec. 29, 2020

Dear all, Apologies for the cross-posting. A postdoctoral position is available in the Williamson and Thathiah laboratories at the University of Pittsburgh School of Medicine to investigate the links between hearing loss and the pathophysiology of Alzheimer’s disease (AD). The information from our senses is used throughout everyday life to guide the decisions we make and the actions that we take. For example, the sound of sirens when driving leads to a decision regarding an appropriate motor action (whether or not, and where, to pull over). The neural circuits that underlie these cognitive processes (accumulation of sensory evidence, short-term memory, perception decision-making, etc.) can be severely altered by disease. Hearing loss is prevalent in >40% of individuals older than 60 years and is considered to be the most heavily contributing modifiable risk factor to dementia. It is our hope that by identifying and studying the neural circuits involved, we will provide insight to drive subsequent therapeutic intervention strategies that may lead to the repair (or prevention) of damage. The Williamson Laboratory uses a variety of state-of-the-art tools to probe the neural circuits of awake mice, including two-photon calcium imaging and high-channel count electrophysiology (both with single-cell optogenetic perturbations), head-fixed virtual reality behaviors, and statistical approaches for neural characterization. A significant focus of the lab is to understand how sensory information is used to guide purposeful behavior in models of health and disease. Details on the research focus and approaches of the Williamson laboratory can be found here: https://www.williamsonlaboratory.com/research/ The Thathiah Laboratory uses molecular, cellular, and behavioral approaches along with optogenetic tools to investigate the mechanisms of AD pathogenesis. Recently, the Thathiah lab teamed up with the Williamson lab to investigate the putative causal relationship between hearing loss, disease pathogenesis, and cognitive impairment using our complementary research approaches in AD mouse models. Details on the research focus of the Thathiah laboratory can be found here: https://www.neurobio.pitt.edu/people/amantha-thathiah Both laboratories are embedded within the Departments of Neurobiology and Otolaryngology, are members of the University of Pittsburgh Brain Institute, the Pittsburgh Hearing Research Center, and are affiliated with the Center for Neuroscience (CNUP) and the Center for the Neural Basis of Cognition (CNBC). The Thathiah laboratory is a member of the Pittsburgh Institute for Neurodegenerative Diseases (PIND), the Alzheimer’s Disease Research Center (ADRC), and the Aging Institute. Postdoctoral fellows will be part of a highly supportive and diverse research environment with excellent career development opportunities. The University of Pittsburgh was ranked third in terms of total NIH funding received in 2018. The Global Livability Index (The Economist) recently ranked Pittsburgh as the second most livable city in America. The University of Pittsburgh School of Medicine is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, creed, sex, sexual orientation, gender identity, national origin, ancestry, age, veteran status, disability unrelated to job requirements, genetic information, military service, or other protected status. Requirements: Applicants must have a Ph.D. in Neuroscience or a relevant field and must be eligible for employment in the US. We are looking for individuals with an excellent record of research achievements and expertise at the intersection of two or more of the following areas: electrophysiology, two-photon imaging, quantitative behavior, and computational neuroscience. Experience with molecular and biochemical techniques is preferred but not required. Excellent verbal and written communication skills, technical expertise, and scientific creativity are essential. Applications will continue until the position is filled. Contact: Interested candidates should send a brief statement of research interests, a current CV, and the names and contact information of three references to: Dr. Ross Williamson: rsw(a)pitt.edu<mailto:rsw@pitt.edu> Dr. Amantha Thathiah: amantha(a)pitt.edu<mailto:amantha@pitt.edu> Thanks, Ross ---------------------------------------------------------------------------------------------------------- Ross S. Williamson, Ph.D. | Assistant Professor | Otolaryngology, Neurobiology Pittsburgh Hearing Research Center | Center for the Neural Basis of Cognition University of Pittsburgh | Biomedical Science Tower | W1448 www.williamsonlaboratory.com<http://www.williamsonlaboratory.com>

1 0