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Call for community project proposals and mentors for INCF's participation in GSoC 2021 - expression of interest due January 15
by Malin Sandström 04 Jan '21

04 Jan '21

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

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Postdoctoral fellow – Systems Neuroscience of Alzheimer’s Disease
by Williamson, Ross S 29 Dec '20

29 Dec '20

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>

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Postdoc at International Centre for Translational Eye Research
by Andrzej Foik 28 Dec '20

28 Dec '20

Dear all, I would like to repost our announcement about the postdoc we are looking for. we are looking for a postdoc in the neuroinformatics or bioinformatics area. Please, spread the word to your friends if you can. The Ophthalmic Biology Group searches for candidates with a Ph.D. degree experienced in computational biology techniques such as neuronal network modeling, electrophysiological data analyses and/or bioinformatics, and DNA/protein modeling. Candidates should be interested in translational research and the development of new therapies to cure blindness or other diseases. The postdoctoral scholar will have a direct impact on lab development and its success in publishing in high impact factor journals. The person will be also responsible for performing dynamic research to create a competitive research group. The position will be assigned to the Ophthalmic Biology Group led by Andrzej Foik Ph.D. focusing on the development of new viral therapies, visual information processing in the visual system before and after plasticity that happens due to vision recovery or disease. https://euraxess.ec.europa.eu/jobs/580785 https://ichf.edu.pl/en/job/international-centre-for-translational-eye-resea… Best regards, Andrzej Foik -- Andrzej Foik, PhD Group Leader Ophthalmic Biology Group International Centre for Translational Eye Research (ICTER) Institute of Physical Chemistry PAS ul. Kasprzaka 44/52, 01-224 Warszawa mobile: +48 695 497 065 office: +48 22 343 3204 email: afoik(a)ichf.edu.pl; andrzejfoik(a)gmail.com NIP: 525-000-87-55 www.icter.pl The controller of your personal data is the Institute of Physical Chemistry of the Polish Academy of Sciences with its registered office in Warsaw, NIP: 5250008755 (the "Institute"). The Institute will process your data for the purpose of carrying out scientific and research activities, providing services and contact with the Institute, on the basis of a contract (in connection with the performance of the contract or in order to take action on your request before the contract is concluded – Article 6, paragraph 1, letter b) of GDPR), the legitimate interest of the Institute (Article 6, paragraph 1, letter f) of the GDPR) and legal provisions (Article 6, paragraph 1, letter c) of the GDPR) - depending on the circumstances. You have the right to request access to your data, receive a copy of it; rectify (correct) it; delete it; limit its processing; transfer it; lodge a complaint to the supervisory body; withdraw your consent for processing at any time (withdrawal of consent does not affect the lawfulness of the processing carried out prior to its withdrawal) or to lodge an objection to data processing. More information is available on the Institute's website. http://ichf.edu.pl/gen_inf/gen_en/GDPR%20-%20General%20Information%20Clause… -- Andrzej Foik, PhD Group Leader Ophthalmic Biology Group International Centre for Translational Eye Research (ICTER) Institute of Physical Chemistry PAS ul. Kasprzaka 44/52, 01-224 Warszawa mobile: +48 695 497 065 office: +48 22 343 3204 email: afoik(a)ichf.edu.pl; andrzejfoik(a)gmail.com NIP: 525-000-87-55 www.icter.pl The controller of your personal data is the Institute of Physical Chemistry of the Polish Academy of Sciences with its registered office in Warsaw, NIP: 5250008755 (the "Institute"). The Institute will process your data for the purpose of carrying out scientific and research activities, providing services and contact with the Institute, on the basis of a contract (in connection with the performance of the contract or in order to take action on your request before the contract is concluded – Article 6, paragraph 1, letter b) of GDPR), the legitimate interest of the Institute (Article 6, paragraph 1, letter f) of the GDPR) and legal provisions (Article 6, paragraph 1, letter c) of the GDPR) - depending on the circumstances. You have the right to request access to your data, receive a copy of it; rectify (correct) it; delete it; limit its processing; transfer it; lodge a complaint to the supervisory body; withdraw your consent for processing at any time (withdrawal of consent does not affect the lawfulness of the processing carried out prior to its withdrawal) or to lodge an objection to data processing. More information is available on the Institute's website. http://ichf.edu.pl/gen_inf/gen_en/GDPR%20-%20General%20Information%20Clause…

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New Journal: Mathematical Neuroscience and Applications
by Zachary Kilpatrick 27 Dec '20

27 Dec '20

We are pleased to announce the creation of "Mathematical Neuroscience and Applications". The aim of this new journal is to publish the best work in mathematical neuroscience and its applications and making it broadly available to the scientific community in a completely open fashion, i.e. at no costs for readers and authors (no APCs). The webpage of the journal can be found at https://mna.episciences.org/ <https://secure-web.cisco.com/1Th57tM0Q4wnQK5WU9a83gEk5eiepY75pxIXyIVdMZmATN…> where more information such as how to submit an article, or the list of Editorial Board Members, https://mna.episciences.org/review/staff <https://secure-web.cisco.com/1CXJhkD3WpGFVRfTHEqp6vfR8XHQDkEeIIbSjzi2e5bXzh…> , is available. This is the Diamond Open Access model which is made possible in our case thanks to the support of Episciences, https://www.episciences.org/# <https://secure-web.cisco.com/1EwusptV_q2y1ZQTKNt9O1K0__jJocYNjvm6c6ar0ARXwJ…> Editorial Board Members of MNA are looking forward to publishing your work. Feel free to reach out to us with any questions. Olivier Faugeras (Editor in Chief), Inria, France Peter Ashwin, University of Exeter, UK Paul Bressloff, University of Utah, USA Stephen Coombes, University of Nottingham, UK Carina Curto, Pennsylvania State University, USA Susanne Ditlevsen, University of Copenhagen, Denmark Antonio Galves, University of São Paulo, Brasil Zachary Kilpatrick, University of Colorado Boulder, USA Carlo Laing, Massey University, Auckland, New Zealand Eva Löcherbach, Paris I University, France Andre Longtin, University of Ottawa, Canada Benoit Perthame, Sorbonne University, France Patricia Reynaud-Bouret, Côte d'Azur University, France Andrey Shilnikov, Georgia State University, USA Wilhelm Stannat, Technische Universität, Berlin, Germany Etienne Tanré, Inria, France Michèle Thieullen, Sorbonne University, France Stephan A Van Gils, Universiteit Twente, Netherlands Romain Veltz, Inria, France Martin Wechselberger, University of Sydney, Australia

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ANDA 2020 - G-Node Advanced Neural Data Analysis Course, April 14-30, 2020, Jülich, Germany
by Thomas Wachtler 23 Dec '20

23 Dec '20

ANDA 2020 - G-NODE ADVANCED NEURAL DATA ANALYSIS COURSE April 14 - 30, 2020 Haus Overbach, Jülich-Barmen, Germany Techniques to record neuronal data from populations of neurons are rapidly improving. Simultaneous recordings from hundreds of channels are possible while animals perform complex behavioral tasks. The analysis of such massive and complex data becomes increasingly challenging. This advanced course aims at providing deeper training in state-of-the-art analysis approaches in systems neuroscience. The course is addressed to excellent master and PhD students and young researchers who are interested in learning advanced techniques in data analytics and in getting hands-on experience in the analysis of electrophysiological data. Internationally renowned researchers will give lectures on statistical data analysis and data mining methods with accompanying exercises. Students will define and perform their own analyses on provided data to solve a challenge. Participants are required to have a strong interest in data analysis, a background in a mathematical or related field, knowledge of algebra, matrix operations, and statistics, and need to have solid programming experience (preferably in Python). FACULTY · Moshe Abeles, Hebrew Univ. Jerusalem, Israel · Michael Denker, Jülich Research Center, Germany · Udo Ernst, Univ. Bremen, Germany · Sonja Grün, Jülich Research Center, Germany · Adam Kohn, Albert Einstein College of Medicine, New York, USA · Jakob Macke, TU Munich, Germany · Luca Mazzucato, Univ. of Oregon, Eugene, USA · Martin Nawrot, Univ. of Cologne, Germany · Yifat Prut, Hebrew Univ. Jerusalem, Israel · Hansjörg Scherberger, German Primate Center, Göttingen, Germany · Thomas Wachtler, LMU Munich, Germany TOPICS COVERED Single neuron properties and statistics · Stochastic processes · Surrogate methods · Detection of spatio-temporal patterns · Unitary Events · Statistical analysis of massively parallel spike data · Higher-order correlation analyses · Elephant toolbox · Spike-LFP relationship · Population coding · State space analysis · Machine learning · Data mining · Research data management and reproducibility REQUIREMENTS Applicants should be familiar with linear algebra, probability, differential and integral calculus and experienced using Python or Matlab. Preparatory reading material will be provided. Students should bring their own laptops and should be able to install software on their system. Students that do not have a suitable laptop should indicate this immediately after acceptance to the course. We will be able to provide a small number of laptops for the time of the course. COURSE FEE A course fee of 1000 Euros will be charged to cover costs for accommodation and meals. Limited financial support may be available for students that otherwise would not be able to attend, which is to be indicated in the application. HOUSING Accommodation in 2-bed rooms for students will be provided at the course site. HOW TO APPLY The application should include · a letter of motivation (max 1 page) · curriculum vitae (please indicate the relevant courses you have taken) · description of programming experience · a letter of recommendation. Please send all documents as a single PDF file to <advanced-course(a)g-node.org>. APPLICATION DEADLINE Applications must be received by NOVEMBER 15, 2019. Early application is encouraged. For further information see http://www.g-node.org/anda

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Open Position at Goettingen University - Postdoctoral Researcher (f/m/d) - SPP 2205
by von Behren, Christina 22 Dec '20

22 Dec '20

Dear list, We would like to draw your attention to the postdoc opportunity below: The Department of Data-driven Analysis of Biological Networks at the Georg-August-Universität Göttingen invites applications for a position as Postdoctoral Researcher (f/m/d) This position is available starting from March 1st, 2021. It is a full time position with a limited contract of 3 years with the possibility of an extension for one additional year. Salary and working hours will be according to the German grade 13 TV-L (100 %, currently 39,80 hours per week). The position will be associated with the group of Prof. Michael Wibral. We are recruiting a Postdoc for the interdisciplinary research project "Evolutionary Convergence of Hierarchical Information Processing" funded by the German Research Foundation (DFG) within the research initiative SPP2205 "Evolutionary optimization of neuronal processing". The project aims to establish the common information theoretic principles of computation in hierarchical neural systems that are conserved across species from drosophila, via rodents to primates and humans. We are looking for candidates with an excellent PhD in neuroscience, cognitive science, physics, computer science or a related field who are committed to pursuing a career in research. The successful applicant will develop and apply novel information theoretic measures to electrophysiological neural recordings and calcium imaging signals to investigate signatures of predictive hierarchical information processing. The ideal candidate should have excellent skills in scientific writing, experience with the application of information theory to biological data, and should have demonstrated her/his ability to work independently. Prior experience with predictive coding theory and experiments are plus. Proven coding skills in a language relevant to data analysis (e.g. Python, Julia, R, Scala, Java), prior experience with research-data management systems (RDMS) are also considered as an advantage. We expect the job holder to establish a local database that organizes the vast amount of research data in this project. We offer the opportunity to become a member of a vibrant community dedicated to innovative research and teaching at the frontier of the exact and biological sciences, and to connect to the latest developments in information theory, including partial information decompositions. The Göttingen Campus is a leading center of biophysics and neuroscience in Europe hosting numerous internationally renowned research institutions, including the University and its Medical Center, the three life science Max Planck Institutes, the European Neuroscience Institute, the German Primate Center, and the Bernstein Center for Computational Neuroscience (BCCN) Göttingen. The University of Göttingen is an equal opportunities employer and places particular emphasis on fostering career opportunities for women. Qualified women are therefore strongly encouraged to apply in fields in which they are underrepresented. The university has committed itself to being a family-friendly institution and supports their employees in balancing work and family life. The mission of the University is to employ a greater number of severely disabled persons. Applications from severely disabled persons with equivalent qualifications will be given preference. Please submit your application in digital form only and send all relevant documents in one single PDF-document, including a letter of interest, your curriculum vitae with a list of publications, copies of your certificates and contact information of at least two references to christina.vonbehren(a)uni-goettingen.de<mailto:christina.vonbehren@uni-goettingen.de> by January 15th, 2021. If you have any questions, please contact Prof. Dr. Michael Wibral, via e-mail: michael.wibral(a)uni-goettingen.de<mailto:michael.wibral@uni-goettingen.de>. Please note: With submission of your application, you accept the processing of your applicant data in terms of data-protection law. Further information on the legal basis and data usage is provided in the Information General Data Protection Regulation (GDPR)<https://www.uni-goettingen.de/de/document/download/e0b7459b97d917e68e3464b8…> ------ Campus Institute for Dynamics of Biological Networks Bernstein Centre for Computational Neuroscience Goettingen University of Goettingen Postal address: Max Planck Institute of Experimental Medicine Hermann-Rein-Str. 3 37075 Goettingen Germany

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Scientist position in modeling at the Allen Institute
by Anton Arkhipov 22 Dec '20

22 Dec '20

Join us to analyze world-class experimental data and build the next generation of brain models! This opening is in the lab of Anton Arkhipov at the Allen Institute (Seattle, WA). One position is already taken, but one is still available: Scientist I - Bio-realistic Modeling of Reconstructed Cortical Tissue See details and apply here: https://alleninstitute.hrmdirect.com/employment/job-opening.php?req=1415274 The Scientist will focus on data analysis and modeling of structure, activity, and computations in mouse cortical circuits. This project will take advantage of unprecedented experimental datasets from the Allen Institute that contain a systematic characterization of synaptic connections between the cell types (https://portal.brain-map.org/explore/connectivity/synaptic-physiology) and a connectome of individual neurons coupled with dense recordings of activity in the mouse visual cortex (https://microns-explorer.org<https://microns-explorer.org/>). The Scientist will work collaboratively with colleagues to integrate these data into new, highly realistic network models of cortical circuits, use the models to explore theoretical predictions, and provide them as a resource to fuel future theoretical, modeling, and experimental work in the community.

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[JOB] Postdoctoral Fellow in Concussion Neuroscience, Machine learning and Cloud Computing
by Franco Pestilli 22 Dec '20

22 Dec '20

We would appreciate if you could share the ad below to relevant list. Drs. Nicholas Port and Franco Pestilli are seeking a Postdoctoral Fellow or Research Associate to join a multi-institutional team of Neuroscientists, Computer Scientists, and Engineers to work on a unique project to apply Machine learning and Cloud computing to improve our understanding of concussion and mild Traumatic Brain Injury. Applicants are invited to apply for this research Postdoctoral Fellow or Research Associate, non-tenure track position with a proposed start date of summer/fall 2021. The primary goal of the project is to use brainlife.io, and advanced machine learning methods to analyze behavioral and clinical outcomes, anatomical and diffusion weighted imaging from a large dataset (the NCAA/DOD CARE Consortium Advanced Research Core). The plan is to build predictive modeling tools available on brainlife.io that can be freely used by clinicians around the world to help in patient care management. Opportunities exist to join several additional concussion, machine learning, informatics and neuroimaging projects with the labs of Drs. Port and Pestilli. The position will be based in Dr. Port’s new, state-of-the-art laboratory within the dedicated Research Center for Elite Athletic Development in the new 66,000 square-foot South-End-Zone edition to Indiana University’s Memorial Stadium (https://iuhoosiers.com/facilities/the-excellence-academy/21 https://president.iu.edu/media/photos/2018/excellence-academy-dedication/in…) A major research university, Indiana University currently enrolls over 38,000 undergraduates and 10,000 graduate and professional students on the Bloomington campus, and has over 114,000 students in the University system. The School of Optometry, Program in Neuroscience and Cognitive Science Program are internationally recognized, vibrant research programs with a very collegial environment. The Department of Psychological and Brain Sciences has a research dedicated 3T Prisma, which Dr. Port uses regularly. A diverse community, Bloomington is located in a beautifully wooded and hilly area of the state, where cultural and recreational opportunities abound, housing costs are low, schools are excellent, and commute times are short. Additional information on the community of Bloomington can be found at https://www.visitbloomington.com/. The Postdoctoral Fellow position requires a PhD in Neuroscience, Computer Science, Engineering, Informatics, Vision Science or related scientific field by the time of appointment. For the Research Associate position, a minimum of a Masters degrees and 5+ year of appropriate work experience is required. Salary and rank will be commensurate with qualifications and experience. For consideration, please submit a letter of application, curriculum vita, and the names and contact information for at least three references. Interested candidates should review the application requirements and submit their application at: http://indiana.peopleadmin.com/postings/10224 Applications received by Jan 11, 2021, will be assured priority consideration; however, the search will remain open until the position is filled. Best regards, Franco FRANCO PESTILLI, PhD | Associate Professor Department of Psychology <https://liberalarts.utexas.edu/psychology/index.php> | College of Liberal Arts <https://liberalarts.utexas.edu/> | The University of Texas at Austin <https://www.utexas.edu/> he/him | pestilli(a)utexas.edu <mailto:pestilli@utexas.edu> | web <https://liberalarts.utexas.edu/psychology/faculty/fp4834> | github <https://github.com/francopestilli> | brainlife.io <https://brainlife.io/>

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Tenure-track faculty position in computational/theoretical neuroscience at UChicago
by Brent Doiron 21 Dec '20

21 Dec '20

*Tenure-track Faculty in Computational/Theoretical NeuroscienceThe University of Chicago: Biological Sciences Division: Department of Neurobiology* Position Description The University of Chicago's Grossman Center for Quantitative Biology and Human Behavior and the Department of Neurobiology seek faculty in computational/theoretical neuroscience. The appointee will be a core member of the newly-launched Grossman Center for Quantitative Biology and Human Behavior and will lead a ‘dry’ computational lab alongside a growing group of other computational neuroscientists. The Grossman Center seeks faculty who will establish deep and extensive collaborations with the vibrant experimental neuroscience community at the University of Chicago. Those developing computational models and analysis methods at the cellular, circuits, systems, or cognitive levels are especially welcome to apply. Appointment as a tenure-track assistant professor is expected, but we will consider appointments as a tenured associate or full professor. The University of Chicago is currently engaged in a major expansion in neuroscience, with computational neuroscience being an area of focus. The University offers a rich intellectual environment that includes a strong translational neuroscience community and affiliations with Argonne National Laboratory and the Marine Biological Laboratory in Woods Hole. The Division, other academic units of the University, and the School of Medicine, are all contained within one compact campus in Chicago's Hyde Park. Appointees will have access to state-of-the-art core facilities and to outstanding colleagues and graduate students affiliated with numerous degree-granting programs within and outside the biological sciences. Prior to the start of employment, qualified applicants must have a doctoral degree or equivalent. To be considered, those interested must apply through the University of Chicago’s Academic Recruitment job board, which uses Interfolio to accept applications: http://apply.interfolio.com/82120. Applicants must upload a CV including a bibliography, contact information for 3 references, a statement outlining research goals, and a teaching statement that can include a description of the candidate’s experience in teaching diverse students [the University’s Diversity Statement can be found at https://provost.uchicago.edu/statements-diversity] Review of complete applications will begin February 1 2021 and continue until the position is filled. Equal Employment Opportunity Statement We seek a diverse pool of applicants who wish to join an academic community that places the highest value on rigorous inquiry and encourages diverse perspectives, experiences, groups of individuals, and ideas to inform and stimulate intellectual challenge, engagement, and exchange. The University’s Statements on Diversity are at https://provost.uchicago.edu/statements-diversity. The University of Chicago is an Affirmative Action/Equal Opportunity/Disabled/Veterans Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, status as an individual with a disability, protected veteran status, genetic information, or other protected classes under the law. For additional information please see the University's Notice of Nondiscrimination. Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-1032 or email equalopportunity(a)uchicago.edu with their request. -- Brent Doiron Professor of Neurobiology and Statistics Director of the Grossman Center for Quantitative Biology and Human Behavior University of Chicago Chicago IL

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Postdoctoral Position at MassachusettsGeneral Hospital
by Xin Yu 21 Dec '20

21 Dec '20

*Postdoctoral Research Fellow Position at Massachusetts General Hospital* The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology at Massachusetts General Hospital is offering a postdoctoral position based on an NIH-funded Brain Initiative project developing novel multi-modal neuroimaging methodology in animal models. This position is open from Jan 1st. 2021 until filled. Potential candidates will be considered based on the following two research directions: *Research Direction #1 Multi-modal neuroimaging in animal brains, (Biologists/biomedical engineers/electrophysiologists) * a) Implement the MRI/EEG/calcium recording methods to specify brain state fluctuation correlated to pupil dynamics in awake rodents b) Target specific nuclei with deep brain optogenetic stimulation methods to study circuit-specific brain state neuromodulation. c) Develop an advanced fiber-optic imaging device for MRI compatible concurrent brain dynamic signal recordings, e.g., Ca2+, Glutamate, dopamine, and other neuromodulators. Experience with viral transfection, 2-PM or optical fiber recordings, or *in vivo. / in vitro. *electrophysiology in animal models (rodents) is highly desirable. The candidates should bear experience or strong interests in brain functional imaging, e.g. task-based BOLD fMRI. *Research Direction #2 Advanced fMRI and computational method development (Bio-engineering and computational neuroscientists)* a) Develop and optimize the high spatiotemporal fMRI method with high field MRI (>11.7T). b) Advanced resting-state fMRI analysis method development based on the neural network-based learning schemes. (being familiar with recurrent neural network design and implementation, e.g. ESN, GRU, et al.) c) Machine learning-based multi-modal brain signal dynamic signal analysis, e.g. LFP, Calcium, fMRI, pupil dynamics, et al. Candidates with strong computational skills and fMRI data processing experience are highly encouraged to apply for this position. The candidate should have strong teamwork skills to fit in a multi-disciplinary group. Please send your CV, contact information of three references, and a cover letter describing your background, interests, and research goals to Dr. Yu by e-mail: xyu9(a)mgh.harvard.edu. Please include “Postdoc Application for Multi-modal fMRI” in the subject line of your email. We welcome trainees with high motivation, curiosity, and scientific maturity. Also, Dr. Yu’s lab has extensive experience to support trainees to apply for international scholarships and help junior researchers to build their academic careers. Here is the selected publication in 2019-20 from Yu lab: 1. Chen Y, Sobczak F, Pais-Roldán P, Schwarz C, Koretsky AP, Yu X. Mapping the Brain-Wide Network Effects by Optogenetic Activation of the Corpus Callosum. Cereb Cortex. 2020 Oct 01; 30(11):5885-5898. PMID: *32556241 <https://www.ncbi.nlm.nih.gov/pubmed/32556241>*. 2. Sobczak F, He Y, Sejnowski TJ, Yu X. Predicting the fMRI Signal Fluctuation with Recurrent Neural Networks Trained on Vascular Network Dynamics. Cereb Cortex. 2020 Sep 17. PMID: *32940658 <https://www.ncbi.nlm.nih.gov/pubmed/32940658>*. 3. Drew PJ, Mateo C, Turner KL, Yu X, Kleinfeld D. Ultra-slow Oscillations in fMRI and Resting-State Connectivity: Neuronal and Vascular Contributions and Technical Confounds. Neuron. 2020 09 09; 107(5):782-804. PMID: *32791040 <https://www.ncbi.nlm.nih.gov/pubmed/32791040>*. 4. Pais-Roldán P, Takahashi K, Sobczak F, Chen Y, Zhao X, Zeng H, Jiang Y, Yu X. Indexing brain state-dependent pupil dynamics with simultaneous fMRI and optical fiber calcium recording. Proc Natl Acad Sci U S A. 2020 03 24; 117(12):6875-6882. PMID: *32139609 <https://www.ncbi.nlm.nih.gov/pubmed/32139609>*. 5. Ovsepian SV, Jiang Y, Sardella TCP, Malekzadeh-Najafabadi J, Burton NC, Yu X, Ntziachristos V. Visualizing cortical response to optogenetic stimulation and sensory inputs using multispectral handheld optoacoustic imaging. Photoacoustics. 2020 Mar; 17:100153. 6. Handwerker J, Pérez-Rodas M, Beyerlein M, Vincent F, Beck A, Freytag N, Yu X, Pohmann R, Anders J, Scheffler K. A CMOS NMR needle for probing brain physiology with high spatial and temporal resolution. Nat Methods. 2020 01; 17(1):64-67. PMID: *31768059 <https://www.ncbi.nlm.nih.gov/pubmed/31768059>*. 7. Chen X, Sobczak F, Chen Y, Jiang Y, Qian C, Lu Z, Ayata C, Logothetis NK, Yu X. Mapping optogenetically-driven single-vessel fMRI with concurrent neuronal calcium recordings in the rat hippocampus. Nat Commun. 2019 11 20; 10(1):5239. PMID: *31748553 <https://www.ncbi.nlm.nih.gov/pubmed/31748553>*. 8. He Y, Wang M, Yu X. High spatiotemporal vessel-specific hemodynamic mapping with multi-echo single-vessel fMRI. J Cereb Blood Flow Metab. 2020 Oct; 40(10):2098-2114. PMID: *31696765 <https://www.ncbi.nlm.nih.gov/pubmed/31696765>*. 9. Chen Y, Pais-Roldan P, Chen X, Frosz MH, Yu X. MRI-guided robotic arm drives optogenetic fMRI with concurrent Ca2+ recording. Nat Commun. 2019 06 10; 10(1):2536. PMID: *31182714 <https://www.ncbi.nlm.nih.gov/pubmed/31182714>*. 10. Pais-Roldán P, Edlow BL, Jiang Y, Stelzer J, Zou M, Yu X. Multimodal assessment of recovery from coma in a rat model of diffuse brainstem tegmentum injury. Neuroimage. 2019 04 01; 189:615-630. PMID: *30708105 <https://www.ncbi.nlm.nih.gov/pubmed/30708105>*.

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