TY - JOUR A1 - Petkova, Mariela D. A1 - Januszewski, Michał A1 - Blakely, Tim A1 - Herrera, Kristian J. A1 - Schuhknecht, Gregor F.P. A1 - Tiller, Robert A1 - Choi, Jinhan A1 - Schalek, Richard L. A1 - Boulanger-Weill, Jonathan A1 - Peleg, Adi A1 - Wu, Yuelong A1 - Wang, Shuohong A1 - Troidl, Jakob A1 - Vohra, Sumit Kumar A1 - Wei, Donglai A1 - Lin, Zudi A1 - Bahl, Armin A1 - Tapia, Juan Carlos A1 - Iyer, Nirmala A1 - Miller, Zachary T. A1 - Hebert, Kathryn B. A1 - Pavarino, Elisa C. A1 - Taylor, Milo A1 - Deng, Zixuan A1 - Stingl, Moritz A1 - Hockling, Dana A1 - Hebling, Alina A1 - Wang, Ruohong C. A1 - Zhang, Lauren L. A1 - Dvorak, Sam A1 - Faik, Zainab A1 - King, Jr., Kareem I. A1 - Goel, Pallavi A1 - Wagner-Carena, Julian A1 - Aley, David A1 - Chalyshkan, Selimzhan A1 - Contreas, Dominick A1 - Li, Xiong A1 - Muthukumar, Akila V. A1 - Vernaglia, Marina S. A1 - Carrasco, Teodoro Tapia A1 - Melnychuck, Sofia A1 - Yan, TingTing A1 - Dalal, Ananya A1 - DiMartino, James A1 - Brown, Sam A1 - Safo-Mensa, Nana A1 - Greenberg, Ethan A1 - Cook, Michael A1 - Finley, Samantha A1 - Flynn, Miriam A. A1 - Hopkins, Gary Patrick A1 - Kovalyak, Julie A1 - Leonard, Meghan A1 - Lohff, Alanna A1 - Ordish, Christopher A1 - Scott, Ashley L. A1 - Takemura, Satoko A1 - Smith, Claire A1 - Walsh, John J. A1 - Berger, Daniel R. A1 - Pfister, Hanspeter A1 - Berg, Stuart A1 - Knecht, Christopher A1 - Meissner, Geoffrey W. A1 - Korff, Wyatt A1 - Ahrens, Misha B A1 - Jain, Viren A1 - Lichtman, Jeff W. A1 - Engert, Florian T1 - A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain JF - bioRxiv N2 - We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing >180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the dataset’s utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. Y1 - 2025 U6 - https://doi.org/10.1101/2025.06.10.658982 ER - TY - JOUR A1 - Noé, Frank A1 - Horenko, Illia A1 - Schütte, Christof A1 - Smith, J. T1 - Hierarchical Analysis of Conformational Dynamics in Biomolecules JF - J. Chem. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/37/ U6 - https://doi.org/10.1063/1.2714539 VL - 126 IS - 15 SP - 155102 ER - TY - JOUR A1 - Noé, Frank A1 - Smith, J. A1 - Schütte, Christof T1 - A network-based approach to biomolecular dynamics JF - From Computational Biophysics to Systems Biology (CBSB07). Editors Y1 - 2007 UR - http://publications.imp.fu-berlin.de/319/ VL - NIC Series 36 PB - John von Neumann Institute for Computing, Jülich ER - TY - JOUR A1 - Cournia, Zoe A1 - Allen, Toby W. A1 - Andricioaei, Ioan A1 - Antonny, Bruno A1 - Baum, Daniel A1 - Brannigan, Grace A1 - Buchete, Nicolae-Viorel A1 - Deckman, Jason T. A1 - Delemotte, Lucie A1 - del Val, Coral A1 - Friedman, Ran A1 - Gkeka, Paraskevi A1 - Hege, Hans-Christian A1 - Hénin, Jérôme A1 - Kasimova, Marina A. A1 - Kolocouris, Antonios A1 - Klein, Michael L. A1 - Khalid, Syma A1 - Lemieux, Joanne A1 - Lindow, Norbert A1 - Roy, Mahua A1 - Selent, Jana A1 - Tarek, Mounir A1 - Tofoleanu, Florentina A1 - Vanni, Stefano A1 - Urban, Sinisa A1 - Wales, David J. A1 - Smith, Jeremy C. A1 - Bondar, Ana-Nicoleta T1 - Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory JF - Journal of Membrane Biology Y1 - 2015 U6 - https://doi.org/10.1007/s00232-015-9802-0 VL - 248 IS - 4 SP - 611 EP - 640 ER -