From 50c6838868e8264ce5ef98f4d16ed0178d6ca9c9 Mon Sep 17 00:00:00 2001 From: Philipp Schlegel Date: Thu, 24 Oct 2024 11:49:45 +0100 Subject: [PATCH] docs: update publications --- publications.md | 272 +++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 220 insertions(+), 52 deletions(-) diff --git a/publications.md b/publications.md index 293cf2fb..a2860262 100644 --- a/publications.md +++ b/publications.md @@ -4,69 +4,237 @@ NAVis has been used in a range of high-profile publications. See below for a (pr Want to see your work listed here? Open an [Issue](https://github.com/navis-org/navis/issues), start a [Discussion](https://github.com/navis-org/navis/discussions) or open a PR to tell us about it! -## 2023 -1. _Interactions between specialized gain control mechanisms in olfactory processing._ Asa Barth-Maron, Isabel D’Alessandro, Rachel I. Wilson, Current Biology (2023); https://doi.org/10.1016/j.cub.2023.10.041 - -2. _Bisected graph matching improves automated pairing of bilaterally homologous neurons from connectomes._ Benjamin D. Pedigo, Michael Winding, Carey E. Priebe, Joshua T. Vogelstein; Network Neuroscience (2023); doi: https://doi.org/10.1162/netn_a_00287 - -3. _Vimo - Visual Analysis of Neuronal Connectivity Motifs_. Troidl, Jakob, Simon Warchol, Jinhan Choi, Jordan Matelsky, Nagaraju Dhanyasi, Xueying Wang, Brock Wester et al., IEEE transactions on visualization and computer graphics (2023). - -4. _BIFROST: a method for registering diverse imaging datasets._ Brezovec et al., bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.09.544408 - -5. _Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila._ Philipp Schlegel, Yijie Yin, Alexander S. Bates, Sven Dorkenwald, Katharina Eichler, Paul Brooks, [...] Davi D. Bock, Gregory S.X.E. Jefferis, bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546055 - -6. _Neuronal wiring diagram of an adult brain._ Dorkenwald S, Matsliah A, [...] Seung HS, Murthy M; FlyWire Consortium, bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546656. +## 2024 + +
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  1. + Whole-brain annotation and multi-connectome cell typing of Drosophila. Schlegel, P., Yin, Y., Bates, A.S. et al. Nature 634, 139–152 (2024). https://doi.org/10.1038/s41586-024-07686-5 +
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  1. + Neuronal wiring diagram of an adult brain. Dorkenwald, S., Matsliah, A., Sterling, A.R. et al. Nature 634, 124–138 (2024). https://doi.org/10.1038/s41586-024-07558-y +
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  1. + Heterogeneity of synaptic connectivity in the fly visual system.Cornean, J., Molina-Obando, S., Gür, B. et al. Nat Commun 15, 1570 (2024). https://doi.org/10.1038/s41467-024-45971-z +
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  1. + A Drosophila computational brain model reveals sensorimotor processing. Shiu, P.K., Sterne, G.R., Spiller, N. et al. Nature 634, 210–219 (2024). https://doi.org/10.1038/s41586-024-07763-9 +
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  1. + Ganguly, I., Heckman, E.L., Litwin-Kumar, A. et al. Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body. Nat Commun 15, 5698 (2024). https://doi.org/10.1038/s41467-024-49616-z +
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  1. + Connectome-driven neural inventory of a complete visual system. Aljoscha Nern, Frank Lösche, Shin-ya Takemura, [...] Stuart Berg, Gerald M Rubin, Michael B Reiser; bioRxiv (2024); doi: https://doi.org/10.1101/2024.04.16.589741 +
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-7. _Lineages to circuits: the developmental and evolutionary architecture of information channels into the central complex._ Kandimalla, P., Omoto, J.J., Hong, E.J. et al., J Comp Physiol (2023); https://doi.org/10.1007/s00359-023-01616-y - -8. _A network-based method for extracting the organization of brain-wide circuits from reconstructed connectome datasets_ K.K.H. Manjunatha, M. Bruzzone, G. Nicoletti, S. Suweis, M. dal Maschio bioRxiv (2023); doi: https://doi.org/10.1101/2023.05.21.541471 - -9. _Multisensory learning binds modality-specific neurons into a cross-modal memory engram._ Zeynep Okray, Pedro F. Jacob, Ciara Stern, Kieran Desmond, Nils Otto, Paola Vargas-Gutierrez, Scott Waddell, bioRxiv (2022); doi: https://doi.org/10.1101/2022.07.08.499174 - -10. _Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body._ Ganguly I, Heckman EL, Litwin-Kumar A, Clowney EJ, Behnia R, bioRxiv (2023); doi: https://doi.org/10.1101/2023.10.12.561793 - -11. _Synaptic and peptidergic connectomes of the Drosophila circadian clock._ Nils Reinhard, Ayumi Fukuda, Giulia Manoli, Emilia Derksen, Aika Saito, Gabriel Möller, Manabu Sekiguchi, Dirk Rieger, Charlotte Helfrich-Förster, Taishi Yoshii, Meet Zandawala, bioRxiv (2023); doi: https://doi.org/10.1101/2023.09.11.557222 - -12. _Heterogeneity of synaptic connectivity in the fly visual system._ Jacqueline Cornean, Sebastian Molina-Obando, Burak Gür, Annika Bast, Giordano Ramos-Traslosheros, Jonas Chojetzki, Lena Lörsch, Maria Ioannidou, Rachita Taneja, Christopher Schnaitmann, Marion Silies, bioRxiv (2023); doi: https://doi.org/10.1101/2023.08.29.555204 +## 2023 -13. _Hue selectivity from recurrent circuitry in Drosophila._ Matthias P Christenson, Álvaro Sanz Díez, Sarah L Heath, Maia Saavedra-Weisenhaus, Atsuko Adachi, L.F. Abbott, Rudy Behnia, bioRxiv (2023); doi: https://doi.org/10.1101/2023.07.12.548573 +
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  1. + Synaptic connectome of the Drosophila circadian clock. Nils Reinhard, Ayumi Fukuda, [...] Taishi Yoshii, Meet Zandawala; bioRxiv (2023); doi: https://doi.org/10.1101/2023.09.11.557222 +
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  1. + Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation. Elizabeth C. Marin, Billy J. Morris, Tomke Stürner [...] David Shepherd, Gregory S.X.E. Jefferis; bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.05.543407 +
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  1. + Interactions between specialized gain control mechanisms in olfactory processing. Asa Barth-Maron, Isabel D’Alessandro, Rachel I. Wilson, Current Biology (2023); https://doi.org/10.1016/j.cub.2023.10.041 +
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  1. + Bisected graph matching improves automated pairing of bilaterally homologous neurons from connectomes. Benjamin D. Pedigo, Michael Winding, Carey E. Priebe, Joshua T. Vogelstein; Network Neuroscience (2023); doi: https://doi.org/10.1162/netn_a_00287 +
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  1. + Vimo - Visual Analysis of Neuronal Connectivity Motifs. Troidl, Jakob, Simon Warchol, Jinhan Choi, Jordan Matelsky, Nagaraju Dhanyasi, Xueying Wang, Brock Wester et al., IEEE transactions on visualization and computer graphics (2023). +
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  1. + BIFROST: a method for registering diverse imaging datasets. Brezovec et al., bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.09.544408 +
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  1. + Lineages to circuits: the developmental and evolutionary architecture of information channels into the central complex. Kandimalla, P., Omoto, J.J., Hong, E.J. et al., J Comp Physiol (2023); https://doi.org/10.1007/s00359-023-01616-y +
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  1. + A network-based method for extracting the organization of brain-wide circuits from reconstructed connectome datasets. K.K.H. Manjunatha, M. Bruzzone, G. Nicoletti, S. Suweis, M. dal Maschio bioRxiv (2023); doi: https://doi.org/10.1101/2023.05.21.541471 +
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  1. + Multisensory learning binds modality-specific neurons into a cross-modal memory engram. Zeynep Okray, Pedro F. Jacob, Ciara Stern, Kieran Desmond, Nils Otto, Paola Vargas-Gutierrez, Scott Waddell, bioRxiv (2022); doi: https://doi.org/10.1101/2022.07.08.499174 +
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  1. + Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body. Ganguly I, Heckman EL, Litwin-Kumar A, Clowney EJ, Behnia R, bioRxiv (2023); doi: https://doi.org/10.1101/2023.10.12.561793 +
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  1. + Synaptic and peptidergic connectomes of the Drosophila circadian clock. Nils Reinhard, Ayumi Fukuda, Giulia Manoli, Emilia Derksen, Aika Saito, Gabriel Möller, Manabu Sekiguchi, Dirk Rieger, Charlotte Helfrich-Förster, Taishi Yoshii, Meet Zandawala, bioRxiv (2023); doi: https://doi.org/10.1101/2023.09.11.557222 +
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  1. + Heterogeneity of synaptic connectivity in the fly visual system. Jacqueline Cornean, Sebastian Molina-Obando, Burak Gür, Annika Bast, Giordano Ramos-Traslosheros, Jonas Chojetzki, Lena Lörsch, Maria Ioannidou, Rachita Taneja, Christopher Schnaitmann, Marion Silies, bioRxiv (2023); doi: https://doi.org/10.1101/2023.08.29.555204 +
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  1. + Hue selectivity from recurrent circuitry in Drosophila. Matthias P Christenson, Álvaro Sanz Díez, Sarah L Heath, Maia Saavedra-Weisenhaus, Atsuko Adachi, L.F. Abbott, Rudy Behnia, bioRxiv (2023); doi: https://doi.org/10.1101/2023.07.12.548573 +
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## 2022 -14. _FlyWire: online community for whole-brain connectomics._ Dorkenwald, S., McKellar, C.E., Macrina, T. et al., Nat Methods (2022). https://doi.org/10.1038/s41592-021-01330-0 - -15. _Synaptic wiring motifs in posterior parietal cortex support decision-making._ Kuan et al., bioRxiv (2022); doi: https://doi.org/10.1101/2022.04.13.488176 - -16. _A Survey of Visualization and Analysis in High‐Resolution Connectomics._ Beyer, Johanna, et al., Computer Graphics Forum. (2022); doi: https://doi.org/10.1111/cgf.14574 - -17. _Eye structure shapes neuron function in Drosophila motion vision._ Arthur Zhao, Eyal Gruntman, Aljoscha Nern, Nirmala A. Iyer, Edward M. Rogers, Sanna Koskela, Igor Siwanowicz, Marisa Dreher, Miriam A. Flynn, Connor W. Laughland, Henrique D.F. Ludwig, Alex G. Thomson, Cullen P. Moran, Bruck Gezahegn, Davi D. Bock, Michael B. Reiser, bioRxiv (2022); doi: https://doi.org/10.1101/2022.12.14.520178 - -18. _Dendrite architecture determines mitochondrial distribution patterns in vivo._ Eavan J. Donovan, Anamika Agrawal, Nicole Liberman, Jordan I. Kalai, Nicholas J. Chua, Elena F. Koslover, Erin L. Barnhart, bioRxiv (2022); doi: https://doi.org/10.1101/2022.07.01.497972 - -19. _Structured sampling of olfactory input by the fly mushroom body._ Zhihao Zheng, Feng Li, Corey Fisher, Iqbal J. Ali, Nadiya Sharifi, Steven Calle-Schuler, Joseph Hsu, Najla Masoodpanah, Lucia Kmecova, Tom Kazimiers, Eric Perlman, Matthew Nichols, Peter H. Li, Viren Jain, Davi D. Bock, Current Biology (2022); doi: https://doi.org/10.1016/j.cub.2022.06.031 - -20. _The connectome of an insect brain._ Winding M, Pedigo BD, Barnes CL, Patsolic HG, Park Y, Kazimiers T, Fushiki A, Andrade IV, Khandelwal A, Valdes-Aleman J, Li F, Randel N, Barsotti E, Correia A, Fetter RD, Hartenstein V, Priebe CE, Vogelstein JT, Cardona A, Zlatic M, Science (2023 ); doi: 10.1126/science.add9330 +
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  1. + Gliotransmission of D-serine promotes thirst-directed behaviors in Drosophila. Annie Park, Vincent Croset, Nils Otto, [...] Scott Waddell; Current Biology (2022); doi: https://doi.org/10.1016/j.cub.2022.07.038 +
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  1. + FlyWire: online community for whole-brain connectomics. Dorkenwald, S., McKellar, C.E., Macrina, T. et al., Nat Methods (2022). https://doi.org/10.1038/s41592-021-01330-0 +
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  1. + Synaptic wiring motifs in posterior parietal cortex support decision-making. Kuan et al., bioRxiv (2022); doi: https://doi.org/10.1101/2022.04.13.488176 +
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  1. + A Survey of Visualization and Analysis in High‐Resolution Connectomics. Beyer, Johanna, et al., Computer Graphics Forum. (2022); doi: https://doi.org/10.1111/cgf.14574 +
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  1. + Eye structure shapes neuron function in Drosophila motion vision. Arthur Zhao, Eyal Gruntman, Aljoscha Nern, Nirmala A. Iyer, Edward M. Rogers, Sanna Koskela, Igor Siwanowicz, Marisa Dreher, Miriam A. Flynn, Connor W. Laughland, Henrique D.F. Ludwig, Alex G. Thomson, Cullen P. Moran, Bruck Gezahegn, Davi D. Bock, Michael B. Reiser, bioRxiv (2022); doi: https://doi.org/10.1101/2022.12.14.520178 +
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  1. + Dendrite architecture determines mitochondrial distribution patterns in vivo. Eavan J. Donovan, Anamika Agrawal, Nicole Liberman, Jordan I. Kalai, Nicholas J. Chua, Elena F. Koslover, Erin L. Barnhart, bioRxiv (2022); doi: https://doi.org/10.1101/2022.07.01.497972 +
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  1. + Structured sampling of olfactory input by the fly mushroom body. Zhihao Zheng, Feng Li, Corey Fisher, Iqbal J. Ali, Nadiya Sharifi, Steven Calle-Schuler, Joseph Hsu, Najla Masoodpanah, Lucia Kmecova, Tom Kazimiers, Eric Perlman, Matthew Nichols, Peter H. Li, Viren Jain, Davi D. Bock, Current Biology (2022); doi: https://doi.org/10.1016/j.cub.2022.06.031 +
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  1. + The connectome of an insect brain. Winding M, Pedigo BD, Barnes CL, Patsolic HG, Park Y, Kazimiers T, Fushiki A, Andrade IV, Khandelwal A, Valdes-Aleman J, Li F, Randel N, Barsotti E, Correia A, Fetter RD, Hartenstein V, Priebe CE, Vogelstein JT, Cardona A, Zlatic M, Science (2023 ); doi: https://doi.org/10.1126/science.add9330 +
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## 2021 -21. _Information flow, cell types and stereotypy in a full olfactory connectome._ Schlegel, Bates et al., eLife (2021); doi: https://doi.org/10.7554/eLife.66018 -22. _A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior._ Nojima T, Rings A, Allen AM, Otto N, Verschut TA, Billeter JC, Neville MC, Goodwin SF. Curr Biol. (2021); doi: https://doi.org/10.1016/j.cub.2020.12.047 +
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  1. + Information flow, cell types and stereotypy in a full olfactory connectome. Schlegel, Bates et al., eLife (2021); doi: https://doi.org/10.7554/eLife.66018 +
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-23. _A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS._ Brandon Mark, Sen-Lin Lai, Aref Arzan Zarin, Laurina Manning, Ashok Litwin-Kumar, Albert Cardona, James W. Truman, Chris Q. Doe, eLife (2021); doi: https://doi.org/10.7554/eLife.67510 +
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  1. + A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior. Nojima T, Rings A, Allen AM, Otto N, Verschut TA, Billeter JC, Neville MC, Goodwin SF. Curr Biol. (2021); doi: https://doi.org/10.1016/j.cub.2020.12.047 +
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-24. _Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy._ Jasper S. Phelps, David Grant Colburn Hildebrand, Brett J. Graham, Aaron T. Kuan, Logan A. Thomas, Tri M. Nguyen, Julia Buhmann, Anthony W. Azevedo, Anne Sustar, Sweta Agrawal, Mingguan Liu, Brendan L. Shanny, Jan Funke, John C. Tuthill, Wei-Chung Allen Lee, -Cell (2021); doi: https://doi.org/10.1016/j.cell.2020.12.013. +
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  1. + A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS. Brandon Mark, Sen-Lin Lai, Aref Arzan Zarin, Laurina Manning, Ashok Litwin-Kumar, Albert Cardona, James W. Truman, Chris Q. Doe, eLife (2021); doi: https://doi.org/10.7554/eLife.67510 +
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  1. + Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. Jasper S. Phelps, David Grant Colburn Hildebrand, Brett J. Graham, Aaron T. Kuan, Logan A. Thomas, Tri M. Nguyen, Julia Buhmann, Anthony W. Azevedo, Anne Sustar, Sweta Agrawal, Mingguan Liu, Brendan L. Shanny, Jan Funke, John C. Tuthill, Wei-Chung Allen Lee, + Cell (2021); doi: https://doi.org/10.1016/j.cell.2020.12.013. +
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-## 2020 -25. _Complete connectomic reconstruction of olfactory projection neurons in the fly brain._ Bates, Alexander S., et al., Current Biology (2020); doi: https://doi.org/10.1016/j.cub.2020.06.042 - -26. _Convergence of distinct subpopulations of mechanosensory neurons onto a neural circuit that elicits grooming._ Stefanie Hampel, Katharina Eichler, Daichi Yamada, Hyunsoo Kim, Mihoko Horigome, Romain Franconville, Davi D. Bock, Azusa Kamikouchi, Andrew M. Seeds, bioRxiv (2020); doi: https://doi.org/10.1101/2020.06.08.141341 - -27. _The Wiring Logic of an Identified Serotonergic Neuron That Spans Sensory Networks._ Kaylynn E. Coates, Steven A. Calle-Schuler, Levi M. Helmick, Victoria L. Knotts, Brennah N. Martik, Farzaan Salman, Lauren T. Warner, Sophia V. Valla, Davi D. Bock, Andrew M. Dacks, Journal of Neuroscience (2020); doi: https://doi.org/10.1523/JNEUROSCI.0552-20.2020 -28. _Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila._ Nils Otto, Markus W. Pleijzier, Isabel C. Morgan, Amelia J. Edmondson-Stait, Konrad J. Heinz, Ildiko Stark, Georgia Dempsey, Masayoshi Ito, Ishaan Kapoor, Joseph Hsu, Philipp M. Schlegel, Alexander S. Bates, Li Feng, Marta Costa, Kei Ito, Davi D. Bock, Gerald M. Rubin, Gregory S.X.E. Jefferis, Scott Waddell, Current Biology (2020); doi: https://doi.org/10.1016/j.cub.2020.05.077 - -29. _The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor._ Turner-Evans DB, Jensen KT, Ali S, Paterson T, Sheridan A, Ray RP, Wolff T, Lauritzen JS, Rubin GM, Bock DD, Jayaraman V., Neuron (2020); doi: https://doi.org/10.1016/j.neuron.2020.08.006 +## 2020 -30. _Connectomics Analysis Reveals First-, Second-, and Third-Order Thermosensory and Hygrosensory Neurons in the Adult Drosophila Brain._ Marin EC, Büld L, Theiss M, Sarkissian T, Roberts RJV, Turnbull R, Tamimi IFM, Pleijzier MW, Laursen WJ, Drummond N, Schlegel P, Bates AS, Li F, Landgraf M, Costa M, Bock DD, Garrity PA, Jefferis GSXE, Curr Biol. (2020); doi: https://doi.org/10.1016/j.cub.2020.06.028 \ No newline at end of file +
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  1. + Complete connectomic reconstruction of olfactory projection neurons in the fly brain. Bates, Alexander S., et al., Current Biology (2020); doi: https://doi.org/10.1016/j.cub.2020.06.042 +
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  1. + Convergence of distinct subpopulations of mechanosensory neurons onto a neural circuit that elicits grooming. Stefanie Hampel, Katharina Eichler, Daichi Yamada, Hyunsoo Kim, Mihoko Horigome, Romain Franconville, Davi D. Bock, Azusa Kamikouchi, Andrew M. Seeds, bioRxiv (2020); doi: https://doi.org/10.1101/2020.06.08.141341 +
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  1. + The Wiring Logic of an Identified Serotonergic Neuron That Spans Sensory Networks. Kaylynn E. Coates, Steven A. Calle-Schuler, Levi M. Helmick, Victoria L. Knotts, Brennah N. Martik, Farzaan Salman, Lauren T. Warner, Sophia V. Valla, Davi D. Bock, Andrew M. Dacks, Journal of Neuroscience (2020); doi: https://doi.org/10.1523/JNEUROSCI.0552-20.2020 +
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  1. + Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila. Nils Otto, Markus W. Pleijzier, Isabel C. Morgan, Amelia J. Edmondson-Stait, Konrad J. Heinz, Ildiko Stark, Georgia Dempsey, Masayoshi Ito, Ishaan Kapoor, Joseph Hsu, Philipp M. Schlegel, Alexander S. Bates, Li Feng, Marta Costa, Kei Ito, Davi D. Bock, Gerald M. Rubin, Gregory S.X.E. Jefferis, Scott Waddell, Current Biology (2020); doi: https://doi.org/10.1016/j.cub.2020.05.077 +
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  1. + The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor. Turner-Evans DB, Jensen KT, Ali S, Paterson T, Sheridan A, Ray RP, Wolff T, Lauritzen JS, Rubin GM, Bock DD, Jayaraman V., Neuron (2020); doi: https://doi.org/10.1016/j.neuron.2020.08.006 +
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  1. + Connectomics Analysis Reveals First-, Second-, and Third-Order Thermosensory and Hygrosensory Neurons in the Adult Drosophila Brain. Marin EC, Büld L, Theiss M, Sarkissian T, Roberts RJV, Turnbull R, Tamimi IFM, Pleijzier MW, Laursen WJ, Drummond N, Schlegel P, Bates AS, Li F, Landgraf M, Costa M, Bock DD, Garrity PA, Jefferis GSXE, Curr Biol. (2020); doi: https://doi.org/10.1016/j.cub.2020.06.028 +
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