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A Connectome of the Adult Drosophila Central Brain

View ORCID ProfileC. Shan Xu, View ORCID ProfileMichal Januszewski, View ORCID ProfileZhiyuan Lu, Shin-ya Takemura, View ORCID ProfileKenneth J. Hayworth, Gary Huang, Kazunori Shinomiya, View ORCID ProfileJeremy Maitin-Shepard, David Ackerman, Stuart Berg, Tim Blakely, View ORCID ProfileJohn Bogovic, Jody Clements, Tom Dolafi, View ORCID ProfilePhilip Hubbard, View ORCID ProfileDagmar Kainmueller, View ORCID ProfileWilliam Katz, Takashi Kawase, Khaled A. Khairy, Laramie Leavitt, View ORCID ProfilePeter H. Li, Larry Lindsey, View ORCID ProfileNicole Neubarth, Donald J. Olbris, Hideo Otsuna, Eric T. Troutman, Lowell Umayam, Ting Zhao, Masayoshi Ito, Jens Goldammer, Tanya Wolff, Robert Svirskas, View ORCID ProfilePhilipp Schlegel, View ORCID ProfileErika R. Neace, View ORCID ProfileChristopher J. Knecht Jr., View ORCID ProfileChelsea X. Alvarado, View ORCID ProfileDennis A. Bailey, View ORCID ProfileSamantha Ballinger, View ORCID ProfileJolanta A Borycz, View ORCID ProfileBrandon S. Canino, Natasha Cheatham, View ORCID ProfileMichael Cook, Marisa Dreher, View ORCID ProfileOctave Duclos, View ORCID ProfileBryon Eubanks, Kelli Fairbanks, View ORCID ProfileSamantha Finley, View ORCID ProfileNora Forknall, View ORCID ProfileAudrey Francis, View ORCID ProfileGary Patrick Hopkins, View ORCID ProfileEmily M. Joyce, View ORCID ProfileSungJin Kim, View ORCID ProfileNicole A. Kirk, View ORCID ProfileJulie Kovalyak, View ORCID ProfileShirley A. Lauchie, View ORCID ProfileAlanna Lohff, View ORCID ProfileCharli Maldonado, View ORCID ProfileEmily A. Manley, View ORCID ProfileSari McLin, View ORCID ProfileCaroline Mooney, View ORCID ProfileMiatta Ndama, View ORCID ProfileOmotara Ogundeyi, View ORCID ProfileNneoma Okeoma, View ORCID ProfileChristopher Ordish, View ORCID ProfileNicholas Padilla, View ORCID ProfileChristopher Patrick, Tyler Paterson, Elliott E. Phillips, View ORCID ProfileEmily M. Phillips, View ORCID ProfileNeha Rampally, View ORCID ProfileCaitlin Ribeiro, View ORCID ProfileMadelaine K Robertson, View ORCID ProfileJon Thomson Rymer, View ORCID ProfileSean M. Ryan, View ORCID ProfileMegan Sammons, Anne K. Scott, View ORCID ProfileAshley L. Scott, View ORCID ProfileAya Shinomiya, Claire Smith, Kelsey Smith, View ORCID ProfileNatalie L. Smith, View ORCID ProfileMargaret A. Sobeski, View ORCID ProfileAlia Suleiman, Jackie Swift, View ORCID ProfileSatoko Takemura, View ORCID ProfileIris Talebi, View ORCID ProfileDorota Tarnogorska, View ORCID ProfileEmily Tenshaw, View ORCID ProfileTemour Tokhi, View ORCID ProfileJohn J. Walsh, Tansy Yang, View ORCID ProfileJane Anne Horne, Feng Li, View ORCID ProfileRuchi Parekh, View ORCID ProfilePatricia K. Rivlin, View ORCID ProfileVivek Jayaraman, Kei Ito, Stephan Saalfeld, Reed George, View ORCID ProfileIan Meinertzhagen, View ORCID ProfileGerald M. Rubin, Harald F. Hess, View ORCID ProfileLouis K. Scheffer, View ORCID ProfileViren Jain, View ORCID ProfileStephen M. Plaza
doi: https://doi.org/10.1101/2020.01.21.911859
C. Shan Xu
Janelia Research Campus, HHMI
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Michal Januszewski
Google Research
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Zhiyuan Lu
Janelia Research Campus, HHMILife Sciences Center, Dalhousie University
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Shin-ya Takemura
Janelia Research Campus, HHMI
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Kenneth J. Hayworth
Janelia Research Campus, HHMI
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Gary Huang
Janelia Research Campus, HHMI
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Kazunori Shinomiya
Janelia Research Campus, HHMI
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Jeremy Maitin-Shepard
Google Research
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David Ackerman
Janelia Research Campus, HHMI
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Stuart Berg
Janelia Research Campus, HHMI
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Tim Blakely
Google Research
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John Bogovic
Janelia Research Campus, HHMI
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Jody Clements
Janelia Research Campus, HHMI
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Tom Dolafi
Janelia Research Campus, HHMI
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Philip Hubbard
Janelia Research Campus, HHMI
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Dagmar Kainmueller
Janelia Research Campus, HHMIMax Delbrueck Center for Molecular Medicine
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William Katz
Janelia Research Campus, HHMI
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Takashi Kawase
Janelia Research Campus, HHMI
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Khaled A. Khairy
Janelia Research Campus, HHMIDepartment of Developmental Neurobiology, St. Jude Childrens Research Hospital
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Laramie Leavitt
Google Research
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Peter H. Li
Google Research
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Larry Lindsey
Google Research
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Nicole Neubarth
Two Six Labs
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Donald J. Olbris
Janelia Research Campus, HHMI
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Hideo Otsuna
Janelia Research Campus, HHMI
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Eric T. Troutman
Janelia Research Campus, HHMI
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Lowell Umayam
Janelia Research Campus, HHMI
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Ting Zhao
Janelia Research Campus, HHMI
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Masayoshi Ito
Janelia Research Campus, HHMIUniversity of Tokyo, Institute for Quantitative Biosciences
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Jens Goldammer
Janelia Research Campus, HHMIInstitute of Zoology, Biocenter Cologne, University of Cologne
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Tanya Wolff
Janelia Research Campus, HHMI
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Robert Svirskas
Janelia Research Campus, HHMI
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Philipp Schlegel
Department of Zoology, University of Cambridge
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Erika R. Neace
Janelia Research Campus, HHMI
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Christopher J. Knecht
Janelia Research Campus, HHMI
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Chelsea X. Alvarado
Janelia Research Campus, HHMI
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Dennis A. Bailey
Janelia Research Campus, HHMI
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Samantha Ballinger
Janelia Research Campus, HHMI
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Jolanta A Borycz
Life Sciences Center, Dalhousie University
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Brandon S. Canino
Janelia Research Campus, HHMI
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Natasha Cheatham
Janelia Research Campus, HHMI
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Michael Cook
Janelia Research Campus, HHMI
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Marisa Dreher
Janelia Research Campus, HHMI
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Octave Duclos
Janelia Research Campus, HHMI
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Bryon Eubanks
Janelia Research Campus, HHMI
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Kelli Fairbanks
Janelia Research Campus, HHMI
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Samantha Finley
Janelia Research Campus, HHMI
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Nora Forknall
Janelia Research Campus, HHMI
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Audrey Francis
Janelia Research Campus, HHMI
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Gary Patrick Hopkins
Janelia Research Campus, HHMI
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Emily M. Joyce
Janelia Research Campus, HHMI
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SungJin Kim
Janelia Research Campus, HHMI
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Nicole A. Kirk
Janelia Research Campus, HHMI
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Julie Kovalyak
Janelia Research Campus, HHMI
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Shirley A. Lauchie
Janelia Research Campus, HHMI
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Alanna Lohff
Janelia Research Campus, HHMI
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Charli Maldonado
Janelia Research Campus, HHMI
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Emily A. Manley
Janelia Research Campus, HHMI
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Sari McLin
Life Sciences Center, Dalhousie University
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Caroline Mooney
Janelia Research Campus, HHMI
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Miatta Ndama
Janelia Research Campus, HHMI
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Omotara Ogundeyi
Janelia Research Campus, HHMI
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Nneoma Okeoma
Janelia Research Campus, HHMI
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Christopher Ordish
Janelia Research Campus, HHMI
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Nicholas Padilla
Janelia Research Campus, HHMI
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Christopher Patrick
Janelia Research Campus, HHMI
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Tyler Paterson
Janelia Research Campus, HHMI
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Elliott E. Phillips
Janelia Research Campus, HHMI
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Emily M. Phillips
Janelia Research Campus, HHMI
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Neha Rampally
Janelia Research Campus, HHMI
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Caitlin Ribeiro
Janelia Research Campus, HHMI
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Madelaine K Robertson
Life Sciences Center, Dalhousie University
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Jon Thomson Rymer
Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Megan Sammons
Janelia Research Campus, HHMI
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Anne K. Scott
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Janelia Research Campus, HHMI
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Aya Shinomiya
Janelia Research Campus, HHMI
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Claire Smith
Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Iris Talebi
Janelia Research Campus, HHMI
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Dorota Tarnogorska
Life Sciences Center, Dalhousie University
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Janelia Research Campus, HHMI
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Temour Tokhi
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Jane Anne Horne
Janelia Research Campus, HHMILife Sciences Center, Dalhousie University
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Kei Ito
Janelia Research Campus, HHMIUniversity of Tokyo, Institute for Quantitative BiosciencesInstitute of Zoology, Biocenter Cologne, University of Cologne
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Stephan Saalfeld
Janelia Research Campus, HHMI
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Janelia Research Campus, HHMI
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Janelia Research Campus, HHMILife Sciences Center, Dalhousie University
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Janelia Research Campus, HHMI
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Louis K. Scheffer
Janelia Research Campus, HHMI
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  • For correspondence: schefferl@janelia.hhmi.org
Viren Jain
Google Research
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Stephen M. Plaza
Janelia Research Campus, HHMI
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Abstract

The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions.

Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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A Connectome of the Adult Drosophila Central Brain
C. Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J. Hayworth, Gary Huang, Kazunori Shinomiya, Jeremy Maitin-Shepard, David Ackerman, Stuart Berg, Tim Blakely, John Bogovic, Jody Clements, Tom Dolafi, Philip Hubbard, Dagmar Kainmueller, William Katz, Takashi Kawase, Khaled A. Khairy, Laramie Leavitt, Peter H. Li, Larry Lindsey, Nicole Neubarth, Donald J. Olbris, Hideo Otsuna, Eric T. Troutman, Lowell Umayam, Ting Zhao, Masayoshi Ito, Jens Goldammer, Tanya Wolff, Robert Svirskas, Philipp Schlegel, Erika R. Neace, Christopher J. Knecht Jr., Chelsea X. Alvarado, Dennis A. Bailey, Samantha Ballinger, Jolanta A Borycz, Brandon S. Canino, Natasha Cheatham, Michael Cook, Marisa Dreher, Octave Duclos, Bryon Eubanks, Kelli Fairbanks, Samantha Finley, Nora Forknall, Audrey Francis, Gary Patrick Hopkins, Emily M. Joyce, SungJin Kim, Nicole A. Kirk, Julie Kovalyak, Shirley A. Lauchie, Alanna Lohff, Charli Maldonado, Emily A. Manley, Sari McLin, Caroline Mooney, Miatta Ndama, Omotara Ogundeyi, Nneoma Okeoma, Christopher Ordish, Nicholas Padilla, Christopher Patrick, Tyler Paterson, Elliott E. Phillips, Emily M. Phillips, Neha Rampally, Caitlin Ribeiro, Madelaine K Robertson, Jon Thomson Rymer, Sean M. Ryan, Megan Sammons, Anne K. Scott, Ashley L. Scott, Aya Shinomiya, Claire Smith, Kelsey Smith, Natalie L. Smith, Margaret A. Sobeski, Alia Suleiman, Jackie Swift, Satoko Takemura, Iris Talebi, Dorota Tarnogorska, Emily Tenshaw, Temour Tokhi, John J. Walsh, Tansy Yang, Jane Anne Horne, Feng Li, Ruchi Parekh, Patricia K. Rivlin, Vivek Jayaraman, Kei Ito, Stephan Saalfeld, Reed George, Ian Meinertzhagen, Gerald M. Rubin, Harald F. Hess, Louis K. Scheffer, Viren Jain, Stephen M. Plaza
bioRxiv 2020.01.21.911859; doi: https://doi.org/10.1101/2020.01.21.911859
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A Connectome of the Adult Drosophila Central Brain
C. Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J. Hayworth, Gary Huang, Kazunori Shinomiya, Jeremy Maitin-Shepard, David Ackerman, Stuart Berg, Tim Blakely, John Bogovic, Jody Clements, Tom Dolafi, Philip Hubbard, Dagmar Kainmueller, William Katz, Takashi Kawase, Khaled A. Khairy, Laramie Leavitt, Peter H. Li, Larry Lindsey, Nicole Neubarth, Donald J. Olbris, Hideo Otsuna, Eric T. Troutman, Lowell Umayam, Ting Zhao, Masayoshi Ito, Jens Goldammer, Tanya Wolff, Robert Svirskas, Philipp Schlegel, Erika R. Neace, Christopher J. Knecht Jr., Chelsea X. Alvarado, Dennis A. Bailey, Samantha Ballinger, Jolanta A Borycz, Brandon S. Canino, Natasha Cheatham, Michael Cook, Marisa Dreher, Octave Duclos, Bryon Eubanks, Kelli Fairbanks, Samantha Finley, Nora Forknall, Audrey Francis, Gary Patrick Hopkins, Emily M. Joyce, SungJin Kim, Nicole A. Kirk, Julie Kovalyak, Shirley A. Lauchie, Alanna Lohff, Charli Maldonado, Emily A. Manley, Sari McLin, Caroline Mooney, Miatta Ndama, Omotara Ogundeyi, Nneoma Okeoma, Christopher Ordish, Nicholas Padilla, Christopher Patrick, Tyler Paterson, Elliott E. Phillips, Emily M. Phillips, Neha Rampally, Caitlin Ribeiro, Madelaine K Robertson, Jon Thomson Rymer, Sean M. Ryan, Megan Sammons, Anne K. Scott, Ashley L. Scott, Aya Shinomiya, Claire Smith, Kelsey Smith, Natalie L. Smith, Margaret A. Sobeski, Alia Suleiman, Jackie Swift, Satoko Takemura, Iris Talebi, Dorota Tarnogorska, Emily Tenshaw, Temour Tokhi, John J. Walsh, Tansy Yang, Jane Anne Horne, Feng Li, Ruchi Parekh, Patricia K. Rivlin, Vivek Jayaraman, Kei Ito, Stephan Saalfeld, Reed George, Ian Meinertzhagen, Gerald M. Rubin, Harald F. Hess, Louis K. Scheffer, Viren Jain, Stephen M. Plaza
bioRxiv 2020.01.21.911859; doi: https://doi.org/10.1101/2020.01.21.911859

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