skip to content

Peer-reviewed publications


*/#: these authors contributed equally


Peer-reviewed publications


Julia Buhmann, Arlo Sheridan, Caroline Malin-Mayor, Philipp Schlegel, Stephan Gerhard, Tom Kazimiers, Renate Krause, Tri M. Nguyen, Larissa Heinrich, Wei-Chung Allen Lee, Rachel Wilson, Stephan Saalfeld, Gregory JefferisDavi Bock, Srinivas Turaga, Matthew Cook, Jan Funke (2021) Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM DatasetNature Methods (preprint)

Philipp Schlegel*, Alexander S. Bates*, Tomke Stürner#Sridhar Jagannathan#Nikolas DrummondJoseph HsuLaia Serratosa CapdevilaAlexandre JavierElizabeth C. Marin, Asa Barth-Maron, Imaan F. M. TamimiFeng LiGerald M. Rubin, Stephen M. Plaza, Marta CostaGregory S. X. E. Jefferis (2021) Information flow, cell types and stereotypy in a full olfactory connectomeeLife (preprinttwitter thread)



Nojima T, Rings A, Allen AM, Otto N, Verschut TA, Billeter JC, Neville MC, Goodwin SF (2021) A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior. Current Biology

Feng Li, Jack W Lindsey, Elizabeth C Marin, Nils Otto, Marisa Dreher, Georgia Dempsey, Ildiko Stark, Alexander S Bates, Markus William Pleijzier, Philipp Schlegel, Aljoscha Nern, Shin-ya Takemura, Nils Eckstein, Tansy Yang, Audrey Francis, Amalia Braun, Ruchi Parekh, Marta Costa, Louis K Scheffer, Yoshi Aso, Gregory SXE Jefferis, Larry F Abbott, Ashok Litwin-Kumar, Scott Waddell, Gerald M Rubin (2020) The connectome of the adult Drosophila mushroom body provides insights into function, eLife (preprint)

Scheffer, Louis K and Xu, C Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J and Huang, Gary B and Shinomiya, Kazunori and Maitlin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip M and Katz, William T and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A and Leavitt, Laramie and Li, Peter H and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J and Otsuna, Hideo and Trautman, Eric T and Ito, Masayoshi and Bates, Alexander S and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika and Knecht, Christopher J and Alvarado, Chelsea X and Bailey, Dennis A and Ballinger, Samantha and Borycz, Jolanta A and Canino, Brandon S and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M and Kim, SungJin and Kirk, Nicole A. and Kovalyak, Julie and Lauchie, Shirley and Lohff, Alanna and Maldonado, Charli and Manley, Emily A and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher M and Paterson, Tyler and Phillips, Elliott E. and Phillips, Emily M. and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K. and Rymer, Jon Thomson and Ryan, Sean M. and Sammons, Megan and Scott, Anne K. and Scott, Ashley L. and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L. and Sobeski, Margaret A. and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J. and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K and Jayaraman, Vivek and Costa, Marta and Jefferis, Gregory SXE and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian and Rubin, Gerald M and Hess, Harald F and Jain, Viren and Plaza, Stephen M (2020) A connectome and analysis of the adult Drosophila central brain​eLife (preprint)

Alexander S. Bates*, Philipp Schlegel*, Ruairi J.V. Roberts, Nikolas Drummond, Imaan F.M. Tamimi, Robert Turnbull, Xincheng Zhao, Elizabeth C. Marin, Patricia D. Popovici, Serene Dhawan, Arian Jamasb, Alexandre Javier, Laia Serratosa Capdevila, Feng Li, Gerald M. Rubin, Scott Waddell, Davi D. Bock, Marta Costa and Gregory S.X.E. Jefferis (2020) Complete Connectomic Reconstruction of Olfactory Projection Neurons in the Fly Brain, Current Biology (preprint, twitter thread)

Elizabeth C. Marin, Laurin Büld, Maria Theiss, Tatevik Sarkissian, Ruairí J.V. Roberts, Robert Turnbull, Imaan F.M. Tamimi, Markus W. Pleijzier, Willem J. Laursen, Nik Drummond, Philipp Schlegel, Alexander S. Bates, Feng Li, Matthias Landgraf, Marta Costa, Davi D. Bock, Paul A. Garrity and Gregory S.X.E. Jefferis (2020) Connectomics Analysis Reveals First-, Second-, and Third-Order Thermosensory and Hygrosensory Neurons in the Adult Drosophila Brain, Current Biology (preprint, twitter thread)

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 and Scott Waddell (2020) Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila, Current Biology (preprint)

Alexander S. Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory S. X. E. Jefferis (2020) The natverse, a versatile computational toolbox to combine and analyse neuroanatomical dataeLife (preprint)



S. Sayin, J.-F. De Backer, K.P. Siju, M.E. Wosniack, L.P. Lewis, L.-M. Frisch, B. Gansen, P. Schlegel, A. Edmondson-Stait, N. Sharifi, C.B. Fisher, S.A. Calle-Schuler, J.S. Lauritzen, D.D. Bock, M. Costa, G.S.X.E. Jefferis, J. Gjorgjieva, I.C. Grunwald Kadow (2019). A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila. Neuron (preprint)

Shahar Frechter, Alexander Shakeel Bates, Sina Tootoonian, Michael-John Dolan, James D Manton, Arian Rokkum Jamasb, Johannes Kohl, Davi D. BockGregory SXE Jefferis (2019). Functional and anatomical specificity in a higher olfactory centreeLife (preprint)

Michael-John Dolan, Shahar Frechter, Alexander Shakeel Bates, Chuntao Dan, Paavo Huoviala, Ruairi JV Roberts, Philipp Schlegel, Serene Dhawan, Remy Tabano, Heather Dionne, Christina Christoforou, Kari Close, Ben Sutcliffe, Bianca Giuliani, Feng LiMarta Costa, Gudrun Ihrke, Geoffrey Meissner, Davi D. Bock, Yoshinori Aso, Gerald M. Rubin*Gregory SXE Jefferis* (2019). Neurogenetic dissection of the Drosophila lateral horn reveals output, functions and interaction with the mushroom bodyeLife (preprint)

Alexander Shakeel Bates, Jasper Janssens, Gregory SXE Jefferis and Stein Aerts (2019). Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics​Current Opinion in Neurobiology​



Michael-John Dolan*, Ghislain Belliart-Guérin*, Alexander Shakeel Bates, Shahar Frechter, Aurélie Lampin-Saint-Amaux, Yoshinori Aso, Ruairí JV Roberts, Philipp Schlegel, Allan Wong, Adnan Hammad, Davi D. Bock, Gerald M. Rubin, Thomas Preat, Pierre-Yves Plaçais and Gregory SXE Jefferis (2018) Communication from Learned to Innate Olfactory Processing Centers Is Required for Memory Retrieval in Drosophila. Neuron (preprint)

Johannes Felsenberg, Pedro F. Jacob, Thomas Walker, Oliver Barnstedt, Amelia J. Edmondson-Stait, Markus W. Pleijzier, Nils Otto, Philipp Schlegel, Nadiya Sharifi, Emmanuel Perisse, Carlas S. Smith, J. Scott Lauritzen, Marta Costa, Gregory SXE Jefferis, Davi D. Bock and Scott Waddell (2018) Integration of Parallel Opposing Memories Underlies Memory Extinction. Cell

Zhihao Zheng*, J. Scott Lauritzen*, Eric Perlman, Camenzind G. Robinson, Matthew Nichols, Daniel Milkie, Omar Torrens, John Price, Corey B. Fisher, Nadiya Sharifi, Steven A. Calle-Schuler, Lucia Kmecova, Iqbal J. Ali, Bill Karsh, Eric T. Trautman, John A. Bogovic, Philipp Hanslovsky, Gregory SXE Jefferis, Michael Kazhdan, Khaled Khairy, Stephan Saalfeld, Richard D. Fetter and Davi D. Bock (2018). A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell (preprint)



Philipp Schlegel*, Marta Costa*, Gregory SXE Jefferis (2017) Learning from Connectomics on the flyCurrent Opinion in Insect Science, 24:96–105

Elizabeth Marin & Marta Costa (2017) Sensory Neurobiology: Wet Fly FishingCurrent Biology, 27:R833–R852



Nils Eckstein, Alexander S. Bates, Michelle Du, Volker Hartenstein, Gregory S. X. E. Jefferis, Jan Funke (2020) Neurotransmitter Classification from Electron Microscopy Images at Synaptic Sites in DrosophilabioRxiv 

Peter H. Li, Larry F. Lindsey, Michal Januszewski, Zhihao Zheng, Alexander Shakeel Bates, István Taisz, Mike Tyka, Matthew Nichols, Feng Li, Eric Perlman, Jeremy Maitin-Shepard, Tim Blakely, Laramie Leavitt, Gregory SXE Jefferis, Davi D. Bock and Viren Jain (2019) Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local RealignmentbioRxiv

Paavo Huoviala, Michael-John Dolan*, Fiona M. Love*, Shahar Frechter, Ruairí J.V. Roberts, Zane Mitrevica, Philipp Schlegel, Alexander Shakeel Bates, Yoshinori Aso, Tiago Rodrigues, Hannah Cornwall, Marcus Stensmyr, Davi D. Bock, Gerald M. Rubin, Marta Costa, Gregory SXE Jefferis (2018) Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending outputbioRxiv