Staff Profiles

Ali Cetin, Ph.D.

Assistant Investigator

Ali Haydar Cetin joined the Allen Institute in 2013 as an assistant investigator in the research and development group. Before joining the Allen Institute he worked as a Postdoctoral Fellow in the lab of Ed Callaway at the Salk Institute for Biological Studies, San Diego where he developed viral vectors for optogenetic manipulations and monosynaptic circuit tracing to understand the connectivity within the nervous system. At the Allen Institute he is leading research efforts focusing on the development, optimization and execution of novel methodologies in order to understand the network connectivity within the mouse visual system using molecular genetic approaches. Cetin received a B.S. in molecular biology and genetics from the Bilkent University in Ankara, Turkey, and a Ph.D. at the Max Planck Institute for Medical Research in Heidelberg, Germany.


Research Interests

Our research is focused on understanding neuroanatomical and functional connectivity within the visual system. In order to reach this goal we are developing and utilizing novel molecular genetic tools that will allow fine scale mapping, quantification and perturbation of individual connections within the mouse visual system. Our major emphasis is generation and optimization of viral vectors and other genetically modified tools and using these in order to help understand the visual information processing.


  • Molecular Neurobiology
  • Genetics
  • Neuroanatomy
  • Viral Vectors

Research Programs

  • Research & Development

Selected Publications View on PUBMED

Connectional architecture of a mouse hypothalamic circuit node controlling social behavior

Proceedings of the National Academy of Sciences
March 21, 2019

Lo L, Kim D, Yao S, Cetin A, Harris JA, Zeng H, Anderson DJ, Weissbourd B

Epigenetic landscape and AAV targeting of human neocortical cell classes

February 19, 2019

Mich JK, Hess EE, Graybuck LT, Somasundaram S, Miller JA, Ding Y, Shapovalova NV, Fong O, Yao S, Mortrud M, Chong P, Bertagnolli D, Goldy J, Casper T, Kroll M, Hodge RD, Bakken TE, Yao Z, Dee N, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Gradinaru V, Sunkin SM, Zeng H, Lein ES, Tasic B, Ting JT, Levi BP

Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons

Nature Neuroscience
March 5, 2018

Chatterjee S, Sullivan H, MacLennan BJ, Xu R, Hou Y, Lavin TK, Lea N, Michalski J, Babcock K, Dietrich S, Matthews GA, Beyeler A, Calhoon GG, Glober G, Whitesell J, Yao S, Cetin A, Harris J, Zeng H, Tye K, Reid RC, Wickersham IR

Shared and distinct transcriptomic cell types across neocortical areas

October 31, 2018

Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H

Identification of preoptic sleep neurons using retrograde labelling and gene profiling

May 17, 2017

Chung S, Weber F, Zhong P, Tan CL, Nguyen TN, Beier KT, Hörmann N, Chang WC, Zhang Z, Do JP, Yao S, Krashes MJ, Tasic B, Cetin A, Zeng H, Knight ZA, Luo L, Dan Y

Optical control of retrogradely infected neurons using drug regulated lentiviral vectors

Journal of Neurophysiology
February 2014

Cetin AH, Callaway EM

Tracing inputs to inhibitory or excitatory neurons of mouse and cat visual cortex with a targeted rabies virus

Current Biology
September 2013

Liu Y, Ehrengruber M, Negwer M, Shao H, Cetin A, Lyon D

Optogenetics through windows on the brain in the nonhuman primate

Journal of Neurophysiology
September 2013

Ruiz O, Lustig B, Nassi J, Cetin A, Reynolds J, Albright T, Callaway EM, Stoner GR, Roe AW

Imaging light responses of retinal ganglion cells in the living mouse eye

Journal of Neurophysiology
May 2013

Yin L, Geng Y, Osakada F, Sharma R, Cetin AH, Callaway EM, Williams DR, Merigan WH

Evoked axonal oxytocin release in the central amygdala attenuates fear response

February 2012

Knobloch HS, Charlet A, Hoffmann LC, Eliava M, Khrulev S, Cetin AH, Schwarz MK, Stoop R, Seeburg PH, Grinevich V

New Rabies Virus Variants for Monitoring and Manipulating Activity and Gene Expression in Defined Neural Circuits

August 2011

Osakada F, Mori T, Cetin AH, Marshel JH, Virgen B, Callaway EM

Monosynaptic circuit tracing in vivo through Cre-dependent targeting and complementation of modified rabies virus

December 2010

Wall NR, Wickersham IR, Cetin A, De La Parra M, Callaway EM

Viral vectors: a wide range of choices and high levels of service

Handbook of Experimental Pharmacology

Osten P, Grinevich V, Cetin A.

Postsynaptic excitability is necessary for strengthening of cortical sensory responses during experience-dependent development

Nature Neuroscience
September 2006

Komai S, Licznerski P, Cetin A, Waters J, Denk W, Brecht M, Osten P

Stereotaxic gene delivery in the rodent brain

Nature Protocols

Cetin A, Komai S, Eliava M, Seeburg PH, Osten P