Publications

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Lin W, Gandhi S, Bhattarai P, Kasa K, Kizil C, Zhang Y. Combining high throughput array synthesis and growth algorithm to discover TNF-α binders with new structures and properties. European Journal of Medical Chemistry. 2023. 248:115078. doi:10.1016/j.ejmech.2022.115078.

Siddiqui T, Celikkaya H, Atasavum ZT, Popova S, Freudenberg U, Werner C, Kizil C. Three-Dimensional Biohybrid StarPEG-Heparin Hydrogel Cultures for Modeling Human Neuronal Development and Alzheimer’s Disease Pathology. Methods in Molecular Biology. 2023. 2561:159-170. doi: 10.1007/978-1-0716-2655-9_8.

Felsky D, Santa-Maria I, Cosacak MI, French L, Schneider JA, Bennett DA, De Jager PL, Kizil C, Tosto G. The Caribbean-Hispanic Alzheimer’s disease brain transcriptome reveals ancestry-specific disease mechanisms. Neurobiology of Disease. 2022. 176:105938. doi: 10.1016/j.nbd.2022.105938.

Kim YA, Siddiqui T, Blaze J, Cosacak MI, Winters T, Kumar A, Tein E, Sproul AA, Teich AF, Bartolini F, Akbarian S, Kizil C, Hargus G, Santa-Maria I. RNA methyltransferase NSun2 deficiency promotes neurodegeneration through epitranscriptomic regulation of tau phosphorylation. Acta Neuropathologica. 2022. doi: 10.1007/s00401-022-02511-7.

Bhattarai P, Turgutalp B, Kizil C. Zebrafish as an Experimental and Preclinical Model for Alzheimer’s Disease. ACS Chemical Neuroscience. 2022. doi: 10.1021/acschemneuro. 2c00583.

Lee AJ, Raghavan NS, Bhattarai P, Siddiqui T, Sariya S, Reyes-Dumeyer D, Flowers XE, Cardoso SAL, De Jager PL, Bennett DA, Schneider JA, Menon V, Wang Y, Lantigua RA, Medrano M, Rivera D, Jiménez-Velázquez IZ, Kukull WA, Brickman AM, Manly JJ, Tosto G, Kizil C*, Vardarajan BN*, Mayeux R*. FMNL2 regulates gliovascular interactions and is associated with vascular risk factors and cerebrovascular pathology in Alzheimer’s disease. Acta Neuropathologica. 2022 Jul;144(1):59-79. doi: 10.1007/s00401-022-02431-6. * equal contribution. Open access.

Turgutalp B, Bhattarai P, Ercetin T, Luise C, Reis R, Gurdal EE, Isaak A, Biriken D, Dinter E, Sipahi H, Schepmann D, Junker A, Wünsch B, Sippl W, Gulcan HO, Kizil C*, Yarim M*. Discovery of Potent Cholinesterase Inhibition-Based Multi-Target-Directed Lead Compounds for Synaptoprotection in Alzheimer’s Disease. Journal of Medicinal Chemistry. 2022. 65(18):12292-12318. doi: 10.1021/acs.jmedchem.2c01003.  * equal contribution

Kizil C, Sariya S, Kim YA, Rajabli F, Martin E, Reyes-Dumeyer D, Vardarajan B, Maldonado A, Haines JL, Mayeux R, Jiménez-Velázquez IZ, Santa-Maria I, Tosto G. Admixture Mapping of Alzheimer’s disease in Caribbean Hispanics identifies a new locus on 22q13.1. Molecular Psychiatry. 2022. 27(6):2813-2820. doi: 10.1038/s41380-022-01526-6.

Cosacak MI, Bhattarai P, De Jager PL, Menon V, Tosto G, Kizil C. Single Cell/Nucleus Transcriptomics Comparison in Zebrafish and Humans Reveals Common and Distinct Molecular Responses to Alzheimer’s Disease. Cells. 2022. 11(11):1807. doi: 10.3390/cells11111807. Open access.

D’Gama PP, Qiu T, Cosacak MI, Rayamajhi D, Konac A, Hansen JN, Ringers C, Acuña-Hinrichsen F, Hui SP, Olstad EW, Chong YL, Lim CKA, Gupta A, Ng CP, Nilges BS, Kashikar ND, Wachten D, Liebl D, Kikuchi K, Kizil C, Yaksi E, Roy S, Jurisch-Yaksi N. Diversity and function of motile ciliated cell types within ependymal lineages of the zebrafish brain. Cell Reports. 2021. 37(1):109775. doi: 10.1016/j.celrep.2021.109775. Open access.

Siddiqui T, Bhattarai P, Popova S, Cosacak MI, Sariya S, Zhang Y, Mayeux R, Tosto G, Kizil C. KYNA/Ahr Signaling Suppresses Neural Stem Cell Plasticity and Neurogenesis in Adult Zebrafish Model of Alzheimer’s Disease. Cells. 2021. 10(10):2748. doi: 10.3390/cells10102748. Open access.

Chang W, Pedroni A, Bertuzzi M, Kizil C, Simon A, Ampatzis K. Locomotion dependent neuron-glia interactions control neurogenesis and regeneration in the adult zebrafish spinal cord. Nature Communications. 2021. 12(1):4857. doi: 10.1038/s41467-021-25052-1. Open access.

Cosacak MI, Bhattarai P, Kizil C. Protocol for Dissection and Dissociation of Zebrafish Telencephalon for Single-Cell Sequencing. STAR Protocols. 2020. 1(1):100042. doi: 10.1016/j.xpro.2020.100042. Open access.

Fore S, Acuña-Hinrichsen F, Mutlu KA, Bartoszek EM, Serneels B, Faturos NG, Chau KTP, Cosacak MI, Verdugo CD, Palumbo F, Ringers C, Jurisch-Yaksi N, Kizil C, Yaksi E. Functional properties of habenular neurons are determined by developmental stage and sequential neurogenesis. Science Advances. 2020. 6(36):eaaz3173. doi: 10.1126/sciadv.aaz3173. Open access.

Jurisch-Yaksi N, Yaksi E, Kizil C. Radial glia in the zebrafish brain: Functional, structural, and physiological comparison with the mammalian glia. Glia. 2020. 68(12):2451-2470. doi: 10.1002/glia.23849.

Mashkaryan V, Siddiqui T, Popova S, Cosacak MI, Bhattarai P, Brandt K, Govindarajan N, Petzold A, Reinhardt S, Dahl A, Lefort R, Kizil C. Type 1 Interleukin-4 Signaling Obliterates Mouse Astroglia in vivo but Not in vitro. Frontiers in Cell and Developmental Biology. 2020. 8:114. doi:10.3389/fcell.2020.00114. Open access.

Bhattarai P, Cosacak MI, Mashkaryan V, Demir S, Popova SD, Govindarajan N, Brandt K, Zhang Y, Chang W, Ampatzis K, Kizil C. Neuron-glia interaction through Serotonin-BDNF-NGFR axis enables regenerative neurogenesis in Alzheimer’s model of adult zebrafish brain. PLoS Biology. 2020. 18(1):e3000585. doi: 10.1371/journal.pbio.3000585. Open access.

Cosacak MI, Bhattarai P, Kizil C. Alzheimer’s disease, neural stem cells and neurogenesis: cellular phase at single-cell level. Neural Regeneration Research. 2020. 15(5):824-827. doi: 10.4103/1673-5374.268896. 

Diaz Verdugo C, Myren-Svelstad S, Aydin E, Van Hoeymissen E, Deneubourg C, Vanderhaeghe S, Vancraeynest J, Pelgrims R, Cosacak MI, Muto A, Kizil C, Kawakami K, Jurisch-Yaksi N, Yaksi E. Glia-neuron interactions underlie state transitions to generalized seizures. Nature Communications. 2019. 10(1):3830. doi: 10.1038/s41467-019-11739-z. Open access.

Cosacak MI, Bhattarai P, Reinhardt S, Petzold A, Dahl A, Zhang Y, Kizil C. Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish Brain Model of Amyloid Toxicity. Cell Reports. 2019 Apr 23;27(4):1307-1318.e3. doi: 10.1016/j.celrep.2019.03.090. Open access.

Diaz Verdugo C, Myren-Svelstad S, Aydin E, Van Hoeymissen E, Deneubourg C, Vanderhaeghe S, Vancraeynest J, Pelgrims R, Cosacak MI, Muto A, Kizil C, Kawakami K, Jurisch-Yaksi N, Yaksi E. Glia-neuron interactions underlie state transitions  to generalized seizures. Nature Communications. 2019 Aug 23;10(1):3830. doi: 10.1038/s41467-019-11739-z. Open access.

Cosacak MI, Bhattarai P, Kizil C. Alzheimer’s disease, neural stem cells and neurogenesis: cellular phase at single-cell level. Neural Regeneration Research. 2020 May;15(5):824-827. doi: 10.4103/1673-5374.268896. Open access.

Celikkaya H, Cosacak MI, Papadimitriou C, Popova S, Bhattarai P, Biswas SN, Siddiqui T, Wistorf S, Nevado-Alcalde I, Naumann L, Mashkaryan V, Brandt K, Freudenberg U, Werner C, Kizil C. (2019) GATA3 Promotes the Neural Progenitor State but Not Neurogenesis in 3D Traumatic Injury Model of Primary Human Cortical Astrocytes. Frontiers in Cellular Neuroscience. 13:23. doi:10.3389/fncel.2019.00023. Open access.

Reinhardt L, Kordes S, Reinhardt P, Glatza M, Baumann M, Drexler HCA, Menninger S, Zischinsky G, Eickhoff J, Fröb C, Bhattarai P, Arulmozhivarman G, Marrone L, Janosch A, Adachi K, Stehling M, Anderson EN, Abo-Rady M, Bickle M, Pandey UB, Reimer MM, Kizil C, Schöler HR, Nussbaumer P, Klebl B, Sterneckert JL. (2019) Dual Inhibition of GSK3β and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo. Stem Cell Reports. 12(3):502-517. doi: 10.1016/j.stemcr.2019.01.015. Open access.

Kizil C, Bhattarai P. (2018) Is Alzheimer’s Also a Stem Cell Disease? – The Zebrafish Perspective. Frontiers in Cell and Developmental Biology. 6:159. doi:10.3389/fcell.2018.00159. Open Access.

Papadimitriou C, Celikkaya H, Cosacak MI, Mashkaryan V, Bray L, Bhattarai P, Brandt K, Hollak H, Chen X, He S, Antos CL, Lin W, Thomas AK, Dahl A, Kurth T, Friedrichs J, Zhang Y, Freudenberg U, Werner C, Kizil C. (2018) 3D Culture Method for Alzheimer’s Disease Modeling Reveals Interleukin-4 Rescues Aβ42-Induced Loss of Human Neural Stem Cell Plasticity. Developmental Cell. 46(1):85-101.e8. doi: 10.1016/j.devcel.2018.06.005.

Kizil, C. (2018). Mechanisms of pathology-induced neural stem cell plasticity and neural regeneration in adult zebrafish brain.  Current Pathobiology Reports. 10.1007/s40139-018-0158-x (PDF)

Cosacak, MI, Yigit, H, Kizil, C, Akgul, B. (2018) Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos. Genes 9:82. 10.3390/genes9020082. (PDF)

Kizil, C. (2018). Turkish Medical Association central council detained for demanding peace. Lancet. PubMed 10.1016/S0140-6736(18)30201-0 (PDF)

Cosacak MI, Bhattarai P, Bocova L, Dzewas T, Mashkaryan V, Papadimitriou C, Brandt K, Hollak H, Antos CL, Kizil C. (2017). Human TAUP301L overexpression results in TAU hyperphosphorylation without neurofibrillary tangles in adult zebrafish brain. Scientific Reports. 7(1), 12959. PubMed 10.1038/s41598-017-13311-5 (PDF)

Bhattarai P, Thomas AK, Mashkaryan V, Cosacak MI, Papadimitriou C, Zhang Y, Kizil C. (2017) Modeling Amyloid-beta42 toxicity and neurodegeneration in adult zebrafish brain. JoVE. 128. PubMed 10.3791/56014

Bhattarai P, Thomas AK, Zhang Y, Kizil C. (2017). The effects of ageing on Amyloid-b42-induced neurodegeneration and regeneration in adult zebrafish brain. Neurogenesis. 4(1):e1322666. PubMed 10.1080/23262133.2017.1322666 (PDF)

Kizil C. (2017) An existential threat. New Scientist. 234(3121):24-25. doi: 1016/S0262-4079(17)30727-3. Link

Bhattarai P, Thomas AK, Cosacak MI, Papadimitriou C, Mashkaryan V, Froc C, Reinhardt S, Kurth T, Dahl A, Zhang Y, Kizil C. (2016) IL4/STAT6 activates neural stem cells in response to Amyloid-b42 aggregation in adult zebrafish brain. Cell Reports, 17(4): 941-948. PubMed 10.1016/j.celrep.2016.09.075 (PDF)

Tincer, G., Mashkaryan, V., Bhattarai, P., Kizil, C. (2016). Neural stem/progenitor cells in Alzheimer’s disease. The Yale Journal of Biology and Medicine, 89(1), 23–35. PubMed

Kizil C. (2016) Degrees of freedom. New Scientist. 231(3084):20-21. doi: 1016/S0262-4079(16)31366-5. Link

Kizil C*, Alberts B, Ayata P, Blobel G, Capecchi M, Clark MM, Curl R, Freiwald WA, Hoffmann R, Mucida D, Nestler EJ, Skotheim JM, Trautmann A, zur Hausen H, Altindis E. (2016). Government: Concern grows for Turkey’s academics. Nature. 529(7587):466. doi: 10.1038/529466a. (*Corresponding author). PubMed

Kizil C*, Kyritsis N, Brand M. (2015) Effects of inflammation on stem cells: together they strive? EMBO Reports. 16(4):416-26. (corresponding author). PubMed 10.15252/embr.201439702

Cosacak MI, Papadimitriou C, Kizil C. (2014). Regeneration, plasticity and induced molecular programs in adult zebrafish brain. BioMed Research International. 2015:769763. PubMed 10.1155/2015/769763

Kizil C, Iltzsche A, Thomas AK, Bhattarai P, Zhang Y, Brand M. (2015) Efficient Cargo Delivery into Adult Brain Tissue Using Short Cell-Penetrating Peptides. PLoS One. 10(4):e0124073. PubMed

Kizil C, Küchler B, Yan JJ, Ozhan G, Moro E, Argenton F, Brand M, Weidinger G, Antos CL. (2014) Simplet/Fam53b is required for Wnt signal transduction by regulating β-catenin nuclear localization. Development. 141(18):3529-39. PubMed

Kyritsis N*, Kizil C*, Brand M. (2014) The role of neuroinflammation in central nervous system regeneration. Trends in Cell Biology. 24(2):128-35 (* equal contribution). PubMed

Kizil C#, Iltzsche A, Kaslin J, Brand M. (2013) Micromanipulation of gene expression in the adult zebrafish brain using cerebroventricular microinjection of morpholino oligonucleotides. JoVE. e50415 (# Corresponding author) PubMed

Altindis E, Alpar MA, Aksay E, Beckwith J, Bökel C, Curl RF, Darnell RB, Elledge SJ, Erman B, Frahm J, Goff SP, Greengard P, Hoffmann R, Ilhan B, Kaslin J, Lipkin SM, Poulopoulou C, Raz E, Rubin MA, Salturk M, Schrock RR, Trautmann A, Unutmaz D, Weinstein H, Kizil C*. (2013) Turkey must end violent response to protests. Science. 341(6143):236. (*Corresponding author) PubMed

Kizil C, Kyritsis N, Dudczig S, Kroehne V, Freudenreich F, Kaslin J, Brand M. (2012) Regenerative neurogenesis from neural progenitor cells requires injury-induced expression of Gata3. Developmental Cell. 23(6): 1230-1237. PubMed

  • Related Commentary: Strähle U, Schmidt R. (2012) A universal program for tissue regeneration? Developmental Cell. 23(6):1123-4.  PubMed

Kyritsis N, Kizil C, Kroehne V, Zocher S, Kaslin J, Freudenreich D, Iltzsche A, Brand M. (2012) Acute inflammation initiates the regenerative response in the adult zebrafish brain. Science. 338(6112): 1353-1356. PubMed

  • Related commentary: Stella N. (2012) Neuroscience. Inflammation to rebuild a brain. Science. 338(6112):1303-4. PubMed
  • Related commentary: Cui Y, Li J, Arias-Carrión O, Yuan TF. (2012) Utilizing neuro-inflammation: turning degeneration to regeneration. CNS Neurol Disord Drug Targets. 11(8):953-4. PubMed

Kizil C, Dudczig S, Kyritsis N, Machate A, Blaesche J, Kroehne V, Brand M. (2012). The chemokine receptor cxcr5 regulates the regenerative neurogenesis response in the adult zebrafish brain. Neural Development 7:27. PubMed

Kizil C, Kaslin J, Kroehne V, Brand M. (2012) Adult neurogenesis and brain regeneration in zebrafish. Developmental Neurobiology 72(3):429-461. PubMed

Kizil C, Brand M (2011) Cerebroventricular Microinjection (CVMI) into Adult Zebrafish Brain Is an Efficient Misexpression Method for Forebrain Ventricular Cells. PLoS ONE 6(11): e27395. PubMed

Kizil C. (2011) Academic autonomy: more freedom for Turkish science. Nature. 477(7366):538. PubMed

Kizil C. (2011) Turkish science seeks freedom. Science. 334(6055):452-3. PubMed

Kizil C, Otto GW, Geisler R, Nüsslein-Volhard C, Antos CL. (2009). Simplet controls cell proliferation and gene transcription during zebrafish caudal fin regeneration. Developmental Biology. 325(2):329-40. PubMed

Correspondences reflect the authors’ opinions and should be considered as readers contribution with no endorsement.

Photo by Steve Johnson
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