Publications

2022

Yap K, Chung TH, Makeyev EV (2022) Analysis of RNA-containing compartments by hybridization and proximity labeling in cultured human cells. STAR Protoc 3: 101139
Yap K, Chung TH, Makeyev EV (2022) Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments. Mol Cell 82: 463-478.e11
Barkus C, Bergmann C, Branco T, Carandini M, Chadderton PT, Galiñanes GL, Gilmour G, Huber D, Huxter JR, Khan AG, King AJ, Maravall M, O'Mahony T, Ragan CI, Robinson ESJ, Schaefer AT, Schultz SR, Sengpiel F, Prescott MJ (2022) Refinements to rodent head fixation and fluid/food control for neuroscience Journal of Neuroscience Methods

Leaman S, Marichal N, Berninger B (2022) Reprogramming cellular identity in vivo. Development 149
Poort J, Wilmes KA, Blot A, Chadwick A, Sahani M, Clopath C, Mrsic-Flogel TD, Hofer SB, Khan AG (2022) Learning and attention increase visual response selectivity through distinct mechanisms. Neuron 110: 686-697.e6

2021

Llorca A, Marín O (2021) Orchestrated freedom: new insights into cortical neurogenesis. Curr Opin Neurobiol 66: 48-56
Ucar B, Kajtez J, Foidl BM, Eigel D, Werner C, Long KR, Emnéus J, Bizeau J, Lomora M, Pandit A, Newland B, Humpel C (2021) Biomaterial based strategies to reconstruct the nigrostriatal pathway in organotypic slice co-cultures. Acta Biomater 121: 250-262
Lipovsek M, Bardy C, Cadwell CR, Hadley K, Kobak D, Tripathy SJ (2021) Patch-seq: Past, Present, and Future. J Neurosci 41: 937-946
Galliano E, Hahn C, Browne LP, R Villamayor P, Tufo C, Crespo A, Grubb MS (2021) Brief Sensory Deprivation Triggers Cell Type-Specific Structural and Functional Plasticity in Olfactory Bulb Neurons. J Neurosci 41: 2135-2151
Moglie MJ, Marcovich I, Corradi J, Carpaneto Freixas AE, Gallino S, Plazas PV, Bouzat C, Lipovsek M, Elgoyhen AB (2021) Loss of Choline Agonism in the Inner Ear Hair Cell Nicotinic Acetylcholine Receptor Linked to the α10 Subunit. Front Mol Neurosci 14: 639720
Pollak TA, Vincent A, Iyegbe C, Coutinho E, Jacobson L, Rujescu D, Stone J, Jezequel J, Rogemond V, Jamain S, Groc L, David A, Egerton A, Kahn RS, Honnorat J, Dazzan P, Leboyer M, McGuire P (2021) Relationship Between Serum NMDA Receptor Antibodies and Response to Antipsychotic Treatment in First-Episode Psychosis. Biol Psychiatry 90: 9-15
Patkee PA, Baburamani AA, Long KR, Dimitrova R, Ciarrusta J, Allsop J, Hughes E, Kangas J, McAlonan GM, Rutherford MA, De Vita E (2021) Neurometabolite mapping highlights elevated myo-inositol profiles within the developing brain in down syndrome. Neurobiol Dis 153: 105316
Díaz-Caneja CM, State MW, Hagerman RJ, Jacquemont S, Marín O, Bagni C, Umbricht D, Simonoff E, de Andrés-Trelles F, Kaale A, Pandina G, Gómez-Mancilla B, Wang PP, Cusak J, Siafis S, Leucht S, Parellada M, Loth E, Charman T, Buitelaar JK, Murphy D, Arango C (2021) A white paper on a neurodevelopmental framework for drug discovery in autism and other neurodevelopmental disorders. Eur Neuropsychopharmacol 48: 49-88
Herrero-Navarro Á, Puche-Aroca L, Moreno-Juan V, Sempere-Ferràndez A, Espinosa A, Susín R, Torres-Masjoan L, Leyva-Díaz E, Karow M, Figueres-Oñate M, López-Mascaraque L, López-Atalaya JP, Berninger B, López-Bendito G (2021) Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming. Sci Adv 7
Salam S, Tacconelli S, Smith BN, Mitchell JC, Glennon E, Nikolaou N, Houart C, Vance C (2021) Identification of a novel interaction of FUS and syntaphilin may explain synaptic and mitochondrial abnormalities caused by ALS mutations. Sci Rep 11: 13613
Lattke M, Goldstone R, Ellis JK, Boeing S, Jurado-Arjona J, Marichal N, MacRae JI, Berninger B, Guillemot F (2021) Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture. Nat Commun 12: 4335
Aviña-Padilla K, Ramírez-Rafael JA, Herrera-Oropeza GE, Muley VY, Valdivia DI, Díaz-Valenzuela E, García-García A, Varela-Echavarría A, Hernández-Rosales M (2021) Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Front Genet 12: 654256
Sharif N, Calzolari F, Berninger B (2021) Direct In Vitro Reprogramming of Astrocytes into Induced Neurons. Methods Mol Biol 2352: 13-29
Mastrolia V, Al Massadi O, de Pins B, Girault JA (2021) Pyk2 in dorsal hippocampus plays a selective role in spatial memory and synaptic plasticity. Sci Rep 11: 16357
Stricker SH, Berninger B, Götz M (2021) Editorial overview: Fluidity of cell fates - from reprogramming to repair. Curr Opin Genet Dev 70: iii-v
Calzolari F, Berninger B (2021) cAAVe phaenomena: Beware of appearances! Cell 184: 5303-5305
Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Rabaneda LG, García-Lira C, Grand T, Briz V, Velasco ER, Andero R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I (2021) Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. Elife 10
Long KR, Huttner WB (2021) The Role of the Extracellular Matrix in Neural Progenitor Cell Proliferation and Cortical Folding During Human Neocortex Development. Front Cell Neurosci 15: 804649

Eigel D, Schuster R, Männel MJ, Thiele J, Panasiuk MJ, Andreae LC, Varricchio C, Brancale A, Welzel PB, Huttner WB, Werner C, Newland B, Long KR (2021) Sulfonated cryogel scaffolds for focal delivery in ex-vivo brain tissue cultures. Biomaterials 271: 120712

Tuvikene J, Esvald EE, Rähni A, Uustalu K, Zhuravskaya A, Avarlaid A, Makeyev EV, Timmusk T (2021) Intronic enhancer region governs transcript-specific Bdnf expression in rodent neurons. Elife 10
Shi Y, Wang M, Mi D, Lu T, Wang B, Dong H, Zhong S, Chen Y, Sun L, Zhou X, Ma Q, Liu Z, Wang W, Zhang J, Wu Q, Marín O, Wang X (2021) Mouse and humans share conserved transcriptional programs for interneuron development Science

Lentini C, d'Orange M, Marichal N, Trottmann MM, Vignoles R, Foucault L, Verrier C, Massera C, Raineteau O, Conzelmann KK, Rival-Gervier S, Depaulis A, Berninger B, Heinrich C (2021) Reprogramming reactive glia into interneurons reduces chronic seizure activity in a mouse model of mesial temporal lobe epilepsy. Cell Stem Cell 28: 2104-2121.e10
Ellingford RA, Panasiuk MJ, de Meritens ER, Shaunak R, Naybour L, Browne L, Basson MA, Andreae LC (2021) Cell-type-specific synaptic imbalance and disrupted homeostatic plasticity in cortical circuits of ASD-associated Chd8 haploinsufficient mice. Mol Psychiatry 26: 3614-3624
Chadwick A, Khan A, Poort J, Blot A, Hofer S, Mrsic-Flogel T, Sahani M (2021) Learning shapes cortical dynamics to enchance integration of relevant sensory input bioRxiv

Braga L, Ali H, Secco I, Chiavacci E, Neves G, Goldhill D, Penn R, Jimenez-Guardeño JM, Ortega-Prieto AM, Bussani R, Cannatà A, Rizzari G, Collesi C, Schneider E, Arosio D, Shah AM, Barclay WS, Malim MH, Burrone J, Giacca M (2021) Drugs that inhibit TMEM16 proteins block SARS-CoV-2 spike-induced syncytia. Nature

Gonzalez Sabater V, Rigby M, Burrone J (2021) Voltage-gated potassium channels ensure action potential shape fidelity in distal axons. J Neurosci

Gordon PM, Hamid F, Makeyev EV, Houart C (2021) A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons. Nat Commun 12: 1918
Anette Wu, Vinay Maddula, Ann Chen Xi Yu, Rahul Goel, Haruna Shimizu, Chung-Liang Chien, Richard Wingate, Mandeep Gill Sagoo, Heike Kielstein, Hannes Traxler, Cecilia Brassett, Jens Waschke, Fransziska Vielmuth, Kevin Keay, Mina Zeroual, Takeshi Sakurai, Jorgen Olsen, Salma El-Batti, Suvi Viranta-Kovanen, Shuji Kitahara, Carol Kunzel, Paulette Bernd & Geoffroy P.J.C. Noel  (2021) An Observation of Healthcare Professions Students’ Perceptions During the COVID-19 Pandemic Medical Science Educator

2020

Lagogiannis K, Diana G, Meyer MP (2020) Learning steers the ontogeny of an efficient hunting sequence in zebrafish larvae. Elife 9
Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou HJ, Fletcher RB, Das D, Street K, de Bezieux HR, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR (2020) Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Sci Adv 6
Briscoe J, Marín O (2020) Looking at neurodevelopment through a big data lens. Science 369
Knüfer A, Diana G, Walsh GS, Clarke JD, Guthrie S (2020) Cadherins regulate nuclear topography and function of developing ocular motor circuitry. Elife 9
Bostock MP, Prasad AR, Chaouni R, Yuen AC, Sousa-Nunes R, Amoyel M, Fernandes VM (2020) An Immobilization Technique for Long-Term Time-Lapse Imaging of Explanted Drosophila Tissues. Front Cell Dev Biol 8: 590094
Exposito-Alonso D, Osório C, Bernard C, Pascual-García S, Del Pino I, Marín O, Rico B (2020) Subcellular sorting of neuregulins controls the assembly of excitatory-inhibitory cortical circuits. Elife 9

Symonds AC, Buckley CE, Williams CA, Clarke JDW (2020) Coordinated assembly and release of adhesions builds apical junctional belts during de novo polarisation of an epithelial tube. Development 147
Lipovsek M, Browne L, Grubb MS (2020) Protocol for Patch-Seq of Small Interneurons. STAR Protoc 1: 100146
Court R, Namiki S, Armstrong JD, Börner J, Card G, Costa M, Dickinson M, Duch C, Korff W, Mann R, Merritt D, Murphey RK, Seeds AM, Shirangi T, Simpson JH, Truman JW, Tuthill JC, Williams DW, Shepherd D (2020) A Systematic Nomenclature for the Drosophila Ventral Nerve Cord. Neuron 107: 1071-1079.e2
Pop S, Chen CL, Sproston CJ, Kondo S, Ramdya P, Williams DW (2020) Extensive and diverse patterns of cell death sculpt neural networks in insects. Elife 9
Patel DS, Diana G, Entchev EV, Zhan M, Lu H, Ch'ng Q (2020) A Multicellular Network Mechanism for Temperature-Robust Food Sensing. Cell Rep 33: 108521
Ivy Usansky Patrycja Jaworska Ludovica Asti Fiona N Kenny Carl Hobbs Vasiliki Sofra Hanfei Song Malcolm Logan Anthony Graham Tanya J Shaw (2020) A developmental basis for the anatomical diversity of dermis in homeostasis and wound repair The Journal of Pathology 253 Issue 3: 315-325

Pan-Vazquez A, Wefelmeyer W, Gonzalez Sabater V, Neves G, Burrone J (2020) Activity-Dependent Plasticity of Axo-axonic Synapses at the Axon Initial Segment. Neuron 106: 265-276.e6

Muraina IA, Bury NR, Scott A, Graham A, Hogstrand C (2020) The zebrafish Znt1asa17 mutant reveals roles of zinc transporter-1a in embryonic development. J Trace Elem Med Biol 60: 126496
Adnan G, Rubikaite A, Khan M, Reber M, Suetterlin P, Hindges R, Drescher U (2020) The GTPase Arl8B Plays a Principle Role in the Positioning of Interstitial Axon Branches by Spatially Controlling Autophagosome and Lysosome Location. J Neurosci 40: 8103-8118

Sahara S, Kodama T, Stevens CF (2020) A common rule governing differentiation kinetics of mouse cortical progenitors. Proc Natl Acad Sci U S A 117: 15221-15229

Marcovich I, Moglie MJ, Carpaneto Freixas AE, Trigila AP, Franchini LF, Plazas PV, Lipovsek M, Elgoyhen AB (2020) Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors. Mol Biol Evol 37: 1070-1089
Moore R, Alexandre P (2020) Delta-Notch Signaling: The Long and The Short of a Neuron's Influence on Progenitor Fates. J Dev Biol 8
Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E (2020) Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Development
Ramos SI, Makeyev EV, Salierno M, Kodama T, Kawakami Y, Sahara S (2020) Tuba8 Drives Differentiation of Cortical Radial Glia into Apical Intermediate Progenitors by Tuning Modifications of Tubulin C Termini. Dev Cell 52: 477-491.e8

Maierbrugger KT, Sousa-Nunes R, Bateman JM (2020) The mTOR pathway component Unkempt regulates neural stem cell and neural progenitor cell cycle in the Drosophila central nervous system. Dev Biol 461: 55-65
Pegge J, Tatsinkam AJ, Rider CC, Bell E (2020) Heparan sulfate proteoglycans regulate BMP signalling during neural crest induction. Dev Biol 460: 108-114
Kainov YA, Makeyev EV (2020) A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells. Nat Commun 11: 361
Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S (2020) Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome. Curr Biol
Shum C, Dutan L, Annuario E, Warre-Cornish K, Taylor SE, Taylor RD, Andreae LC, Buckley NJ, Price J, Bhattacharyya S, Srivastava DP (2020) Δ9-tetrahydrocannabinol and 2-AG decreases neurite outgrowth and differentially affects ERK1/2 and Akt signaling in hiPSC-derived cortical neurons. Mol Cell Neurosci 103: 103463
Armstrong EC, Caruso A, Servadio M, Andreae LC, Trezza V, Scattoni ML, Fernandes C (2020) Assessing the developmental trajectory of mouse models of neurodevelopmental disorders: Social and communication deficits in mice with Neurexin 1α deletion. Genes Brain Behav 19: e12630

Wu A, Noël GPJC, Wingate R, Kielstein H, Sakurai T, Viranta-Kovanen S, Chien C-L, Traxler H, Waschke J, Vielmuth F, Sagoo MG, Kitahara S, Kato Y, Keay KA, Olsen J, Bernd P (2020) An International Partnership of 12 Anatomy Departments: Improving Global Health through Internationalization of Medical Education. Annals of Global Health 86(1): 27: 1-14

2019

Youli Hu, Thomas Butts, Subathra Poopalasundaram, Anthony Graham, Pierre-Marc Bouloux (2019) Extracellular matrix protein anosmin-1 modulates olfactory ensheathing cell maturation in chick olfactory bulb development Eur J Neurosci 50(9): 3472-3486

Anthony Graham Subathra Poopalasundaram Victoria Shone Clemens Kiecker (2019) A reappraisal of the numbering of the pharyngeal arches Journal of Anatomy 235 Issue 6: 1019-1023

Namba T, Dóczi J, Pinson A, Xing L, Kalebic N, Wilsch-Bräuninger M, Long KR, Vaid S, Lauer J, Bogdanova A, Borgonovo B, Shevchenko A, Keller P, Drechsel D, Kurzchalia T, Wimberger P, Chinopoulos C, Huttner WB (2019) Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis. Neuron

Kiecker C, Clarke J, Bell E (2019) Teaching embryology through science fiction and role-play. Med Educ 53: 519
Hanzel M, Rook V, Wingate RJT (2019) Mitotic granule cell precursors undergo highly dynamic morphological transitions throughout the external germinal layer of the chick cerebellum. Sci Rep 9: 15218

Iulianella A, Wingate RJ, Moens CB, Capaldo E (2019) The generation of granule cells during the development and evolution of the cerebellum. Dev Dyn 248: 506-513
Connolly KJ, O'Hare MB, Mohammed A, Aitchison KM, Anthoney NC, Taylor MJ, Stewart BA, Tuxworth RI, Tear G (2019) The neuronal ceroid lipofuscinosis protein Cln7 functions in the postsynaptic cell to regulate synapse development. Sci Rep 9: 15592
Bachmann C, Noreen F, Voermans NC, Schär PL, Vissing J, Fock JM, Bulk S, Kusters B, Moore SA, Beggs AH, Mathews KD, Meyer M, Genetti CA, Meola G, Cardani R, Mathews E, Jungbluth H, Muntoni F, Zorzato F, Treves S (2019) Aberrant regulation of epigenetic modifiers contributes to the pathogenesis in patients with selenoprotein N-related myopathies. Hum Mutat 40: 962-974
Cai P, Li Z, Keneth ES, Wang L, Wan C, Jiang Y, Hu B, Wu YL, Wang S, Lim CT, Makeyev EV, Magdassi S, Chen X (2019) Differential Homeostasis of Sessile and Pendant Epithelium Reconstituted in a 3D-Printed "GeminiChip". Adv Mater 31: e1900514
Thams S, Lowry ER, Larraufie MH, Spiller KJ, Li H, Williams DJ, Hoang P, Jiang E, Williams LA, Sandoe J, Eggan K, Lieberam I, Kanning KC, Stockwell BR, Henderson CE, Wichterle H (2019) A Stem Cell-Based Screening Platform Identifies Compounds that Desensitize Motor Neurons to Endoplasmic Reticulum Stress. Mol Ther 27: 87-101

Brosig A, Fuchs J, Ipek F, Kroon C, Schrötter S, Vadhvani M, Polyzou A, Ledderose J, van Diepen M, Holzhütter HG, Trimbuch T, Gimber N, Schmoranzer J, Lieberam I, Rosenmund C, Spahn C, Scheerer P, Szczepek M, Leondaritis G, Eickholt BJ (2019) The Axonal Membrane Protein PRG2 Inhibits PTEN and Directs Growth to Branches. Cell Rep 29: 2028-2040.e8

Pang CC, Kiecker C, O'Brien JT, Noble W, Chang RC (2019) Ammon's Horn 2 (CA2) of the Hippocampus: A Long-Known Region with a New Potential Role in Neurodegeneration. Neuroscientist 25: 167-180
Staudt N, Giger FA, Fielding T, Hutt JA, Foucher I, Snowden V, Hellich A, Kiecker C, Houart C (2019) Pineal progenitors originate from a non-neural territory limited by FGF signalling. Development 146

Cheung A, Trevers KE, Reyes-Corral M, Antinucci P, Hindges R (2019) Expression and Roles of Teneurins in Zebrafish. Front Neurosci 13: 158

Lipovsek M, Grubb MS (2019) Boosting adult neurogenesis to enhance sensory performance. EMBO J 38
Graham A, Poopalasundaram S, Shone V, Kiecker C (2019) A reappraisal and revision of the numbering of the pharyngeal arches. J Anat 235: 1019-1023
Hu Y, Butts T, Poopalasundaram S, Graham A, Bouloux PM (2019) Extracellular matrix protein anosmin-1 modulates olfactory ensheathing cell maturation in chick olfactory bulb development. Eur J Neurosci 50: 3472-3486
Araya C, Häkkinen HM, Carcamo L, Cerda M, Savy T, Rookyard C, Peyriéras N, Clarke JDW (2019) Publisher Correction: Cdh2 coordinates Myosin-II dependent internalisation of the zebrafish neural plate. Sci Rep 9: 7699
Wu T, Duan F, Yang W, Liu H, Caballero A, Fernandes de Abreu DA, Dar AR, Alcedo J, Ch'ng Q, Butcher RA, Zhang Y (2019) Pheromones Modulate Learning by Regulating the Balanced Signals of Two Insulin-like Peptides. Neuron 104: 1095-1109.e5
Denaxa M, Neves G, Burrone J, Pachnis V (2019) Transplantation of Chemogenetically Engineered Cortical Interneuron Progenitors into Early Postnatal Mouse Brains. J Vis Exp
Pérez-Brangulí F, Buchsbaum IY, Pozner T, Regensburger M, Fan W, Schray A, Börstler T, Mishra H, Gräf D, Kohl Z, Winkler J, Berninger B, Cappello S, Winner B (2019) Human SPG11 cerebral organoids reveal cortical neurogenesis impairment. Hum Mol Genet 28: 961-971
Kalamakis G, Brüne D, Ravichandran S, Bolz J, Fan W, Ziebell F, Stiehl T, Catalá-Martinez F, Kupke J, Zhao S, Llorens-Bobadilla E, Bauer K, Limpert S, Berger B, Christen U, Schmezer P, Mallm JP, Berninger B, Anders S, Del Sol A, Marciniak-Czochra A, Martin-Villalba A (2019) Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain. Cell 176: 1407-1419.e14
Kang E, Song J, Lin Y, Park J, Lee JH, Hussani Q, Gu Y, Ge S, Li W, Hsu KS, Berninger B, Christian KM, Song H, Ming GL (2019) Interplay between a Mental Disorder Risk Gene and Developmental Polarity Switch of GABA Action Leads to Excitation-Inhibition Imbalance. Cell Rep 28: 1419-1428.e3
Wong FK, Marín O (2019) Developmental Cell Death in the Cerebral Cortex. Annu Rev Cell Dev Biol 35: 523-542
Llorca A, Ciceri G, Beattie R, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marin O (2019) A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. Elife 8