Publications

2024

Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke GL, Tong AHY, Chan K, Ha KCH, Blencowe BJ, Moffat J, Greenblatt JF (2024) Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 52: 4483-4501
Zhuravskaya A, Yap K, Hamid F, Makeyev EV (2024) Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 25: 162

Horton S, Mastrolia V, Jackson RE, Kemlo S, Pereira Machado PM, Carbajal MA, Hindges R, Fleck RA, Aguiar P, Neves G, Burrone J (2024) Excitatory and inhibitory synapses show a tight subcellular correlation that weakens over development. Cell Rep 43: 114361

Li JD, Taipale M, Blencowe BJ (2024) Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25. Mol Cell
Mateus JC, Sousa MM, Burrone J, Aguiar P (2024) Beyond a Transmission Cable-New Technologies to Reveal the Richness in Axonal Electrophysiology. J Neurosci 44

Marín O (2024) Parvalbumin interneuron deficits in schizophrenia. Eur Neuropsychopharmacol 82: 44-52

Gogou C, Beugelink JW, Frias CP, Kresik L, Jaroszynska N, Drescher U, Janssen BJC, Hindges R, Meijer DH (2024) Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition. Nat Commun 15: 3648

Pellegrini L, Silva-Vargas V, Patrizi A (2024) Breakthroughs in choroid plexus and CSF biology from the first European Choroid plexus Scientific Forum (ECSF). Fluids Barriers CNS 21: 43

Li S, Shea QTK, Ling YT, Zheng YP (2024) Investigation of 3D vessel reconstruction under Doppler imaging with phantoms: Towards reconstruction of the Circle of Willis. Ultrasonics 141: 107332

Perez-Sisques L, Bhatt S, Matuleviciute R, Gileadi T, Kramar E, Graham A, Garcia FG, Keiser A, Matheos DP, Cain JA, Pittman AM, Andreae LC, Fernandes C, Wood MA, Giese KP, Basson MA (2024) The intellectual disability risk gene Kdm5b regulates long term memory consolidation in the hippocampus. J Neurosci

Ellingford RA, Tojo M, Basson MA, Andreae LC (2024) Male-Dominant Effects of Chd8 Haploinsufficiency on Synaptic Phenotypes during Development in Mouse Prefrontal Cortex. ACS Chem Neurosci 15: 1635-1642

Cole N, Harvey M, Myers-Joseph D, Gilra A, Khan A (2024) Prediction error signals in anterior cingulate cortex drive task-switching bioRxiv

Mòdol L, Moissidis M, Selten M, Oozeer F, Marín O (2024) Somatostatin interneurons control the timing of developmental desynchronization in cortical networks. Neuron

Folgueira M, Clarke JDW (2024) Telencephalic eversion in embryos and early larvae of four teleost species. Evol Dev 26: e12474

Cubillos P, Ditzer N, Kolodziejczyk A, Schwenk G, Hoffmann J, Schütze TM, Derihaci RP, Birdir C, Köllner JE, Petzold A, Sarov M, Martin U, Long KR, Wimberger P, Albert M (2024) The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex. EMBO J

Makeyev EV, Huang S (2024) The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. Nucleus 15: 2306777

Read E, Hindges R (2024) A novel locomotion-based prepulse inhibition assay in zebrafish larvae. MicroPubl Biol 2024

Ganier C, Mazin P, Herrera-Oropeza G, Du-Harpur X, Blakeley M, Gabriel J, Predeus AV, Cakir B, Prete M, Harun N, Darrigrand JF, Haiser A, Wyles S, Shaw T, Teichmann SA, Haniffa M, Watt FM, Lynch MD (2024) Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma. Proc Natl Acad Sci U S A 121: e2313326120

Rodríguez-Moreno CB, Cañeque-Rufo H, Flor-García M, Terreros-Roncal J, Moreno-Jiménez EP, Pallas-Bazarra N, Bressa C, Larrosa M, Cafini F, Llorens-Martín M (2024) Azithromycin preserves adult hippocampal neurogenesis and behavior in a mouse model of sepsis. Brain Behav Immun 117: 135-148

Myers-Joseph D, Wilmes KA, Fernandez-Otero M, Clopath C, Khan AG (2024) Disinhibition by VIP interneurons is orthogonal to cross-modal attentional modulation in primary visual cortex. Neuron 112: 628-645.e7

2023

Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ (2023) Global detection of human variants and isoforms by deep proteome sequencing. Nat Biotechnol 41: 1776-1786
Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR, Blencowe BJ, Lambowitz AM, Schimmel P (2023) Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 25: 592-603
Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ (2023) Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 83: 4222-4238.e10
Cheesbrough A, Harley P, Riccio F, Wu L, Song W, Lieberam I (2023) A scalable human iPSC-based neuromuscular disease model on suspended biobased elastomer nanofiber scaffolds. Biofabrication 15

Mishra S, Dabaja M, Akhlaq A, Pereira B, Marbach K, Rovcanin M, Chandra R, Caballero A, Fernandes de Abreu D, Ch'ng Q, Alcedo J (2023) Specific sensory neurons and insulin-like peptides modulate food type-dependent oogenesis and fertilization in Caenorhabditis elegans. Elife 12: e83224.

Zeng B, Liu Z, Lu Y, Zhong S, Qin S, Huang L, Zeng Y, Li Z, Dong H, Shi Y, Yang J, Dai Y, Ma Q, Sun L, Bian L, Han D, Chen Y, Qiu X, Wang W, Marín O, Wu Q, Wang Y, Wang X (2023) The single-cell and spatial transcriptional landscape of human gastrulation and early brain development. Cell Stem Cell 30: 851-866.e7.

Kainov Y, Zhuravskaya A, Makeyev EV (2023) Protocol for auxin-inducible depletion of the RNA-binding protein PTBP1 in mouse embryonic stem cells. STAR Protoc 4: 102644.

Beltrán Arranz A, Berninger B (2023) Seizing hope: Advancing cell therapy for pharmaco-resistant epilepsy toward the clinic. Cell Stem Cell 30: 1287-1289.

Felske T, Tocco C, Péron S, Harb K, Alfano C, Galante C, Berninger B, Studer M (2023) Lmo4 synergizes with Fezf2 to promote direct in vivo reprogramming of upper layer cortical neurons and cortical glia towards deep-layer neuron identities. PLoS Biol 21(8): e3002237.

Chadwick A, Khan AG, Poort J, Blot A, Hofer SB, Mrsic-Flogel TD, Sahani M (2023) Learning shapes cortical dynamics to enhance integration of relevant sensory input. Neuron 111: 106-120.e10.

Choi S, Schilder BM, Abbasova L, Murphy AE, Skene NG (2023) EpiCompare: R package for the comparison and quality control of epigenomic peak files. Bioinform Adv 3: vbad049.

Puhl CJ, Wefelmeyer W, Burrone J (2023) Cholinergic Stimulation Modulates the Functional Composition of CA3 Cell Types in the Hippocampus. J Neurosci 43: 4972-4983.

Williams J, Hurling C, Munir S, Harley P, Machado CB, Cujba AM, Alvarez-Fallas M, Danovi D, Lieberam I, Sancho R, Beales P, Watt FM (2023) Modelling renal defects in Bardet-Biedl syndrome patients using human iPS cells. Front Cell Dev Biol 11: 1163825.

Fan W, Jurado-Arjona J, Alanis-Lobato G, Péron S, Berger C, Andrade-Navarro MA, Falk S, Berninger B (2023) The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation. EMBO J : e110384.

Compans B, Burrone J (2023) Chandelier cells shine a light on the formation of GABAergic synapses. Curr Opin Neurobiol 80: 102697.

Harley P, Paredes-Redondo A, Grenci G, Viasnoff V, Lin YY, Lieberam I (2023) 3D Compartmentalised Human Pluripotent Stem Cell-derived Neuromuscular Co-cultures. Bio Protoc 13: e4624.

Jetsonen E, Didio G, Winkel F, Llach Pou M, Boj C, Kuczynski-Noyau L, Võikar V, Guirado R, Taira T, Lauri SE, Castrén E, Umemori J (2023) Activation of TrkB in Parvalbumin interneurons is required for the promotion of reversal learning in spatial and fear memory by antidepressants. Neuropsychopharmacology 48: 1021-1030.

Iannone C, Kainov Y, Zhuravskaya A, Hamid F, Nojima T, Makeyev EV (2023) PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells. Mol Cell 83: 203-218.e9.

Massimo M, Barelli C, Moreno C, Collesi C, Holloway RK, Crespo B, Zentilin L, Williams A, Miron VE, Giacca M, Long KR (2023) Haemorrhage of human foetal cortex associated with SARS-CoV-2 infection. Brain 146: 1175-1185.

Poopalasundaram S, Richardson J, Graham A (2023) Key separable events in the remodelling of the pharyngeal arches. J Anat 243: 100-109.

Berzanskyte I, Riccio F, Machado CB, Bradbury EJ, Lieberam I (2023) Enrichment of human embryonic stem cell-derived V3 interneurons using an Nkx2-2 gene-specific reporter. Sci Rep 13: 2008.

Kebschull JM, Casoni F, Consalez GG, Goldowitz D, Hawkes R, Ruigrok TJH, Schilling K, Wingate R, Wu J, Yeung J, Uusisaari MY (2023) Cerebellum Lecture: the Cerebellar Nuclei-Core of the Cerebellum. Cerebellum.

Cameron D, Mi D, Vinh NN, Webber C, Li M, Marín O, O'Donovan MC, Bray NJ (2023) Single-Nuclei RNA Sequencing of 5 Regions of the Human Prenatal Brain Implicates Developing Neuron Populations in Genetic Risk for Schizophrenia. Biol Psychiatry 93: 157-166.

2022

Nabeel-Shah S, Lee H, Ahmed N, Burke GL, Farhangmehr S, Ashraf K, Pu S, Braunschweig U, Zhong G, Wei H, Tang H, Yang J, Marcon E, Blencowe BJ, Zhang Z, Greenblatt JF (2022) SARS-CoV-2 nucleocapsid protein binds host mRNAs and attenuates stress granules to impair host stress response. iScience 25: 103562
Barutcu AR, Wu M, Braunschweig U, Dyakov BJA, Luo Z, Turner KM, Durbic T, Lin ZY, Weatheritt RJ, Maass PG, Gingras AC, Blencowe BJ (2022) Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol Cell 82: 1035-1052.e9
Fagg WS, Liu N, Braunschweig U, Pereira de Castro KL, Chen X, Ditmars FS, Widen SG, Donohue JP, Modis K, Russell WK, Fair JH, Weirauch MT, Blencowe BJ, Garcia-Blanco MA (2022) Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. Nucleic Acids Res 50: 5313-5334
Song J, Nabeel-Shah S, Pu S, Lee H, Braunschweig U, Ni Z, Ahmed N, Marcon E, Zhong G, Ray D, Ha KCH, Guo X, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF (2022) Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Mol Cell 82: 3135-3150.e9
Kelava I, Chiaradia I, Pellegrini L, Kalinka AT, Lancaster MA (2022) Androgens increase excitatory neurogenic potential in human brain organoids. Nature 602: 112-116
Kostadinov D, Häusser M (2022) Reward signals in the cerebellum: Origins, targets, and functional implications. Neuron 110: 1290-1303
Hindges R, Lele Z (2022) Editorial: Cell adhesion molecules in neural development and disease. Front Neurosci 16: 1112300
Browne LP, Crespo A, Grubb MS (2022) Rapid presynaptic maturation in naturally regenerating axons of the adult mouse olfactory nerve. Cell Rep 41: 111750
Galante C, Marichal N, Scarante FF, Ghayad LM, Shi Y, Schuurmans C, Berninger B, Péron S (2022) Enhanced proliferation of oligodendrocyte progenitor cells following retrovirus mediated Achaete-scute complex-like 1 overexpression in the postnatal cerebral cortex in vivo. Front Neurosci 16: 919462
Sainsbury TTJ, Diana G, Meyer MP (2022) Topographically localised modulation of tectal cell spatial tuning by complex natural scenes. eNeuro
Moore RE, Pop S, Alleyne C, Clarke JDW (2022) Microtubules are not required to generate a nascent axon in embryonic spinal neurons in vivo. EMBO Rep 23: e52493
Cheung A, Schachermayer G, Biehler A, Wallis A, Missaire M, Hindges R (2022) Teneurin paralogues are able to localise synaptic sites driven by the intracellular domain and have the potential to form cis-heterodimers. Front Neurosci 16: 915149
Nikolaou N, Gordon PM, Hamid F, Taylor R, Lloyd-Jones J, Makeyev EV, Houart C (2022) Cytoplasmic pool of U1 spliceosome protein SNRNP70 shapes the axonal transcriptome and regulates motor connectivity. Curr Biol

Taylor R, Hamid F, Fielding T, Gordon PM, Maloney M, Makeyev EV, Houart C (2022) Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS. Nat Commun 13: 6994

Richard Taylor, Fursham Hamid, Triona Fielding, Patricia M. Gordon, Megan Maloney, Eugene V. Makeyev & Corinne Houart (2022) Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS Nature Communications

Nikolas Nikolaou, Patricia M. Gordon, Fursham Hamid, Richard Taylor, Joshua Lloyd-Jones, Eugene V. Makeyev, Corinne Houart (2022) Cytoplasmic pool of U1 spliceosome protein SNRNP70 shapes the axonal transcriptome and regulates motor connectivity Current Biology

Cheung A., Schachermayer G., Biehler A., Wallis A., Missaire M. & Hindges R. (2022) Teneurin paralogues are able to localise synaptic sites driven by the intracellular domain and have the potential to form cis-heterodimers Frontiers in Neuroscience

Poobalasingam T, Bianco F, Oozeer F, Gordon-Weeks PR (2022) The drebrin/EB3 pathway regulates cytoskeletal dynamics to drive neuritogenesis in embryonic cortical neurons. J Neurochem 160: 185-202
Marín O, Moreno N (2022) Agustín González, an Inspirational Leader in Spanish Comparative Neuroanatomy. Brain Behav Evol 96: 174-180
Sheardown E, Torres-Perez JV, Anagianni S, Fraser SE, Vallortigara G, Butterworth B, Miletto-Petrazzini ME, Brennan CH (2022) Characterizing ontogeny of quantity discrimination in zebrafish. Proc Biol Sci 289: 20212544
Newland B, Long KR (2022) Cryogel scaffolds: soft and easy to use tools for neural tissue culture. Neural Regen Res 17: 1981-1983
Tufo C, Poopalasundaram S, Dorrego-Rivas A, Ford MC, Graham A, Grubb MS (2022) Development of the mammalian main olfactory bulb. Development 149
Jackson RE, Compans B, Burrone J (2022) Correlative Live-Cell and Super-Resolution Imaging to Link Presynaptic Molecular Organisation With Function. Front Synaptic Neurosci 14: 830583
Byrne DJ, Lipovsek M, Crespo A, Grubb MS (2022) Brief sensory deprivation triggers plasticity of dopamine-synthesising enzyme expression in genetically labelled olfactory bulb dopaminergic neurons. Eur J Neurosci 56: 3591-3612
Sreenivasan V, Serafeimidou-Pouliou E, Exposito-Alonso D, Bercsenyi K, Bernard C, Bae SE, Oozeer F, Hanusz-Godoy A, Edwards RH, Marín O (2022) Input-specific control of interneuron numbers in nascent striatal networks. Proc Natl Acad Sci U S A 119: e2118430119
Dorrego-Rivas A, Grubb MS (2022) The axon initial segment as a source of neuropathic pain. Brain 145: 1574-1575
Cooper A, Berninger B (2022) Gatekeeping astrocyte identity. Elife 11
Kelkar M, Bohec P, Smith MB, Sreenivasan V, Lisica A, Valon L, Ferber E, Baum B, Salbreux G, Charras G (2022) Spindle reorientation in response to mechanical stress is an emergent property of the spindle positioning mechanisms. Proc Natl Acad Sci U S A 119: e2121868119
Dorrego-Rivas A, Grubb MS (2022) Developing and maintaining a nose-to-brain map of odorant identity. Open Biol 12: 220053
Jackson RE, Compans B, Burrone J (2022) Corrigendum: Correlative Live-Cell and Super-Resolution Imaging to Link Presynaptic Molecular Organisation With Function. Front Synaptic Neurosci 14: 953045
Wong FK, Selten M, Rosés-Novella C, Sreenivasan V, Pallas-Bazarra N, Serafeimidou-Pouliou E, Hanusz-Godoy A, Oozeer F, Edwards R, Marín O (2022) Serotonergic regulation of bipolar cell survival in the developing cerebral cortex. Cell Rep 40: 111037
Leschik J, Gentile A, Cicek C, Péron S, Tevosian M, Beer A, Radyushkin K, Bludau A, Ebner K, Neumann I, Singewald N, Berninger B, Lessmann V, Lutz B (2022) Brain-derived neurotrophic factor expression in serotonergic neurons improves stress resilience and promotes adult hippocampal neurogenesis. Prog Neurobiol 217: 102333
Velásquez ZD, Rojas-Barón L, Larrazabal C, Salierno M, Gärtner U, Pervizaj-Oruqaj L, Herold S, Hermosilla C, Taubert A (2022) Corrigendum: Neospora caninum infection triggers S-phase arrest and alters nuclear characteristics in primary bovine endothelial host cells. Front Cell Dev Biol 10: 1025995
Hamid F, Alasoo K, Vilo J, Makeyev E (2022) Functional Annotation of Custom Transcriptomes. Methods Mol Biol 2537: 149-172
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