Publications

2024

Best AJ, Braunschweig U, Wu M, Farhangmehr S, Pasculescu A, Lim JJ, Comsa LC, Jen M, Wang J, Datti A, Wrana JL, Cordes SP, Al-Awar R, Han H, Blencowe BJ (2024) High-throughput sensitive screening of small molecule modulators of microexon alternative splicing using dual Nano and Firefly luciferase reporters. Nat Commun

Lim JJ, Vining KH, Mooney DJ, Blencowe BJ (2024) Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR. Proc Natl Acad Sci U S A

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

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

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

Li JD, Taipale M, Blencowe BJ (2024) Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25. Mol Cell

Beau M, Herzfeld DJ, Naveros F, Hemelt ME, D'Agostino F, Oostland M, Sánchez-López A, Chung YY, Michael Maibach , Kyranakis S, Stabb HN, Martínez Lopera MG, Lajko A, Zedler M, Ohmae S, Hall NJ, Clark BA, Cohen D, Lisberger SG, Kostadinov D, Hull C, Häusser M, Medina JF (2024) A deep-learning strategy to identify cell types across species from high-density extracellular recordings. bioRxiv

Mateus JC, Sousa MM, Burrone J, Aguiar P (2024) Beyond a Transmission Cable-New Technologies to Reveal the Richness in Axonal Electrophysiology. J Neurosci

Marín O (2024) Parvalbumin interneuron deficits in schizophrenia. Eur Neuropsychopharmacol

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

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

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

Pérez-Sisqués L, Bhatt SU, Matuleviciute R, Gileadi TE, 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

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

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

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

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

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

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

2023

Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J (2023) Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon

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

Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR (2023) RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep

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

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

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

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

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

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

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

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

Sezener E, Grabska-Barwińska A, Kostadinov D, Beau M, Krishnagopal S, Budden D, Hutter D, Veness J, Botvinick M, Clopath C, Häusser M, Latham PE (2023) A rapid and efficient learning rule for biological neural circuits. bioRxiv.

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

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

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

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

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

Rigby M, Grillo FW, Compans B, Neves G, Gallinaro J, Nashashibi S, Horton S, Pereira Machado PM, Carbajal MA, Vizcay-Barrena G, Levet F, Sibarita JB, Kirkland A, Fleck RA, Clopath C, Burrone J (2023) Multi-synaptic boutons are a feature of CA1 hippocampal connections in the stratum oriens. Cell Rep

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

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

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

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

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

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

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

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

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

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

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

Han H, Best AJ, Braunschweig U, Mikolajewicz N, Li JD, Roth J, Chowdhury F, Mantica F, Nabeel-Shah S, Parada G, Brown KR, O'Hanlon D, Wei J, Yao Y, Zid AA, Comsa LC, Jen M, Wang J, Datti A, Gonatopoulos-Pournatzis T, Weatheritt RJ, Greenblatt JF, Wrana JL, Irimia M, Gingras AC, Moffat J, Blencowe BJ (2022) Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis. Mol Cell

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

Kelava I, Chiaradia I, Pellegrini L, Kalinka AT, Lancaster MA (2022) Androgens increase excitatory neurogenic potential in human brain organoids. Nature

Kostadinov D, Häusser M (2022) Reward signals in the cerebellum: Origins, targets, and functional implications. Neuron

Hindges R, Lele Z (2022) Editorial: Cell adhesion molecules in neural development and disease. Front Neurosci

Browne LP, Crespo A, Grubb MS (2022) Rapid presynaptic maturation in naturally regenerating axons of the adult mouse olfactory nerve. Cell Rep

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

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

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

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

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

Mossink B, van Rhijn JR, Wang S, Linda K, Vitale MR, Zöller JEM, van Hugte EJH, Bak J, Verboven AHA, Selten M, Negwer M, Latour BL, van der Werf I, Keller JM, Klein Gunnewiek TM, Schoenmaker C, Oudakker A, Anania A, Jansen S, Lesch KP, Frega M, van Bokhoven H, Schubert D, Nadif Kasri N (2022) Cadherin-13 is a critical regulator of GABAergic modulation in human stem-cell-derived neuronal networks. Mol Psychiatry

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

Marín O, Moreno N (2022) Agustín González, an Inspirational Leader in Spanish Comparative Neuroanatomy. Brain Behav Evol

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

Newland B, Long KR (2022) Cryogel scaffolds: soft and easy to use tools for neural tissue culture. Neural Regen Res

Tufo C, Poopalasundaram S, Dorrego-Rivas A, Ford MC, Graham A, Grubb MS (2022) Development of the mammalian main olfactory bulb. Development

Jackson RE, Compans B, Burrone J (2022) Correlative Live-Cell and Super-Resolution Imaging to Link Presynaptic Molecular Organisation With Function. Front Synaptic Neurosci

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

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

Dorrego-Rivas A, Grubb MS (2022) The axon initial segment as a source of neuropathic pain. Brain

Cooper A, Berninger B (2022) Gatekeeping astrocyte identity. Elife

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

Dorrego-Rivas A, Grubb MS (2022) Developing and maintaining a nose-to-brain map of odorant identity. Open Biol

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

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

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

Messina A, Potrich D, Perrino M, Sheardown E, Miletto Petrazzini ME, Luu P, Nadtochiy A, Truong TV, Sovrano VA, Fraser SE, Brennan CH, Vallortigara G (2022) Quantity as a Fish Views It: Behavior and Neurobiology. Front Neuroanat

Ma S, Skarica M, Li Q, Xu C, Risgaard RD, Tebbenkamp ATN, Mato-Blanco X, Kovner R, Krsnik Ž, de Martin X, Luria V, Martí-Pérez X, Liang D, Karger A, Schmidt DK, Gomez-Sanchez Z, Qi C, Gobeske KT, Pochareddy S, Debnath A, Hottman CJ, Spurrier J, Teo L, Boghdadi AG, Homman-Ludiye J, Ely JJ, Daadi EW, Mi D, Daadi M, Marín O, Hof PR, Rasin MR, Bourne J, Sherwood CC, Santpere G, Girgenti MJ, Strittmatter SM, Sousa AMM, Sestan N (2022) Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science

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

Hamid F, Alasoo K, Vilo J, Makeyev E (2022) Functional Annotation of Custom Transcriptomes. Methods Mol Biol

Yap K, Chung TH, Makeyev EV (2022) Analysis of RNA-containing compartments by hybridization and proximity labeling in cultured human cells. STAR Protoc

Yap K, Chung TH, Makeyev EV (2022) Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments. Mol Cell