Papers

2025

• Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesionsFeng R, Spieth L, Liu L, Berghoff S, Franz J, Liu Q, Wang Z, Tiwari V, Vitale S, Frerich SImmunity · 2025
• An atypical atherogenic chemokine that promotes advanced atherosclerosis and hepatic lipogenesisEl Bounkari O, Zan C, Yang B, Ebert S, Wagner J, Bugar E, Kramer N, Bourilhon P, Kontos C, Zarwel MNature Communications · 2025
• Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 miceRezaei A, Kocsis-Jutka V, Gunes ZI, Zeng Q, Kislinger G, Bauernschmitt F, Isilgan HB, Parisi LR, Kaya T, Franzenburg SNature Communications · 2025
• Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegenerationMurray ME, Smith C, Menon V, Keene CD, Lein E, Hawrylycz M, Aguzzi A, Benedetti B, Brose K, Caetano-Anolles KNeuron · 2025
• Accelerating Biomedical Discoveries in Aging and Neurodegeneration Through Transformative NeuropathologyMurray ME, Smith C, Menon V, Keen CD, Lein ES, Hawrylycz M, Aguzzi A, Benedetti B, Brose K, Caetano-Anolles KPreprint · 2025

2024

• Continued dysfunction of capillary pericytes promotes no-reflow after experimental stroke in vivoShrouder JJ, Calandra GM, Filser S, Varga DP, Besson-Girard S, Mamrak U, Dorok M, Bulut-Impraim B, Seker FB, Gesierich BBrain · 2024doi.org/10.1093/brain/awad401
• Innate immune memory after brain injury drives inflammatory cardiac dysfunctionSimats A, Zhang S, Messerer D, Chong F, Beşkardeş S, Chivukula AS, Cao J, Besson-Girard S, Montellano FA, Morbach CCell · 2024doi.org/10.1016/j.cell.2023.08.013
• Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous systemTiwari V, Prajapati B, Asare Y, Damkou A, Ji H, Liu L, Naser N, Gouna G, Leszczyńska KB, Mieczkowski JImmunity · 2024doi.org/10.1016/j.immuni.2024.07.013
• T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosisKedia S, Ji H, Feng R, Androvic P, Spieth L, Liu L, Franz J, Zdiarstek H, Anderson KP, Kaboglu CNature Neuroscience · 2024
• Implementation and validation of single-cell genomics experiments in neuroscienceColonna M, Konopka G, Liddelow SA, Nowakowski T, Awatramani R, Bateup HS, Cadwell CR, Caglayan E, Chen JL, Gillis JNature Neuroscience · 2024doi.org/10.1038/s41593-024-01814-0
• Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discoveryBonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis MNature Neuroscience · 2024doi.org/10.1038/s41593-024-01806-0
• Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous systemAdameyko I, Bakken T, Bhaduri A, Chhatbar C, Filbin MG, Gate D, Hochgerner H, Kim CN, Krull J, La Manno GNature Neuroscience · 2024doi.org/10.1038/s41593-024-01827-9

2023

• Distinct molecular profiles of skull bone marrow in health and neurological disordersKolabas ZI, Kuemmerle LB, Perneczky R, Förstera B, Ulukaya S, Ali M, Kapoor S, Bartos LM, Büttner M, Caliskan OSCell · 2023doi.org/10.1016/j.cell.2023.07.009
• Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injuryAndrovic P, Schifferer M, Perez Anderson K, Cantuti-Castelvetri L, Jiang H, Ji H, Liu L, Gouna G, Berghoff SA, Besson-Girard SNature Communications · 2023doi.org/10.1038/s41467-023-39447-9
• High-resolution RNA sequencing from PFA-fixed microscopy sectionsJi H, Besson-Girard S, Androvic P, Bulut B, Liu L, Wang Y, Gokce ONeural Repair: Methods and Protocols · 2023doi.org/10.1007/978-1-0716-2926-0_16
• Pathways linking aging and atheroprotection in Mif‐deficient atherosclerotic miceKrammer C, Yang B, Reichl S, Besson‐Girard S, Ji H, Bolini V, Schulte C, Noels H, Schlepckow K, Jocher GThe FASEB journal · 2023doi.org/10.1096/fj.202200056R

2022

• Heterocomplexes between the atypical chemokine MIF and the CXC-motif chemokine CXCL4L1 regulate inflammation and thrombus formationBrandhofer M, Hoffmann A, Blanchet X, Siminkovitch E, Rohlfing AK, El Bounkari O, Nestele JA, Bild A, Kontos C, Hille KCellular and molecular life sciences · 2022doi.org/10.1007/s00018-022-04539-0
• ADAM10 and ADAM17 promote SARS‐CoV‐2 cell entry and spike protein‐mediated lung cell fusionJocher G, Grass V, Tschirner SK, Riepler L, Breimann S, Kaya T, Oelsner M, Hamad MS, Hofmann LI, Blobel CPEMBO reports · 2022doi.org/10.15252/embr.202154305
• CD8+ T cells induce interferon-responsive oligodendrocytes and microglia in white matter agingKaya T, Mattugini N, Liu L, Ji H, Cantuti-Castelvetri L, Wu J, Schifferer M, Groh J, Martini R, Besson-Girard SNature Neuroscience · 2022doi.org/10.1038/s41593-022-01183-6
• Microglia states and nomenclature: A field at its crossroadsPaolicelli RC, Sierra A, Stevens B, Tremblay ME, Aguzzi A, Ajami B, Amit I, Audinat E, Bechmann I, Bennett MNeuron · 2022doi.org/10.1016/j.neuron.2022.10.020
• T cells induce interferon-responsive oligodendrocytes during white matter agingKaya T, Mattugini N, Liu L, Ji H, Besson-Girard S, Kaiji S, Liesz A, Gokce O, Simons MbioRxiv · 2022
• Spatial transcriptomics-correlated electron microscopyAndrovic P, Schifferer M, Anderson KP, Cantuti-Castelvetri L, Ji H, Liu L, Besson-Girard S, Knoferle J, Simons M, Gokce ObioRxiv · 2022
• T cells modulate the microglial response to brain ischemiaBenakis C, Simats A, Tritschler S, Heindl S, Besson-Girard S, Llovera G, Pinkham K, Kolz A, Ricci A, Theis FJeLife · 2022doi.org/10.7554/eLife.82031

2021

• TREM2-dependent lipid droplet biogenesis in phagocytes is required for remyelinationGouna G, Klose C, Bosch-Queralt M, Liu L, Gokce O, Schifferer M, Cantuti-Castelvetri L, Simons MJournal of Experimental Medicine · 2021
• White matter aging drives microglial diversitySafaiyan S, Besson-Girard S, Kaya T, Cantuti-Castelvetri L, Liu L, Ji H, Schifferer M, Gouna G, Usifo F, Kannaiyan NNeuron · 2021doi.org/10.1016/j.neuron.2021.01.027
• Dissociation of microdissected mouse brain tissue for artifact free single-cell RNA sequencingLiu L, Besson-Girard S, Ji H, Gehring K, Bulut B, Kaya T, Usifo F, Simons M, Gokce OSTAR protocols · 2021doi.org/10.1016/j.xpro.2021.100590
• Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammationKolabas ZI, Kuemmerle LB, Perneczky R, Förstera B, Büttner M, Caliskan OS, Ali M, Rong Z, Mai H, Hummel SbioRxiv · 2021

2020

• Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous systemCantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, Kallio K, Kaya T, Anastasina M, Smura TBioRxiv · 2020
• Designed CXCR4 mimic acts as a soluble chemokine receptor that blocks atherogenic inflammation by agonist-specific targetingKontos C, El Bounkari O, Krammer C, Sinitski D, Hille K, Zan C, Yan G, Wang S, Gao Y, Brandhofer MNature Communications · 2020doi.org/10.1038/s41467-020-19764-z
• Continuous and discrete neuron types of the adult murine striatumStanley G, Gokce O, Malenka RC, Südhof TC, Quake SRNeuron · 2020doi.org/10.1016/j.neuron.2019.11.004
• Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivityCantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, van der Meer F, Kallio K, Kaya T, Anastasina MScience · 2020doi.org/10.1126/science.abd2985

2019

• Characterization of the Nuclease Activity of MIF Proteins: A 02-10Bulut B, Besson-Girard S, Usifo F, Bernhagen J, Gokce OActa Physiologica · 2019
• scRNA-Seq Identifies MIF as Master Regulator of B Cell Fate: OS 08-06Besson-Girard S, Krammer C, Reichl S, Usifo F, Bernhagen J, Gokce OActa Physiologica · 2019
• Effects Of Mif-Deficiency On Age-Related B Cell Phenotypes And Population Diversity In AtherosclerosisKrammer C, Besson-Girard S, Gokce O, Schulte C, El Bounkari O, Bernhagen JAtherosclerosis · 2019
• Discrete and continuous cell identities of the adult murine striatumStanley G, Gokce O, Malenka RC, Südhof TC, Quake SRBioRxiv · 2019
• The multitasking potential of alarmins and atypical chemokinesKapurniotu A, Gokce O, Bernhagen JFrontiers in medicine · 2019doi.org/10.3389/fmed.2019.00003

2018

• High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysisWang W, Penland L, Gokce O, Croote D, Quake SRBMC genomics · 2018
• Autism-associated neuroligin-4 mutation selectively impairs glycinergic synaptic transmission in mouse brainstem synapsesZhang B, Gokce O, Hale WD, Brose N, Südhof TCJournal of Experimental Medicine · 2018doi.org/10.1084/jem.20172162

2017

• Developmental plasticity shapes synaptic phenotypes of autism-associated neuroligin-3 mutations in the calyx of HeldZhang B, Seigneur E, Wei P, Gokce O, Morgan J, Südhof TMolecular Psychiatry · 2017doi.org/10.1038/mp.2016.157

2016

• Cellular taxonomy of the mouse striatum as revealed by single cell RNA sequencingStanley G, Gokce O, Treutlein B, Sudhof TC, Quake SBiophysical Journal · 2016
• Cellular taxonomy of the mouse striatum as revealed by single-cell RNA-seqGokce O, Stanley GM, Treutlein B, Neff NF, Camp JG, Malenka RC, Rothwell PE, Fuccillo MV, Südhof TC, Quake SRCell Reports · 2016doi.org/10.1016/j.celrep.2016.06.059
• Novel Neuron Types and Anatomical Organization of the Striatum Revealed by Single-Cell RNA-SeqStanley G, Gökce O, Treutlein B, Quake S, Sudhof TMolecular Biology of the Cell · 2016

2015

• Single-cell mRNA profiling reveals cell-type-specific expression of neurexin isoformsFuccillo MV, Földy C, Gökce O, Rothwell PE, Sun GL, Malenka RC, Südhof TCNeuron · 2015doi.org/10.1016/j.neuron.2015.06.028
• Neuroligins sculpt cerebellar Purkinje-cell circuits by differential control of distinct classes of synapsesZhang B, Chen LY, Liu X, Maxeiner S, Lee SJ, Gokce O, Südhof TCNeuron · 2015doi.org/10.1016/j.neuron.2015.07.020

2014

• Autism-associated neuroligin-3 mutations commonly impair striatal circuits to boost repetitive behaviorsRothwell PE, Fuccillo MV, Maxeiner S, Hayton SJ, Gokce O, Lim BK, Fowler SC, Malenka RC, Südhof TCCell · 2014doi.org/10.1016/j.cell.2014.04.045
• A potent and selective Sirtuin 1 inhibitor alleviates pathology in multiple animal and cell models of Huntington's diseaseSmith MR, Syed A, Lukacsovich T, Purcell J, Barbaro BA, Worthge SA, Wei SR, Pollio G, Magnoni L, Scali CHuman molecular genetics · 2014doi.org/10.1093/hmg/ddu010
• Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencingTreutlein B, Gokce O, Quake SR, Südhof TCProceedings of the National Academy of Sciences · 2014doi.org/10.1073/pnas.1403244111

2013

• Fused 3-hydroxy-3-trifluoromethylpyrazoles inhibit mutant Huntingtin toxicityLa Rosa S, Benicchi T, Bettinetti L, Ceccarelli I, Diodato E, Federico C, Fiengo P, Franceschini D, Gokce O, Heitz FACS medicinal chemistry letters · 2013doi.org/10.1021/ml400251g
• Membrane-tethered monomeric neurexin LNS-domain triggers synapse formationGokce O, Südhof TCThe Journal of neuroscience · 2013doi.org/10.1523/JNEUROSCI.1232-13.2013

2011

• Decreased striatal RGS2 expression is neuroprotective in Huntington's disease (HD) and exemplifies a compensatory aspect of HD-induced gene regulationSeredenina T, Gokce O, Luthi-Carter RPloS one · 2011

2010

• Diminished activity-dependent BDNF expression underlies cortical neuron microcircuit hypoconnectivity resulting from exposure to mutant huntingtin fragmentsGambazzi L, Gokce O, Seredenina T, Katsyuba E, Runne H, Markram H, Giugliano M, Luthi-Carter RJ. Pharmacol. Exp. Ther · 2010doi.org/10.1124/jpet.110.167551
• A06 Effects of mutant huntingtin on cortical neuron connectivity and activity dependent gene expressionSeredenina T, Gambazzi L, Gokce O, Katsyuba E, Runne H, Markram H, Giugliano M, Luthi-Carter RJournal of Neurology, Neurosurgery & Psychiatry · 2010
• A10 SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesisTaylor D, Pallos J, Lambert E, Amore A, Parker A, Moffitt H, Smith D, Runne H, Gokce O, Kuhn AJournal of Neurology, Neurosurgery & Psychiatry · 2010
• Decreased Lin7b expression in layer 5 pyramidal neurons may contribute to impaired corticostriatal connectivity in huntington diseaseZucker B, Kama JA, Kuhn A, Thu D, Orlando LR, Dunah AW, Gokce O, Taylor DM, Lambeck J, Friedrich BJournal of Neuropathology & Experimental Neurology · 2010doi.org/10.1097/NEN.0b013e3181ed7a41
• SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesisLuthi-Carter R, Taylor DM, Pallos J, Lambert E, Amore A, Parker A, Moffitt H, Smith DL, Runne H, Gokce OProceedings of the National Academy of Sciences · 2010doi.org/10.1073/pnas.1002924107
• Diminished activity-dependent brain-derived neurotrophic factor expression underlies cortical neuron microcircuit hypoconnectivity resulting from exposure to mutant huntingtin fragmentsGambazzi L, Gokce O, Seredenina T, Katsyuba E, Runne H, Markram H, Giugliano M, Luthi-Carter RThe Journal of pharmacology and experimental therapeutics · 2010

2009

• Diminished hippocalcin expression in Huntington’s disease brain does not account for increased striatal neuronGokce O, Nicole DJOURNAL OF NEUROCHEMISTRY · 2009
• Diminished hippocalcin expression in Huntington’s disease brain does not account for increased striatal neuron vulnerability as assessed in primary neuronsRudinskiy N, Kaneko YA, Beesen AA, Gokce O, Régulier E, Déglon N, Luthi‐Carter RJournal of neurochemistry · 2009
• Short-term striatal gene expression responses to brain-derived neurotrophic factor are dependent on MEK and ERK activationGokce O, Runne H, Kuhn A, Luthi-Carter RPlos one · 2009

2008

• The ratio of monomeric to aggregated forms of Aβ40 and Aβ42 is an important determinant of amyloid-β aggregation, fibrillogenesis, and toxicityJan A, Gokce O, Luthi-Carter R, Lashuel HAJournal of Biological Chemistry · 2008
• Dysregulation of gene expression in primary neuron models of Huntington's disease shows that polyglutamine-related effects on the striatal transcriptome may not be dependent on brain circuitryRunne H, Régulier E, Kuhn A, Zala D, Gokce O, Perrin V, Sick B, Aebischer P, Déglon N, Luthi-Carter RThe journal of neuroscience · 2008

2004

• Krev1 Interaction Trapped-1/Cerebral Cavernous Malformation-1 protein expression during early angiogenesisGuzeloglu-Kayisli O, Kayisli UA, Amankulor NM, Voorhees JR, Gokce O, Diluna ML, Laurans MS, Luleci G, Gunel MJournal of Neurosurgery: Pediatrics · 2004