Publications

Asma Ull O, Kaandorp MPT, Jakab A, Kim HG (2026)
Developmental Brain Age Estimation From MRI Data: A Systematic Review of Deep Learning Approaches and Open Datasets
J Magn Reson Imaging, 650-671

Bürgi N, Aydogan G, Konovalov A, Ruff CC (2026)
A neural fingerprint of adaptive mentalization
Nature Neurosience, 934-944

Hu J, Moisa M, Ruff CC (2026)
Augmentation of frontoparietal gamma-band phase coupling enhances human altruistic behavior
PLOS Biology, e3003602

Raduner N, Providoli C, Di Pietro SV, Schneebeli M, ..., Casimiro E, Bedi S, Karipidis I, von Rhein M, Raschle NM, Ruff C, Brem S (2026)
Neural and behavioural differences in multisensory statistical and reinforcement learning across development and task variants Imaging Neuroscience, 1117

Wicki S, Canziani A, Poggi G, Argunşah AÖ, Karayannis T, Pryce CR (2026)
Development of visual-stimulus reversal learning-memory in mice is dependent on social interaction
iScience, 114864

Bachmann-Gagescu R, Sayer JA (2025)
Tackling ciliary specialization to understand phenotypic variability in human primary ciliopathies
Journal of Cell Science, jcs264177

Calangiu I, Kollmorgen S, Reppas J, Mante V (2025)
Prospective and retrospective representations of saccadic movements in primate prefrontal cortex
Cell Reports, 115289

Disselhoff V, Jakab A, Latal B, Schnider B, Wehrle MF, Hagman C, EpoKidsResearch Group (2025)
Inhibition abilities and functional brain connectivity in school-aged term-born and preterm-born children
Pediatric Research, 315-324

Ehrler M, O’Gorman R, Wehrle FM, Speckert A, Jakab A, Kretschmar O, Latal B (2025)Learning from those who thrive: protective factors and neuroimaging markers in adolescents with complex congenital heart disease and with a favorable neurodevelopmental profile. Child Neuropsychology, 613–634

Eschment M, Mercey O, ..., Rauch A, Guichard P, Hamel V, Bachmann-Gagescu R (2025)CEP290 deficiency disrupts ciliary axonemal architecture in human iPSC-derived brain organoids
Journal of Cell Science, jcs264092

Figueiro-Silva J, Eschment M, ..., Rauch A, Bachmann-Gagescu R (2025)
CRISPR/Cas9-mediated generation of two isogenic CEP290-mutated iPSC lines
Stem Cell Research, 103781

Fraga-González G, Haller P, Willinger D, Gehring V, Frei N, Brem S (2025)
Functional brain activations correlated with association strength and prediction error during novel symbol-speech sound learning
Imaging Neuroscience, imag_a_0039

Garbelli M, Chen Z (2025)
Food dye for optical clearing and in vivo imaging
Kidney International , 776-778

Groos D, Reuss AM, Rupprecht P, Stachniak T, Lewis C, Han S, ..., Karayannis T, Aguzzi A, Helmchen F (2025)
A distinct hypothalamus-habenula circuit governs risk preference
Nature Neuroscience, 361-373

Haenseler W, Eschment M, Evans B, Brasili M, Figueiro-Silva J, Roethlisberger F, ..., Müller M, Cowley SA, Bachmann-Gagescu R (2025)Differences in neuronal ciliation rate and ciliary content revealed by systematic imaging-based analysis of hiPSC-derived models across protocols. 
Frontiers Cell and Development Biology, 1516596

Han S, Helmchen F (2025)
Coordinated multi-level adaptations across neocortical areas during task learning
Nature Communications ,7719

Haugg A, Frei N, Lutz C, Di Pietro SV, Karipidis II, Brem S (2025)
The structural covariance of reading-related brain regions in adults and children with typical or poor reading skills
Developmental Cognitive Neuroscience, 101522

Kapetaniou GE, Moisa M, Ruff CC, Tobler PN, Soutschek A (2025)
Frontopolar Cortex Interacts With Dorsolateral Prefron-tal Cortex to Causally Guide Metacognition
Human Brain Mapping, e70146

Lugrin C, Hu J, Ruff CC (2025)
 A computational account of multiple motives guiding context-dependent prosocial behavior
PLOS Computational Biology, e1013032

Lugrin C, Konovalov A, Ruff CC (2025)
Manipulating attention facilitates cooperation
Commun Psychology, 39

Naert T, Yamamoto T, Han S, Röck R, Horn M, Bethge P, Vladimirov N, Voigt FF, Figuieiro-Silva J, Bachmann-Gagescu R, Vleminckx K, Helmchen F, Lienkamp SS (2025)
Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates
Nature Biotechnology, 14

Payette K, Steger C, ... Bach Cuadra M, Jakab A (2025)
Multi-Center Fetal Brain Tissue Annotation (FeTA) Challenge 2022 Results
IEEE Transactions on Medical Imaging, 1257-1272

Raduner N, Providoli C, Di Pietro SV, Schneebeli M, Karipidis II, Casimiro E, Bedi S, von Rhein M, Raschle NM, Ruff C, Brem S (2025)Growing minds, integrating senses: Neural and computational insights into age-related changes in au-dio-visual and tactile-visual learning in childrenDevelopmental Cognitive Neuroscience, 101622

Raschle NM, Borbás R, ...., Konrad K, Stadler C (2025)Losing Control: Prefrontal Emotion Regulation Is Related to Symptom Severity and Predicts Treatment-Related Symptom Change in Adolescent Girls With Conduct DisorderBiological Psychiatry: Cognitive Neuroscience and Neuroimaging, 80–93

Speckert A, Gianinazzi L, Kollmorgen S, Hagmann C, Grehten P, Kottke R, Natalucci G, Latal B, …, Jabkab A (2025)Atlas-independent brain connectome analysis at voxel-level granularity: graph convolutional networks for etiology clas-sification in newborns
NeuroImage, 121568

Speckert A, Payette K, Knirsch W, von Rhein M, …, Spina Bifida Study Group Zurich, Latal B, Jakab A (2025)Altered Connectome Topology in Newborns at Risk for Cognitive Developmental Delay: A Cross‐Etiologic Study
Human Brain Mapping, e70084

Steger C, Boegeholz A, Latal B, …, Jakab A, Reinehr M, Knirsch W (2025)Placental histology, perioperative brain devel-opment, and neurodevelopmental outcome at 1 year of age in patients undergoing neonatal cardiac surgery—is there an association? Frontiers Cardiovascular Medicine, 1556289

Wu Y, Korobeynyk VI, ..., Jessberger S (2025)
Multimodal transcriptomics reveal neurogenic aging trajectories and age-related regional inflammation in the dentate gyrus.
Nature Neuroscience, 30

Yusifov E, Schaettin M, Dumoulin A, Bachmann-Gagescu R, Stoeckli ET (2025)
The primary cilium gene CPLANE1 is required for peripheral nervous system development
Developmental Biology,106-121

Aydogan G, Ruff CC (2024)
New Insights from Gene Expression Patterns on the Neurobiological Basis of Risky Behaviour
Nature Mental Health 2, 1273–1274

Bonte M, Brem S (2024)
Unraveling individual differences in learning potential: A dynamic framework for the case of reading development
Developmental Cognitive Neuroscience 66, 101362

Cai L, Argunşah AÖ, Damilou A, Karayannis T (2024)
A nasal chemosensation-dependent critical window for somatosensory development
Science 384, 652-660

Damilou A, Cai L, Argunşah AÖ, Han S, Kanatouris G, Karatsoli M, Hanley O, Gesuita L, Kollmorgen S, Helmchen F, Karayannis T (2024)
Developmental Cajal-Retzius cell death contributes to the maturation of layer 1 cortical inhibition and somatosensory processing
Nature Communications 15, 650

Ehrler M, Speckert A, Kretschmar O, Tuura O’Gorman R, Latal B, Jakab A (2024) The cumulative impact of clinical risk on brain networks and associations with executive function impairments in adolescents with congenital heart diseaseHuman Brain Mapping, e70028

Han S, Helmchen F (2024) Behaviour-relevant top-down cross-modal predictions in mouse neocortex
Nature Neuroscience 27, 298–308

Holfeld A, Schuster D, Sesterhenn F, Stalder P, Haenseler W, ..., Picotti P (2024) Systematic identification of structure-specific protein–protein interactions
 Mol Syst Biol

Ji H, Payette K, Speckert A, ..., Latal B, SPINA BIFIDA STUDY GROUP ZURICH, Jakab A (2024) Thalamic connectivity topography in newborns with spina bifida: association with neurological functional level but not developmental outcome at 2 years Cerebral Cortex bhad438

Kolokotronis K, Suter A-A, Ivanovski I, Frey T, Bahr A, Rauch A, Steindl K (2024) DPF2-related Coffin-Siris syndrome type 7 in two generations 
European Journal of Medical Genetics 69

Nair AG*, Bollmohr N*, Schökle L, Keim J, Melero JMM, Müller M (2024)
Presynaptic quantal size enhancement counteracts post-tetanic release depression 
J Physiol.

Noble AR, Masek M, Hofmann C, Cuoco A, Rusterholz TDS, Ozkoc H, Greter NR, Phelps IG, Vladimirov N, Kollmorgen S, Stoeckli E, Bachmann-Gagescu R (2024)
Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system
Biol Open 13(11): bio060421.

Speckert A, Ji H, Payette K, Grehten P, Kottke R, Ackermann S, ... , Jakab A (2024)
OSBA: An open neonatal neuroimaging atlas and template for spina bifida aperta
Data, 9(9), 107

Toyofuku A, Ehrler M, Naef N, Schmid AS, Kretschmar O, Latal B, O'Gorman Tuura R (2024) Heart rate variability and cognitive functions in adolescents with complex congenital heart disease. Pediatr Res 97, pp. 1103–1113

Vladimirov N, Voigt FF, Naert T, Araujo GR, Cai R, Reuss AM, Zhao S, Schmid p, Hildebrand S, Schaettin M, Groos D, Mateos JM, Bethge Ph, Yamamoto T, Aerne V, Roebroeck A, Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F (2024) The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples  Nature Communications 15, 2679

Voigt FF, Reuss AM, Naert T, Hildebrand S, Schaettin M, Hotz AL, Whitehead L, Bahl A, Neuhauss SC, Roebroeck A, Stoeckli ET, Lienkamp SS, Aguzzi A, Helmchen F (2024). Reflective multi-immersion microscope objectives inspired by the Schmidt telescope. Nature Biotechnology, 42(1), pp.65-71.

Yusifov E, Schaettin M, Dumoulin A, Bachmann-Gagescu R, Stoeckli ET (2024).
The primary cilium gene CPLANE1 is required for peripheral nervous system development. Dev Biol. Epub 2024 Dec 16.

 

Asadollahi R, Delvendahl I, Muff R, ..., Bachmann-Gagescu R, ..., Müller M, Rauch A (2023)
Pathogenic SCN2A variants cause early-stage dysfunction in patient-derived neurons
Human Molecular Genetics 32(13):2192-2204

Barretto-García M, de Hollander G, Grueschow M, Polanía R, Woodford M, Ruff CC (2023) Individual risk attitudes arise from noise in neurocognitive magnitude representations Nature Human Behavior 1-17

Baum S, …, Vladimirov N, Walsworth RL, Watanabe H (2023) Mineral detection of neutrinos and dark matter. A whitepaper  Physics of the Dark Universe 41: 101245 .

Di Pietro SV, Karipidis II, Pleisch G, Brem S (2023) Neurodevelopmental trajectories of letter and speech sound processing from preschool to the end of elementary schoolDevelopmental Cognitive Neuroscience 61:101255

Di Pietro SV, Williger D, Frei N, Lutz C, Coraj S, Schneider C, Stämpfli P, Brem S (2023) Disentangling influences of dyslexia, development, and reading experience on effective brain connectivity in childrenNeuroImage 268:119869

Egger M, Luo W, Cruz-Ochoa N, Lukacsovich D, Varga C, Que L, Maloveczky G, Winterer J, Kaur R, Lukacsovich T, Földy C (2023) Commissural dentate granule cell projections and their rapid formation in the adult brain. PNAS Nexus, 2(4):pgad088.

Frey T, Ivanovski I, Bahr A, Zweier M, Laube J, Luchsinger I, Steindl K, Rauch A (2023) A very mild phenotype in six individuals of a three-generation family with the novel HRAS variant c.176C > G p.(Ala59Gly): Emergence of a new HRAS-related RASopathy distinct from Costello syndrome American Journal of Medical Genetics Part A, 191(8):2074-2082

Hu J, Konovalov A, Ruff CC  (2023)   A unified neural account of contextual and individual differences in altruism eLife 12:e80667 This study used methods developed within the AdaBD project NumRisk

Lewis CM, Hoffmann A, Helmchen F (2023)Linking brain activity across scales with simultaneous opto- and electrophysiology, Neurophotonics 11(3):033403  Review

Payette K, Hongwei L, de Dumast P, Licando E, Ji H, …, Jakab A (2023) Fetal brain tissue annotation and segmentation challenge results Medical Image Analysis 88: 102833

Royall LN, Machado D, Jessberger S, Denoth-Lippuner A (2023) Asymmetric inheritance of centrosomes maintains stem cell properties in human neural progenitor cellseLife12:e83157
This study used methods developed within the AdaBD project on organoids

Voigt F, Reuss A, Naert T, Hildebrand S, Schaettin M,  Hotz A, Whitehead L, Bahl A, Neuhauss S, Roebroeck A, Stoeckli E, Lienkamp S, Aguzzi A, Helmchen F (2023) Reflective multi-immersion microscope objectives inspired by the Schmidt telescope Nature Biotechnology

Wilhelm M*, Sych Y*, Fomins A, Alatorre Warren JL, Lewis CM, Serratosa Capdevila L, Boehringer R, Amadei EA, Grewe BF, O'Connor EC, Hall B, Helmchen F (2023) Striatum-projecting prefrontal cortex neurons support working memory maintenance Nature Communications 14: 7016. (* equal contribution)
AdaBD supported this study with important equipment

Baeriswyl T, Schaettin M, Leoni S, Dumoulin A, Stoeckli ET (2022) Endoglycan Regulates Purkinje Cell Migration by Balancing Cell-Cell Adhesion Frontiers in Neuroscience 16, 894962

Denoth-Lippuner A, Royall LN, Gonzalez-Bohorquez D, Machado D, Jessberger S (2022) Injection and electroporation of plasmid DNA into human cortical organoids. STAR Protocols 3, 101129. 

Diederich B, Müllenbroich C, Vladimirov N, Bowman R, Stirling J, Reynaud EG (2022) CAD we share? Publishing reproducible microscope hardware. Nature Methods 19, 1026–1030 

Fraga-González G, Di Pietro SV, Pleisch G, Walitza S, Brandeis- D, Karipidis Il, Brem S (2022)  Visual Occipito-Temporal N1 Sensitivity to Digits Across Elementary School. Frontiers in Human Neuroscience 16 : 887413. 

Gonzalez-Bohorquez D, Gallego Lopez IM, Jaeger BN, Pfammatter S, Bowers M, Semenkovich CF, Jessberger S (2022)  FASN-dependent de novo lipogenesis is required for brain development. PNAS 119.

Kebiri H, Canales-Rodríguez EJ, Lajous H, de Dumast P, Girard G, Alemán-Gómez Y, Koob M, Jakab A, Bach Cuadra M (2022) Through-Plane Super-Resolution With Autoencoders in Diffusion Magnetic Resonance Imaging of the Developing Human Brain. Front Neurol. 13:827816

Luo W, Cruz-Ochoa NA, Seng C, Egger M, Lukacsovich D, Lukacsovich T and Földy C (2022) Pcdh11x controls target specification of mossy fiber sprouting Frontiers in Neuroscience 16:888362. 

Muttathukunnel P, Frei P, Perry S, Dickman D, Müller M (2022) Rapid homeostatic modulation of transsynaptic nanocolumn rings. PNAS 119. 

Karipidis II, Pleisch G, Di Pietro SV, Fraga-González G, Brem S (2021) Developmental Trajectories of Letter and Speech Sound Integration During Reading Acquisition. Front. Psychol., 16 November 2021. 

Araujo GA, Baudis L, Bowden N, ..., Vladimirov N, Walkup K, Wittweg C, Zhang X (2025)
Nuclear recoil detection with color centers in bulk lithium fluoride
arXiv

Aydogan G, Kollmorgen S, Mante V, Linnér RK, Kleim B, Nave G, Ruff CC (2025)
Long-Term Imprint of Prenatal War Trauma on Brain Structure: Evidence from Genetically Informed Neuroimaging
bioRxiv

Bedi S, de Hollander G, Raduner N, Helmchen F, Brem S, Konovalov A, Ruff CC (2025)
Separable neurocomputational mechanisms underlying multisensory learning
bioRxiv

Bedi S, de Hollander G, Ruff CC (2025)
Probability weighting arises from boundary repulsions of cognitive noise
bioRxiv

de Hollander G, Grueschow M, Hennel F, Ruff CC (2025)
Rapid Changes in Risk Attitudes Originate from Bayesian Inference on Parietal Magnitude Representations
bioRxiv

Prat-Carrabin A, de Hollander G, Bedi S, Gershman SJ, Ruff CC (2025)
Distributed range adaptation in human parietal encoding of numbers
bioRxiv

Renkert MF, de Hollander G, Aydogan G, Bedi S, Lamm C, Ruff CC (2025)
Acute stress reduces risk-aversion by changing magnitude perception
bioRxiv

Reuss AM, Groos D, ..., Vladimirov N, Bethge P, Reimann R, Helmchen F, Rupprecht P, Aguzzi A (2025)
aDISCO: A clearing method to enable 3D microscopy of large archival paraffin-embedded human tissue blocks
bioRxiv

Schoenfeld G, Kollmorgen S, Lewis C, Bethge P, Reuss AM, Aguzzi A, Mante V, Helmchen F (2021) Dendritic integration of sensory and reward information facilitates learning.
bioRxiv

Underlined: AdaBD researchers
*: Equal contribution