SFARI Gene: an evolving database for the autism research community

AutDB: a gene reference resource for autism research

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Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

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A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

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Consensus Paper: Pathological Role of the Cerebellum in Autism

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Rodent models in neuroscience research: is it a rat race?

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FlyBase: a guided tour of highlighted features

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Common DNA methylation alterations in multiple brain regions in autism

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Emerging connections between cerebellar development, behaviour and complex brain disorders

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Clustering autism: using neuroanatomical differences in 26 mouse models to gain insight into the heterogeneity

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Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders

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Precise temporal regulation of alternative splicing during neural development

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Fundamental Elements in Autism: From Neurogenesis and Neurite Growth to Synaptic Plasticity

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Genomic architecture of autism from comprehensive whole-genome sequence annotation

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Genome-wide detection of tandem DNA repeats that are expanded in autism

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Genomics, convergent neuroscience and progress in understanding autism spectrum disorder

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A Quantitative Framework to Evaluate Modeling of Cortical Development by Neural Stem Cells

Stein, J. L., de la Torre-Ubieta, L., Tian, Y., Parikshak, N. N., Hernández, I. A., Marchetto, M. C., Baker, D. K., Lu, D., Hinman, C. R., Lowe, J. K., et al. (2014) · Neuron · doi:10.1016/j.neuron.2014.05.035 · Cited by 201 · see citing works

Distinct subnetworks of the thalamic reticular nucleus

Li, Y., López-Huerta, V. G., Adiconis, X., Levandowski, K. M., Choi, S., Simmons, S., Arias-García, M. A., Guo, B., Yao, A. Y., Blosser, T. R., et al. (2020) · Nature · doi:10.1038/s41586-020-2504-5 · Cited by 208 · see citing works

New roles for the cerebellum in health and disease

Reeber, S. L., Otis, T. S., & Sillitoe, R. (2013) · Frontiers in Systems Neuroscience · doi:10.3389/fnsys.2013.00083 · Cited by 193 · see citing works

AutismKB: an evidence-based knowledgebase of autism genetics

Xu, L.-M., Li, J.-R., Huang, Y., Zhao, M., Tang, X., & Wei, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1145 · Cited by 179 · see citing works

Genetic Effects on Cerebellar Structure Across Mouse Models of Autism Using a Magnetic Resonance Imaging Atlas

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Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development

Nowakowski, T. J., Rani, N., Golkaram, M., Zhou, H. R., Alvarado, B., Huch, K., West, J. A., Leyrat, A., Pollen, A. A., Kriegstein, A. R., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0265-3 · Cited by 166 · see citing works

Molecular and network-level mechanisms explaining individual differences in autism spectrum disorder

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Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

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Pathway Network Analyses for Autism Reveal Multisystem Involvement, Major Overlaps with Other Diseases and Convergence upon MAPK and Calcium Signaling

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A myelin-related transcriptomic profile is shared by Pitt–Hopkins syndrome models and human autism spectrum disorder

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Cerebellar associative sensory learning defects in five mouse autism models

Kloth, A. D., Badura, A., Li, A., Cherskov, A., Connolly, S. G., Giovannucci, A., Bangash, M. A., Grasselli, G., Peñagarikano, O., Piochon, C., et al. (2015) · eLife · doi:10.7554/elife.06085 · Cited by 146 · see citing works

TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons

Caubit, X., Gubellini, P., Andrieux, J., Roubertoux, P. L., Metwaly, M., Jacq, B., Fatmi, A., Had‐Aissouni, L., Kwan, K. Y., Salin, P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3681 · Cited by 140 · see citing works

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders

Codina‐Solà, M., Rodríguez‐Santiago, B., Homs, A., Santoyo‐López, J., Rigau, M., Laín, G. A., Campo, M. D., Gener, B., Gabau, E., Botella, M. P., et al. (2015) · Molecular Autism · doi:10.1186/s13229-015-0017-0 · Cited by 132 · see citing works

Cohesin-dependence of neuronal gene expression relates to chromatin loop length

Calderon, L., Weiss, F. D., Beagan, J. A., Oliveira, M. S., Georgieva, R., Wang, Y.-F., Carroll, T. S., Dharmalingam, G., Gong, W., Tossell, K., et al. (2022) · eLife · doi:10.7554/elife.76539 · Cited by 132 · see citing works

Salivary miRNA profiles identify children with autism spectrum disorder, correlate with adaptive behavior, and implicate ASD candidate genes involved in neurodevelopment

Hicks, S. D., Ignacio, C., Gentile, K. L., & Middleton, F. A. (2016) · BMC Pediatrics · doi:10.1186/s12887-016-0586-x · Cited by 128 · see citing works

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

Chen, J., Swofford, R., Johnson, J., Cummings, B. B., Rogel, N., Lindblad-Toh, K., Haerty, W., Palma, F. D., & Regev, A. (2019) · Genome Research · doi:10.1101/gr.237636.118 · Cited by 128 · see citing works

Genome‐wide Association Study of Autism Spectrum Disorder in the East Asian Populations

Liu, X., Shimada, T., Otowa, T., Wu, Y., Kawamura, Y., Tochigi, M., Iwata, Y., Umekage, T., Toyota, T., Maekawa, M., et al. (2015) · Autism Research · doi:10.1002/aur.1536 · Cited by 115 · see citing works

Spontaneous and Induced Animal Models for Cancer Research

Onaciu, A., Munteanu, R. A., Munteanu, V. C., Gulei, D., Ráduly, L., Feder, R., Pîrlog, R., Atanasov, A. G., Korban, S. S., Irimie, A., et al. (2020) · Diagnostics · doi:10.3390/diagnostics10090660 · Cited by 112 · see citing works

Decomposition of phenotypic heterogeneity in autism reveals underlying genetic programs

Litman, A., Sauerwald, N., Snyder, L. G., Foss‐Feig, J. H., Park, C. Y., Hao, Y., Dinstein, I., Theesfeld, C. L., & Troyanskaya, O. G. (2025) · Nature Genetics · doi:10.1038/s41588-025-02224-z · Cited by 116 · see citing works

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

Takeuchi, A., Iida, K., Tsubota, T., Hosokawa, M., Denawa, M., Brown, J. B., Ninomiya, K., Ito, M., Kimurâ, H., Abe, T., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.141 · Cited by 102 · see citing works

Domestic dog lineages reveal genetic drivers of behavioral diversification

Dutrow, E. V., Serpell, J. A., & Ostrander, E. A. (2022) · Cell · doi:10.1016/j.cell.2022.11.003 · Cited by 94 · see citing works

Large-scale methylation domains mark a functional subset of neuronally expressed genesPreprint

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Proteomic Analysis of Post-synaptic Density Fractions from Shank3 Mutant Mice Reveals Brain Region Specific Changes Relevant to Autism Spectrum Disorder

Reim, D., Distler, U., Halbedl, S., Verpelli, C., Sala, C., Bockmann, J., Tenzer, S., Boeckers, T. M., & Schmeißer, M. J. (2017) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2017.00026 · Cited by 81 · see citing works

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

Mordaunt, C. E., Jianu, J. M., Laufer, B. I., Zhu, Y., Hwang, H., Dunaway, K. W., Bakulski, K. M., Feinberg, J. I., Volk, H. E., Lyall, K., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00785-8 · Cited by 86 · see citing works

ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism

Berto, S., Usui, N., Konopka, G., & Fogel, B. L. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw110 · Cited by 80 · see citing works

DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders

Christian, D. L., Wu, D. Y., Martin, J. R., Moore, J. R., Liu, Y. R., Clemens, A. W., Nettles, S. A., Kirkland, N. M., Papouin, T., Hill, C. A., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108416 · Cited by 78 · see citing works

Copy number variants in autism spectrum disorders

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Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF

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Effect Sizes of Deletions and Duplications on Autism Risk Across the Genome

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Single-base resolution of mouse offspring brain methylome reveals epigenome modifications caused by gestational folic acid

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The role of Pax6 in brain development and its impact on pathogenesis of autism spectrum disorder

Kikkawa, T., Casingal, C. R., Chun, S. H., Shinohara, H. M., Hiraoka, K., & Osumi, N. (2018) · Brain Research · doi:10.1016/j.brainres.2018.02.041 · Cited by 66 · see citing works

Rho GTPase Regulators and Effectors in Autism Spectrum Disorders: Animal Models and Insights for Therapeutics

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Targeted massively parallel sequencing of autism spectrum disorder-associated genes in a case control cohort reveals rare loss-of-function risk variants

Griswold, A. J., Dueker, N., Booven, D. V., Rantus, J. A., Jaworski, J. M., Slifer, S. H., Schmidt, M. A., Hulme, W. F., Konidari, I., Whitehead, P. L., et al. (2015) · Molecular Autism · doi:10.1186/s13229-015-0034-z · Cited by 62 · see citing works

KDM5A mutations identified in autism spectrum disorder using forward genetics

Hayek, L. E., Tuncay, İ. O., Nijem, N., Russell, J. L., Ludwig, S. M., Kaur, K. J., Li, X., Anderton, P. D., Tang, M., Gerard, A., et al. (2020) · eLife · doi:10.7554/elife.56883 · Cited by 59 · see citing works

What we can learn from a genetic rodent model about autism

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Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression

Casanova, M., Sharp, J. L., Chakraborty, H., Sumi, N. S., & Casanova, M. F. (2016) · Molecular Autism · doi:10.1186/s13229-016-0082-z · Cited by 60 · see citing works

Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality

Zito, A., Lualdi, M., Granata, P., Cocciadiferro, D., Novelli, A., Alberio, T., Casalone, R., & Fasano, M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.577623 · Cited by 60 · see citing works

MACROD2 gene associated with autistic-like traits in a general population sample

Jones, R., Cadby, G., Blangero, J., Abraham, L. J., Whitehouse, A., & Moses, E. K. (2014) · Psychiatric Genetics · doi:10.1097/ypg.0000000000000052 · Cited by 60 · see citing works

A Revolutionizing Approach to Autism Spectrum Disorder Using the Microbiome

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Thirty Years’ History since the Discovery of Pax6: From Central Nervous System Development to Neurodevelopmental Disorders

Ochi, S., Manabe, S., Kikkawa, T., & Osumi, N. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23116115 · Cited by 58 · see citing works

Copy‐number variation in the pathogenesis of autism spectrum disorder

Shishido, E., Aleksić, B., & Ozaki, N. (2013) · Psychiatry and Clinical Neurosciences · doi:10.1111/pcn.12128 · Cited by 58 · see citing works

AutDB: a platform to decode the genetic architecture of autism

Pereanu, W., Larsen, E. C., Das, I., Estévez, M. A., Sarkar, A. A., Spring-Pearson, S., Kollu, R., Basu, S. N., & Banerjee‐Basu, S. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1093 · Cited by 54 · see citing works

NEXMIF/KIDLIA Knock-out Mouse Demonstrates Autism-Like Behaviors, Memory Deficits, and Impairments in Synapse Formation and Function

Gilbert, J. P., O’Connor, M. G., Templet, S., Moghaddam, M., Ioschpe, A. D. V., Sinclair, A., Zhu, L., Xu, W., & Man, H. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.0222-19.2019 · Cited by 54 · see citing works

Transcriptomic analysis of genetically defined autism candidate genes reveals common mechanisms of action

Lanz, T. A., Guilmette, E., Gosink, M. M., Fischer, J. E., Fitzgerald, L. W., Stephenson, D. T., & Pletcher, M. T. (2013) · Molecular Autism · doi:10.1186/2040-2392-4-45 · Cited by 52 · see citing works

Genotator: A disease-agnostic tool for genetic annotation of disease

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Genetic mechanisms of regression in autism spectrum disorder

Tammimies, K. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.04.022 · Cited by 53 · see citing works

Patient-derived iPSC-cerebral organoid modeling of the 17q11.2 microdeletion syndrome establishes CRLF3 as a critical regulator of neurogenesis

Wegscheid, M. L., Anastasaki, C., Hartigan, K. A., Cobb, O. M., Papke, J. B., Traber, J. N., Morris, S. M., & Gutmann, D. H. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109315 · Cited by 50 · see citing works

RNA‐binding proteins involved in RNA localization and their implications in neuronal diseases

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Genetics studies indicate that neural induction and early neuronal maturation are disturbed in autism

Casanova, M., & Casanova, M. F. (2014) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2014.00397 · Cited by 46 · see citing works

Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin

Weiss, F. D., Calderón, L., Wang, Y.-F., Georgieva, R., Guo, Y., Cvetešić, N., Kaur, M., Dharmalingam, G., Krantz, I. D., Lenhard, B., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23141-9 · Cited by 46 · see citing works

Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders

Shin, D. S., Kim, C. N., Ross, J. M., Hennick, K. M., Wu, S., Paranjape, N., Leonard, R., Wang, J. C., Keefe, M. G., Pavlovic, B. J., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.01.010 · Cited by 46 · see citing works

CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation

Sood, S., Weber, C. M., Hodges, H. C., Krokhotin, A., Shalizi, A., & Crabtree, G. R. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921963117 · Cited by 42 · see citing works

SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data

Arpi, M. N. T., & Simpson, T. I. (2022) · Scientific Reports · doi:10.1038/s41598-022-14077-1 · Cited by 41 · see citing works

Spatiotemporal dynamics of the postnatal developing primate brain transcriptome

Bakken, T. E., Miller, J. A., Luo, R., Bernard, A., Bennett, J. L., Lee, C., Bertagnolli, D., Parikshak, N., Smith, K. A., Sunkin, S. M., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv166 · Cited by 40 · see citing works

Genetic aetiologies for childhood speech disorder: novel pathways co-expressed during brain development

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Mapping cis-regulatory elements in human neurons links psychiatric disease heritability and activity-regulated transcriptional programs

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SnapShot: Genetics of Autism

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Behavioral and neuroanatomical approaches in models of neurodevelopmental disorders: opportunities for translation

Silverman, J. L., & Ellegood, J. (2018) · Current Opinion in Neurology · doi:10.1097/wco.0000000000000537 · Cited by 35 · see citing works

Abnormal Levels of Metal Micronutrients and Autism Spectrum Disorder: A Perspective Review

Behl, S., Mehta, S., & Pandey, M. K. (2020) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2020.586209 · Cited by 37 · see citing works

Animal model integration to AutDB, a genetic database for autism

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Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex

Berto, S., & Nowick, K. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy149 · Cited by 36 · see citing works

Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation

Bakulski, K. M., Dou, J., Feinberg, J. I., Aung, M. T., Ladd‐Acosta, C., Volk, H. E., Newschaffer, C. J., Croen, L., Hertz‐Picciotto, I., Levy, S. E., et al. (2021) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2021.775390 · Cited by 35 · see citing works

Autism-specific PTEN p.Ile135Leu variant and an autism genetic background combine to dysregulate cortical neurogenesis

Fu, S., Bury, L. A. D., Eum, J., & Wynshaw-Boris, A. J. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.03.015 · Cited by 36 · see citing works

Functional and clinical studies reveal pathophysiological complexity of CLCN4-related neurodevelopmental condition

Palmer, E. E., Pusch, M., Picollo, A., Forwood, C., Nguyen, M. H., Suckow, V., Gibbons, J., Hoff, A., Sigfrid, L., Mégarbané, A., et al. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01852-9 · Cited by 33 · see citing works

Specification of human brain regions with orthogonal gradients of WNT and SHH in organoids reveals patterning variations across cell lines

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Resources available for autism research in the big data era: a systematic review

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