Systems-level multi-omics dissection of syndromic and idiopathic autism reveals distinct regulatory architectures, candidate molecular signatures, and potential therapeutic targets

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1074 · Cited by 8,056 · see citing works

cytoHubba: identifying hub objects and sub-networks from complex interactome

Chin, C.-H., Chen, S., Wu, H.-H., Ho, C.-W., Ko, M., & Lin, C. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-s4-s11 · Cited by 6,635 · see citing works

Cytoscape 2.8: new features for data integration and network visualization

Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., & Ideker, T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq675 · Cited by 4,770 · see citing works

Global prevalence of autism: A systematic review update

Zeidan, J., Fombonne, E., Scorah, J., Ibrahim, A., Durkin, M. S., Saxena, S., Yusuf, A., Shih, A., & Elsabbagh, M. (2022) · Autism Research · doi:10.1002/aur.2696 · Cited by 3,117 · see citing works

Synaptic, transcriptional and chromatin genes disrupted in autism

Study, T. D., De Rubeis, S., Autism, H. M. C. F., UK10K Consortium, The Autism Sequencing Consortium, He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Ercument Cicek, A., et al. (2014) · Nature · doi:10.1038/nature13772 · Cited by 2,746 · see citing works

A travel guide to Cytoscape plugins

Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,496 · see citing works

admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties

Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty707 · Cited by 1,441 · see citing works

Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci

Sanders, S. J., He, X., Willsey, A. J., Ercan-Sencicek, A. G., Samocha, K. E., Cicek, A. E., Murtha, M. T., Bal, V. H., Bishop, S. L., Dong, S., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.09.016 · Cited by 1,430 · see citing works

MicroRNAs 103 and 107 regulate insulin sensitivity

Trajkovski, M., Hausser, J., Soutschek, J., Bhat, B., Akin, A., Zavolan, M., Heim, M. H., & Stoffel, M. (2011) · Nature · doi:10.1038/nature10112 · Cited by 1,000 · see citing works

miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions

Huang, H., Lin, Y.-C.-D., Cui, S., Tang, Y., Tang, Y., Xu, J., Bao, J., Li, Y., Wen, J., Zuo, H., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1079 · Cited by 979 · see citing works

The Cerebellum, Sensitive Periods, and Autism

Wang, S. S. ‐., Kloth, A. D., & Badura, A. (2014) · Neuron · doi:10.1016/j.neuron.2014.07.016 · Cited by 829 · see citing works

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

Bernier, R., Golzio, C., Xiong, B., Stessman, H. A., Coe, B. P., Penn, O., Witherspoon, K., Gerdts, J., Baker, C., Vulto-van Silfhout, A. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.06.017 · Cited by 798 · see citing works

A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment

Rybak‐Wolf, A., Fuchs, H. R., Smirnova, L., Brandt, C., Pohl, E. E., Nitsch, R., & Wulczyn, F. G. (2008) · Nature Cell Biology · doi:10.1038/ncb1759 · Cited by 788 · see citing works

Deep-Learning-Based Drug–Target Interaction Prediction

Wen, M., Zhang, Z., Niu, S., Sha, H., Yang, R., Yun, Y., & Lü, H. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00618 · Cited by 583 · see citing works

The Cerebellum and Neurodevelopmental Disorders

Stoodley, C. J. (2016) · The Cerebellum · doi:10.1007/s12311-015-0715-3 · Cited by 409 · see citing works

The MicroRNA-17-92 Family of MicroRNA Clusters in Development and Disease

Concepcion, C. P., Bonetti, C., & Ventura, A. (2012) · The Cancer Journal · doi:10.1097/ppo.0b013e318258b60a · Cited by 286 · see citing works

Heterogeneous dysregulation of microRNAs across the autism spectrum

Abu-Elneel, K., Liu, T., Gazzaniga, F. S., Nishimura, Y., Wall, D. P., Geschwind, D. H., Lao, K., & Kosik, K. S. (2008) · neurogenetics · doi:10.1007/s10048-008-0133-5 · Cited by 271 · see citing works

Getting to the cores of autism

Iakoucheva, L. M., Muotri, A. R., & Sebat, J. (2019) · Cell · doi:10.1016/j.cell.2019.07.037 · Cited by 260 · see citing works

Reward system dysfunction in autism spectrum disorders

Kohls, G., Schulte-Rüther, M., Nehrkorn, B., Müller, K., Fink, G. R., Kamp-Becker, I., Herpertz-Dahlmann, B., Schultz, R. T., & Konrad, K. (2013) · Social Cognitive and Affective Neuroscience · doi:10.1093/scan/nss033 · Cited by 259 · see citing works

miRmine: a database of human miRNA expression profiles

Panwar, B., Omenn, G. S., & Guan, Y. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx019 · Cited by 198 · see citing works

Applications of transformer-based language models in bioinformatics: a survey

Zhang, S., Fan, R., Liu, Y., Chen, S., Liu, Q., & Zeng, W. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad001 · Cited by 176 · see citing works

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

Phan, B. N., Bohlen, J. F., Davis, B. A., Ye, Z., Chen, H.-Y., Mayfield, B., Sripathy, S. R., Page, S. C., Campbell, M. N., Smith, H. L., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-019-0578-x · Cited by 144 · see citing works

Recent developments in the genetics of autism spectrum disorders

Murdoch, J. D., & State, M. W. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.02.003 · Cited by 132 · see citing works

Genetic causes of syndromic and non‐syndromic autism

Çağlayan, A. O. (2010) · Developmental Medicine & Child Neurology · doi:10.1111/j.1469-8749.2009.03523.x · Cited by 123 · see citing works

The ubiquitin hybrid gene UBA52 regulates ubiquitination of ribosome and sustains embryonic development

Kobayashi, M., Oshima, S., Maeyashiki, C., Nibe, Y., Otsubo, K., Matsuzawa, Y., Nemoto, Y., Nagaishi, T., Okamoto, R., Tsuchiya, K., et al. (2016) · Scientific Reports · doi:10.1038/srep36780 · Cited by 123 · see citing works

CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language

Blok, L. S., Rousseau, J., Twist, J., Ehresmann, S., Takaku, M., Venselaar, H., Rodan, L. H., Nowak, C. B., Douglas, J., Swoboda, K. J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06014-6 · Cited by 120 · see citing works

The emerging role of microRNAs in schizophrenia and autism spectrum disorders

Mellios, N., & Sur, M. (2012) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2012.00039 · Cited by 120 · see citing works

Reciprocal signaling between translational control pathways and synaptic proteins in autism spectrum disorders

Santini, E., & Klann, E. (2014) · Science Signaling · doi:10.1126/scisignal.2005832 · Cited by 118 · see citing works

miRNAs in brain development

Petri, R., Malmevik, J., Fasching, L., Åkerblom, M., & Jakobsson, J. (2013) · Experimental Cell Research · doi:10.1016/j.yexcr.2013.09.022 · Cited by 109 · see citing works

Placebo-Controlled Study of the D4/5-HT2A Antagonist Fananserin in the Treatment of Schizophrenia

Truffinet, P., Tamminga, C. A., Fabre, L. F., Meltzer, H. Y., re, M.-E. R. ⁄., & Papillon-Downey, C. (1999) · American Journal of Psychiatry · doi:10.1176/ajp.156.3.419 · Cited by 94 · see citing works

Genes and Pathways Regulated by Androgens in Human Neural Cells, Potential Candidates for the Male Excess in Autism Spectrum Disorder

Quartier, A., Chatrousse, L., Redin, C. E., Keime, C., Haumesser, N., Maglott, A., Brino, L., Gras, S. L., Benchoua, A., Mandel, J., et al. (2018) · Biological Psychiatry · doi:10.1016/j.biopsych.2018.01.002 · Cited by 86 · see citing works

Idiopathic Autism: Cellular and Molecular Phenotypes in Pluripotent Stem Cell-Derived Neurons

Liu, X., Campanac, E., Cheung, H., Ziats, M. N., Canterel-Thouennon, L., Raygada, M. J., Baxendale, V., Pang, A. L., Yang, L., Swedo, S. E., et al. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-9961-8 · Cited by 81 · see citing works

mTOR signalling pathway - A root cause for idiopathic autism?

Ganesan, H., Balasubramanian, V., Iyer, M., Venugopal, A., Subramaniam, M. D., Cho, S.-G., & Vellingiri, B. (2019) · BMB Reports · doi:10.5483/bmbrep.2019.52.7.137 · Cited by 73 · see citing works

The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders

Turner, T. N., & Eichler, E. E. (2018) · Trends in Neurosciences · doi:10.1016/j.tins.2018.11.002 · Cited by 69 · see citing works

Atypical miRNA expression in temporal cortex associated with dysregulation of immune, cell cycle, and other pathways in autism spectrum disorders

Ander, B. P., Barger, N., Stamova, B. S., Sharp, F. R., & Schumann, C. M. (2015) · Molecular Autism · doi:10.1186/s13229-015-0029-9 · Cited by 68 · see citing works

Detection of molecular signatures and pathways shared in inflammatory bowel disease and colorectal cancer: A bioinformatics and systems biology approach

Al-Mustanjid, M., Mahmud, S., Royel, M. R. I., Rahman, M. H., Islam, T., Rahman, M. R., & Moni, M. A. (2020) · Genomics · doi:10.1016/j.ygeno.2020.06.001 · Cited by 61 · see citing works

Clinically Precedented Protein Kinases: Rationale for Their Use in Neurodegenerative Disease

Benn, C., & Dawson, L. A. (2020) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2020.00242 · Cited by 57 · see citing works

New Candidates for Autism/Intellectual Disability Identified by Whole-Exome Sequencing

Bruno, L. P., Doddato, G., Valentino, F., Baldassarri, M., Tita, R., Fallerini, C., Bruttini, M., Rizzo, C. L., Mencarelli, M. A., Mari, F., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413439 · Cited by 57 · see citing works

Syndromic Autism Revisited: Review of the Literature and Lessons Learned

Ziats, C. A., Patterson, W. G., & Friez, M. J. (2020) · Pediatric Neurology · doi:10.1016/j.pediatrneurol.2020.06.011 · Cited by 55 · see citing works

Interactions between the lipidome and genetic and environmental factors in autism

Yap, C. X., Henders, A. K., Alvares, G. A., Giles, C., Huynh, K., Nguyen, A., Wallace, L. M., McLaren, T., Yang, Y., Hernandez, L. M., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02271-1 · Cited by 53 · see citing works

mTOR Suppresses Macroautophagy During Striatal Postnatal Development and Is Hyperactive in Mouse Models of Autism Spectrum Disorders

Lieberman, O. J., Cartocci, V., Pigulevskiy, I., Molinari, M., Carbonell, J., Broseta, M. B., Post, M. R., Sulzer, D., Borgkvist, A., & Santini, E. (2020) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2020.00070 · Cited by 47 · see citing works

Genetic common variants associated with cerebellar volume and their overlap with mental disorders: a study on 33,265 individuals from the UK-Biobank

Chambers, T., Escott‐Price, V., Legge, S. E., Baker, E. A., Singh, K. D., Walters, J., Caseras, X., & Anney, R. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01443-8 · Cited by 45 · see citing works

Inhibition of microRNA-103a inhibits the activation of astrocytes in hippocampus tissues and improves the pathological injury of neurons of epilepsy rats by regulating BDNF

Zheng, P., Bin, H., & Chen, W. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0821-2 · Cited by 44 · see citing works

Pathology and Astrocytes in Autism

Vakilzadeh, G., & Martínez‐Cerdeño, V. (2023) · Neuropsychiatric Disease and Treatment · doi:10.2147/ndt.s390053 · Cited by 43 · 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

Genetic Influences on the Developing Young Brain and Risk for Neuropsychiatric Disorders

Alex, A. M., Buß, C., Davis, E. P., Campos, G. D. L., Donald, K. A., Fair, D. A., Gaab, N., Gao, W., Gilmore, J. H., Girault, J. B., et al. (2023) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.01.013 · Cited by 41 · see citing works

Pharmacological mTOR inhibitors in ameliorating Alzheimer’s disease: current review and perspectives

Xie, P.-L., Zheng, M.-Y., Han, R., Chen, W., & Mao, J.-H. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2024.1366061 · Cited by 39 · see citing works

Integrative multi-omics analysis of autism spectrum disorder reveals unique microbial macromolecules interactions

Osama, A., Anwar, A. M., Ezzeldin, S., Ahmed, E., Mahgoub, S., Ibrahim, O., Ibrahim, S., Abdelhamid, I. A., Bakry, U., Diab, A. A., et al. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.01.036 · Cited by 36 · see citing works

Synaptogenesis

Petzoldt, A. G., & Sigrist, S. J. (2014) · Current Biology · doi:10.1016/j.cub.2014.10.024 · Cited by 33 · see citing works

Design protein-protein interaction network and protein-drug interaction network for common cancer diseases: A bioinformatics approach

Hasan, M. R., Paul, B. K., Ahmed, K., & Bhuyian, T. (2020) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2020.100311 · Cited by 33 · see citing works

Role for Chromatin Remodeling Factor Chd1 in Learning and Memory

Schoberleitner, I., Mutti, A., Sah, A., Wille, A., Gimeno-Valiente, F., Piatti, P., Kharitonova, M. V., Torres, L., López‐Rodas, G., Liu, J. J., et al. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00003 · Cited by 24 · see citing works

Heterogeneity of Autism Characteristics in Genetic Syndromes: Key Considerations for Assessment and Support

Jenner, L., Richards, C., Howard, R., & Moss, J. F. (2023) · Current Developmental Disorders Reports · doi:10.1007/s40474-023-00276-6 · Cited by 24 · see citing works

Post-transcriptional regulation in cranial neural crest cells expands developmental potential

Keuls, R. A., Oh, Y. S., Patel, I., & Parchem, R. J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2212578120 · Cited by 19 · see citing works

Elucidation of Abnormal Extracellular Regulated Kinase (ERK) Signaling and Associations with Syndromic and Non-syndromic Autism

Tiwari, A., Rahi, S., & Mehan, S. (2020) · Current Drug Targets · doi:10.2174/1389450121666201020155010 · Cited by 19 · see citing works

Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes

Kimura, H., Nakatochi, M., Aleksić, B., Guevara, J., Toyama, M., Hayashi, Y., Kato, H., Kushima, I., Morikawa, M., Ishizuka, K., et al. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-02033-6 · Cited by 17 · see citing works

Drug repurposing candidates to treat core symptoms in autism spectrum disorder

Koch, E. M., & Demontis, D. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.995439 · Cited by 16 · see citing works

Multi-omics study reveals differential expression and phosphorylation of autophagy-related proteins in autism spectrum disorder

Deri, E., Ojha, S. K., Kartawy, M., Khaliulin, I., & Amal, H. (2025) · Scientific Reports · doi:10.1038/s41598-025-95860-8 · Cited by 15 · see citing works

MicroRNA and MicroRNA-Target Variants Associated with Autism Spectrum Disorder and Related Disorders

Wong, A. D., Zhou, A., Cao, X., Mahaganapathy, V., Azaro, M. A., Gwin, C., Wilson, S., Buyske, S. G., Bartlett, C. W., Flax, J. F., et al. (2022) · Genes · doi:10.3390/genes13081329 · Cited by 14 · see citing works

Identification of miRNA-mRNA Network in Autism Spectrum Disorder Using a Bioinformatics Method

Noroozi, R., Dinger, M. E., Fatehi, R., Taheri, M. N., & Ghafouri‐Fard, S. (2020) · Journal of Molecular Neuroscience · doi:10.1007/s12031-020-01695-5 · Cited by 12 · see citing works

Computational network analysis of two popular skin cancers provides insights into the molecular mechanisms and reveals common therapeutic targets

Mahmud, M. S., Paul, B. K., Hasan, M. R., Islam, K. M. T., Mahmud, S., & Mahmud, S. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e41688 · Cited by 10 · see citing works

PHA-665752’s Antigrowth and Proapoptotic Effects on HSC-3 Human Oral Cancer Cells

Yadav, A. K., Wang, S., Shin, Y., & Jang, B. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052871 · Cited by 9 · see citing works

UnCOT-AD: Unpaired Cross-Omics Translation Enables Multi-Omics Integration for Alzheimer’s Disease Prediction

Abir, A. R., Dip, S. A., & Zhang, L. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf438 · Cited by 9 · see citing works

Experimental and clinical tests of FDA-approved kinase inhibitors for the treatment of neurological disorders (update 2024)

Aliashrafzadeh, H., Liu, D., Alba, S. D., Akbar, I., Lui, A., Vanleuven, J., Martin, R. M., Wang, Z., & Liu, D. (2025) · Exploration of Drug Science · doi:10.37349/eds.2025.1008116 · Cited by 5 · see citing works

Comprehensive multi‐omics mapping of immune perturbations in autism spectrum disorder

Yan, C., Feng, F., Lan, C., Luo, G., Jiang, X., Wang, H., Chen, Y., Yang, Y., Deng, L., Huang, X., et al. (2025) · Clinical and Translational Medicine · doi:10.1002/ctm2.70552 · Cited by 3 · see citing works

DrugMAP: Deep Multimodal Transformers for Drug-Target Mechanism of Action Prediction

Das, R., Jana, S., Dey, A., Corre, P. L., Marc Cuggia, A., Maulik, U., & Bandyopadhyay, S. (2025) · IEEE Transactions on Artificial Intelligence · doi:10.1109/tai.2025.3565671 · Cited by 2 · see citing works

Integrated cortical and plasma proteomic analysis of Cntnap2 knockout mice and human models of autism spectrum disorder: Potential involvement of galectin-3-binding protein

Sayson, L. V., Lee, H. J., Campomayor, N. B., Balataria, S., Kim, M., Cho, A., Yi, E. C., Lee, C. R., Kim, B.-N., Cheong, J. H., et al. (2025) · Neuroscience · doi:10.1016/j.neuroscience.2025.09.052 · Cited by 1 · see citing works

A Brain-Penetrant mTOR Kinase Inhibitor for the Treatment of Neurological Disorders

Trauner, D. H., & Arp, C. J. (2021) · Synfacts · doi:10.1055/s-0040-1719413 · Cited by 1 · see citing works

Biological hierarchy from genotype to phenotype in syndromic and non-syndromic autism spectrum disorder

Qing, Z., Yin, Z., Chen, B., Rao, Z., Yin, D., Li, D., Lu, Y., Shi, M., Li, S., Xu, Y., et al. (2026) · Frontiers in Neuroscience · doi:10.3389/fnins.2026.1964684

A Systems-Level Multi-Omics Dissection of Syndromic and Idiopathic Autism Reveals Distinct Regulatory Architectures, Molecular Biomarkers, and Therapeutic VulnerabilitiesPreprint

Rudhra, O., & Singh, S. K. (2026) · Research Square · doi:10.21203/rs.3.rs-9067110/v1

Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes

Zhang, J., Ji, G., Gao, X., & Guan, J. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05278-0 · Cited by 6 · see citing works

Integrated Transcriptome Analyses Revealed Key Target Genes in Mouse Models of Autism

Duan, W., Wang, K., Duan, Y., Chu, X., Ma, R., Hu, P., & Xiong, B. (2019) · Autism Research · doi:10.1002/aur.2240 · Cited by 27 · see citing works

Biological hierarchy from genotype to phenotype in syndromic and non-syndromic autism spectrum disorder

Qing, Z., Yin, Z., Chen, B., Rao, Z., Yin, D., Li, D., Lu, Y., Shi, M., Li, S., Xu, Y., et al. (2026) · Frontiers in Neuroscience · doi:10.3389/fnins.2026.1964684

Identification of target hub genes and construction of a novel miRNA regulatory network in autism spectrum disorder by integrated analysis

Zhu, J., Meng, H., & Li, Y. (2023) · Medicine · doi:10.1097/md.0000000000034420 · Cited by 3 · see citing works