Paternally inherited cis-regulatory structural variants are associated with autism

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

PLINK: a tool set for whole-genome association and population-based linkage analyses.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437

Analyzing real-time PCR data by the comparative CT method

Schmittgen, T. D., & Livak, K. J. (2008) · Nature Protocols · doi:10.1038/nprot.2008.73 · Cited by 26,190

A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,508

Analysis of protein-coding genetic variation in 60,706 humans

Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587

Finding the missing heritability of complex diseases

Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368

Versatile and open software for comparing large genomes

Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254

Insights into the molecular basis of wooden breast based on comparative analysis of fast- and slow-growth broilersPreprint

Hubert, S. M., Williams, T. J., & Athrey, G. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/356683 · Cited by 15

Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission

Breuss, M. W., Yang, X., Stanley, V., McEvoy‐Venneri, J., Xu, X., Morales, A. J., & Gleeson, J. G. (2022) · eLife · doi:10.7554/elife.78459 · Cited by 13

Strategies for dissecting the complexity of neurodevelopmental disorders

Sun, J., Noss, S., Banerjee, D., Das, M., & Girirajan, S. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.10.009 · Cited by 10

Whole-genome sequencing identifies novel genes for autism in Chinese trios

Chang, S., Liu, J. J., Zhao, Y., Pang, T., Zheng, X., Song, Z., Zhang, A., Gao, X., Luo, L., Guo, Y., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-023-2564-8 · Cited by 13

Using coding and non-coding rare variants to target candidate genes in patients with severe tinnitus

Gallego‐Martinez, A., Escalera‐Balsera, A., Trpchevska, N., Robles-Bolívar, P., Román-Naranjo, P., Frejo, L., Perez‐Carpena, P., Bulla, J., Gallus, S., Canlon, B., et al. (2022) · npj Genomic Medicine · doi:10.1038/s41525-022-00341-w · Cited by 12

Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity

Sun, Y. H., Cui, H., Song, C. W., Shen, J. T., Zhuo, X., Wang, R. H., Yu, X., Ndamba, R., Mu, Q., Gu, H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36354-x · Cited by 12

Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells

Ross, P. J., Mok, R. S. F., Smith, B. S., Rodrigues, D. C., Mufteev, M., Scherer, S. W., & Ellis, J. (2020) · Molecular Autism · doi:10.1186/s13229-020-00333-6 · Cited by 12

Genome wide analysis of rare copy number variations in alcohol abuse or dependence

Rodríguez-López, J., Flórez, G., Blanco, V., Pereiro, C., Fernández, J. M., Fariñas, E., Estévez, V., Gómez-Trigo, J., Gurriarán, X., Calvo, R. C., et al. (2018) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2018.06.001 · Cited by 11

nanotatoR: a tool for enhanced annotation of genomic structural variants

Bhattacharya, S., Barseghyan, H., Délot, E. C., & Vilain, E. J. N. (2021) · BMC Genomics · doi:10.1186/s12864-020-07182-w · Cited by 9

Integrated Functional Analysis Implicates Syndromic and Rare Copy Number Variation Genes as Prominent Molecular Players in Pathogenesis of Autism Spectrum Disorders

Ashitha, S. N. M., & Ramachandra, N. B. (2020) · Neuroscience · doi:10.1016/j.neuroscience.2020.04.051 · Cited by 10

Inter-chromosomal insertions at Xq27.1 associated with retinal dystrophy induce dysregulation of LINC00632 and CDR1as/ciRS-7

Gardner, J. C., Jovanovic, K., Ottaviani, D., Melo, U. S., Jackson, J., Guarascio, R., Ziaka, K., Hau, K.-L., Lane, A., Taylor, R. L., et al. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.01.007 · Cited by 10

Transcription Pause and Escape in Neurodevelopmental Disorders

Eigenhuis, K. N., Somsen, H. B., & van den Berg, D. L. C. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.846272 · Cited by 8

A linkage and exome study of multiplex families with bipolar disorder implicates rare coding variants of ANK3 and additional rare alleles at 10q11-q21

Claudio Toma, A., Shaw, A. D., Heath, A., Pierce, K. D., Mitchell, P. B., Schofield, P. R., & Fullerton, J. M. (2021) · Journal of Psychiatry and Neuroscience · doi:10.1503/jpn.200083 · Cited by 10

Genetics of Pathologic Myopia

Zhang, Q. (2021) · Springer eBooks · doi:10.1007/978-3-030-74334-5_4 · Cited by 10

Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments

Alibutud, R., Hansali, S., Cao, X., Zhou, A., Mahaganapathy, V., Azaro, M. A., Gwin, C., Wilson, S., Buyske, S. G., Bartlett, C. W., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241713248 · Cited by 9

GABA Signaling Pathway-associated Gene PLCL1 Rare Variants May be Associated with Autism Spectrum Disorders

Zheng, F., Liu, G., Dang, T., Chen, Q., An, Y., Wu, M., Kong, X., Qiu, Z., & Wu, B.-L. (2021) · Neuroscience Bulletin · doi:10.1007/s12264-021-00707-7 · Cited by 9

Autism genetics perturb prenatal neurodevelopment through a hierarchy of broadly-expressed and brain-specific genesPreprint

Gazestani, V., Chiang, A. W. T., Courchesne, E., & Lewis, N. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.23.112623 · Cited by 7

Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era

Zaghi, M., Banfi, F., Bellini, E. N., & Sessa, A. (2021) · Biomolecules · doi:10.3390/biom11111713 · Cited by 8

Evidence of transgenerational effects on autism spectrum disorder using multigenerational space-time cluster detection

Steed, R. R., Bakian, A. V., Smith, K. R., Wan, N., Brewer, S., Medina, R., & VanDerslice, J. A. (2022) · International Journal of Health Geographics · doi:10.1186/s12942-022-00313-4 · Cited by 9

Complex de novo structural variants are an underestimated cause of rare disorders

Jung, H., Yang, T.-P., Walker, S., Danecek, P., Garcia-Salinas, O. I., Neville, M. D. C., Christopher, J., Cortés‐Ciriano, I., Firth, H. V., Scally, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64722-2 · Cited by 8

Evidence for parent-of-origin effects in autism spectrum disorder: a narrative review

Ryan, N., & Heron, E. A. (2023) · Journal of Applied Genetics · doi:10.1007/s13353-022-00742-8 · Cited by 8

Genetic Variant Analyses Identify Novel Candidate Autism Risk Genes from a Highly Consanguineous Cohort of 104 Families from Oman

Gupta, V. R., Ben‐Mahmoud, A., Idris, A. B., Hottenga, J., Habbab, W., Alsayegh, A., Kim, H., Al‐Mamari, W., & Stanton, L. W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252413700 · Cited by 10

The Autism Palette: Combinations of Impairments Explain the Heterogeneity in ASD

Fóthi, Á., Lörincz, A., & Soorya, L. V. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.503462 · Cited by 9

Elucidation of molecular pathogenesis and drug development for psychiatric disorders from rare disease-susceptibility variants

Kimura, H., Mori, D., Aleksić, B., & Ozaki, N. (2020) · Neuroscience Research · doi:10.1016/j.neures.2020.11.008 · Cited by 7

Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression

Ashouri, S., Wong, J. H., Nakagawa, H., Shimada, M., Tokunaga, K., & Fujimoto, A. (2021) · Human Genetics · doi:10.1007/s00439-021-02291-2 · Cited by 5

Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients

McQuerry, J. A., Mclaird, M., Hartin, S. N., Means, J. C., Johnston, J. J., Pastinen, T., & Younger, S. T. (2022) · Scientific Reports · doi:10.1038/s41598-022-11589-8 · Cited by 6

NeuroCNVscore: a tissue-specific framework to prioritise the pathogenicity of CNVs in neurodevelopmental disorders

Liu, X., Xu, W., Leng, F., Zhang, P., Guo, R., Zhang, Y., Hao, C., Ni, X., & Li, W. (2023) · BMJ Paediatrics Open · doi:10.1136/bmjpo-2023-001966 · Cited by 5

The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genomePreprint

Lee, Y.-L., Bouwman, A. C., Harland, C., Bosse, M., Moreira, G. C. M., Veerkamp, R. F., Mullaart, E., Cambisano, N., Groenen, M. A. M., Karim, L., et al. (2023) · Genome Research · doi:10.1101/gr.277884.123 · Cited by 7

Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations

Nair, S., Li, X., Anderson, T., & Platt, R. N. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf127 · Cited by 6

Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes

Lu, Y., Wang, X., Yu, H., Li, J., Jiang, Z., Chen, B., Lu, Y., Wang, W., Han, C., Ouyang, Y., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00152 · Cited by 5

Autism Spectrum Disorders: Analysis of Mobile Elements at 7q11.23 Williams–Beuren Region by Comparative Genomics

Cupaioli, F. A., Fallerini, C., Mencarelli, M. A., Perticaroli, V., Filippini, V., Mari, F., Renieri, A., & Mezzelani, A. (2021) · Genes · doi:10.3390/genes12101605 · Cited by 5

Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment

Okay, K., Varış, P. Ü., Miral, S., Pavlopoulou, A., Oktay, Y., & Karakülah, G. (2022) · Journal of Autism and Developmental Disorders · doi:10.1007/s10803-022-05636-6 · Cited by 5

Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly

Fu, C. S., Ngo, J., Zhang, S., Lu, L., Miron, A., Schafer, S. T., Gage, F. H., Jin, F., Schumacher, F. R., & Wynshaw-Boris, A. J. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac300 · Cited by 5

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem RepeatsPreprint

Jakubosky, D. A., Smith, E. N., D’Antonio, M., Bonder, M. J., Greenwald, W. W. Y., D’Antonio‐Chronowska, A., Matsui, H., Stegle, O., Montgomery, S. B., DeBoever, C., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/713198 · Cited by 5

SVFX: a machine-learning framework to quantify the pathogenicity of structural variantsPreprint

Kumar, S., Harmanci, A. O., Vytheeswaran, J., & Gerstein, M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/739474 · Cited by 5

Expectations and blind spots for structural variation detection from short-read alignment and long-read assemblyPreprint

Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.03.168831 · Cited by 5

Genetic modifiers and ascertainment drive variable expressivity of complex disordersPreprint

Jensen, M., Smolen, C., Tyryshkina, A., Pizzo, L., Banerjee, D., Oetjens, M. T., Shimelis, H., Taylor, C. M., Pounraja, V. K., Song, H., et al. (2024) · medRxiv · doi:10.1101/2024.08.27.24312158 · Cited by 5

Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism

Mortazavi, M., Guevara, J., Diaz, J., Tran, S. S., Jam, H. Z., Reeves, C., Batalov, S., Jepsen, K., Bainbridge, M., Besterman, A. D., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101186 · Cited by 11

Autismus-Spektrum-Störung im Erwachsenenalter

Thaler, H., & Falter‐Wagner, C. M. (2023) · Fortschritte der Neurologie · Psychiatrie · doi:10.1055/a-1898-5347 · Cited by 4

Potential clinical applications of advanced genomic analysis in cerebral palsy

Lewis, S. A., Ruttenberg, A., Iyiyol, T., Kong, N., Jin, S. C., & Kruer, M. C. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105229 · Cited by 5

Systematic assessment of structural variant annotation tools for genomic interpretation

Liu, X., Gu, L., Hao, C., Xu, W., Leng, F., Zhang, P., & Li, W. (2024) · Life Science Alliance · doi:10.26508/lsa.202402949 · Cited by 4

Generation and characterization of a knockout mouse of an enhancer of EBF3

Hurtado, E. C., Wotton, J. M., Gulka, A. O. D., Burke, C., Ng, J. K., Bah, I., Manuel, J. G., Heins, H. B., Murray, S. A., Gorkin, D. U., et al. (2025) · Biology Open · doi:10.1242/bio.062070 · Cited by 6

Why are individuals with autism spectrum disorder at risk group for unhealthy weight?

Trambacz-Oleszak, S. (2019) · Anthropological Review · doi:10.2478/anre-2019-0023 · Cited by 4

Burden re-analysis of neurodevelopmental disorder cohorts for prioritization of candidate genes

Smal, N., Majdoub, F., Janssens, K., Reyniers, E., Meuwissen, M. E. C., Ceulemans, B., Northrup, H., Hill, J. B., Liu, L., Errichiello, E., et al. (2024) · European Journal of Human Genetics · doi:10.1038/s41431-024-01661-4 · Cited by 4

SV 2 : Accurate Structural Variation Genotyping and De Novo Mutation Detection from Whole GenomesPreprint

Antaki, D., Brandler, W. M., & Sebat, J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/113498 · Cited by 4

Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis -Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic VariationPreprint

Cherry, T. J., Yang, M. G., Harmin, D. A., Tao, P., Timms, A. E., Bauwens, M., Allikmets, R. L., Jones, E., Chen, R., Baere, E. D., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/412361 · Cited by 4

Identification of essential regulatory elements in the human genomePreprint

Wells, A. C., Heckerman, D. E., Torkamani, A., Li, Y., Ren, B., Telenti, A., & di Iulio, J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/444562 · Cited by 5

Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum DisorderPreprint

Borges-Monroy, R., Chu, C., Dias, C., Choi, J., Lee, S., Gao, Y., Shin, T., Park, P. J., Walsh, C. A., & Lee, E. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.29.428895 · Cited by 4

Observational methods for human studies of transgenerational effects

Steed, R. R., Wan, N., Bakian, A. V., Medina, R., Brewer, S., Smith, K. R., & VanDerslice, J. A. (2024) · Epigenetics · doi:10.1080/15592294.2024.2366065 · Cited by 3

Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort

Zhang, Y., Chien, W. T., Chan, J. Y., Cheung, T., He, Z., Yip, K.-H., Chan, D. F.-Y., Chong, J. S. C., Waye, M. M. Y., Chair, S. Y., et al. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.05.043 · Cited by 3

The post-diagnostics world: charting a path for pediatric genomic medicine in the twenty-first century

Bonkowsky, J. L., Pastinen, T., & White, P. (2022) · Pediatric Research · doi:10.1038/s41390-022-02144-2 · Cited by 3

Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation

Liang, D., Aygün, N., Matoba, N., Ideraabdullah, F., Love, M. I., & Stein, J. L. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac207 · Cited by 2

Combining multi-omics approaches to prioritize the variant-regulated functional long non-coding RNAs in autism spectrum disorder

Wang, H., Wu, X., Chen, Y., Hou, F., Zhu, K., Jiang, Q., Xiao, P., Zhang, Q., Xiang, Z., Fan, Y., et al. (2022) · Asian Journal of Psychiatry · doi:10.1016/j.ajp.2022.103357 · Cited by 4

Emerging role of epigenetics in human neurodevelopmental disorders

Mastrototaro, G., Sessa, A., & Zaghi, M. (2023) · Elsevier eBooks · doi:10.1016/b978-0-443-18661-5.00022-1 · Cited by 3

Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humansPreprint

Jakubosky, D. A., D’Antonio, M., Bonder, M. J., Smail, C., Donovan, M. K. R., Greenwald, W. W. Y., D’Antonio‐Chronowska, A., Matsui, H., Stegle, O., Smith, E. N., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/714477 · Cited by 3

Contribution of de novo retroelements to birth defects and childhood cancersPreprint

Chu, C., Ljungström, V., Tran, A. V., Jin, H., & Park, P. J. (2024) · medRxiv · doi:10.1101/2024.04.15.24305733 · Cited by 3

Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India

Shah, J., Mondal, D., Jain, D. K., Mhatre, P., Patel, K., Iyer, A., Pandya, M., Menghani, B., Dave, G., Sheth, J. J., et al. (2025) · BMC Medical Genomics · doi:10.1186/s12920-025-02204-6 · Cited by 3

Regulation of RNA transcript elongation in metazoans and its relevance to disease

Mimoso, C. A., Fianu, I., & Adelman, K. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-026-01003-w · Cited by 2

Revisiting the genetic architecture of autism spectrum disorders in the genomic era: Insights from East Asian studies

Qiu, Z., & Du, A. (2024) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2024.102936 · Cited by 2

Shared rare genetic variants in multiplex autism families suggest a social memory gene under selection

Lee, K. S., Lee, T., Kim, M., Ignatova, E., Ban, H., Sung, M. K., Kim, Y., Kim, Y., Han, J., & Choi, J. K. (2025) · Scientific Reports · doi:10.1038/s41598-024-83839-w · Cited by 2

Prenatal, perinatal, and environmental risk factors contribute to the high prevalence of autism spectrum disorder in northeastern Bangladesh

Mourosi, J. T., Anwar, S., Islam, M. T., Vanakker, O. M., & Hosen, M. J. (2025) · International Journal of Developmental Disabilities · doi:10.1080/20473869.2025.2452858 · Cited by 3

Prioritizing de novo autism risk variants with calibrated gene- and variant-scoring models

Jiang, Y., Urresti, J., Pagel, K. A., Pramod, A. B., Iakoucheva, L. M., & Predrag Radivojac, A. (2021) · Human Genetics · doi:10.1007/s00439-021-02356-2 · Cited by 2

Molecular diagnosis of autism spectrum disorder through whole exome sequencing

de Almeida, T. F. (2019) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2019.tde-04022019-092804 · Cited by 2

Multi-hit autism genomic architecture evidenced from consanguineous families with involvement of FEZF2 and mutations in high-risk genesPreprint

Bensaid, M., Loe-Mie, Y., Lepagnol-Bestel, A.-M., Han, W., Santpere, G., Klarić, T., Plançon, C., Roudies, R., Benhima, I., Tarik, N., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/759480 · Cited by 3

Genome-wide analysis of Structural Variants in Parkinson’s Disease using Short-Read Sequencing dataPreprint

Billingsley, K. J., Ding, J., Jerez, P. Á., Illarionova, A., Grenn, F. P., Makarious, M. B., Moore, A. K., Vitale, D., Reed, X., Hernandez, D. G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.22.504867 · Cited by 2

Finding Genetic Regulators, Forecasting Function

Szewczak, L. (2018) · Cell · doi:10.1016/j.cell.2018.06.043 · Cited by 1

LEO1 haploinsufficiency is associated with developmental delays and autism spectrum disorder

Ung, E. C., & Borja, N. A. (2025) · Journal of Human Genetics · doi:10.1038/s10038-025-01410-5 · Cited by 1

Genetic analysis of neurodegenerative diseases

Grassano, M., Schindler, A. B., Traynor, B. J., & Scholz, S. W. (2026) · Journal of Clinical Investigation · doi:10.1172/jci199840 · Cited by 1

Molecular testing in autism spectrum disorder

Fernandez, B. A., Marshall, C. R., Vorstman, J. A. S., & Scherer, S. W. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-822824-1.00016-x · Cited by 2

Categorical misalignment: Making autism(s) in big data biobanking

Metcalf, K. (2024) · Social Studies of Science · doi:10.1177/03063127241288223 · Cited by 1

Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 familiesPreprint

Whelan, C. W., Handsaker, R. E., Genovese, G., Kashin, S., Lek, M., Hughes, J. D., McElwee, J. J., Lenardo, M. J., MacArthur, D. G., & McCarroll, S. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.03.235358 · Cited by 1

Large-scale sequencing study of de novo regulatory Tandem Repeats (TRs) identifies new ASD (Autism Spectrum Disorders) candidate genes integrating gene expression mapping, brain scRNA-seq and organoid models.Preprint

Fontenla, M. C. R., Carballo-Pacoret, P., Dominguez-Alonso, S., Gonzalez-Peñas, J., Parellada, M., Arango, C., & Carracedo, Á. (2026) · Research Square · doi:10.21203/rs.3.rs-8374597/v1 · Cited by 1

Likelihood-Based Computational Approaches for Association Studies in Statistical Genetics.

Ting, B. W. (2020) · NCSU Libraries Repository (North Carolina State University Libraries)

Copy numbers of 45S and 5S ribosomal DNA arrays lack meaningful correlation in humansPreprint

Hall, A. N., Turner, T. N., & Queitsch, C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.06.189753

Failure to approach, autism

Pfaff, D. W. (2020) · Elsevier eBooks · doi:10.1016/b978-0-323-85861-8.00002-5

Investigation of Genetic and Clinical Heterogeneity in Subtypes of Autism Spectrum Disorder

Chan, A. J. S. (2020) · TSpace (University of Toronto)

AIM in Genomic Basis of Medicine: Applications

Kamada, M., & Okuno, Y. (2021) · Springer eBooks · doi:10.1007/978-3-030-58080-3_264-1

Structural variation in genomes and its role in disease

Vlaar, J. M. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/902

Inference of cell-type specific imprinted regulatory elements and genes during human neuronal differentiationPreprint

Liang, D., Aygün, N., Matoba, N., Ideraabdullah, F. Y., Love, M. I., & Stein, J. (2021) · bioRxiv · doi:10.1101/2021.10.04.463060

AIM in Genomic Basis of Medicine: Applications

Kamada, M., & Okuno, Y. (2022) · Springer eBooks · doi:10.1007/978-3-030-64573-1_264

Structural variants in the bovine genome

Lee, Y.-L. (2022) · doi:10.18174/566496

Faculty Opinions recommendation of Paternally inherited cis-regulatory structural variants are associated with autism.

Stankiewicz, P. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733081240.793545433

Autism spectrum disorder: understanding the impact of SNPs on biological pathways in the fetal and adult cortexPreprint

Golovina, E., Fadason, T., Lints, T., Walker, C. G., Vickers, M. H., & O'Sullivan, J. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.03.433667

Faculty Opinions recommendation of Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development.

Mefford, H. C. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736437709.793571951

Faculty Opinions recommendation of Inherited and de novo genetic risk for autism impacts shared networks.

Alkuraya, F. S. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736388363.793563929

Faculty Opinions recommendation of Inherited and de novo genetic risk for autism impacts shared networks.

Kooy, R. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736388363.793564139

Genetic etiologies of autism: Unpacking pathogenic mechanisms and characteristics

Hudac, C. M., Friedman, N. R., & Turner, T. N. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-816393-1.00001-4

Evidence of Transgenerational Effects on Autism Spectrum Disorder Using Multigenerational Space-Time Cluster DetectionPreprint

Steed, R. R., Bakian, A. V., Smith, K. R., Wan, N., Brewer, S., & VanDerslice, J. A. (2022) · Research Square · doi:10.21203/rs.3.rs-1852813/v1

Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephalyPreprint

Wynshaw-Boris, A. J., Fu, C., Ngo, J., Zhang, S., Lu, L., Miron, A., Schafer, S. T., Gage, F. H., Jin, F., & Schumacher, F. (2022) · Research Square · doi:10.21203/rs.3.rs-2009452/v1

Genetics and Epigenetics of ASD

Mojarad, B. A., Qaiser, F., & Yuen, R. K. C. (2023) · Springer eBooks · doi:10.1007/978-3-031-20792-1_18 · Cited by 2

Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models

Pan, C., Rahn, R., Heller, D., & Reinert, K. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad071

Deciphering the role of germline complex de novo structural variations in rare disordersPreprint

Jung, H., Yang, T.-P., Walker, S., Danecek, P., Salinas, I. G., Neville, M. D. C., Firth, H. V., Scally, A., Hurles, M. E., Campbell, P. J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.03.587925

Abordagens alternativas para caracterização da arquitetura genética do transtorno do espectro autista

Costa, C. I. S. (2024) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2024.tde-22082024-180122

Insights into the role of cis-regulatory elements of 5-HT2A gene in gene expression and regulation: an in silico approach

Bhogegowda, K. K. H., Niketh, S., Thyloor, R., & Kolgi, R. R. (2024) · Research in Biotechnology · doi:10.25081/rib.2024.v15.9081

Deciphering the Non-Coding Genome in Autism Spectrum Disorders (ASD): A Study of De Novo and Rare Inherited Variants through Targeted Sequencing in Regulatory RegionsPreprint

Dominguez-Alonso, S., Trotta, J. P., González‐Peñas, J., Fernández‐Prieto, M., Parellada, M., Arango, C., Carracedo, Á., & Rodriguez‐Fontenla, C. (2024) · medRxiv · doi:10.1101/2024.10.14.24315434

Long read whole genome sequencing-based discovery of complex structural variants and their role in aetiology of non-syndromic autism spectrum disorder in IndiaPreprint

Shah, J., Mondal, D., Jain, D. K., Mhatre, P., Patel, K., Iyer, A., Pandya, M., Menghani, B., Dave, G., Sheth, J. J., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-5950423/v1

Analysis of epigenetic mutation of AGTR2 gene responsible for Autism across three generation: An exploratory studyPreprint

Misra, P., Bhardwaj, L., Kumar, V., & Chauhan, K. (2025) · Research Square · doi:10.21203/rs.3.rs-7040442/v1

SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies

Peng, W., Zhang, L., Tang, B., Liang, J., Liu, Z., Ye, L., Yuan, Y., Wang, Y., Tan, R., Lin, N., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03730-3

Coding and noncoding de novo variation converge on developmental trajectories of cortical layer 5–6 neurons in autism spectrum disorderPreprint

Elkon, R., England, E. M., & Shemesh, S. (2025) · Research Square · doi:10.21203/rs.3.rs-7841641/v1

Additional file 1 of Evidence of transgenerational effects on autism spectrum disorder using multigenerational space-time cluster detection

Steed, R. R., Bakian, A. V., Smith, K. R., Wan, N., Brewer, S., Medina, R., & VanDerslice, J. (2022) · Figshare · doi:10.6084/m9.figshare.21268919

Inherited variation contributes to autism

Zahn, L. M. (2018) · Science · doi:10.1126/science.360.6386.280-d

Disparity between Maternal and Paternal Contributions to Inherited Risk for Autism

Antaki, D. (2018) · eScholarship (California Digital Library)

Dysregulation of heterochromatin caused by genomic structural variants may be central to autism spectrum disorder

Garvin, M. R., & Kainer, D. (2025) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2025.1553575 · Cited by 5

An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

Williams, S. M., An, J., Edson, J., Watts, M. E., Murigneux, V., Whitehouse, A., Jackson, C. J., Bellgrove, M. A., Cristino, A. S., & Claudianos, C. (2018) · Molecular Psychiatry · doi:10.1038/s41380-018-0049-x · Cited by 77

Excess of rare, inherited truncating mutations in autism

Krumm, N., Turner, T. N., Baker, C., Vives, L., Mohajeri, K., Witherspoon, K., Raja, A., Coe, B. P., Stessman, H. A., He, Z.-X., et al. (2015) · Nature Genetics · doi:10.1038/ng.3303 · Cited by 587