Chromatin accessibility dynamics in a model of human forebrain development

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259 · see citing works

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Biological insights from 108 schizophrenia-associated genetic loci

Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works

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 · cited 1× · see citing works

An atlas of genetic correlations across human diseases and traits

ReproGen Consortium, Bulik-Sullivan, B., Psychiatric Genomics Consortium, Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3, Finucane, H. K., Anttila, V., Gusev, A., Day, F. R., Loh, P.-R., Duncan, L., et al. (2015) · Nature Genetics · doi:10.1038/ng.3406 · Cited by 4,255 · see citing works

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399 · see citing works

Snakemake—a scalable bioinformatics workflow engine

Köster, J., & Rahmann, S. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts480 · Cited by 2,780 · see citing works

Partitioning heritability by functional annotation using genome-wide association summary statistics

ReproGen Consortium, Finucane, H. K., Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.-R., Anttila, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3404 · Cited by 2,604 · see citing works

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4396 · Cited by 2,496 · see citing works

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

Zhang, Y., Sloan, S. A., Clarke, L. E., Caneda, C., Plaza, C. A., Blumenthal, P. D., Vogel, H., Steinberg, G. K., Edwards, M. S. B., Li, G., et al. (2016) · Neuron · doi:10.1016/j.neuron.2015.11.013 · Cited by 2,295 · see citing works

Spatio-temporal transcriptome of the human brain

Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., et al. (2011) · Nature · doi:10.1038/nature10523 · Cited by 2,084 · see citing works

Chromatin accessibility and the regulatory epigenome

Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793 · see citing works

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

Paşca, A. M., Sloan, S. A., Clarke, L. E., Tian, Y., Makinson, C. D., Huber, N., Kim, C. H., Park, J.-Y., O'Rourke, N. A., Nguyen, K. D., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3415 · Cited by 1,609 · see citing works

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

GERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552 · see citing works

Uniquely Hominid Features of Adult Human Astrocytes

Oberheim, N. A., Takano, T., Han, X., He, W., Lin, J. H. C., Wang, F., Xu, Q., Wyatt, J. D., Pilcher, W., Ojemann, J. G., et al. (2009) · The Journal of Neuroscience · doi:10.1523/jneurosci.4707-08.2009 · Cited by 1,488 · see citing works

Assembly of functionally integrated human forebrain spheroids

Birey, F., Andersen, J., Makinson, C. D., Islam, S., Wei, W., Huber, N., Fan, H. C., Metzler, K. R. C., Panagiotakos, G., Thom, N., et al. (2017) · Nature · doi:10.1038/nature22330 · Cited by 1,365 · see citing works

Distribution and intensity of constraint in mammalian genomic sequence

Cooper, G. M., Stone, E. A., Asimenos, G., Green, E. D., Batzoglou, S., & Sidow, A. (2005) · Genome Research · doi:10.1101/gr.3577405 · Cited by 1,359 · see citing works

Transcriptional landscape of the prenatal human brain

Miller, J. A., Ding, S.-L., Sunkin, S. M., Smith, K. A., Ng, L., Szafer, A., Ebbert, A., Riley, Z. L., Royall, J. J., Aiona, K., et al. (2014) · Nature · doi:10.1038/nature13185 · Cited by 1,325 · see citing works

The chromatin accessibility landscape of primary human cancers

Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230 · see citing works

DNA-Binding Specificities of Human Transcription Factors

Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P. M. A., Morgunova, E. Y., Enge, M., Taipale, M., Wei, G., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.009 · Cited by 1,228 · see citing works

Interneuron cell types are fit to function

Kepecs, A., & Fishell, G. (2014) · Nature · doi:10.1038/nature12983 · Cited by 1,110 · see citing works

VISTA Enhancer Browser—a database of tissue-specific human enhancers

Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080 · see citing works

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism

Parikshak, N. N., Luo, R., Zhang, A., Won, H., Lowe, J. K., Chandran, V., Horvath, S., & Geschwind, D. H. (2013) · Cell · doi:10.1016/j.cell.2013.10.031 · Cited by 1,039 · see citing works

The origin and specification of cortical interneurons

Wonders, C. P., & Anderson, S. A. (2006) · Nature Reviews Neuroscience · doi:10.1038/nrn1954 · Cited by 980 · see citing works

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

Nowakowski, T. J., Bhaduri, A., Pollen, A. A., Alvarado, B., Mostajo-Radji, M. A., Di Lullo, E., Haeussler, M., Sandoval-Espinosa, C., Liu, S. J., Velmeshev, D., et al. (2017) · Science · doi:10.1126/science.aap8809 · Cited by 964 · see citing works

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

Mathelier, A., Fornes, O., Arenillas, D. J., Chen, C.-Y., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1176 · Cited by 937 · see citing works

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism

Willsey, A. J., Sanders, S. J., Li, M., Dong, S., Tebbenkamp, A. T., Muhle, R. A., Reilly, S. K., Lin, L., Fertuzinhos, S., Miller, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.020 · Cited by 934 · see citing works

Single-cell genomics identifies cell type–specific molecular changes in autism

Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D. H., & Kriegstein, A. R. (2019) · Science · doi:10.1126/science.aav8130 · Cited by 927 · see citing works

Molecular Identity of Human Outer Radial Glia during Cortical Development

Pollen, A. A., Nowakowski, T. J., Chen, J., Retallack, H., Sandoval-Espinosa, C., Nicholas, C. R., Shuga, J., Liu, S. J., Oldham, M. C., Diaz, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.004 · Cited by 908 · see citing works

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

Silbereis, J. C., Pochareddy, S., Zhu, Y., Li, M., & Sestan, N. (2016) · Neuron · doi:10.1016/j.neuron.2015.12.008 · Cited by 818 · see citing works

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science · doi:10.1126/science.aat7615 · Cited by 810 · see citing works

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789 · see citing works

Organoid single-cell genomic atlas uncovers human-specific features of brain development

Kanton, S., Boyle, M. J., He, Z., Santel, M., Weigert, A., Sanchís-Calleja, F., Guijarro, P., Sidow, L., Fleck, J. S., Han, D., et al. (2019) · Nature · doi:10.1038/s41586-019-1654-9 · Cited by 761 · see citing works

Biased gene conversion and the evolution of mammalian genomic landscapes

Duret, L., & Galtier, N. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150001 · Cited by 737 · see citing works

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2018) · Cell · doi:10.1016/j.cell.2018.03.074 · Cited by 670 · see citing works

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

Sloan, S. A., Darmanis, S., Huber, N., Khan, T. A., Birey, F., Caneda, C., Reimer, R., Quake, S. R., Barres, B. A., & Paşca, S. P. (2017) · Neuron · doi:10.1016/j.neuron.2017.07.035 · Cited by 593 · see citing works

Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

Paşca, S. P., Portmann, T., Voineagu, I., Yazawa, M., Shcheglovitov, A., Paşca, A. M., Cord, B., Palmer, T. D., Chikahisa, S., Nishino, S., et al. (2011) · Nature Medicine · doi:10.1038/nm.2576 · Cited by 585 · see citing works

Chromosome conformation elucidates regulatory relationships in developing human brain

Won, H., de la Torre-Ubieta, L., Stein, J. L., Parikshak, N. N., Huang, J., Opland, C. K., Gandal, M. J., Sutton, G. J., Hormozdiari, F., Lu, D., et al. (2016) · Nature · doi:10.1038/nature19847 · Cited by 584 · see citing works

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

Adey, A., Morrison, H. G., Asan, Xu, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-12-r119 · Cited by 566 · see citing works

DNA-dependent formation of transcription factor pairs alters their binding specificity

Jolma, A., Yin, Y., Nitta, K. R., Dave, K., Popov, A. N., Taipale, M., Enge, M., Kivioja, T., Morgunova, E. Y., & Taipale, J. (2015) · Nature · doi:10.1038/nature15518 · Cited by 555 · see citing works

Forces shaping the fastest evolving regions in the human genome

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020168 · Cited by 511 · see citing works

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

Jaffe, A. E., Gao, Y., Deep-Soboslay, A., Tao, R., Hyde, T. M., Weinberger, D. R., & Kleinman, J. E. (2016) · Nature Neuroscience · doi:10.1038/nn.4181 · Cited by 511 · see citing works

The rise of three-dimensional human brain cultures

Pașca, S. P. (2018) · Nature · doi:10.1038/nature25032 · Cited by 509 · see citing works

Reliability of human cortical organoid generation

Yoon, S.-J., Elahi, L. S., Pașca, A. M., Marton, R. M., Gordon, A., Revah, O., Miura, Y., Walczak, E. M., Holdgate, G. M., Fan, H. C., et al. (2019) · Nature Methods · doi:10.1038/s41592-018-0255-0 · Cited by 507 · see citing works

Generation and assembly of human brain region-specific three-dimensional cultures

Sloan, S. A., Andersen, J., Pașca, A. M., Birey, F., & Pașca, S. P. (2018) · Nature Protocols · doi:10.1038/s41596-018-0032-7 · Cited by 490 · see citing works

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

Zeng, H., Shen, E. H., Hohmann, J. G., Oh, S. W., Bernard, A., Royall, J. J., Glattfelder, K. J., Sunkin, S. M., Morris, J. A., Guillozet-Bongaarts, A. L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.052 · Cited by 426 · see citing works

Predicting the molecular complexity of sequencing libraries

Daley, T., & Smith, A. D. (2013) · Nature Methods · doi:10.1038/nmeth.2375 · Cited by 378 · see citing works

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

de la Torre-Ubieta, L., Stein, J. L., Won, H., Opland, C. K., Liang, D., Lu, D., & Geschwind, D. H. (2018) · Cell · doi:10.1016/j.cell.2017.12.014 · Cited by 353 · see citing works

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

Kvon, E. Z., Kamneva, O. K., Melo, U. S., Barozzi, I., Osterwalder, M., Mannion, B. J., Tissières, V., Pickle, C. S., Plajzer-Frick, I., Lee, E. A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.028 · Cited by 339 · see citing works

Biased gene conversion: implications for genome and sex evolution

Marais, G. A. B. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(03)00116-1 · Cited by 332 · see citing works

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Preissl, S., Fang, R., Huang, H., Zhao, Y., Raviram, R., Gorkin, D. U., Zhang, Y., Sos, B. C., Afzal, V., Dickel, D. E., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0079-3 · Cited by 332 · see citing works

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

Stergachis, A. B., Neph, S. J., Reynolds, A. P., Humbert, R., Miller, B. G., Paige, S. L., Vernot, B., Cheng, J. B., Thurman, R. E., Sandstrom, R. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.020 · Cited by 331 · see citing works

Optogenetic control of Drosophila using a red-shifted channelrhodopsin reveals experience-dependent influences on courtship

Inagaki, H. K., Jung, Y., Hoopfer, E. D., Wong, A. M., Mishra, N., Lin, J. Y., Tsien, R. Y., & Anderson, D. J. (2014) · Nature Methods · doi:10.1038/nmeth.2765 · Cited by 321 · see citing works

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.048 · Cited by 319 · see citing works

Multiple Autism-Linked Genes Mediate Synapse Elimination via Proteasomal Degradation of a Synaptic Scaffold PSD-95

Tsai, N.-P., Wilkerson, J. R., Guo, W., Maksimova, M. A., DeMartino, G. N., Cowan, C. W., & Huber, K. M. (2012) · Cell · doi:10.1016/j.cell.2012.11.040 · Cited by 316 · see citing works

Lhx2 Selector Activity Specifies Cortical Identity and Suppresses Hippocampal Organizer Fate

Mangale, V. S., Hirokawa, K. E., Satyaki, P. R. V., Gokulchandran, N., Chikbire, S., Subramanian, L., Shetty, A. S., Martynoga, B., Paul, J., Mai, M. V., et al. (2008) · Science · doi:10.1126/science.1151695 · Cited by 316 · see citing works

DNA-dependent formation of transcription factor pairs alters their binding specificity

Jolma, A., Yin, Y., Nitta, K. R., Dave, K., Popov, A. N., Taipale, M., Enge, M., Kivioja, T., Morgunova, E. Y., & Taipale, J. (2016) · Nature · doi:10.1038/nature18912 · Cited by 314 · see citing works

Id proteins in cell growth and tumorigenesis

Sikder, H. A., Devlin, M. K., Dunlap, S., Ryu, B., & Alani, R. M. (2003) · Cancer Cell · doi:10.1016/s1535-6108(03)00141-7 · Cited by 309 · see citing works

Transcriptome and epigenome landscape of human cortical development modeled in organoids

Amiri, A., Coppola, G., Scuderi, S., Wu, F., Roychowdhury, T., Liu, F., Pochareddy, S., Shin, Y., Safi, A., Song, L., et al. (2018) · Science · doi:10.1126/science.aat6720 · Cited by 302 · see citing works

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

Johnson, M. B., Wang, P. P., Atabay, K. D., Murphy, E. A., Doan, R. N., Hecht, J. L., & Walsh, C. A. (2015) · Nature Neuroscience · doi:10.1038/nn.3980 · Cited by 288 · see citing works

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

Zhou, J., Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0420-0 · Cited by 287 · see citing works

Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo

Li, H., Radford, J. C., Ragusa, M. J., Shea, K. L., McKercher, S. R., Zaremba, J. D., Soussou, W., Nie, Z., Kang, Y., Nakanishi, N., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802876105 · Cited by 254 · see citing works

Many human accelerated regions are developmental enhancers

Capra, J. A., Erwin, G. D., McKinsey, G., Rubenstein, J. L. R., & Pollard, K. S. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0025 · Cited by 235 · see citing works

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

Maurano, M. T., Haugen, E., Sandstrom, R. S., Vierstra, J. D., Shafer, A., Kaul, R., & Stamatoyannopoulos, J. A. (2015) · Nature Genetics · doi:10.1038/ng.3432 · Cited by 211 · see citing works

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

Romero, I. G., Pavlovic, B. J., Hernando-Herraez, I., Zhou, X., Ward, M. C., Banovich, N. E., Kagan, C. L., Burnett, J. E., Huang, C. H., Mitrano, A., et al. (2015) · eLife · doi:10.7554/elife.07103 · Cited by 194 · see citing works

Molecular Control of Neurogenesis: A View from the Mammalian Cerebral CortexPreprint

Martynoga, B., Drechsel, D., & Guillemot, F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a008359 · Cited by 187 · see citing works

Annual Research Review: Development of the cerebral cortex: implications for neurodevelopmental disorders

Rubenstein, J. L. R. (2010) · Journal of Child Psychology and Psychiatry · doi:10.1111/j.1469-7610.2010.02307.x · Cited by 170 · see citing works

Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci

Forrest, M. P., Zhang, H., Moy, W., McGowan, H., Leites, C., Dionisio, L. E., Xu, Z., Shi, J., Sanders, A. R., Greenleaf, W. J., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.07.008 · Cited by 118 · see citing works

Malformations of Cerebral Cortex Development: Molecules and Mechanisms

Juric‐Sekhar, G., & Hevner, R. F. (2019) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012927 · Cited by 116 · see citing works

The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders

Chen, C., Meng, Q., Xia, Y., Ding, C., Wang, L., Dai, R., Cheng, L., Gunaratne, P. H., Gibbs, R. A., Min, S., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aat8178 · Cited by 107 · see citing works

Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

Levchenko, А., Kanapin, A. A., Samsonova, A. A., & Gainetdinov, R. R. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx240 · Cited by 103 · see citing works

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome

Kostka, D., Hubisz, M. J., Siepel, A., & Pollard, K. S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr279 · Cited by 102 · see citing works

Id4 is required for the correct timing of neural differentiation

Bedford, L., Walker, R., Kondo, T., van Crüchten, I., King, E. R., & Sablitzky, F. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.02.001 · Cited by 91 · see citing works

TBR1 regulates autism risk genes in the developing neocortex

Notwell, J. H., Heavner, W. E., Darbandi, S. F., Katzman, S., McKenna, W. L., Ortiz-Londono, C. F., Tastad, D., Eckler, M. J., Rubenstein, J. L. R., McConnell, S. K., et al. (2016) · Genome Research · doi:10.1101/gr.203612.115 · Cited by 74 · see citing works

c-fos proto-oncogene expression in astrocytes associated with differentiation or proliferation but not depolarization

Hisanaga, K., Sagar, S. M., Hicks, K. J., Swanson, R. A., & Sharp, F. R. (1990) · Molecular Brain Research · doi:10.1016/0169-328x(90)90011-2 · Cited by 69 · see citing works

Functional and Molecular Characterization of the Role of CTCF in Human Embryonic Stem Cell Biology

Balakrishnan, S. K., Witcher, M., Berggren, W. T., & Emerson, B. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042424 · Cited by 26 · see citing works

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.039 · Cited by 478 · see citing works

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Corces, M. R., Shcherbina, A., Kundu, S., Gloudemans, M. J., Frésard, L., Granja, J. M., Louie, B. H., Eulalio, T., Shams, S., Bagdatli, S. T., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-00721-x · Cited by 358 · see citing works

Long-term maturation of human cortical organoids matches key early postnatal transitions

Gordon, A., Yoon, S., Tran, S. S., Makinson, C. D., Park, J. Y., Andersen, J., Valencia, A. M., Horvath, S., Xiao, X. G., Huguenard, J. R., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00802-y · Cited by 352 · see citing works

Inferring and perturbing cell fate regulomes in human brain organoids

Fleck, J. S., Jansen, S. M. J., Wollny, D., Zenk, F., Seimiya, M., Jain, A., Okamoto, R., Santel, M., He, Z., Camp, J. G., et al. (2023) · Nature · doi:10.1038/s41586-022-05279-8 · Cited by 315 · see citing works

Human cerebral organoids — a new tool for clinical neurology research

Eichmüller, O. L., & Knoblich, J. A. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00723-9 · Cited by 260 · see citing works

Single-cell epigenomics reveals mechanisms of human cortical development

Ziffra, R. S., Kim, C. N., Ross, J. M., Wilfert, A. B., Turner, T. N., Haeussler, M., Casella, A. M., Przytycki, P. F., Keough, K. C., Shin, D. S., et al. (2021) · Nature · doi:10.1038/s41586-021-03209-8 · Cited by 267 · see citing works

Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

Uzquiano, A., Kedaigle, A. J., Pigoni, M., Paulsen, B. D. S., Adiconis, X., Kim, K., Faits, T., Nagaraja, S., Antón-Bolaños, N., Gerhardinger, C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.010 · Cited by 250 · see citing works

Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes

Armand, E. J., Li, J., Xie, F., Luo, C., & Mukamel, E. A. (2021) · Neuron · doi:10.1016/j.neuron.2020.12.010 · Cited by 241 · see citing works

Human brain organogenesis: Toward a cellular understanding of development and disease

Kelley, K. W., & Pașca, S. P. (2021) · Cell · doi:10.1016/j.cell.2021.10.003 · Cited by 233 · see citing works

Genomics, convergent neuroscience and progress in understanding autism spectrum disorder

Willsey, H. R., Willsey, A. J., Wang, B., & State, M. W. (2022) · Nature reviews. Neuroscience · doi:10.1038/s41583-022-00576-7 · Cited by 229 · see citing works

Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution

Herring, C. A., Simmons, R. K., Freytag, S., Poppe, D., Moffet, J. J. D., Pflueger, J., Buckberry, S., Vargas-Landín, D. B., Clément, O., Goñi, E., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.039 · Cited by 226 · see citing works

A transcription factor atlas of directed differentiation

Joung, J., Ma, S., Tay, T., Geiger-Schuller, K., Kirchgatterer, P. C., Verdine, V. K., Guo, B., Arias-García, M. A., Allen, W. E., Singh, A., et al. (2023) · Cell · doi:10.1016/j.cell.2022.11.026 · Cited by 223 · see citing works

Chromatin accessibility profiling methods

Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206 · see citing works

ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids

Bowles, K. R., Silva, M. C., Whitney, K., Bertucci, T., Berlind, J. E., Lai, J. D., Garza, J. C., Boles, N. C., Mahali, S., Strang, K. H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.003 · Cited by 175 · see citing works

Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application

Chen, Y., Liang, R., Li, Y., Jiang, L., Ma, D., Luo, Q., & Song, G. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-02030-9 · Cited by 174 · see citing works

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

Liu, C. X., Li, R., Li, Y., Lin, X., Zhao, K., Liu, Q., Wang, S., Yang, X., Shi, X., Ma, Y., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.04.009 · Cited by 171 · see citing works

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Spanier, K. I., Bravo González-Blas, C., Quan, X. J., Papasokrati, D., Hulselmans, G., Makhzami, S., et al. (2021) · doi:10.1101/2021.08.11.454937 · Cited by 170 · see citing works

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Gomez, A. E., Aughey, G., Spanier, K. I., De Rop, F. V., González-Blas, C. B., Dionne, M., et al. (2022) · Nature · doi:10.1038/s41586-021-04262-z · Cited by 170 · see citing works

Single-cell genomics and regulatory networks for 388 human brains

Emani, P. S., Liu, J. J., Clarke, D., Jensen, M., Warrell, J., Gupta, C., Meng, R., Lee, C.-Y., Xu, S., Dursun, C., et al. (2024) · Science · doi:10.1126/science.adi5199 · Cited by 168 · see citing works

Brain organoids: an ensemble of bioassays to investigate human neurodevelopment and disease

Sidhaye, J., & Knoblich, J. A. (2020) · Cell Death and Differentiation · doi:10.1038/s41418-020-0566-4 · Cited by 167 · see citing works

Modelling human brain development and disease with organoids

Birtele, M., Lancaster, M. A., & Quadrato, G. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00804-1 · Cited by 161 · see citing works

Developments and Opportunities for 3D Bioprinted Organoids

Ren, Y., Yang, X., Ma, Z., Sun, X., Zhang, Y.-X., Li, W., Yang, H., Qiang, L., Yang, Z.-Z., Liu, Y.-H., et al. (2021) · International Journal of Bioprinting · doi:10.18063/ijb.v7i3.364 · Cited by 104 · see citing works

Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells

Tian, F., Cheng, Y., Zhou, S., Wang, Q., Monavarfeshani, A., Gao, K., Jiang, W., Kawaguchi, R., Wang, Q., Tang, M., et al. (2022) · Neuron · doi:10.1016/j.neuron.2022.06.003 · Cited by 125 · see citing works

Advancing models of neural development with biomaterials

Roth, J. G., Huang, M. S., Li, T. L., Feig, V. R., Jiang, Y., Cui, B., Greely, H. T., Bao, Z., Pașca, S. P., & Heilshorn, S. C. (2021) · Nature reviews. Neuroscience · doi:10.1038/s41583-021-00496-y · Cited by 120 · see citing works

Multi-omic profiling of the developing human cerebral cortex at the single-cell level

Zhu, K., Bendl, J. M., Rahman, S., Vicari, J. M., Coleman, C., Clarence, T., Latouche, O., Tsankova, N. M., Li, A., Brennand, K., et al. (2023) · Science Advances · doi:10.1126/sciadv.adg3754 · Cited by 116 · see citing works

The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective

Mossink, B., Negwer, M., Schubert, D., & Nadif Kasri, N. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-020-03714-5 · Cited by 114 · see citing works

SEdb 2.0: a comprehensive super-enhancer database of human and mouse

Wang, Y., Song, C., Zhao, J., Zhang, Y., Zhao, X., Feng, C., Zhang, G., Zhu, J., Wang, F., Qian, F., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac968 · Cited by 111 · see citing works

3D Brain Organoids: Studying Brain Development and Disease Outside the Embryo

Velasco, S., Paulsen, B. D. S., & Arlotta, P. (2020) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-070918-050154 · Cited by 107 · see citing works

Human fetal brain self-organizes into long-term expanding organoids

Hendriks, D. F. G., Pagliaro, A., Andreatta, F., Ma, Z., van Giessen, J., Massalini, S., López‐Iglesias, C., van Son, G. J. F., DeMartino, J., Damen, M. J. A., et al. (2024) · Cell · doi:10.1016/j.cell.2023.12.012 · Cited by 106 · see citing works

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

Hu, B., Won, H., Mah, W., Park, R. B., Kassim, B., Spiess, K., Kozlenkov, A., Crowley, C. A., Pochareddy, S., The PsychENCODE Consortium, et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24243-0 · Cited by 103 · see citing works

Upgrading the Physiological Relevance of Human Brain Organoids

Dosso, A. D., Urenda, J.-P., Nguyen, T., & Quadrato, G. (2020) · Neuron · doi:10.1016/j.neuron.2020.08.029 · Cited by 87 · see citing works

Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity

Shi, X., Li, Y., Yuan, Q., Tang, S., Guo, S., Zhang, Y., He, J., Zhang, X., Han, M., Liu, Z., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29857-6 · Cited by 101 · see citing works

Non-synaptic function of the autism spectrum disorder-associated gene SYNGAP1 in cortical neurogenesis

Birtele, M., Dosso, A. D., Xu, T., Nguyen, T. N., Wilkinson, B., Hosseini, N., Nguyen, S. C., Urenda, J., Knight, G. T., Rojas, C., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01477-3 · Cited by 99 · see citing works

Shared heritability of human face and brain shape

Naqvi, S., Sleyp, Y., Hoskens, H., Indencleef, K., Spence, J. P., Bruffaerts, R., Radwan, A., Eller, R. J., Richmond, S., Shriver, M. D., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00827-w · Cited by 96 · see citing works

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

Ma, S., & Zhang, Y. (2020) · Molecular Biomedicine · doi:10.1186/s43556-020-00009-w · Cited by 88 · see citing works

Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., Wang, H., Bie, X., Jiang, J., Feng, X., et al. (2023) · Genome biology · doi:10.1186/s13059-022-02844-2 · Cited by 87 · see citing works

Self-organized tissue mechanics underlie embryonic regulation

Caldarelli, P., Chamolly, A., Villedieu, A., Alegria-Prévot, O., Phan, C., Gros, J., & Corson, F. (2024) · Nature · doi:10.1038/s41586-024-07934-8 · Cited by 87 · see citing works

Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells

Sarropoulos, I., Sepp, M., Frömel, R., Leiss, K., Trost, N., Leushkin, E. V., Okonechnikov, K., Joshi, P. K., Giere, P., Kutscher, L. M., et al. (2021) · Science · doi:10.1126/science.abg4696 · Cited by 77 · see citing works

Advances in development and application of human organoids

Shankaran, A., Prasad, K., Chaudhari, S., Brand, A. M., & Satyamoorthy, K. (2021) · 3 Biotech · doi:10.1007/s13205-021-02815-7 · Cited by 74 · see citing works

Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability

Bae, T., Fasching, L., Wang, Y., Shin, J. H., Šuvakov, M., Jang, Y., Norton, S., Dias, C., Mariani, J., Jourdon, A., et al. (2022) · Science · doi:10.1126/science.abm6222 · Cited by 74 · see citing works

Recent advances in gene therapy for neurodevelopmental disorders with epilepsy

Turner, T. J., Zourray, C., Schorge, S., & Lignani, G. (2021) · Journal of Neurochemistry · doi:10.1111/jnc.15168 · Cited by 71 · see citing works

Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases

Gupta, C., Chandrashekar, P. B., Jin, T., He, C., Khullar, S., Chang, Q., & Wang, D. (2022) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-022-09438-w · Cited by 64 · see citing works

Neurodevelopmental disorders—high-resolution rethinking of disease modeling

Khodosevich, K., & Sellgren, C. M. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01876-1 · Cited by 64 · see citing works

A beginner’s guide on the use of brain organoids for neuroscientists: a systematic review

Mulder, L., Depla, J. A., Sridhar, A., Wolthers, K. C., Pajkrt, D., & de Sá, R. V. (2023) · Stem Cell Research & Therapy · doi:10.1186/s13287-023-03302-x · Cited by 62 · see citing works

Single-cell transcriptomic landscape of the developing human spinal cord

Andersen, J., Thom, N., Shadrach, J. L., Chen, X., Onesto, M. M., Amin, N. D., Yoon, S.-J., Li, L., Greenleaf, W. J., Müller, F., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01311-w · Cited by 61 · see citing works

Impact of alcohol exposure on neural development and network formation in human cortical organoids

Adams, J. W., Negraes, P. D., Truong, J., Tran, T. H., Szeto, R. A., Guerra, B. S., Herai, R. H., Teodorof‐Diedrich, C., Spector, S. A., Campo, M. D., et al. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01862-7 · Cited by 58 · see citing works

AUTS2 Syndrome: Molecular Mechanisms and Model Systems

Biel, A., Castanza, A. S., Rutherford, R., Fair, S. R., Chifamba, L., Wester, J. C., Hester, M. E., & Hevner, R. F. (2022) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2022.858582 · Cited by 56 · see citing works

Identification of visual cortex cell types and species differences using single-cell RNA sequencing

Wei, J.-R., Hao, Z.-Z., Xu, C., Huang, M., Tang, L., Xu, N., Liu, R., Shen, Y., Teichmann, S. A., Miao, Z., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34590-1 · Cited by 55 · see citing works

Brain organoid protocols and limitations

Zhao, H. H., & Haddad, G. G. (2024) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2024.1351734 · Cited by 51 · see citing works

Vascularized human brain organoid on-chip.

Tan, S.-Y., Feng, X.-H., Cheng, L. K. W., & Wu, A. (2023) · Lab on a Chip · doi:10.1039/d2lc01109c · Cited by 49 · see citing works

Development and Application of Brain Region–Specific Organoids for Investigating Psychiatric Disorders

Zhang, Z., Wang, X., Park, S. S., Song, H., & Ming, G. (2022) · Biological Psychiatry · doi:10.1016/j.biopsych.2022.12.015 · Cited by 49 · see citing works

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Zhao, L., Chen, J., Zhang, Z., Wu, W., Lin, X., Gao, M., Yang, Y., Zhao, P., Xu, S., Yang, C., et al. (2024) · Advanced Science · doi:10.1002/advs.202401383 · Cited by 49 · see citing works

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Dorado, G., Gálvez, S., Tham, T. E. R., Sánchez, V. F. V., & Hernández, P. (2021) · Biomolecules · doi:10.3390/biom11081111 · Cited by 48 · see citing works

Review of multi-omics data resources and integrative analysis for human brain disorders

Dong, X., Liu, C., & Dozmorov, M. (2021) · Briefings in Functional Genomics · doi:10.1093/bfgp/elab024 · Cited by 47 · see citing works

Neuronal fate acquisition and specification: time for a change

Bonnefont, J., & Vanderhaeghen, P. (2021) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2020.12.006 · Cited by 47 · see citing works

Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat

Zhang, H., Jin, Z., Cui, F., Zhao, L., Zhang, X., Chen, J., Zhang, J., Li, Y., Li, Y., Niu, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44003-6 · Cited by 45 · see citing works

Patient-Derived Midbrain Organoids to Explore the Molecular Basis of Parkinson's Disease

Galet, B., Cheval, H., & Ravassard, P. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.01005 · Cited by 45 · see citing works

Brain organoids: A promising model to assess oxidative stress‐induced central nervous system damage

Oyefeso, F. A., Muotri, A. R., Wilson, C. G., & Pecaut, M. J. (2021) · Developmental Neurobiology · doi:10.1002/dneu.22828 · Cited by 44 · see citing works

Application of Fused Organoid Models to Study Human Brain Development and Neural Disorders

Chen, A., Guo, Z., Fang, L., & Bian, S. (2020) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2020.00133 · Cited by 44 · see citing works

Targeting epigenetic dysregulation in autism spectrum disorders

Herrera, M. L., Paraíso‐Luna, J., Bustos-Martínez, I., & Barco, Á. (2024) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2024.06.004 · Cited by 43 · see citing works

Human in vitro models for understanding mechanisms of autism spectrum disorder

Gordon, A., & Geschwind, D. H. (2020) · Molecular Autism · doi:10.1186/s13229-020-00332-7 · Cited by 43 · see citing works

Computational Identification of Ligand-Receptor Pairs That Drive Human Astrocyte Development

Voss, A. J., Lanjewar, S. N., Sampson, M. M., King, A. T., Hill, E. J., Sing, A., Sojka, C., Bhatia, T. N., Spangle, J. M., & Sloan, S. A. (2022) · Nature Neuroscience · doi:10.1038/s41593-023-01375-8 · Cited by 41 · see citing works

Developmental convergence and divergence in human stem cell models of autism

Gordon, A., Yoon, S., Bicks, L. K., Martín, J. M., Pintacuda, G., Arteaga, S. A., Wamsley, B., Guo, Q., Elahi, L. S., Dolmetsch, R. E., et al. (2026) · Nature · doi:10.1038/s41586-025-10047-5 · Cited by 41 · see citing works

What Have Organoids and Assembloids Taught Us About the Pathophysiology of Neuropsychiatric Disorders?

Levy, R. J., & Pașca, S. P. (2022) · Biological Psychiatry · doi:10.1016/j.biopsych.2022.11.017 · Cited by 40 · see citing works

Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain

Lee, D. R., Rhodes, C. T., Mitra, A., Zhang, Y., Maric, D., Dale, R. K., & Petros, T. J. (2022) · eLife · doi:10.7554/elife.71864 · Cited by 39 · see citing works

Deconstructing and reconstructing the human brain with regionally specified brain organoids

Xiang, Y., Çakır, B., & Park, I. (2020) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2020.05.023 · Cited by 38 · see citing works

DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype-phenotype prediction

Chandrashekar, P. B., Alatkar, S., Wang, J., Hoffman, G. E., He, C., Jin, T., Khullar, S., Bendl, J., Fullard, J. F., Roussos, P., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01248-6 · Cited by 37 · see citing works

Mechanistic insights into the role of plant polyphenols and their nano-formulations in the management of depression

Kabra, A., Garg, R., Brimson, J. M., Živković, J., Almawash, S., Ayaz, M., Nawaz, A., Hassan, S. S. U., & BUNGAU, S. G. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.1046599 · Cited by 37 · see citing works

Histone Variants and Histone Modifications in Neurogenesis

Zhang, M., Zhao, J., Lv, Y., Wang, W., Feng, C., Zou, W., Su, L., & Jiao, J. (2020) · Trends in Cell Biology · doi:10.1016/j.tcb.2020.09.003 · Cited by 37 · see citing works

Mcm2 promotes stem cell differentiation via its ability to bind H3-H4

Xu, X., Hua, X., Brown, K., Ren, X., & Zhang, Z. (2022) · eLife · doi:10.7554/elife.80917 · Cited by 36 · see citing works

Transcending toward Advanced 3D-Cell Culture Modalities: A Review about an Emerging Paradigm in Translational Oncology

Farhat, J., Pandey, I., & Alwahsh, M. (2021) · Cells · doi:10.3390/cells10071657 · Cited by 35 · see citing works

Brain organoids: Human 3D models to investigate neuronal circuits assembly, function and dysfunction

Tambalo, M., & Lodato, S. (2020) · Brain Research · doi:10.1016/j.brainres.2020.147028 · Cited by 34 · see citing works

Polycomb‐mediated gene regulation in human brain development and neurodevelopmental disorders

Bölicke, N., & Albert, M. (2022) · Developmental Neurobiology · doi:10.1002/dneu.22876 · Cited by 34 · see citing works

An epigenome atlas of neural progenitors within the embryonic mouse forebrain

Rhodes, C. T., Thompson, J. J., Mitra, A., Asokumar, D., Lee, D. R., Lee, D. J., Zhang, Y., Jason, E., Dale, R., Rocha, P. P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31793-4 · Cited by 33 · see citing works

Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells

Wang, B., Starr, A. L., & Fraser, H. B. (2023) · eLife · doi:10.7554/elife.89594 · Cited by 33 · see citing works

Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution

Sahinyan, K., Blackburn, D. M., Simon, M.-M., Lazure, F., Kwan, T., Bourque, G., & Soleimani, V. D. (2022) · eLife · doi:10.7554/elife.72792 · Cited by 32 · see citing works

The Effects of Environmental Adversities on Human Neocortical Neurogenesis Modeled in Brain Organoids

Sarieva, K., & Mayer, S. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.686410 · Cited by 30 · see citing works

Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

Guerin, L. N., Barnett, K. R., & Hodges, E. C. (2021) · Nature Protocols · doi:10.1038/s41596-021-00608-z · Cited by 28 · see citing works

Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids

Noack, F., Vangelisti, S., Ditzer, N., Chong, F., Albert, M., & Bonev, B. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01296-5 · Cited by 26 · see citing works

The dynamics of chromatin architecture in brain development and function

Harabula, I., & Pombo, A. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.008 · Cited by 25 · see citing works

Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells

Blair, J. D., Hartman, A., Zenk, F. L., Wahle, P., Brancati, G., Dalgarno, C., Treutlein, B., & Satija, R. (2025) · Nature Communications · doi:10.1038/s41467-025-56590-7 · Cited by 25 · see citing works

Mapping the developmental trajectory of human astrocytes reveals divergence in glioblastoma

Sojka, C., Wang, H. V., Bhatia, T. N., Li, Y., Chopra, P., Sing, A., Voss, A. J., King, A. T., Wang, F., Joseph, K., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-024-01583-9 · Cited by 24 · see citing works

Scalable production of human cortical organoids using a biocompatible polymer

Narazaki, G., Miura, Y., Pavlov, S. D., Thete, M. V., Roth, J. G., Avar, M., Shin, S., Kim, J., Hudáčová, Z., Heilshorn, S. C., et al. (2025) · Nature Biomedical Engineering · doi:10.1038/s41551-025-01427-3 · Cited by 24 · see citing works

Epigenetics modifiers: potential hub for understanding and treating neurodevelopmental disorders from hypoxic injury

Cristancho, A. G., & Marsh, E. D. (2020) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-020-09344-z · Cited by 24 · see citing works

A matter of space and time: Emerging roles of disease-associated proteins in neural development

Panagiotakos, G., & Pașca, S. P. (2021) · Neuron · doi:10.1016/j.neuron.2021.10.035 · Cited by 24 · see citing works

Modeling Developmental Brain Diseases Using Human Pluripotent Stem Cells-Derived Brain Organoids – Progress and Perspective

Bhattacharya, A., Choi, W. W. Y., Muffat, J., & Li, Y. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167386 · Cited by 24 · see citing works

Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids

Cappuccio, G., Khalil, S. M., Osenberg, S., Li, F., & Maletić‐Savatić, M. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1181965 · Cited by 24 · see citing works

Microenvironment-Driven Dynamic Chromatin Changes in Glioblastoma Recapitulate Early Neural Development at Single-Cell Resolution

Pine, A. R., Cirigliano, S. M., Singhania, R., Nicholson, J., da Silva, B., Leslie, C. S., & Fine, H. A. (2023) · Cancer Research · doi:10.1158/0008-5472.can-22-2872 · Cited by 23 · see citing works

Epigenetics of neural differentiation: Spotlight on enhancers

Giacoman-Lozano, M., Meléndez-Ramírez, C., Martínez-Ledesma, E., Durán, R. C., & Velasco, I. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1001701 · Cited by 22 · see citing works

Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth

Tang, X., Wang, Z., Khutsishvili, D., Cheng, Y., Wang, J., Tang, J., & Ma, S. (2023) · Cell Systems · doi:10.1016/j.cels.2023.09.004 · Cited by 22 · see citing works

Implementation and validation of single-cell genomics experiments in neuroscience

Colonna, M., Konopka, G., Liddelow, S. A., Nowakowski, T. J., Awatramani, R. B., Bateup, H. S., Cadwell, C. R., Caglayan, E., Chen, J. L., Gillis, J., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01814-0 · Cited by 22 · see citing works

Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid

Lewis, E. M. A., Kaushik, K., Sandoval, L. A., Antony, I., Dietmann, S., & Kroll, K. L. (2021) · Neurochemistry International · doi:10.1016/j.neuint.2021.105039 · Cited by 22 · see citing works

Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells

Kim, S., Seo, S., Stein-O’Brien, G., Jaishankar, A., Ogawa, K., Micali, N., Luria, V., Karger, A., Wang, Y., Kim, H., et al. (2024) · Stem Cell Reports · doi:10.1016/j.stemcr.2024.07.004 · Cited by 21 · see citing works

Complex in vitro models positioned for impact to drug testing in pharma: a review

Kang, S., Chen, E. C., Cifuentes, H., Co, J. Y., Cole, G., Graham, J. C., Hsia, I., Kiyota, T., Klein, J. A., Kroll, K. T., et al. (2024) · Biofabrication · doi:10.1088/1758-5090/ad6933 · Cited by 21 · see citing works

Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits

Chawla, A., Nagy, C., & Turecki, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147612 · Cited by 20 · see citing works

Development of bioinformatics and multi-omics analyses in organoids

Ha, D., Kong, J., Kim, D., Lee, K., Lee, J., Park, M., Ahn, H., Oh, Y., & Kim, S. (2022) · BMB Reports · doi:10.5483/bmbrep.2022-0155 · Cited by 20 · see citing works

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

Xie, F., Armand, E. J., Yao, Z., Liu, H., Bartlett, A., Behrens, M. M., Li, Y. E., Lucero, J. D., Luo, C., Nery, J. R., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100342 · Cited by 20 · see citing works

Models for evaluating glioblastoma invasion along white matter tracts

Li, Y. O., Wang, J., Song, S.-R., Lv, S., Qin, J., & Yu, S. (2023) · Trends in biotechnology · doi:10.1016/j.tibtech.2023.09.005 · Cited by 20 · see citing works

Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids

Capauto, D., Wang, Y., Wu, F., Norton, S., Mariani, J., Inoue, F., Crawford, G. E., Ahituv, N., Abyzov, A. S., & Vaccarino, F. M. (2024) · Scientific Reports · doi:10.1038/s41598-024-54302-7 · Cited by 20 · see citing works

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 20 · see citing works

Organoids recapitulate brain development

Zahn, L. M. (2020) · Science · doi:10.1126/science.367.6476.401-i

Characterizing the epigenomic landscape of the developing human cortex at single-cell resolution

Ziffra, R. S. (2021) · eScholarship (California Digital Library)

Single-cell epigenomics reveals mechanisms of human cortical development

Ziffra, R. S., Kim, C. N., Ross, J. M., Wilfert, A. B., Turner, T. N., Haeussler, M., Casella, A. M., Przytycki, P. F., Keough, K. C., Shin, D. S., et al. (2021) · Nature · doi:10.1038/s41586-021-03209-8 · Cited by 267 · see citing works

Organoid single-cell genomic atlas uncovers human-specific features of brain development

Kanton, S., Boyle, M. J., He, Z., Santel, M., Weigert, A., Sanchís-Calleja, F., Guijarro, P., Sidow, L., Fleck, J. S., Han, D., et al. (2019) · Nature · doi:10.1038/s41586-019-1654-9 · Cited by 761 · see citing works

Single cell epigenomic atlas of the developing human brain and organoids

Ziffra, R. S., Kim, C. N., Wilfert, A., Turner, T. N., Haeussler, M., Casella, A. M., Przytycki, P. F., Kreimer, A., Pollard, K. S., Ament, S. A., et al. (2019) · doi:10.1101/2019.12.30.891549 · Cited by 33 · see citing works