Miller, E. L., Hargreaves, D. C., Kadoch, C., Chang, C.-Y., Calarco, J. P., Hodges, C., Buenrostro, J. D., Cui, K., Greenleaf, W. J., Zhao, K. & Crabtree, G. R. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol advance online publication, 10.1038/nsmb.3384 http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb.3384.html - supplementary-information (2017).

Chen, J., Yu, J. T., Wojta, K., Wang, H. F., Zetterberg, H., Blennow, K., Yokoyama, J. S., Weiner, M. W., Kramer, J. H., Rosen, H., Miller, B. L., Coppola, G., Boxer, A. L. & Alzheimer's Disease Neuroimaging, I. Genome-wide association study identifies MAPT locus influencing human plasma tau levels. Neurology, 10.1212/WNL.0000000000003615 (2017).https://www.ncbi.nlm.nih.gov/pubmed/28100725

Kadoch, C., Williams, R. T., Calarco, J. P., Miller, E. L., Weber, C. M., Braun, S. M., Pulice, J. L., Chory, E. J. & Crabtree, G. R. Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states. Nat Genet 49, 213-222, 10.1038/ng.3734 (2017).https://www.ncbi.nlm.nih.gov/pubmed/27941796

Wu, Y. E., Parikshak, N. N., Belgard, T. G. & Geschwind, D. H. Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder. Nat Neurosci 19, 1463-1476, 10.1038/nn.4373 (2016).https://www.ncbi.nlm.nih.gov/pubmed/27571009

Sun, W., Poschmann, J., Cruz-Herrera Del Rosario, R., Parikshak, N. N., Hajan, H. S., Kumar, V., Ramasamy, R., Belgard, T. G., Elanggovan, B., Wong, C. C., Mill, J., Geschwind, D. H. & Prabhakar, S. Histone Acetylome-wide Association Study of Autism Spectrum Disorder. Cell 167, 1385-1397 e1311, 10.1016/j.cell.2016.10.031 (2016).https://www.ncbi.nlm.nih.gov/pubmed/27863250

Parikshak, N. N., Swarup, V., Belgard, T. G., Irimia, M., Ramaswami, G., Gandal, M. J., Hartl, C., Leppa, V., Ubieta, L. T., Huang, J., Lowe, J. K., Blencowe, B. J., Horvath, S. & Geschwind, D. H. Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 540, 423-427, 10.1038/nature20612 (2016).https://www.ncbi.nlm.nih.gov/pubmed/27919067

Marbach, D., Lamparter, D., Quon, G., Kellis, M., Kutalik, Z. & Bergmann, S. Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Nat Methods 13, 366-370, 10.1038/nmeth.3799 (2016).https://www.ncbi.nlm.nih.gov/pubmed/26950747

Lamparter, D., Marbach, D., Rueedi, R., Kutalik, Z. & Bergmann, S. Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PLoS Comput Biol 12, e1004714, 10.1371/journal.pcbi.1004714 (2016).https://www.ncbi.nlm.nih.gov/pubmed/26808494

Heimberg, G., Bhatnagar, R., El-Samad, H. & Thomson, M. Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. Cell Syst 2, 239-250, 10.1016/j.cels.2016.04.001 (2016).https://www.ncbi.nlm.nih.gov/pubmed/27135536

Hanson-Smith, V. & Johnson, A. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories. PLoS Comput Biol 12, e1004976, 10.1371/journal.pcbi.1004976 (2016).https://www.ncbi.nlm.nih.gov/pubmed/27472806

Chandran, V., Coppola, G., Nawabi, H., Omura, T., Versano, R., Huebner, E. A., Zhang, A., Costigan, M., Yekkirala, A., Barrett, L., Blesch, A., Michaelevski, I., Davis-Turak, J., Gao, F., Langfelder, P., Horvath, S., He, Z., Benowitz, L., Fainzilber, M., Tuszynski, M., Woolf, C. J. & Geschwind, D. H. A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program. Neuron 89, 956-970, 10.1016/j.neuron.2016.01.034 (2016).https://www.ncbi.nlm.nih.gov/pubmed/26898779

Wang, G. Z., Belgard, T. G., Mao, D., Chen, L., Berto, S., Preuss, T. M., Lu, H., Geschwind, D. H. & Konopka, G. Correspondence between Resting-State Activity and Brain Gene Expression. Neuron 88, 659-666, 10.1016/j.neuron.2015.10.022 (2015)

Cho, S. H., Chen, J. A., Sayed, F., Ward, M. E., Gao, F., Nguyen, T. A., Krabbe, G., Sohn, P. D., Lo, I., Minami, S., Devidze, N., Zhou, Y., Coppola, G. & Gan, L. SIRT1 deficiency in microglia contributes to cognitive decline in aging and neurodegeneration via epigenetic regulation of IL-1beta. J Neurosci 35, 807-818, 10.1523/JNEUROSCI.2939-14.2015 (2015).https://www.ncbi.nlm.nih.gov/pubmed/25589773

Chen, J. A., Wang, Q., Davis-Turak, J., Li, Y., Karydas, A. M., Hsu, S. C., Sears, R. L., Chatzopoulou, D., Huang, A. Y., Wojta, K. J., Klein, E., Lee, J., Beekly, D. L., Boxer, A., Faber, K. M., Haase, C. M., Miller, J., Poon, W. W., Rosen, A., Rosen, H., Sapozhnikova, A., Shapira, J., Varpetian, A., Foroud, T. M., Levenson, R. W., Levey, A. I., Kukull, W. A., Mendez, M. F., Ringman, J., Chui, H., Cotman, C., DeCarli, C., Miller, B. L., Geschwind, D. H. & Coppola, G. A multiancestral genome-wide exome array study of Alzheimer disease, frontotemporal dementia, and progressive supranuclear palsy. JAMA Neurol 72, 414-422, 10.1001/jamaneurol.2014.4040 (2015).https://www.ncbi.nlm.nih.gov/pubmed/25706306

Chen, J. A., Penagarikano, O., Belgard, T. G., Swarup, V. & Geschwind, D. H. The emerging picture of autism spectrum disorder: genetics and pathology. Annu Rev Pathol 10, 111-144, 10.1146/annurev-pathol-012414-040405 (2015).https://www.ncbi.nlm.nih.gov/pubmed/25621659

Chen, J. A., Coppola, G. in Brain Mapping: An Encyclopedic Reference Vol. 3  (ed A. W. Toga) 1037-1047 (Academic Press: Elsevier, 2015).

Painter, M. W., Brosius Lutz, A., Cheng, Y. C., Latremoliere, A., Duong, K., Miller, C. M., Posada, S., Cobos, E. J., Zhang, A. X., Wagers, A. J., Havton, L. A., Barres, B., Omura, T. & Woolf, C. J. Diminished Schwann cell repair responses underlie age-associated impaired axonal regeneration. Neuron 83, 331-343, 10.1016/j.neuron.2014.06.016 (2014).https://www.ncbi.nlm.nih.gov/pubmed/25033179

Li, Y., Chen, J. A., Sears, R. L., Gao, F., Klein, E. D., Karydas, A., Geschwind, M. D., Rosen, H. J., Boxer, A. L., Guo, W., Pellegrini, M., Horvath, S., Miller, B. L., Geschwind, D. H. & Coppola, G. An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy. PLoS Genet 10, e1004211, 10.1371/journal.pgen.1004211 (2014).https://www.ncbi.nlm.nih.gov/pubmed/24603599

Howard, C. J., Hanson-Smith, V., Kennedy, K. J., Miller, C. J., Lou, H. J., Johnson, A. D., Turk, B. E. & Holt, L. J. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. Elife 3, 10.7554/eLife.04126 (2014).https://www.ncbi.nlm.nih.gov/pubmed/25310241

Belgard, T. G., Jankovic, I., Lowe, J. K. & Geschwind, D. H. Population structure confounds autism genetic classifier. Mol Psychiatry 19, 405-407, 10.1038/mp.2013.34 (2014).https://www.ncbi.nlm.nih.gov/pubmed/23546168

Seitan, V.*, Faure, A.J.*, Zhan, Y., McCord, R., Lajoie, B., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A., Flicek, P., Dekker, J. & Merkenschlager, M. Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments. Genome Research 23: 2066–2077 (2013).http://dx.doi.org/10.1101/gr.161620.113

Parikshak, N. N., Luo, R., Zhang, A., Won, H., Lowe, J. K., Chandran, V., Horvath, S. & Geschwind, D. H. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008-1021, 10.1016/j.cell.2013.10.031 (2013).https://www.ncbi.nlm.nih.gov/pubmed/24267887

Hoerder-Suabedissen, A., Oeschger, F. M., Krishnan, M. L., Belgard, T. G., Wang, W. Z., Lee, S., Webber, C., Petretto, E., Edwards, A. D. & Molnar, Z. Expression profiling of mouse subplate reveals a dynamic gene network and disease association with autism and schizophrenia. Proc Natl Acad Sci U S A 110, 3555-3560, 10.1073/pnas.1218510110 (2013).https://www.ncbi.nlm.nih.gov/pubmed/23401504

Belgard, T. G., Montiel, J. F., Wang, W. Z., García-Moreno, F., Margulies, E. H., Ponting, C. P. & Molnár, Z. Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors. Proceedings of the National Academy of Sciences 110, 13150-13155, 10.1073/pnas.1307444110 (2013).http://www.pnas.org/content/110/32/13150.abstract

Dykhuizen, E. C., Hargreaves, D. C., Miller, E. L., Cui, K., Korshunov, A., Kool, M., Pfister, S., Cho, Y. J., Zhao, K. & Crabtree, G. R. BAF complexes facilitate decatenation of DNA by topoisomerase IIalpha. Nature 497, 624-627, 10.1038/nature12146 (2013).https://www.ncbi.nlm.nih.gov/pubmed/23698369

Nellaker, C., Keane, T. M., Yalcin, B., Wong, K., Agam, A., Belgard, T. G., Flint, J., Adams, D. J., Frankel, W. N. & Ponting, C. P. The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol 13, R45, 10.1186/gb-2012-13-6-r45 (2012).https://www.ncbi.nlm.nih.gov/pubmed/22703977

Faure, A. J., Schmidt, D., Watt, S., Schwalie, P. C., Wilson, M. D., Xu, H., Ramsay, R. G., Odom, D. T. & Flicek, P. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Res 22, 2163-2175, 10.1101/gr.136507.111 (2012).https://www.ncbi.nlm.nih.gov/pubmed/22780989

Hathaway, N. A., Bell, O., Hodges, C., Miller, E. L., Neel, D. S. & Crabtree, G. R. Dynamics and memory of heterochromatin in living cells. Cell 149, 1447-1460, 10.1016/j.cell.2012.03.052 (2012).https://www.ncbi.nlm.nih.gov/pubmed/22704655

Wuchty, S., Arjona, D., Li, A., Kotliarov, Y., Walling, J., Ahn, S., Zhang, A., Maric, D., Anolik, R., Zenklusen, J. C. & Fine, H. A. Prediction of Associations between microRNAs and Gene Expression in Glioma Biology. PLoS One 6, e14681, 10.1371/journal.pone.0014681 (2011)

Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., Furlotte, N. A., Eskin, E., Nellaker, C., Whitley, H., Cleak, J., Janowitz, D., Hernandez-Pliego, P., Edwards, A., Belgard, T. G., Oliver, P. L., McIntyre, R. E., Bhomra, A., Nicod, J., Gan, X., Yuan, W., van der Weyden, L., Steward, C. A., Bala, S., Stalker, J., Mott, R., Durbin, R., Jackson, I. J., Czechanski, A., Guerra-Assuncao, J. A., Donahue, L. R., Reinholdt, L. G., Payseur, B. A., Ponting, C. P., Birney, E., Flint, J. & Adams, D. J. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289-294, 10.1038/nature10413 (2011).https://www.ncbi.nlm.nih.gov/pubmed/21921910

Belgard, T. G., Marques, A. C., Oliver, P. L., Abaan, H. O., Sirey, T. M., Hoerder-Suabedissen, A., Garcia-Moreno, F., Molnar, Z., Margulies, E. H. & Ponting, C. P. A transcriptomic atlas of mouse neocortical layers. Neuron 71, 605-616, 10.1016/j.neuron.2011.06.039 (2011).https://www.ncbi.nlm.nih.gov/pubmed/21867878

Wuchty, S., Zhang, A., Walling, J., Ahn, S., Li, A., Quezado, M., Oberholtzer, C., Zenklusen, J. C. & Fine, H. A. Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. J Biomed Inform 43, 945-952, 10.1016/j.jbi.2010.08.011 (2010)