Publications


Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging

Leeman D.S., Hebestreit K., Ruetz T., Webb A.E., McKay A., Pollina E.A., Dulken B.W., Zhao X., Yeo R.W., Ho T.T., Mahmoudi S., Devarajan K., Passegué E., Rando T.A., Frydman J., Brunet A. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science 10.1126/science.aag3048 (2018).

http://science.sciencemag.org/content/359/6381/1277.full

 

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons

Shi Y., Lin S., Staats K.A., Li Y., Chang W.H., Hung S.T., Hendricks E., Linares G.R., Wang Y., Son E.Y., Wen X., Kisler K., Wilkinson B., Menendez L., Sugawara T., Woolwine P., Huang M., Cowan M.J., Ge B., Koutsodendris N., Sandor K.P., Komberg J., Vangoor V.R., Senthilkumar K., Hennes V., Seah C., Nelson A.R., Cheng T.Y., Lee S.J., August P.R., Chen J.A., Wisniewski N., Hanson-Smith V., Belgard T.G., Zhang A., Coba M., Grunseich C., Ward M.E., van den Berg L.H., Pasterkamp R.J., Trotti D., Zlokovic B.V., Ichida J.K. Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons. Nat Med 10.1038/nm.4490 (2018).

https://www.ncbi.nlm.nih.gov/pubmed/29400714

 

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol advance online publication

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 (2017).

http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb.3384.html - supplementary-information

 

& Alzheimer's Disease Neuroimaging, I. Genome-wide association study identifies MAPT locus influencing human plasma tau levels

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

 

Polycomb complex opposition on heterochromatin in normal and oncogenic states

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

 

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

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

 

A multiancestral genome-wide exome array study of Alzheimer disease, frontotemporal dementia, and progressive supranuclear palsy

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

 

The emerging picture of autism spectrum disorder: genetics and pathology

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

 

in Brain Mapping: An Encyclopedic Reference Vol. 3  (ed A. W. Toga)

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

 

Diminished Schwann cell repair responses underlie age-associated impaired axonal regeneration

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).

 

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

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

 

A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program

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

 

Correspondence between Resting-State Activity and Brain Gene Expression

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)

 

SIRT1 deficiency in microglia contributes to cognitive decline in aging and neurodegeneration via epigenetic regulation of IL-1beta

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

 

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. 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

 

Expression profiling of mouse subplate reveals a dynamic gene network and disease association with autism and schizophrenia

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

 

Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors

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

 

BAF complexes facilitate decatenation of DNA by topoisomerase IIalpha

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

 

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

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

 

A transcriptomic atlas of mouse neocortical layers

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

 

Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology

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)

https://www.ncbi.nlm.nih.gov/pubmed/25033179

 

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

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

 

Dynamics and memory of heterochromatin in living cells

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

 

Histone Acetylome-wide Association Study of Autism Spectrum Disorder

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

 

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

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

 

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

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

 

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

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

 

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

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

 

An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy

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

 

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

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

 

D. H. Population structure confounds autism genetic classifier

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

 

Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments

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

 

Prediction of Associations between microRNAs and Gene Expression in Glioma Biology

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)

 

Mouse genomic variation and its effect on phenotypes and gene regulation

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