Selected Recent Publications

Stanley Center Publications

Below are selected publications related to key areas of interest to Stanley Center investigators, including: CommentaryGenetics, Neurobiology, and Clinical Research.

Click here for a special focus on schizophrenia research at the Stanley Center

Commentary

Hyman, S. E. (2021). Wringing Biological Insight From Polygenic SignalsBiological Psychiatry. 89(1), 8-10. 

Hyman S. E. (2021). Use of mouse models to investigate the contributions of CNVs associated with schizophrenia and autism to disease mechanisms. Current opinion in genetics & development, 68, 99–105. 

Hyman S. E. (2021). Psychiatric Disorders: Grounded in Human Biology but Not Natural Kinds. Perspectives in biology and medicine, 64(1), 6–28.

Aida, T., Feng G. (2020). The dawn of non-human primate models for neurodevelopmental disorders. Current Opinion Genetic Development 65, 160-168. 

Feng, G., Jensen, F. E., Greely, H. T., Okano, H., Treue, S., Roberts, A. C., Fox, J. G., Caddick, S., Poo, M. M., Newsome, W. T., Morrison, J. H. (2020). Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research. Proceedings of the National Acadamies of Science. 

Nehme, R., Barrett, L.E. (2020) Using human pluripotent stem cell models to study autism in the era of big data Molecular Austism 11:21

Feng G, Jensen FE, Greely HT, Okano H, Treue S, Roberts AC, Fox JG, Caddick S, Poo MM, Newsome WT, Morrison JH. (2020) Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research. Proc Natl Acad Sci Online ahead of print.

Velasco S, Paulsen B, Arlotta P. 3D Brain Organoids: Studying Brain Development and Disease Outside the Embryo. Annu Rev Neurosci. 2020 Jul 8;43:375-389.  

Liddelow SA, Marsh SE, Stevens B. Microglia and Astrocytes in Disease: Dynamic Duo or Partners in Crime? Trends Immunol. 2020 Sep;41(9):820-835.

Martin, A.R., Daly, M.J., Robinson, E.B., Hyman, S.E., Neale, B.M. (2019) Predicting Polygenic Risk of Psychiatric Disorders Biol Psychiatry 86:97-109

Martin, A.R., Kanai, M., Kamatani, Y., Okada, Y., Neale, B.M., and Daly, M.J. (2019) Clinical use of current polygenic risk scores may exacerbate health disparities Nature Genetics 51, 584–591

Wilton, D.K., Dissing-Olesen, L., Stevens, B. (2019) Neuron-Glia Signaling in Synapse Elimination Annu Rev Neurosci 42:107-127

Hyman, S.E. (2018) The daunting polygenicity of mental illness: making a new map Philosophical Transactions of the Royal Society B: Biological Sciences 373, 20170031

Farahany, N.A., Greely, H.T., Hyman, S., Koch, C., Grady, C., Pașca, S.P., Sestan, N., Arlotta, P., Bernat, J.L., Ting, J., et al (2018) The ethics of experimenting with human brain tissue Nature 556, 429–432

Kaiser, T., and Feng, G. (2015) Modeling psychiatric disorders for developing effective treatments Nature Medicine 21, 979–988

Genetics

Atkinson, E. G., Maihofer, A. X., Kanai, M., Martin, A. R., Karczewski, K. J., Santoro, M. L., Ulirsch, J. C., Kamatani, Y., Okada, Y., Finucane, H. K., Koenen, K. C., Nievergelt, C. M., Daly, M. J., Neale, B. M. (2021). Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power. Nature Genetics53195204.

Bigdeli, T. B., Genovese, G., Georgakopoulos, .P, Meyers, J. L., Peterson, R. E., Iyegbe, C. O., Medeiros, H., Valderrama, J., Achtyes, E. D., Kotov, R., Stahl, E. A., Abbott, C., Azevedo, M. H., Belliveau, R. A., Bevilacqua, E., Bromet, E. J., Byerley, W., Carvalho, C. B., Chapman, S. B., DeLisi, L. E., Dumont ,A. L., O'Dushlaine, C., Evgrafov, O. V., Fochtmann, L. J., Gage, D., Kennedy, J. L., Kinkead, B., Macedo, A., Moran, J. L., Morley, C. P., Dewan, M. J., Nemesh, J., Perkins, D. O., Purcell, S. M., Rakofsky, J. J., Scolnick, E. M., Sklar, B. M., Sklar, P., Smoller, J. W., Sullivan, P. F., Macciardi, F., Marder, S. R., Gur, R. C., Gur, R. E., Braff, D. L.; Consortium on the Genetics of Schizophrenia (COGS), Investigators, Nicolini, H., Escamilla, M. A., Vawter, M. P., Sobell, J. L., Malaspina, D., Lehrer, D. S., Buckley, P. F., Rapaport, M. H., Knowles, J. A.; Genomic Psychiatry Cohort (GPC) Consortium, Fanous, A. H., Pato, M. T., McCarroll, S. A., Pato, C. N. (2020). Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry. Molecular Psychiatry 25(10), 2455-2467.

Demontis, D., Walters, R., Martin, J., Mattheisen, M., Als, T., Agerbo, E., Baldursson, G., Belliveau, R., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Cerrato, F., Chambert, K., Churchhouse, C., Dumont, A., Eriksson, N., Gandal, M., Goldstein, J. , Grasby, K., Grove, J., Gudmundsson, O. O., Hansen, C. S., Hauberg, M. E., Hollegaard, M. V., Howrigan, D. P., Huang, H., Maller, J. B., Martin, A. R., Martin, N., Moran, J., Pallesen, J., Palmer, D., Pedersen, C., Pedersen, M., Poterba, T., Poulsen, J., Ripke, S., Robinson, E., Satterstrom, F., Stefansson, H., Stevens, C., Turley, P., Walters, G., Won, H., Wright, M.; ADHD Working Group of the Psychiatric Genomics Consortium (PGC); Early Lifecourse & Genetic Epidemiology (EAGLE) Consortium; 23andMe Research Team, et al. (2019). Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorderNat Genet 51,63-75.

Feng, Y-CA, Howrigan, D., Abbott, L., Tashman, K., Cerrato, F., Singh, T., Heyne, H., Byrnes, A., Churchhouse, C., Watts, N., et al. (2019). Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 IndividualsAmerican Journal of Human Genetics 105, 267–282.

Finucane, H., Reshef, Y., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P., Lareau, C., Shoresh, N., Genovese, G., Saunders, A., Macosko, E., Pollack, S.; Brainstorm Consortium, Perry, J., Buenrostro, J., Bernstein, B., Raychaudhuri, S., McCarroll, S., Neale, B., Price, A. (2018) Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell typesNat Genet 50, 621-629.

Grove, J., Ripke, S., Als, T., Mattheisen, M., Walters, R., Won, H., Pallesen, J., Agerbo, E., Andreassen, O, Anney, R., Awashti, S., Belliveau, R., Bettella, F., Buxbaum, J., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Cerrato, F., Chambert, K., Christensen, J., Churchhouse, C., Dellenvall, K., Demontis, D., De Rubeis, S., Devlin, B., Djurovic, S., Dumont, A. L., Goldstein, J. I., Hansen, C. S., Hauberg, M., Hollegaard, M., Hope, S., Howrigan, D., Huang, H., Hultman, C., Klei, L., Maller, J., Martin,J., Martin, A.  Moran, J., Nyegaard, M., Nærland, T., Palmer, D., Palotie, A., Pedersen, C., Pedersen, M., Poterba, T., Poulsen, J., Pourcain, B., Qvist, P., Rehnström, K., Reichenberg, A., Reichert, J., Robinson, E., Roeder, K., Roussos, P., Saemundsen, E., Sandin, S., Satterstrom, F., Davey Smith, G., Stefansson, H., Steinberg, S., Stevens, C., Sullivan, P., Turley, P., Walters, G., Xu, X.; Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium; et al. (2019). Identification of common genetic risk variants for autism spectrum disorderNat Genet 51,431-444.

Hess, J. L., Tylee, D. S., Mattheisen, M., Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Børglum, A. D., Als, T. D., Grove, J., Werge, T., Mortensen, P. B., Mors, O., Nordentoft, M., Hougaard, D. M., Byberg-Grauholm, J., Bækvad-Hansen, M., Greenwood, T. A., Tsuang, M. T., Curtis, D., Steinberg, S., Sigurdsson, E., … Glatt, S. J. (2021). A polygenic resilience score moderates the genetic risk for schizophrenia. Molecular psychiatry, 26(3), 800–815. 

Howrigan, D., Rose, S., Samocha, K., Fromer, M., Cerrato, F., Chen,W., Churchhouse, C., Chambert, K., Chandler, S., Daly, M., Dumont, A., Genovese, G., Hwu, H., Laird, N., Kosmicki, J., Moran, J., Roe, C., Singh,T., Wang, S., Faraone, S., Glatt, S., McCarroll, S. , Tsuang, M., Neale, B. (2020). Exome sequencing in schizophrenia-affected parent-offspring trios reveals risk conferred by protein-coding de novo mutationsNat Neurosci 23:185-193.

Kamitaki N, Sekar A, Handsaker RE, de Rivera H, Tooley K, Morris DL, Taylor KE, Whelan CW, Tombleson P, Loohuis LMO; Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke M, Kimberly RP, Kaufman KM, Harley JB, Langefeld CD, Seidman CE, Pato MT, Pato CN, Ophoff RA, Graham RR, Criswell LA, Vyse TJ, McCarroll SA. (2020) Complement genes contribute sex-biased vulnerability in diverse disordersNature. 582:577-581

Lam, M., Chen, C., Li, Z., Martin, A., Bryois, J., Ma, X., Gaspar, H., Ikeda, M., Benyamin, B., Brown, B., Liu, R., Zhou, W., Guan, L., Kamatani, Y., Kim, S., Kubo, M., Kusumawardhani, A., Liu, C, Ma, H., Periyasamy, S., Takahashi, A., Xu, Z., Yu, H., Zhu, F.; Schizophrenia Working Group of the Psychiatric Genomics Consortium; et al. (2019). Comparative genetic architectures of schizophrenia in East Asian and European populationsNat Genet 51,1670-1678.

Loh, P. R., Genovese, G., McCarroll, S. A. (2020). Monogenic and polygenic inheritance become instruments for clonal selection. Nature 584(7819), 136-141.  

Martin, A. R., Atkinson, E. G., Chapman, S. B., Stevenson, A., Stroud, R. E., Abebe, T., Akena, D., Alemayehu, M., Ashaba, F. K., Atwoli, L., Bowers, T., Chibnik, L. B., Daly, M. J., DeSmet, T., Dodge, S., Fekadu, A., Ferriera, S., Gelaye, B., Gichuru, S., Injera, W. E., … NeuroGAP-Psychosis Study Team (2021). Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. American journal of human genetics, 108(4), 656–668. 

Martin, A. R., Gignoux, C. R., Walters, R. K., Wojcik, G. L., Neale, B. M., Gravel, S., Daly, M. J., Bustamante, C. D., Kenny, E. E. (2020). Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. American Journal of Human Genetics 107(4), 788-789. 

Mullins, N., & Huang, H. (2021). Genetic Architecture of Bipolar Disorder in Individuals of Han Chinese and European Ancestries. JAMA psychiatry, 78(3), 248–249. 

Nievergelt, C., Maihofer, A., Klengel, T., Atkinson, E., Chen, C., Choi, K., Coleman, J., Dalvie, S., Duncan, L., Gelernter, J., Levey, D., Logue, M., Polimanti, R., Provost, A., Ratanatharathorn, A., Stein, M., Torres, K., et al. (2019). International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk lociNat Commun 10, 4558.

Peterson, R., Kuchenbaecker, K., Walters, R., Chen, C., Popejoy, A., Periyasamy, S., Lam, M., Iyegbe, C., Strawbridge, R., Brick, L., Carey, C.E., Martin, A.R., et al. (2019). Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and RecommendationsCell 179, 589–603.

Saarentaus, E. C., Havulinna, A. S., Mars, N., Ahola-Olli, A., Kiiskinen, T., Partanen, J., Ruotsalainen, S., Kurki, M., Urpa, L. M., Chen, L., Perola, M., Salomaa, V., Veijola, J., Männikkö, M., Hall, I. M., Pietiläinen, O., Kaprio, J., Ripatti, S., Daly, M., & Palotie, A. (2021). Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants. Molecular psychiatry, Advance online publication. 

Wang, Q. S., Kelley, D. R., Ulirsch, J., Kanai, M., Sadhuka, S., Cui, R., Albors, C., Cheng, N., Okada, Y., Biobank Japan Project, Aguet, F., Ardlie, K. G., MacArthur, D. G., & Finucane, H. K. (2021). Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. Nature communications, 12(1), 3394. https://doi.org/10.1038/s41467-021-23134-8

Satterstrom, F., Kosmicki, J., Wang, J., Breen, M., De Rubeis, S., An, J., Peng, M., Collins, R., Grove, J., Klei, L., Stevens, C., Reichert, J., Mulhern, M., Artomov, M., Gerges, S., Sheppard, B., Xu, X., Bhaduri, A., Norman, U., Brand, H., Schwartz, G., Nguyen, R., Guerrero, E., Dias, C.; Autism Sequencing Consortium; iPSYCH-Broad Consortium, Betancur, C., Cook, E., Gallagher, L., Gill, M., Sutcliffe, J., Thurm, A., Zwick, M., Børglum, A., State, M., Cicek, A., Talkowski, M., Cutler, D., Devlin, B., Sanders, S., Roeder, K., Daly, M., Buxbaum, J. (2020). Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of AutismCell 180:568-584.

Satterstrom, F., Walters, R., Singh, T., Wigdor, E., Lescai, F., Demontis, D., Kosmicki, J., Grove, J., Stevens, C., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Palmer, D., Maller, J.; iPSYCH-Broad Consortium, Nordentoft, M., Mors, O., Robinson, E. , Hougaard, D., Werge, T., Bo Mortensen, P., Neale, B., Børglum, A., Daly, M. (2019). Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variantsNat Neurosci 22,1961-1965.

Stahl, E., Breen, G., Forstner, A., McQuillin, A., Ripke, S., Trubetskoy, V., Mattheisen, M., Wang, Y., Coleman, J., Gaspar, H., de Leeuw, C., Steinberg, S., Pavlides, J., Trzaskowski, M., Byrne, E., Pers, T., Holmans, P., Richards, A., et al, (2019). Genome-wide association study identifies 30 loci associated with bipolar disorderNat Genet 51, 793-803.

Stevenson, A., Akena, D., Stroud, R., Atwoli, L., Campbell, M., Chibnik, L., Kwobah, E., Kariuki, S., Martin, A., de Menil, V., Newton, C., Sibeko, G., Stein, D., Teferra, S., Zingela, Z., Koenen, K. (2019) Neuropsychiatric Genetics of African Populations-Psychosis (NeuroGAP-Psychosis): a case-control study protocol and GWAS in Ethiopia, Kenya, South Africa and UgandaBMJ Open 9:e025469

Taylor, J., Debost, J., Morton, S., Wigdor, E., Heyne, H., Lal, D., Howrigan, D., Bloemendal, A., Larsen, J., Kosmicki, J., Weiner, D., Homsy, J., Seidman, J., Seidman, C., Agerbo, E., McGrath, J., Mortensen, P., Petersen, L., Daly, M., Robinson, E. B. (2019). Paternal-age-related de novo mutations and risk for five disordersNature Communications 10, 3043.

Thyme, S., Pieper, L, Li, E., Pandey, S., Wang, Y., Morris, N., Sha, C., Choi, J., Herrera, K., Soucy, E., Zimmerman, S., Randlett, O., Greenwood, J., McCarroll, S., Schier, A. (2019). Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared FunctionsCell 177, 478-491

Yu, D., Sul, J., Tsetsos, F., Nawaz, M., Huang, A., Zelaya, I., Illmann, C., Osiecki, L., Darrow, S., Hirschtritt, M., et al. (2019). Interrogating the Genetic Determinants of Tourette’s Syndrome and Other Tic Disorders Through Genome-Wide Association StudiesAmerican Journal of Psychiatry 176, 217–227.

Selected preprints:

Carey, C., Huang, Y., Strong, R., Aslibekyan, S., Gentleman, R., Smoller, J., Wilmer, J., Robinson, E., Germine, L. (2020). Shared and distinct genetic influences between cognitive domains and psychiatric disorder risk based on genome-wide data. bioRxiv 2020.09.16.297408.

Lam, M., Thompson, M., Li, B., Edwards, A. C., Chen, C.-Y., Ge, T., Cai, N., Bigdeli, T., Lencz, T., Kendler, K., Huang, H. (2020). Elucidating the Joint Genetic Architecture of Mood Disorder and Schizophrenia. medRxiv 2020.09.14.20193870.

Martin, A. R., Atkinson, E. G., Chapman, S. B., Stevenson, A., Stroud, R. E., Abebe, T., Akena, D., Alemayehu, M., Ashaba, F. K., Atwoli, L., Bowers, T., Chibnik, L. B., Daly, M. J., DeSmet, T., Dodge, S., Fekadu, A., Ferriera, S., Gelaye, B., … Gichuru, S. (2020). Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. bioRxiv 2020.04.27.064832.

Mullins, N., Forstner, A. J., O’Connell, K. S., Coombes, B., Coleman, J. R. I., Qiao, Z., Als, T. D., Bigdeli, T. B., Børte, S., Bryois, J., Charney, A. W., Drange, O. K., Gandal, M. J., Hagenaars, S. P., Ikeda, M., Kamitaki, N., Kim, M., Krebs, K., … Panagiotaropoulou, G. (2020). Genome-wide association study of over 40,000 bipolar disorder cases provides novel biological insights. medRxiv 2020.09.17.20187054.

Schizophrenia Working Group of the Psychiatric Genomics Consortium, Ripke, S., Walters, J.TR., O'Donovan, M.C. (2020). Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia. medRxiv 2020.09.12.20192922.

Singh, T., Poterba, T., Curtis, D., Akil, H., Al Eissa, M., Barchas, J. D., Bass, N., Bigdeli, T. B., Breen, G., Bromet, E. J., Buckley, P. F., Bunney, W. E., Bybjerg-Grauholm, J., Byerley, W. F., Chapman, S. B., Chen, W. J., Churchhouse, C., Craddock, N., Curtis, C., … Daly, M. J. (2020). Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia. medRxiv 2020.09.18.20192815.

Wang, Q. S., Kelley, D. R., Ulirsch, J., Kanai, M., Sadhuka, S., Cui, R., Albors, C., Cheng, N., Okada, Y., Aguet, F., Ardlie, K. G., MacArthur, D. G., and Finucane, H. K. (2020). Leveraging supervised learning for functionally-informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. bioRxiv 2020.10.20.347294.

Neurobiology

Tools and technologies:

Adam, Y., Kim, J., Lou, S., Zhao, Y., Brinks, D., Wu, H., Mostajo-Radji, M., Kheifets, S.,Parot, V.,Chettih, S.,Williams, K., Farhi, S., Madisen, L.,  Harvey, C., Zeng, H., Arlotta, P., Campbell, R.,  Cohen, A. (2019). Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics. Nature 569, 413-417.

Albanese, A., Swaney, J. M., Yun, D. H., Evans, N. B., Antonucci, J. M., Velasco, S., Sohn, C. H., Arlotta, P., Gehrke, L., Chung, K. (2020). Multiscale 3D phenotyping of human cerebral organoids. Scientific Reports. 10(1):21487. 

Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic Acids Res. 2020 Jan 10;48(1):e4. 

Cable, D. M., Murray, E., Zou, L. S., Goeva, A., Macosko, E. Z., Chen, F., & Irizarry, R. A. (2021). Robust decomposition of cell type mixtures in spatial transcriptomics. Nature biotechnology, Advance online publication. 

Di Bella, D. J., Habibi, E., Stickels, R. R., Scalia, G., Brown, J., Yadollahpour, P., Yang, S. M., Abbate, C., Biancalani, T., Macosko, E. Z., Chen, F., Regev, A., & Arlotta, P. (2021). Molecular logic of cellular diversification in the mouse cerebral cortex. Nature, Advance online publication. 

Eid, F. E., Elmarakeby, H. A., Chan, Y. A., Fornelos, N., ElHefnawi, M., Van Allen, E. M., Heath, L. S., & Lage, K. (2021). Systematic auditing is essential to debiasing machine learning in biology. Communications biology, 4(1), 183. 

Hammond, T., Dufort, C., Dissing-Olesen, L., Giera, S., Young, A., Wysoker, A., Walker, A., Gergits, F., Segel, M., Nemesh, J., Saunders, A., Macosko, E., Franklin, R., Piao, X., McCarroll, S., Stevens, B. (2019). Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes. Immunity 50, 253-271.

Hazelbaker DZ, Beccard A, Angelini G, Mazzucato P, Messana A, Lam D, Eggan K, Barrett LE. A multiplexed gRNA piggyBac transposon system facilitates efficient induction of CRISPRi and CRISPRa in human pluripotent stem cells. Sci Rep. 2020 Jan 20;10(1):635.

Huang, Q., Chan, K., Tobey, I., Chan, Y., Poterba, T., Boutros, C., Balazs, A., Daneman, R., Bloom, J., Seed, C., Deverman, B. (2019). Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHPB capsids. PLOS One 101371.

Jin, X., Simmons, S. K., Guo, A., Shetty, A. S., Ko, M., Nguyen, L., Jokhi, V., Robinson, E., Oyler, P., Curry, N., Deangeli, G., Lodato, S., Levin, J. Z., Regev, A., Zhang, F., Arlotta, P. (2020). In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science. 370(6520):eaaz6063. 

Koopmans, F., van Nierop, P., Andres-Alonso, M., Byrnes, A., Cijsouw, T., Coba, M., Cornelisse, L., Farrell, R., Goldschmidt, H., Howrigan, D., et al. (2019). SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron 103, 217–234.

Krienen, F. M., Goldman, M., Zhang, Q., C. H. Del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., Wu, C., Lutservitz, A., Mullally, C. D., Reed, N., Bien, E., Bortolin, L., Fernandez-Otero, M., Lin, J. D., Wysoker, A., Nemesh, J., Kulp, D., Burns, M., Tkachev, V., Smith, R., Walsh, C. A., Dimidschstein, J., Rudy, B., Kean, L. S., Berretta, S., Fishell, G., Feng, G., McCarroll, S. A. (2020). Innovations present in the primate interneuron repertoire. Nature. 586(7828):262-269. doi: 10.1038/s41586-020-2781-z.

Liu, J., Gao, C., Sodicoff, J., Kozareva, V., Macosko, E. Z., Welch, J. D. (2020). Jointly defining cell types from multiple single-cell datasets using LIGER. Nature Protocols.15(11):3632-3662.

Pintacuda, G., Lassen, F. H., Hsu, Y. H., Kim, A., Martín, J. M., Malolepsza, E., Lim, J. K., Fornelos, N., Eggan, K. C., & Lage, K. (2021). Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. Nature communications, 12(1), 2580. 

Pintacuda, G., Martín, J. M., & Eggan, K. C. (2021). Mind the translational gap: using iPS cell models to bridge from genetic discoveries to perturbed pathways and therapeutic targets. Molecular autism, 12(1), 10. 

Rodriques, S., Stickels, R., Goeva, A., Martin, C., Murray, E., Vanderburg, C., Welch, J., Chen, L. M., Chen, F., Macosko, E. (2019). Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467.

Smith, E. J., Farshim, P. P., Flomen, R., Jones, S. T., McAteer, S. J., Deverman, B. E., Gradinaru, V., & Bates, G. P. (2021). Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery. Brain communications, 3(2), fcab105. 

Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., Arlotta, P., Macosko, E. Z., & Chen, F. (2021). Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature biotechnology, 39(3), 313–319. 

Tomov, M. L., O'Neil, A., Abbasi, H. S., Cimini, B. A., Carpenter, A. E., Rubin, L. L., & Bathe, M. (2021). Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications biology, 4(1), 786. 

Velasco, S., Kedaigle, A. J., Simmons, S., Nash, A., Rocha, M., Quadrato, G., Paulsen, B., Nguyen, L., Adiconis, X., Regev, A., Levin, J.Z., Arlotta, P. (2019). Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature 570, 523–527.

Velasco, S., Paulsen, B., Arlotta, P. (2020) 3D Brain Organoids: Studying Brain Development and Disease Outside the Embryo. Annual Review of Neuroscience. 43:375-389.

Vormstein-Schneider D, Lin JD, Pelkey KA, Chittajallu R, Guo B, Arias-Garcia MA, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken TP, Smith J, Ibrahim LA, M Astro KJ, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi GA, Gorissen BL, Yuan X, Zaghloul KA, Devinsky O, Sabatini BL, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain CJ, Fishell G, Dimidschstein J. Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans. Nat Neurosci. 2020 Aug 17. 

Welch, J., Kozareva, V., Ferreira, A., Vanderburg, C., Martin, C., and Macosko, E. (2019). Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity. Cell 177, 1873–1887.

Ximerakis, M., Lipnick, S., Innes, B. T., Simmons, S. K., Adiconis, X., Dionne, D., Mayweather, B., Nguyen, L., Niziolek, Z., Ozek, C., Butty, V., Isserlin, R., Buchanan, S., Levine, S., Regev, A., Bader, G., Levin, J., Rubin, L. (2019), Single-cell transcriptomic profiling of the aging mouse brain, Nat Neurosci 22:1696-1708

Hazelbaker, D. Z., Beccard, A., Mazzucato, P., Angelini, G., Messana, A., Lam, D., Eggan, K., and Barrett, L. E. (2019). Multiplexed and inducible gene modulation in human pluripotent stem cells by CRISPR interference and activation. bioRxiv 603951

Insights into disease mechanisms:

Amal, H., Barak, B., Bhat, V., Gong, G., Joughin, B. A., Wang, X., Wishnok, J. S., Feng, G., Tannenbaum, S. R. (2020). Shank3 mutation in a mouse model of autism leads to changes in the S-nitroso-proteome and affects key proteins involved in vesicle release and synaptic function. Molecular Psychiatry 25(8), 1835-1848.

Barak, B., Zhang, Z., Liu, Y., Nir, A., Trangle, S., Ennis, M., Levandowski, K., Wang, D., Quast, K., Boulting, G., et al. (2019). Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioral and myelin alterations rescuable by a remyelinating drug. Nature Neuroscience 22, 700–708.

Chen Q, Deister CA, Gao X, Guo B, Lynn-Jones T, Chen N, Wells MF, Liu R, Goard MJ, Dimidschstein J, Feng S, Shi Y, Liao W, Lu Z, Fishell G, Moore CI, Feng G. (2020) Dysfunction of cortical GABAergic neurons leads to sensory hyper-reactivity in a Shank3 mouse model of ASD. Nat Neurosci. 23:520-532

Du, J., Simmons, S., Brunklaus, A., Adiconis, X., Hession, C., Fu, Z., Li, Y., Shema, R., Møller, R., Barak, B., Feng, G., Meisler, M., Sanders, S., Lerche, H., Campbell, A., McCarroll, S., Levin, J., Lal, D. (2019). Differential excitatory vs. inhibitory SCN expression at single cell level regulates brain sodium channel function in neurodevelopmental disorders. Eur J Paediatr Neurol.  Dec 28 2019 [Epub ahead of print]

Guo, B., Chen, J., Chen, Q., Ren, K., Feng, D., Mao, H., Yao, H., Yang, J., Liu, H., Liu, Y., et al. (2019). Anterior cingulate cortex dysfunction underlies social deficits in Shank3 mutant mice. Nature Neuroscience 22, 1223–1234.

Krienen FM, Goldman M, Zhang Q, C H Del Rosario R, Florio M, Machold R, Saunders A, Levandowski K, Zaniewski H, Schuman B, Wu C, Lutservitz A, Mullally CD, Reed N, Bien E, Bortolin L, Fernandez-Otero M, Lin JD, Wysoker A, Nemesh J, Kulp D, Burns M, Tkachev V, Smith R, Walsh CA, Dimidschstein J, Rudy B, S Kean L, Berretta S, Fishell G, Feng G, McCarroll SA. Innovations present in the primate interneuron repertoire. Nature. 2020 Oct;586(7828):262-269. 

Mealer, R. G., Jenkins, B. G., Chen, C. Y., Daly, M. J., Ge, T., Lehoux, S., Marquardt, T., Palmer, C. D., Park, J. H., Parsons, P. J., Sackstein, R., Williams, S. E., Cumming,s R. D., Scolnick, E. M., Smoller, J.W. (2020). The schizophrenia risk locus in SLC39A8 alters brain metal transport and plasma glycosylation. Scientific Reports 10(1), 13162. 

Mealer, R. G., Williams, S. E., Daly, M. J., Scolnick, E. M., Cummings, R. D., Smoller, J. W. (2020). Glycobiology and schizophrenia: a biological hypothesis emerging from genomic research. Molecular Psychiatry 25(12), 3129-3139. 

Nakajima, M., Schmitt, L., Halassa, M. (2019). Prefrontal cortex regulates sensory filtering through a basal ganglia-to-thalamus pathway. Neuron 103, 445–458.

Nakajima, M., Schmitt, L., Feng, G., Halassa, M. (2019). Combinatorial targeting of distributed forebrain networks reverses noise hypersensitivity in a model of Autism Spectrum Disorder. Neuron 104, 488–500.

Roy, D. S., Zhang, Y., Aida, T., Choi, S., Chen, Q., Hou, Y., Lea, N. E., Skaggs, K. M., Quay, J. C., Liew, M., Maisano, H., Le, V., Jones, C., Xu, J., Kong, D., Sullivan, H. A., Saunders, A., McCarroll, S. A., Wickersham, I. R., & Feng, G. (2021). Anterior thalamic dysfunction underlies cognitive deficits in a subset of neuropsychiatric disease models. Neuron, S0896-6273(21)00420-7. Advance online publication. 

Scott-Hewitt, N., Perrucci, F., Morini, R., Erreni, M., Mahoney, M., Witkowska, A., Carey, A., Faggiani, E., Schuetz, L. T., Mason, S., Tamborini, M., Bizzotto, M., Passoni, L., Filipello, F., Jahn, R., Stevens, B., Matteoli, M. (2020). Local externalization of phosphatidylserine mediates developmental synaptic pruning by microglia. EMBO Journal. 39(16):e105380. 

Wallace J, Lord J, Dissing-Olesen L, Stevens B, Murthy VN. Microglial depletion disrupts normal functional development of adult-born neurons in the olfactory bulb. Elife. 2020 Mar 9;9:e50531. 

Yang, S. M., Michel, K., Jokhi, V., Nedivi, E., Arlotta, P. (2020). Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. Science 370. (6523):eabd2109. doi: 10.1126/science.abd2109. PMID: 33335032.

Yilmaz, M., Yalcin, E., Presumey, J., Aw, E., Ma, M., Whelan, C. W., Stevens, B., McCarroll, S. A., Carroll, M. C. (2021). Overexpression of schizophrenia susceptibility factor human complement C4A promotes excessive synaptic loss and behavioral changes in mice. Nature Neuroscience.  24(2), 214–224. print.

Zhou, Y., Sharma, J., Ke, Q., Landman, R., Yuan, J., Chen, H., Hayden, D., Fisher, J., Jiang, M., Menegas, W., et al. (2019). Atypical behavior and connectivity in SHANK3-mutant macaques. Nature 570, 326–331.

Zonouzi, M., Berger, D., Jokhi, V., Kedaigle, A., Lichtman, J., and Arlotta, P. (2019). Individual oligodendrocytes show bias for inhibitory axons in the neocortex. Cell Reports 27, 2799–2808.

Kamitaki, N., Sekar, A., Handsaker, R., de Rivera, H., Tooley, K., Morris, D., Taylor, K., Whelan, C., Tombleson, P., Olde Loohuis, L.;Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, M., Kimberly, R., Kaufman, K., Harley, J., Langefeld, C.,  Seidman, C., Pato, M., Pato, C., Ophoff, R.,  Graham, R.,  Criswell, L., Vyse, T., McCarroll, S. (2019). Complement component 4 genes contribute sex-specific vulnerability in diverse illnesses. bioRxiv 761718

Wallace, J., Lord, J., Dissing-Olesen, L., Stevens, B., and Murthy, V. (2019). Microglia are necessary for normal functional development of adult-born neurons in the olfactory bulb. bioRxiv 714337

Selected preprints:

Di Bella, D. J., Habibi, E., Yang, S.-M., Stickels, R. R., Brown, J., Yadollahpour, P., Chen, F., Macosko, E. Z., Regev, A., & Arlotta, P. (2020). Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex. bioRxiv 2020.07.02.185439

Mitchell, J. M., Nemesh, J., Ghosh, S., Handsaker, R. E., Mello, C. J., Meyer, D., Raghunathan, K., de Rivera, H., Tegtmeyer, M., Hawes, D., Neumann, A., Nehme, R., Eggan, K., & McCarroll, S. A. (2020). Mapping genetic effects on cellular phenotypes with “cell villages.” bioRxiv 2020.06.29.174383

Paulsen, B., Velasco, S., Kedaigle, A. J., Pigoni, M., Quadrato, G., Deo, A., Adiconis, X., Uzquiano, A., Kim, K., Simmons, S. K., Tsafou, K., Albanese, A., Sartore, R., Abbate, C., Tucewicz, A., Smith, S., Chung, K., Lage, K., Regev, A., … Arlotta, P. (2020). Human brain organoids reveal accelerated development of cortical neuron classes as a shared feature of autism risk genes. bioRxiv 2020.11.10.376509

Pintacuda, G., Lassen, F. H., Hsu, Y.-H. H., Kim, A., Martín, J. M., Malolepsza, E., Lim, J. K., Fornelos, N., Eggan, K. C., & Lage, K. (2020). Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data. bioRxiv 2020.05.04.076034

Clinical and Therapeutics

Draffin, J. E., Sánchez-Castillo, C., Fernández-Rodrigo, A., Sánchez-Sáez, X., Ávila, J., Wagner, F. F., Esteban, J. A. (2021). GSK3α, not GSK3β, drives hippocampal NMDAR-dependent LTD via tau-mediated spine anchoring. EMBO Journal. 40(2):e105513. 

Feseha, S., Timic Stamenic, T., Wallace, D., Tamag, C., Yang, L., Pan, J. Q., Todorovic, S. M. (2020). Global genetic deletion of CaV3.3 channels facilitates anaesthetic induction and enhances isoflurane-sparing effects of T-type calcium channel blockers. Scientific Reports.10(1):21510. 

Ghoshal, A., Uygun, D., Yang, L., McNally, J., Lopez-Huerta, V., Arias-Garcia, M., Baez-Nieto, D., Allen, A., Fitzgerald, M., Choi, S., et al. (2020). Effects of a patient-derived de novo coding alteration of CACNA1I in mice connect a schizophrenia risk gene with sleep spindle deficits. Translational Psychiatry 10:29.

Guo, S-M., Veneziano, R., Gordonov, S., Li, L., Danielson, E., Perez de Arce, K., Park, D., Kulesa, A., Wamhoff, E-C., Blainey, P., et al. (2019). Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes. Nature Communications 10, 4337.

Heyne, H. O., Baez-Nieto, D., Iqbal, S., Palmer, D. S., Brunklaus, A., May, P.; Epi25 Collaborative, Johannesen, K. M., Lauxmann, S., Lemke, J. R., Møller, R. S., Pérez-Palma, E., Scholl, U. I., Syrbe, S., Lerche, H., Lal, D., Campbell, A. J., Wang, H. R., Pan, J., Daly, M. J. (2020). Predicting functional effects of missense variants in voltage-gated sodium and calcium channels. Science Translational Medicine.

Hwang, H., Szucs, M. J., Ding, L. J., Allen, A., Ren, X., Haensgen, H., Gao, F., Rhim, H., Andrade, A., Pan, J. Q., Carr, S. A., Ahmad, R., & Xu, W. (2021). Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome. Biological psychiatry, 89(3), 256–269.

Iqbal, S., Pérez-Palma, E., Jespersen, J. B., May, P., Hoksza, D., Heyne, H. O., Ahmed, S. S., Rifat, Z. T., Rahman, M. S., Lage, K., Palotie, A., Cottrell, J. R., Wagner, F. F., Daly, M. J., Campbell, A. J., Lal, D. (2020) Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. Proceedings of the National Academy of Sciences of the United States of America. 117(45):28201-28211. 

Madison, J. M., Duong, K., Vieux, E. F., Udeshi, N. D., Iqbal, S., Requadt, E., Fereshetian, S., Lewis, M. C., Gomes, A. S., Pierce, K. A., Platt, R. J., Zhang, F., Campbell, A. J., Lal, D., Wagner, F. F., Clish, C. B., Carr, S. A., Sheng, M., Scolnick, E. M., Cottrell, J. R. (2020) Regulation of purine metabolism connects KCTD13 to a metabolic disorder with autistic features. iScience. 24(1):101935.

McCamphill, P.K., Stoppel, L.J., Senter, R.K., Lewis, M.C., Heynen, A.J., et al. (2020). Selective inhibition of glycogen synthase kinase 3α corrects pathophysiology in a mouse model of fragile X syndrome. Science Translational Medicine 12, 544.

Reidenbach, A. G., Mesleh, M. F., Casalena, D., Vallabh, S. M., Dahlin, J. L., Leed, A. J., Chan, A. I., Usanov, D. L., Yehl, J. B., Lemke, C. T., Campbell, A. J., Shah, R. N., Shrestha, O. K., Sacher, J. R., Rangel, V. L., Moroco, J. A., Sathappa, M., Nonato, M. C., Nguyen, K. T., Wright, S. K., Liu, D. R., Wagner, F. F., Kaushik, V. K., Auld, D. S., Schreiber, S. L., Minikel, E. V. (2020) Multimodal small-molecule screening for human prion protein binders. Journal of Biological Chemistry. 295(39):13516-13531.

Sorek, M., Oweis, W., Nissim-Rafinia, M., Maman, M., Simon, S., Hession, C. C., Adiconis, X., Simmons, S. K., Sanjana, N. E., Shi, X., Lu, C., Pan, J. Q., Xu, X., Pouladi, M. A., Ellerby, L. M., Zhang, F., Levin, J. Z., & Meshorer, E. (2021). Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity. Genome biology, 22(1), 73.