bioRxiv Channel: Simons Foundation Autism Research Initiative (SFARI) https://biorxiv.org This feed contains articles for bioRxiv Channel "Simons Foundation Autism Research Initiative (SFARI)" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population ]]> https://biorxiv.org/cgi/content/short/027771v1?rss=1" Elise B Robinson Beate St Pourcain Verneri Anttila Jack Kosmicki Brendan Bulik-Sullivan Jakob Grove Julian Maller Kaitlin E Samocha Stephan Sanders Stephan Ripke Joanna Martin Mads V Hollegaard Thomas Werge David M Hougaard Benjamin M Neale David Evans David Skuse Preben Bo Mortensen Anders Borglum Angelica Ronald George Davey Smith Mark J Daly 2015-09-29 doi:10.1101/027771 Cold Spring Harbor Laboratory Press 2015-09-29 <![CDATA[ Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families ]]> https://biorxiv.org/cgi/content/short/127043v1?rss=1" Werling, D. M. Brand, H. An, J.-Y. Stone, M. R. Glessner, J. T. Zhu, L. Collins, R. L. Dong, S. Layer, R. M. Markenscoff-Papadimitriou, E.-C. Farrell, A. Schwartz, G. B. Currall, B. B. Dea, J. Duhn, C. Erdman, C. Gilson, M. Handsaker, R. E. Kashin, S. Klei, L. Mandell, J. D. Nowakowski, T. J. Liu, Y. Pochareddy, S. Smith, L. Walker, M. F. Wang, H. Z. Waterman, M. J. He, X. Kriegstein, A. R. Rubenstein, J. L. Sestan, N. McCarroll, S. A. Neale, B. M. Coon, H. Willsey, A. J. Buxbaum, J. D. Daly, M. J. State, M. W. Quinlan, A. Marth, G. T. Roeder, K. Devli 2017-04-13 doi:10.1101/127043 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Homozygous loss of autism-risk gene CNTNAP2 results in reduced local and long-range prefrontal functional connectivity ]]> https://biorxiv.org/cgi/content/short/060335v1?rss=1" Adam Liska Ryszard Gomolka Mara Sabbioni Alberto Galbusera Stefano Panzeri Maria Luisa Scattoni Alessandro Gozzi 2016-06-29 doi:10.1101/060335 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Brainwide Mapping Of Endogenous Serotonergic Transmission Via Chemogenetic-fMRI ]]> https://biorxiv.org/cgi/content/short/122770v1?rss=1" Giorgi, A. Migliarini, S. Gritti, M. Galbusera, A. Maddaloni, G. De Luca, M. A. Tonini, R. Gozzi, A. Pasqualetti, M. 2017-04-03 doi:10.1101/122770 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Comprehensive Analysis of Two Shank3 and the Cacna1c Mouse Models of Autism Spectrum Disorder ]]> https://biorxiv.org/cgi/content/short/068866v1?rss=1" Patricia A Kabitzke Daniela Brunner Dansha He Pamela A Fazio Kimberly Cox Jane Sutphen Lucinda Thiede Emily Sabath Taleen Hanania Vadim Alexandrov Randall Rasmusson Will Spooren Anirvan Ghosh Pamela Feliciano Barbara Biemans Marta Benedetti Alice Luo Clayton 2016-09-02 doi:10.1101/068866 Cold Spring Harbor Laboratory Press 2016-09-02 <![CDATA[ Excessive ERK-dependent synaptic clustering with enhanced motor learning in the MECP2 duplication syndrome mouse model of autism ]]> https://biorxiv.org/cgi/content/short/100875v1?rss=1" Ash, R. T. Buffington, S. A. Park, J. Costa-Mattioli, M. Zoghbi, H. Y. Smirnakis, S. M. 2017-01-16 doi:10.1101/100875 Cold Spring Harbor Laboratory Press 2017-01-16 <![CDATA[ Frequency and complexity of de novo structural mutation in autism ]]> https://biorxiv.org/cgi/content/short/030270v1?rss=1" William M Brandler Danny Antaki Madhusudan Gujral Amina Noor Gabriel Rosanio Timothy R Chapman Daniel J Barrera Guan Ning Lin Dheeraj Malhotra Amanda C Watts Lawrence C Wong Jasper A Estabillo Therese E Gadomski Oanh Hong Karin V Fuentes Fajardo Abhishek Bhandari Renius Owen Michael Baughn Jeffrey Yuan Terry Solomon Alexandra G Moyzis Stephan J Sanders Gail E Reiner Keith K Vaux Charles M Strom Kang Zhang Alysson R Muotri Natacha Akshoomoff Suzanne M Leal Karen Pierce Eric Courchesne Lilia M Iakoucheva Christina Corsello Jonathan Sebat 2015-10-30 doi:10.1101/030270 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Paternally inherited noncoding structural variants contribute to autism ]]> https://biorxiv.org/cgi/content/short/102327v1?rss=1" Brandler, W. M. Antaki, D. Gujral, M. Kleiber, M. L. Maile, M. S. Hong, O. Chapman, T. R. Tan, S. Tandon, P. Pang, T. Tang, S. C. Vaux, K. K. Yang, Y. Harrington, E. Juul, S. Turner, D. J. Kingsmore, S. F. Gleeson, J. G. Kakaradov, B. Telenti, A. Venter, J. C. Corominas, R. Cormand, B. Rueda, I. Messer, K. S. Nievergelt, C. M. Arranz, M. J. Courchesne, E. Pierce, K. Muotri, A. R. Iakoucheva, L. M. Hervas, A. Corsello, C. Sebat, J. 2017-03-29 doi:10.1101/102327 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ Exonic somatic mutations contribute risk for autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/083428v1?rss=1" Krupp, D. R. Barnard, R. A. Duffourd, Y. Evans, S. Bernier, R. Riviere, J.-B. Fombonne, E. O'Roak, B. J. 2016-10-26 doi:10.1101/083428 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders ]]> https://biorxiv.org/cgi/content/short/089342v1?rss=1" Weiner, D. J. Wigdor, E. M. Ripke, S. Walters, R. K. Kosmicki, J. A. Grove, J. Samocha, K. E. Goldstein, J. Okbay, A. Bybjerg-Gauholm, J. Werge, T. Hougaard, D. M. Taylor, J. Skuse, D. Devlin, B. Anney, R. Sanders, S. Bishop, S. Bo Mortensen, P. Borglum, A. Davey Smith, G. Daly, M. J. Robinson, E. B. 2016-11-23 doi:10.1101/089342 Cold Spring Harbor Laboratory Press 2016-11-23 <![CDATA[ Contribution of de novo non-coding mutations to autism and identification of risk genes from whole-genome sequencing of affected families ]]> https://biorxiv.org/cgi/content/short/077578v1?rss=1" Yuwen Liu A. Ercument Cicek Yanyu Liang Jinchen Li Rebecca A Muhle Nicholas Knoblauch Martina Krenzer Yue Mei Yan Wang Yi Jiang Even Geller Zhongshan Li Iuliana Ionita-Laza Jinyu Wu Kun Xia James P Noonan Zhong Sheng Sun Xin He 2016-09-26 doi:10.1101/077578 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes ]]> https://biorxiv.org/cgi/content/short/058826v1?rss=1" Chaolin Zhang Yufeng Shen 2016-06-14 doi:10.1101/058826 Cold Spring Harbor Laboratory Press 2016-06-14 <![CDATA[ Exaggerated CpH Methylation in the Autism-Affected Brain ]]> https://biorxiv.org/cgi/content/short/069120v1?rss=1" Shannon E Ellis Simone Gupta Anna Moes Andrew B West Dan E Arking 2016-08-11 doi:10.1101/069120 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Transcriptome Analysis of Cortical Tissue Reveals Shared Sets of Down-Regulated Genes in Autism and Schizophrenia ]]> https://biorxiv.org/cgi/content/short/029132v1?rss=1" Shannon E Ellis Rebecca Panitch Andrew West Dan E Arking 2015-10-14 doi:10.1101/029132 Cold Spring Harbor Laboratory Press 2015-10-14 <![CDATA[ CNView: a visualization and annotation tool for copy number variation from whole-genome sequencing ]]> https://biorxiv.org/cgi/content/short/049536v1?rss=1" Ryan L Collins Matthew R Stone Harrison Brand Joseph T Glessner Michael E Talkowski 2016-04-20 doi:10.1101/049536 Cold Spring Harbor Laboratory Press 2016-04-20 <![CDATA[ High-risk Autism Spectrum Disorder Utah pedigrees: a novel Shared Genomic Segments analysis. ]]> https://biorxiv.org/cgi/content/short/134957v1?rss=1" Darlington, T. Bilder, D. Morgan, J. Jerominski, L. Rajamanickam, V. Sargent, R. Camp, N. J. Coon, H. H. 2017-05-09 doi:10.1101/134957 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Damaging Mutations are Associated with Diminished Motor Skills and IQ in Children on the Autism Spectrum ]]> https://biorxiv.org/cgi/content/short/141200v1?rss=1" Buja, A. Volfovsky, N. Krieger, A. Lord, C. Lash, A. Wigler, M. Iossifov, I. 2017-05-23 doi:10.1101/141200 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ De novo indels within introns contribute to ASD incidence ]]> https://biorxiv.org/cgi/content/short/137471v1?rss=1" Munoz, A. Yamrom, B. Lee, Y.-h. Andrews, P. Marks, S. Lin, K.-T. Wang, Z. Krainer, A. R. Darnell, R. B. Wigler, M. Iossifov, I. 2017-05-24 doi:10.1101/137471 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Native KCC2 Interactome Reveals PACSIN1 As A Critical Regulator Of Synaptic Inhibition ]]> https://biorxiv.org/cgi/content/short/142265v1?rss=1" Mahadevan, V. Khademullah, C. S. Dargaei, Z. Chevrier, J. Uvarov, P. Kwan, J. Bagshaw, R. D. Pawson, T. Emili, A. De Koninck, Y. Anggono, V. Airaksinen, M. Woodin, M. A. 2017-05-25 doi:10.1101/142265 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Distinctive Behavioural Anomalies, Structural Brain Phenotypes And Cortical Hyper-Connectivity In Chd8-Deficient Mice ]]> https://biorxiv.org/cgi/content/short/143552v1?rss=1" Suetterlin, P. Hurley, S. Mohan, C. Riegman, K. L. H. Caruso, A. Pagani, M. Ellegood, J. Galbusera, A. Crespo-Enriquez, I. Michetti, C. Ellingford, R. Brock, O. Delogu, A. Francis-West, P. Lerch, J. P. Scattoni, M. L. Gozzi, A. Fernandes, C. Basson, A. 2017-05-29 doi:10.1101/143552 Cold Spring Harbor Laboratory Press 2017-05-29 <![CDATA[ Indexcov: fast coverage quality control for whole-genome sequencing ]]> https://biorxiv.org/cgi/content/short/148296v1?rss=1" Pedersen, B. S. Collins, R. L. Talkwoski, M. E. Quinlan, A. R. 2017-06-09 doi:10.1101/148296 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Mutational sequencing for accurate count and long-range assembly ]]> https://biorxiv.org/cgi/content/short/149740v1?rss=1" Kumar, V. Rosenbaum, J. Wang, Z. Forcier, T. Ronemus, M. Wigler, M. Levy, D. 2017-06-13 doi:10.1101/149740 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Normal CA1 place fields but discoordinated network discharge in a Fmr1-null mouse model of fragile X syndrome ]]> https://biorxiv.org/cgi/content/short/152462v1?rss=1" Sparks, F. T. Talbot, Z. N. Dvorak, D. Curran, B. M. Alarcon, J. M. Fenton, A. A. 2017-06-20 doi:10.1101/152462 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Control of recollection by slow gamma dominating medium gamma in hippocampus CA1 ]]> https://biorxiv.org/cgi/content/short/152488v1?rss=1" Dvorak, D. Radwan, B. Sparks, F. T. Talbot, Z. N. Fenton, A. A. 2017-06-20 doi:10.1101/152488 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Distinct contributions of three GABAergic interneuron populations to a mouse model of Rett Syndrome. ]]> https://biorxiv.org/cgi/content/short/155382v1?rss=1" Mossner, J. Batista-Brito, R. Pant, R. Cardin, J. 2017-06-25 doi:10.1101/155382 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ An insula-central amygdala circuit for behavioral inhibition ]]> https://biorxiv.org/cgi/content/short/156216v1?rss=1" Schiff, H. C. Bouhuis, A. L. Yu, K. Penzo, M. A. Li, H. He, M. Li, B. 2017-06-26 doi:10.1101/156216 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium ]]> https://biorxiv.org/cgi/content/short/160499v1?rss=1" Sanders, S. J. Neale, B. M. Huang, H. Werling, D. M. An, J.-Y. Dong, S. - Whole Genome Sequencing for Psychiatric Disorders, Abecasis, G. Arguello, P. A. Blangero, J. Boehnke, M. Daly, M. Eggan, K. Geschwind, D. H. Glahn, D. Goldstein, D. B. Gur, R. E. Handsaker, R. E. McCarroll, S. A. Ophoff, R. A. Palotie, A. Pato, C. Sabatti, C. State, M. W. Willsey, A. J. Hyman, S. E. Addington, A. Lehner, T. Freimer, N. B. 2017-07-07 doi:10.1101/160499 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ Abnormal Speech Motor Control in Individuals with 16p11.2 Deletions ]]> https://biorxiv.org/cgi/content/short/165316v1?rss=1" 70%) in individuals with the 600 kb BP4-BP5 16p11.2 deletion; however, the mechanisms that drive these deficits are unclear, limiting our ability to target interventions and advance treatment. This study examined fundamental aspects of speech motor control in participants with the 16p11.2 deletion. To assess capacity for control of voice, we examined how accurately and quickly subjects changed the pitch of their voice within a trial to correct for a transient perturbation of the pitch of their auditory feedback. When compared to sibling controls, 16p11.2 deletion carriers show an over-exaggerated pitch compensation response to unpredictable mid-vocalization pitch perturbations. We also examined sensorimotor adaptation of speech by assessing how subjects learned to adapt their sustained productions of formants (speech spectral peak frequencies important for vowel identity), in response to consistent changes in their auditory feedback during vowel production. Deletion carriers show reduced sensorimotor adaptation to sustained vowel identity changes in auditory feedback. These results together suggest that 16p11.2 deletion carriers have fundamental impairments in the basic mechanisms of speech motor control and these impairments may partially explain the deficits in speech and language in these individuals. ]]> Demopoulos, C. Kothare, H. Mizuiri, D. Henderson-Sabes, J. Fregeau, B. Tjernagel, J. Houde, J. Sherr, E. Nagarajan, S. S. 2017-07-18 doi:10.1101/165316 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Increased axonal bouton stability during learning in the mouse model of MECP2 duplication syndrome ]]> https://biorxiv.org/cgi/content/short/186239v1?rss=1" Ash, R. T. Fahey, P. G. Park, J. Zoghbi, H. Y. Smirnakis, S. M. 2017-09-08 doi:10.1101/186239 Cold Spring Harbor Laboratory Press 2017-09-08 <![CDATA[ Genetic analysis of very obese children with autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/185900v1?rss=1" Cortes, H. D. Wevrick, R. 2017-09-12 doi:10.1101/185900 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Inhibitory neuron diversity originates from cardinal classes shared across germinal zones. ]]> https://biorxiv.org/cgi/content/short/105312v1?rss=1" Mayer, C. Hafemeister, C. Bandler, R. C. Machold, R. Fishell, G. Satija, R. 2017-02-02 doi:10.1101/105312 Cold Spring Harbor Laboratory Press 2017-02-02 <![CDATA[ TiSAn: Tissue Specific Variant Annotation ]]> https://biorxiv.org/cgi/content/short/141408v1?rss=1" Vervier, K. Michaelson, J. J. 2017-05-24 doi:10.1101/141408 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ De novo damaging coding mutations are strongly associated with obsessive-compulsive disorder and overlap with autism ]]> https://biorxiv.org/cgi/content/short/127712v1?rss=1" Cappi, C. Oliphant, M. E. Peter, Z. Zai, G. Sullivan, C. A. Gupta, A. R. Hoffman, E. J. Virdee, M. Willsey, A. J. Shavitt, R. G. Miguel, E. C. Kennedy, J. L. Richter, M. A. Fernandez, T. V. 2017-09-21 doi:10.1101/127712 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Paternal-age-related de novo mutations and risk for five disorders ]]> https://biorxiv.org/cgi/content/short/192740v1?rss=1" Taylor, J. Debost, J.-C. P. G. Morton, S. U. Wigdor, E. M. Heyne, H. O. Lal, D. Howrigan, D. P. Bloemendal, A. Larsen, J. T. Kosmicki, J. A. Weiner, D. J. Pediatric Cardiac Genomics Consortium, Homsy, J. Seidman, J. G. Seidman, C. E. Agerbo, E. McGrath, J. J. Mortensen, P. B. Petersen, L. Daly, M. J. Robinson, E. B. 2017-09-22 doi:10.1101/192740 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Quantification of autism recurrence risk by direct assessment of paternal sperm mosaicism ]]> https://biorxiv.org/cgi/content/short/208165v1?rss=1" 90x) whole genome sequencing of four paternal sperm samples, which detected 12/355 transmitted de novo single nucleotide variants that were mosaic above 2% AF, and more than two dozen additional, non-transmitted mosaic variants in paternal sperm. Our results demonstrate that germline mosaicism is an underestimated phenomenon, which has important implications for clinical practice and in understanding the basis of human disease. Genetic analysis of sperm can assess individualized recurrence risk following the birth of a child with a de novo disease, as well as the risk in any male planning to have children. ]]> Breuss, M. Kleiber, M. George, R. D. Antaki, D. James, K. N. Ball, L. L. Hong, O. Garcia, C. A. B. Musaev, D. Nguyen, A. McEvoy-Venneri, J. Knox, R. Sticca, E. Devinsky, O. Gymrek, M. Sebat, J. Gleeson, J. G. 2017-10-24 doi:10.1101/208165 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Single-cell transcriptomic catalog of mouse cortical development ]]> https://biorxiv.org/cgi/content/short/208744v1?rss=1" Loo, L. Simon, J. M. McCoy, E. S. Niehaus, J. K. Zylka, M. J. 2017-10-25 doi:10.1101/208744 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Prediction and interpretation of deleterious coding variants in terms of protein structural stability ]]> https://biorxiv.org/cgi/content/short/210120v1?rss=1" Ancien, F. Pucci, F. Godfroid, M. Rooman, M. 2017-10-27 doi:10.1101/210120 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Impaired perceptual learning in Fragile X syndrome is mediated by parvalbumin neuron dysfunction in V1 and is reversible. ]]> https://biorxiv.org/cgi/content/short/217414v1?rss=1" Goel, A. Cantu, D. Guilfoyle, J. Chaudhari, G. R. Newadkar, A. Todisco, B. Alba, D. d. Kourdougli, N. Schmitt, L. M. Pedapati, E. Erickson, C. A. Portera-Cailliau, C. 2017-11-13 doi:10.1101/217414 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Structural disruption of genomic regions containing ultraconserved elements is associated with neurodevelopmental phenotypes ]]> https://biorxiv.org/cgi/content/short/233197v1?rss=1" McCole, R. B. Saylor, W. Redin, C. Fonseka, C. Y. Brand, H. Erceg, J. Talkowski, M. E. Wu, C.- t. 2017-12-13 doi:10.1101/233197 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Neuron-specific cTag-CLIP reveals cell-specific diversity of functional RNA regulation in the brain ]]> https://biorxiv.org/cgi/content/short/244905v1?rss=1" Saito, Y. Yuan, Y. Zucker-Scharff, I. Fak, J. J. Tajima, Y. Licatalosi, D. D. Darnell, R. B. 2018-01-08 doi:10.1101/244905 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ A master regulatory network restoring brain glutamate homeostasis is coordinately activated in stroke ]]> https://biorxiv.org/cgi/content/short/245928v1?rss=1" Kobayashi, M. Anderson, C. Benakis, C. Moore, M. J. Mele, A. Fak, J. J. Park, C. Y. Zhou, P. Anrather, J. Iadecola, C. Darnell, R. B. 2018-01-10 doi:10.1101/245928 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors ]]> https://biorxiv.org/cgi/content/short/209478v1?rss=1" Manheimer, K. B. Patel, N. Richter, F. Gorham, J. Tai, A. C. Homsy, J. Boskovski, M. T. Parfenov, M. Goldmuntz, E. Chung, W. K. Brueckner, M. Tristani-Firouzi, M. Srivastava, D. Seidman, J. G. Seidman, C. E. Gelb, B. D. Sharp, A. J. 2017-10-26 doi:10.1101/209478 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Two-Photon Imaging of Striatum Demonstrates Distinct Functions for Striosomes and Matrix in Reinforcement Learning ]]> https://biorxiv.org/cgi/content/short/199497v1?rss=1" Bloem, B. Huda, R. Sur, M. Graybiel, A. M. 2017-11-24 doi:10.1101/199497 Cold Spring Harbor Laboratory Press 2017-11-24 <![CDATA[ Elevated polygenic burden for autism is associated with differential DNA methylation at birth. ]]> https://biorxiv.org/cgi/content/short/225193v1?rss=1" Hannon, E. Schendel, D. Ladd-Acosta, C. Grove, J. iPSYCH-Broad ASD Group, Hansen, C. S. Andrews, S. V. Hougaard, D. Bresnahan, M. Mors, O. Hollegaard, M. V. Baekvad-Hansen, M. Hornig, M. Mortensen, P. B. Borglum, A. Werge, T. Pedersen, M. G. Nordentoft, M. Buxbaum, J. Fallin, D. Bybjerg-Grauholm, J. Reichenberg, A. Mill, J. 2017-11-26 doi:10.1101/225193 Cold Spring Harbor Laboratory Press 2017-11-26 <![CDATA[ Precise temporal regulation of alternative splicing during neural development ]]> https://biorxiv.org/cgi/content/short/247601v1?rss=1" Weyn-Vanhentenryck, S. M. Feng, H. Ustianenko, D. Duffie, R. Yan, Q. Jacko, M. Martinez, J. C. Goodwin, M. Zhang, X. Hengst, U. Lomvardas, S. Swanson, M. S. Zhang, C. 2018-01-14 doi:10.1101/247601 Cold Spring Harbor Laboratory Press 2018-01-14 <![CDATA[ Spatio-Temporal Gene Discovery For Autism Spectrum Disorder ]]> https://biorxiv.org/cgi/content/short/256693v1?rss=1" Norman, U. Cicek, A. E. 2018-01-30 doi:10.1101/256693 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Nucleosome turnover is sufficient to establish varied histone methylation states ]]> https://biorxiv.org/cgi/content/short/256321v1?rss=1" Chory, E. J. Calarco, J. P. Hathaway, N. A. Bell, O. Neel, D. Crabtree, G. R. 2018-01-31 doi:10.1101/256321 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders ]]> https://biorxiv.org/cgi/content/short/257758v1?rss=1" Pizzo, L. Jensen, M. Polyak, A. Rosenfeld, J. A. Mannik, K. Krishnan, A. McCready, E. Pichon, O. Le Caignec, C. Van Dijck, A. Pope, K. Voorhoeve, E. Yoon, J. Stankiewicz, P. Cheung, S. W. Pazuchanics, D. Huber, E. Kumar, V. Kember, R. Mari, F. Curro, A. Castiglia, L. Galesi, O. Avola, E. Mattina, T. Fichera, M. Mandara, L. Vincent, M. Nizon, M. Mercier, S. Beneteau, C. Blesson, S. Martin-Coignard, D. Mosca-Boidron, A.-L. Caberg, J. H. Bucan, M. Zeesman, S. Nowaczyk, M. J. M. Lefebvre, M. Faivre, L. Callier, P. Skinner, C. Keren, B. Perrine, C. Pronte 2018-02-01 doi:10.1101/257758 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ MVP: predicting pathogenicity of missense variants by deep neural networks ]]> https://biorxiv.org/cgi/content/short/259390v1?rss=1" Qi, H. Chen, C. Zhang, H. Long, J. J. Chung, W. K. Guan, Y. Shen, Y. 2018-02-02 doi:10.1101/259390 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Common risk variants identified in autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/224774v1?rss=1" Grove, J. Ripke, S. Als, T. D. Mattheisen, M. Walters, R. Won, H. Pallesen, J. Agerbo, E. Andreassen, O. A. Anney, R. Belliveau, R. Bettella, F. Buxbaum, J. D. Bybjerg-Grauholm, J. Baekved-Hansen, M. Cerrato, F. Chambert, K. Christensen, J. H. Churchhouse, C. Dellenvall, K. Demontis, D. De Rubeis, S. Devlin, B. Djurovic, S. Dumont, A. Goldstein, J. Hansen, C. S. Hauberg, M. E. Hollegaard, M. V. Hope, S. Howrigan, D. P. Huang, H. Hultman, C. Klei, L. Maller, J. Martin, J. Martin, A. R. Moran, J. Nyegaard, M. Naerland, T. Palmer, D. S. Palotie, A. Peders 2017-11-25 doi:10.1101/224774 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ Simple genetic models for autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/017301v1?rss=1" Swagatam Mukhopadhyay Michael Wigler Dan Levy 2015-03-30 doi:10.1101/017301 Cold Spring Harbor Laboratory Press 2015-03-30 <![CDATA[ Maturation Trajectories of Cortical Resting-State Networks Depend on the Mediating Frequency Band ]]> https://biorxiv.org/cgi/content/short/264416v1?rss=1" Khan, S. Hashmi, J. Mamashli, F. Michmizos, K. Kitzbichler, M. Bharadwaj, H. Bekhti, Y. Ganesan, S. Garel, K. A. Whitfield-Gabrieli, S. Gollub, R. Kong, J. Vaina, L. M. Rana, K. Stufflebeam, S. Hamalainen, M. Kenet, T. 2018-02-13 doi:10.1101/264416 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ ASD and ADHD have a similar burden of rare protein-truncating variants ]]> https://biorxiv.org/cgi/content/short/277707v1?rss=1" Satterstrom, F. K. Walters, R. K. Singh, T. Wigdor, E. M. Lescai, F. Demontis, D. Kosmicki, J. A. Grove, J. Stevens, C. Bybjerg-Grauholm, J. Baekvad-Hansen, M. Palmer, D. S. Maller, J. B. iPSYCH-Broad Consortium, Nordentoft, M. Mors, O. Robinson, E. B. Hougaard, D. M. Werge, T. M. Bo Mortensen, P. Neale, B. M. Borglum, A. D. Daly, M. J. 2018-03-06 doi:10.1101/277707 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ A reference haplotype panel for genome-wide imputation of short tandem repeats ]]> https://biorxiv.org/cgi/content/short/277673v1?rss=1" Saini, S. Mitra, I. Gymrek, M. 2018-03-06 doi:10.1101/277673 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Disentangling genetic overlap between Attention-Deficit/Hyperactivity Disorder, literacy and language ]]> https://biorxiv.org/cgi/content/short/276527v1?rss=1" Verhoef, E. Demontis, D. Burgess, S. Shapland, C. Y. Dale, P. S. Okbay, A. Neale, B. M. Faraone, S. V. iPSYCH-Broad-PGC ADHD Consortium, Stergiakouli, E. Davey Smith, G. Fisher, S. E. Borglum, A. St Pourcain, B. 2018-03-05 doi:10.1101/276527 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Intellectual phenotypes in autism strongly correlate with gene dosage changes and exon locations of truncating mutations ]]> https://biorxiv.org/cgi/content/short/270850v1?rss=1" Chiang, A. H. Chang, J. Vitkup, D. 2018-04-17 doi:10.1101/270850 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Rbfox1 mediates cell-type-specific splicing in cortical interneurons ]]> https://biorxiv.org/cgi/content/short/305904v1?rss=1" Jaglin, X. H. Wamsley, B. Favuzzi, E. Quattracolo, G. Negro, M. Yusef, N. Khodadadi-Jamayran, A. Rudy, B. Fishell, G. 2018-04-21 doi:10.1101/305904 Cold Spring Harbor Laboratory Press 2018-04-21 <![CDATA[ Increased excitation-inhibition ratio stabilizes synapse and circuit excitability in four autism mouse models. ]]> https://biorxiv.org/cgi/content/short/317693v1?rss=1" Antoine, M. W. Schnepel, P. Langberg, T. Feldman, D. E. 2018-05-09 doi:10.1101/317693 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knock-Out Mice ]]> https://biorxiv.org/cgi/content/short/319368v1?rss=1" Das Sharma, S. Metz, J. B. Li, H. Hobson, B. D. Hornstein, N. Sulzer, D. Tang, G. Sims, P. A. 2018-05-10 doi:10.1101/319368 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Whole-genome deep learning analysis reveals causal role of noncoding mutations in autism ]]> https://biorxiv.org/cgi/content/short/319681v1?rss=1" Zhou, J. Park, C. Theesfeld, C. Yuan, Y. Sawicka, K. Darnell, J. Scheckel, C. Fak, J. Tajima, Y. Darnell, R. Troyanskaya, O. 2018-05-11 doi:10.1101/319681 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Dynamics of social representation in the mouse prefrontal cortex ]]> https://biorxiv.org/cgi/content/short/321182v1?rss=1" Levy, D. R. Tamir, T. Kaufman, M. Weissbrod, A. Schneidman, E. Yizhar, O. 2018-05-14 doi:10.1101/321182 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Nested oscillatory dynamics in cortical organoids model early human brain network development ]]> https://biorxiv.org/cgi/content/short/358622v1?rss=1" Trujillo, C. A. Gao, R. Negraes, P. D. Chaim, I. A. Domissy, A. Vandenberghe, M. Devor, A. Yeo, G. W. Voytek, B. Muotri, A. R. 2018-06-29 doi:10.1101/358622 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ The autism-associated gene Scn2a plays an essential role in synaptic stability and learning ]]> https://biorxiv.org/cgi/content/short/366781v1?rss=1" Spratt, P. Ben-Shalom, R. Keeshen, C. Burke, K. Clarkson, R. Sanders, S. Bender, K. 2018-07-10 doi:10.1101/366781 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Bidirectional control of orienting behavior by distinct prefrontal circuits ]]> https://biorxiv.org/cgi/content/short/307009v1?rss=1" Huda, R. Sipe, G. O. Adam, E. Breton-Provencher, V. Pho, G. Gunter, L. Wickersham, I. R. Sur, M. 2018-04-25 doi:10.1101/307009 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Autism-associated Shank3 is essential for homeostatic plasticity and neuronal circuit stability ]]> https://biorxiv.org/cgi/content/short/365445v1?rss=1" Tatavarty, V. Torrado Pacheco, A. Lin, H. Miska, N. J. Hengen, K. B. Wagner, F. F. Turrigiano, G. G. 2018-07-09 doi:10.1101/365445 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice ]]> https://biorxiv.org/cgi/content/short/260083v1?rss=1" Tong, D. Chen, R. Lu, Y. Li, W. Zhang, Y. Lin, J. He, L. Dang, T. Shan, S. Xu, X. Zhang, Y. Zhang, C. Du, Y. Zhou, W.-H. Wang, X. Qiu, Z. 2018-02-05 doi:10.1101/260083 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo ]]> https://biorxiv.org/cgi/content/short/401604v1?rss=1" Rieger, M. A. King, D. M. Cohen, B. A. Dougherty, J. D. 2018-08-27 doi:10.1101/401604 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Integrative cross-species analyses identify deficits in habituation learning as a widely affected mechanism in Autism ]]> https://biorxiv.org/cgi/content/short/285981v1?rss=1" Fenckova, M. Asztalos, L. Cizek, P. Singgih, E. L. Blok, L. E. R. Glennon, J. C. IntHout, J. Zweier, C. Eichler, E. E. Bernier, R. Asztalos, Z. Schenck, A. 2018-03-20 doi:10.1101/285981 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ Altered dendritic spine function and integration in a mouse model of Fragile X Syndrome ]]> https://biorxiv.org/cgi/content/short/396986v1?rss=1" Booker, S. A. Domanski, A. P. Dando, O. R. Jackson, A. D. Isaac, J. T. Hardingham, G. E. Wyllie, D. J. Kind, P. C. 2018-08-21 doi:10.1101/396986 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Using multiple measurements of tissue to estimate individual- and cell-type-specific gene expression via deconvolution ]]> https://biorxiv.org/cgi/content/short/379099v1?rss=1" Wang, J. Devlin, B. Roeder, K. 2018-07-27 doi:10.1101/379099 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Whole genome sequencing in multiplex families reveals novel inherited and de novo genetic risk in autism ]]> https://biorxiv.org/cgi/content/short/338855v1?rss=1" Ruzzo, E. K. Perez-Cano, L. Jung, J.-Y. Wang, L.-k. Kashef-Haghighi, D. Hartl, C. Hoekstra, J. Leventhal, O. Gandal, M. J. Paskov, K. Stockham, N. Polioudakis, D. Lowe, J. K. Geschwind, D. H. Wall, D. P. 2018-06-06 doi:10.1101/338855 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/cgi/content/short/484113v1?rss=1" Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. 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. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Deletion of autism risk gene Shank3 disrupts prefrontal connectivity ]]> https://biorxiv.org/cgi/content/short/409284v1?rss=1" Pagani, M. Bertero, A. Liska, A. Galbusera, A. Sabbioni, M. Scattoni, M. L. Pasqualetti, M. Gozzi, A. 2018-09-06 doi:10.1101/409284 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Non-monotonic regulation of gene expression, neural progenitor fate and brain growth by the chromatin remodeller CHD8 ]]> https://biorxiv.org/cgi/content/short/469031v1?rss=1" Hurley, S. Mohan, C. Suetterlin, P. Ellegood, J. Rudari, F. Lerch, J. P. Fernandes, C. Basson, M. A. 2018-11-12 doi:10.1101/469031 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ A machine-learning approach for accurate detection of copy-number variants from exome sequencing ]]> https://biorxiv.org/cgi/content/short/460931v1?rss=1" Kumar, V. Jensen, M. Jayakar, G. Kelkar, N. Girirajan, S. 2018-11-02 doi:10.1101/460931 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ An interaction-based model for neuropsychiatric features of copy-number variants ]]> https://biorxiv.org/cgi/content/short/459958v1?rss=1" Jensen, M. Girirajan, S. 2018-11-02 doi:10.1101/459958 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ Calculating the Effects of Autism Risk Gene Variants on Dysfunction of Biological Processes Identifies Clinically-Useful Information ]]> https://biorxiv.org/cgi/content/short/449819v1?rss=1" Veatch, O. J. Mazzotti, D. R. Sutcliffe, J. S. Schultz, R. T. Abel, T. Tunc, B. Assouline, S. G. Brodkin, E. S. Michaelson, J. J. Nickl-Jockschat, T. Warren, Z. E. Malow, B. A. Pack, A. I. 2018-10-22 doi:10.1101/449819 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ Forecasting autism gene discovery with machine learning and genome-scale data ]]> https://biorxiv.org/cgi/content/short/370601v1?rss=1" Brueggeman, L. Koomar, T. Michaelson, J. 2018-07-16 doi:10.1101/370601 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Reduced frontal gamma power at 24 months is associated with better expressive language in toddlers at risk for autism ]]> https://biorxiv.org/cgi/content/short/430421v1?rss=1" Wilkinson, C. L. Levin, A. R. Gabard-Durnam, L. J. Tager-Flusberg, H. Nelson, C. A. 2018-09-29 doi:10.1101/430421 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution ]]> https://biorxiv.org/cgi/content/short/500934v1?rss=1" Pollen, A. A. Bhaduri, A. Andrews, M. G. Nowakowski, T. J. Meyerson, O. S. Mostajo-Radji, M. A. Di Lullo, E. Alvarado, B. Bedolli, M. Dougherty, M. L. Fiddes, I. T. Kronenberg, Z. N. Shuga, J. Leyrat, A. A. West, J. A. Bershteyn, M. Lowe, C. B. Pavolvic, B. J. Salama, S. R. Haussler, D. Eichler, E. Kriegstein, A. A. 2018-12-19 doi:10.1101/500934 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Exome sequencing of 457 autism families recruited online provides evidence for novel ASD genes ]]> https://biorxiv.org/cgi/content/short/516625v1?rss=1" Feliciano, P. Zhou, X. Astrovskaya, I. Turner, T. Wang, T. Brueggeman, L. Barnard, R. Hsieh, A. Snyder, L. G. Muzny, D. Sabo, A. The SPARK Consortium, Gibbs, R. Eichler, E. O'Roak, B. Michaelson, J. Volfovsky, N. Shen, Y. Chung, W. 2019-01-09 doi:10.1101/516625 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Both rare and common genetic variants contribute to autism in the Faroe Islands ]]> https://biorxiv.org/cgi/content/short/363853v1?rss=1" Leblond, C. Cliquet, F. Carton, C. Huguet, G. Mathieu, A. Kergrohen, T. Buratti, J. Lemiere, N. Cuisset, L. Bienvenu, T. Boland, A. Deleuze, J.-F. Stora, T. Biskupstoe, R. Halling, J. Andorsdottir, G. Billstedt, E. Gillberg, C. Bourgeron, T. 2018-07-06 doi:10.1101/363853 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ mTOR suppresses macroautophagy during postnatal development of the striatum. ]]> https://biorxiv.org/cgi/content/short/536680v1?rss=1" Lieberman, O. Pigulevskiy, I. Post, M. Sulzer, D. Santini, E. 2019-01-31 doi:10.1101/536680 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Enhanced population coding for rewarded choices in the medial frontal cortex of the mouse ]]> https://biorxiv.org/cgi/content/short/429852v1?rss=1" Siniscalchi, M. J. Wang, H. Kwan, A. C. 2018-09-28 doi:10.1101/429852 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ Oligogenic effects of 16p11.2 copy number variation on craniofacial development ]]> https://biorxiv.org/cgi/content/short/540732v1?rss=1" Qiu, Y. Arbogast, T. Martin Lorenzo, S. Li, H. Shih, T. Ellen, R. Hong, O. Cho, S. Shanta, O. Timothy, P. Corsello, C. Deutsch, C. K. Chevalier, C. Davis, E. E. Iakoucheva, L. M. Herault, Y. Katasanis, N. Messer, K. Sebat, J. 2019-02-05 doi:10.1101/540732 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Shared polygenetic variation between ASD and ADHD exerts opposite association patterns with educational attainment ]]> https://biorxiv.org/cgi/content/short/580365v1?rss=1" Verhoef, E. Grove, J. Shapland, C. Y. Demontis, D. Burgess, S. Rai, D. Borglum, A. D. St Pourcain, B. 2019-03-17 doi:10.1101/580365 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ Robust and replicable measurement for prepulse inhibition of the acoustic startle response ]]> https://biorxiv.org/cgi/content/short/601500v1?rss=1" Miller, E. A. Kastner, D. B. Grzybowski, M. N. Dwinell, M. R. Geurts, A. M. Frank, L. M. 2019-04-07 doi:10.1101/601500 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Impaired KCC2 phosphorylation leads to neuronal network dysfunction and neurodevelopmental pathogenesis. ]]> https://biorxiv.org/cgi/content/short/606566v1?rss=1" Pisella, L. Gaiarsa, J.-L. Diabira, D. Zhang, J. Khalilov, I. Duan, J. Kahle, K. Medyna, I. 2019-04-12 doi:10.1101/606566 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Single-cell analysis of Foxp1-driven mechanisms essential for striatal development ]]> https://biorxiv.org/cgi/content/short/611780v1?rss=1" Anderson, A. G. Kulkarni, A. Harper, M. Konopka, G. 2019-04-18 doi:10.1101/611780 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Cortical Foxp2 supports behavioral flexibility and developmental dopamine D1 receptor expression ]]> https://biorxiv.org/cgi/content/short/624973v1?rss=1" Co, M. Hickey, S. L. Kulkarni, A. Harper, M. Konopka, G. 2019-05-02 doi:10.1101/624973 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Psychotic symptoms in 16p11.2 copy number variant carriers ]]> https://biorxiv.org/cgi/content/short/621250v1?rss=1" Jutla, A. Turner, J. B. Green Snyder, L. Chung, W. K. Veenstra-VanderWeele, J. 2019-05-05 doi:10.1101/621250 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Maternal experience-dependent cortical plasticity in mice is circuit- and stimulus-specific and requires Mecp2 ]]> https://biorxiv.org/cgi/content/short/655035v1?rss=1" Lau, B. Y. B. Krishnan, K. Huang, Z. J. Shea, S. D. 2019-05-30 doi:10.1101/655035 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Mutually exclusive autism mutations point to the circadian clock and PI3K signaling pathways ]]> https://biorxiv.org/cgi/content/short/653527v1?rss=1" Manning, H. O'Roak, B. J. Babur, O. 2019-05-30 doi:10.1101/653527 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Diminished cortical excitation during perceptual impairments in a mouse model of autism ]]> https://biorxiv.org/cgi/content/short/657189v1?rss=1" Del Rosario, J. Speed, A. Arrowood, H. Motz, C. Pardue, M. Haider, B. 2019-06-03 doi:10.1101/657189 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Ketamine disinhibits dendrites and enhances calcium signals in prefrontal dendritic spines ]]> https://biorxiv.org/cgi/content/short/659292v1?rss=1" Ali, F. Gerhard, D. M. Sweasy, K. Pothula, S. Pittenger, C. Duman, R. S. Kwan, A. C. 2019-06-03 doi:10.1101/659292 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Predicting Functional Effects of Missense Variants in Voltage-Gated Sodium and Calcium Channels ]]> https://biorxiv.org/cgi/content/short/671453v1?rss=1" 100.000 cases and controls. Ultimately, functional prediction of missense variants in clinically relevant genes will facilitate precision medicine in clinical practice. ]]> Heyne, H. Palmer, D. Iqbal, S. Baez-Nieto, D. Brunklaus, A. the Epi25 Collaborative, Johannesen, K. Lauxmann, S. Lemke, J. Moller, R. Perez-Palma, E. Scholl, U. Syrbe, S. Lerche, H. May, P. Lal, D. Campbell, A. Pan, J. Wang, H.-R. Daly, M. 2019-06-14 doi:10.1101/671453 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ The human-specific BOLA2 duplication modifies iron homeostasis and anemia predisposition in chromosome 16p11.2 autism patients ]]> https://biorxiv.org/cgi/content/short/693952v1?rss=1" Giannuzzi, G. Schmidt, P. J. Porcu, E. Willemin, G. Munson, K. M. Nuttle, X. Earl, R. Chrast, J. Hoekzema, K. Risso, D. Mannik, K. De Nittis, P. Baratz, E. D. 16p11.2 Consortium, Herault, Y. Gao, X. Philpott, C. C. Bernier, R. A. Kutalik, Z. Fleming, M. D. Eichler, E. E. Reymond, A. 2019-07-05 doi:10.1101/693952 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Variants in the degron of AFF3 cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy ]]> https://biorxiv.org/cgi/content/short/693937v1?rss=1" Voisin, N. Schnur, R. E. Douzgou, S. Hiatt, S. M. Rustad, C. F. Brown, N. J. Earl, D. L. Keren, B. Levchenko, O. Geuer, S. Amor, D. Brusco, A. Bebin, E. M. Cappuccio, G. Charrow, J. Chatron, N. Cooper, G. M. Dadali, E. Delafontaine, J. Del Giudice, E. Douglas, G. Funari, T. Giannuzzi, G. Guex, N. Heron, D. Holla, O. L. Hurst, A. C. E. Juusola, J. Kronn, D. Lavrov, A. Lee, C. Merckoll, E. Mikhaleva, A. Norman, J. Pradervand, S. Sanders, V. Sirchia, F. Takenouchi, T. Tanaka, A. J. Taska-Tench, H. Tonne, E. Tveten, K. Vitiello, G. Uehara, T. Nava, C. Y 2019-07-17 doi:10.1101/693937 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Systemizing is genetically correlated with autism and is genetically distinct from social autistic traits ]]> https://biorxiv.org/cgi/content/short/228254v1?rss=1" Warrier, V. Toro, R. Chakrabarti, B. iPSYCH-Broad Autism Group, Borglum, A. Grove, J. the 23andMe Research Team, Hinds, D. Bourgeron, T. Baron-Cohen, S. 2017-12-03 doi:10.1101/228254 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Reduced sleep pressure in young children with autism ]]> https://biorxiv.org/cgi/content/short/706135v1?rss=1" Arazi, A. Meiri, G. Danan, D. Michaelovski, A. Flusser, H. Menashe, I. Tarasiuk, A. Dinstein, I. 2019-07-22 doi:10.1101/706135 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Systematic phenomics analysis of ASD-associated genes reveals shared functions and parallel networks underlying reversible impairments in habituation learning ]]> https://biorxiv.org/cgi/content/short/687194v1?rss=1" McDiarmid, T. A. Belmadani, M. Liang, j. Meili, F. Mathews, E. A. Mullen, G. P. Rand, J. B. Mizumoto, K. Haas, K. Pavlidis, P. Rankin, C. H. 2019-06-30 doi:10.1101/687194 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ Gene discoveries in autism are biased towards comorbidity with intellectual disability ]]> https://biorxiv.org/cgi/content/short/715755v1?rss=1" 100) had lower frequencies of CNVs (p=0.065) and LGD variants (p=0.021) compared with individuals who manifested both autism and ID (IQ<70). These data indicated that de novo LGD variants conferred a 1.53-fold higher risk (p=0.035) towards comorbid ID, while LGD mutations specifically disrupting autism-associated genes conferred a 4.85-fold increased risk (p=0.011) for comorbid ID. Furthermore, de novo LGD variants in individuals with high-functioning autism were more likely to disrupt genes with little functional relevance towards neurodevelopment, as demonstrated by evidence from pathogenicity metrics, expression patterns in the developing brain, and mouse model phenotypes. Overall, our data suggest that de novo pathogenic variants disrupting genes associated with autism contribute towards autism and ID comorbidity, while other genetic factors are likely to be causal for high-functioning autism. ]]> Jensen, M. Smolen, C. Girirajan, S. 2019-07-26 doi:10.1101/715755 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11.2 locus ]]> https://biorxiv.org/cgi/content/short/716415v1?rss=1" Männik, K. Arbogast, T. Lepamets, M. Lepik, K. Pellaz, A. Ademi, H. Kupchinsky, Z. A. Ellegood, J. Attanasio, C. Messina, A. Rotman, S. Martin-Brevet, S. Dubruc, E. Chrast, J. Lerch, J. P. Qiu, L. R. Laisk, T. The 16p11.2 European Consortium, The Simons VIP Consortium, The eQTLGen Consortium, Henkelman, M. R. Jacquemont, S. Herault, Y. Lindgren, C. M. Peterson, H. Stehle, J. C. Katsanis, N. Kutalik, Z. Nef, S. Draganski, B. Davis, E. E. Mägi, R. Reymond, A. 2019-07-26 doi:10.1101/716415 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Brain-wide visual habituation networks in wild type and fmr1 zebrafish ]]> https://biorxiv.org/cgi/content/short/722074v1?rss=1" Marquez-Legorreta, E. Constantin, L. Piber, M. Favre-Bulle, I. A. Taylor, M. Vanwalleghem, G. Scott, E. 2019-08-06 doi:10.1101/722074 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Altered brain-wide auditory networks in fmr1-mutant larval zebrafish ]]> https://biorxiv.org/cgi/content/short/722082v1?rss=1" Constantin, L. Poulsen, R. Favre-Bulle, I. A. Taylor, M. Sun, B. Goodhill, G. Vanwalleghem, G. Scott, E. 2019-08-05 doi:10.1101/722082 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify candidate risk genes and biological pathways ]]> https://biorxiv.org/cgi/content/short/730952v1?rss=1" Fernandez, T. V. Williams, Z. P. Kline, T. Rajendran, S. Augustine, F. Wright, N. Sullivan, C. A. W. Olfson, E. Abdallah, S. B. Liu, W. Hoffman, E. J. Gupta, A. R. Singer, H. S. 2019-08-13 doi:10.1101/730952 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Placental neurosteroids shape cerebellar development and social behaviour ]]> https://biorxiv.org/cgi/content/short/730150v1?rss=1" Vacher, C.-M. O'Reilly, J. J. Salzbank, J. Lacaille, H. Bakalar, D. Sebaoui-Illoul, S. Liere, P. Clarkson-Paredes, C. Sasaki, T. Sathyanesan, A. Imamura Kawasawa, Y. Popratiloff, A. Hashimoto-Torii, K. Gallo, V. Schumacher, M. Penn, A. A. 2019-08-13 doi:10.1101/730150 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Human cerebral organoids capture the spatiotemporal complexity and disease dynamics of UBE3A ]]> https://biorxiv.org/cgi/content/short/742213v1?rss=1" Sen, D. Voulgaropoulos, A. Drobna, Z. Keung, A. J. 2019-08-22 doi:10.1101/742213 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution ]]> https://biorxiv.org/cgi/content/short/744540v1?rss=1" LU, L. Liu, X. Huang, W.-K. Giusti-Rodriguez, P. Cui, J. Zhang, S. Xu, W. Wen, Z. Ma, S. Rosen, J. D. Xu, Z. Bartels, C. Riki Kawaguchi, R. Hu, M. Scacheri, P. Rong, Z. Li, Y. Sullivan, P. F. Song, H. Ming, G.-l. Li, Y. Jin, F. 2019-08-22 doi:10.1101/744540 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types ]]> https://biorxiv.org/cgi/content/short/762500v1?rss=1" Van Driesche, S. J. Sawicka, K. Zhang, C. Hung, S. K. Y. Park, C. Y. Fak, J. J. Yang, C. Darnell, R. B. Darnell, J. C. 2019-09-09 doi:10.1101/762500 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Deletion of a non-canonical promoter regulatory element causes loss of Scn1a expression and epileptic phenotypes in mice ]]> https://biorxiv.org/cgi/content/short/766634v1?rss=1" Haigh, J. L. Adhikari, A. Copping, N. A. Stradleigh, T. W. Wade, A. A. Catta-Preta, R. F. Su-Feher, L. Zdilar, I. Morse, S. J. Fenton, T. A. Nguyen, A. B. Quintero, D. M. Sramek, M. Carter, J. L. Gompers, A. Lambert, J. T. Canales, C. P. Pennacchio, L. Visel, A. Dickel, D. Silverman, J. L. Nord, A. S. 2019-09-12 doi:10.1101/766634 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ A sex difference in the composition of the rodent postsynaptic density ]]> https://biorxiv.org/cgi/content/short/802538v1?rss=1" Mastro, T. L. Preza, A. Basu, S. Chattarji, S. Till, S. M. Kind, P. C. Kennedy, M. B. 2019-10-12 doi:10.1101/802538 Cold Spring Harbor Laboratory Press 2019-10-12 <![CDATA[ Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction ]]> https://biorxiv.org/cgi/content/short/800011v1?rss=1" Post, K. L. Belmadani, M. Ganguly, P. Meili, F. Dingwall, R. McDiarmid, T. A. Meyers, W. M. Herrington, C. Young, B. P. Callaghan, D. B. Rogic, S. Edwards, M. Niciforovic, A. Cau, A. Rankin, C. OConnor, T. P. Bamji, S. X. Loewen, C. J. Allan, D. W. Pavlidis, P. Haas, K. 2019-10-10 doi:10.1101/800011 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Acute and repeated intranasal oxytocin differentially modulate brain-wide functional connectivity ]]> https://biorxiv.org/cgi/content/short/798025v1?rss=1" Pagani, M. De Felice, A. Montani, C. Galbusera, A. Papaleo, F. Gozzi, A. 2019-10-09 doi:10.1101/798025 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Genetic Rescue of Fragile X Syndrome Links FMRP Deficiency to Codon Optimality-Dependent RNA Destabilization ]]> https://biorxiv.org/cgi/content/short/801449v1?rss=1" Shu, H. R. Donnard, E. Liu, B. Richter, J. 2019-10-10 doi:10.1101/801449 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ An open resource of structural variation for medical and population genetics ]]> https://biorxiv.org/cgi/content/short/578674v1?rss=1" Collins, R. L. Brand, H. Karczewski, K. J. Zhao, X. Alflödi, J. Khera, A. V. Francioli, L. C. Gauthier, L. D. Wang, H. Watts, N. A. Solomonson, M. O'Donnell-Luria, A. Baumann, A. Munshi, R. Lowther, C. Walker, M. Whelan, C. Huang, Y. Brookings, T. Sharpe, T. Stone, M. R. Valkanas, E. Fu, J. Tiao, G. Laricchia, K. M. Stevens, C. Gupta, N. Margolin, L. The Genome Aggregation Database (gnomAD) Productio, The gnomAD Consortium, Spertus, J. A. Taylor, K. D. Lin, H. J. Rich, S. S. Post, W. Chen, Y.-D. I. Rotter, J. I. Nusbaum, C. Philippakis, A. Lander, E 2019-03-14 doi:10.1101/578674 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Dynamic preferences account for inter-animal variability during the continual learning of a cognitive task ]]> https://biorxiv.org/cgi/content/short/808006v1?rss=1" Kastner, D. B. Miller, E. A. Yang, Z. Roumis, D. K. Liu, D. F. Frank, L. M. Dayan, P. 2019-10-17 doi:10.1101/808006 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ MEF2C hypofunction in neuronal and neuroimmune populations cooperate to produce MEF2C haploinsufficiency syndrome-like behaviors in mice ]]> https://biorxiv.org/cgi/content/short/824151v1?rss=1" Harrington, A. J. Bridges, C. M. Blankenship, K. Assali, A. Berto, S. Siemsen, B. M. Moore, H. W. Cho, J. Y. Tsvetkov, E. Thielking, A. Konopka, G. Everman, D. B. Scofield, M. Skinner, S. A. Cowan, C. W. 2019-10-30 doi:10.1101/824151 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/835678v1?rss=1" Huang, K. Wu, Y. Shin, J. Zheng, Y. Fotuhi Siahpirani, A. Lin, Y. Ni, Z. Chen, J. You, J. Keles, S. Wang, D. Roy, S. Lu, Q. 2019-11-08 doi:10.1101/835678 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ G-Graph: An interactive genomic graph viewer ]]> https://biorxiv.org/cgi/content/short/803015v1?rss=1" Andrews, P. A. Alexander, J. Kendall, J. Wigler, M. 2019-11-18 doi:10.1101/803015 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Multiplexed single-cell autism modeling reveals convergent mechanisms altering neuronal differentiation ]]> https://biorxiv.org/cgi/content/short/862680v1?rss=1" Lalli, M. A. Avey, D. Dougherty, J. D. Milbrandt, J. Mitra, R. D. 2019-12-03 doi:10.1101/862680 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Massively parallel disruption of enhancers active during human corticogenesis ]]> https://biorxiv.org/cgi/content/short/852673v1?rss=1" Geller, E. Gockley, J. Emera, D. Uebbing, S. Cotney, J. Noonan, J. P. 2019-12-02 doi:10.1101/852673 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Neuropsychiatric mutations delineate functional brain connectivity dimensions contributing to autism and schizophrenia ]]> https://biorxiv.org/cgi/content/short/862615v1?rss=1" Moreau, C. Urchs, S. Orban, P. Schramm, C. Dumas, G. Labbe, A. Huguet, G. Douard, E. Quirion, P.-O. Lin, A. Kushan, L. Grot, S. Luck, D. Mendrek, A. Potvin, S. Stip, E. Bourgeron, T. Evans, A. C. SimonsVIP Consortium, Bearden, C. E. Bellec, P. Jacquemont, S. 2019-12-06 doi:10.1101/862615 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Increased variability but intact integration during visual navigation in Autism Spectrum Disorder ]]> https://biorxiv.org/cgi/content/short/2019.12.28.890004v1?rss=1" Noel, J.-P. Lakshminarasimhan, K. J. Park, H. Angelaki, D. 2019-12-28 doi:10.1101/2019.12.28.890004 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Regulation of Prefrontal Patterning, Connectivity and Synaptogenesis by Retinoic Acid ]]> https://biorxiv.org/cgi/content/short/2019.12.31.891036v1?rss=1" Shibata, M. Pattabiraman, K. Lorente-Galdos, B. Andreijevic, D. Xing, X. Sousa, A. M. M. Santpere, G. Sestan, N. 2019-12-31 doi:10.1101/2019.12.31.891036 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ The stability flexibility tradeoff and the dark side of detail ]]> https://biorxiv.org/cgi/content/short/2020.01.03.894014v1?rss=1" Nassar, M. R. Troiani, V. 2020-01-03 doi:10.1101/2020.01.03.894014 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism ]]> https://biorxiv.org/cgi/content/short/801076v1?rss=1" Richter, J. Huber, K. Shah, S. Molinaro, G. Liu, B. Wang, R. 2019-10-10 doi:10.1101/801076 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Intrinsic excitation-inhibition imbalance affects medial prefrontal cortex differently in autistic men versus women ]]> https://biorxiv.org/cgi/content/short/2020.01.16.909531v1?rss=1" Trakoshis, S. Martinez-Canada, P. Rocchi, F. Canella, C. You, W. Chakrabarti, B. Ruigrok, A. N. Bullmore, E. Suckling, J. Markicevic, M. Zerbi, V. MRC AIMS Consortium, Baron-Cohen, S. Panzeri, S. Gozzi, A. Lai, M.-C. Lombardo, M. V. 2020-01-27 doi:10.1101/2020.01.16.909531 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Homeostatic Plasticity Commonly Fails at the Intersection of Autism-Gene Mutations and a Novel Class of Common Phenotypic Modifier ]]> https://biorxiv.org/cgi/content/short/2020.01.31.927665v1?rss=1" Genc, O. An, J. Y. Fetter, R. D. Kulik, Y. Zunino, G. Sanders, S. J. Davis, G. W. 2020-01-31 doi:10.1101/2020.01.31.927665 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional? ]]> https://biorxiv.org/cgi/content/short/2020.02.02.931337v1?rss=1" Mulvey, B. Lagunas, T. Dougherty, J. D. 2020-02-03 doi:10.1101/2020.02.02.931337 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Recent ultra-rare inherited mutations identify novel autism candidate risk genes ]]> https://biorxiv.org/cgi/content/short/2020.02.10.932327v1?rss=1" Wilfert, A. B. Turner, T. N. Murali, S. C. Hsieh, P. Sulovari, A. Wang, T. Coe, B. P. Guo, H. Hoekzema, K. Bakken, T. E. Winterkorn, L. H. Evani, U. S. Byrska-Bishop, M. Earl, R. K. Bernier, R. A. The SPARK Consortium, Zody, M. C. Eichler, E. E. 2020-02-11 doi:10.1101/2020.02.10.932327 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling ]]> https://biorxiv.org/cgi/content/short/2020.02.07.939256v1?rss=1" Amar, M. Pramod, A. B. Herrera, V. M. Yu, N.-K. Qiu, L. R. Zhang, P. Moran-Losada, P. Trujillo, C. A. Ellegood, J. Urresti, J. Chau, K. Diedrich, J. Chen, J. Gutierrez, J. Sebat, J. Ramanathan, D. Lerch, J. P. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-02-12 doi:10.1101/2020.02.07.939256 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Natural selection influenced the genetic architecture of brain structure, behavioral and neuropsychiatric traits ]]> https://biorxiv.org/cgi/content/short/2020.02.26.966531v1?rss=1" Wendt, F. R. Pathak, G. A. Overstreet, C. Tylee, D. S. Gelernter, J. Atkinson, E. G. Polimanti, R. 2020-02-27 doi:10.1101/2020.02.26.966531 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ The contribution of de novo tandem repeat mutations to autism spectrum disorders ]]> https://biorxiv.org/cgi/content/short/2020.03.04.974170v1?rss=1" Mitra, I. Mousavi, N. Ma, N. Lamkin, M. Yanicky, R. Shleizer-Burko, S. Gymrek, M. 2020-03-05 doi:10.1101/2020.03.04.974170 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Aberrant Sensory Encoding in Patients with Autism ]]> https://biorxiv.org/cgi/content/short/2020.03.04.976191v1?rss=1" Noel, J.-P. Zhang, L.-Q. Stocker, A. Angelaki, D. 2020-03-05 doi:10.1101/2020.03.04.976191 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing. ]]> https://biorxiv.org/cgi/content/short/2020.03.14.992032v1?rss=1" Kerschbamer, E. Tripathi, T. Erdin, S. Salviato, E. Di Leva, F. Sebestyen, E. Arnoldi, M. Benelli, M. Gusella, J. F. Piazza, S. Demichelis, F. Talkowski, M. E. Ferrari, F. Biagioli, M. 2020-03-16 doi:10.1101/2020.03.14.992032 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Multi-parametric analysis of 58 SYNGAP1 variants reveal impacts on GTPase signaling, localization and protein stability ]]> https://biorxiv.org/cgi/content/short/2020.04.21.053686v1?rss=1" Meili, F. Wei, W. J. Sin, W.-C. Dascalu, I. Callaghan, D. B. Rogic, S. Meyers, W. M. Pavlidis, P. Haas, K. 2020-04-22 doi:10.1101/2020.04.21.053686 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data ]]> https://biorxiv.org/cgi/content/short/2020.05.04.076034v1?rss=1" Pintacuda, G. Lassen, F. H. Hsu, Y.-H. H. Kim, A. Martin, J. M. Malolepsza, E. Lim, J. K. Fornelos, N. Eggan, K. C. Lage, K. 2020-05-05 doi:10.1101/2020.05.04.076034 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Cell-type-specific synaptic imbalance and disrupted homeostatic plasticity in cortical circuits of ASD-associated Chd8 haploinsufficient mice ]]> https://biorxiv.org/cgi/content/short/2020.05.14.093187v1?rss=1" Ellingford, R. A. Rabeshala de Meritens, E. Shaunak, R. Naybour, L. Basson, M. A. Andreae, L. C. 2020-05-14 doi:10.1101/2020.05.14.093187 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Multitask learning on comorbid disorders improves gene risk prediction for Autism Spectrum Disorder and Intellectual Disability ]]> https://biorxiv.org/cgi/content/short/2020.06.13.150201v1?rss=1" Beyreli, I. Karakahya, O. Cicek, A. E. 2020-06-15 doi:10.1101/2020.06.13.150201 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data ]]> https://biorxiv.org/cgi/content/short/2020.06.15.153031v1?rss=1" Chen, S. Zhou, X. Byington, E. Bruce, S. L. Zhang, H. Shen, Y. 2020-06-16 doi:10.1101/2020.06.15.153031 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism ]]> https://biorxiv.org/cgi/content/short/2020.06.25.172262v1?rss=1" Urresti, J. Zhang, P. Moran-Losada, P. Yu, N.-K. Negraes, P. D. Trujillo, C. A. Antaki, D. Amar, M. Chau, K. Pramod, A. B. Diedrich, J. Tejwani, L. Romero, S. Sebat, J. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.25.172262 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Isoform transcriptome of developing human brain provides new insights into autism risk variants ]]> https://biorxiv.org/cgi/content/short/2020.06.27.175489v1?rss=1" Chau, K. Zhang, P. Urresti, J. Amar, M. Pramod, A. B. Thomas, A. Corominas, R. Lin, G. N. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.27.175489 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders ]]> https://biorxiv.org/cgi/content/short/2020.07.10.195859v1?rss=1" Christian, D. L. Wu, D. Y. Martin, J. R. Moore, J. R. Liu, Y. R. Clemens, A. W. Nettles, S. A. Kirkland, N. M. Hill, C. A. Wozniak, D. F. Dougherty, J. D. Gabel, H. W. 2020-07-13 doi:10.1101/2020.07.10.195859 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ FOXP1 negatively regulates intrinsic excitability in D2 striatal projection neurons by promoting inwardly rectifying and leak potassium currents ]]> https://biorxiv.org/cgi/content/short/2020.07.21.213173v1?rss=1" Khandelwal, N. Cavalier, S. Rybalchenko, V. Kulkarni, A. Anderson, A. G. Konopka, G. Gibson, J. R. 2020-07-21 doi:10.1101/2020.07.21.213173 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data ]]> https://biorxiv.org/cgi/content/short/2020.08.05.238949v1?rss=1" Wang, J. Roeder, K. Devlin, B. 2020-08-06 doi:10.1101/2020.08.05.238949 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Systematic evaluation of genome sequencing as a first-tier diagnostic test for prenatal and pediatric disorders ]]> https://biorxiv.org/cgi/content/short/2020.08.12.248526v1?rss=1" Lowther, C. Valkanas, E. Giordano, J. L. Wang, H. Z. Currall, B. B. O'Keefe, K. Collins, R. L. Zhao, X. Austin-Tse, C. A. Evangelista, E. Aggarwal, V. Lucente, D. Gauthier, L. D. Tolonen, C. Sahakian, N. An, J.-Y. Dong, S. Norton, M. E. MacKenzie, T. Devlin, B. Gilmore, K. Powell, B. Brandt, A. Vetrini, F. DiVito, M. Goldstein, D. B. Sanders, S. J. MacArthur, D. G. Hodge, J. C. O'Donnell-Luria, A. Rehm, H. Vora, N. Levy, B. Brand, H. Wapner, R. Talkowski, M. E. 2020-08-13 doi:10.1101/2020.08.12.248526 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ The organization and developmental establishment ofcortical interneuron presynaptic circuits ]]> https://biorxiv.org/cgi/content/short/2020.09.17.302117v1?rss=1" Pouchelon, G. Bollmann, Y. Fisher, E. Agba, C. K. Xu, Q. Ritola, K. D. Mirow, A. M. Kim, S. Cossart, R. Fishell, G. 2020-09-17 doi:10.1101/2020.09.17.302117 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ A causal study of bumetanide on a marker of excitatory-inhibitory balance in the human brain ]]> https://biorxiv.org/cgi/content/short/2020.09.22.304279v1?rss=1" Botch, T. L. Spiegel, A. Ricciardi, C. Robertson, C. E. 2020-09-23 doi:10.1101/2020.09.22.304279 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ A cross-species link between mTOR-related synaptic pathology and functional hyperconnectivityin autism ]]> https://biorxiv.org/cgi/content/short/2020.10.07.329292v1?rss=1" Pagani, M. Bertero, A. Trakoshis, S. Ulysse, L. Locarno, A. Miseviciute, I. De Felice, A. Canella, C. Supekar, K. Galbusera, A. Menon, V. Tonini, R. Deco, G. Lombardo, M. V. Pasqualetti, M. Gozzi, A. 2020-10-08 doi:10.1101/2020.10.07.329292 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families ]]> https://biorxiv.org/cgi/content/short/2020.10.06.329011v1?rss=1" Belyeu, J. R. Brand, H. Wang, H. Zhao, X. Pedersen, B. S. Feusier, J. Gupta, M. Nicholas, T. J. Baird, L. Devlin, B. Sanders, S. J. Jorde, L. B. Talkowski, M. E. Quinlan, A. R. 2020-10-08 doi:10.1101/2020.10.06.329011 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Heterozygous deletion of SYNGAP enzymatic domains in rats causes selective learning, social and seizure phenotypes ]]> https://biorxiv.org/cgi/content/short/2020.10.14.339192v1?rss=1" Katsanevaki, D. Till, S. M. Buller-Peralta, I. Watson, T. C. Nawaz, M. S. Arkell, D. Tiwari, S. Kapgal, V. Biswal, S. Smith, J. A. Anstey, N. J. Mizen, L. Perentos, N. Jones, M. W. Cousin, M. A. Chattarji, S. Gonzalez-Sulser, A. Hardt, O. Wood, E. R. Kind, P. C. 2020-10-14 doi:10.1101/2020.10.14.339192 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Temporal stability of human sperm mosaic mutations results in life-long threat of transmission to offspring ]]> https://biorxiv.org/cgi/content/short/2020.10.14.339796v1?rss=1" Yang, X. Breuss, M. W. Xu, X. Antaki, D. James, K. N. Stanley, V. Ball, L. L. George, R. D. Wirth, S. A. Cao, B. Nguyen, A. McEvoy-Venneri, J. Chai, G. Nahas, S. Van Der Kraan, L. Ding, Y. Sebat, J. Gleeson, J. G. 2020-10-14 doi:10.1101/2020.10.14.339796 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes ]]> https://biorxiv.org/cgi/content/short/2020.10.15.340588v1?rss=1" Zerbi, V. Pagani, M. Markicevic, M. Matteoli, M. Pozzi, D. Fagiolini, M. Bozzi, Y. Galbusera, A. Scattoni, M. L. Provenzano, G. Banerjee, A. Helmchen, F. Basson, A. Ellegood, J. Lerch, J. Rudin, M. Gozzi, A. Wenderoth, N. 2020-10-15 doi:10.1101/2020.10.15.340588 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex ]]> https://biorxiv.org/cgi/content/short/2020.10.14.339200v1?rss=1" Jeffries, A. R. Leung, S. K. Castanho, I. Moore, K. Davies, J. Dempster, E. Bray, N. J. O'Neill, P. Tseng, E. J. Ahmed, Z. Collier, D. Prabhakar, S. Scalkwyk, L. Gandal, M. Hannon, E. Mill, J. 2020-10-15 doi:10.1101/2020.10.14.339200 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Regulation of neural gene expression by estrogen receptor alpha ]]> https://biorxiv.org/cgi/content/short/2020.10.21.349290v1?rss=1" Gegenhuber, B. Wu, M. V. Bronstein, R. Tollkuhn, J. 2020-10-21 doi:10.1101/2020.10.21.349290 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Spatial modulation of dark versus bright stimulus responses in mouse visual cortex ]]> https://biorxiv.org/cgi/content/short/2020.10.27.353573v1?rss=1" Williams, B. Del Rosario, J. Coletta, S. Murlin, E. K. Muzzu, T. Speed, A. Meyer-Baese, L. Saleem, A. B. Haider, B. 2020-10-28 doi:10.1101/2020.10.27.353573 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Brunner syndrome associated MAOA dysfunction in human dopaminergic neurons results in NMDAR hyperfunction and increased network activity. ]]> https://biorxiv.org/cgi/content/short/2020.10.28.359224v1?rss=1" Shi, Y. van Rhijn, J.-R. Bormann, M. Mossink, B. Frega, M. Recaioglu, H. Hakobjan, M. Klein Gunnewiek, T. M. Schoenmaker, C. Palmer, E. Faivre, L. Kittel-Schneider, S. Schubert, D. Brunner, H. Franke, B. Nadif Kasri, N. 2020-10-29 doi:10.1101/2020.10.28.359224 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ A configurable model of the synaptic proteome reveals the molecular mechanisms of disease co-morbidity. ]]> https://biorxiv.org/cgi/content/short/2020.10.27.356899v1?rss=1" Sorokina, O. McLean, C. Croning, M. D. Heil, K. F. Wysochka, E. He, X. Sterratt, D. C. Grant, S. Simpson, I. Armstrong, J. D. 2020-10-27 doi:10.1101/2020.10.27.356899 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Neural basis of opioid-induced respiratory depression and its rescue ]]> https://biorxiv.org/cgi/content/short/2020.10.28.359893v1?rss=1" Liu, S. Kim, D.-I. Oh, T. G. Pao, G. M. Kim, J. H. Palmiter, R. D. Banghart, M. M. Lee, K.-F. Evans, R. M. Han, S. 2020-10-29 doi:10.1101/2020.10.28.359893 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants ]]> https://biorxiv.org/cgi/content/short/2020.11.03.365395v1?rss=1" Miller, D. E. Sulovari, A. Wang, T. Loucks, H. Hoekzema, K. Munson, K. M. Lewis, A. P. Almanza Fuerte, E. P. Paschal, C. R. Thies, J. Bennett, J. T. Glass, I. Dipple, K. M. Patterson, K. Bonkowski, E. S. Nelson, Z. Squire, A. Sikes, M. Beckman, E. Bennett, R. L. Earl, D. Lee, W. Allikmets, R. Perlman, S. J. Chow, P. Hing, A. V. Adam, M. P. Sun, A. Lam, C. Chang, I. University of Washington Center for Mendelian Genomics, Cherry, T. Chong, J. X. Bamshad, M. J. Nickerson, D. A. Mefford, H. C. Doherty, D. Eichler, E. E. 2020-11-04 doi:10.1101/2020.11.03.365395 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Sex-specific stress-related behavioral phenotypes and central amygdala dysfunction in a mouse model of 16p11.2 microdeletion ]]> https://biorxiv.org/cgi/content/short/2020.11.12.380501v1?rss=1" Giovanniello, J. R. Ahrens, S. Yu, K. Li, B. 2020-11-15 doi:10.1101/2020.11.12.380501 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior ]]> https://biorxiv.org/cgi/content/short/2020.11.11.378893v1?rss=1" Raiders, S. Black, E. C. Bae, A. MacFarlane, S. Shaham, S. Singhvi, A. 2020-11-12 doi:10.1101/2020.11.11.378893 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse neocortex ]]> https://biorxiv.org/cgi/content/short/2020.11.18.389171v1?rss=1" Liang, L. Fazel Darbandi, S. Pochareddy, S. Gulden, F. O. Gilson, M. C. Sheppard, B. K. Sahagun, A. An, J.-Y. Werling, D. M. Rubenstein, J. L. R. Sestan, N. Bender, K. Sanders, S. J. 2020-11-18 doi:10.1101/2020.11.18.389171 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ The need to connect: Acute social isolation causes neural craving responses similar to hunger. ]]> https://biorxiv.org/cgi/content/short/2020.03.25.006643v1?rss=1" Tomova, L. Wang, K. Thompson, T. Matthews, G. Takahashi, A. Tye, K. Saxe, R. 2020-03-26 doi:10.1101/2020.03.25.006643 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Can machine learning aid in identifying disease genes? The case of autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/2020.11.26.394676v1?rss=1" Gunning, M. Pavlidis, P. 2020-11-27 doi:10.1101/2020.11.26.394676 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Developmental loss of ErbB4 in PV interneurons disrupts state-dependent cortical circuit dynamics. ]]> https://biorxiv.org/cgi/content/short/2020.12.09.418590v1?rss=1" Batista-Brito, R. Majumdar, A. Nuno, A. Vinck, M. Cardin, J. A. 2020-12-10 doi:10.1101/2020.12.09.418590 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Chromatin remodeler Arid1a regulates subplate neuron identity and wiring of cortical connectivity ]]> https://biorxiv.org/cgi/content/short/2020.12.14.422645v1?rss=1" Doyle, D. Z. Lam, M. M. Qalieh, A. Qalieh, Y. Sorel, A. Funk, O. H. Kwan, K. Y. 2020-12-14 doi:10.1101/2020.12.14.422645 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Drosophila functional screening of de novo variants in autism uncovers deleterious variants and facilitates discovery of rare neurodevelopmental diseases ]]> https://biorxiv.org/cgi/content/short/2020.12.30.424813v1?rss=1" Marcogliese, P. C. Deal, S. L. Andrews, J. Harnish, J. M. Bhavana, V. H. Graves, H. K. Jangam, S. Luo, X. Liu, N. Bei, D. Chao, Y.-H. Hull, B. Lee, P.-T. Pan, H. Longley, C. M. Chao, H.-T. Chung, H. Haelterman, N. A. Kanca, O. Manivannan, S. N. Rossetti, L. Z. Gerard, A. Schwaibold, E. M. C. Guerrini, R. Vetro, A. England, E. Murali, C. N. Barakat, T. S. van Dooren, M. F. Wilke, M. van Slegtenhorst, M. Lesca, G. Sabatier, I. Chatron, N. Brownstein, C. A. Madden, J. A. Agrawal, P. B. Keller, R. Pavinato, L. Brusco, A. Rosenfeld, J. A. Marom, R. Wangler, 2021-01-01 doi:10.1101/2020.12.30.424813 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Broad transcriptomic dysregulation across the cerebral cortex in ASD ]]> https://biorxiv.org/cgi/content/short/2020.12.17.423129v1?rss=1" Haney, J. R. Wamsley, B. Chen, G. T. Parhami, S. Emani, P. S. Chang, N. Hoftman, G. D. de Alba, D. Kale, G. Ramaswami, G. Hartl, C. L. Jin, T. Wang, D. Ou, J. Wu, Y. E. Parikshak, N. N. Swarup, V. Belgard, T. G. Gerstein, M. Pasaniuc, B. Gandal, M. J. Geschwind, D. H. 2020-12-18 doi:10.1101/2020.12.17.423129 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Human neuronal networks on micro-electrode arrays are a highly robust tool to study disease-specific genotype-phenotype correlations in vitro ]]> https://biorxiv.org/cgi/content/short/2021.01.20.427439v1?rss=1" Mossink, B. Verboven, A. H. A. van Hugte, E. J. H. Klein Gunnewiek, T. M. Parodi, G. Linda, K. Schoenmaker, C. Kleefstra, T. Kozicz, T. van Bokhoven, H. Schubert, D. Nadif Kasri, N. Frega, M. 2021-01-21 doi:10.1101/2021.01.20.427439 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells ]]> https://biorxiv.org/cgi/content/short/2021.02.02.429423v1?rss=1" Spratt, P. W. Ben-Shalom, R. Sahagun, A. Keeshen, C. M. Sanders, S. J. Bender, K. J. 2021-02-02 doi:10.1101/2021.02.02.429423 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Customized de novo mutation detection for any variant calling pipeline: SynthDNM ]]> https://biorxiv.org/cgi/content/short/2021.02.10.427198v1?rss=1" Lian, A. Guevara, J. Xia, K. Sebat, J. 2021-02-10 doi:10.1101/2021.02.10.427198 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Mice Make Targeted Saccades ]]> https://biorxiv.org/cgi/content/short/2021.02.10.430669v1?rss=1" Zahler, S. H. Taylor, D. E. Adams, J. M. Feinberg, E. H. 2021-02-11 doi:10.1101/2021.02.10.430669 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ fmr1 mutation interacts with sensory experience to alter the early development of behavior and sensory coding in zebrafish ]]> https://biorxiv.org/cgi/content/short/2021.03.16.435742v1?rss=1" Zhu, S. McCullough, M. Pujic, Z. Sibberas, J. Sun, B. Bucknall, B. Avitan, L. Goodhill, G. 2021-03-17 doi:10.1101/2021.03.16.435742 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ NRF1 Association with AUTS2-Polycomb Mediates Specific Gene Activation in the Brain ]]> https://biorxiv.org/cgi/content/short/2021.03.30.437620v1?rss=1" Liu, S. Aldinger, K. A. Cheng, C. V. Kiyama, T. Dave, M. McNamara, H. K. Caraffi, S. G. Ivanovski, I. Errichiello, E. Zweier, C. Zuffardi, O. Schneider, M. Papavasiliou, A. S. Perry, M. S. Cho, M. T. Weber, A. Swale, A. Badea, T. C. Mao, C.-A. Garavelli, L. Dobyns, W. B. Reinberg, D. 2021-03-30 doi:10.1101/2021.03.30.437620 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Microglia complement signaling promotes neuronal elimination and normal brain functional connectivity ]]> https://biorxiv.org/cgi/content/short/2021.03.31.437118v1?rss=1" Deivasigamani, S. Miteva, M. T. Natale, S. Gutierrez-Barragan, D. Basilico, B. Di Angelantonio, S. Pape, C. Bolasco, G. Galbusera, A. Gozzi, A. Ragozzino, D. Gross, C. T. 2021-04-02 doi:10.1101/2021.03.31.437118 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes ]]> https://biorxiv.org/cgi/content/short/2021.04.07.438852v1?rss=1" Markenscoff, E. Binyameen, F. Whalen, S. Price, J. Lim, K. Catta-Preta, R. Pai, E. L.-L. Mu, X. Xu, D. Pollard, K. S. Nord, A. State, M. W. Rubenstein, J. L. R. 2021-04-08 doi:10.1101/2021.04.07.438852 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome ]]> https://biorxiv.org/cgi/content/short/2020.08.18.253443v1?rss=1" Lombardo, M. V. Eyler, L. Pramparo, T. Gazestani, V. H. Hagler, D. J. Chen, C.-H. Dale, A. M. Seidlitz, J. Bethlehem, R. A. I. Bertelsen, N. Carter Barnes, C. Lopez, L. Campbell, K. Lewis, N. E. Pierce, K. Courchesne, E. 2020-08-18 doi:10.1101/2020.08.18.253443 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ ASXL3 controls cortical neuron fate specification through extrinsic self-renewal pathways ]]> https://biorxiv.org/cgi/content/short/2021.07.20.452995v1?rss=1" McGrath, B. T. Wu, P. Salvi, S. Girgla, N. Xu, C. Zhu, J. KC, R. Tsan, Y.-C. Moccia, A. Srivastava, A. Zhou, X. Bielas, S. L. 2021-07-21 doi:10.1101/2021.07.20.452995 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Towards Preclinical Validation of Arbaclofen (R-baclofen) Treatment for 16p11.2 Deletion Syndrome ]]> https://biorxiv.org/cgi/content/short/2023.05.01.538987v1?rss=1" Gundersen, B. B. O'Brien, W. T. Schaffler, M. D. Schultz, M. N. Tsukahara, T. Lorenzo, S. M. Nalesso, V. Clayton, A. H. L. Abel, T. Crawley, J. N. Datta, S. R. Herault, Y. 2023-05-02 doi:10.1101/2023.05.01.538987 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ Cell-type-specificity of isoform diversity in the developing human neocortex informs mechanisms of neurodevelopmental disorders ]]> https://biorxiv.org/cgi/content/short/2023.03.25.534016v1?rss=1" 7,000 novel exons, expanding the proteome by 92,422 putative proteoforms. We uncovered thousands of isoform switches during cortical neurogenesis predicted to impact RNA regulatory domains or protein structure and implicating previously uncharacterized RNA-binding proteins in cellular identity and neuropsychiatric disease. At the single-cell level, early-stage excitatory neurons exhibited the greatest isoform diversity, and isoform-centric single-cell clustering led to the identification of previously uncharacterized cell states. We systematically assessed the contribution of transcriptomic features, and localized cell and spatio-temporal transcript expression signatures across neuropsychiatric disorders, revealing predominant enrichments in dynamic isoform expression and utilization patterns and that the number and complexity of isoforms per gene is strongly predictive of disease. Leveraging this resource, we re-prioritized thousands of rare de novo risk variants associated with autism spectrum disorders (ASD), intellectual disability (ID), and neurodevelopmental disorders (NDDs), more broadly, to potentially more severe consequences and revealed a larger proportion of cryptic splice variants with the expanded transcriptome annotation provided in this study. CONCLUSIONOur study offers a comprehensive landscape of isoform diversity in the human neocortex during development. This extensive cataloging of novel isoforms and splicing events sheds light on the underlying mechanisms of neurodevelopmental disorders and presents an opportunity to explore rare genetic variants linked to these conditions. The implications of our findings extend beyond fundamental neuroscience, as they provide crucial insights into the molecular basis of developmental brain disorders and pave the way for targeted therapeutic interventions. To facilitate exploration of this dataset we developed an online portal (https://sciso.gandallab.org/). ]]> Patowary, A. 2023-03-26 doi:10.1101/2023.03.25.534016 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ Neuron cilia constrain glial regulators to microdomains around distal neurons ]]> https://biorxiv.org/cgi/content/short/2023.03.18.533255v1?rss=1" Ray, S. Gurung, P. Manning, R. S. Kravchuk, A. Singhvi, A. 2023-03-19 doi:10.1101/2023.03.18.533255 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Electrophysiological indices of hierarchical speech processing differentially reflect the comprehension of speech in noise ]]> https://biorxiv.org/cgi/content/short/2023.03.30.534927v1?rss=1" Synigal, S. R. Anderson, A. J. Lalor, E. C. 2023-03-31 doi:10.1101/2023.03.30.534927 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Molecular cascades and cell-type specific signatures in ASD revealed by single cell genomics ]]> https://biorxiv.org/cgi/content/short/2023.03.10.530869v1?rss=1" Wamsley, B. Bicks, L. Cheng, Y. Kawaguchi, R. Quintero, D. Grundman, J. Liu, J. Xiao, S. Hawken, N. Margolis, M. Mazariegos, S. Geschwind, D. H. 2023-03-10 doi:10.1101/2023.03.10.530869 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics ]]> https://biorxiv.org/cgi/content/short/2023.03.16.532307v1?rss=1" Weinreb, C. Osman, M. A. M. Zhang, L. Lin, S. Pearl, J. Annapragada, S. Conlin, E. Gillis, W. F. Jay, M. Ye, S. Mathis, A. Mathis, M. W. Pereira, T. Linderman, S. W. Datta, S. R. 2023-03-17 doi:10.1101/2023.03.16.532307 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Mouse models of SYNGAP1-related intellectual disability ]]> https://biorxiv.org/cgi/content/short/2023.05.25.542312v1?rss=1" A. While reduction in Syngap1 mRNA varies from 30-50% depending on the specific mutation, both models show [~]50% reduction in Syngap1 protein, have deficits in synaptic plasticity, and recapitulate key features of SRID including hyperactivity and impaired working memory. These data suggest that half the amount of SYNGAP1 protein is key to the pathogenesis of SRID. These results provide a resource to study SRID and establish a framework for the development of therapeutic strategies for this disorder. Significance StatementSYNGAP1 is a protein enriched at excitatory synapses in the brain that is an important regulator of synapse structure and function. SYNGAP1 mutations cause SYNGAP1-related intellectual disability (SRID), a neurodevelopmental disorder with cognitive impairment, social deficits, seizures, and sleep disturbances. To explore how SYNGAP1 mutations found in humans lead to disease, we generated the first knock-in mouse models with causal SRID variants: one with a frameshift mutation and a second with an intronic mutation that creates a cryptic splice acceptor site. Both models show decreased Syngap1 mRNA and Syngap1 protein and recapitulate key features of SRID including hyperactivity and impaired working memory. These results provide a resource to study SRID and establish a framework for the development of therapeutic strategies. HighlightsO_LITwo mouse models with SYNGAP1-related intellectual disability (SRID) mutations found in humans were generated: one with a frameshift mutation that results in a premature stop codon and the other with an intronic mutation resulting in a cryptic splice acceptor site and premature stop codon. C_LIO_LIBoth SRID mouse models show 35[~]50% reduction in mRNA and [~]50% reduction in Syngap1 protein. C_LIO_LIBoth SRID mouse models display deficits in synaptic plasticity and behavioral phenotypes found in people. C_LIO_LIRNA-seq confirmed cryptic splice acceptor activity in one SRID mouse model and revealed broad transcriptional changes also identified in Syngap1+/- mice. C_LIO_LINovel SRID mouse models generated here provide a resource and establish a framework for development of future therapeutic intervention. C_LI ]]> Araki, Y. Gerber, E. E. Rajkovich, K. E. Hong, I. Johnson, R. C. Lee, H.-K. Kirkwood, A. Huganir, R. L. 2023-05-25 doi:10.1101/2023.05.25.542312 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants ]]> https://biorxiv.org/cgi/content/short/2023.01.31.526505v1?rss=1" Einson, J. Glinos, D. Boerwinkle, E. Castaldi, P. Darbar, D. de Andrade, M. Ellinor, P. Fornage, M. Gabriel, S. Germer, S. Gibbs, R. Hersh, C. Johnsen, J. Kaplan, R. Konkle, B. Kooperberg, C. Nassir, R. Loos, R. J. F. Meyers, D. A. Mitchell, B. D. Psaty, B. Vasan, R. S. Rich, S. S. Rienstra, M. Rotter, J. I. Saferali, A. Shoemaker, M. B. Silverman, E. Smith, A. V. Mohammadi, P. Castel, S. E. Iossifov, I. Lappalainen, T. 2023-01-31 doi:10.1101/2023.01.31.526505 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ HAT: de novo variant calling for highly accurate short-read and long-read sequencing data ]]> https://biorxiv.org/cgi/content/short/2023.01.27.525940v1?rss=1" Ng, J. K. Turner, T. N. 2023-01-28 doi:10.1101/2023.01.27.525940 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Epithelia delimits glial apical polarity against mechanical shear to maintain glia-neuron architecture ]]> https://biorxiv.org/cgi/content/short/2022.12.26.521704v1?rss=1" Martin, C. G. Bent, J. S. Singhvi, A. 2022-12-27 doi:10.1101/2022.12.26.521704 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Systematic multi-trait AAV capsid engineering for efficient gene delivery ]]> https://biorxiv.org/cgi/content/short/2022.12.22.521680v1?rss=1" Eid, F.-E. Chen, A. T. Chan, K. Y. Huang, Q. Zheng, Q. Tobey, I. G. Pacouret, S. Brauer, P. P. Keyes, C. Powell, M. Johnston, J. Zhao, B. Lage, K. Tarantal, A. F. Chan, Y. A. Deverman, B. E. 2022-12-22 doi:10.1101/2022.12.22.521680 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Quantifying constraint in human mitochondrial DNA ]]> https://biorxiv.org/cgi/content/short/2022.12.16.520778v1?rss=1" Lake, N. J. Liu, W. Battle, S. L. Laricchia, K. M. Tiao, G. Compton, A. G. Cowie, S. Christodoulou, J. Thorburn, D. R. Zhao, H. Arking, D. E. Sunyaev, S. R. Lek, M. 2022-12-19 doi:10.1101/2022.12.16.520778 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Robust hierarchically organized whole-brain patterns of dysconnectivity in schizophrenia spectrum disorders observed after Personalized Intrinsic Network Topography ]]> https://biorxiv.org/cgi/content/short/2022.12.13.520333v1?rss=1" Dickie, E. W. Shahab, S. Hawco, C. Miranda, D. Herman, G. Argyelan, M. Ji, J. L. W. Jeyachandra, J. Anticevic, A. Malhotra, A. K. Voineskos, A. N. 2022-12-15 doi:10.1101/2022.12.13.520333 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ An in vivo platform for rebuilding functional neocortical tissue ]]> https://biorxiv.org/cgi/content/short/2022.12.09.519776v1?rss=1" Quezada, A. Ward, C. Bader, E. R. Zolotavin, P. Altun, E. Hong, S. Killian, N. Xie, C. Batista-Brito, R. Hebert, J. M. 2022-12-11 doi:10.1101/2022.12.09.519776 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Regulation of stress-induced sleep fragmentation by preoptic glutamatergic neurons ]]> https://biorxiv.org/cgi/content/short/2022.11.30.518589v1?rss=1" Smith, J. Honig-Frand, A. Antila, H. Weber, F. Chung, S. 2022-12-01 doi:10.1101/2022.11.30.518589 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ A new theoretical framework jointly explains behavioral and neural variability across subjects performing flexible decision-making ]]> https://biorxiv.org/cgi/content/short/2022.11.28.518207v1?rss=1" Pagan, M. Tang, V. D. Aoi, M. C. Pillow, J. W. Mante, V. Sussillo, D. Brody, C. D. 2022-11-28 doi:10.1101/2022.11.28.518207 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Transcriptional diversity in synaptic gene sets is sufficient to discriminate cortical neuronal identity ]]> https://biorxiv.org/cgi/content/short/2022.11.25.517899v1?rss=1" Roig Adam, A. Martinez Lopez, J. van der Spek, S. The SYNGO consortium, Sullivan, P. F. Smit, A. Verhage, M. Hjerling-Leffler, J. 2022-11-25 doi:10.1101/2022.11.25.517899 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Deficits in integrative NMDA receptors caused by Grin1 disruption can be rescued in adulthood ]]> https://biorxiv.org/cgi/content/short/2022.11.22.517556v1?rss=1" Venkatesan, S. Binko, M. A. Mielnik, C. A. Ramsey, A. J. Lambe, E. K. 2022-11-23 doi:10.1101/2022.11.22.517556 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Sex-biasing influence of autism-associated Ube3a gene overdosage at connectomic, behavioral and transcriptomic levels ]]> https://biorxiv.org/cgi/content/short/2022.10.25.513747v1?rss=1" Montani, C. Pagani, M. De Guzman, E. Balasco, L. Alvino, F. De Felice, A. Galbusera, A. Nickl-Jockstat, T. Lau, P. Borsotti, N. Pasqualetti, M. Mattioni, L. Provenzano, G. Bozzi, Y. Lombardo, M. Gozzi, A. 2022-10-25 doi:10.1101/2022.10.25.513747 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Cell type-specific assessment of cholesterol distribution in models of neurodevelopmental disorders ]]> https://biorxiv.org/cgi/content/short/2022.11.16.516849v1?rss=1" Czernecki, C. Dixit, S. Riezman, I. Innocenti, S. Pfrieger, F. Riezman, H. Scheiffele, P. 2022-11-17 doi:10.1101/2022.11.16.516849 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ A single-cell trajectory atlas of striatal development ]]> https://biorxiv.org/cgi/content/short/2022.11.18.517098v1?rss=1" Anderson, A. G. Kulkarni, A. Konopka, G. 2022-11-18 doi:10.1101/2022.11.18.517098 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Ventral striatal dopamine encodes unique properties of visual stimuli in mice ]]> https://biorxiv.org/cgi/content/short/2022.09.20.508670v1?rss=1" Gonzalez, L. S. Fisher, A. A. Cotella, E. M. Robinson, J. E. 2022-09-22 doi:10.1101/2022.09.20.508670 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Data-driven dissection of the Fever Effect in Autism Spectrum Disorder ]]> https://biorxiv.org/cgi/content/short/2022.06.16.496362v1?rss=1" Muller, E. Shalev, I. Bachmat, E. Eran, A. 2022-06-17 doi:10.1101/2022.06.16.496362 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Ketamine induces multiple individually distinct whole-brain functional connectivity signatures ]]> https://biorxiv.org/cgi/content/short/2022.11.01.514692v1?rss=1" Moujaes, F. Ji, J. L. Rahmati, M. Burt, J. Schleifer, C. H. Adkinson, B. Savic, A. Santamauro, N. Tamayo, Z. Diehl, C. Kolobaric, A. Flynn, M. Rieser, N. M. Fonteneau, C. Camarro, T. Xu, J. Cho, Y. Repovs, G. Fineberg, S. Morgan, P. Seifritz, E. Vollenweider, F. X. Krystal, J. Murray, J. D. Preller, K. H. Anticevic, A. 2022-11-01 doi:10.1101/2022.11.01.514692 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids ]]> https://biorxiv.org/cgi/content/short/2022.10.24.513565v1?rss=1" Popova, G. Retallack, H. Kim, C. N. Shin, D. Wang, A. DeRisi, J. J. Nowakowski, T. J. 2022-10-24 doi:10.1101/2022.10.24.513565 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes ]]> https://biorxiv.org/cgi/content/short/2022.11.05.515231v1?rss=1" Castro, C. P. Diehl, A. G. Boyle, A. P. 2022-11-05 doi:10.1101/2022.11.05.515231 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Mapping human social brain specialisation beyond the neuron using multimodal imaging in human infants ]]> https://biorxiv.org/cgi/content/short/2022.11.08.514512v1?rss=1" Siddiqui, M. Pinti, P. Brigadoi, S. Lloyd-Fox, S. Elwell, C. E. Johnson, M. H. Tachtsidis, I. Jones, E. J. 2022-11-09 doi:10.1101/2022.11.08.514512 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ QuNex -- An Integrative Platform forReproducible Neuroimaging Analytics ]]> https://biorxiv.org/cgi/content/short/2022.06.03.494750v1?rss=1" Ji, J. L. Demsar, J. Fonteneau, C. Tamayo, Z. Pan, L. Kraljic, A. Matkovic, A. Purg, N. Helmer, M. Warrington, S. Sotiropoulos, S. Harms, M. Murray, J. D. Anticevic, A. Repovs, G. 2022-06-05 doi:10.1101/2022.06.03.494750 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ In vivo proximity ligation reveals endogenous candidate interactors of Neurexin's intracellular domain ]]> https://biorxiv.org/cgi/content/short/2022.09.27.509791v1?rss=1" Schaan Profes, M. Tiroumalechetty, A. Patel, N. Lauar, S. S. Sidoli, S. Kurshan, P. 2022-09-28 doi:10.1101/2022.09.27.509791 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Rapid specification of human pluripotent stem cells to functional astrocytes ]]> https://biorxiv.org/cgi/content/short/2022.08.25.505166v1?rss=1" Lendemeijer, B. Unkel, M. Mossink, B. Hijazi, S. Sampedro, S. G. Shpak, G. Slump, D. E. van den Hout, M. C. G. N. van IJcken, W. F. J. Bindels, E. M. J. Hoogendijk, W. J. G. Nadif Kasri, N. de Vrij, F. M. S. Kushner, S. A. 2022-08-26 doi:10.1101/2022.08.25.505166 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Single-cell brain organoid screening identifies developmental defects in autism ]]> https://biorxiv.org/cgi/content/short/2022.09.15.508118v1?rss=1" Li, C. Fleck, J. S. Martins-Costa, C. Burkard, T. R. Stuempflen, M. Vertesy, A. Peer, A. M. Esk, C. Elling, U. Kasprian, G. Corsini, N. S. Treutlein, B. Knoblich, J. A. 2022-09-15 doi:10.1101/2022.09.15.508118 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Dysregulation of mTOR Signaling Mediates Common Neurite and Migration Defects in Both Idiopathic and 16p11.2 Deletion Autism Neural Precursor Cells ]]> https://biorxiv.org/cgi/content/short/2022.09.17.508382v1?rss=1" Prem, S. Dev, B. Peng, C. Mehta, M. Alibutud, R. Connacher, R. J. St. Thomas, M. Zhou, X. Matteson, P. Xing, J. Millonig, J. DiCicco-Bloom, E. 2022-09-20 doi:10.1101/2022.09.17.508382 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Variation in glutamate and GABA genes and their association with brain structure and chemistry in autism ]]> https://biorxiv.org/cgi/content/short/2022.05.25.493390v1?rss=1" Naaijen, J. Arenella, M. Zoellner, H. J. Puts, N. Lythgoe, D. J. Brandeis, D. Durston, S. Poelmans, G. Ruisch, I. H. Buitelaar, J. K. 2022-05-25 doi:10.1101/2022.05.25.493390 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Physical and functional convergence of the autism risk genes Scn2a and Ank2 in neocortical pyramidal cell dendrites ]]> https://biorxiv.org/cgi/content/short/2022.05.31.494205v1?rss=1" Nelson, A. D. Catalfio, A. M. Gupta, J. M. Min, L. Caballero-Floran, R. N. Dean, K. P. Elvira, C. C. Derderian, K. D. Kyoung, H. Sahagun, A. Sanders, S. J. Bender, K. Jenkins, P. M. 2022-05-31 doi:10.1101/2022.05.31.494205 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Ankyrin-B is lipid-modified by S-palmitoylation to promote dendritic membrane scaffolding of voltage-gated sodium channel Nav1.2 in neurons ]]> https://biorxiv.org/cgi/content/short/2022.06.01.494444v1?rss=1" Gupta, J. P. Jenkins, P. M. 2022-06-02 doi:10.1101/2022.06.01.494444 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Peripheral Auditory Nerve Impairment in a Mouse Model of Syndromic Autism ]]> https://biorxiv.org/cgi/content/short/2022.06.02.494499v1?rss=1" McChesney, N. Barth, J. L. Rumschlag, J. A. Tan, J. Harrington, A. Noble, K. McClaskey, C. Elvis, P. Vaena, S. Romeo, M. Harris, K. C. Cowan, C. W. Lang, H. 2022-06-03 doi:10.1101/2022.06.02.494499 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes ]]> https://biorxiv.org/cgi/content/short/2022.07.10.498576v1?rss=1" Liu, F. Liang, C. Li, Z. Zhao, S. Shangguan, S. Yuan, H. Yao, R. Qin, Z. Zhang, S. Zou, L. Gao, Z. Chen, Q. Wen, S. Peng, J. Yin, F. Chen, F. Qiu, X. Luo, J. Xie, Y. Lu, D. Zhang, Y. Xie, H. Wang, H. Cui, X. Wang, J. Huang, H. Liu, R. Sun, X. Chen, C. Wu, N. Liu, C. Shen, Y. Gusella, J. F. Chen, X. 2022-07-11 doi:10.1101/2022.07.10.498576 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ CDKL5 deficiency slows synaptic vesicle endocytosis ]]> https://biorxiv.org/cgi/content/short/2022.03.15.484308v1?rss=1" Kontaxi, C. Davenport, E. C. Kind, P. C. Cousin, M. A. 2022-03-16 doi:10.1101/2022.03.15.484308 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK Biobank ]]> https://biorxiv.org/cgi/content/short/2022.08.25.504851v1?rss=1" Babadi, M. Fu, J. M. Lee, S. K. Smirnov, A. N. Gauthier, L. D. Walker, M. Benjamin, D. I. Karczewski, K. J. Wong, I. Collins, R. L. Sanchis-Juan, A. Brand, H. Banks, E. Talkowski, M. E. 2022-08-26 doi:10.1101/2022.08.25.504851 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Rare CNVs and phenome-wide profiling: a tale of brain-structural divergence and phenotypical convergence ]]> https://biorxiv.org/cgi/content/short/2022.04.23.489093v1?rss=1" Kopal, J. Kumar, K. Saltoun, K. Modenato, C. Moreau, C. A. Martin-Brevet, S. Huguet, G. Jean-Louis, M. Martin, C.-O. Saci, Z. Younis, N. Tamer, P. Douard, E. A. Maillard, A. Rodriguez-Herreros, B. Pain, A. Richetin, S. Kushan, L. Silva, A. I. van den Bree, M. B. Linden, D. E. Owen, M. J. Hall, J. Lippe, S. Draganski, B. Sonderby, I. E. Andreassen, O. A. Glahn, D. C. Thompson, P. Bearden, C. E. Jacquemont, S. Bzdok, D. 2022-04-25 doi:10.1101/2022.04.23.489093 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Fine-grained topographic organization within somatosensory cortex during resting-state and emotional face-matching task and its association with ASD traits ]]> https://biorxiv.org/cgi/content/short/2022.04.26.489525v1?rss=1" Isakoglou, C. Haak, K. V. Wolfers, T. Floris, D. L. Llera, A. Oldehinkel, M. Forde, N. J. Oakley, B. F. M. Tillmann, J. Holt, R. J. Moessnang, C. Loth, E. Bourgeron, T. Baron-Cohen, S. Charman, T. Banaschewski, T. Murphy, D. G. M. Buitelaar, J. K. Marquand, A. F. Beckmann, C. F. EU-AIMS LEAP Group, 2022-04-27 doi:10.1101/2022.04.26.489525 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ CLARITY increases sensitivity and specificity of fluorescence immunostaining in long-term archived human brain tissue ]]> https://biorxiv.org/cgi/content/short/2022.04.27.489700v1?rss=1" View larger version (79K): org.highwire.dtl.DTLVardef@1732df2org.highwire.dtl.DTLVardef@cda615org.highwire.dtl.DTLVardef@152b44aorg.highwire.dtl.DTLVardef@ba972a_HPS_FORMAT_FIGEXP M_FIG Summary of the main advantages of hCLARITY. CLARITY was applied on human post mortem brain tissue in direct comparison to untreated sections (minus CLARITY). Owing to removal of lipids during the clearing with SDS and the resulting reduction in light scattering, cleared sections were less opaque. The denaturing effect of the detergent SDS most likely results in better accessibility of certain epitopes. The major benefits of hCLARITY were found in an increased sensitivity and specificity of antibodies for neuronal cells. The adapted hCLARITY protocol is compatible with staining techniques for confocal microscopy, super-resolution microscopy, and light microscopy. C_FIG ]]> Woelfle, S. Deshpande, D. Feldengut, S. Roselli, F. Deisseroth, K. Michaelis, J. Böckers, T. Schoen, M. 2022-04-29 doi:10.1101/2022.04.27.489700 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Oxytocin attenuates microglial activation and restores social and non-social memory in the APP/PS1 mouse model of Alzheimer's disease ]]> https://biorxiv.org/cgi/content/short/2022.05.07.491031v1?rss=1" Selles, M. C. Fortuna, J. T. S. de Faria, Y. P. R. Longo, B. M. Froemke, R. Chao, M. V. Ferreira, S. T. 2022-05-08 doi:10.1101/2022.05.07.491031 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Saturated reconstruction of living brain tissue ]]> https://biorxiv.org/cgi/content/short/2022.03.16.484431v1?rss=1" Velicky, P. Miguel, E. Michalska, J. M. Wei, D. Lin, Z. Watson, J. F. Troidl, J. Beyer, J. Ben-Simon, Y. Sommer, C. Jahr, W. Cenameri, A. Broichhagen, J. Grant, S. G. N. Jonas, P. Novarino, G. Pfister, H. Bickel, B. Danzl, J. G. 2022-03-18 doi:10.1101/2022.03.16.484431 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamocortical visual system ]]> https://biorxiv.org/cgi/content/short/2022.05.19.491028v1?rss=1" Shin, D. Peelman, K. Del Rosario, J. Haider, B. 2022-05-20 doi:10.1101/2022.05.19.491028 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ ASD modelling in organoids reveals imbalance of excitatory cortical neuron subtypes during early neurogenesis ]]> https://biorxiv.org/cgi/content/short/2022.03.19.484988v1?rss=1" Jourdon, A. Wu, F. Mariani, J. Capauto, D. Norton, S. Tomasini, L. Amiri, A. Suvakov, M. Schreiner, J. Jang, Y. Nguyen, C. K. Cummings, E. M. Han, G. Powell, K. Szekely, A. McPartland, J. C. Pelphrey, K. Chawarska, K. Ventola, P. Abyzov, A. Vaccarino, F. M. 2022-03-20 doi:10.1101/2022.03.19.484988 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Dissociable Cellular and Genetic Mechanisms of Cortical Thinning at Different Life Stages ]]> https://biorxiv.org/cgi/content/short/2022.03.21.484899v1?rss=1" 60 years) in the patterns of association between inter-regional profiles of cortical thickness and expression profiles of marker genes for CA1 and S1 pyramidal cells, astrocytes, and microglia. Gene ontology and enrichment analyses indicated that each of the three life-stages was associated with different biological processes and cellular components: synaptic modeling in early life, neurotransmission in mid-life, and neurodegeneration in late-life. These findings provide mechanistic insights into age-related cortical thinning during typical development and aging. ]]> Modabbernia, A. Vidal-Pineiro, D. Agartz, I. Andreassen, O. A. Ayesa-Arriola, R. Bertolino, A. Boomsma, D. I. Bourque, J. Breier, A. Brouwer, R. M. Buitelaar, J. K. Canales-Rodriguez, E. J. Caseras, X. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Zubicaray, G. I. Dickie, E. W. Dima, D. Frenzel, S. Fisher, S. E. Franke, B. Glahn, D. C. Grabe, H.-J. Grotegerd, D. Gruber, O. Guerrero-Pedraza, A. Gur, R. E. Gur, R. C. Hartman, C. A. Hoekstra, P. J. Hulshoff Pol, H. E. Jahanshad, N. Jernigan, T. L. Jiang, J. Kalnin, A. J. Kochan, N. A. Mazoyer, 2022-03-22 doi:10.1101/2022.03.21.484899 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Mobile elements in human population-specific genome and phenotype divergence ]]> https://biorxiv.org/cgi/content/short/2022.03.25.485726v1?rss=1" Kojima, S. Koyama, S. Ka, M. Saito, Y. Parrish, E. H. Endo, M. Takata, S. Mizukoshi, M. Hikino, K. Takeda, A. Gelinas, A. F. Heaton, S. M. Koide, R. Kamada, A. J. Noguchi, M. Hamada, M. Biobank Japan Project Consortium, Kamatani, Y. Murakawa, Y. Ishigaki, K. Nakamura, Y. Ito, K. Terao, C. Momozawa, Y. Parrish, N. F. 2022-03-27 doi:10.1101/2022.03.25.485726 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Glial dysregulation in human brain in Fragile X-related disorders ]]> https://biorxiv.org/cgi/content/short/2022.03.29.486195v1?rss=1" Dias, C. M. Talukdar, M. Akula, S. Walsh, K. G. Walsh, C. A. 2022-03-29 doi:10.1101/2022.03.29.486195 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ CRISPR activation rescues abnormalities in SCN2A haploinsufficiency-associated autism spectrum disorder ]]> https://biorxiv.org/cgi/content/short/2022.03.30.486483v1?rss=1" Tamura, S. Nelson, A. D. Spratt, P. W. Kyoung, H. Zhou, X. Li, Z. Zhao, J. Holden, S. S. Sahagun, A. Keeshen, C. M. Lu, C. Hamada, E. C. Ben-Shalom, R. Pan, J. Q. Paz, J. T. Sanders, S. J. Matharu, N. Ahituv, N. Bender, K. J. 2022-04-01 doi:10.1101/2022.03.30.486483 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ De novo human brain enhancers created by single nucleotide mutations ]]> https://biorxiv.org/cgi/content/short/2021.07.04.451055v1?rss=1" Li, S. Hannenhalli, S. Ovcharenko, I. 2021-07-05 doi:10.1101/2021.07.04.451055 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Gut Enterochromaffin Cells are Critical Drivers of Visceral Pain and Anxiety ]]> https://biorxiv.org/cgi/content/short/2022.04.04.486775v1?rss=1" Bayrer, J. R. Castro, J. Venkataramen, A. Touhara, K. K. Rossen, N. D. Morrie, R. D. Hendry, A. Madden, J. Braverman, K. Schober, G. Brizuela, M. Bueno Silva, C. Ingraham, H. A. Brierley, S. M. Julius, D. 2022-04-05 doi:10.1101/2022.04.04.486775 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Spatial and temporal autocorrelation weave human brain networks ]]> https://biorxiv.org/cgi/content/short/2021.06.01.446561v1?rss=1" Shinn, M. Hu, A. Turner, L. Noble, S. Achard, S. Anticevic, A. Scheinost, D. Constable, R. T. Lee, D. Bullmore, E. T. Murray, J. D. 2021-06-01 doi:10.1101/2021.06.01.446561 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding ]]> https://biorxiv.org/cgi/content/short/2022.02.13.480215v1?rss=1" Fang, W. Bell, C. M. Sapirstein, A. Asami, S. Leeper, K. Zack, D. J. Ji, H. Kalhor, R. 2022-02-14 doi:10.1101/2022.02.13.480215 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Autism is associated with inter-individual variations of gray and white matter morphology ]]> https://biorxiv.org/cgi/content/short/2022.02.16.480649v1?rss=1" Mei, T. Forde, N. J. Floris, D. L. Dell'Acqua, F. Stones, R. Ilioska, I. Durston, S. Moessnang, C. Banaschewski, T. Holt, R. J. Baron-Cohen, S. Rausch, A. Loth, E. Oakley, B. Charman, T. Ecker, C. Murphy, D. G. M. the EU-AIMS LEAP group, Beckmann, C. F. Llera, A. Buitelaar, J. K. 2022-02-17 doi:10.1101/2022.02.16.480649 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Patterns of connectome variability in autism across five functional activation tasks. Fndings from the LEAP project ]]> https://biorxiv.org/cgi/content/short/2022.02.22.481408v1?rss=1" Looden, T. Floris, D. L. Llera Arenas, A. Chauvin, R. J. Charman, T. Banaschewski, T. Murphy, D. Marquand, A. F. Buitelaar, J. K. Beckmann, C. F. the AIMS-2-TRIALS group, 2022-02-23 doi:10.1101/2022.02.22.481408 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ EphB1 controls proper long-range cortical axon guidance through a cell non-autonomous role in GABAergic cells ]]> https://biorxiv.org/cgi/content/short/2022.02.28.482352v1?rss=1" Assali, A. Chenaux, G. Cowan, C. W. 2022-03-01 doi:10.1101/2022.02.28.482352 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Measuring the response to visually presented faces in the human lateral prefrontal cortex ]]> https://biorxiv.org/cgi/content/short/2022.03.06.483119v1?rss=1" Nikel, L. Sliwinska, M. Kucuk, E. Ungerleider, L. Pitcher, D. 2022-03-07 doi:10.1101/2022.03.06.483119 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Multi-omic analysis along the gut-brain axis points to a functional architecture of autism ]]> https://biorxiv.org/cgi/content/short/2022.02.25.482050v1?rss=1" Morton, J. T. Jin, D.-m. Mills, R. Shao, Y. Rahman, G. Harold-Berding, K. Needham, B. D. Zurita, M. F. David, M. Averina, O. Kovtun, A. Noto, A. Mussap, M. Wang, M. Frank, D. Li, E. Zhou, W. Fanos, V. Danilenko, V. Wall, D. P. Cardenas, P. A. Baldeon, M. xavier, r. j. Mazmanian, S. Knight, R. Gilbert, J. Donovan, S. Lawley, T. Carpenter, B. Bonneau, R. Taroncher-Oldenburg, G. 2022-02-26 doi:10.1101/2022.02.25.482050 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Molecular and connectomic vulnerability shape cross-disorder cortical abnormalities ]]> https://biorxiv.org/cgi/content/short/2022.01.21.476409v1?rss=1" Hansen, J. Y. Shafiei, G. Y. Vogel, J. W. Smart, K. Bearden, C. E. Hoogman, M. Franke, B. van Rooij, D. Buitelaar, J. McDonald, C. R. Sisodiya, S. Schmaal, L. Veltman, D. J. van den Heuvel, O. A. Stein, D. J. van Erp, T. G. Ching, C. Andreassen, O. A. Hajek, T. Opel, N. Modinos, G. Aleman, A. van der Werf, Y. Jahanshad, N. Thomopoulos, S. I. Thompson, P. M. Carson, R. E. Dagher, A. Misic, B. 2022-01-21 doi:10.1101/2022.01.21.476409 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Astrocyte glutamate transport is modulated by motor learning and regulates neuronal correlations and movement encoding by motor cortex neurons ]]> https://biorxiv.org/cgi/content/short/2022.01.20.477039v1?rss=1" Delepine, C. Li, K. Shih, J. Gaudeaux, P. Sur, M. 2022-01-21 doi:10.1101/2022.01.20.477039 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Variability in sampling of cortex-wide neural dynamics explains individual differences in functional connectivity and behavioral phenotype ]]> https://biorxiv.org/cgi/content/short/2022.01.24.477572v1?rss=1" MacDowell, C. J. Briones, B. A. Lenzi, M. J. Gustison, M. L. Buschman, T. J. 2022-01-25 doi:10.1101/2022.01.24.477572 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene. ]]> https://biorxiv.org/cgi/content/short/2021.11.21.469432v1?rss=1" Kostic, M. Raymond, J. J. Henry, B. Tumkaya, T. Khlghatyan, J. Dvornik, J. Hsiao, J. Cheon, S. H. Chung, J. Sun, Y. Dolmetsch, R. Worringer, K. A. Ihry, R. 2021-11-23 doi:10.1101/2021.11.21.469432 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ The PAIR-R24M Dataset for Multi-animal 3D Pose Estimation ]]> https://biorxiv.org/cgi/content/short/2021.11.23.469743v1?rss=1" Marshall, J. D. Klibaite, U. Gellis, A. J. Aldarondo, D. E. Olveczky, B. P. Dunn, T. W. 2021-11-25 doi:10.1101/2021.11.23.469743 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders ]]> https://biorxiv.org/cgi/content/short/2021.12.17.473207v1?rss=1" Baker, B. H. Zhang, S. Simon, J. M. McLarnan, S. M. Chung, W. K. Pearson, B. L. 2021-12-20 doi:10.1101/2021.12.17.473207 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Sex significantly impacts the function of major depression-linked variants in vivo ]]> https://biorxiv.org/cgi/content/short/2021.11.01.466849v1?rss=1" 1,000 variants from >30 MDD loci, identifying extensive sex-by-allele effects in mature hippocampal neurons and suggesting sex-differentiated impacts of genetic risk may underlie sex bias in disease. Unbiased informatics approaches indicated that functional MDD variants recurrently disrupt sex hormone receptor binding sequences. We confirmed this with MPRAs in neonatal brains, comparing brains undergoing the masculinizing hormone surge to hormonally-quiescent juveniles. Our study provides novel insights into the influence of age, biological sex, and cell type on regulatory-variant function, and provides a framework for in vivo parallel assays to functionally define interactions between organismal variables like sex and regulatory variation. One-Sentence SummaryMassively parallel assays in vivo identified extensive functional and sex-interacting common variants in depression risk loci. ]]> Mulvey, B. Selmanovic, D. Dougherty, J. D. 2021-11-04 doi:10.1101/2021.11.01.466849 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Cortical wiring by synapse-specific control of local protein synthesis ]]> https://biorxiv.org/cgi/content/short/2021.11.12.468364v1?rss=1" Bernard, C. Exposito-Alonso, D. Selten, M. Sanalidou, S. Hanusz-Godoy, A. Oozeer, F. Maeso, P. Rico, B. Marin, O. 2021-11-13 doi:10.1101/2021.11.12.468364 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Adaptation and serial choice bias are unaltered in autism ]]> https://biorxiv.org/cgi/content/short/2021.09.13.460060v1?rss=1" Bosch, E. Fritsche, M. Utzerath, C. Buitelaar, J. K. de Lange, F. P. 2021-09-15 doi:10.1101/2021.09.13.460060 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Dual color mesoscopic imaging reveals spatiotemporally heterogeneous coordination of cholinergic and neocortical activity. ]]> https://biorxiv.org/cgi/content/short/2020.12.09.418632v1?rss=1" Lohani, S. Moberly, A. H. Benisty, H. Landa, B. Jing, M. Li, Y. Higley, M. Cardin, J. A. 2020-12-11 doi:10.1101/2020.12.09.418632 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Computational Fingerprints: Modeling Interactions Between Brain Regions as Points in a Function Space ]]> https://biorxiv.org/cgi/content/short/2021.09.28.462195v1?rss=1" Poskanzer, C. Anzellotti, S. 2021-09-30 doi:10.1101/2021.09.28.462195 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ A general framework for identifying rare variant combinations in complex disorders ]]> https://biorxiv.org/cgi/content/short/2021.10.01.462832v1?rss=1" Pounraja, V. K. Girirajan, S. 2021-10-01 doi:10.1101/2021.10.01.462832 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Biophysical Kv channel alterations dampen excitability of cortical PV interneurons and contribute to network hyperexcitability in early Alzheimer's ]]> https://biorxiv.org/cgi/content/short/2021.10.25.465789v1?rss=1" Olah, V. J. Goettemoeller, A. M. Dimidschstein, J. Rowan, M. J. 2021-10-26 doi:10.1101/2021.10.25.465789 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ MeCP2 deletion impaired layer 2/3-dominant dynamic reorganization of cortical circuit during motor skill learning ]]> https://biorxiv.org/cgi/content/short/786822v1?rss=1" Yue, Y. Xu, P. Liu, Z. Chen, Z. Su, J. Chen, A. Ash, R. Barut, E. Simha, R. Smirnakis, S. M. Zeng, C. Lu, H. 2019-09-30 doi:10.1101/786822 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Differences in social brain function in autism spectrum disorder are linked to the serotonin transporter ]]> https://biorxiv.org/cgi/content/short/2021.05.28.446151v1?rss=1" Wong, N. M. L. Dipasquale, O. Turkheimer, F. E. Findon, J. L. Wichers, R. H. Dimitrov, M. Murphy, C. M. Stoencheva, V. Robertson, D. M. Murphy, D. G. Daly, E. McAlonan, G. M. 2021-05-28 doi:10.1101/2021.05.28.446151 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ The ciliary gene INPP5E confers dorsal telencephalic identity to human cortical organoids by negatively regulating Sonic Hedgehog signalling ]]> https://biorxiv.org/cgi/content/short/2021.06.06.447245v1?rss=1" Schembs, L. Willems, A. Hasenpusch-Theil, K. Cooper, J. D. Whiting, K. Burr, K. Bostrand, S. M. K. Selvaraj, B. T. Chandran, S. Theil, T. 2021-06-06 doi:10.1101/2021.06.06.447245 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Computational Neuroimaging of Cognition-Emotion Interactions: Affective and Task-similar Interference Differentially Impact Working Memory ]]> https://biorxiv.org/cgi/content/short/2021.06.03.446811v1?rss=1" Ji, J. L. Repovs, G. Yang, G. J. Savic, A. Murray, J. D. Anticevic, A. 2021-06-03 doi:10.1101/2021.06.03.446811 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Identifying developing interneurons as a potential target for multiple genetic autism risk factors in human and rodent forebrain. ]]> https://biorxiv.org/cgi/content/short/2021.06.03.446920v1?rss=1" Yang, Y. Booker, S. A. Clegg, J. M. Quintana-Urzainqui, I. Sumera, A. Kozic, Z. R. Dando, O. R. Martin Lorenzo, S. Herault, Y. Kind, P. C. Price, D. J. Pratt, T. 2021-06-03 doi:10.1101/2021.06.03.446920 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Atypical gaze patterns in autism are heterogeneous across subjects but reliable within individuals ]]> https://biorxiv.org/cgi/content/short/2021.07.01.450793v1?rss=1" Keles, U. Kliemann, D. Byrge, L. Saarimaki, H. Paul, L. K. Kennedy, D. P. Adolphs, R. 2021-07-02 doi:10.1101/2021.07.01.450793 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Interpreting Polygenic Score Effects in Sibling Analysis ]]> https://biorxiv.org/cgi/content/short/2021.07.16.452740v1?rss=1" 50%) attenuations in the associations between polygenic scores and phenotypes compared to non-sibling models, consistent with researchers expectations about bias reduction. This paper explores these expectations by using family (quad) data and simulations that include indirect genetic effect processes and evaluates the ability of sibling models to uncover direct genetic effects. We find that sibling models, in general, fail to uncover direct genetic effects; indeed, these models have both upward and downward biases that are difficult to sign in typical data. When genetic nurture effects exist, sibling models create "measurement error" that attenuate associations between polygenic scores and phenotypes. As the correlation between direct and indirect effect changes, this bias can increase or decrease. Our findings suggest that interpreting results from sibling analysis aimed at uncovering direct genetic effects should be treated with caution. ]]> Fletcher, J. Wu, Y. Li, T. Lu, Q. 2021-07-17 doi:10.1101/2021.07.16.452740 Cold Spring Harbor Laboratory Press 2021-07-17 <![CDATA[ Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids ]]> https://biorxiv.org/cgi/content/short/2021.02.18.431674v1?rss=1" Sen, D. Voulgaropoulos, A. Keung, A. J. 2021-02-19 doi:10.1101/2021.02.18.431674 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Somatosensory processing deficits and altered cortico-hippocampal connectivity in Shank3b-/- mice ]]> https://biorxiv.org/cgi/content/short/2021.02.28.433258v1?rss=1" Balasco, L. Pagani, M. Pangrazzi, L. Schlosman, E. Mattioni, L. Galbusera, A. Provenzano, G. Gozzi, A. Bozzi, Y. 2021-02-28 doi:10.1101/2021.02.28.433258 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Generation of fate patterns via intercellular forces ]]> https://biorxiv.org/cgi/content/short/2021.04.30.442205v1?rss=1" Nunley, H. Xue, X. Fu, J. Lubensky, D. K. 2021-05-01 doi:10.1101/2021.04.30.442205 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ NeuroSCORE: A Genome-wide Omics-Based Model to Identify Candidate Disease Genes of the Central Nervous System ]]> https://biorxiv.org/cgi/content/short/2021.02.04.429640v1?rss=1" Davis, K. W. Bilancia, C. G. Martin, M. Vanzo, R. Rimmasch, M. Hom, Y. Uddin, M. Serrano, M. 2021-02-06 doi:10.1101/2021.02.04.429640 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Gamete simulation improves polygenic transmission disequilibrium analysis ]]> https://biorxiv.org/cgi/content/short/2020.10.26.355602v1?rss=1" Chen, J. You, J. Zhao, Z. Ni, Z. Huang, K. Wu, Y. Fletcher, J. Lu, Q. 2020-10-27 doi:10.1101/2020.10.26.355602 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo. ]]> https://biorxiv.org/cgi/content/short/2020.08.24.265389v1?rss=1" Liu, Y. Fischer, A. D. St. Pierre, C. L. Macias-Velasco, J. F. Lawson, H. A. Dougherty, J. D. 2020-08-24 doi:10.1101/2020.08.24.265389 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Identifying cell type specific driver genes in autism-associated copy number loci from cerebral organoids ]]> https://biorxiv.org/cgi/content/short/2020.11.15.375386v1?rss=1" Lim, E. T. 2020-11-17 doi:10.1101/2020.11.15.375386 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder ]]> https://biorxiv.org/cgi/content/short/2021.01.29.428895v1?rss=1" 60% not previously reported and 158 de novo retrotransposition events identified in whole genome sequencing (WGS) data of 2,288 families with ASD from the Simons Simplex Collection (SSC). As expected, the overall burden of de novo events was similar between ASD individuals and unaffected siblings, with 1 de novo insertion per 29, 104, and 192 births for Alu, L1, and SVA respectively, and 1 de novo insertion per 20 births total, while the location of transposon insertions differed between ASD and unaffected individuals. ASD cases showed more de novo L1 insertions than expected in ASD genes, and we also found de novo intronic retrotransposition events in known syndromic ASD genes in affected individuals but not in controls. Additionally, we observed exonic insertions in genes with a high probability of being loss-of-function intolerant, including a likely causative exonic insertion in CSDE1, only in ASD individuals. Although de novo retrotransposition occurs less frequently than single nucleotide and copy number variants, these findings suggest a modest, but important, impact of intronic and exonic retrotransposition mutations in ASD and highlight the utility of developing specific bioinformatic tools for high-throughput detection of transposable element insertions. ]]> Borges Monroy, R. Chu, C. Dias, C. Choi, J. Lee, S. Gao, Y. Shin, T. Park, P. J. Walsh, C. A. Lee, E. A. 2021-01-31 doi:10.1101/2021.01.29.428895 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data ]]> https://biorxiv.org/cgi/content/short/2021.01.29.428754v1?rss=1" Navarro, M. Simpson, I. 2021-02-01 doi:10.1101/2021.01.29.428754 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families ]]> https://biorxiv.org/cgi/content/short/2020.08.03.235358v1?rss=1" Whelan, C. W. Handsaker, R. E. Genovese, G. Kashin, S. Lek, M. Hughes, J. McElwee, J. Lenardo, M. MacArthur, D. McCarroll, S. A. 2020-08-04 doi:10.1101/2020.08.03.235358 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Demyelination induces selective vulnerability of inhibitory networks in multiple sclerosis ]]> https://biorxiv.org/cgi/content/short/2020.09.17.302042v1?rss=1" Zoupi, L. Booker, S. A. Eigel, D. Werner, C. Kind, P. C. Spires-Jones, T. Newland, B. Williams, A. 2020-09-19 doi:10.1101/2020.09.17.302042 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model ]]> https://biorxiv.org/cgi/content/short/2020.02.09.940965v1?rss=1" Ward, T. R. Zhang, X. Leung, L. C. Zhou, B. Muench, K. Roth, J. G. Khechaduri, A. Plastini, M. J. Charlton, C. Pattni, R. Ho, S. Ho, M. Huang, Y. Hallmayer, J. F. Mourrain, P. Palmer, T. D. Urban, A. E. 2020-02-10 doi:10.1101/2020.02.09.940965 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Structural neuroplasticity after sleep loss modifies behavior and requires neurexin and neuroligin ]]> https://biorxiv.org/cgi/content/short/2023.06.20.545788v1?rss=1" View larger version (34K): org.highwire.dtl.DTLVardef@2320c4org.highwire.dtl.DTLVardef@3c3b86org.highwire.dtl.DTLVardef@67dc96org.highwire.dtl.DTLVardef@c3033d_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractGABAergic morphologic and behavioral plasticity induced by developmental sleep deprivation depends on the conserved autism genes, nrx-1 and nlg-1 A) Sleep depriving male C. elegans during all larval sleep periods in development (aptf-1 or npr-1) or selectively inhibiting sleep during L4-adult molt (vibration or RIS silencing) results in an increase in DVB outgrowth. B) Mutations in nrx-1 (and nlg-1 in npr-1 animals) prevent sleep deprivation induced morphologic plasticity changes. C) DVB neurite outgrowth results in a functional change in spicule protraction rate as a result of increased GABAergic inhibitory signaling, which also depends on nrx-1 and nlg-1. C_FIG ]]> Cowen, M. H. Raizen, D. M. Hart, M. P. 2023-06-24 doi:10.1101/2023.06.20.545788 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Compensation between FOXP transcription factors maintains proper striatal function ]]> https://biorxiv.org/cgi/content/short/2023.06.26.546567v1?rss=1" Ahmed, N. I. Khandelwal, N. Anderson, A. G. Kulkarni, A. Gibson, J. Konopka, G. 2023-06-26 doi:10.1101/2023.06.26.546567 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Developmental molecular controls over arealization of descending cortical motor pathways ]]> https://biorxiv.org/cgi/content/short/2023.06.29.546438v1?rss=1" Abe, P. Lavalley, A. Morassut, I. Klingler, E. Santinha, A. J. Platt, R. J. Jabaudon, D. 2023-06-30 doi:10.1101/2023.06.29.546438 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Reprogramming method does not impact the neuronal differentiation potential of 16p11.2 deletion patient iPSCs ]]> https://biorxiv.org/cgi/content/short/2023.07.07.548182v1?rss=1" Wells, M. F. Guss, E. Zhou, H. Sun, B. Martinez, H. Akopian, V. Noggle, S. Paull, D. Moore, J. Sheldon, M. Sommer, J. Benedetti, M. Meissner, A. Eggan, K. 2023-07-08 doi:10.1101/2023.07.07.548182 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ The organisation and turnover of synaptic proteins within molecular supercomplexes. ]]> https://biorxiv.org/cgi/content/short/2023.07.13.548866v1?rss=1" Morris, K. Bulovaite, E. Kaizuka, T. Adams, C. Komiyama, N. Grant, S. G. N. Horrocks, M. H. 2023-07-13 doi:10.1101/2023.07.13.548866 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Distinct roles of putative excitatory and inhibitory neurons in the macaque inferior temporal cortex in core object recognition behavior ]]> https://biorxiv.org/cgi/content/short/2023.08.01.551579v1?rss=1" Sanghavi, S. Kar, K. 2023-08-03 doi:10.1101/2023.08.01.551579 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Characterizing Subcortical Structural Heterogeneity in Autism ]]> https://biorxiv.org/cgi/content/short/2023.08.28.554882v1?rss=1" MacDonald, D. N. Bedford, S. A. Olafson, E. Park, M. T. M. Devenyi, G. A. Tullo, S. Patel, R. Anagnostou, E. Baron-Cohen, S. Bullmore, E. T. Chura, L. R. Craig, M. C. Ecker, C. Floris, D. L. Holt, R. J. Lenroot, R. Lerch, J. P. Lombardo, M. V. Murphy, D. G. M. Raznahan, A. Ruigrok, A. N. V. Smith, E. Shinohara, R. T. Spencer, M. D. Suckling, J. Taylor, M. J. Thurm, A. MRC AIMS Consortium, Lai, M.-C. Chakravarty, M. M. 2023-08-29 doi:10.1101/2023.08.28.554882 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Single cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism ]]> https://biorxiv.org/cgi/content/short/2023.09.22.559056v1?rss=1" Perez, Y. Velmeshev, D. Wang, L. White, M. Siebert, C. Baltazar, J. Dutton, N. G. Wang, S. Haeussler, M. Chamberlain, S. Kriegstein, A. 2023-09-22 doi:10.1101/2023.09.22.559056 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI ]]> https://biorxiv.org/cgi/content/short/2024.02.08.579330v1?rss=1" Chorbadjiev, L. Cokol, M. Weinstein, Z. Shi, K. Fleisch, C. Dimitrov, N. Mladenov, S. Xu, S. Hall, J. Ford, S. Lee, Y.-h. Yamrom, B. Marks, S. Munoz, A. Lash, A. Volfovsky, N. Iossifov, I. 2024-02-11 doi:10.1101/2024.02.08.579330 Cold Spring Harbor Laboratory Press 2024-02-11