S
Shan Dong
Researcher at University of California, San Francisco
Publications - 24
Citations - 10331
Shan Dong is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Exome sequencing & Copy-number variation. The author has an hindex of 17, co-authored 24 publications receiving 7221 citations. Previous affiliations of Shan Dong include Yale University & Tongji University.
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Journal ArticleDOI
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
Chen Xie,Xizeng Mao,Jiaju Huang,Yang Ding,Jianmin Wu,Shan Dong,Lei Kong,Ge Gao,Chuan-Yun Li,Liping Wei +9 more
TL;DR: A web server, KOBAS 2.0, is reported, which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations, which allows for both ID mapping and cross-species sequence similarity mapping.
Journal ArticleDOI
The contribution of de novo coding mutations to autism spectrum disorder
Ivan Iossifov,Brian J. O'Roak,Stephen Sanders,Stephen Sanders,Michael Ronemus,Niklas Krumm,Dan Levy,Holly A.F. Stessman,Kali Witherspoon,Laura Vives,Karynne E. Patterson,Joshua D. Smith,Bryan W. Paeper,Deborah A. Nickerson,Jeanselle Dea,Shan Dong,Shan Dong,Luis E. Gonzalez,Jeffrey D. Mandell,Shrikant Mane,Michael T. Murtha,Catherine A.W. Sullivan,Michael F. Walker,Zainulabedin Waqar,Liping Wei,A. Jeremy Willsey,A. Jeremy Willsey,Boris Yamrom,Yoon-ha Lee,Ewa A. Grabowska,Ertugrul Dalkic,Ertugrul Dalkic,Zihua Wang,Steven Marks,Peter Andrews,Anthony Leotta,Jude Kendall,Inessa Hakker,Julie Rosenbaum,Beicong Ma,Linda Rodgers,Jennifer Troge,Giuseppe Narzisi,Seungtai Yoon,Michael C. Schatz,Kenny Ye,W. Richard McCombie,Jay Shendure,Evan E. Eichler,Evan E. Eichler,Matthew W. State,Matthew W. State,Michael Wigler +52 more
TL;DR: It is estimated that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation.
Journal ArticleDOI
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.
Stephen Sanders,Xin He,A. Jeremy Willsey,A. Gulhan Ercan-Sencicek,Kaitlin E. Samocha,Kaitlin E. Samocha,A. Ercument Cicek,A. Ercument Cicek,Michael T. Murtha,Vanessa H. Bal,Somer L. Bishop,Shan Dong,Arthur P. Goldberg,Cai Jinlu,John F. Keaney,Lambertus Klei,Jeffrey D. Mandell,Daniel Moreno-De-Luca,Christopher S. Poultney,Elise B. Robinson,Elise B. Robinson,Louw Smith,Tor Solli-Nowlan,Mack Y. Su,Nicole A. Teran,Michael F. Walker,Donna M. Werling,Arthur L. Beaudet,Rita M. Cantor,Eric Fombonne,Daniel H. Geschwind,Dorothy E. Grice,Catherine Lord,Jennifer K. Lowe,Shrikant Mane,Donna M. Martin,Eric M. Morrow,Michael E. Talkowski,James S. Sutcliffe,Christopher A. Walsh,Timothy W. Yu,David H. Ledbetter,Christa Lese Martin,Edwin H. Cook,Joseph D. Buxbaum,Mark J. Daly,Mark J. Daly,Bernie Devlin,Kathryn Roeder,Matthew W. State +49 more
TL;DR: Analysis of de novo CNVs from the full Simons Simplex Collection replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci, including 6 CNV regions.
Journal ArticleDOI
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
F. Kyle Satterstrom,F. Kyle Satterstrom,Jack A. Kosmicki,Jiebiao Wang,Michael S. Breen,Silvia De Rubeis,Joon Yong An,Joon Yong An,Minshi Peng,Ryan Collins,Jakob Grove,Jakob Grove,Lambertus Klei,Christine Stevens,Jennifer Reichert,Maureen Mulhern,Mykyta Artomov,Sherif Gerges,Brooke Sheppard,Xinyi Xu,Aparna Bhaduri,Utku Norman,Harrison Brand,Grace Schwartz,Rachel Nguyen,Elizabeth E. Guerrero,Caroline Dias,Branko Aleksic,Richard Anney,Mafalda Barbosa,Somer L. Bishop,Alfredo Brusco,Jonas Bybjerg-Grauholm,Angel Carracedo,Marcus C.Y. Chan,Andreas G. Chiocchetti,Brian H.Y. Chung,Hilary Coon,Michael L. Cuccaro,Aurora Currò,Bernardo Dalla Bernardina,Ryan N. Doan,Enrico Domenici,Shan Dong,Chiara Fallerini,Montserrat Fernández-Prieto,Giovanni Battista Ferrero,Christine M. Freitag,Menachem Fromer,J. Jay Gargus,Daniel H. Geschwind,Elisa Giorgio,Javier González-Peñas,Stephen J. Guter,Danielle Halpern,Emily Hansen-Kiss,Xin He,Gail E. Herman,Irva Hertz-Picciotto,David M. Hougaard,Christina M. Hultman,Iuliana Ionita-Laza,Suma Jacob,Jesslyn Jamison,Astanand Jugessur,Miia Kaartinen,Gun Peggy Knudsen,Alexander Kolevzon,Itaru Kushima,So Lun Lee,Terho Lehtimäki,Elaine T. Lim,Carla Lintas,W. Ian Lipkin,Diego Lopergolo,Fátima Lopes,Yunin Ludena,Patrícia Maciel,Per Magnus,Behrang Mahjani,Nell Maltman,Dara S. Manoach,Gal Meiri,Idan Menashe,Judith Miller,Nancy J. Minshew,Eduarda Montenegro M. de Souza,Danielle de Paula Moreira,Eric M. Morrow,Ole Mors,Preben Bo Mortensen,Matthew W. Mosconi,Pierandrea Muglia,Benjamin M. Neale,Merete Nordentoft,Norio Ozaki,Aarno Palotie,Mara Parellada,Maria Rita Passos-Bueno,Margaret A. Pericak-Vance,Antonio M. Persico,Isaac N. Pessah,Kaija Puura,Abraham Reichenberg,Alessandra Renieri,Evelise Riberi,Elise B. Robinson,Elise B. Robinson,Kaitlin E. Samocha,Sven Sandin,Sven Sandin,Susan L. Santangelo,Susan L. Santangelo,Gerry Schellenberg,Stephen W. Scherer,Sabine Schlitt,Rebecca J. Schmidt,Lauren M. Schmitt,Isabela Maya Wahys Silva,Tarjinder Singh,Tarjinder Singh,Paige M. Siper,Moyra Smith,Gabriela Soares,Camilla Stoltenberg,Pål Surén,Ezra Susser,John A. Sweeney,Peter Szatmari,Lara Tang,Flora Tassone,Karoline Teufel,Elisabetta Trabetti,Maria del Pilar Trelles,Christopher A. Walsh,Lauren A. Weiss,Thomas Werge,Donna M. Werling,Emilie M. Wigdor,Emilie M. Wigdor,Emma Wilkinson,A. Jeremy Willsey,Timothy W. Yu,Mullin H.C. Yu,Ryan Yuen,Elaine Cristina Zachi,Esben Agerbo,Thomas Damm Als,Vivek Appadurai,Marie Bækvad-Hansen,Rich Belliveau,Alfonso Buil,Caitlin E. Carey,Felecia Cerrato,Kimberly Chambert,Claire Churchhouse,Claire Churchhouse,Søren Dalsgaard,Ditte Demontis,Ashley Dumont,Jacqueline I. Goldstein,Christine Søholm Hansen,Mads E. Hauberg,Mads E. Hauberg,Mads E. Hauberg,Mads V. Hollegaard,Daniel P. Howrigan,Hailiang Huang,Julian Maller,Alicia R. Martin,Joanna Martin,Manuel Mattheisen,Jennifer L. Moran,Jonatan Pallesen,Duncan S. Palmer,Carsten Bøcker Pedersen,Marianne Giørtz Pedersen,Timothy Poterba,Jesper Buchhave Poulsen,Stephan Ripke,Andrew J. Schork,Wesley K. Thompson,Patrick Turley,Raymond K. Walters,Catalina Betancur,Edwin H. Cook,Louise Gallagher,Michael Gill,James S. Sutcliffe,Audrey Thurm,Michael E. Zwick,Anders D. Børglum,Matthew W. State,A. Ercument Cicek,A. Ercument Cicek,Michael E. Talkowski,David J. Cutler,Bernie Devlin,Stephen Sanders,Kathryn Roeder,Mark J. Daly,Joseph D. Buxbaum +201 more
TL;DR: The largest exome sequencing study of autism spectrum disorder (ASD) to date, using an enhanced analytical framework to integrate de novo and case-control rare variation, identifies 102 risk genes at a false discovery rate of 0.1 or less, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.
Journal ArticleDOI
Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism
A. Jeremy Willsey,A. Jeremy Willsey,Stephen Sanders,Stephen Sanders,Mingfeng Li,Shan Dong,Shan Dong,Andrew T.N. Tebbenkamp,Rebecca A. Muhle,Steven K. Reilly,Leon Lin,Sofia Fertuzinhos,Jeremy A. Miller,Michael T. Murtha,Candace Bichsel,Wei Niu,Justin Cotney,A. Gulhan Ercan-Sencicek,Jake Gockley,Abha R. Gupta,Wenqi Han,Xin He,Ellen J. Hoffman,Lambertus Klei,Jing Lei,Wenzhong Liu,Li Liu,Cong Lu,Xuming Xu,Ying Zhu,Shrikant Mane,Ed S. Lein,Liping Wei,James P. Noonan,Kathryn Roeder,Bernie Devlin,Nenad Sestan,Matthew W. State +37 more
TL;DR: Coexpression networks are constructed based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood and demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons.