Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families.

[1]  J. Gusella,et al.  Disruption of MBD5 contributes to a spectrum of psychopathology and neurodevelopmental abnormalities , 2014, Molecular Psychiatry.

[2]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[3]  J. Rosenfeld,et al.  Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder , 2013, European Journal of Human Genetics.

[4]  Wei Niu,et al.  Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism , 2013, Cell.

[5]  William Stafford Noble,et al.  Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome , 2013, Nucleus.

[6]  Sharmila Banerjee-Basu,et al.  SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs) , 2013, Molecular Autism.

[7]  E. Chen,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[8]  Wei Wu,et al.  From neural development to cognition: unexpected roles for chromatin , 2013, Nature Reviews Genetics.

[9]  Scott B. Selleck,et al.  Global increases in both common and rare copy number load associated with autism , 2013, Human molecular genetics.

[10]  David C. Atkins,et al.  A tutorial on count regression and zero-altered count models for longitudinal substance use data. , 2013, Psychology of addictive behaviors : journal of the Society of Psychologists in Addictive Behaviors.

[11]  Bradley P. Coe,et al.  Estimates of penetrance for recurrent pathogenic copy-number variations , 2012, Genetics in Medicine.

[12]  Charlotte Soneson,et al.  A comparison of methods for differential expression analysis of RNA-seq data , 2013, BMC Bioinformatics.

[13]  Christian Gilissen,et al.  Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. , 2012, American journal of human genetics.

[14]  Yuan Tian,et al.  Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. , 2012, American journal of human genetics.

[15]  A. Reymond,et al.  KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant , 2012, Nature.

[16]  H. Sive,et al.  Zebrafish homologs of genes within 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes , 2012, Disease Models & Mechanisms.

[17]  Toshiro K. Ohsumi,et al.  Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries , 2012, Cell.

[18]  Kenny Q. Ye,et al.  De Novo Gene Disruptions in Children on the Autistic Spectrum , 2012, Neuron.

[19]  Chris Williams,et al.  RNA-SeQC: RNA-seq metrics for quality control and process optimization , 2012, Bioinform..

[20]  Michael F. Walker,et al.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism , 2012, Nature.

[21]  Evan T. Geller,et al.  Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.

[22]  J. Baio.  Prevalence of autism spectrum disorders--Autism and Developmental Disabilities Monitoring Network, 14 sites, United States, 2008. , 2012, Morbidity and mortality weekly report. Surveillance summaries.

[23]  Peter Langfelder,et al.  Fast R Functions for Robust Correlations and Hierarchical Clustering. , 2012, Journal of statistical software.

[24]  Bradley P. Coe,et al.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations , 2012, Nature.

[25]  Roberto Sacco,et al.  Genome-wide expression studies in Autism spectrum disorder, Rett syndrome, and Down syndrome , 2012, Neurobiology of Disease.

[26]  I. Voineagu.  Gene expression studies in autism: Moving from the genome to the transcriptome and beyond , 2012, Neurobiology of Disease.

[27]  Steven P Lund,et al.  Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates , 2012, Statistical applications in genetics and molecular biology.

[28]  Min Zhao,et al.  AutismKB: an evidence-based knowledgebase of autism genetics , 2011, Nucleic Acids Res..

[29]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[30]  Mark D. Robinson,et al.  Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design , 2012 .

[31]  J. Rosenfeld,et al.  Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder. , 2011, American journal of human genetics.

[32]  P. Elliott,et al.  Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus , 2011, Nature.

[33]  Andreas Buja,et al.  Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism , 2011, Proceedings of the National Academy of Sciences.

[34]  M. O’Driscoll,et al.  The consequences of structural genomic alterations in humans: genomic disorders, genomic instability and cancer. , 2011, Seminars in cell & developmental biology.

[35]  M. Salit,et al.  Synthetic Spike-in Standards for Rna-seq Experiments Material Supplemental Open Access License Commons Creative , 2022 .

[36]  Gregory M. Cooper,et al.  A Copy Number Variation Morbidity Map of Developmental Delay , 2011, Nature Genetics.

[37]  S. Zhong,et al.  High-throughput illumina strand-specific RNA sequencing library preparation. , 2011, Cold Spring Harbor protocols.

[38]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[39]  Kathryn Roeder,et al.  Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism , 2011, Neuron.

[40]  S. Horvath,et al.  Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology , 2011, Nature.

[41]  Jeff H. Chang,et al.  The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq , 2011 .

[42]  R. Hennekam,et al.  The atypical 16p11.2 deletion: A not so atypical microdeletion syndrome? , 2011, American journal of medical genetics. Part A.

[43]  Wei Liu,et al.  Statistical Applications in Genetics and Molecular Biology Linear Combination Test for Hierarchical Gene Set Analysis , 2011 .

[44]  M. Daly,et al.  Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology , 2011, PLoS genetics.

[45]  R. Evans,et al.  Esrrg functions in early branch generation of the ureteric bud and is essential for normal development of the renal papilla , 2010, Human molecular genetics.

[46]  Alan Agresti,et al.  Categorical Data Analysis , 2003 .

[47]  William N. Venables,et al.  Modern Applied Statistics with S , 2010 .

[48]  N. Friedman,et al.  Comprehensive comparative analysis of strand-specific RNA sequencing methods , 2010, Nature Methods.

[49]  Gary D Bader,et al.  Functional impact of global rare copy number variation in autism spectrum disorders , 2010, Nature.

[50]  A. Reymond,et al.  The effect of translocation-induced nuclear reorganization on gene expression. , 2010, Genome research.

[51]  Stephen R. Williams,et al.  Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures , 2010, European Journal of Human Genetics.

[52]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[53]  D Gianola,et al.  Technical note: an R package for fitting generalized linear mixed models in animal breeding. , 2010, Journal of animal science.

[54]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[55]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[56]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

[57]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[58]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[59]  J. Lupski,et al.  Mechanisms for human genomic rearrangements , 2008, PathoGenetics.

[60]  Edwin H. Cook,et al.  Copy-number variations associated with neuropsychiatric conditions , 2008, Nature.

[61]  Joshua M. Korn,et al.  Association between microdeletion and microduplication at 16p11.2 and autism. , 2008, The New England journal of medicine.

[62]  D. Pinto,et al.  Structural variation of chromosomes in autism spectrum disorder. , 2008, American journal of human genetics.

[63]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[64]  Alex Magee,et al.  Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. , 2006, American journal of human genetics.

[65]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Hiroaki Kitano,et al.  The PANTHER database of protein families, subfamilies, functions and pathways , 2004, Nucleic Acids Res..

[67]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[68]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[69]  Standards, Guidelines and Best Practices for Rna-seq V1.0 (june 2011) the Encode Consortium , 2022 .