组会分享的文献列表 Paper presentation for Journal club


分享时间 演讲人                文献题目 PMID
(Date) (Presenter)                (Article Title)
       
    表达谱&单细胞测序 Expression & single cell related  
2020-06-12 蔡文翔 "Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease", Nat Gen 2020 May 32341526
2020-07-21 陈宇璨 "Brain cell type–specific enhancer–promoter interactome maps and disease-risk association", Science 2019 Nov Science
TBD TBD "Conserved cell types with divergent features in human versus mouse cortex", Nature 2019 July 31435019
TBD TBD "Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits", Nat Genetics 2019 May 31086352
TBD TBD "Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex", bioRxiv 2019 Mar bioRxiv
TBD TBD "A statistical framework for cross-tissue transcriptome-wide association analysis", Nat Genet. 2019 Mar 30804563
TBD TBD "Cell lineage inference from SNP and scRNA-Seq data", Nucleic Acids Res. 2019, Mar 30820578
TBD TBD "Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells", Nat Biotech 2018, Oct 30320766
TBD TBD "A test metric for assessing single-cell RNA-seq batch correction", Nat Method 2019, Jan 30573817
2019-11-01 姜雪 "Single-cell transcriptomic analysis of Alzheimer’s disease", Nature 2019, June 31042697
2019-06-21 陈淼 "Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures", Cell Reports 2019, Feb 30811995
2019-04-12 陈亮 "Single-cell reconstruction of the early maternal–fetal interface in humans", Nature 2018, Nov 30429548
2019-03-22 方钰 "Integrative functional genomic analysis of human brain development and neuropsychiatric risks", Science 2018, Dec 30545854
2019-01-02 宋炜宸 "Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.", Science 2018, Dec 30545856
2018-11-8 宋炜宸 "Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region", Science 2018, Oct 30385464
2018-10-18 方钰 "Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis", Nat Neurosci. 2018 Aug 30050107
2018-7-26 宋炜宸 "Genetic identification of brain cell types underlying schizophrenia", Nat Genet. 2018 Jun 29785013
2018-3-6 王卫娣 Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex, Science. 2017 Dec 29217575
       
    机器学习 Machine leaning & deep learning related  
2022-9-30 宋炜宸 "A sequence-based global map of regulatory activity for deciphering human genetics", Nat Genet. 2022, July Nat Genet.
TBD TBD "A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action", Cell 2019, May Cell
TBD TBD "End-to-End Differentiable Learning of Protein Structure", Cell Systems 2019, April Cell Systems
TBD TBD "A primer on deep learning in genomics", Nat Genetics 2019, Jan 3047844
TBD TBD "Deep learning in biomedicine", Nat Biotech 2018, Oct 30188539
TBD TBD "Single-cell RNA-seq denoising using a deep count autoencoder", Nat Comm 2019, Jan 30674886
TBD TBD "Using multiple measurements of tissue to estimate cell-type-specific gene expression via deconvolution", biorxiv 2018, Dec biorxiv
TBD TBD "Can Deep Learning Improve Genomic Prediction of Complex Human Traits?", Genetics 2019, Jan XXX
TBD TBD "Using deep learning to model the hierarchical structure and function of a cell", Nat Method 2018, April 29505029
TBD TBD "Deep learning is combined with massive-scale citizen science to improve large-scale image classification", Nat Biotech 2018, Oct 30125267
2020-05-02 潘伟豪 "Automated analysis of immunohistochemistry images identifies candidate location biomarkers for cancers", Proc Natl Acad Sci U S A. 2014, Dec 25489103
2020-01-03 钱威 "Predicting the clinical impact of human mutation with deep neural networks", Nat Gen 2018, Aug 30038395
2019-04-12 钱威 "Predicting Splicing from Primary Sequence with Deep Learning", Cell 2019, Jan 30661751
       
    组学和集成分析 Omic & intergrative analysis related  
TBD TBD "DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits", Genome biology 2019, Dec Genome biology
TBD TBD "Genes with High Network Connectivity Are Enriched for Disease Heritability", AJHG 2019, May Cell
TBD TBD "Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities", Cell 2019, May Cell
2019-12-06 陈宇璨 "A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data", Nat. Neurosci 2019, April 30988527
TBD TBD "A reference map of the human protein interactome", BioRxiv 2019, April BioRxiv
TBD TBD "GeNets: a unified web platform for network-based genomic analyses", Nat. Methods 2018, Jun 29915188
TBD TBD "A Computational Framework for Genome-wide Characterization of the Human Disease Landscape", Cell Systems 2019, Feb 30685436
TBD TBD "Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues", Mol Syst Biol. 2019, Feb 30777893
TBD TBD "Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets", Molecular Systems Biology 2018, June 29925568
2019-11-01 王卫娣 "Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders", Genome Medicine 2019, Nov Genome Medicine
2019-06-05 王卫娣 "Gene expression imputation across multiple brain regions provides insights into schizophrenia risk", Nature Genetics 2019, Apr 30911161
2019-05-10 宋炜宸 "Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis", Cell 2015, Jul 26095251
2019-04-19 陈淼 "Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism", Nature 2016, Dec 27919067
2019-04-19 陈淼 "Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq", Science 2015, Feb 25700174
2019-04-19 姜雪 "Comprehensive functional genomic resource and integrative model for the human brain", Science 2018, Dec 30545857
2019-03-15 陈淼 "A deep proteome and transcriptome abundance atlas of 29 healthy human tissues", Mol Syst Biol. 2019, Feb 30777892
2019-02-27 钱威 "Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set", Nat Comm 2019, Jan 30602777
2019-02-27 陈淼 "An integrative tissue-network approach to identify and test human disease genes", Nat Biotech 2018, Oct 30346941
2019-01-09 钱威 "A resource of variant effect predictions of single nucleotide variants in model organisms", Molecular Systems Biology 2018, Dec 30573687
2019-01-09 陈淼 "Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders", Cell Systems 2017, Aug 28822752
       
    疾病和突变 Disease variant related  
TBD TBD "Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer", AJHG 2019, May 31006514
TBD TBD "Genetic compensation triggered by mutant mRNA degradation", Nature 2019, April Nature
TBD TBD "Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions", Cell 2019, March Cell
TBD TBD "Genome-wide analysis reveals extensive genetic overlap between schizophrenia, bipolar disorder, and intelligence", Mol Psy 2019, Jan 30610197
TBD TBD "Characterizing the Major Structural Variant Alleles of the Human Genome", Cell 2019, Jan 30661756
TBD TBD "ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties", Mol Psy 2018, Feb 28044064
TBD TBD "Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk", Nat Genet 2018, Sep 30127527
TBD TBD "Genomic Patterns of De Novo Mutation in Simplex Autism", Cell 2017, Oct 28965761
TBD TBD "Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples", Nat Gen 2017, Feb 28191890
TDB TDB "Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk", bioRxiv 2018, Nov bioRxiv
2020-07-03 宋炜宸 "Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders", Cell 2019, Dec 3183502
2020-01-03 蔡文翔 "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition", Nature Neurosci 2018, Dec 30455454
2019-07-09 王卫娣 "High-throughput identification of human SNPs affecting regulatory element activity", Nature Genetics 2019, Jun 31253979
2019-06-21 钱威 "Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk", Nature Genetics 2019, Jun 31133750
2019-06-05 姜雪 "Genomic Analysis in the Age of Human Genome Sequencing", Cell 2019, Mar 30901550
2019-05-27 赵晶晶 "Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood", Cell 2019, April Cell
2019-05-10 蔡文翔 "Postnatal Tshz3 Deletion Drives Altered Corticostriatal Function and Autism Spectrum Disorder-like Behavior", Biol Psychiatry 2019, Mar 31060802
2019-03-22 钱威 "Characterizing mutagenic effects of recombination through a sequence-level genetic map", Science 2019, Jan 30679340
2019-01-09 王卫娣 "Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity", Nat. Gen 2018, Dec 30559488
2018-6-26 王卫娣 "Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes", Cell. 2018 Jun 29906448
       
    可变剪切&非编码 Splicing & noncoding related  
TBD TBD "Axonogenesis Is Coordinated by Neuron-Specific Alternative Splicing Programming and Splicing Regulator PTBP2", Neuron 2019, Feb 30733148
TBD TBD "Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis", Cell 2018, Feb 29474919
TBD TBD "The human noncoding genome defined by genetic diversity", Nat Genet 2018, Sep 29483654
TBD TBD "Whole-genome sequencing of quartet families with autism spectrum disorder", Nat Med 2015, Feb 25621899
TBD TBD "An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder", Nat Genet 2018, May 29700473
TBD TBD "Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing", Cell 2019, Jan 30661752
2019-03-29 赵晶晶 "Intron retention is a source of neoepitopes in cancer", Nat Biotech 2018, Aug 30114007
2019-01-02 赵晶晶 "Rbfox1 Mediates Cell-type-Specific Splicing in Cortical Interneurons", Neuron 2018, Nov 30318414
2019-01-16 陈亮 "The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes", Sci Transl Med 2018, Dec 30545965
2019-01-02 姜雪 "Whole-genome sequencing in autism identifies hot spots for de novo germline mutation", Cell 2012, Dec 23260136
2018-12-27 陈亮 "Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations", Nat Genet 2018, Nov 30297966
2018-7-5 赵晶晶 "Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism", Nature. 2016 27919067
2018-5-4 王卫娣 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression, Nat Genet. 2018 Apr 29610481
       
2018
2018-11-1 王卫娣 "The UK Biobank resource with deep phenotyping and genomic data", Nature 2018, Oct 30305743
2018-10-25 姜雪 "Genome-wide association studies of brain imaging phenotypes in UK Biobank", Nature 2018, Oct 30305740
2018-9-26 赵晶晶 "Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes", Am J Hum Genet. 2017 Sep 28867141
2018-9-10 程影 "Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk", Nat Genet. 2018 Sep 30127527
2018-8-2 陈亮 Prevalence of rearrangements in the 22q11.2 region and population-based risk of neuropsychiatric and developmental disorders in a Danish population: a case-cohort study, Lancet Psychiatry. 2018 Jul 29886042
2018-7-19 王卫娣 "An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders", Nat Genet. 2018 Jul 29892012
2018-7-3 方钰 "Analysis of shared heritability in common disorders of the brain", Science. 2018 Jun 29930110
2018-6-22 程影 "Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder", Mol Psychiatry. 2018 Apr 28322282
2018-6-3 方钰 "De novo mutations in regulatory elements in neurodevelopmental disorders", Nature. 2018 Mar 29562236
2018-5-13 陈亮 "Copy Number Variation in Obsessive-Compulsive Disorder and Tourette Syndrome: A Cross-Disorder Study", J Am Acad Child Adolesc Psychiatry. 2014 Aug 25062598
2018-5-6 宋炜宸 "An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder", Nat Genet. 2018 May 29700473
2018-4-22 赵晶晶 Excess translation of epigenetic regulators contributes to Fragile X Syndrome and is alleviated by Brd4 inhibition, Cell. 2017 Sep 28823556
2018-4-7 程影 Interactome analysis reveals ZNF804A, a schizophrenia risk gene, as a novel component of protein translational machinery critical for embryonic neurodevelopment, Mol Psychiatry. 2018 28924186
2018-3-30 方钰 Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap, Science. 2018 Feb 29439242
2018-3-9 王卫娣 Damaging de novo mutations diminish motor skills in children on the autism spectrum, PNAS 2018 Feb 29434036
2018-1-16 程影 Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia, Nat Genet. 2017 Nov 28991256