非监督式人工智能自组织学习

  工具概括

      灵感起源于人脑认知，该人工智能神经网络算法通过非监督方式，神经网络上各个神经元根据输入训练数据集（如多维生物组学数据）进行竞争性学习训练调整，实现从高维输入到低维输出（2D输出），相关前期工作发表在Developmental Cell（2010）、Biochemical Biophysical Research Communications（2014），并受邀撰写人工智能领域专著《Applications of Self-organizing Maps》第9章节。受天然形成蜂巢特殊结构启发，结合毕加索的立体主义，创造性地构建“超正六边形”及其衍生的一系列2D拓扑结构，实现调控组学立体主义，形成了基于自组织学习拓扑优化算法的多维组学数据聚类、整合与可视化展示的新体系（iScience 2018），发布于Bioconductor，迄今下载量为5万7千余次，并成功地应用于基因表达的遗传调控研究（Genomics Proteomics Bioinformatics 2019）、新冠宿主的多组学动态图谱可视化展示（Cell Discovery 2021）。


      同名艺术作品荣获第22届国际分子生物学智能系统ISMB年会“最佳艺术品奖（Best Artwork Award）”。此外，为了揭示异常转录因子在急性早幼粒细胞白血病发生中的分子调控网络，通过多组学研究手段（ChIP-seq、RNA-seq等技术），绘制了PML/RARa融合蛋白靶基因全图谱绘制并重新定义其异常转录调控机制，发现新的调控靶基因GFI1，并开展了体内外实验验证（Blood 2021）。近期，成功地应用于急性T淋巴细胞白血病患者转录组队列研究（PNAS 2022）。


  论文发表

    Genomic evidence supports the recognition of endometriosis as an inflammatory systemic disease and reveals disease-specific therapeutic potentials of targeting neutrophil degranulation
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    Frontiers in Immunology 2022

    DOI: 10.3389/fimmu.2022.758440

    Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases

    Proceedings of the National Academy of Sciences 2022

    DOI: 10.1073/pnas.2120787119

    A PML/RARα direct target atlas redefines transcriptional deregulation in acute promyelocytic leukemia

    Blood 2021

    DOI: 10.1182/blood.2020005698

    Genetic prioritization, therapeutic repositioning and cross-disease comparisons reveal inflammatory targets tractable for kidney stone disease

    Frontiers in Immunology 2021

    DOI: 10.3389/fimmu.2021.687291

    Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19

    Cell Discovery 2021

    DOI: 10.1038/s41421-021-00274-1

    A genetics-led approach defines the drug target landscape of 30 immune-related traits
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    Nature Genetics 2019

    DOI: 10.1038/s41588-019-0456-1

    I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data

    Genomics, Proteomics and Bioinformatics 2019

    DOI: 10.1016/j.gpb.2018.10.006

    Regulatory genomic data cubism

    iScience 2018

    DOI: 10.1016/j.isci.2018.04.017

    Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy

    Nature Communications 2014

    DOI: 10.1038/ncomms5741

    The 'dnet' approach promotes emerging research on cancer patient survival

    Genome Medicine 2014

    DOI: 10.1186/s13073-014-0064-8

    supraHex: An R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map

    Biochemical and Biophysical Research Communications 2014

    DOI: 10.1016/j.bbrc.2013.11.103

    The evolution of human cells in terms of protein innovation

    Molecular Biology and Evolution 2014

    DOI: 10.1093/molbev/mst139

    Preferential eradication of acute myelogenous leukemia stem cells by fenretinide

    Proceedings of the National Academy of Sciences 2013

    DOI: 10.1073/pnas.1302352110

    Using self-organizing maps to visualize, filter and cluster multidimensional bio-omics data

    Developments and Applications of Self-Organizing Maps 2012

    DOI: 10.5772/51702

    An interferon-related signature in the transcriptional core response of human macrophages to mycobacterium tuberculosis infection

    PLoS ONE 2012

    DOI: 10.1371/journal.pone.0038367

    A topology-preserving selection and clustering approach to multidimensional biological data

    OMICS : A Journal of Integrative Biology 2011

    DOI: 10.1089/omi.2010.0066

    Transcriptome analysis of early organogenesis in human embryos

    Developmental Cell 2010

    DOI: 10.1016/j.devcel.2010.06.014

    Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome reveal novel molecular mechanism

    Endocrine-Related Cancer 2009

    DOI: 10.1677/ERC-08-0325

    Converting redox signaling to apoptotic activities by stress-responsive regulators HSF1 and NRF2 in fenretinide treated cancer cells

    PloS ONE 2009

    DOI: 10.1371/journal.pone.0007538

    Transcriptome and proteome analyses of drug interactions with natural products

    Current Drug Metabolism 2008

    DOI: 10.2174/138920008786927802

    Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia

    Blood 2006

    DOI: 10.1182/blood-2005-06-2318