媒体报道与论文清单

  媒体报道


      2022年6月，转化医学网媒体报道《Nucleic Acids Research丨PiER：专属于遗传靶点量化推荐的在线服务工具》，并转载于网易、腾讯等多家新闻媒体。
      2022年5月，BioArtMED媒体报道《NAR丨方海自主研发在线服务工具PiER，零编程实现遗传靶点计算转化》。

      2021年11月，BioArt媒体报道《NAR丨方海发布免疫疾病遗传靶点数据库“优先指数”，助力计算转化医学研究》。

      2019年6月，BioArt媒体报道《Nature Genetics丨方海博士等研发药物治疗靶点优先指数，使以遗传学为导向的GWAS医学转化研究更靠近临床现实》。

  论文清单


    OpenXGR: a web-server update for genomic summary data interpretation

    Nucleic Acids Research 2023

    DOI: 10.1093/nar/gkad357

    The dcGO domain-centric ontology database in 2023: new website and extended annotations for protein structural domains

    Journal of Molecular Biology 2023

    DOI: 10.1016/j.jmb.2023.168093

    Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis

    Cell Genomics 2023

    DOI: 10.1016/j.xgen.2023.100306

    Diverse rescue potencies of p53 mutations to ATO are predetermined by intrinsic mutational properties

    Science Translational Medicine 2023

    DOI: 10.1126/scitranslmed.abn9155

    Hypothesis-free phenotype prediction within a genetics-first framework

    Nature Communications 2023

    DOI: 10.1038/s41467-023-36634-6

    When cancer drug resistance meets metabolomics (bulk, single-cell and/or spatial): Progress, potential, and perspective

    Frontiers in Oncology 2023

    DOI: 10.3389/fonc.2022.1054233

    PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions

    Nucleic Acids Research 2022

    DOI: 10.1093/nar/gkac379

    Priority index: database of genetic targets in immune-mediated disease

    Nucleic Acids Research 2022

    DOI: 10.1093/nar/gkab994

    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

    Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance

    Genome Biology 2022

    DOI: 10.1186/s13059-022-02702-1

    Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation

    Oncogene 2022

    DOI: 10.1038/s41388-022-02516-2

    A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

    Cell 2022

    DOI: 10.1016/j.cell.2022.01.012

    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

    Transcriptome-based molecular subtypes and differentiation hierarchies improve the classification framework of acute myeloid leukemia

    Proceedings of the National Academy of Sciences 2022

    DOI: 10.1073/pnas.2211429119

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

    Blood 2021

    DOI: 10.1182/blood.2020005698

    Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort

    EBioMedicine 2021

    DOI: 10.1016/j.ebiom.2021.103716

    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

    Distinct immune signatures discriminate between asymptomatic and presymptomatic SARS-CoV-2pos subjects

    Cell Research 2021

    DOI: 10.1038/s41422-021-00562-1

    Genetic Interaction Network Interpretation: A Tidy Data Science Perspective

    Epistasis: Methods and Protocols 2021

    DOI: 10.1007/978-1-0716-0947-7_22

    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

    Integration of genomic and transcriptomic markers improves the prognosis prediction of acute promyelocytic leukemia

    Clinical Cancer Research 2021

    DOI: 10.1158/1078-0432.CCR-20-4375

    Genomic insights into myasthenia gravis identify distinct immunological mechanisms in early and late onset disease

    Annals of Neurology 2021

    DOI: 10.1002/ana.26169

    Transcriptomic analysis of inflammatory cardiomyopathy identifies molecular signatures of disease and informs in silico prediction of a network-based rationale for therapy

    Frontiers in Immunology 2021

    DOI: 10.3389/fimmu.2021.640837

    From genome-wide association studies to rational drug target prioritisation in inflammatory arthritis

    Lancet Rheumatology 2020

    DOI: 10.1016/S2665-9913(19)30134-1

    Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

    Nature Medicine 2020

    DOI: 10.1038/s41591-019-0734-6

    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

    The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Genome Biology 2019

    DOI: 10.1186/s13059-019-1835-8

    The association between endometriosis and autoimmune diseases: a systematic review and meta-analysis

    Human Reproduction Update 2019

    DOI: 10.1093/humupd/dmz012

    Regulatory genomic data cubism

    iScience 2018

    DOI: 10.1016/j.isci.2018.04.017

    Unique transcriptome signatures and GM-CSF expression in lymphocytes from patients with spondyloarthritis

    Nature Communications 2017

    DOI: 10.1038/s41467-017-01771-2

    XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
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    Genome Medicine 2016

    DOI: 10.1186/s13073-016-0384-y

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Genome biology 2016

    DOI: 10.1186/s13059-016-1037-6

    Evolution of the calcium-based intracellular signalling system

    Genome Biology and Evolution 2016

    DOI: 10.1093/gbe/evw139

    Genome-wide studies identify a novel interplay between AML1 and AML1/ETO in t(8;21) acute myeloid leukemia

    Blood 2016

    DOI: 10.1182/blood-2015-03-626671

    A predictive computational framework for direct reprogramming between human cell types

    Nature Genetics 2016

    DOI: 10.1038/ng.3487

    Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

    Biochimie 2015

    DOI: 10.1016/j.biochi.2015.05.003

    A proteome quality index

    Environmental Microbiology 2015

    DOI: 10.1111/1462-2920.12622

    The SUPERFAMILY 1.75 database in 2014: a doubling of data

    Nucleic Acids Research 2015

    DOI: 10.1093/nar/gku1041

    The ‘dnet’ approach promotes emerging research on cancer patient survival

    Genome Medicine 2014

    DOI: 10.1186/s13073-014-0064-8

    The Evolution of Human Cells in Terms of Protein Innovation

    Molecular Biology and Evolution 2014

    DOI: 10.1093/molbev/mst139

    dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

    PLoS Computational Biology 2014

    DOI: 10.1371/journal.pcbi.1003929

    Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy

    Nature Communications 2014

    DOI: 10.1038/ncomms5741

    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

    A promoter-level mammalian expression atlas

    Nature 2014

    DOI: 10.1038/nature13182

    A large-scale evaluation of computational protein function prediction

    Nature Methods 2013

    DOI: 10.1038/nmeth.2340

    A disease-drug-phenotype matrix inferred by walking on a functional domain network

    Molecular BioSystems 2013

    DOI: 10.1039/c3mb25495j

    A daily-updated tree of (sequenced) life as a reference for genome research

    Scientific Reports 2013

    DOI: 10.1038/srep02015

    A domain-centric solution to functional genomics via dcGO Predictor

    BMC Bioinformatics 2013

    DOI: 10.1186/1471-2105-14-S3-S9

    dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

    Nucleic Acids Research 2013

    DOI: 10.1093/nar/gks1080

    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

    SUPERFAMILY 1.75 including a domain-centric gene ontology method

    Nucleic Acids Research 2011

    DOI: 10.1093/nar/gkq1130

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

    OMICS : A Journal of Integrative Biology 2011

    DOI: 10.1089/omi.2010.0066

    An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro

    BMC Systems Biology 2011

    DOI: 10.1186/1752-0509-5-108

    Transcriptome analysis of early organogenesis in human embryos

    Developmental Cell 2010

    DOI: 10.1016/j.devcel.2010.06.014

    PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia

    Cancer Cell 2010

    DOI: 10.1016/j.ccr.2009.12.045

    p21-Activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration

    Endocrine 2010

    DOI: 10.1007/S12020-010-9324-6

    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