{"id":83,"date":"2018-10-29T14:41:33","date_gmt":"2018-10-29T14:41:33","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/kuanhuanglab\/?page_id=83"},"modified":"2025-10-22T21:28:26","modified_gmt":"2025-10-22T21:28:26","slug":"publication","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/kuanhuanglab\/publication\/","title":{"rendered":"Publication"},"content":{"rendered":"<p>[et_pb_section fb_built=&#8221;1&#8243; _builder_version=&#8221;4.16&#8243; global_colors_info=&#8221;{}&#8221;][et_pb_row _builder_version=&#8221;4.16&#8243; background_size=&#8221;initial&#8221; background_position=&#8221;top_left&#8221; background_repeat=&#8221;repeat&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_column type=&#8221;4_4&#8243; _builder_version=&#8221;4.16&#8243; custom_padding=&#8221;|||&#8221; global_colors_info=&#8221;{}&#8221; custom_padding__hover=&#8221;|||&#8221;][et_pb_code _builder_version=&#8221;4.27.4&#8243; global_colors_info=&#8221;{}&#8221;]<!-- Google tag (gtag.js) --><!-- [et_pb_line_break_holder] --><script src=\"https:\/\/www.googletagmanager.com\/gtag\/js?id=G-848HQGTE7Z\"><\/script><!-- [et_pb_line_break_holder] --><script><!-- [et_pb_line_break_holder] -->  window.dataLayer = window.dataLayer || [];<!-- [et_pb_line_break_holder] -->  function gtag(){dataLayer.push(arguments);}<!-- [et_pb_line_break_holder] -->  gtag('js', new Date());<!-- [et_pb_line_break_holder] --><!-- [et_pb_line_break_holder] -->  gtag('config', 'G-848HQGTE7Z');<!-- [et_pb_line_break_holder] --><\/script><!-- [et_pb_line_break_holder] --><script src=\"https:\/\/ajax.googleapis.com\/ajax\/libs\/jquery\/3.1.0\/jquery.min.js\"><\/script><!-- [et_pb_line_break_holder] --><!-- [et_pb_line_break_holder] --><script type='text\/javascript' src='https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js'><\/script><!-- [et_pb_line_break_holder] --><script type=\"text\/javascript\" src=\"\/\/cdn.plu.mx\/widget-popup.js\"><\/script>[\/et_pb_code][et_pb_text admin_label=&#8221;Text&#8221; _builder_version=&#8221;4.27.4&#8243; text_line_height=&#8221;1.5em&#8221; header_3_text_color=&#8221;#006ac1&#8243; background_size=&#8221;initial&#8221; background_position=&#8221;top_left&#8221; background_repeat=&#8221;repeat&#8221; vertical_offset_tablet=&#8221;0&#8243; horizontal_offset_tablet=&#8221;0&#8243; hover_enabled=&#8221;0&#8243; text_font_size_tablet=&#8221;&#8221; text_font_size_phone=&#8221;&#8221; text_font_size_last_edited=&#8221;on|desktop&#8221; z_index_tablet=&#8221;0&#8243; text_text_shadow_horizontal_length_tablet=&#8221;0px&#8221; text_text_shadow_vertical_length_tablet=&#8221;0px&#8221; text_text_shadow_blur_strength_tablet=&#8221;1px&#8221; link_text_shadow_horizontal_length_tablet=&#8221;0px&#8221; link_text_shadow_vertical_length_tablet=&#8221;0px&#8221; link_text_shadow_blur_strength_tablet=&#8221;1px&#8221; ul_text_shadow_horizontal_length_tablet=&#8221;0px&#8221; ul_text_shadow_vertical_length_tablet=&#8221;0px&#8221; ul_text_shadow_blur_strength_tablet=&#8221;1px&#8221; 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header_4_text_shadow_blur_strength_tablet=&#8221;1px&#8221; header_5_text_shadow_horizontal_length_tablet=&#8221;0px&#8221; header_5_text_shadow_vertical_length_tablet=&#8221;0px&#8221; header_5_text_shadow_blur_strength_tablet=&#8221;1px&#8221; header_6_text_shadow_horizontal_length_tablet=&#8221;0px&#8221; header_6_text_shadow_vertical_length_tablet=&#8221;0px&#8221; header_6_text_shadow_blur_strength_tablet=&#8221;1px&#8221; box_shadow_horizontal_tablet=&#8221;0px&#8221; box_shadow_vertical_tablet=&#8221;0px&#8221; box_shadow_blur_tablet=&#8221;40px&#8221; box_shadow_spread_tablet=&#8221;0px&#8221; global_colors_info=&#8221;{}&#8221; sticky_enabled=&#8221;0&#8243;]<\/p>\n<p><script type=\"text\/javascript\" src=\"https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js\"><\/script> <script src=\"https:\/\/ajax.googleapis.com\/ajax\/libs\/jquery\/3.1.0\/jquery.min.js\"><\/script><\/p>\n<p><script type=\"text\/javascript\" src=\"\/\/cdn.plu.mx\/widget-popup.js\"><\/script> <script type=\"text\/javascript\" src=\"https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js\"><\/script><\/p>\n<h1>PUBLICATIONS (selected)<\/h1>\n<blockquote>\n<p><strong>Huang Members (Volunteer or Mount Sinai) <span style=\"color: #800080\"><span style=\"color: #333333\">| *Co-first Authors | #Co-corresponding Authors | &#8220;Consortium authorship<\/span><\/span><\/strong><\/p>\n<p><strong>Complete &amp; updated lists of publications on <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=kuan-lin+huang&amp;sort=date&amp;size=200\">PubMed<\/a> or <a href=\"https:\/\/scholar.google.com\/citations?user=jLvQLMcAAAAJ\">Google Scholar<\/a><\/strong><\/p>\n<\/blockquote>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41593-025-02063-5\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41593-025-02063-5\">Globally accessible platforms for the exchange of research findings and career development.<\/a><br \/>Salamero-Boix A<span style=\"color: #800080\"><span style=\"color: #333333\">*#<\/span><\/span>, Contreras Castillo E<span style=\"color: #800080\"><span style=\"color: #333333\">*#<\/span><\/span>, Lin CJ<span style=\"color: #800080\"><span style=\"color: #333333\">*#<\/span><\/span>, <strong>Huang KL<\/strong><span style=\"color: #800080\"><span style=\"color: #333333\">*#<\/span><\/span><br \/><em>Nature Neuroscience<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1126\/science.adm7066\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.science.org\/doi\/10.1126\/science.adm7066\">Machine learning-based penetrance of genetic variants.<\/a><br \/>Forrest IS, Vy HMT, Rocheleau G, Jordan DM, Petrazzini BO, Nadkarni GN, Cho JH, Ganapathi M, <strong>Huang KL<\/strong>, Chung WK, Do R<br \/><em>Science<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41588-025-02212-3\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41588-025-02212-3\">Using large-scale population-based data to improve disease risk assessment of clinical variants.<\/a><br \/>Forrest IS, <strong>Huang KL<\/strong>, Eggington JM, Chung WK, Jordan DM, Do R<br \/><em>Nature Genetics<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41467-025-58796-1\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41467-025-58796-1\">A clinical benchmark of public self-supervised pathology foundation models.<\/a><br \/>Campanella G, Chen S, Singh M, Verma R, Muehlstedt S, Zeng J, Stock A, Croken M, Veremis B, <strong>Elmas A<\/strong>, Shujski I, Neittaanm\u00e4ki N, <strong>Huang KL<\/strong>, Kwan R, Houldsworth J, Schoenfeld AJ, Vanderbilt C<br \/><em>Nature Communications<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.cell.2025.03.026\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1016\/j.cell.2025.03.026\">Precision proteogenomics reveals pan-cancer impact of germline variants.<\/a><br \/>Martins Rodrigues F, Terekhanova NV, Imbach KJ, Clauser KR, Esai Selvan M, Mendizabal I, Geffen Y, Akiyama Y, Maynard M, Yaron TM, Li Y, Cao S, Storrs EP, Gonda OS, Gaite-Reguero A, Govindan A, Kawaler EA, Wyczalkowski MA, Klein RJ, Turhan B, Krug K, Mani DR, Leprevost FDV, Nesvizhskii AI, Carr SA, Feny\u00f6 D, Gillette MA, Colaprico A, Iavarone A, Robles AI, <strong>Huang KL<\/strong>, Kumar-Sinha C, Aguet F, Lazar AJ, Cantley LC, Marigorta UM, G\u00fcm\u00fc\u015f ZH, Bailey MH, Getz G, Porta-Pardo E, Ding L; Clinical Proteomic Tumor Analysis Consortium<br \/><em>Cell<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1158\/1078-0432.CCR-24-2785\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1158\/1078-0432.CCR-24-2785\">Germline Pathogenic DROSHA Variants Are Linked to Pineoblastoma and Wilms Tumor Predisposition.<\/a><br \/>Fiorica PN, Golmard L, Kim J, Bao R, Lin FY, Roy A, Pribnow A, Perrino MR, Masliah-Planchon J, Michalak-Provost S, Wong J, Filser M, Stoppa-Lyonnet D, Bourdeaut F, Brahimi A, Ingster O, Saulnier Sholler G, Jackson SA, Sasaki MM, Fowler T, Ng A, Corbett RJ, Kaufman RS, Haley JS, Carey DJ, <strong>Huang KL<\/strong>, Diskin SJ, Rokita JL, Al-Kateb H, McGee RB, Schiffman JD, Chen KS, Stewart DR, Williams Parsons D, Plon SE, Schultz KAP, Onel K<br \/><em>Clinical Cancer Research<\/em> 2025.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1093\/gigascience\/giae113\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1093\/gigascience\/giae113\">Mutation impact on mRNA versus protein expression across human cancers.<\/a><br \/><strong>Liu Y<span style=\"color: #800080\"><span style=\"color: #333333\">*<\/span><\/span><\/strong>, <strong>Elmas A<span style=\"color: #800080\"><span style=\"color: #333333\">*<\/span><\/span><\/strong>, <strong>Huang KL<\/strong><br \/><em>GigaScience<\/em> 2025. [<a href=\"https:\/\/github.com\/Huang-lab\/pQTL\">GitHub<\/a>]<\/p>\n<h3>2024<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1101\/2024.11.11.619147\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1101\/2024.11.11.619147\">Master regulators governing protein abundance across ten human cancer types.<\/a><br \/><strong>Wang Z<\/strong>, <strong>Wojciechowicz M, Rosen J<\/strong>, <strong>Elmas A<\/strong>, Song WM, <strong>Liu Y<\/strong>, <strong>Huang KL<\/strong><br \/><em>bioRxiv<\/em> [Preprint] 2024.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1101\/2024.10.17.618926\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1101\/2024.10.17.618926\">Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine.<\/a><br \/><strong>Elmas A<\/strong>, Layden HM, Ellis JD, Bartlett LN, Zhao X, Kawabata-Iwakawa R, Obinata H, Hiebert SW, <strong>Huang KL<\/strong><br \/><em>bioRxiv<\/em> [Preprint] 2024.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1101\/2024.10.17.618945\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1101\/2024.10.17.618945\">Deletions Rate-Limit Breast and Ovarian Cancer Initiation.<\/a><br \/><strong>Houlahan KE<span style=\"color: #800080\"><span style=\"color: #333333\">*<\/span><\/span>, Bihie M<span style=\"color: #800080\"><span style=\"color: #333333\">*<\/span><\/span>, Greatti Y<span style=\"color: #800080\"><span style=\"color: #333333\">*<\/span><\/span>, Contreras JG, Fulop DJ<\/strong>, Lopez G, Huang HH, Van Loo P, Curtis C, Boutros PC, <strong>Huang KL<\/strong><br \/><em>bioRxiv<\/em> [Preprint] 2024.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.isci.2024.110640\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1016\/j.isci.2024.110640\">Structural analysis of genomic and proteomic signatures reveal dynamic expression of intrinsically disordered regions in breast cancer.<\/a><br \/><strong>Zatorski N<\/strong>, Sun Y, <strong>Elmas A<\/strong>, Dallago C, Karl T, Stein D, Rost B, <strong>Huang KL<\/strong>, Walsh M, Schlessinger A<br \/><em>iScience<\/em> 2024.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.3390\/ijms25137376\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.3390\/ijms25137376\">Associations of Circulating Biomarkers with Disease Risks: A Two-Sample Mendelian Randomization Study.<\/a><br \/><strong>Elmas A<\/strong>, Spehar K, Do R, Castellano JM, <strong>Huang KL<\/strong><br \/><em>International Journal of Molecular Sciences<\/em> 2024.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"10.46471\/gigabyte.126\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/gigabytejournal.com\/articles\/126\">Get Free Copy: a multi-repository search platform for biomedical publications<\/a><br \/><strong>Kosimkhujaev N<\/strong>, <strong>Huang KL<\/strong><br \/><em>GigaByte<\/em> 2024. [<a href=\"https:\/\/getfreecopy.com\/\">GetFreeCopy<\/a>][<a href=\"http:\/\/gigasciencejournal.com\/blog\/llms-openboxscience-getfreecopy\/\">GigaScience Editor BlogPost<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s43856-024-00437-7\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s43856-024-00437-7\">Machine learning models identify predictive features of patient mortality across dementia types<\/a><br \/><strong>Zhang J<\/strong>, Luo S, Miller Z, Chan KCG, <strong>Huang KL<\/strong><br \/><em>Communications Medicine<\/em> 2024. [<a href=\"https:\/\/github.com\/Huang-lab\/dementia-survival-prediction\">GitHub<\/a>][<a href=\"https:\/\/health.mountsinai.org\/blog\/ai-spotlight-predicting-risk-of-death-in-dementia-patients\/\">Mount Sinai AI BlogPost<\/a>]<\/p>\n<h3>2023<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1186\/s13045-023-01517-2\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1186\/s13045-023-01517-2\">Multiscale protein networks systematically identify aberrant protein interactions and oncogenic regulators in seven cancer types.<\/a><br \/>Song WM, <strong>Elmas A<\/strong>, Farias R, Xu P, Zhou X, Hopkins B, <strong>Huang KL<\/strong>, Zhang B<br \/><em>Journal of Hematology &amp; Oncology<\/em> 2023.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1007\/s00262-023-03381-y\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s00262-023-03381-y\">Using EGFR amplification to stratify recurrent glioblastoma treated with immune checkpoint inhibitors.<\/a><br \/>Friedman JS,<strong> Jun T<\/strong>, Rashidipour O, <strong>Huang KL<\/strong>, Ellis E, Kadaba P, Belani P, Nael K, Tsankova NM, Sebra R, Hormigo A<br \/><em>Cancer Immunology, Immunotherapy<\/em> 2023.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41586-022-05598-w\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41586-022-05598-w\">Pan-cancer analysis of whole genomes.<\/a><br \/><strong>ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium&#8221;<\/strong><br \/><em>Nature<\/em> 2023.<\/p>\n<h3>2022<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.3389\/fcimb.2022.933190\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2022.933190\/full\">Multiethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes.<\/a><br \/><strong>Jun T<\/strong>, Mathew D, Sharma N, Nirenberg S, Huang HH, Kovatch P, Wherry EJ, <strong>Huang KL<\/strong><br \/><em>Frontiers in Cellular and Infection Microbiology<\/em> 2022.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.3389\/fonc.2022.814120\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fonc.2022.814120\/full\">Proteomic Analyses Identify Therapeutic Targets in Hepatocellular Carcinoma.<\/a><br \/><strong>Elmas A<\/strong>, Lujambio A, <strong>Huang KL<\/strong><br \/><em>Frontiers in Oncology<\/em> 2022.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.chaos.2022.111927\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1016\/j.chaos.2022.111927\">Modeling COVID-19 dynamic using a two-strain model with vaccination.<\/a><br \/><strong>de Le\u00f3n UA<\/strong>, Avila-Vales E, <strong>Huang KL<\/strong><br \/><em>Chaos, Solitons &amp; Fractals<\/em> 2022.<\/p>\n<h3>2021<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.3390\/cancers13184572\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.mdpi.com\/2072-6694\/13\/18\/4572\">Genomic Determinants of Homologous Recombination Deficiency across Human Cancers<\/a><br \/><span style=\"color: #800080\"><strong>Qing T<\/strong><\/span>, <span style=\"color: #800080\"><strong>X Wang<\/strong><\/span>, <strong>Jun T<\/strong>, Ding L, Pusztai L#, <strong>Huang KL#<\/strong>.<br \/><em>Cancers<\/em> 2021.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1186\/s13073-021-00964-1\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-021-00964-1\">Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes<\/a><br \/><strong>Wang Z<\/strong>, Fan X, Shen Y, Pagadala MS, <strong>Signer R<\/strong>, Cygan KJ, Fairbrother WG, Carter H, Chung WK#, <strong>Huang KL#<\/strong>.<br \/><em>Genome Medicine<\/em> 2021. [<a href=\"https:\/\/github.com\/WangZishan\/TCGASecondaryPredisposition\">GitHub]<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41598-021-93126-7\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41598-021-93126-7\">Prediction of individual COVID-19 diagnosis using baseline demographics and lab data<\/a><br \/><strong><span style=\"color: #800080\">Zhang J<\/span>, Jun T<\/strong>, <strong><span style=\"color: #800080\">Frank J<\/span><\/strong>, Nirenberg S, Kovatch P, <strong>Huang KL<\/strong>.<br \/><em>Scientific Reports<\/em> 2021. [<a href=\"https:\/\/github.com\/Huang-lab\/covid19-diagnosis-prediction\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s43856-021-00006-2\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s43856-021-00006-2.epdf\">Analysis of sex-speci\ufb01c risk factors and clinical outcomes in COVID-19<\/a><br \/><strong>Jun T<\/strong>, Nirenberg S, <strong>Weinberger T<\/strong>, <span style=\"color: #800080\"><strong>Sharma N<\/strong><\/span>, Pujadas E, Cordon-Cardo C, Kovatch P, <strong>Huang KL<\/strong>.<br \/><em>Communications Medicine<\/em> 2021. [<a href=\"https:\/\/github.com\/Huang-lab\/SParCS\/tree\/master\/MSSM_COVID\/R\">GitHub<\/a>] [<a href=\"https:\/\/www.news-medical.net\/news\/20200803\/Research-explains-recognized-sex-differences-in-COVID-19-outcomes.aspx\">News<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.2147\/CMAR.S311548\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.dovepress.com\/the-functional-hallmarks-of-cancer-predisposition-genes-peer-reviewed-fulltext-article-CMAR\">The Functional Hallmarks of Cancer Predisposition Genes<\/a><br \/><strong>Capellini A*<\/strong>, <strong>Williams M*<\/strong>, Onel K#, <strong>Huang KL#<\/strong>.<br \/><em>Cancer Manag Res.<\/em>\u00a02021.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41598-021-91713-2\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41598-021-91713-2\">Genetic dependency of Alzheimer\u2019s disease-associated genes across cells and tissue types<\/a><br \/><strong>Jaladanki SK*<\/strong>, <strong>Elmas A*<\/strong>, <strong>Malave GS<\/strong>, <strong>Huang KL<\/strong>.<br \/><em>Scientific Reports<\/em> 2021.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.isci.2021.102550\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2589004221005186\">Phenome-wide and expression quantitative trait locus associations of COVID-19 genetic risk loci<\/a><br \/><strong>Moon C<\/strong>, Schilder BM, Raj T, <strong>Huang KL<\/strong>.<br \/><em>iScience<\/em> 2021.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.xcrm.2021.100276\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S266637912100104X\">Diverse Immune Response of DNA Damage Repair-Deficient Tumors<\/a><br \/><span style=\"color: #800080\"><strong>Qing T<\/strong><\/span>, <strong>Jun T<\/strong>, Lindblad KE, Lujambio A, Marczyk M, Pusztai L#, <strong>Huang KL#<\/strong>.<br \/><em>Cell Reports Medicine<\/em> 2021. [<a href=\"https:\/\/github.com\/tao-qing\/DDRImmune\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41467-021-22481-w\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41467-021-22481-w\">Systematic discovery of spatially interacting phosphorylation sites and mutations in cancer<\/a><br \/><strong>Huang KL#<\/strong>, Scott AD, Zhou DC, Wang LB, Weerasinghe A, <strong>Elmas A<\/strong>, Liu R, Sengupta S, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Feny\u00f6 D, Chen K, Mills G, Ding L#.<br \/><em>Nature Communications<\/em> 2021. [<a href=\"https:\/\/github.com\/ding-lab\/hotspot3d\">GitHub for software<\/a>][<a href=\"https:\/\/github.com\/ding-lab\/HotPho_Analysis\">GitHub for analysis scripts<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1142\/9789811232701_0017\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/9789811232701_0017\">AeQTL: eQTL analysis using region-based aggregation of rare variants<\/a><br \/><span style=\"color: #800080\"><strong>Dong G<\/strong><\/span>, Wendl M, Zhang B, Ding L,<strong> Huang KL<\/strong>.<br \/><em>Pac Symp Biocomput.<\/em> 2021. <em>[<a href=\"https:\/\/github.com\/Huang-lab\/AeQTL\">GitHub<\/a>]<\/em><\/p>\n<h3>2020<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.cell.2020.11.004\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S009286742031463X\">Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors<\/a><br \/>Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O&#8217;Donnell T, Chakraborty L, Samstein R, <strong>Huang KL<\/strong>, Blank SV, Greenbaum B, Bhardwaj N.<br \/><em>Cell<\/em>\u00a02020.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41467-020-18534-1\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32968074\/\">Risk prediction of late-onset Alzheimer&#8217;s disease implies an oligogenic architecture<\/a><br \/>Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, Goate AM, Marcora E,<b>\u00a0Huang KL<\/b>, Porter T, Laws SM; Australian Imaging Biomarkers and Lifestyle (AIBL) Study, Sachdev PS, Mather KA, Armstrong NJ, Thalamuthu A, Brodaty H, Yengo L, Yang J, Wray NR, McRae AF, Visscher PM.<br \/><em>Nature Communications<\/em>\u00a02020.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1186\/s13073-020-00744-3\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-020-00744-3\">Ancestry-Specific Predisposing Germline Variants in Cancer<\/a><br \/><span class=\"highwire-citation-author first\"><span class=\"nlm-surname\"><span style=\"color: #800080\"><strong>Oak N<\/strong><\/span><\/span><\/span>,\u00a0Cherniack AD, Mashl RJ; TCGA Analysis Network, Hirsch FR, Ding L, Beroukhim R, G\u00fcm\u00fc\u015f ZH, Plon SE, <strong>Huang KL.<\/strong><br \/><em>Genome Medicine<\/em> 2020. [<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.04.14.032557v1\">bioRxiv<\/a>][<a href=\"https:\/\/github.com\/Huang-lab\/AncestralCancerPredisposition\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1111\/ahg.12389\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1111\/ahg.12389\">Genotype Concordance and Polygenic Risk Score Estimation across Consumer Genetic Testing Data<\/a><br \/><span style=\"color: #800080\"><strong>Batra P<\/strong><\/span>, <strong>Huang KL.<\/strong><br \/><em>Annals of Human Genetics<\/em> 2020. [<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/795666v2\">bioRxiv<\/a>][<a href=\"https:\/\/github.com\/Huang-lab\/AncestralCancerPredisposition\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.ccell.2020.04.012\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.cell.com\/cancer-cell\/pdf\/S1535-6108(20)30211-7.pdf\">Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer\u00a0<\/a><br \/>Carrot-Zhang J*, Chambwe N*, Damrauer JS*, Knijnenburg TA*, Robertson AG*, Yau C*, Zhou W*, Berger AC*, <strong>Huang KL<\/strong>*, Newberg JY*, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E, Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R.<br \/><em>Cancer Cell <\/em>2020.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1371\/journal.pcbi.1007723\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1007723\">Ten Simple Rules for landing on the right job after your PhD or postdoc<\/a><br \/><strong>Huang KL<\/strong>.<br \/><em>PLoS Computational Biology<\/em> 2020. [<a href=\"https:\/\/www.youtube.com\/watch?v=O6HZJgqhxA4\">YouTube<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41586-020-1969-6\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/doi.org\/10.1038\/s41586-020-1969-6\">Pan-cancer analysis of whole genomes<\/a><br \/><strong>ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium&#8221;<\/strong>.<br \/><em>Nature<\/em> 2020.<\/p>\n<h3>2019<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1074\/mcp.RA118.001243\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1535947620340639\">Regulated phosphosignaling associated with breast cancer subtypes and druggability<\/a><br \/><strong>Huang KL<span style=\"color: #800080\"><span style=\"color: #333333\">#<\/span><\/span><\/strong>, Wu Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Ellis MJ, Fenyo\u0308 D, Chen F, Townsend RR, Carr SA, Ding L<span style=\"color: #800080\"><span style=\"color: #333333\">#.<\/span><\/span><br \/><em>Molecular and Cellular Proteomics<\/em> 2019. [<a href=\"https:\/\/github.com\/ding-lab\/phosphoproteomics\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1002\/hep.30677\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/aasldpubs.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/hep.30677\">Mannose Phosphate Isomerase and Mannose Regulate Hepatic Stellate Cell Activation and Fibrosis in Zebrafish and Humans<\/a><br \/>DeRossi C, Bambino K, Morrison J, Sakarin I, Villacorta-Martin C, Zhang C, Ellis JL, Fiel MI, Ybanez M, Lee YA, <strong>Huang KL<\/strong>, Yin C, Sakaguchi TF, Friedman SL, Villanueva A, Chu J.<br \/><em>Hepatology<\/em> 2019.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1371\/journal.pgen.1008049\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.1008049\">Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity<\/a><br \/>Adamovich AI, Banerjee T, Wingo M, Duncan K, Ning J, Martins Rodrigues F, <strong>Huang KL<\/strong>, Lee C, Chen F, Ding L, Parvin JD.<br \/><em>PLoS Genetics<\/em> 2019.<\/p>\n<h3>2018<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1002\/humu.23668\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/humu.23668\">Framework for microRNA variant annotation and prioritization using human population and disease datasets<\/a><br \/>Oak N, Ghosh R, <strong>Huang KL<\/strong>, Wheeler DA, Ding L, Plon SE.<br \/><em>Human Mutation<\/em>. 2018 Oct 10. [<a href=\"https:\/\/github.com\/nroak\/ADmiRE\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1093\/bioinformatics\/bty649\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/bty649\/25542157\/bty649.pdf\">CharGer: Clinical Characterization of Germline Variants<\/a><br \/>Scott AD#, <strong>Huang KL<\/strong>, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski M, Ding L#.<br \/><em>Bioinformatics<\/em>. 2018 Aug 9.\u00a0[<a href=\"https:\/\/github.com\/ding-lab\/CharGer\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1186\/s13073-018-0564-z\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-018-0564-z\">Integrative omics analyses broaden treatment targets in human cancer<\/a><br \/>Sengupta S*, Sun SQ*, <strong>Huang KL<\/strong>, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Feny\u00f6 D, Townsend RR, Dipersio JF, Chen F, Ding L.<br \/><em>Genome Medicine<\/em>. 2018 Jul 27;10(1):60.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.cell.2018.03.039\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.cell.com\/action\/showPdf?pii=S0092-8674%2818%2930363-5\">Pathogenic Germline Variants in 10,389 Adult Cancers<\/a><br \/><strong> Huang KL<\/strong>, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F#, Ding L#.<br \/><em>Cell<\/em>. 2018 Apr 5;173(2):355-370.e14. [<a href=\"https:\/\/github.com\/ding-lab\/PanCanAtlasGermline\">GitHub<\/a>] [Controlled-access variant-call data available: <a href=\"https:\/\/gdc.cancer.gov\/about-data\/publications\/PanCanAtlas-Germline-AWG\">GDC<\/a>] [Presentation: <a href=\"https:\/\/www.youtube.com\/watch?v=-jDVm8_x-zM&amp;t=6s\">YouTube<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1016\/j.cell.2018.03.033\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867418303131\">Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics<\/a><br \/>Ding L#, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, <strong>Huang KL<\/strong>, Tokheim C, Cort\u00e9s-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA#, Getz G#; Cancer Genome Atlas Research Network.<br \/><em>Cell<\/em>. 2018 Apr 5;173(2):305-320.e10.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/s41422-018-0019-5\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41422-018-0019-5\">Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types<\/a><br \/>Cao Y, Zhou W, Li L, Wang J, Gao Z, Jiang Y, Jiang X, Shan A, Bailey MH, <strong>Huang<\/strong> <strong>KL<\/strong>, Sun SQ, McLellan MD, Niu B, Wang W, Ding L, Ning G.<br \/><em>Cell Research<\/em>. 2018 May;28(5):601-604.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1158\/0008-5472.CAN-17-1990\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"http:\/\/cancerres.aacrjournals.org\/content\/78\/10\/2732\">Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers<\/a><br \/>Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, <strong>Huang KL<\/strong>, Yoon CJ, Ding L, Feny\u00f6 D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.<br \/><em>Cancer Research<\/em>. 2018 May 15;78(10):2732-2746.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/d41586-018-01076-4\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/d41586-018-01076-4\">Most popular public searches on gene names<\/a><br \/><strong>Huang KL<\/strong>.<br \/><em> Nature<\/em>. 2018 Jan 25;553(7689):405. [<a href=\"go.nature.com\/2dsjvdm\">Gene Google Trend Data<\/a>]<\/p>\n<h3>2017<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1126\/scisignal.aam8065\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"http:\/\/stke.sciencemag.org\/content\/10\/491\/eaam8065\">Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner<\/a><br \/>Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR,<strong> Huang<\/strong> <strong>KL<\/strong>, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Feny\u00f6 D, Held JM.<br \/><em>Science Signalling<\/em>. 2017 Aug 8;10(491).<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/nn.4587\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/nn.4587\">A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer&#8217;s disease<\/a><br \/><strong>Huang KL*<\/strong>, Marcora E*, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, van der Lee S, Del-Aguila JL, Fernandez MV, Iba\u00f1ez L; International Genomics of Alzheimer&#8217;s Project; Alzheimer&#8217;s Disease Neuroimaging Initiative, Sims R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM.<br \/><em>Nature Neuroscience<\/em>. 2017 Aug;20(8):1052-1061. [<a href=\"https:\/\/github.com\/kuanlinhuang\/AD_SPI1_project\">GitHub<\/a>][<a href=\"https:\/\/www.youtube.com\/watch?v=3XiOkwo0X_4&amp;t=2s\">YouTube<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1101\/gr.211656.116\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/genome.cshlp.org\/content\/27\/8\/1450.full\">GenomeVIP: a cloud platform for genomic variant discovery and interpretation<\/a><br \/>Mashl RJ, Scott AD, <strong>Huang KL<\/strong>, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny\u00f6 D, Raphael BJ, Wendl MC, Ding L.<br \/><em>Genome Research<\/em>. 2017 Aug;27(8):1450-1459.\u00a0[<a href=\"https:\/\/github.com\/ding-lab\/GenomeVIP\">GitHub<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/ncomms14864\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/ncomms14864\/\">Proteogenomic integration reveals therapeutic targets in breast cancer xenografts<\/a><br \/><strong>Huang KL<\/strong>*, Li S*, Mertins P*, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Feny\u00f6 D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA#, Ellis MJ#, Ding L#.<br \/><em>Nature Communications<\/em>. 2017 Mar 28;8:14864. [<a href=\"https:\/\/github.com\/kuanlinhuang\/PDXNatComm2017\">GitHub<\/a>][<a href=\"https:\/\/mountsinai.box.com\/s\/3gzbcvizzfy9oev54yarysqxjwl6r47o\">Shared multi-omic data for the PDX cohort<\/a>][<a href=\"https:\/\/www.youtube.com\/watch?v=c3QaJ19sjS4\">YouTube<\/a>]<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1007\/s00401-017-1685-y\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/link.springer.com\/article\/10.1007%2Fs00401-017-1685-y\">Genome-wide association study identifies four novel loci associated with Alzheimer&#8217;s endophenotypes and disease modifiers<\/a><br \/>Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, <strong>Huang KL<\/strong>, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O&#8217;Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VM, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF; Alzheimer\u2019s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Genetic Consortium (ADGC), Kauwe JS, Goate AM, Cruchaga C.<br \/><em>Acta Neuropathol<\/em>. 2017 May;133(5):839-856.<\/p>\n<h3>2016<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1186\/s12883-016-0742-9\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/bmcneurol.biomedcentral.com\/articles\/10.1186\/s12883-016-0742-9\">Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40<\/a><br \/>Deming Y, Black K, Carrell D, Cai Y, Del-Aguila JL, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Bertelsen S, <strong>Huang KL<\/strong>, Sutphen CL, Tarawneh R, Fagan AM, Holtzman DM, Morris JC, Goate AM, Dougherty JD, Cruchaga C.<br \/><em>BMC<\/em> <em> Neurology<\/em>. 2016 Nov 10;16(1):217.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/nature18003\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/nature18003\">Proteogenomics connects somatic mutations to <\/a>signalling<a href=\"https:\/\/www.nature.com\/articles\/nature18003\"> in breast cancer<\/a><br \/>Mertins P*, Mani DR*, Ruggles KV*, Gillette MA*, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, <strong>Huang KL<\/strong>, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Feny\u00f6 D, Ellis MJ<sup>#<\/sup>, Carr SA<sup>#<\/sup>; NCI CPTAC.<br \/><em>Nature<\/em>. 2016 Jun 2;534(7605):55-62.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/nm.4002\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/nm.4002\">Systematic discovery of complex insertions and deletions in human cancers<\/a><br \/>Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, <strong>Huang KL<\/strong>, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L.<br \/><em>Nature Medicine<\/em>. 2016 Jan;22(1):97-104.<\/p>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.4149\/205_150601N306\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"http:\/\/www.elis.sk\/index.php?page=shop.product_details&amp;flypage=flypage.tpl&amp;product_id=4569&amp;category_id=85&amp;option=com_virtuemart&amp;vmcchk=1&amp;Itemid=1\">Pan-cancer methylation and expression profiling of adenocarcinomas revealed epigenetic silencing in the WNT signaling pathway<\/a><br \/>Li J*, <strong>Huang KL<\/strong>*, Zhang T, Li H, Zhao J, Wang H.<br \/><em>Neoplasma<\/em>. 2016.<\/p>\n<h3>2015<\/h3>\n<div class=\"altmetric-embed\" style=\"float: right\" data-badge-type=\"donut\" data-badge-popover=\"right\" data-doi=\"doi.org\/10.1038\/ncomms10086\" data-hide-no-mentions=\"true\">\u00a0<\/div>\n<p><a href=\"https:\/\/www.nature.com\/articles\/ncomms10086\/\">Patterns and functional implications of rare germline variants across 12 cancer types<\/a><br \/>Lu C*, Xie M*, Wendl MC*, Wang J*, McLellan MD*, Leiserson MD*, <strong>Huang KL<\/strong>, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L.<br \/><em>Nature Communications<\/em>. 2015 Dec 22;6:10086.<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p>PUBLICATIONS (selected) Huang Members (Volunteer or Mount Sinai) | *Co-first Authors | #Co-corresponding Authors | &#8220;Consortium authorship Complete &amp; updated lists of publications on PubMed or Google Scholar \u00a0 Globally accessible platforms for the exchange of research findings and career development.Salamero-Boix A*#, Contreras Castillo E*#, Lin CJ*#, Huang KL*#Nature Neuroscience 2025. \u00a0 Machine learning-based penetrance [&hellip;]<\/p>\n","protected":false},"author":300,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"[et_pb_section bb_built=\"1\" _builder_version=\"3.0.47\"][et_pb_row _builder_version=\"3.0.47\" background_size=\"initial\" background_position=\"top_left\" background_repeat=\"repeat\"][et_pb_column type=\"4_4\"][et_pb_code _builder_version=\"3.19.10\"]<script src=\"https:\/\/ajax.googleapis.com\/ajax\/libs\/jquery\/3.1.0\/jquery.min.js\"><\/script><!-- [et_pb_line_break_holder] --><!-- [et_pb_line_break_holder] --><script type='text\/javascript' src='https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js'><\/script>[\/et_pb_code][et_pb_text _builder_version=\"3.19.10\" background_size=\"initial\" background_position=\"top_left\" background_repeat=\"repeat\" text_font_size=\"12px\" text_font_size_last_edited=\"on|desktop\" text_line_height=\"1.5em\"]\r\n\r\n<p><script type=\"text\/javascript\" src=\"https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js\"><\/script><br \/><script src=\"https:\/\/ajax.googleapis.com\/ajax\/libs\/jquery\/3.1.0\/jquery.min.js\"><\/script><\/p><h1>PUBLICATIONS<\/h1><p><strong>Lab Members |\u00a0<span style=\"color: #800080\">Mentored Members\u00a0with External Affiliations\u00a0<span style=\"color: #333333\">| *Co-first Authors | #Co-corresponding Authors<\/span><\/span><\/strong><\/p><div class=\"page\" title=\"Page 1\"><div class=\"layoutArea\"><div class=\"column\"><h3>2019<\/h3><p>Ancestry-Specific Predisposing Germline Variants in Cancer.<br \/><span style=\"color: #800080\"><strong>Oak N<\/strong><\/span>, Gu\u0308mu\u0308s\u0327 ZH, Ding L, Plon SE, TCGA Analysis Network, <strong>Huang KL.<\/strong><br \/>In review. [<a href=\"https:\/\/github.com\/Huang-lab\/AncestralCancerPredisposition\">GitHub<\/a>]\u00a0<\/p><p><span class=\"hljs-tag\"><<span class=\"hljs-title\">div<\/span> <span class=\"hljs-attribute\">class<\/span>=<span class=\"hljs-value\">'altmetric-embed'<\/span> <span class=\"hljs-attribute\">data-badge-type<\/span>=<span class=\"hljs-value\">'donut'<\/span> <span class=\"hljs-attribute\">data-doi<\/span>=<span class=\"hljs-value\">\"10.1038\/nature.2012.9872\"<\/span>><\/span><span class=\"hljs-tag\"><\/<span class=\"hljs-title\">div<\/span>><\/span><\/p><\/div><\/div><\/div><p>AeQTL: eQTL analysis using region-based aggregation of rare variants.<br \/><span style=\"color: #800080\"><strong>Dong G<\/strong><\/span>, Wendl MC, Zhang B, Ding L, <strong>Huang KL.<\/strong><br \/>In revision. [<a href=\"https:\/\/github.com\/Huang-lab\/AeQTL\">GitHub<\/a>]<\/p><p>Systematic discovery of spatially interacting phosphorylation sites and mutations in cancer.<br \/><strong>Huang KL<\/strong>, Scott AD, Weerasinghe A, Liu R, Zhou DC, Wang LB, Sengupta S, Lai CW, Wu Y, Ruggles K, Payne SH, Raphael B, Feny\u00f6 D, Chen K, Mills G, Ding L.<br \/>In revision. [<a href=\"https:\/\/github.com\/ding-lab\/HotPho_Analysis\">GitHub<\/a>]<\/p><p>Regulated phosphosignaling associated with breast cancer subtypes and druggability.<br \/><strong>Huang KL<span style=\"color: #800080\"><span style=\"color: #333333\">#<\/span><\/span><\/strong>, Wu Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Ellis MJ, Fenyo\u0308 D, Chen F, Townsend RR, Carr SA, Ding L<span style=\"color: #800080\"><span style=\"color: #333333\">#.<\/span><\/span><br \/><em>Molecular and Cellular Proteomics<\/em> 2019. [<a href=\"https:\/\/github.com\/ding-lab\/phosphoproteomics\">GitHub<\/a>]<\/p><p>Mannose Phosphate Isomerase and Mannose Regulate Hepatic Stellate Cell Activation and Fibrosis in Zebrafish and Humans. <br \/>DeRossi C, Bambino K, Morrison J, Sakarin I, Villacorta-Martin C, Zhang C, Ellis JL, Fiel MI, Ybanez M, Lee YA, <strong>Huang KL<\/strong>, Yin C, Sakaguchi TF, Friedman SL, Villanueva A, Chu J. <br \/><em>Hepatology<\/em> 2019.\u00a0<\/p><p>Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity. <br \/>Adamovich AI, Banerjee T, Wingo M, Duncan K, Ning J, Martins Rodrigues F, <strong>Huang KL<\/strong>, Lee C, Chen F, Ding L, Parvin JD. <br \/><em>PLoS Genetics<\/em> 2019.<\/p><h3>2018<\/h3><p><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/humu.23668\">Framework for microRNA variant annotation and prioritization using human population and disease datasets.<\/a><br \/>Oak N, Ghosh R, <strong>Huang KL<\/strong>, Wheeler DA, Ding L, Plon SE.<br \/><em>Hum Mutat<\/em>. 2018 Oct 10. [<a href=\"https:\/\/github.com\/nroak\/ADmiRE\">GitHub<\/a>]<\/p><p><a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/bty649\/25542157\/bty649.pdf\">CharGer: Clinical Characterization of Germline Variants.<\/a><br \/>Scott AD#, <strong>Huang KL<\/strong>, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski M, Ding L#.<br \/><em>Bioinformatics<\/em>. 2018 Aug 9.\u00a0[<a href=\"https:\/\/github.com\/ding-lab\/CharGer\">GitHub<\/a>]<\/p><p><a href=\"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-018-0564-z\">Integrative omics analyses broaden treatment targets in human cancer.<\/a><br \/>Sengupta S*, Sun SQ*, <strong>Huang KL<\/strong>, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Feny\u00f6 D, Townsend RR, Dipersio JF, Chen F, Ding L.<br \/><em>Genome Med<\/em>. 2018 Jul 27;10(1):60.<\/p><p><a href=\"https:\/\/www.cell.com\/action\/showPdf?pii=S0092-8674%2818%2930363-5\">Pathogenic Germline Variants in 10,389 Adult Cancers.<\/a><br \/><strong> Huang KL<\/strong>, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F##, Ding L#.<br \/><em>Cell<\/em>. 2018 Apr 5;173(2):355-370.e14. [<a href=\"https:\/\/github.com\/ding-lab\/PanCanAtlasGermline\">GitHub<\/a>][<a href=\"https:\/\/gdc.cancer.gov\/about-data\/publications\/PanCanAtlas-Germline-AWG\">GDC (controlled-access germline data)<\/a>]<\/p><p><a href=\"https:\/\/www.cell.com\/action\/showPdf?pii=S0092-8674%2818%2930313-1\">Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.<\/a><br \/>Ding L#, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, <strong>Huang KL<\/strong>, Tokheim C, Cort\u00e9s-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA#, Getz G#; Cancer Genome Atlas Research Network.<br \/><em>Cell<\/em>. 2018 Apr 5;173(2):305-320.e10.<\/p><p><a href=\"https:\/\/www.nature.com\/articles\/s41422-018-0019-5\">Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types.<\/a><br \/>Cao Y, Zhou W, Li L, Wang J, Gao Z, Jiang Y, Jiang X, Shan A, Bailey MH, <strong>Huang<\/strong> <strong>KL<\/strong>, Sun SQ, McLellan MD, Niu B, Wang W, Ding L, Ning G.<br \/><em>Cell Res<\/em>. 2018 May;28(5):601-604.<\/p><p><a href=\"http:\/\/cancerres.aacrjournals.org\/content\/78\/10\/2732\">Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers.<\/a><br \/>Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, <strong>Huang KL<\/strong>, Yoon CJ, Ding L, Feny\u00f6 D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.<br \/><em>Cancer Res<\/em>. 2018 May 15;78(10):2732-2746.<\/p><p><a href=\"https:\/\/www.nature.com\/articles\/d41586-018-01076-4\">Most popular public searches on gene names.<\/a><br \/><strong>Huang KL<\/strong>.<br \/><em> Nature<\/em>. 2018 Jan 25;553(7689):405. 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