液态活检

Malaria extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes. Mantel, PY, Hjelmqvist, D, Nilsson, S, Ravel, D, Ribeiro, M, Grüring, C, Ma, S, Padmanabhan, P, Trachtenberg, AJ, Ankarklev, J, Brancucci, N, Huttenhower, C, Duraisingh, MT, Ghiran, I, Kuo, WP, Martinelli, R, Marti, M., Nature Communications, 2016 a. Emerging technologies in extracellular vesicle-based molecular diagnostics. Jia S, Zocco D, Samuels ML, Chou MF, Chammas R, Skog J, Zarovni N, Momen-Heravi F, Kuo WP. Expert Rev Mol Diagn. 2014;14(3):307-21.

Short Course in Extracellular Vesicles – The Transition from Tissue to Liquid Biopsies. Lötvall J, Skog J, Vlassov AV, Sacido AA, Rohde E, Gere J, Kuo WP. Journal of Circulating Biomarkers. 2014, 3 (8), 1-5.

Detection Of Human c-Myc and EGFR Amplifications in Circulating Extracellular Vesicles in Mouse Tumour Models. Balaj L, Momen-Heravi F, Chen W, Sivaraman S, Zhang X, Ludwig N, Meese E, Wurdinger T, Noske D, Charest A, Hochberg FH, Vandertop P, Skog J, Kuo WP. Journal of Circulating Biomarkers. 2014, 3 (6), 1-7. Extracellular vesicles as shuttles of tumor biomarkers and anti-tumor drugs. Zocco D, Ferruzzi P, Cappello F, Kuo WP, Fais S. Front Oncol. 2014;4:267.

Current methods for the isolation of extracellular vesicles. Momen-Heravi F, Balaj L, Alian S, Mantel PY, Halleck AE, Trachtenberg AJ, Soria CE, Oquin S, Bonebreak CM, Saracoglu E, Skog J, Kuo WP. Biol Chem. 2013, 394(10):1253-62.

Alternative methods for characterization of extracellular vesicles. Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M, Distel RJ, Ivanov AR, Skog J, Kuo WP. Front Physiol. 2012;3:354. Impact of biofluid viscosity on size and sedimentation efficiency of the isolated microvesicles. Momen-Heravi F, Balaj L, Alian S, Trachtenberg AJ, Hochberg FH, Skog J, Kuo WP. Front Physiol. 2012;3:162.

新一代测序

Genomic landscape and genetic het¬erogeneity in gastric adenocarcinoma revealed by whole-genome sequencing. Swee Seong Wong, Kyoung-Mee Kim, Jason C. Ting, Kun Yu, Jake Fu Shawn Liu, Razvan Cristescu, Michael Nebozhyn, Lara Gong, Yong Gang Yue , Jian Wang , Chen Ronghua, Andrey Loboda, James Hardwick, Xiaoqiao Liu, Hongyue Dai, Jin JG, Xiang S. Ye , So Young Kang, In Gu Do, Joon Oh Park, Tae Sung Sohn, Christoph Reinhard , Jeeyun Lee, Sung Kim & Amit Aggarwal. Nature Communications, 2014. 5.

The draft genome of the large yellow croaker reveals well-developed innate immunity. Changwen Wu, Di Zhang, Mengyuan Kan, Zhengmin Lv, Aiyi Zhu, Yongquan Su, Daizhan Zhou, Jianshe Zhang , Zhou Zhang, Meiying Xu , Lihua Jiang, Baoying Guo, Ting Wang, Changfeng Chi , Yong Mao, Jiajian Zhou , Xinxiu Yu, Hailing Wang, Xiaoling Weng, Jin JG, Junyi Ye, Lin He & Yun Liu., Nature Communications, 2014. 5.

Clinical application of whole-genome sequencing in patients with primary immunodeficiency. Mousallem T, Urban TJ, McSweeney KM, Kleinstein SE, Zhu M, Adeli M, Parrott RE, Roberts JL, Krueger B, Buckley RH, Goldstein DB., Journal of Allergy and Clinical Immunology, 2015. 136(2): p. 476-479. e6.

Using ERDS to infer copy-number variants in high-coverage genomes. Zhu M, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, Ruzzo EK, Gumbs CE, Singh A, Feng S, Shianna KV and Goldstein DB., The American Journal of Human Genetics, 2012. 91(3): p. 408-421.

Prioritizing genetic variants for causality on the basis of preferential linkage disequilibrium. Zhu Q, Ge D, Heinzen E, Dickson S, Urban TJ,Zhu M, Maia JM, Zhao Q, Shianna K, Goldstein DB., The American Journal of Human Genetics, 2012. 91(3): p. 422-434.

生物信息分析

AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L. BMC Bioinformatics. 2011;12:75.

Error margin analysis for feature gene extraction. Chow CK, Zhu HL, Lacy J, Kuo WP. BMC Bioinformatics. 2010; 11: 241.

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP. BMC Genomics. 2007;8:153.

Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data. Galante PA, Trimarchi J, Cepko CL, de Souza SJ, Ohno-Machado L, Kuo WP. Bioinformatics. 2007;23(7):903-5.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. MAQC Consortium. Nat Biotechnol. 2006;24(9):1151-61. (Kuo WP is one of the key contributors)

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. Nat Biotechnol. 2006;24(7):832-40.

Analysis of matched mRNA measurements from two different microarray technologies. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Bioinformatics. 2002;18(3):405-12.

生物标志物

Endothelial and circulating placental C19MC microRNAs distinguish propranolol-responsive infantile hemangioma from other vascular anomalies. Strub GM, Kirsh AL, Whipple MW, Kuo WP, Keller RB, Kapur RP, Perkins JA, Majesky MW. JCI Insight. 2016 Sep 8;1(14):e88856. doi: 10.1172/jci.insight.88856.

Epithelialization of mouse ovarian tumor cells originating in the fallopian tube stroma. Hua Y, Choi PW, Trachtenberg AJ, Ng AC, Kuo WP, Ng SK, Dinulescu DM, Matzuk MM, Berkowitz RS, Ng SW., Oncotarget. 2016 Sep 1. doi: 10.18632/oncotarget.11808.

Molecular Changes in Endometriosis-Associated Ovarian Clear Cell Carcinoma. Worley, MJ, Liu, S, Hua, Y, Kwok, JS, Samuel, A, Hou, L, Shoni, M, Lu, S, Sandberg, EM, Keryan, A, Wu, D, Ng, SK, Kuo WP, Parra-Herran, CE, Tsui, SK, Welch, W, Crum, C, Berkowitz, RS and Ng, SW., Eur J Cancer. 2015 Jun 6. pii: S0959-8049(15)00442-6. doi: 10.1016/j.ejca.2015.05.011.

NAD+ protects against EAE by regulating CD4+ T-cell differentiation. Tullius SG, Biefer HR, Li S, Trachtenberg AJ, Edtinger K, Quante M, Krenzien F, Uehara H, Yang X, Kissick HT, Kuo WP, Ghiran I, de la Fuente MA, Arredouani MS, Camacho V, Tigges JC, Toxavidis V, El Fatimy R, Smith BD, Vasudevan A, ElKhal A., Nat Commun. 2014 Oct 7;5:5101. doi: 10.1038/ncomms6101.

Genomewide Study of Salivary MicroRNAs for Detection of Oral Cancer. Momen-Heravi F, Trachtenberg AJ, Kuo WP, Cheng YS. J Dent Res. 2014 Apr 9;93(7 suppl):86S-93S.

miR-30-5p Functions as a Tumor Suppressor and Novel Therapeutic Tool by Targeting the Oncogenic Wnt/β-Catenin/BCL9 Pathway. Zhao JJ, Lin J, Zhu D, Wang X, Brooks D, Chen M, Chu ZB, Takada K, Ciccarelli B, Admin S, Tao J, Tai YT, Treon S, Pinkus G,Kuo WP, Hideshima T, Bouxsein M, Munshi N, Anderson K, Carrasco R. Cancer Res. 2014 Mar 15;74(6):1801-13. doi: 10.1158/0008-5472.CAN-13-3311-T. Epub 2014 Mar 5.

Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion.Wang G, Lunardi A, Zhang J, Chen Z, Ala U, Webster KA, Tay Y, Gonzalez-Billalabeitia E, Egia A, Shaffer DR, Carver B, Liu XS, Taulli R,Kuo WP, Nardella C, Signoretti S, Cordon-Cardo C, Gerald WL, Pandolfi PP. Nat Genet. 2013 Jun 2. doi: 10.1038/ng.2654.

A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue. Wang S, Wang L, Bayaxi N, Li J, Verhaegh W, Janevski A, Varadan V, Ren Y, Merkle D, Meng X, Gao X, Wang H, Ren J, Kuo WP, Dimitrova N, Wu Y, Zhu H. Gut. 2013;62(2):280-9.

Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients. Thompson AJ, Clark PJ, Singh A, Ge D, Fellay J, Zhu M, Zhu Q, Urban TJ, Patel K, Tillmann HL, Naggie S, Afdhal NH, Jacobson IM, Esteban R, Poordad F, Lawitz EJ, McCone J, Shiffman ML, Galler GW, King JW, Kwo PY, Shianna KV, Noviello S, Pedicone LD, Brass CA, Albrecht JK, Sulkowski MS, Goldstein DB, McHutchison JG, Muir AJ, Journal of Hepatology, 2012. 56(2): p. 313-319.

Isthmin is a novel secreted angiogenesis inhibitor that inhibits tumor growth in mice. Xiang W, Ke Z, Zhang Y, Cheng GH, Irwan ID, Sulochana KN, Potturi P, Wang Z, Yang H, Wang J, Zhuo L, Kini RM, Ge R. J Cell Mol Med, 2009, Oct 29.

The first but not the second thrombospondin type 1 repeat of ADAMTS5 functions as an angiogenesis inhibitor. Sharghi-Namini S, Fan H, Sulochana KN, Potturi P, Xiang W, Chong YS, Wang Z, Yang H, Ge R, Biochem Biophys Res Commun. 2008. 371(2):215-9.

Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications. Hasina R, Whipple ME, Martin LE, Kuo WP, Ohno-Machado L, Lingen MW. (2008) Lab Invest. Apr;88(4):342-53. Epub 2008 Feb 18.