Publications | (Eric) Zhang Chen

Chen EZ, Dong X, Wu J, Jiang H, Li X, Rong R. Lesion attributes segmentation for melanoma detection with multi-task U-Net. IEEE International Symposium on Biomedical Imaging (ISBI), 2019.

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Jiang H, Rong R, Wu J, Li X, Dong X, Chen EZ. Skin lesion segmentation with improved C-UNet networks. bioRxiv, 2018.

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Li X, Wu J, Jiang H, Chen EZ, Dong X, Rong R. Skin lesion classification via combining deep learning features and clinical criteria representations. bioRxiv, 2018.

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Wu J, Li X, Chen EZ, Jiang H, Dong X, Rong R. What evidence does deep learning model use to classify skin lesions?. arXiv, 2018.

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Ni J, Shen TC, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I. A role for bacterial urease in gut dysbiosis and Crohn’s disease. Science Translational Medicine, 2017.

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Chen EZ, Bushman FD, Li H. A model-based approach for species abundance quantification based on shotgun metagenomic data. Statistics in Biosciences, 2017.

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Chen EZ, Li H. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics, 2016.

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Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe, 2015.

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Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, Penubarthi S, Sun H, Baldwin DA, Fraser NW. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection. PLoS ONE, 2015.

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Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Comparative effectiveness of nutritional and biological therapy in north american children with active Crohnʼs disease. Inflammatory Bowel Diseases, 2015.

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Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut, 2014.

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Zheng YWL, Chan KCA, Sun H, Jiang P, Su X, Chen EZ, Lun FMF, Hung ECW, Lee V, Wong J, Lai PBS, Li C-K, Chiu RWK, Lo YMD. Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model. Clinical Chemistry, 2012.

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Xu C, Lu X, Chen EZ, He Z, Uyunbilig B, Li G, Ma Y, Hui L, Xie B, Gao Y, Ding X, Hu Y, Hu P, Han J-DJ, Wang X. Genome-wide roles of Foxa2 in directing liver specification. Journal of Molecular Cell Biology, 2012.

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Lu L, Zhou L, Chen EZ, Sun K, Jiang P, Wang L, Su X, Sun H, Wang H. A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS ONE, 2012.

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Van Abel D, Hölzel DR, Jain S, Lun FMF, Zheng YWL, Chen EZ, Sun H, Chiu RWK, Lo YMD, van Dijk M, Oudejans CBM. SFRS7-mediated splicing of tau exon 10 is directly regulated by STOX1A in glial cells. PLoS ONE, 2011.

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Chen EZ, Chiu RWK, Sun H, Akolekar R, Chan KCA, Leung TY, Jiang P, Zheng YWL, Lun FMF, Chan LYS, Jin Y, Go ATJI, Lau ET, To WWK, Leung WC, Tang RYK, Au-Yeung SKC, Lam H, Kung YY, Zhang X, van Vugt JMG, Minekawa R, Tang MHY, Wang J, Oudejans CBM, Lau TK, Nicolaides KH, Lo YMD. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS ONE, 2011.

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Lu L, Zhou L, Chen EZ, Sun K, Jiang P. Genome-wide identification of TF-miRNA regulatory networks in myogenesis. IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011.

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Jiang P, Sun X, Chen EZ, Sun K, Chiu RWK, Lo YMD, Sun H. Methy-Pipe: An integrated bioinformatics data analysis pipeline for whole genome methylome analysis. IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010.

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Lo YMD, Chan KCA, Sun H, Chen EZ, Jiang P, Lun FMF, Zheng YW, Leung TY, Lau TK, Cantor CR, Chiu RWK. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Science Translational Medicine, 2010.

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Fei T, Xia K, Li Z, Zhou B, Zhu S, Chen H, Zhang J, Chen Z, Xiao H, Han J-DJ, Chen Y-G. Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination. Genome Research, 2010.

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Han J-DJ, Liu Y, Xue H, Xia K, Yu H, Zhu S, Chen Z, Zhang W, Huang Z, Jin C, Xian B, Li J, Hou L, Han Y, Niu C, Alcon TC. Developmental systems biology flourishing on new technologies. Journal of Genetics and Genomics, 2008.

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