Article
Computer Science, Artificial Intelligence
Sheetal Rajpal, Ankit Rajpal, Arpita Saggar, Ashok K. Vaid, Virendra Kumar, Manoj Agarwal, Naveen Kumar
Summary: Breast cancer, a heterogeneous disease with high mortality, requires early diagnosis and treatment. Epigenomic changes, specifically DNA methylation, impact gene expression in breast cancer subtypes. This study proposes a two-stage biomarker discovery framework, XAI-MethylMarker, to identify a small set of biomarkers for breast cancer classification. A deep-learning network, MethylNet, is used for dimensionality reduction and classification, and a biomarker discovery algorithm, MethylBDA, analyzes the MethylNet model to discover 52 biomarkers. The classification accuracy achieved is 0.8145 +/- 0.07 through cross-validation. Gene set analysis reveals clinically relevant biomarkers associated with druggable genes, prognostic outcomes, and enriched pathways in distinct breast cancer subtypes.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Paula Lucia Farre, Rocio Belen Duca, Cintia Massillo, Guillermo Nicolas Dalton, Karen Daniela Grana, Kevin Gardner, Ezequiel Lacunza, Adriana De Siervi
Summary: Breast cancer is the leading cause of death by cancer in women globally. A miRNA signature deregulated in preclinical and clinical BCa models was identified for potential biomarker discovery, useful for BCa diagnosis and/or prognosis. Certain miRNAs were up-regulated and down-regulated in BCa, showing negative correlation with the expression of related genes. Genes such as GAB1, GNG12, HBP1, and SESN1 have been found to have expression levels related to patient survival in aggressive BCa subtypes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Xuanyi Wang, Zixuan Chai, Guizhi Pan, Youjin Hao, Bo Li, Ting Ye, Yinghong Li, Fei Long, Lixin Xia, Mingwei Liu
Summary: ExoBCD is the first well-corroborated knowledge base for exosomal studies of breast cancer, integrating a large number of annotation entries and exosomal molecules information, providing rich data on experimental biology and gene expression patterns.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Multidisciplinary Sciences
Yaqing Jiao, Cindy See Wai Tong, Timothy H. Rainer
Summary: Clinicians need reliable outcome predictors to improve the prognosis of septic patients. Mouse models are widely used in sepsis research for novel prognostic biomarker discovery, but current models and biomarker platforms do not achieve sufficient clinical performance for use in humans.
Article
Multidisciplinary Sciences
Xiangning Chen, Justin M. Balko, Fei Ling, Yabin Jin, Anneliese Gonzalez, Zhongming Zhao, Jingchun Chen
Summary: In this study, a new approach called candidate extraction from convolutional neural network (CNN) elements (CECE) was used to discover biomarkers for triple negative breast cancers (TNBCs). A set of 21 genes able to classify TNBCs into two major classes with distinct overall survival rates was identified. The results demonstrate that the spatial patterns learned by CNN models can be utilized to discover interacting biomarkers otherwise unlikely to be identified by traditional approaches.
Article
Cell Biology
Yingan Zhao, Yingjue Zhang, Chen Dai, Kai Hong, Yangyang Guo
Summary: This study established a 13-gene signature and robust nomogram to predict the prognosis of breast cancer patients. The research showed that patients with high-risk breast cancer had poorer survival and the signature was an independent prognostic factor. This can be beneficial for the diagnosis and treatment of breast cancer.
Article
Oncology
Xiaojun Zhang, Mengke Niu, Tianye Li, Yuze Wu, Jinnan Gao, Ming Yi, Kongming Wu
Summary: S100A8/A9 is significantly increased in basal-like and Her2-overexpressed subtypes of breast cancer, predicting poor prognosis. The tumor suppressor DACH1 inhibits the expression of S100A8/A9. The combination of S100A8/A9 and DACH1 predicts the overall survival of breast cancer patients more accurately.
BIOMARKER RESEARCH
(2023)
Article
Oncology
Zeyu Xing, Dongcai Lin, Yuting Hong, Zihuan Ma, Hongnan Jiang, Ye Lu, Jiale Sun, Jiarui Song, Li Xie, Man Yang, Xintong Xie, Tianyu Wang, Hong Zhou, Xiaoqi Chen, Xiang Wang, Jidong Gao
Summary: This study aimed to uncover novel useful genetic biomarkers and establish a risk signature for breast cancer to aid in determining clinical strategies.
FRONTIERS IN ONCOLOGY
(2023)
Article
Obstetrics & Gynecology
K. Lundin, J. G. ESHRE Addons Working Grp, J. G. Bentzen, G. Bozdag, T. Ebner, J. Harper, N. Le Clef, A. Moffett, S. Norcross, N. P. Polyzos, S. Rautakallio-Hokkanen, I Sfontouris, K. Sermon, N. Vermeulen, A. Pinborg
Summary: This study focused on the safety and efficacy of add-ons used in ART treatment. The study formulated 42 recommendations covering various aspects such as diagnosis, laboratory tests, and clinical management. However, most of the recommendations were based on low-quality evidence.
HUMAN REPRODUCTION
(2023)
Article
Immunology
Junshuai Xue, Delin Ma, Jianjun Jiang, Yang Liu
Summary: Various immune/inflammatory indicators have been studied for their diagnostic and prognostic value in venous thromboembolism (VTE), with the neutrophil/lymphocyte ratio (NLR) showing promising predictive capability. Further investigations are needed to determine the reliability and stability of other indicators such as platelet/lymphocyte ratio (PLR) and systemic immune/inflammatory index (SII). Overall, this review provides new insights and clinical guidance for the diagnosis and treatment of VTE.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Xujun Ruan, Yan Wang, Lirong Zhou, Qiuling Zheng, Haiping Hao, Dandan He
Summary: The discovery of disease biomarker based on untargeted metabolomics is important for studying pathological mechanisms and facilitating early disease diagnosis. This study evaluated the sample preparation, data processing procedure, and metabolite identification strategy for the discovery of breast cancer biomarkers. The optimized strategy simplified the process of exploring differential metabolites, laying a foundation for biomarker discovery and disease mechanism studies.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Oncology
A. Gilmour, R. Cutress, A. Gandhi, D. Harcourt, K. Little, J. Mansell, J. Murphy, E. Pennery, R. Tillett, R. Vidya, L. Martin
Summary: The guidelines aim to provide the best oncoplastic and reconstructive practice in breast surgery for breast cancer patients, hoping to benefit multidisciplinary teams and other professionals involved in this clinical practice area.
Article
Immunology
Xiangyu Sun, Xin Fu, Shouping Xu, Pengfei Qiu, Zhidong Lv, Mingke Cui, Qiang Zhang, Yingying Xu
Summary: This study investigated the expression of OLR1 in breast cancer tissues and its correlation with clinical outcomes, finding that OLR1 upregulation was associated with worse prognosis and tumor infiltration. Additionally, OLR1 may regulate immunity-related pathways, particularly macrophage polarization, affecting the survival of breast cancer patients.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Immunology
Qing Peng, Tingyu Wen, Dongyang Liu, Suguo Wang, Xinting Jiang, Shiju Zhao, Gaozhong Huang
Summary: This study comprehensively analyzed DSN1 expression in different molecular subtypes or stages of breast cancer, and found that upregulation of DSN1 was strongly associated with poor prognosis and decreased survival in breast cancer. Significant differences in DSN1 expression were also observed in different pathological subtypes and stages of breast cancer.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Medicine, General & Internal
Marta Sanchez-Marteles, Jorge Rubio-Gracia, Natacha Pena-Fresneda, Vanesa Garces-Horna, Borja Gracia-Tello, Luis Martinez-Lostao, Silvia Crespo-Aznarez, Juan Ignacio Perez-Calvo, Ignacio Gimenez-Lopez
Summary: The study found that the changes in serum sST2 concentration in COVID-19 patients were closely related to patient prognosis, and a concentration above 58.9 ng/mL could predict whether patients would be admitted to the ICU or die. This suggests that early measurement of sST2 helps identify high-risk patients.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Medicine, Research & Experimental
Tingting Du, Lun Yang, Heng Luo, Peng Zhou, Hu Mei, Jiekun Xuan, Qinghe Xing, Baitang Ning, Donna L. Mendrick, Leming Shi
BIOMARKERS IN MEDICINE
(2015)
Review
Medicine, Research & Experimental
Yuanting Zheng, Tao Qing, Yunjie Song, Jinhang Zhu, Ying Yu, Weiwei Shi, Lajos Pusztai, Leming Shi
BIOMARKERS IN MEDICINE
(2015)
Article
Biochemical Research Methods
Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick, Huixiao Hong
BMC BIOINFORMATICS
(2015)
Article
Biotechnology & Applied Microbiology
Zhiguang Li, Taichun Qin, Kejian Wang, Michael Hackenberg, Jian Yan, Yuan Gao, Li-Rong Yu, Leming Shi, Zhenqiang Su, Tao Chen
Article
Mathematical & Computational Biology
Christopher J. Mitchell, Derese Getnet, Min-Sik Kim, Srikanth S. Manda, Praveen Kumar, Tai-Chung Huang, Sneha M. Pinto, Raja Sekhar Nirujogi, Mio Iwasaki, Patrick G. Shaw, Xinyan Wu, Jun Zhong, Raghothama Chaerkady, Arivusudar Marimuthu, Babylakshmi Muthusamy, Nandini A. Sahasrabuddhe, Rajesh Raju, Caitlyn Bowman, Ludmila Danilova, Jevon Cutler, Dhanashree S. Kelkar, Charles G. Drake, T. S. Keshava Prasad, Luigi Marchionni, Peter N. Murakami, Alan F. Scott, Leming Shi, Jean Thierry-Mieg, Danielle Thierry-Mieg, Rafael Irizarry, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey
BMC SYSTEMS BIOLOGY
(2015)
Article
Biochemical Research Methods
Heng Luo, Tingting Du, Peng Zhou, Lun Yang, Hu Mei, Huiwen Ng, Wenqian Zhang, Mao Shu, Weida Tong, Leming Shi, Donna L. Mendrick, Huixiao Hong
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2015)
Article
Biotechnology & Applied Microbiology
Wenqian Zhang, Ying Yu, Falk Hertwig, Jean Thierry-Mieg, Wenwei Zhang, Danielle Thierry-Mieg, Jian Wang, Cesare Furlanello, Viswanath Devanarayan, Jie Cheng, Youping Deng, Barbara Hero, Huixiao Hong, Meiwen Jia, Li Li, Simon M. Lin, Yuri Nikolsky, Andre Oberthuer, Tao Qing, Zhenqiang Su, Ruth Volland, Charles Wang, May D. Wang, Junmei Ai, Davide Albanese, Shahab Asgharzadeh, Smadar Avigad, Wenjun Bao, Marina Bessarabova, Murray H. Brilliant, Benedikt Brors, Marco Chierici, Tzu-Ming Chu, Jibin Zhang, Richard G. Grundy, Min Max He, Scott Hebbring, Howard L. Kaufman, Samir Lababidi, Lee J. Lancashire, Yan Li, Xin X. Lu, Heng Luo, Xiwen Ma, Baitang Ning, Rosa Noguera, Martin Peifer, John H. Phan, Frederik Roels, Carolina Rosswog, Susan Shao, Jie Shen, Jessica Theissen, Gian Paolo Tonini, Jo Vandesompele, Po-Yen Wu, Wenzhong Xiao, Joshua Xu, Weihong Xu, Jiekun Xuan, Yong Yang, Zhan Ye, Zirui Dong, Ke K. Zhang, Ye Yin, Chen Zhao, Yuanting Zheng, Russell D. Wolfinger, Tieliu Shi, Linda H. Malkas, Frank Berthold, Jun Wang, Weida Tong, Leming Shi, Zhiyu Peng, Matthias Fischer
Article
Biotechnology & Applied Microbiology
Charles Wang, Binsheng Gong, Pierre R. Bushel, Jean Thierry-Mieg, Danielle Thierry-Mieg, Joshua Xu, Hong Fang, Huixiao Hong, Jie Shen, Zhenqiang Su, Joe Meehan, Xiaojin Li, Lu Yang, Haiqing Li, Pawel P. Labaj, David P. Kreil, Dalila Megherbi, Stan Gaj, Florian Caiment, Joost van Delft, Jos Kleinjans, Andreas Scherer, Viswanath Devanarayan, Jian Wang, Yong Yang, Hui-Rong Qian, Lee J. Lancashire, Marina Bessarabova, Yuri Nikolsky, Cesare Furlanello, Marco Chierici, Davide Albanese, Giuseppe Jurman, Samantha Riccadonna, Michele Filosi, Roberto Visintainer, Ke K. Zhang, Jainying Li, Jui-Hua Hsieh, Daniel L. Svoboda, James C. Fuscoe, Youping Deng, Leming Shi, Richard S. Paules, Scott S. Auerbach, Weida Tong
NATURE BIOTECHNOLOGY
(2014)
Article
Biotechnology & Applied Microbiology
Sheng Li, Pawel P. Labaj, Paul Zumbo, Peter Sykacek, Wei Shi, Leming Shi, John Phan, Po-Yen Wu, May Wang, Charles Wang, Danielle Thierry-Mieg, Jean Thierry-Mieg, David P. Kreil, Christopher E. Mason
NATURE BIOTECHNOLOGY
(2014)
Article
Biotechnology & Applied Microbiology
Zhenqiang Su, Pawel P. Labaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Shi, Charles Wang, Gary P. Schroth, Robert A. Setterquist, John F. Thompson, Wendell D. Jones, Wenzhong Xiao, Weihong Xu, Roderick V. Jensen, Reagan Kelly, Joshua Xu, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong, Nadereh Jafari, Stan Letovsky, Yang Liao, Fei Lu, Edward J. Oakeley, Zhiyu Peng, Craig A. Praul, Javier Santoyo-Lopez, Andreas Scherer, Tieliu Shi, Gordon K. Smyth, Frank Staedtler, Peter Sykacek, Xin-Xing Tan, E. Aubrey Thompson, Jo Vandesompele, May D. Wang, Jian Wang, Russell D. Wolfinger, Jiri Zavadil, Scott S. Auerbach, Wenjun Bao, Hans Binder, Thomas Blomquist, Murray H. Brilliant, Pierre R. Bushel, Weimin Cain, Jennifer G. Catalano, Ching-Wei Chang, Tao Chen, Geng Chen, Rong Chen, Marco Chierici, Tzu-Ming Chu, Djork-Arne Clevert, Youping Deng, Adnan Derti, Viswanath Devanarayan, Zirui Dong, Joaquin Dopazo, Tingting Du, Hong Fang, Yongxiang Fang, Mario Fasold, Anita Fernandez, Matthias Fischer, Pedro Furio-Tari, James C. Fuscoe, Florian Caiment, Stan Gaj, Jorge Gandara, Huan Gao, Weigong Ge, Yoichi Gondo, Binsheng Gong, Meihua Gong, Zhuolin Gong, Bridgett Green, Chao Guo, Lei Guo, Li-Wu Guo, James Hadfield, Jan Hellemans, Sepp Hochreiter, Meiwen Jia, Min Jian, Charles D. Johnson, Suzanne Kay, Jos Kleinjans, Samir Lababidi, Shawn Levy, Quan-Zhen Li, Li Li, Li Li, Peng Li, Yan Li, Haiqing Li, Jianying Li, Shiyong Li, Simon M. Lin, Francisco J. Lopez, Xin Lu, Heng Luo, Xiwen Ma, Joseph Meehan, Dalila B. Megherbi, Nan Mei, Bing Mu, Baitang Ning, Akhilesh Pandey, Javier Perez-Florido, Roger G. Perkins, Ryan Peters, John H. Phan, Mehdi Pirooznia, Feng Qian, Tao Qing, Lucille Rainbow, Philippe Rocca-Serra, Laure Sambourg, Susanna-Assunta Sansone, Scott Schwartz, Ruchir Shah, Jie Shen, Todd M. Smith, Oliver Stegle, Nancy Stralis-Pavese, Elia Stupka, Yutaka Suzuki, Lee T. Szkotnicki, Matthew Tinning, Bimeng Tu, Joost van Deft, Alicia Vela-Boza, Elisa Venturini, Stephen J. Walker, Liqing Wan, Wei Wang, Jinhui Wang, Jun Wang, Eric D. Wieben, James C. Willey, Po-Yen Wu, Jiekun Xuan, Yong Yang, Zhan Ye, Ye Yin, Ying Yu, Yate-Ching Yuan, John Zhang, Ke K. Zhang, Wenqian Zhang, Wenwei Zhang, Yanyan Zhang, Chen Zhao, Yuanting Zheng, Yiming Zhou, Paul Zumbo, Weida Tong, David P. Kreil, Christopher E. Mason, Leming Shi
NATURE BIOTECHNOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Heng Luo, Ping Zhang, Hui Huang, Jialiang Huang, Emily Kao, Leming Shi, Lin He, Lun Yang
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Jinhang Zhu, Geng Chen, Sibo Zhu, Suqing Li, Zhuo Wen, Bin Li, Yuanting Zheng, Leming Shi
SCIENTIFIC REPORTS
(2016)
Meeting Abstract
Oncology
M. Peifer, F. Hertwig, F. Roels, D. Dreidax, M. Gartlgruber, R. Menon, B. Hero, A. Schramm, J. H. Schulte, C. Herrmann, R. J. O'Sullivan, F. Westermann, R. K. Thomas, M. Fischer
ONCOLOGY RESEARCH AND TREATMENT
(2016)
Article
Biochemical Research Methods
Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, Donna L. Mendrick, Huixiao Hong
BIOINFORMATICS AND BIOLOGY INSIGHTS
(2015)
Meeting Abstract
Environmental Sciences
P. R. Bushel, C. Wang, B. Gong, J. Thierry-Mieg, D. Thierry-Mieg, J. Xu, H. Fang, D. P. Kreil, D. Megherbi, J. Li, R. S. Paules, L. Shi, S. S. Auerbach, W. Tong
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2014)