Search Results - "JIANHUA RUAN"

Robust edge-based biomarker discovery improves prediction of breast cancer metastasis by Adnan, Nahim, Lei, Chengwei, Ruan, Jianhua

“…The abundance of molecular profiling of breast cancer tissues entailed active research on molecular marker-based early diagnosis of metastasis. Recently there…”
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Characterization and identification of microRNA core promoters in four model species by Zhou, Xuefeng, Ruan, Jianhua, Wang, Guandong, Zhang, Weixiong

“…MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and…”
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Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance by Bi, Mingjun, Zhang, Zhao, Jiang, Yi-Zhou, Xue, Pengya, Wang, Hu, Lai, Zhao, Fu, Xiaoyong, De Angelis, Carmine, Gong, Yue, Gao, Zhen, Ruan, Jianhua, Jin, Victor X., Marangoni, Elisabetta, Montaudon, Elodie, Glass, Christopher K., Li, Wei, Huang, Tim Hui-Ming, Shao, Zhi-Ming, Schiff, Rachel, Chen, Lizhen, Liu, Zhijie

“…Acquired therapy resistance is a major problem for anticancer treatment, yet the underlying molecular mechanisms remain unclear. Using an established breast…”
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The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia by Lovelace, Dawn L, Gao, Zhen, Mutoji, Kazadi, Song, Yuntao Charlie, Ruan, Jianhua, Hermann, Brian P

“…Spermatogonial stem cells (SSCs) maintain spermatogenesis throughout adulthood through balanced self-renewal and differentiation, yet the regulatory logic of…”
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A general co-expression network-based approach to gene expression analysis: comparison and applications by Ruan, Jianhua, Dean, Angela K, Zhang, Weixiong

“…Co-expression network-based approaches have become popular in analyzing microarray data, such as for detecting functional gene modules. However, co-expression…”
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A top-performing algorithm for the DREAM3 gene expression prediction challenge by Ruan, Jianhua

“…A wealth of computational methods has been developed to address problems in systems biology, such as modeling gene expression. However, to objectively evaluate…”
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Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation by Mitsuya, Kohzoh, Parker, Ashley N, Liu, Lu, Ruan, Jianhua, Vissers, Margreet C M, Myatt, Leslie

“…The inflammatory and metabolic derangements of obesity in pregnant women generate an adverse intrauterine environment, increase pregnancy complications and…”
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Manipulation of the Plant Host by the Geminivirus AC2/C2 Protein, a Central Player in the Infection Cycle by Guerrero, Jennifer, Regedanz, Elizabeth, Lu, Liu, Ruan, Jianhua, Bisaro, David M, Sunter, Garry

“…Geminiviruses are a significant group of emergent plant DNA viruses causing devastating diseases in food crops worldwide, including the Southern United States,…”
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Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency [version 2; peer review: 2 approved] by Zand, Maryam, Ruan, Jianhua

“…The advancement in single-cell RNA sequencing technologies allow us to obtain transcriptome at single cell resolution. However, the original spatial context of…”
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Mutation of the conserved late element in geminivirus CP promoters abolishes Arabidopsis TCP24 transcription factor binding and decreases H3K27me3 levels on viral chromatin by Williams, Jacqueline, Regedanz, Elizabeth, Lucinda, Natalia, Nava Fereira, Alba Ruth, Lacatus, Gabriela, Berger, Mary, O'Connell, Nels, Coursey, Tami, Ruan, Jianhua, Bisaro, David M, Sunter, Garry

“…In geminiviruses belonging to the genus Begomovirus, coat protein (CP) expression depends on viral AL2 protein, which derepresses and activates the CP promoter…”
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Logo2PWM: a tool to convert sequence logo to position weight matrix by Gao, Zhen, Liu, Lu, Ruan, Jianhua

“…position weight matrix (PWM) and sequence logo are the most widely used representations of transcription factor binding site (TFBS) in biological sequences…”
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Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases by Ray, Monika, Ruan, Jianhua, Zhang, Weixiong

“…Because of its polygenic nature, Alzheimer's disease is believed to be caused not by defects in single genes, but rather by variations in a large number of…”
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Comparison of attitudes toward disability and people with disability among caregivers, the public, and people with disability: findings from a cross-sectional survey by Zheng, Qiaolan, Tian, Qi, Hao, Chun, Gu, Jing, Tao, Jianting, Liang, Zuoyi, Chen, Xinlin, Fang, Jiqian, Ruan, Jianhua, Ai, Qiuxiang, Hao, Yuantao

“…A negative attitude toward disability is one of the potential barriers for people with disability (PWD) to achieve social equality. Although numerous studies…”
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The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications by Liu, Xiaoming, Xie, Lei, Wu, Zhijin, Wang, Kai, Zhao, Zhongming, Ruan, Jianhua, Zhi, Degui

“…The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10-12, 2018, in Los Angeles, California, USA. The…”
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The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications by Wu, Zhijin, Yan, Jingwen, Wang, Kai, Liu, Xiaoming, Guo, Yan, Zhi, Degui, Ruan, Jianhua, Zhao, Zhongming

“…The sixth International Conference on Intelligent Biology and Medicine (ICIBM) took place in Los Angeles, California, USA on June 10-12, 2018. This conference…”
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Comparative evaluation of network features for the prediction of breast cancer metastasis by Adnan, Nahim, Liu, Zhijie, Huang, Tim H M, Ruan, Jianhua

“…Discovering a highly accurate and robust gene signature for the prediction of breast cancer metastasis from gene expression profiling of primary tumors is one…”
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A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks by Gao, Zhen, Zhao, Ruizhe, Ruan, Jianhua

“…Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery…”
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Adipokines Deregulate Cellular Communication via Epigenetic Repression of Gap Junction Loci in Obese Endometrial Cancer by Polusani, Srikanth R, Huang, Yi-Wen, Huang, Guangcun, Chen, Chun-Wei, Wang, Chiou-Miin, Lin, Li-Ling, Osmulski, Pawel, Lucio, Nicholas D, Liu, Lu, Hsu, Ya-Ting, Zhou, Yufan, Lin, Chun-Lin, Aguilera-Barrantes, Irene, Valente, Philip T, Kost, Edward R, Chen, Chun-Liang, Shim, Eun Yong, Lee, Sang Eun, Ruan, Jianhua, Gaczynska, Maria E, Yan, Pearlly, Goodfellow, Paul J, Mutch, David G, Jin, Victor X, Nicholson, Bruce J, Huang, Tim H-M, Kirma, Nameer B

“…Emerging evidence indicates that adipose stromal cells (ASC) are recruited to enhance cancer development. In this study, we examined the role these adipocyte…”
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The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools by Liu, Zhandong, Zheng, W Jim, Allen, Genevera I, Liu, Yin, Ruan, Jianhua, Zhao, Zhongming

“…The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight…”
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An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots by Ruan, Jianhua, Stormo, Gary D., Zhang, Weixiong

“…Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several…”
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