Search Results - "JUNBAI WANG"

The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data by Wang, Junbai

“…To further understand the implementation of hyperparameters re-estimation technique in Bayesian hierarchical model, we added two more prior assumptions over…”
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Frequent somatic mutations of KMT2D (MLL2) and CARD11 genes in primary cold agglutinin disease by Małecka, Agnieszka, Trøen, Gunhild, Tierens, Anne, Østlie, Ingunn, Małecki, Jędrzej, Randen, Ulla, Wang, Junbai, Berentsen, Sigbjørn, Tjønnfjord, Geir E., Delabie, Jan M. A.

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Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information by Wang, Junbai

“…In parallel with the quick development of high-throughput technologies, in vivo (vitro) experiments for genome-wide identification of protein-DNA interactions…”
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Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance by Zhou, Yufan, Gerrard, Diana L., Wang, Junbai, Li, Tian, Yang, Yini, Fritz, Andrew J., Rajendran, Mahitha, Fu, Xiaoyong, Stein, Gary, Schiff, Rachel, Lin, Shili, Frietze, Seth, Jin, Victor X.

“…Recent studies have demonstrated that chromatin architecture is linked to the progression of cancers. However, the roles of 3D structure and its dynamics in…”
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Social stress in rats promotes transcriptional mitochondrial changes of the adrenal tissue by Zylla, Terese Elisabeth, Wang, Junbai, Gjerstad, Johannes

“…Previous observations suggest that strong social stressors, that is, repeated social defeat, could initiate functional changes in the…”
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abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis by Ali, Omer, Farooq, Amna, Yang, Mingyi, Jin, Victor X, Bjørås, Magnar, Wang, Junbai

“…Transcription factor (TF) binding motifs are identified by high throughput sequencing technologies as means to capture Protein-DNA interactions. These motifs…”
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BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors by Wang, Junbai, Morigen

“…We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study…”
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Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data by Yang, Mingyi, Ali, Omer, Bjørås, Magnar, Wang, Junbai

“…Millions of single nucleotide variants (SNVs) exist in the human genome; however, it remains challenging to identify functional SNVs associated with diseases…”
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Nuclear IL-33 restrains the early conversion of fibroblasts to an extracellular matrix-secreting phenotype by Gatti, Francesca, Mia, Sobuj, Hammarström, Clara, Frerker, Nadine, Fosby, Bjarte, Wang, Junbai, Pietka, Wojciech, Sundnes, Olav, Hol, Johanna, Kasprzycka, Monika, Haraldsen, Guttorm

“…Interleukin (IL)-33 is a cytokine that appears to mediate fibrosis by signaling via its receptor ST2 (IL-33R/IL1RL1). It is also, however, a protein that after…”
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Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma by Batmanov, Kirill, Wang, Wei, Bjørås, Magnar, Delabie, Jan, Wang, Junbai

“…The contribution of mutations in regulatory regions to tumorigenesis has been the subject of many recent studies. We propose a new framework for integrative…”
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BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts by Batmanov, Kirill, Delabie, Jan, Wang, Junbai

“…Most of somatic mutations in cancer occur outside of gene coding regions. These mutations may disrupt the gene regulation by affecting protein-DNA interaction…”
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Integrating whole genome sequencing, methylation, gene expression, topologically associated domain information in regulatory mutation prediction: A study of follicular lymphoma by Farooq, Amna, Trøen, Gunhild, Delabie, Jan, Wang, Junbai

“…[Display omitted] A major challenge in human genetics is of the analysis of the interplay between genetic and epigenetic factors in a multifactorial disease…”
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Mapping nucleosome and chromatin architectures: A survey of computational methods by Fang, Kun, Wang, Junbai, Liu, Lu, Jin, Victor X.

“…With ever-growing genomic sequencing data, the data variabilities and the underlying biases of the sequencing technologies pose significant computational…”
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Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53 by Wang, Junbai, Tian, Tianhai

“…The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major…”
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Exploring the potential effect of paricalcitol on markers of inflammation in de novo renal transplant recipients by Pihlstrøm, Hege Kampen, Ueland, Thor, Michelsen, Annika E, Aukrust, Pål, Gatti, Franscesca, Hammarström, Clara, Kasprzycka, Monika, Wang, Junbai, Haraldsen, Guttorm, Mjøen, Geir, Dahle, Dag Olav, Midtvedt, Karsten, Eide, Ivar Anders, Hartmann, Anders, Holdaas, Hallvard

“…Following a successful renal transplantation circulating markers of inflammation may remain elevated, and systemic inflammation is associated with worse…”
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Author Correction: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance by Zhou, Yufan, Gerrard, Diana L., Wang, Junbai, Li, Tian, Yang, Yini, Fritz, Andrew J., Rajendran, Mahitha, Fu, Xiaoyong, Stein, Gary, Schiff, Rachel, Lin, Shili, Frietze, Seth, Jin, Victor X.

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology by Lan, Xun, Adams, Christopher, Landers, Mark, Dudas, Miroslav, Krissinger, Daniel, Marnellos, George, Bonneville, Russell, Xu, Maoxiong, Wang, Junbai, Huang, Tim H-M, Meredith, Gavin, Jin, Victor X

“…Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for…”
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Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops by Zhou, Yufan, Cheng, Xiaolong, Yang, Yini, Li, Tian, Li, Jingwei, Huang, Tim H-M, Wang, Junbai, Lin, Shili, Jin, Victor X

“…Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic…”
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Metabolic reprogramming is associated with flavopiridol resistance in prostate cancer DU145 cells by Li, Xiaoran, Lu, Jie, Kan, Quancheng, Li, Xiaoli, Fan, Qiong, Li, Yaqing, Huang, Ruixia, Slipicevic, Ana, Dong, Hiep Phuc, Eide, Lars, Wang, Junbai, Zhang, Hongquan, Berge, Viktor, Goscinski, Mariusz Adam, Kvalheim, Gunnar, Nesland, Jahn M., Suo, Zhenhe

“…Flavopiridol (FP) is a pan-cyclin dependent kinase inhibitor, which shows strong efficacy in inducing cancer cell apoptosis. Although FP is potent against most…”
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Adhesion molecule protein signature in ovarian cancer effusions is prognostic of patient outcome by Kim, Geoffrey, Davidson, Ben, Henning, Ryan, Wang, Junbai, Yu, Minshu, Annunziata, Christina, Hetland, Thea, Kohn, Elise C.

“…BACKGROUND: Ovarian cancer cells in malignant effusions lack attachment to solid‐phase matrix substrata and receive survival stimuli through cell–cell and…”
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