Search Results - "Bi, Yingtao"

A comparative study of evaluating missing value imputation methods in label-free proteomics by Jin, Liang, Bi, Yingtao, Hu, Chenqi, Qu, Jun, Shen, Shichen, Wang, Xue, Tian, Yu

“…The presence of missing values (MVs) in label-free quantitative proteomics greatly reduces the completeness of data. Imputation has been widely utilized to…”
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A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples by Chen, Wanqiu, Zhao, Yongmei, Chen, Xin, Yang, Zhaowei, Xu, Xiaojiang, Bi, Yingtao, Chen, Vicky, Li, Jing, Choi, Hannah, Ernest, Ben, Tran, Bao, Mehta, Monika, Kumar, Parimal, Farmer, Andrew, Mir, Alain, Mehra, Urvashi Ann, Li, Jian-Liang, Moos, Malcolm, Xiao, Wenming, Wang, Charles

“…Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge…”
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Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates by Farkas, Marina, Hashimoto, Hideharu, Bi, Yingtao, Davuluri, Ramana V., Resnick-Silverman, Lois, Manfredi, James J., Debler, Erik W., McMahon, Steven B.

“…The tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate…”
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Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques by Macyszyn, Luke, Akbari, Hamed, Pisapia, Jared M, Da, Xiao, Attiah, Mark, Pigrish, Vadim, Bi, Yingtao, Pal, Sharmistha, Davuluri, Ramana V, Roccograndi, Laura, Dahmane, Nadia, Martinez-Lage, Maria, Biros, George, Wolf, Ronald L, Bilello, Michel, O'Rourke, Donald M, Davatzikos, Christos

“…MRI characteristics of brain gliomas have been used to predict clinical outcome and molecular tumor characteristics. However, previously reported imaging…”
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Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation by Calvert, Andrea E., Chalastanis, Alexandra, Wu, Yongfei, Hurley, Lisa A., Kouri, Fotini M., Bi, Yingtao, Kachman, Maureen, May, Jasmine L., Bartom, Elizabeth, Hua, Youjia, Mishra, Rama K., Schiltz, Gary E., Dubrovskyi, Oleksii, Mazar, Andrew P., Peter, Marcus E., Zheng, Hongwu, James, C. David, Burant, Charles F., Chandel, Navdeep S., Davuluri, Ramana V., Horbinski, Craig, Stegh, Alexander H.

“…Oncogenic mutations in two isocitrate dehydrogenase (IDH)-encoding genes (IDH1 and IDH2) have been identified in acute myelogenous leukemia, low-grade glioma,…”
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Immune landscapes associated with different glioblastoma molecular subtypes by Martinez-Lage, Maria, Lynch, Timothy M, Bi, Yingtao, Cocito, Carolina, Way, Gregory P, Pal, Sharmistha, Haller, Josephine, Yan, Rachel E, Ziober, Amy, Nguyen, Aivi, Kandpal, Manoj, O'Rourke, Donald M, Greenfield, Jeffrey P, Greene, Casey S, Davuluri, Ramana V, Dahmane, Nadia

“…Recent work has highlighted the tumor microenvironment as a central player in cancer. In particular, interactions between tumor and immune cells may help drive…”
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Fibroblast activation protein expression by stromal cells and tumor-associated macrophages in human breast cancer by Tchou, Julia, Zhang, Paul J, Bi, Yingtao, Satija, Celine, Marjumdar, Rajrupa, Stephen, Tom L, Lo, Albert, Chen, Haiying, Mies, Carolyn, June, Carl H, Conejo-Garcia, Jose, Puré, Ellen

“…Summary Fibroblast activation protein (FAP) has long been known to be expressed in the stroma of breast cancer. However, very little is known if the magnitude…”
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Identifying the ubiquitination targets of E6AP by orthogonal ubiquitin transfer by Wang, Yiyang, Liu, Xianpeng, Zhou, Li, Duong, Duc, Bhuripanyo, Karan, Zhao, Bo, Zhou, Han, Liu, Ruochuan, Bi, Yingtao, Kiyokawa, Hiroaki, Yin, Jun

“…E3 ubiquitin (UB) ligases are the ending modules of the E1–E2-E3 cascades that transfer UB to cellular proteins and regulate their biological functions…”
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Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes by Liu, Xianpeng, Zhao, Bo, Sun, Limin, Bhuripanyo, Karan, Wang, Yiyang, Bi, Yingtao, Davuluri, Ramana V., Duong, Duc M., Nanavati, Dhaval, Yin, Jun, Kiyokawa, Hiroaki

“…Protein ubiquitination is mediated sequentially by ubiquitin activating enzyme E1, ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. Uba1 was thought to…”
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Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients by Jin, Liang, Macoritto, Michael, Wang, Jing, Bi, Yingtao, Wang, Fei, Suarez-Fueyo, Abel, Paez-Cortez, Jesus, Hu, Chenqi, Knight, Heather, Mascanfroni, Ivan, Staron, Matthew M, Schwartz Sterman, Annette, Houghton, Jean Marie, Westmoreland, Susan, Tian, Yu

“…Crohn's disease (CD) is a subtype of inflammatory bowel disease (IBD) characterized by transmural disease. The concept of transmural healing (TH) has been…”
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Immunopathogenesis of hidradenitis suppurativa and response to anti-TNF-α therapy by Lowe, Margaret M, Naik, Haley B, Clancy, Sean, Pauli, Mariela, Smith, Kathleen M, Bi, Yingtao, Dunstan, Robert, Gudjonsson, Johann E, Paul, Maia, Harris, Hobart, Kim, Esther, Shin, Uk Sok, Ahn, Richard, Liao, Wilson, Hansen, Scott L, Rosenblum, Michael D

“…Hidradenitis suppurativa (HS) is a highly prevalent, morbid inflammatory skin disease with limited treatment options. The major cell types and inflammatory…”
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Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia by Glass, Carolyn, Wuertzer, Charles, Cui, Xiaohui, Bi, Yingtao, Davuluri, Ramana, Xiao, Ying-Yi, Wilson, Michael, Owens, Kristina, Zhang, Yi, Perkins, Archibald

“…The ecotropic virus integration site 1 (EVI1) transcription factor is associated with human myeloid malignancy of poor prognosis and is overexpressed in 8-10%…”
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Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma by Walsh, Alice M, Kapoor, Gurpreet S, Buonato, Janine M, Mathew, Lijoy K, Bi, Yingtao, Davuluri, Ramana V, Martinez-Lage, Maria, Simon, M Celeste, O'Rourke, Donald M, Lazzara, Matthew J

“…Glioblastoma multiforme (GBM) is notoriously resistant to therapy, and the development of a durable cure will require the identification of broadly relevant…”
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IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data by Kim, Hyunsoo, Bi, Yingtao, Pal, Sharmistha, Gupta, Ravi, Davuluri, Ramana V

“…mRNA-Seq technology has revolutionized the field of transcriptomics for identification and quantification of gene transcripts not only at gene level but also…”
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Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model by Malchenko, Sergey, Sredni, Simone Treiger, Bi, Yingtao, Margaryan, Naira V, Boyineni, Jerusha, Mohanam, Indra, Tomita, Tadanori, Davuluri, Ramana V, Soares, Marcelo B

“…Recently, we described a new animal model of CNS primitive neuroectodermal tumors (CNS-PNET), which was generated by orthotopic transplantation of human Radial…”
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The efficiency of logistic regression compared to normal discriminant analysis under class-conditional classification noise by Bi, Yingtao, Jeske, Daniel R.

“…In many real world classification problems, class-conditional classification noise (CCC-Noise) frequently deteriorates the performance of a classifier that is…”
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Tree-based position weight matrix approach to model transcription factor binding site profiles by Bi, Yingtao, Kim, Hyunsoo, Gupta, Ravi, Davuluri, Ramana V

“…Most of the position weight matrix (PWM) based bioinformatics methods developed to predict transcription factor binding sites (TFBS) assume each nucleotide in…”
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Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis by Shilpi, Arunima, Bi, Yingtao, Jung, Segun, Patra, Samir K., Davuluri, Ramana V.

“…Introduction Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for…”
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Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow by Jin, Liang, Wang, Fei, Wang, Xue, Harvey, Bohdan P, Bi, Yingtao, Hu, Chenqi, Cui, Baoliang, Darcy, Anhdao T, Maull, John W, Phillips, Ben R, Kim, Youngjae, Jenkins, Gary J, Sornasse, Thierry R, Tian, Yu

“…Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease. Plasma biomarkers are critical for understanding disease mechanisms, treatment…”
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Immunopathogenesis of hidradenitis suppurativa and response to anti-TNF-α therapy by Lowe, Margaret M, Naik, Haley B, Clancy, Sean, Pauli, Mariela, Smith, Kathleen M, Bi, Yingtao, Dunstan, Robert, Gudjonsson, Johann E, Paul, Maia, Harris, Hobart, Kim, Esther, Shin, Uk Sok, Ahn, Richard, Liao, Wilson, Hansen, Scott L, Rosenblum, Michael D

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