Search Results - "Xu, Joshua"

Towards accurate and reliable resolution of structural variants for clinical diagnosis by Liu, Zhichao, Roberts, Ruth, Mercer, Timothy R, Xu, Joshua, Sedlazeck, Fritz J, Tong, Weida

“…Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs…”
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The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance by Wang, Charles, Gong, Binsheng, Bushel, Pierre R, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Xu, Joshua, Fang, Hong, Hong, Huixiao, Shen, Jie, Su, Zhenqiang, Meehan, Joe, Li, Xiaojin, Yang, Lu, Li, Haiqing, Łabaj, Paweł P, Kreil, David P, Megherbi, Dalila, Gaj, Stan, Caiment, Florian, van Delft, Joost, Kleinjans, Jos, Scherer, Andreas, Devanarayan, Viswanath, Wang, Jian, Yang, Yong, Qian, Hui-Rong, Lancashire, Lee J, Bessarabova, Marina, Nikolsky, Yuri, Furlanello, Cesare, Chierici, Marco, Albanese, Davide, Jurman, Giuseppe, Riccadonna, Samantha, Filosi, Michele, Visintainer, Roberto, Zhang, Ke K, Li, Jianying, Hsieh, Jui-Hua, Svoboda, Daniel L, Fuscoe, James C, Deng, Youping, Shi, Leming, Paules, Richard S, Auerbach, Scott S, Tong, Weida

“…A comparison of RNA-seq and microarray data from samples treated with diverse drugs highlights a dependency of cross-platform concordance on treatment effect…”
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HetEnc: a deep learning predictive model for multi-type biological dataset by Wu, Leihong, Liu, Xiangwen, Xu, Joshua

“…Researchers today are generating unprecedented amounts of biological data. One trend in current biological research is integrated analysis with multi-platform…”
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The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine by Mercer, Tim R, Xu, Joshua, Mason, Christopher E, Tong, Weida

“…The founding project, MAQC Phase I, was initiated in 2005 by the FDA’s National Center for Toxicological Research (NCTR) to evaluate the reliability of…”
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Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method by Yu, Ying, Zhang, Naixin, Mai, Yuanbang, Ren, Luyao, Chen, Qiaochu, Cao, Zehui, Chen, Qingwang, Liu, Yaqing, Hou, Wanwan, Yang, Jingcheng, Hong, Huixiao, Xu, Joshua, Tong, Weida, Dong, Lianhua, Shi, Leming, Fang, Xiang, Zheng, Yuanting

“…Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora…”
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Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis by Liu, Zhichao, Roberts, Ruth, Mercer, Timothy R., Xu, Joshua, Sedlazeck, Fritz J., Tong, Weida

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Evaluating Alternative Registration Planes in Imageless, Computer-Assisted Navigation Systems for Direct Anterior Total Hip Arthroplasty by Farey, John E, Chai, Yuan, Xu, Joshua, Maes, Vincent, Sadeghpour, Ameneh, Baker, Neri A, Vigdorchik, Jonathan M, Walter, William L

“…(1) Background: Imageless computer navigation systems have the potential to improve the accuracy of acetabular cup position in total hip arthroplasty (THA)…”
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Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA by Wu, Leihong, Ingle, Taylor, Liu, Zhichao, Zhao-Wong, Anna, Harris, Stephen, Thakkar, Shraddha, Zhou, Guangxu, Yang, Junshuang, Xu, Joshua, Mehta, Darshan, Ge, Weigong, Tong, Weida, Fang, Hong

“…Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e.,…”
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Laminectomy and fusion vs laminoplasty for multi-level cervical myelopathy: a systematic review and meta-analysis by Phan, Kevin, Scherman, Daniel B., Xu, Joshua, Leung, Vannessa, Virk, Sohaib, Mobbs, Ralph J.

“…Background Surgical approaches for multi-level cervical spondylotic myelopathy (CSM) include posterior cervical surgery via laminectomy and fusion (LF) or…”
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Polydimethylsiloxane core–polycaprolactone shell nanofibers as biocompatible, real-time oxygen sensors by Xue, Ruipeng, Behera, Prajna, Xu, Joshua, Viapiano, Mariano S., Lannutti, John J.

“…•PDMS ‘core’ nanofibers can be created via encapsulation within a PCL ‘shell’.•PDMS is ideal for oxygen sensing as it allows for very rapid oxygen…”
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DLI-IT: a deep learning approach to drug label identification through image and text embedding by Liu, Xiangwen, Meehan, Joe, Tong, Weida, Wu, Leihong, Xu, Xiaowei, Xu, Joshua

“…Drug label, or packaging insert play a significant role in all the operations from production through drug distribution channels to the end consumer. Image of…”
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The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors by Liu, Lina, Vujovic, Ana, Deshpande, Nandan P., Sathe, Shashank, Anande, Govardhan, Chen, He Tian Tony, Xu, Joshua, Minden, Mark D., Yeo, Gene W., Unnikrishnan, Ashwin, Hope, Kristin J., Lu, Yu

“…Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival…”
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance by Ren, Luyao, Duan, Xiaoke, Dong, Lianhua, Zhang, Rui, Yang, Jingcheng, Gao, Yuechen, Peng, Rongxue, Hou, Wanwan, Liu, Yaqing, Li, Jingjing, Yu, Ying, Zhang, Naixin, Shang, Jun, Liang, Fan, Wang, Depeng, Chen, Hui, Sun, Lele, Hao, Lingtong, Scherer, Andreas, Nordlund, Jessica, Xiao, Wenming, Xu, Joshua, Tong, Weida, Hu, Xin, Jia, Peng, Ye, Kai, Li, Jinming, Jin, Li, Hong, Huixiao, Wang, Jing, Fan, Shaohua, Fang, Xiang, Zheng, Yuanting, Shi, Leming

“…Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets…”
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Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome by Reis, Andre L M, Deveson, Ira W, Madala, Bindu Swapna, Wong, Ted, Barker, Chris, Xu, Joshua, Lennon, Niall, Tong, Weida, Mercer, Tim R

“…Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the…”
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Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA by Gong, Binsheng, Lababidi, Samir, Kusko, Rebecca, Bouri, Khaled, Prezek, Sarah, Thovarai, Vishal, Prasanna, Anish, Maier, Ezekiel J., Golkaram, Mahdi, Sun, Xingqiang, Kyriakidis, Konstantinos, Kitajima, João Paulo, Ebrahim Sahraeian, Sayed Mohammad, Guo, Yunfei, Johanson, Elaine, Jones, Wendell, Tong, Weida, Xu, Joshua

“…Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S…”
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Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies by Gong, Binsheng, Kusko, Rebecca, Jones, Wendell, Tong, Weida, Xu, Joshua

“…The lack of suitable reference genomic material to enable a transparent cross-lab study of oncopanels inspired the SEQC2 Oncopanel Sequencing Working Group to…”
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DNA sequence analysis of plasmids from multidrug resistant Salmonella enterica serotype Heidelberg isolates by Han, Jing, Lynne, Aaron M, David, Donna E, Tang, Hailin, Xu, Joshua, Nayak, Rajesh, Kaldhone, Pravin, Logue, Catherine M, Foley, Steven L

“…Salmonella enterica serovar Heidelberg is among the most detected serovars in swine and poultry, ranks among the top five serotypes associated with human…”
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Orbital approaches for treatment of carotid cavernous fistulas: A systematic review by Phan, Kevin, BSc, M Phil, Xu, Joshua, BSc, Leung, Vannessa, MBBS, Teng, Ian, B Med, Sheik-Ali, Sharaf, Maharaj, Monish, B Med, Mobbs, Ralph, MBBS, MS, FRACS, Rao, Prashanth J., MBBS, FRACS, PhD

“…Abstract Carotid cavernous fistulas (CCFs) are abnormal connections between the carotid arteries and the cavernous sinus. CCFs often present with double…”
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Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells by Craig, Daniel J, Morrison, Thomas, Khuder, Sadik A, Crawford, Erin L, Wu, Leihong, Xu, Joshua, Blomquist, Thomas M, Willey, James C

“…Standardized Nucleic Acid Quantification for SEQuencing (SNAQ-SEQ) is a novel method that utilizes synthetic DNA internal standards spiked into each sample…”
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Accuracy of acetabular component alignment with surgical guidance systems during hip arthroplasty by Xu, Joshua, Veltman, Ewout S, Chai, Yuan, Walter, William L

“…Navigation in total hip arthroplasty has been shown to improve acetabular positioning and can decrease the incidence of mal-positioned acetabular components…”
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