VICTOR: Validation and inspection of cell type annotation through optimal regression

Authors: Chia-Jung Chang, Chih-Yuan Hsu, Qi Liu, Yu Shyr

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 3270-3280 (2024)

Subject Terms: Single-cell RNA sequencing analysis, Assessment of annotation quality, Cell type annotation, Elastic-net regularized regression, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037024002873; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/3b3bcb8ee2c645ed971aefdf6b926d85

Afatinib and Necitumumab in EGFR-Mutant NSCLC with Acquired Resistance to Tyrosine Kinase Inhibitors

Authors: Nathaniel J. Myall, MD, Jennifer G. Whisenant, PhD, Joel W. Neal, MD, PhD, Wade T. Iams, MD, Karen L. Reckamp, MD, Sally York, MD, PhD, Lynne D. Berry, PhD, Yu Shyr, PhD, Leora Horn, MD, Heather A. Wakelee, MD, Sukhmani K. Padda, MD

Source: JTO Clinical and Research Reports, Vol 6, Iss 2, Pp 100757- (2025)

Subject Terms: Dual EGFR inhibition, Phase I trial, Lung cancer, EGFR-mutated, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666364324001279; https://doaj.org/toc/2666-3643

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aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph

Authors: Jia Li, Yu Shyr, Qi Liu

Source: Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)

Subject Terms: Single-cell and spatial transcriptomics, Clustering, Rare cells, Adaptive k-nearest neighbors, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/72d330b981b141d68ba3fe09704b0048

Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn’s disease

Authors: Jia Li, Alan J. Simmons, Caroline V. Hawkins, Sophie Chiron, Marisol A. Ramirez-Solano, Naila Tasneem, Harsimran Kaur, Yanwen Xu, Frank Revetta, Paige N. Vega, Shunxing Bao, Can Cui, Regina N. Tyree, Larry W. Raber, Anna N. Conner, Jennifer M. Pilat, Justin Jacobse, Kara M. McNamara, Margaret M. Allaman, Gabriella A. Raffa, Alain P. Gobert, Mohammad Asim, Jeremy A. Goettel, Yash A. Choksi, Dawn B. Beaulieu, Robin L. Dalal, Sara N. Horst, Baldeep S. Pabla, Yuankai Huo, Bennett A. Landman, Joseph T. Roland, Elizabeth A. Scoville, David A. Schwartz, M. Kay Washington, Yu Shyr, Keith T. Wilson, Lori A. Coburn, Ken S. Lau, Qi Liu

Source: Nature Communications, Vol 15, Iss 1, Pp 1-19 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/0ba81d63e38741479e8c66302f19cf18

A Phase 1/2 Study to Evaluate the Safety and Activity of Nivolumab in Combination With Vorolanib, a Vascular Endothelial Growth Factor Tyrosine Kinase Inhibitor, in Patients With Refractory Thoracic Tumors

Authors: Kathryn E. Beckermann, MD, PhD, Christine M. Bestvina, MD, Badi El Osta, MD, Rachel E. Sanborn, MD, Hossein Borghaei, MD, Philip Edward Lammers, MD, MSCI, Giovanni Selvaggi, MD, Jennifer G. Whisenant, PhD, Ellen Heimann-Nichols, MBA, Lynne Berry, PhD, Chih-Yuan Hsu, PhD, Yu Shyr, PhD, Leora Horn, MD, MSc, MHPE, Heather Wakelee, MD, FASCO

Source: JTO Clinical and Research Reports, Vol 5, Iss 2, Pp 100619- (2024)

Subject Terms: Lung cancer, Thymic, Small cell, Anti-angiogenic, Nivolumab, PD-1, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666364323001625; https://doaj.org/toc/2666-3643

Access URL: https://doaj.org/article/c6b067ef1dff4f2782f2f6840a59c659

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.

Authors: Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu

Source: PLoS Computational Biology, Vol 20, Iss 1, p e1011786 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011786&type=printable; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/03bbb53df7504b1bb6905fb12c260480

Power and sample sizes estimation in clinical trials with treatment switching in intention-to-treat analysis: a simulation study

Authors: Lejun Deng, Chih-Yuan Hsu, Yu Shyr

Source: BMC Medical Research Methodology, Vol 23, Iss 1, Pp 1-9 (2023)

Subject Terms: Crossover, Intention-to-treat analysis, Randomized controlled trials, Treatment switching, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2288

Access URL: https://doaj.org/article/006c8334060d4a5b984945e08509923e

scDemultiplex: An iterative beta-binomial model-based method for accurate demultiplexing with hashtag oligos

Authors: Li-Ching Huang, Lindsey K. Stolze, Hua-Chang Chen, Alexander Gelbard, Yu Shyr, Qi Liu, Quanhu Sheng

Source: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 4044-4055 (2023)

Subject Terms: Single-cell sequencing, Hashtag oligo (HTO), Demultiplexing, Beta-binomial, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S200103702300288X; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/ff683179d5d44a2a94fa817ffb63d090

Time-Dependent Effects of Clinical Interventions on SARS-CoV-2 Immunity in Patients with Lung Cancer

Authors: Philip C. Mack, Chih-Yuan Hsu, Ananda M. Rodilla, Jorge E. Gomez, Jazz Cagan, Yuanhui Huang, Sooyun Tavolacci, Rajesh M. Valanparambil, Nicholas Rohs, Rachel Brody, Brittney Nichols, Juan Manuel Carreño, Sheena Bhalla, Christian Rolfo, David E. Gerber, Amy Moore, Jennifer C. King, Rafi Ahmed, John D. Minna, Paul A. Bunn, Adolfo García-Sastre, Florian Krammer, Fred R. Hirsch, Yu Shyr

Source: Vaccines, Vol 12, Iss 7, p 713 (2024)

Subject Terms: SARS-CoV-2 antibody levels, lung cancer therapies, time-dependent regression model, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-393X/12/7/713; https://doaj.org/toc/2076-393X

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Breakthrough SARS-CoV-2 infections among patients with cancer following two and three doses of COVID-19 mRNA vaccines: a retrospective observational study from the COVID-19 and Cancer ConsortiumResearch in context

Authors: Toni K. Choueiri, Chris Labaki, Ziad Bakouny, Chih-Yuan Hsu, Andrew L. Schmidt, Gilberto de Lima Lopes, Jr., Clara Hwang, Sunny R.K. Singh, Chinmay Jani, Lisa B. Weissmann, Elizabeth A. Griffiths, Susan Halabi, Ulysses Wu, Stephanie Berg, Timothy E. O'Connor, Trisha M. Wise-Draper, Orestis A. Panagiotou, Elizabeth J. Klein, Monika Joshi, Fares Yared, Miriam Santos Dutra, Na Tosha N. Gatson, Sibel Blau, Harpreet Singh, Rahul Nanchal, Rana R. McKay, Taylor K. Nonato, Ryann Quinn, Samuel M. Rubinstein, Matthew Puc, Blanche H. Mavromatis, Praveen Vikas, Bryan Faller, Howard A. Zaren, Salvatore Del Prete, Karen Russell, Daniel Y. Reuben, Melissa K. Accordino, Christopher R. Friese, Sanjay Mishra, Donna R. Rivera, Yu Shyr, Dimitrios Farmakiotis, Jeremy L. Warner

Source: The Lancet Regional Health. Americas, Vol 19, Iss , Pp 100445- (2023)

Subject Terms: Covid-19, Vaccination, SARS-CoV-2, Cancer, Breakthrough infection, mRNA vaccine, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667193X23000194; https://doaj.org/toc/2667-193X

Access URL: https://doaj.org/article/e370428645e4460e9f6ede1b1e0c1c34

Associations of influenza vaccination with severity of immune-related adverse events in patients with advanced thoracic cancers on immune checkpoint inhibitors

Authors: Emily Pei-Ying Lin, Li-Ching Huang, Jennifer Whisenant, Sally York, Travis Osterman, Jennifer Lewis, Wade Iams, Emily Skotte, Amanda Cass, Chih-Yuan Hsu, Yu Shyr, Leora Horn

Source: ERJ Open Research, Vol 8, Iss 4 (2022)

Subject Terms: Medicine

File Description: electronic resource

Relation: http://openres.ersjournals.com/content/8/4/00684-2021.full; https://doaj.org/toc/2312-0541

Access URL: https://doaj.org/article/42db88a605794c8498181839ee80df4f

Expression of CCL2/CCR2 signaling proteins in breast carcinoma cells is associated with invasive progression

Authors: Wei Bin Fang, Diana Sofia Acevedo, Curtis Smart, Brandon Zinda, Nadia Alissa, Kyle Warren, Garth Fraga, Li-Ching Huang, Yu Shyr, Wei Li, Lu Xie, Vincent Staggs, Yan Hong, Fariba Behbod, Nikki Cheng

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/5e457ae5a93a494ea906c23486258ba4

MetaGSCA: A tool for meta-analysis of gene set differential coexpression.

Authors: Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott Ness, Yu Shyr, Fei Ye

Source: PLoS Computational Biology, Vol 17, Iss 5, p e1008976 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008976&type=printable; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/dfe3d22a633a472d9322b1fe6da9ec96

Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer

Authors: Luigi Formisano, Yao Lu, Alberto Servetto, Ariella B. Hanker, Valerie M. Jansen, Joshua A. Bauer, Dhivya R. Sudhan, Angel L. Guerrero-Zotano, Sarah Croessmann, Yan Guo, Paula Gonzalez Ericsson, Kyung-min Lee, Mellissa J. Nixon, Luis J. Schwarz, Melinda E. Sanders, Teresa C. Dugger, Marcelo Rocha Cruz, Amir Behdad, Massimo Cristofanilli, Aditya Bardia, Joyce O’Shaughnessy, Rebecca J. Nagy, Richard B. Lanman, Nadia Solovieff, Wei He, Michelle Miller, Fei Su, Yu Shyr, Ingrid A. Mayer, Justin M. Balko, Carlos L. Arteaga

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c9a8bb9c2aac44dba476758c76c4a8d4

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

Authors: Jing Wang, Yue Zhao, Xiaofan Zhou, Scott W. Hiebert, Qi Liu, Yu Shyr

Source: BMC Genomics, Vol 19, Iss 1, Pp 1-18 (2018)

Subject Terms: Enhancer, Nascent RNA sequencing, Enhancer regulation, Enhancer prioritization, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-018-5016-z; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/05443fe2874e4f63a3689dcfaf2da9d6

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing

Authors: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-8 (2018)

Subject Terms: RNA-Seq, Sample size, Power analysis, Simulation, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2191-5; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/bcd29130d8e441328a8a47a68052fdd2

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data

Authors: Yan Guo, Shilin Zhao, Quanhu Sheng, David C Samuels, Yu Shyr

Source: BMC Genomics, Vol 18, Iss S6, Pp 37-46 (2017)

Subject Terms: DNA-RNA difference, RNA editing, Single nucleotide variant, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-017-4022-x; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/2f7f8e0104cf4c9dba37dac00e611ea8

A Refractive Distortion Correction Method for 3D Root Reconstruction

Authors: Li, Mu-Wei, Wu, Po-Lung, Lo, Shuen-Fang, Chan, Yung-Kuan, Yu, Shyr-Shen

Source: 2023 Sixth International Symposium on Computer, Consumer and Control (IS3C) IS3C Computer, Consumer and Control (IS3C), 2023 Sixth International Symposium on. :114-117 Jun, 2023

Relation: 2023 Sixth International Symposium on Computer, Consumer and Control (IS3C)

Pan-Cancer Analysis Reveals Common and Specific Relationships between Intragenic miRNAs and Their Host Genes

Authors: Baohong Liu, Yu Shyr, Qi Liu

Source: Biomedicines, Vol 9, Iss 9, p 1263 (2021)

Subject Terms: miRNAs, host genes, coexpression, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2227-9059/9/9/1263; https://doaj.org/toc/2227-9059

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Shanghai Score: A Prognostic and Adjuvant Treatment-evaluating System Constructed for Chinese Patients with Hepatocellular Carcinoma after Curative Resection

Authors: Hui-Chuan Sun, Lu Xie, Xin-Rong Yang, Wei Li, Jian Yu, Xiao-Dong Zhu, Yong Xia, Ti Zhang, Yang Xu, Bo Hu, Li-Ping Du, Ling-Yao Zeng, Jian Ouyang, Wei Zhang, Tian-Qiang Song, Qiang Li, Ying-Hong Shi, Jian Zhou, Shuang-Jian Qiu, Qian Liu, Yi-Xue Li, Zhao-You Tang, Yu Shyr, Feng Shen, Jia Fan

Source: Chinese Medical Journal, Vol 130, Iss 22, Pp 2650-2660 (2017)

Subject Terms: Adjuvant Treatment, Hepatocellular Carcinoma, Prognosis, Shanghai Score, Medicine

File Description: electronic resource

Relation: http://www.cmj.org/article.asp?issn=0366-6999;year=2017;volume=130;issue=22;spage=2650;epage=2660;aulast=Sun; https://doaj.org/toc/0366-6999

Access URL: https://doaj.org/article/ee49e02b78cb40b3853111cc0ae34bd9