Qi Liu

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 42

Top Topics

Benign Prostatic Hyperplasia

Network Analysis

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

Cancer research

Bioinformatics (Oxford, England)

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Christian T Meyer, Brianna N Smith, Jing Wang, Kevin B Teuscher, Brian C Grieb, Gregory Caleb Howard, Alexander James Silver, Shelly L Lorey, Gordon M Stott, William J Moore, Taekyu Lee, Michael R Savona, April M Weissmiller, Qi Liu, Vito Quaranta, Stephen W Fesik, William P Tansey
Expanded profiling of WD repeat domain 5 inhibitors reveals actionable strategies for the treatment of hematologic malignancies. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS computational biology 20 (1) (2024)
Jing Yang, Qi Liu, Yu Shyr
A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer research 84 (4) (2024)
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
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nature communications 15 (1) (2024)
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS computational biology 20 (1) (2024)
Christian T Meyer, Brianna N Smith, Jing Wang, Kevin B Teuscher, Brian C Grieb, Gregory Caleb Howard, Alexander James Silver, Shelly L Lorey, Gordon M Stott, William J Moore, Taekyu Lee, Michael R Savona, April M Weissmiller, Qi Liu, Vito Quaranta, Stephen W Fesik, William P Tansey
Expanded profiling of WD repeat domain 5 inhibitors reveals actionable strategies for the treatment of hematologic malignancies. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
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
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nature communications 15 (1) (2024)
Renjie Jin, Connor M Forbes, Nicole L Miller, John T Lafin, Douglas W Strand, Thomas Case, Justin Merrill Marken Cates, Qi Liu, Marisol Ramirez-Solano, James L Mohler, Robert J Matusik
Transcriptomic analysis of benign prostatic hyperplasia identifies critical pathways in prostatic overgrowth and 5-alpha reductase inhibitor resistance. The Prostate 84 (5) (2024)
Renjie Jin, Connor M Forbes, Nicole L Miller, John T Lafin, Douglas W Strand, Thomas Case, Justin Merrill Marken Cates, Qi Liu, Marisol Ramirez-Solano, James L Mohler, Robert J Matusik
Transcriptomic analysis of benign prostatic hyperplasia identifies critical pathways in prostatic overgrowth and 5-alpha reductase inhibitor resistance. The Prostate 84 (5) (2024)
Jia Li, Yu Shyr, Qi Liu
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome biology 25 (1) (2024)
Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS computational biology 20 (1) (2024)
Jing Yang, Qi Liu, Yu Shyr
A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer research 84 (4) (2024)
Jia Li, Yu Shyr, Qi Liu
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome biology 25 (1) (2024)
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
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nature communications 15 (1) (2024)
Jing Yang, Qi Liu, Yu Shyr
A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer research 84 (4) (2024)
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Christian T Meyer, Brianna N Smith, Jing Wang, Kevin B Teuscher, Brian C Grieb, Gregory Caleb Howard, Alexander James Silver, Shelly L Lorey, Gordon M Stott, William J Moore, Taekyu Lee, Michael R Savona, April M Weissmiller, Qi Liu, Vito Quaranta, Stephen W Fesik, William P Tansey
Expanded profiling of WD repeat domain 5 inhibitors reveals actionable strategies for the treatment of hematologic malignancies. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS computational biology 20 (1) (2024)
Renjie Jin, Connor M Forbes, Nicole L Miller, John T Lafin, Douglas W Strand, Thomas Case, Justin Merrill Marken Cates, Qi Liu, Marisol Ramirez-Solano, James L Mohler, Robert J Matusik
Transcriptomic analysis of benign prostatic hyperplasia identifies critical pathways in prostatic overgrowth and 5-alpha reductase inhibitor resistance. The Prostate (2024)
Jia Li, Yu Shyr, Qi Liu
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome biology 25 (1) (2024)
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Jing Yang, Qi Liu, Yu Shyr
A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer research 84 (4) (2024)
Jing Yang, Qi Liu, Yu Shyr
A large-scale meta-analysis reveals positive feedback between macrophages and T cells that sensitizes tumors to immunotherapy. Cancer research (2023)
Jing Yang, Qi Liu, Yu Shyr
A large-scale meta-analysis reveals positive feedback between macrophages and T cells that sensitizes tumors to immunotherapy. Cancer research (2023)
Jing Yang, Qi Liu, Yu Shyr
A large-scale meta-analysis reveals positive feedback between macrophages and T cells that sensitizes tumors to immunotherapy. Cancer research (2023)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shih-Kai Chu, Shilin Zhao, Yu Shyr, Qi Liu
Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. Briefings in bioinformatics 23 (2) (2022)
Kevin B Teuscher, Somenath Chowdhury, Kenneth M Meyers, Jianhua Tian, Jiqing Sai, Mayme Van Meveren, Taylor M South, John L Sensintaffar, Tyson A Rietz, Soumita Goswami, Jing Wang, Brian C Grieb, Shelly L Lorey, Gregory Caleb Howard, Qi Liu, William J Moore, Gordon M Stott, William P Tansey, Taekyu Lee, Stephen W Fesik
Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Qi Liu, Chih-Yuan Hsu, Jia Li, Yu Shyr
Dysregulated ligand-receptor interactions from single-cell transcriptomics. Bioinformatics (Oxford, England) 38 (12) (2022)
RenJie Jin, Douglas W Strand, Connor M Forbes, Thomas Case, Justin M M Cates, Qi Liu, Marisol Ramirez-Solano, Ginger L Milne, Stephanie Sanchez, Zunyi Y Wang, Dale E Bjorling, Nicole L Miller, Robert J Matusik
The prostaglandin pathway is activated in patients who fail medical therapy for benign prostatic hyperplasia with lower urinary tract symptoms. The Prostate 81 (13) (2021)
Jia Li, Quanhu Sheng, Yu Shyr, Qi Liu
scMRMA: single cell multiresolution marker-based annotation. Nucleic acids research (2021)
Hua-Chang Chen, Jing Wang, Qi Liu, Yu Shyr
A domain damage index to prioritizing the pathogenicity of missense variants. Human mutation 42 (11) (2021)
Bao-Hong Liu, Yu Shyr, Qi Liu
Pan-Cancer Analysis Reveals Common and Specific Relationships between Intragenic miRNAs and Their Host Genes. Biomedicines 9 (9) (2021)
David J Wooten, Sarah M Groves, Darren R Tyson, Qi Liu, Jing S Lim, Reka Albert, Carlos F Lopez, Julien Sage, Vito Quaranta
Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers. PLoS computational biology 15 (10) (2019)