Bing Zhang

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 35

Top Topics

Mass Spectrometry

Top Venues

Nature communications

Tomography (Ann Arbor, Mich.)

Science advances

Nucleic acids research

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

Publications

John M Elizarraras, Yuxing Liao, Zhiao Shi, Qian Zhu, Alexander R Pico, Bing Zhang
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics. Nucleic acids research 52 (W1) (2024)
Chenwei Wang, Bing Zhang
Proteomics Meets Dose Response: A New Paradigm for Deciphering Drug Effects. Cancer research 84 (16) (2024)
John M Elizarraras, Yuxing Liao, Zhiao Shi, Qian Zhu, Alexander R Pico, Bing Zhang
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics. Nucleic acids research (2024)
Chenwei Wang, Bing Zhang
Proteomics Meets Dose-Response: A New Paradigm for Deciphering Drug Effects. Cancer research (2024)
John M Elizarraras, Yuxing Liao, Zhiao Shi, Qian Zhu, Alexander R Pico, Bing Zhang
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics. Nucleic acids research 52 (W1) (2024)
Emel Alkim, Heidi Dowst, Julie C DiCarlo, Lacey E Dobrolecki, Anadulce Hernández-Herrera, David A Hormuth, Yuxing Liao, Apollo McOwiti, Robia G Pautler, Mothaffar Rimawi, Ashley Roark, Ramakrishnan Rajaram Srinivasan, John Virostko, Bing Zhang, Fei Zheng, Daniel L Rubin, Thomas E Yankeelov, Michael T Lewis
Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography (Ann Arbor, Mich.) 9 (2) (2023)
Shuyi Ji, Li Feng, Zile Fu, Gaohua Wu, Yingcheng Wu, Youpei Lin, Dayun Lu, Yuanli Song, Peng Cui, Zijian Yang, Chen Sang, Guohe Song, Shangli Cai, Yuanchuang Li, Hanqing Lin, Shu Zhang, Xiaoying Wang, Shuangjian Qiu, Xiaoming Zhang, Guoqiang Hua, Junqiang Li, Jian Zhou, Zhi Dai, Xiang-Dong Wang, Li Ding, Pei Wang, Daming Gao, Bing Zhang, Henry Rodriguez, Jia Fan, Hans Clevers, Hu Zhou, Yi-Di Sun, Qiang Gao
Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology. Science translational medicine 15 (706) (2023)
Bo Wen, Bing Zhang
PepQuery2 democratizes public MS proteomics data for rapid peptide searching. Nature communications 14 (1) (2023)
Emel Alkim, Heidi Dowst, Julie C DiCarlo, Lacey E Dobrolecki, Anadulce Hernández-Herrera, David A Hormuth, Yuxing Liao, Apollo McOwiti, Robia G Pautler, Mothaffar Rimawi, Ashley Roark, Ramakrishnan Rajaram Srinivasan, John Virostko, Bing Zhang, Fei Zheng, Daniel L Rubin, Thomas E Yankeelov, Michael T Lewis
Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography (Ann Arbor, Mich.) 9 (2) (2023)
Wen Bu, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Amy T Ku, Yiqun Zhang, Weiyu Jiang, Jazmin Urrutia, Wen Jiang, Fei Yue, Luyu Jia, Ahmed Atef Ibrahim, Bing Zhang, Shixia Huang, Yi Li
Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. Science advances 9 (19) (2023)
Wen Bu, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Amy T Ku, Yiqun Zhang, Weiyu Jiang, Jazmin Urrutia, Wen Jiang, Fei Yue, Luyu Jia, Ahmed Atef Ibrahim, Bing Zhang, Shixia Huang, Yi Li
Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. Science advances 9 (19) (2023)
Beom-Jun Kim, Ze-Yi Zheng, Jonathan T Lei, Matthew V Holt, Anran Chen, Jianheng Peng, Diana Fandino, Purba Singh, Hilda Kennedy, Yongchao Dou, María Del Rosario Chica-Parrado, Emmanuel Bikorimana, Dan Ye, Yunguan Wang, Ariella B Hanker, Nada Mohamed, Susan G Hilsenbeck, Bora Lim, Jaya Ruth Asirvatham, Arun Sreekumar, Bing Zhang, George Miles, Meenakshi Anurag, Matthew J Ellis, Eric C Chang
Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor-positive Breast Cancers for Targeted Treatment. Cancer research communications 3 (7) (2023)
Xiangdong Lv, Xuan Lu, Jin Cao, Qin Luo, Yao Ding, Fanglue Peng, Apar Pataer, Dong Lu, Dong Han, Eric Malmberg, Doug W Chan, Xiaoran Wang, Sara R Savage, Sufeng Mao, Jingjing Yu, Fei Peng, Liang Yan, Huan Meng, Laure Maneix, Yumin Han, Yiwen Chen, Wantong Yao, Eric C Chang, Andre Catic, Xia Lin, George Miles, Pengxiang Huang, Zheng Sun, Bryan Burt, Huamin Wang, Jin Wang, Qizhi Cathy Yao, Bing Zhang, Jack A Roth, Bert W O' Malley, Matthew J Ellis, Mothaffar F Rimawi, Haoqiang Ying, Xi Chen
Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors. Science (New York, N.Y.) 381 (6662) (2023)
Emel Alkim, Heidi Dowst, Julie C DiCarlo, Lacey E Dobrolecki, Anadulce Hernández-Herrera, David A Hormuth, Yuxing Liao, Apollo McOwiti, Robia G Pautler, Mothaffar Rimawi, Ashley Roark, Ramakrishnan Rajaram Srinivasan, John Virostko, Bing Zhang, Fei Zheng, Daniel L Rubin, Thomas E Yankeelov, Michael T Lewis
Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography (Ann Arbor, Mich.) 9 (2) (2023)
Hongwen Zhu, Youpei Lin, Dayun Lu, Shisheng Wang, Yuejia Liu, Liangqing Dong, Qian Meng, Jing Gao, Yuqiu Wang, Nixue Song, Yuying Suo, Li Ding, Pei Wang, Bing Zhang, Daming Gao, Jia Fan, Qiang Gao, Hu Zhou
Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma. National science review 10 (8) (2023)
Chang In Moon, John Michael Elizarraras, Jonathan Thomas Lei, Byron Jia, Bing Zhang
ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials. Nucleic acids research (2023)
Wen Bu, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Amy T Ku, Yiqun Zhang, Weiyu Jiang, Jazmin Urrutia, Wen Jiang, Fei Yue, Luyu Jia, Ahmed Atef Ibrahim, Bing Zhang, Shixia Huang, Yi Li
Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. Science advances 9 (19) (2023)
Yongchao Dou, Yuejia Liu, Xinpei Yi, Lindsey K Olsen, Hongwen Zhu, Qiang Gao, Hu Zhou, Bing Zhang
SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics. Nature communications 14 (1) (2023)
Emel Alkim, Heidi Dowst, Julie C DiCarlo, Lacey E Dobrolecki, Anadulce Hernández-Herrera, David A Hormuth, Yuxing Liao, Apollo McOwiti, Robia G Pautler, Mothaffar Rimawi, Ashley Roark, Ramakrishnan Rajaram Srinivasan, John Virostko, Bing Zhang, Fei Zheng, Daniel L Rubin, Thomas E Yankeelov, Michael T Lewis
Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography (Ann Arbor, Mich.) 9 (2) (2023)
Wen Bu, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Amy T Ku, Yiqun Zhang, Weiyu Jiang, Jazmin Urrutia, Wen Jiang, Fei Yue, Luyu Jia, Ahmed Atef Ibrahim, Bing Zhang, Shixia Huang, Yi Li
Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. Science advances 9 (19) (2023)
Emel Alkim, Heidi Dowst, Julie C DiCarlo, Lacey E Dobrolecki, Anadulce Hernández-Herrera, David A Hormuth, Yuxing Liao, Apollo McOwiti, Robia G Pautler, Mothaffar Rimawi, Ashley Roark, Ramakrishnan Rajaram Srinivasan, John Virostko, Bing Zhang, Fei Zheng, Daniel L Rubin, Thomas E Yankeelov, Michael T Lewis
Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography (Ann Arbor, Mich.) 9 (2) (2023)
Meenakshi Anurag, Eric J Jaehnig, Karsten Krug, Jonathan T Lei, Erik J Bergstrom, Beom-Jun Kim, Tanmayi D Vashist, Anh Minh Tran Huynh, Yongchao Dou, Xuxu Gou, Chen Huang, Zhiao Shi, Bo Wen, Viktoriya Korchina, Richard A Gibbs, Donna M Muzny, Harsha Vardhan Doddapaneni, Lacey Elizabeth Dobrolecki, Henry Rodriguez, Ana I Robles, Tara Hiltke, Michael T Lewis, Julie R Nangia, Maryam Nemati Shafaee, Shunqiang Li, Ian S Hagemann, Jeremy Hoog, Bora Lim, C Kent Osborne, D R Mani, Michael A Gillette, Bing Zhang, Gloria V Echeverria, George Miles, Mothaffar F Rimawi, Steven A Carr, Foluso O Ademuyiwa, Shankha Satpathy, Matthew J Ellis
Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. Cancer discovery 12 (11) (2022)
Brian D Lehmann, Antonio Colaprico, Tiago C Silva, Jianjiao Chen, Hanbing An, Yuguang J Ban, Hanchen Huang, Lily Wang, Jamaal L James, Justin M Balko, Paula I Gonzalez Ericsson, Melinda E Sanders, Bing Zhang, Jennifer A Pietenpol, X Steven Chen
Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nature communications 12 (1) (2021)
Dongqing Huang, Sara R Savage, Anna P Calinawan, Chenwei Lin, Bing Zhang, Pei Wang, Timothy K Starr, Michael J Birrer, Amanda G Paulovich
A highly annotated database of genes associated with platinum resistance in cancer. Oncogene 40 (46) (2021)
Jonathan T Lei, Bing Zhang
Proteogenomics drives therapeutic hypothesis generation for precision oncology. British journal of cancer 125 (1) (2021)
Bo Wen, Bing Zhang
Computational Proteomics: Focus on Deep Learning. Proteomics 20 (21-22) (2021)
Kai Li, Antrix Jain, Anna Malovannaya, Bo Wen, Bing Zhang
DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics. Proteomics 20 (21-22) (2020)
Bo Wen, Kai Li, Yun Zhang, Bing Zhang
Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis. Nature communications 11 (1) (2020)
Bo Wen, Wen-Feng Zeng, Yuxing Liao, Zhiao Shi, Sara R Savage, Wen Jiang, Bing Zhang
Deep Learning in Proteomics. Proteomics 20 (21-22) (2020)
Shankha Satpathy, Eric J Jaehnig, Karsten Krug, Beom-Jun Kim, Alexander B Saltzman, Doug W Chan, Kimberly R Holloway, Meenakshi Anurag, Chen Huang, Purba Singh, Ari Gao, Noel Namai, Yongchao Dou, Bo Wen, Suhas V Vasaikar, David Mutch, Mark A Watson, Cynthia Ma, Foluso O Ademuyiwa, Mothaffar F Rimawi, Rachel Schiff, Jeremy Hoog, Samuel Jacobs, Anna Malovannaya, Terry Hyslop, Karl R Clauser, D R Mani, Charles M Perou, George Miles, Bing Zhang, Michael A Gillette, Steven A Carr, Matthew J Ellis
Microscaled proteogenomic methods for precision oncology. Nature communications 11 (1) (2020)
Sara R Savage, Bing Zhang
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clinical proteomics 17 (2020)
Jorge Gómez-Miragaya, Ander Díaz-Navarro, Raul Tonda, Sergi Beltran, Luis Palomero, Marta Palafox, Lacey E Dobrolecki, Chen Huang, Suhas Vasaikar, Bing Zhang, Gerburg M Wulf, Alejandro Collado-Sole, Eva María Trinidad, Purificación Muñoz, Laia Paré, Aleix Prat, Alejandra Bruna, Carlos Caldas, Joaquín Arribas, María Teresa Soler-Monso, Anna Petit, Judith Balmaña, Cristina Cruz, Violeta Serra, Miguel Angel Pujana, Michael T Lewis, Xose S Puente, Eva González-Suárez
Chromosome 12p Amplification in Triple-Negative/BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity. Cancer research 79 (16) (2019)
Bing Zhang, Jeffrey R Whiteaker, Andrew N Hoofnagle, Geoffrey S Baird, Karin D Rodland, Amanda G Paulovich
Clinical potential of mass spectrometry-based proteogenomics. Nature reviews. Clinical oncology 16 (4) (2019)
Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi, Emily S Boja, Catherine E Costello, Benjamin F Cravatt, Catherine Fenselau, Benjamin A Garcia, Ying Ge, Jeremy Gunawardena, Ronald C Hendrickson, Paul J Hergenrother, Christian G Huber, Alexander R Ivanov, Ole N Jensen, Michael C Jewett, Michael P Snyder, Laura L Kiessling, Nevan J Krogan, Martin R Larsen, Joseph A Loo, Rachel R Ogorzalek Loo, Emma Lundberg, Michael J MacCoss, Parag Mallick, Vamsi K Mootha, Milan Mrksich, Tom W Muir, Steven M Patrie, James J Pesavento, Sharon J Pitteri, Henry Rodriguez, Alan Saghatelian, Wendy Sandoval, Hartmut Schlüter, Salvatore Sechi, Sarah A Slavoff, Lloyd M Smith, Michael P Snyder, Paul M Thomas, Mathias Uhlén, Jennifer E Van Eyk, Marc Vidal, David R Walt, Forest M White, Evan R Williams, Therese Wohlschlager, Vicki H Wysocki, Nathan A Yates, Nicolas L Young, Bing Zhang
How many human proteoforms are there? Nature chemical biology 14 (3) (2019)
Ting-Wen Chen, Chi-Ching Lee, Hsuan Liu, Chi-Sheng Wu, Curtis R Pickering, Po-Jung Huang, Jing Wang, Ian Yi-Feng Chang, Yuan-Ming Yeh, Chih-De Chen, Hsin-Pai Li, Ji-Dung Luo, Bertrand Chin-Ming Tan, Timothy En Haw Chan, Chuen Hsueh, Lichieh Julie Chu, Yi-Ting Chen, Bing Zhang, Chia-Yu Yang, Chih-Ching Wu, Chia-Wei Hsu, Lai-Chu See, Petrus Tang, Jau-Song Yu, Wei-Chao Liao, Wei-Fan Chiang, Henry Rodriguez, Jeffrey N Myers, Kai-Ping Chang, Yu-Sun Chang
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nature communications 8 (1) (2017)