Yuanfang Guan

Publication Activity (10 Years)

Years Active: 2008-2023
Publications (10 Years): 33

Top Topics

Differentially Expressed

Top Venues

Briefings Bioinform.

Nat. Mach. Intell.

Publications

Weilin Meng, Xinyuan Zhang, Boshu Ru, Yuanfang Guan
A Machine Learning Approach to Real-World Time to Treatment Discontinuation Prediction. Adv. Intell. Syst. 5 (4) (2023)
Mathieu Chevalley, Jacob Sackett-Sanders, Yusuf Roohani, Pascal Notin, Artemy Bakulin, Dariusz Brzezinski, Kaiwen Deng, Yuanfang Guan, Justin Hong, Michael Ibrahim, Wojciech Kotlowski, Marcin Kowiel, Panagiotis Misiakos, Achille Nazaret, Markus Püschel, Chris Wendler, Arash Mehrjou, Patrick Schwab
The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data. CoRR (2023)
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Computational approaches for detecting disease-associated alternative splicing events. Briefings Bioinform. 24 (3) (2023)
Jason L. Causey, Keyu Li, Xianghao Chen, Wei Dong, Karl Walker, Jake A. Qualls, Jonathan Stubblefield, Jason H. Moore, Yuanfang Guan, Xiuzhen Huang
Spatial Pyramid Pooling With 3D Convolution Improves Lung Cancer Detection. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Yuanfang Guan, Jianxin Wang
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. Nucleic Acids Res. 50 (D1) (2022)
Hongyang Li, Ridvan Eksi, Daiyao Yi, Bradley Godfrey, Lisa R. Mathew, Christopher L. O'Connor, Markus Bitzer, Matthias Kretzler, Rajasree Menon, Yuanfang Guan
Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms. PLoS Comput. Biol. 18 (4) (2022)
Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Weisheng Liu, Shannon Erhardt, Fang-Xiang Wu, Xing-Ming Zhao, Yuanfang Guan, Jun Wang, Daifeng Wang, Bin Hu, Jianxin Wang
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. Briefings Bioinform. 23 (1) (2022)
Xin An, Xi Chen, Daiyao Yi, Hongyang Li, Yuanfang Guan
Representation of molecules for drug response prediction. Briefings Bioinform. 23 (1) (2022)
Hongyang Li, Yuanfang Guan
Multilevel Modeling of Joint Damage in Rheumatoid Arthritis. Adv. Intell. Syst. 4 (11) (2022)
Hongyang Li, Yuanfang Guan
Asymmetric predictive relationships across histone modifications. Nat. Mach. Intell. 4 (3) (2022)
Hanrui Zhang, Xueqing Wang, Hongyang Li, Soham Mehendale, Yuanfang Guan
Auto-annotating sleep stages based on polysomnographic data. Patterns 3 (1) (2022)
Jason L. Causey, Jonathan Stubblefield, Jake A. Qualls, Jennifer Fowler, Lingrui Cai, Karl Walker, Yuanfang Guan, Xiuzhen Huang
An Ensemble of U-Net Models for Kidney Tumor Segmentation With CT Images. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (3) (2022)
James Lu, Brendan Bender, Jin Y. Jin, Yuanfang Guan
Deep learning prediction of patient response time course from early data via neural-pharmacokinetic/pharmacodynamic modelling. Nat. Mach. Intell. 3 (8) (2021)
Konstantin F. Willeke, Paul G. Fahey, Mohammad Bashiri, Laura Hansel, Christoph Blessing, Konstantin-Klemens Lurz, Max F. Burg, Santiago A. Cadena, Zhiwei Ding, Kayla Ponder, Taliah Muhammad, Saumil S. Patel, Kaiwen Deng, Yuanfang Guan, Yiqin Zhu, Kaiwen Xiao, Xiao Han, Simone Azeglio, Ulisse Ferrari, Peter Neri, Olivier Marre, Adrian Hoffmann, Kirill Fedyanin, Kirill Vishniakov, Maxim Panov, Subash Prakash, Kishan Naik, Kantharaju Narayanappa, Alexander S. Ecker, Andreas S. Tolias, Fabian H. Sinz
Retrospective on the SENSORIUM 2022 competition. NeurIPS (Competition and Demos) (2021)
Jennifer Fowler, Jonathan Stubblefield, Jason L. Causey, Jake A. Qualls, Wei Dong, Hongmei Jiang, Karl Walker, Yuanfang Guan, Xiuzhen Huang
Identify differentially expressed genes with large background samples. Int. J. Comput. Biol. Drug Des. 14 (6) (2021)
Bulat Zagidullin, Ziyan Wang, Yuanfang Guan, Esa Pitkänen, Jing Tang
Comparative analysis of molecular fingerprints in prediction of drug combination effects. Briefings Bioinform. 22 (6) (2021)
Solveig K. Sieberts, Jennifer Schaff, Marlena Duda, Bálint Á Pataki, Ming Sun, Phil Snyder, Jean-Francois Daneault, Federico Parisi, Gianluca Costante, Udi Rubin, Peter Banda, Yooree Chae, Elias Chaibub Neto, E. Ray Dorsey, Zafer Aydin, Aipeng Chen, Laura L. Elo, Carlos Espino, Enrico Glaab, Ethan Goan, Fatemeh Noushin Golabchi, Yasin Görmez, Maria K. Jaakkola, Jitendra Jonnagaddala, Riku Klén, Dongmei Li, Christian McDaniel, Dimitri Perrin, Thanneer M. Perumal, Nastaran Mohammadian Rad, Erin Rainaldi, Stefano Sapienza, Patrick Schwab, Nikolai Shokhirev, Mikko S. Venäläinen, Gloria Vergara-Diaz, Yuqian Zhang, Avner G. S. Abrami, Aditya Adhikary, Carla Agurto, Sherry Bhalla, Halil Ibrahim Bilgin, Vittorio Caggiano, Jun Cheng, Eden Deng, Qiwei Gan, Rajan Girsa, Zhi Han, Stephen Heisig, Kun Huang, Samad Jahandideh, Wolfgang Kopp, Christoph F. Kurz, Gregor Lichtner, Raquel Norel, G. P. S. Raghava, Tavpritesh Sethi, Nicholas Shawen, Vaibhav Tripathi, Matthew Tsai, Tongxin Wang, Yi Wu, Jie Zhang, Xinyu Zhang, Yuanjia Wang, Yuanfang Guan, Daniela Brunner, Paolo Bonato, Lara M. Mangravite, Larsson Omberg
Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge. npj Digit. Medicine 4 (2021)
Yuanfang Guan, Hongyang Li, Daiyao Yi, Dongdong Zhang, Changchang Yin, Keyu Li, Ping Zhang
A survival model generalized to regression learning algorithms. Nat. Comput. Sci. 1 (6) (2021)
James Lu, Brendan Bender, Jin Y. Jin, Yuanfang Guan
Deep learning prediction of patient response time course from early data via neural-pharmacokinetic/pharmacodynamic modeling. CoRR (2020)
Yuanfang Guan, Xueqing Wang, Hongyang Li, Zhenning Zhang, Xianghao Chen, Omer Siddiqui, Sara Nehring, Xiuzhen Huang
Detecting Asymmetric Patterns and Localizing Cancers on Mammograms. Patterns 1 (7) (2020)
Hanrui Zhang, Kaiwen Deng, Hongyang Li, Roger L. Albin, Yuanfang Guan
Deep Learning Identifies Digital Biomarkers for Self-Reported Parkinson's Disease. Patterns 1 (3) (2020)
Hongyang Li, Yuanfang Guan
Machine learning empowers phosphoproteome prediction in cancers. Bioinform. 36 (3) (2020)
Jason L. Causey, Yuanfang Guan, Wei Dong, Karl Walker, Jake A. Qualls, Fred W. Prior, Xiuzhen Huang
Lung cancer screening with low-dose CT scans using a deep learning approach. CoRR (2019)
Hong-Dong Li, Tianjian Bai, Erin Sandford, Margit Burmeister, Yuanfang Guan
BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets. Bioinform. 35 (14) (2019)
Ming Tang, Chao Gao, Stephen A. Goutman, Alexandr A. Kalinin, Bhramar Mukherjee, Yuanfang Guan, Ivo D. Dinov
Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics 17 (3) (2019)
Yuanfang Guan
Waking up to data challenges. Nat. Mach. Intell. 1 (1) (2019)
Hongyang Li, Shuai Hu, Nouri Neamati, Yuanfang Guan
TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction. Bioinform. 35 (13) (2019)
Yuanfang Guan, Tingyang Li, Hongjiu Zhang, Fan Zhu, Gilbert S. Omenn
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile. Bioinform. 34 (23) (2018)
Daniel Quang, Yuanfang Guan, Stephen C. J. Parker
YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. Bioinform. 34 (20) (2018)
Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A. Goutman, Bhramar Mukherjee, Ivo D. Dinov, Yuanfang Guan
Complete hazard ranking to analyze right-censored data: An ALS survival study. PLoS Comput. Biol. 13 (12) (2017)
Bharat Panwar, Gilbert S. Omenn, Yuanfang Guan
miRmine: a database of human miRNA expression profiles. Bioinform. 33 (10) (2017)
Hongdong Li, Gilbert S. Omenn, Yuanfang Guan
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Briefings Bioinform. 17 (6) (2016)
Fan Zhu, Bharat Panwar, Yuanfang Guan
Algorithms for modeling global and context-specific functional relationship networks. Briefings Bioinform. 17 (4) (2016)
Fan Zhu, Lihong Shi, James Douglas Engel, Yuanfang Guan
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. Bioinform. 31 (15) (2015)
Hongdong Li, Gilbert S. Omenn, Yuanfang Guan
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. Database J. Biol. Databases Curation 2015 (2015)
Fan Zhu, Yuanfang Guan
Predicting dynamic signaling network response under unseen perturbations. Bioinform. 30 (19) (2014)
Fan Zhu, Lihong Shi, Hongdong Li, Ridvan Eksi, James Douglas Engel, Yuanfang Guan
human erythroid differentiation. Bioinform. 30 (23) (2014)
Ridvan Eksi, Hongdong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan
Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data. PLoS Comput. Biol. 9 (11) (2013)
Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. 9 (3) (2013)
Yuanfang Guan, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K. Wong, John C. Schimenti, Mary Ann Handel, Carol J. Bult, Matthew A. Hibbs, Olga G. Troyanskaya
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes. PLoS Comput. Biol. 8 (9) (2012)
Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species. PLoS Comput. Biol. 6 (3) (2010)
Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations. PLoS Comput. Biol. 6 (11) (2010)
Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya
A Genomewide Functional Network for the Laboratory Mouse. PLoS Comput. Biol. 4 (9) (2008)