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2020 – today
- 2023
[j40]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)- [j39]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) - [i3]Mathieu Chevalley, Jacob Sackett-Sanders, Yusuf H. 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 abs/2308.15395 (2023) - 2022
- [j38]Hongyang Li, Yuanfang Guan:
Multilevel Modeling of Joint Damage in Rheumatoid Arthritis. Adv. Intell. Syst. 4(11) (2022) - [j37]Xin An, Xi Chen, Daiyao Yi, Hongyang Li, Yuanfang Guan:
Representation of molecules for drug response prediction. Briefings Bioinform. 23(1) (2022) - [j36]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) - [j35]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): 710-718 (2022) - [j34]Hongyang Li, Yuanfang Guan:
Asymmetric predictive relationships across histone modifications. Nat. Mach. Intell. 4(3): 288-299 (2022) - [j33]Hanrui Zhang, Xueqing Wang, Hongyang Li, Soham Mehendale, Yuanfang Guan:
Auto-annotating sleep stages based on polysomnographic data. Patterns 3(1): 100371 (2022) - [j32]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) - [j31]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): 1165-1172 (2022) - [j30]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): 1387-1392 (2022) - 2021
- [j29]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) - [j28]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): 411-428 (2021) - [j27]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): 696-704 (2021) - [j26]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): 433-440 (2021) - [j25]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, Earl 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) - [c1]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: 314-333 - 2020
- [j24]Hongyang Li, Yuanfang Guan:
Machine learning empowers phosphoproteome prediction in cancers. Bioinform. 36(3): 859-864 (2020) - [j23]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): 100042 (2020) - [j22]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): 100106 (2020) - [i2]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 abs/2010.11769 (2020)
2010 – 2019
- 2019
- [j21]Hongyang Li, Shuai Hu, Nouri Neamati, Yuanfang Guan:
TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction. Bioinform. 35(13): 2338-2339 (2019) - [j20]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): 2486-2488 (2019) - [j19]Yuanfang Guan:
Waking up to data challenges. Nat. Mach. Intell. 1(1): 67 (2019) - [j18]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): 407-421 (2019) - [i1]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 abs/1906.00240 (2019) - 2018
- [j17]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): 3578-3580 (2018) - [j16]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): 3975-3982 (2018) - 2017
- [j15]Bharat Panwar, Gilbert S. Omenn, Yuanfang Guan:
miRmine: a database of human miRNA expression profiles. Bioinform. 33(10): 1554-1560 (2017) - [j14]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) - 2016
- [j13]Fan Zhu, Bharat Panwar, Yuanfang Guan:
Algorithms for modeling global and context-specific functional relationship networks. Briefings Bioinform. 17(4): 686-695 (2016) - [j12]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): 1024-1031 (2016) - 2015
- [j11]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) - [j10]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): 2537-2544 (2015) - 2014
- [j9]Fan Zhu, Yuanfang Guan:
Predicting dynamic signaling network response under unseen perturbations. Bioinform. 30(19): 2772-2778 (2014) - [j8]Fan Zhu, Lihong Shi, Hongdong Li, Ridvan Eksi, James Douglas Engel, Yuanfang Guan:
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. Bioinform. 30(23): 3325-3333 (2014) - 2013
- [j7]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) - [j6]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) - 2012
- [j5]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): 484-490 (2012) - [j4]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) - 2010
- [j3]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) - [j2]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)
2000 – 2009
- 2008
- [j1]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)
Coauthor Index
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