Yuanfang Guan

45 papers Journal 43Unranked 2
YearRankTypeTitle / Venue / Authors
2025 — conf
The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data.
CLeaR
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
2023 J jnl
A Machine Learning Approach to Real-World Time to Treatment Discontinuation Prediction.
Adv. Intell. Syst.
Weilin Meng, Xinyuan Zhang, Boshu Ru, Yuanfang Guan
2023 J jnl
Computational approaches for detecting disease-associated alternative splicing events.
Briefings Bioinform.
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
2023 J jnl
The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data.
CoRR
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
2022 J jnl
An Ensemble of U-Net Models for Kidney Tumor Segmentation With CT Images.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jason L. Causey, Jonathan W. Stubblefield, Jake A. Qualls, Jennifer Fowler, Lingrui Cai, Karl Walker, Yuanfang Guan, Xiuzhen Huang
2022 J jnl
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.
Briefings Bioinform.
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
2022 J jnl
Asymmetric predictive relationships across histone modifications.
Nat. Mach. Intell.
Hongyang Li, Yuanfang Guan
2022 J jnl
Auto-annotating sleep stages based on polysomnographic data.
Patterns
Hanrui Zhang, Xueqing Wang, Hongyang Li, Soham Mehendale, Yuanfang Guan
2022 J jnl
Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.
PLoS Comput. Biol.
Hongyang Li, Ridvan Eksi, Daiyao Yi, Bradley Godfrey, Lisa R. Mathew, Christopher L. O'Connor, Markus Bitzer, Matthias Kretzler, Rajasree Menon, Yuanfang Guan
2022 J jnl
Multilevel Modeling of Joint Damage in Rheumatoid Arthritis.
Adv. Intell. Syst.
Hongyang Li, Yuanfang Guan
2022 J jnl
Representation of molecules for drug response prediction.
Briefings Bioinform.
Xin An, Xi Chen, Daiyao Yi, Hongyang Li, Yuanfang Guan
2022 J jnl
Spatial Pyramid Pooling With 3D Convolution Improves Lung Cancer Detection.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jason L. Causey, Keyu Li, Xianghao Chen, Wei Dong, Karl Walker, Jake A. Qualls, Jonathan W. Stubblefield, Jason H. Moore, Yuanfang Guan, Xiuzhen Huang
2022 J jnl
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.
Nucleic Acids Res.
Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Yuanfang Guan, Jianxin Wang
2021 J jnl
A survival model generalized to regression learning algorithms.
Nat. Comput. Sci.
Yuanfang Guan, Hongyang Li, Daiyao Yi, Dongdong Zhang, Changchang Yin, Keyu Li, Ping Zhang
2021 J jnl
Comparative analysis of molecular fingerprints in prediction of drug combination effects.
Briefings Bioinform.
Bulat Zagidullin, Ziyan Wang, Yuanfang Guan, Esa Pitkänen, Jing Tang
2021 J jnl
Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.
npj Digit. Medicine
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
2021 J jnl
Deep learning prediction of patient response time course from early data via neural-pharmacokinetic/pharmacodynamic modelling.
Nat. Mach. Intell.
James Lu, Brendan Bender, Jin Y. Jin, Yuanfang Guan
2021 J jnl
Identify differentially expressed genes with large background samples.
Int. J. Comput. Biol. Drug Des.
Jennifer Fowler, Jonathan W. Stubblefield, Jason L. Causey, Jake A. Qualls, Wei Dong, Hongmei Jiang, Karl Walker, Yuanfang Guan, Xiuzhen Huang
2021 — conf
Retrospective on the SENSORIUM 2022 competition.
NeurIPS (Competition and Demos)
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
2020 J jnl
Deep Learning Identifies Digital Biomarkers for Self-Reported Parkinson's Disease.
Patterns
Hanrui Zhang, Kaiwen Deng, Hongyang Li, Roger L. Albin, Yuanfang Guan
2020 J jnl
Deep learning prediction of patient response time course from early data via neural-pharmacokinetic/pharmacodynamic modeling.
CoRR
James Lu, Brendan Bender, Jin Y. Jin, Yuanfang Guan
2020 J jnl
Detecting Asymmetric Patterns and Localizing Cancers on Mammograms.
Patterns
Yuanfang Guan, Xueqing Wang, Hongyang Li, Zhenning Zhang, Xianghao Chen, Omer Siddiqui, Sara Nehring, Xiuzhen Huang
2020 J jnl
Machine learning empowers phosphoproteome prediction in cancers.
Bioinform.
Hongyang Li, Yuanfang Guan
2019 J jnl
BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets.
Bioinform.
Hong-Dong Li, Tianjian Bai, Erin Sandford, Margit Burmeister, Yuanfang Guan
2019 J jnl
Lung cancer screening with low-dose CT scans using a deep learning approach.
CoRR
Jason L. Causey, Yuanfang Guan, Wei Dong, Karl Walker, Jake A. Qualls, Fred W. Prior, Xiuzhen Huang
2019 J jnl
Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering.
Neuroinformatics
Ming Tang, Chao Gao, Stephen A. Goutman, Alexandr A. Kalinin, Bhramar Mukherjee, Yuanfang Guan, Ivo D. Dinov
2019 J jnl
TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction.
Bioinform.
Hongyang Li, Shuai Hu, Nouri Neamati, Yuanfang Guan
2019 J jnl
Waking up to data challenges.
Nat. Mach. Intell.
Yuanfang Guan
2018 J jnl
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile.
Bioinform.
Yuanfang Guan, Tingyang Li, Hongjiu Zhang, Fan Zhu, Gilbert S. Omenn
2018 J jnl
YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU.
Bioinform.
Daniel Quang, Yuanfang Guan, Stephen C. J. Parker
2017 J jnl
Complete hazard ranking to analyze right-censored data: An ALS survival study.
PLoS Comput. Biol.
Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A. Goutman, Bhramar Mukherjee, Ivo D. Dinov, Yuanfang Guan
2017 J jnl
miRmine: a database of human miRNA expression profiles.
Bioinform.
Bharat Panwar, Gilbert S. Omenn, Yuanfang Guan
2016 J jnl
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.
Briefings Bioinform.
Hongdong Li, Gilbert S. Omenn, Yuanfang Guan
2016 J jnl
Algorithms for modeling global and context-specific functional relationship networks.
Briefings Bioinform.
Fan Zhu, Bharat Panwar, Yuanfang Guan
2015 J jnl
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
Hongdong Li, Gilbert S. Omenn, Yuanfang Guan
2015 J jnl
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system.
Bioinform.
Fan Zhu, Lihong Shi, James Douglas Engel, Yuanfang Guan
2014 J jnl
Modeling dynamic functional relationship networks and application to
Bioinform.
Fan Zhu, Lihong Shi, Hongdong Li, Ridvan Eksi, James Douglas Engel, Yuanfang Guan
2014 J jnl
Predicting dynamic signaling network response under unseen perturbations.
Bioinform.
Fan Zhu, Yuanfang Guan
2013 J jnl
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes.
PLoS Comput. Biol.
Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
2013 J jnl
Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data.
PLoS Comput. Biol.
Ridvan Eksi, Hongdong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan
2012 J jnl
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Nucleic Acids Res.
Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
2012 J jnl
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes.
PLoS Comput. Biol.
Yuanfang Guan, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K. Wong, John C. Schimenti, Mary Ann Handel, Carol J. Bult, Matthew A. Hibbs, Olga G. Troyanskaya
2010 J jnl
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.
PLoS Comput. Biol.
Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
2010 J jnl
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.
PLoS Comput. Biol.
Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya
2008 J jnl
A Genomewide Functional Network for the Laboratory Mouse.
PLoS Comput. Biol.
Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya