Dongxiao Zhu - RankMe

126 papers A* 13A 6B 4C 4Journal 69Unranked 29

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Attention Smoothing Is All You Need For Unlearning. CoRR Saleh Zare Zade, Xiangyu Zhou, Sijia Liu, Dongxiao Zhu
2026	A*	`conf`	Not All Tokens Are Meant to Be Forgotten. AAAI Xiangyu Zhou, Yao Qiang, Saleh Zare Zade, Douglas Zytko, Prashant Khanduri, Dongxiao Zhu
2026	J	`jnl`	WalkGPT: Grounded Vision-Language Conversation with Depth-Aware Segmentation for Pedestrian Navigation. CoRR Rafi Ibn Sultan, Hui Zhu, Xiangyu Zhou, Chengyin Li, Prashant Khanduri, Marco Brocanelli, Dongxiao Zhu
2025	A	`conf`	AutoProSAM: Automated Prompting SAM for 3D Multi-Organ Segmentation. WACV Chengyin Li, Rafi Ibn Sultan, Prashant Khanduri, Yao Qiang, Chetty J. Indrin, Dongxiao Zhu
2025	A	`conf`	Automatic Calibration for Membership Inference Attack on Large Language Models. ECAI Saleh Zare Zade, Yao Qiang, Xiangyu Zhou, Hui Zhu, Mohammad Amin Roshani, Prashant Khanduri, Dongxiao Zhu
2025	J	`jnl`	Automatic Calibration for Membership Inference Attack on Large Language Models. CoRR Saleh Zare Zade, Yao Qiang, Xiangyu Zhou, Hui Zhu, Mohammad Amin Roshani, Prashant Khanduri, Dongxiao Zhu
2025	J	`jnl`	BiPVL-Seg: Bidirectional Progressive Vision-Language Fusion with Global-Local Alignment for Medical Image Segmentation. CoRR Rafi Ibn Sultan, Hui Zhu, Chengyin Li, Dongxiao Zhu
2025	J	`jnl`	Collective Consent: Who Needs to Consent to the Donation of Data Representing Multiple People? Proc. ACM Hum. Comput. Interact. Emma Walquist, Isha Datey, Wenqi Zheng, Xiangyu Zhou, Kelly Berishaj, Melissa Mcdonald, Michele Parkhill, Dongxiao Zhu, Douglas Zytko
2025	J	`jnl`	Fluence Map Prediction with Deep Learning: A Transformer-based Approach. CoRR Ujunwa Mgboh, Rafi Ibn Sultan, Dongxiao Zhu, Joshua Kim
2025	J	`jnl`	FluenceFormer: Transformer-Driven Multi-Beam Fluence Map Regression for Radiotherapy Planning. CoRR Ujunwa Mgboh, Rafi Ibn Sultan, Joshua Kim, Kundan Thind, Dongxiao Zhu
2025	A	`conf`	GeoSAM: Fine-Tuning SAM with Multi-Modal Prompts for Mobility Infrastructure Segmentation. ECAI Rafi Ibn Sultan, Chengyin Li, Hui Zhu, Prashant Khanduri, Marco Brocanelli, Dongxiao Zhu
2025	B	`conf`	Interpretability-Aware Vision Transformer. IJCNN Yao Qiang, Chengyin Li, Hui Zhu, Prashant Khanduri, Dongxiao Zhu
2025	A	`conf`	MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training. WACV Chengyin Li, Hui Zhu, Rafi Ibn Sultan, Hassan Bagher-Ebadian, Prashant Khanduri, Chetty J. Indrin, Kundan Thind, Dongxiao Zhu
2025	J	`jnl`	Not All Tokens Are Meant to Be Forgotten. CoRR Xiangyu Zhou, Yao Qiang, Saleh Zare Zade, Douglas Zytko, Prashant Khanduri, Dongxiao Zhu
2024	A*	`conf`	"It's Not What We Were Trying to Get At, but I Think Maybe It Should Be": Learning How to Do Trauma-Informed Design with a Data Donation Platform for Online Dating Sexual Violence. CHI Wenqi Zheng, Emma Walquist, Isha Datey, Xiangyu Zhou, Kelly Berishaj, Melissa Mcdonald, Michele Parkhill, Dongxiao Zhu, Douglas Zytko
2024	A*	`conf`	Benchmark and Neural Architecture for Conversational Entity Retrieval from a Knowledge Graph. WWW Mona Zamiri, Yao Qiang, Fedor Nikolaev, Dongxiao Zhu, Alexander Kotov
2024	—	`conf`	Evaluation of the Segment Anything Model (SAM) for Brain Tumor Segmentation. ISBI Mohammad Peivandi, Jason Zhang, Michael Lu, Chengyin Li, Dongxiao Zhu, Zhifeng Kou
2024	—	`conf`	Fairness-Aware Vision Transformer via Debiased Self-Attention. ECCV (37) Yao Qiang, Chengyin Li, Prashant Khanduri, Dongxiao Zhu
2024	J	`jnl`	Generative LLM Powered Conversational AI Application for Personalized Risk Assessment: A Case Study in COVID-19. CoRR Mohammad Amin Roshani, Xiangyu Zhou, Yao Qiang, Srinivasan Suresh, Steve Hicks, Usha Sethuraman, Dongxiao Zhu
2024	J	`jnl`	Learning to Poison Large Language Models During Instruction Tuning. CoRR Yao Qiang, Xiangyu Zhou, Saleh Zare Zade, Mohammad Amin Roshani, Douglas Zytko, Dongxiao Zhu
2024	A*	`conf`	MFABA: A More Faithful and Accelerated Boundary-Based Attribution Method for Deep Neural Networks. AAAI Zhiyu Zhu, Huaming Chen, Jiayu Zhang, Xinyi Wang, Zhibo Jin, Minhui Xue, Dongxiao Zhu, Kim-Kwang Raymond Choo
2024	J	`jnl`	MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training. CoRR Chengyin Li, Hui Zhu, Rafi Ibn Sultan, Hassan Bagher-Ebadian, Prashant Khanduri, Indrin J. Chetty, Kundan Thind, Dongxiao Zhu
2023	J	`jnl`	Auto-Prompting SAM for Mobile Friendly 3D Medical Image Segmentation. CoRR Chengyin Li, Prashant Khanduri, Yao Qiang, Rafi Ibn Sultan, Indrin J. Chetty, Dongxiao Zhu
2023	J	`jnl`	Fairness-aware Vision Transformer via Debiased Self-Attention. CoRR Yao Qiang, Chengyin Li, Prashant Khanduri, Dongxiao Zhu
2023	J	`jnl`	FedDRO: Federated Compositional Optimization for Distributionally Robust Learning. CoRR Prashant Khanduri, Chengyin Li, Rafi Ibn Sultan, Yao Qiang, Jörg Kliewer, Dongxiao Zhu
2023	—	`conf`	FocalUNETR: A Focal Transformer for Boundary-Aware Prostate Segmentation Using CT Images. MICCAI (3) Chengyin Li, Yao Qiang, Rafi Ibn Sultan, Hassan Bagher-Ebadian, Prashant Khanduri, Indrin J. Chetty, Dongxiao Zhu
2023	J	`jnl`	GeoSAM: Fine-tuning SAM with Sparse and Dense Visual Prompting for Automated Segmentation of Mobility Infrastructure. CoRR Rafi Ibn Sultan, Chengyin Li, Hui Zhu, Prashant Khanduri, Marco Brocanelli, Dongxiao Zhu
2023	J	`jnl`	Hijacking Large Language Models via Adversarial In-Context Learning. CoRR Yao Qiang, Xiangyu Zhou, Dongxiao Zhu
2023	J	`jnl`	Interpretability-Aware Vision Transformer. CoRR Yao Qiang, Chengyin Li, Prashant Khanduri, Dongxiao Zhu
2023	A*	`conf`	Learning Compact Features via In-Training Representation Alignment. AAAI Xin Li, Xiangrui Li, Deng Pan, Yao Qiang, Dongxiao Zhu
2023	J	`jnl`	MFABA: A More Faithful and Accelerated Boundary-based Attribution Method for Deep Neural Networks. CoRR Zhiyu Zhu, Huaming Chen, Jiayu Zhang, Xinyi Wang, Zhibo Jin, Minhui Xue, Dongxiao Zhu, Kim-Kwang Raymond Choo
2023	A*	`conf`	Negative Flux Aggregation to Estimate Feature Attributions. IJCAI Xin Li, Deng Pan, Chengyin Li, Yao Qiang, Dongxiao Zhu
2023	J	`jnl`	Negative Flux Aggregation to Estimate Feature Attributions. CoRR Xin Li, Deng Pan, Chengyin Li, Yao Qiang, Dongxiao Zhu
2023	—	`conf`	Towards Trauma-Informed Data Donation of Sexual Experience in Online Dating to Improve Sexual Risk Detection AI. UIST (Adjunct Volume) Wenqi Zheng, Emma Walquist, Isha Datey, Xiangyu Zhou, Kelly Berishaj, Melissa Mcdonald, Michele Parkhill, Dongxiao Zhu, Douglas Zytko
2023	J	`jnl`	Towards Trustworthy Artificial Intelligence for Equitable Global Health. CoRR Hong Qin, Jude Kong, Wandi Ding, Ramneek Ahluwalia, Christo El-Morr, Zeynep Engin, Jake Okechukwu Effoduh, Rebecca Hwa, Serena Jingchuan Guo, Laleh Seyyed-Kalantari, Sylvia Kiwuwa Muyingo, Candace Makeda Moore, Ravi Parikh, Reva Schwartz, Dongxiao Zhu, Xiaoqian Wang, Yiye Zhang
2022	A*	`conf`	AttCAT: Explaining Transformers via Attentive Class Activation Tokens. NeurIPS Yao Qiang, Deng Pan, Chengyin Li, Xin Li, Rhongho Jang, Dongxiao Zhu
2022	A*	`conf`	Counterfactual Interpolation Augmentation (CIA): A Unified Approach to Enhance Fairness and Explainability of DNN. IJCAI Yao Qiang, Chengyin Li, Marco Brocanelli, Dongxiao Zhu
2022	—	`conf`	Coupling User Preference with External Rewards to Enable Driver-centered and Resource-aware EV Charging Recommendation. ECML/PKDD (4) Chengyin Li, Zheng Dong, Nathan Fisher, Dongxiao Zhu
2022	J	`jnl`	Coupling User Preference with External Rewards to Enable Driver-centered and Resource-aware EV Charging Recommendation. CoRR Chengyin Li, Zheng Dong, Nathan Fisher, Dongxiao Zhu
2022	J	`jnl`	FocalUNETR: A Focal Transformer for Boundary-aware Segmentation of CT Images. CoRR Chengyin Li, Hassan Bagher-Ebadian, Vikram Goddla, Indrin J. Chetty, Dongxiao Zhu
2022	J	`jnl`	Learning Compact Features via In-Training Representation Alignment. CoRR Xin Li, Xiangrui Li, Deng Pan, Yao Qiang, Dongxiao Zhu
2022	J	`jnl`	Saliency Guided Adversarial Training for Learning Generalizable Features with Applications to Medical Imaging Classification System. CoRR Xin Li, Yao Qiang, Chengyin Li, Sijia Liu, Dongxiao Zhu
2022	B	`conf`	Tiny RNN Model with Certified Robustness for Text Classification. IJCNN Yao Qiang, Supriya Tumkur Suresh Kumar, Marco Brocanelli, Dongxiao Zhu
2021	J	`jnl`	Adversarially Robust and Explainable Model Compression with On-Device Personalization for Text Classification. CoRR Yao Qiang, Supriya Tumkur Suresh Kumar, Marco Brocanelli, Dongxiao Zhu
2021	—	`conf`	Defending Against Adversarial Attacks On Medical Imaging Ai System, Classification Or Detection? ISBI Xin Li, Deng Pan, Dongxiao Zhu
2021	A*	`conf`	Explaining Deep Neural Network Models with Adversarial Gradient Integration. IJCAI Deng Pan, Xin Li, Dongxiao Zhu
2021	A*	`conf`	Improving Adversarial Robustness via Probabilistically Compact Loss with Logit Constraints. AAAI Xin Li, Xiangrui Li, Deng Pan, Dongxiao Zhu
2021	J	`jnl`	Tackling ordinal regression problem for heterogeneous data: sparse and deep multi-task learning approaches. Data Min. Knowl. Discov. Lu Wang, Dongxiao Zhu
2020	—	`conf`	COVID-MobileXpert: On-Device COVID-19 Patient Triage and Follow-up using Chest X-rays. BIBM Xin Li, Chengyin Li, Dongxiao Zhu
2020	J	`jnl`	COVID-MobileXpert: On-Device COVID-19 Screening using Snapshots of Chest X-Ray. CoRR Xin Li, Chengyin Li, Dongxiao Zhu
2020	J	`jnl`	Defending against adversarial attacks on medical imaging AI system, classification or detection? CoRR Xin Li, Deng Pan, Dongxiao Zhu
2020	A*	`conf`	Explainable Recommendation via Interpretable Feature Mapping and Evaluation of Explainability. IJCAI Deng Pan, Xiangrui Li, Xin Li, Dongxiao Zhu
2020	J	`jnl`	Explainable Recommendation via Interpretable Feature Mapping and Evaluation of Explainability. CoRR Deng Pan, Xiangrui Li, Xin Li, Dongxiao Zhu
2020	J	`jnl`	Improve SGD Training via Aligning Mini-batches. CoRR Xiangrui Li, Deng Pan, Xin Li, Dongxiao Zhu
2020	J	`jnl`	Improving Adversarial Robustness via Probabilistically Compact Loss with Logit Constraints. CoRR Xin Li, Xiangrui Li, Deng Pan, Dongxiao Zhu
2020	—	`conf`	Interpreting Age Effects of Human Fetal Brain from Spontaneous fMRI Using Deep 3D Convolutional Neural Networks. ISBI Xiangrui Li, Jasmine L. Hect, Moriah E. Thomason, Dongxiao Zhu
2020	A*	`conf`	On the Learning Property of Logistic and Softmax Losses for Deep Neural Networks. AAAI Xiangrui Li, Xin Li, Deng Pan, Dongxiao Zhu
2020	J	`jnl`	On the Learning Property of Logistic and Softmax Losses for Deep Neural Networks. CoRR Xiangrui Li, Xin Li, Deng Pan, Dongxiao Zhu
2020	—	`conf`	Robust Detection of Adversarial Attacks on Medical Images. ISBI Xin Li, Dongxiao Zhu
2020	B	`conf`	Toward Tag-free Aspect Based Sentiment Analysis: A Multiple Attention Network Approach. IJCNN Yao Qiang, Xin Li, Dongxiao Zhu
2020	J	`jnl`	Toward Tag-free Aspect Based Sentiment Analysis: A Multiple Attention Network Approach. CoRR Yao Qiang, Xin Li, Dongxiao Zhu
2019	J	`jnl`	A Deep Active Survival Analysis approach for precision treatment recommendations: Application of prostate cancer. Expert Syst. Appl. Milad Zafar Nezhad, Najibesadat Sadati, Kai Yang, Dongxiao Zhu
2019	J	`jnl`	CRCEN: A Generalized Cost-sensitive Neural Network Approach for Imbalanced Classification. CoRR Xiangrui Li, Dongxiao Zhu
2019	J	`jnl`	Interpreting Age Effects of Human Fetal Brain from Spontaneous fMRI using Deep 3D Convolutional Neural Networks. CoRR Xiangrui Li, Jasmine L. Hect, Moriah E. Thomason, Dongxiao Zhu
2019	J	`jnl`	Multi-task Prediction of Patient Workload. CoRR Mohammad Hessam Olya, Dongxiao Zhu, Kai Yang
2019	—	`conf`	Prioritization of Multi-Level Risk Factors for Obesity. BIBM Lu Wang, Ming Dong, Elizabeth Towner, Dongxiao Zhu
2019	J	`jnl`	Tackling Multiple Ordinal Regression Problems: Sparse and Deep Multi-Task Learning Approaches. CoRR Lu Wang, Dongxiao Zhu
2019	J	`jnl`	Vispi: Automatic Visual Perception and Interpretation of Chest X-rays. CoRR Xin Li, Rui Cao, Dongxiao Zhu
2018	J	`jnl`	A Deep Active Survival Analysis Approach for Precision Treatment Recommendations: Application of Prostate Cancer. CoRR Milad Zafar Nezhad, Najibesadat Sadati, Kai Yang, Dongxiao Zhu
2018	J	`jnl`	A Predictive Approach Using Deep Feature Learning for Electronic Medical Records: A Comparative Study. CoRR Milad Zafar Nezhad, Dongxiao Zhu, Najibesadat Sadati, Kai Yang
2018	J	`jnl`	Clustering over-dispersed data with mixed feature types. Stat. Anal. Data Min. Lu Wang, Dongxiao Zhu, Ming Dong
2018	J	`jnl`	Joint Energy Management and Interference Coordination With Max-Min Fairness in Ultra-Dense HetNets. IEEE Access Jie Zheng, Ling Gao, Haijun Zhang, Dongxiao Zhu, Hai Wang, Quanli Gao, Victor C. M. Leung
2018	—	`conf`	Joint Energy-Efficient Optimization of Downlink and Uplink with eICIC in HetNet. IoTaaS Jie Zheng, Ling Gao, Dongxiao Zhu, Hai Wang, Qian Sun, Jinping Niu, Xiaoya Li, Jianfeng Yang
2018	J	`jnl`	Learning and Interpreting Features to Rank: A Case Study on Age Estimation. Int. J. Multim. Data Eng. Manag. Shixing Chen, Ming Dong, Dongxiao Zhu
2018	J	`jnl`	Leveraging auxiliary measures: a deep multi-task neural network for predictive modeling in clinical research. BMC Medical Informatics Decis. Mak. Xiangrui Li, Dongxiao Zhu, Phillip Levy
2018	J	`jnl`	Multinomial classification with class-conditional overlapping sparse feature groups. Pattern Recognit. Lett. Xiangrui Li, Dongxiao Zhu, Ming Dong
2018	—	`conf`	Obesity risk factors ranking using multi-task learning. BHI Lu Wang, Dongxiao Zhu, Elizabeth Towner, Ming Dong
2018	A	`conf`	Proteus: network-aware web browsing on heterogeneous mobile systems. CoNEXT Jie Ren, Xiaoming Wang, Jianbin Fang, Yansong Feng, Dongxiao Zhu, Zhunchen Luo, Jie Zheng, Zheng Wang
2018	J	`jnl`	Robust feature selection via Pattern Recognit. Lett. Xiangrui Li, Dongxiao Zhu
2017	J	`jnl`	Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse. Quant. Biol. Jiao Chen, Dongxiao Zhu, Yanni Sun
2017	C	`conf`	Modeling Over-Dispersion for Network Data Clustering. ICMLA Lu Wang, Dongxiao Zhu, Ming Dong, Yan Li
2017	A*	`conf`	Multi-task Survival Analysis. ICDM Lu Wang, Yan Li, Jiayu Zhou, Dongxiao Zhu, Jieping Ye
2017	J	`jnl`	Object tracking via Dirichlet process-based appearance models. Neural Comput. Appl. Raed Almomani, Ming Dong, Dongxiao Zhu
2017	—	`conf`	Predictive deep network with leveraging clinical measure as auxiliary task. BIBM Xiangrui Li, Dongxiao Zhu, Phillip Levy
2017	J	`jnl`	SAFS: A Deep Feature Selection Approach for Precision Medicine. CoRR Milad Zafar Nezhad, Dongxiao Zhu, Xiangrui Li, Kai Yang, Phillip Levy
2017	—	`conf`	SDT: A Tree Method for Detecting Patient Subgroups with Personalized Risk Factors. CRI Xiangrui Li, Dongxiao Zhu, Ming Dong, Milad Zafar Nezhad, Alexander T. Janke, Phillip Levy
2017	C	`conf`	SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine. ICMLA Milad Zafar Nezhad, Dongxiao Zhu, Najibesadat Sadati, Kai Yang, Phillip Levi
2017	J	`jnl`	SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine. CoRR Milad Zafar Nezhad, Dongxiao Zhu, Najibesadat Sadati, Kai Yang, Phillip Levy
2017	J	`jnl`	Transcriptome assembly strategies for precision medicine. Quant. Biol. Lu Wang, Lipi R. Acharya, Changxin Bai, Dongxiao Zhu
2016	A	`conf`	A Bayesian hierarchical appearance model for robust object tracking. ICME Raed Almomani, Ming Dong, Dongxiao Zhu
2016	—	`ch.`	Gene-set-based inference of biological network topologies from big molecular profiling data. Big Data over Networks Lipi R. Acharya, Dongxiao Zhu
2016	—	`conf`	Poisson-Markov Mixture Model and Parallel Algorithm for Binning Massive and Heterogenous DNA Sequencing Reads. ISBRA Lu Wang, Dongxiao Zhu, Yan Li, Ming Dong
2016	—	`conf`	SAFS: A deep feature selection approach for precision medicine. BIBM Milad Zafar Nezhad, Dongxiao Zhu, Xiangrui Li, Kai Yang, Phillip Levy
2016	—	`conf`	Text Classification with Topic-based Word Embedding and Convolutional Neural Networks. BCB Haotian Xu, Ming Dong, Dongxiao Zhu, Alexander Kotov, April Idalski Carcone, Sylvie Naar-King
2015	J	`jnl`	Knowledge Discovery Using Big Data in Biomedical Systems. IEEE ACM Trans. Comput. Biol. Bioinform. Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki
2015	J	`jnl`	Network inference through synergistic subnetwork evolution. EURASIP J. Bioinform. Syst. Biol. Lipi R. Acharya, Robert G. Reynolds, Dongxiao Zhu
2014	—	`conf`	A novel semi-supervised learning approach to analyzing metagenomic reads. BCB Yuliang Geng, Xue-wen Chen, Dongxiao Zhu
2014	B	`conf`	GSCA: Reconstructing biological pathway topologies using a cultural algorithms approach. IEEE Congress on Evolutionary Computation Thair Judeh, Thaer Jayyousi, Lipi R. Acharya, Robert G. Reynolds, Dongxiao Zhu
2014	—	`conf`	dSpliceType: A Multivariate Model for Detecting Various Types of Differential Splicing Events Using RNA-Seq. ISBRA Nan Deng, Dongxiao Zhu
2013	—	`conf`	Detecting various types of differential splicing events using RNA-Seq data. BCB Nan Deng, Dongxiao Zhu
2013	—	`conf`	Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets. BCB Thair Judeh, Thaer Jayyousi, Lipi R. Acharya, Robert G. Reynolds, Dongxiao Zhu
2013	—	`conf`	MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions. BCB Tin Chi Nguyen, Dongxiao Zhu
2013	—	`conf`	RNA-Seq analyses to reveal the human transcriptome landscape. BCB Nan Deng, Dongxiao Zhu
2013	J	`jnl`	SPATA: A Seeding and Patching Algorithm for Hybrid Transcriptome Assembly. CoRR Tin Chi Nguyen, Zhiyu Zhao, Dongxiao Zhu
2012	J	`jnl`	GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets. IEEE ACM Trans. Comput. Biol. Bioinform. Lipi R. Acharya, Thair Judeh, Zhansheng Duan, Michael G. Rabbat, Dongxiao Zhu
2012	J	`jnl`	Optimal structural inference of signaling pathways from unordered and overlapping gene sets. Bioinform. Lipi R. Acharya, Thair Judeh, Guangdi Wang, Dongxiao Zhu
2012	J	`jnl`	SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq CoRR Tin Chi Nguyen, Nan Deng, Dongxiao Zhu
2011	J	`jnl`	A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements. IEEE ACM Trans. Comput. Biol. Bioinform. Dongxiao Zhu, Lipi R. Acharya, Hui Zhang
2011	J	`jnl`	SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol. Medicine Guorong Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
2011	—	`conf`	SPATA: A highly accurate GUI tool for de novo transcriptome assembly. BIBM Workshops Tin Chi Nguyen, Zhiyu Zhao, Dongxiao Zhu
2011	—	`conf`	SPATA: A seeding and patching algorithm for de novo transcriptome assembly. BIBM Workshops Zhiyu Zhao, Tin Chi Nguyen, Nan Deng, Kristen Marie Johnson, Dongxiao Zhu
2011	—	`conf`	iQuant: A fast yet accurate GUI tool for transcript quantification. BIBM Workshops Tin Chi Nguyen, Nan Deng, Guorong Xu, Zhansheng Duan, Dongxiao Zhu
2010	J	`jnl`	Improved Bayesian Network inference using relaxed gene ordering. Int. J. Data Min. Bioinform. Dongxiao Zhu, Hua Li
2010	J	`jnl`	svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification. BMC Bioinform. Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, Kun Zhang
2009	—	`conf`	A Generalized Multivariate Approach for Correlation-Based Pattern Discovery from Replicated Molecular Profiling Data. BIBM Dongxiao Zhu, Guorong Xu, Lipi R. Acharya
2009	J	`jnl`	Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation. Int. J. Comput. Biol. Drug Des. Kun Zhang, Wei Fan, Prescott Deininger, Andrea Edwards, Zujia Xu, Dongxiao Zhu
2009	C	`conf`	Estimating an Optimal Correlation Structure from Replicated Molecular Profiling Data Using Finite Mixture Models. ICMLA Lipi R. Acharya, Dongxiao Zhu
2009	J	`jnl`	Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data. BMC Bioinform. Dongxiao Zhu
2007	J	`jnl`	Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. J. Comput. Biol. Dongxiao Zhu, Alfred O. Hero III
2007	C	`conf`	Improvement of Bayesian Network Inference Using a Relaxed Gene Ordering. ICMLA Dongxiao Zhu, Hua Li
2007	J	`jnl`	Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. Bioinform. Dongxiao Zhu, Youjuan Li, Hua Li
2005	—	`conf`	Gene coexpression network discovery with controlled statistical and biological significance. ICASSP (5) Dongxiao Zhu, Alfred O. Hero III
2005	J	`jnl`	High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). J. Comput. Biol. Dongxiao Zhu, Alfred O. Hero III, Zhaohui S. Qin, Anand Swaroop
2005	—	`conf`	Network constrained clustering for gene microarray data. ICASSP (5) Dongxiao Zhu, Alfred O. Hero III
2005	J	`jnl`	Network constrained clustering for gene microarray data. Bioinform. Dongxiao Zhu, Alfred O. Hero III, Hong Cheng, Ritu Khanna, Anand Swaroop
2005	J	`jnl`	Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinform. Dongxiao Zhu, Zhaohui S. Qin