@article{lo200315,
  title={15,000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis},
  author={Lo, Jane and Lee, Sorcheng and Xu, Min and Liu, Feng and Ruan, Hua and Eun, Alvin and He, Yawen and Ma, Weiping and Wang, Weefuen and Wen, Zilong and others},
  journal={Genome Research},
  volume={13},
  number={3},
  pages={455--466},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

@article{xu2003gene,
  title={Gene selection for cancer classification using a hybrid of univariate and multivariate feature selection methods},
  author={Xu, Min and Setiono, Rudy},
  journal={Applied Genomics and Proteomics},
  volume={2},
  number={2},
  pages={79-91},
  year={2003},
  publisher={BioMed Central Ltd}
}

@inproceedings{wei2004hybrid,
  title={A hybrid SOM-SVM method for analyzing zebra fish gene expression},
  author={Wei, Wu and Xin, Liu and Min, Xu and Jinrong, Peng and Setiono, Rudy},
  booktitle={Proceedings of the 17th International Conference on Pattern Recognition, 2004. ICPR 2004.},
  volume={2},
  pages={323--326},
  year={2004},
  organization={IEEE}
}

@article{wu2005hybrid,
  title={A hybrid SOM-SVM approach for the zebrafish gene expression analysis},
  author={Wu, Wei and Liu, Xin and Xu, Min and Peng, Jin-Rong and Setiono, Rudy},
  journal={Genomics, proteomics \& bioinformatics},
  volume={3},
  number={2},
  pages={84--93},
  year={2005},
  publisher={Elsevier}
}

@article{wen2005genome,
  title={Genome-wide identification of female-enriched genes in zebrafish},
  author={Wen, Chaoming and Zhang, Zhenhai and Ma, Weiping and Xu, Min and Wen, Zilong and Peng, Jinrong},
  journal={Developmental dynamics: an official publication of the American Association of Anatomists},
  volume={232},
  number={1},
  pages={171--179},
  year={2005},
  publisher={Wiley Online Library}
}



@article{he2006genome,
  title={Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris: identification of novel cell--cell communication-dependent genes and functions},
  author={He, Ya-Wen and Xu, Min and Lin, Kui and Ng, Yu-Jin Alvin and Wen, Chao-Ming and Wang, Lian-Hui and Liu, Zi-Duo and Zhang, Hai-Bao and Dong, Yi-Hu and Dow, J Maxwell and others},
  journal={Molecular microbiology},
  volume={59},
  number={2},
  pages={610--622},
  year={2006},
  publisher={Wiley Online Library}
}

@article{tu2006further,
  title={Further understanding human disease genes by comparing with housekeeping genes and other genes},
  author={Tu, Zhidong and Wang, Li and Xu, Min and Zhou, Xianghong and Chen, Ting and Sun, Fengzhu},
  journal={BMC genomics},
  volume={7},
  number={1},
  pages={31},
  year={2006},
  publisher={Springer}
}

@article{pan2006integrative,
  title={Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data},
  author={Pan, Fei and Kamath, Kiran and Zhang, Kangyu and Pulapura, Sudip and Achar, Avinash and Nunez-Iglesias, Juan and Huang, Yu and Yan, Xifeng and Han, Jiawei and Hu, Haiyan and others},
  journal={Bioinformatics},
  volume={22},
  number={13},
  pages={1665--1667},
  year={2006},
  publisher={Oxford University Press}
}

@article{he2007xanthomonas,
  title={Xanthomonas campestris cell--cell communication involves a putative nucleotide receptor protein Clp and a hierarchical signalling network},
  author={He, Ya-Wen and Ng, Alvin Yu-Jin and Xu, Min and Lin, Kui and Wang, Lian-Hui and Dong, Yi-Hu and Zhang, Lian-Hui},
  journal={Molecular microbiology},
  volume={64},
  number={2},
  pages={281--292},
  year={2007},
  publisher={Wiley Online Library}
}

@article{xu2008integrative,
  title={An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer},
  author={Xu, Min and Kao, Ming-Chih J and Nunez-Iglesias, Juan and Nevins, Joseph R and West, Mike and Zhou, Xianghong Jasmine},
  journal={BMC genomics},
  volume={9},
  number={Suppl 1},
  pages={S12},
  year={2008},
  publisher={BioMed Central Ltd}
}

@article{xu2008stable,
  title={A stable iterative method for refining discriminative gene clusters},
  author={Xu, Min and Zhu, Mengxia and Zhang, Louxin},
  journal={BMC genomics},
  volume={9},
  number={Suppl 2},
  pages={S18},
  year={2008},
  publisher={BioMed Central Ltd}
}

@inproceedings{xu20093d,
  title={3D rotation invariant features for the characterization of molecular density maps},
  author={Xu, Min and Zhang, Shihua and Alber, Frank},
  booktitle={2009 IEEE International Conference on Bioinformatics and Biomedicine},
  pages={74--78},
  year={2009},
  organization={IEEE}
}

@article{xu2009automatic,
  title={Automatic tracking of protein vesicles},
  author={Xu, Min},
  journal={arXiv preprint arXiv:1506.02083},
  year={2009}
}

@article{xu2009automated,
  title={Automated multidimensional phenotypic profiling using large public microarray repositories},
  author={Xu, Min and Li, Wenyuan and James, Gareth M and Mehan, Michael R and Zhou, Xianghong Jasmine},
  journal={Proceedings of the National Academy of Sciences},
  volume={106},
  number={30},
  pages={12323--12328},
  year={2009},
  publisher={National Acad Sciences}
}

@article{eisenstein2009reading,
  title={Reading between the lines},
  author={Eisenstein, Michael},
  journal={Nature Methods},
  volume={6},
  number={9},
  pages={632--632},
  year={2009},
  publisher={Nature Publishing Group}
}

@article{yip2010closing,
  title={Closing the Genotype-phenotype Gap},
  author={Yip, YL and Section Editor for the IMIA Yearbook Section on Bioinformatics and others},
  journal={Yearbook of medical informatics},
  volume={19},
  number={01},
  pages={82--85},
  year={2010},
  publisher={Georg Thieme Verlag KG}
}

@article{li2010unraveling,
  title={Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets},
  author={Li, Wenyuan and Xu, Min and Zhou, Xianghong Jasmine},
  journal={Journal of biomedical informatics},
  volume={43},
  number={4},
  pages={550--559},
  year={2010},
  publisher={Elsevier}
}

@article{zhang2010fast,
  title={A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps},
  author={Zhang, Shihua and Vasishtan, Daven and Xu, Min and Topf, Maya and Alber, Frank},
  journal={Bioinformatics},
  volume={26},
  number={12},
  pages={i261--i268},
  year={2010},
  publisher={Oxford Univ Press}
}

@article{beck2011exploring,
  title={{Exploring the Spatial and Temporal Organization of a Cell's Proteome}},
  author={Beck, Martin and Topf, Maya and Frazier, Zachary and Tjong, Harianto and Xu, Min and Zhang, Shihua and Alber, Frank},
  journal={Journal of Structural Biology},
  volume={173},
  number={3},
  pages={483--496},
  issn={1047-8477},
  year={2011},
  publisher={Elsevier}
}

@article{xu2011smad1,
  title={Smad1 and its target gene Wif1 coordinate BMP and Wnt signaling activities to regulate fetal lung development},
  author={Xu, Bing and Chen, Cheng and Chen, Hui and Zheng, Song-Guo and Bringas, Pablo and Xu, Min and Zhou, Xianghong and Chen, Di and Umans, Lieve and Zwijsen, An and others},
  journal={Development},
  volume={138},
  number={5},
  pages={925--935},
  year={2011},
  publisher={Oxford University Press for The Company of Biologists Limited}
}

@article{xu2011template,
  title={Template-free detection of macromolecular complexes in cryo electron tomograms},
  author={Xu, Min and Beck, Martin and Alber, Frank},
  journal={Bioinformatics},
  volume={27},
  number={13},
  pages={i69--i76},
  year={2011},
  publisher={Oxford Univ Press}
}

@inproceedings{xu2011gradient,
  title={Gradient-based high precision alignment of cryo-electron subtomograms},
  author={Xu, Min and Alber, Frank},
  booktitle={2011 IEEE International Conference on Systems Biology},
  pages={279--284},
  year={2011},
  organization={IEEE}
}

@article{al2012differential,
  title={Differential trafficking of transport vesicles contributes to the localization of dendritic proteins},
  author={Al-Bassam, Sarmad and Xu, Min and Wandless, Thomas J and Arnold, Don B},
  journal={Cell reports},
  volume={2},
  number={1},
  pages={89--100},
  year={2012},
  publisher={Elsevier}
}

@article{xu2012high-precision,
  title={High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization},
  author={Xu, Min and Alber, Frank},
  journal={BMC Systems Biology},
  volume={6},
  number={Suppl 1},
  pages={S18},
  year={2012},
  publisher={BioMed Central Ltd}
}

@article{xu2012high-throughput,
  title={{High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching}},
  author={Xu, Min and Beck, Martin and Alber, Frank},
  journal={Journal of Structural Biology},
  volume={178},
  number={2},
  pages={152--164},
  year={2012},
  publisher={Elsevier}
}

@article{li2012frequent,
  title={Frequent pattern discovery in multiple biological networks: Patterns and algorithms},
  author={Li, Wenyuan and Hu, Haiyan and Huang, Yu and Li, Haifeng and Mehan, Michael R and Nunez-Iglesias, Juan and Xu, Min and Yan, Xifeng and Zhou, Xianghong Jasmine},
  journal={Statistics in Biosciences},
  volume={4},
  number={1},
  pages={157--176},
  year={2012},
  publisher={Springer}
}

@article{xu2012high,
  title={High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization},
  author={Xu, Min and Alber, Frank},
  journal={BMC systems biology},
  volume={6},
  number={S1},
  pages={S18},
  year={2012},
  publisher={Springer}
}

@article{thalassinos2013conformational,
  title={Conformational states of macromolecular assemblies explored by integrative structure calculation},
  author={Thalassinos, Konstantinos and Pandurangan, Arun Prasad and Xu, Min and Alber, Frank and Topf, Maya},
  journal={Structure},
  volume={21},
  number={9},
  pages={1500--1508},
  year={2013},
  publisher={Elsevier}
}

@article{xu2013automated,
  title={Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms},
  author={Xu, Min and Alber, Frank},
  journal={Bioinformatics},
  volume={29},
  number={13},
  pages={i274--i282},
  year={2013},
  publisher={Oxford Univ Press}
}

@article{xu2015gene,
  title={Gene selection for cancer classification using a hybrid of univariate and multivariate feature selection methods},
  author={Xu, Min and Setiono, Rudy},
  journal={arXiv preprint arXiv:1506.02085},
  year={2015}
}

@article{xu2015novo,
  title={De novo visual proteomics in single cells through pattern mining},
  author={Xu, Min and Tocheva, Elitza I and Chang, Yi-Wei and Jensen, Grant J and Alber, Frank},
  journal={arXiv preprint arXiv:1512.09347},
  year={2015}
}

@article{xu2015integrative,
  title={Integrative analysis of gene expression and phenotype data},
  author={Xu, Min},
  journal={arXiv preprint arXiv:1506.08511},
  year={2015}
}

@article{xu2015global,
  title={Global Gene Expression Analysis Using Machine Learning Methods},
  author={Xu, Min},
  journal={arXiv preprint arXiv:1506.02087},
  year={2015}
}

@article{xu2015automatic,
  title={Automatic tracking of protein vesicles},
  author={Xu, Min},
  journal={arXiv preprint arXiv:1506.02083},
  year={2015}
}


@article{pei2016simulating,
  title={Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking},
  author={Pei, Long and Xu, Min and Frazier, Zachary and Alber, Frank},
  journal={BMC bioinformatics},
  volume={17},
  number={1},
  pages={405},
  year={2016},
  publisher={BioMed Central}
}

@article{xu2017deep,
  title={Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms},
  author={Xu, Min and Chai, Xiaoqi and Muthakana, Hariank and Liang, Xiaodan and Yang, Ge and Zeev-Ben-Mordehai, Tzviya and Xing, Eric},
  journal={Bioinformatics},
  volume={33},
  number={14},
  pages={i13--i22},
  year={2017},
  publisher={Oxford Univ Press},
  doi = {10.1093/bioinformatics/btx230}
}

@article{xu2017experience,
  title={Experience enrichment based task independent reward model},
  author={Xu, Min},
  journal={arXiv preprint arXiv:1705.07460},
  year={2017}
}

@article{frazier2017tomominer,
  title={TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis},
  author={Frazier, Zachary and Xu, Min and Alber, Frank},
  journal={Structure},
  volume={25},
  number={6},
  pages={951--961},
  year={2017},
  publisher={Elsevier}
}

@inproceedings{wang2018image,
  title={Image-derived generative modeling of pseudo-macromolecular structures -- towards statistical assessment of Electron CryoTomography template matching},
  author={Wang, Kaiwen and Zeng, Xiangrui and Liang, Xiaodan and Huo, Zhiguang and Xing, Eric P and Xu, Min},
  booktitle={British Machine Vision Conference (BMVC)},
  year={2018}
}

@inproceedings{liu2018multi,
  title={Multi-task Learning for Macromolecule Classification, Segmentation and Coarse Structural Recovery in Cryo-Tomography},
  author={Liu, Chang and Zeng, Xiangrui and Wang, Kaiwen and Guo, Qiang and Xu, Min},
  booktitle={British Machine Vision Conference (BMVC)},
  year={2018}
}

@inproceedings{zhao2018respond,
  title={Respond-cam: Analyzing deep models for 3d imaging data by visualizations},
  author={Zhao, Guannan and Zhou, Bo and Wang, Kaiwen and Jiang, Rui and Xu, Min},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={485--492},
  year={2018},
  organization={Springer}
}

@article{zhao2018integration,
  title={An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification},
  author={Zhao, Yixiu and Zeng, Xiangrui and Guo, Qiang and Xu, Min},
  journal={Bioinformatics},
  volume={34},
  number={13},
  pages={i227--i236},
  year={2018},
  publisher={Oxford University Press},
  doi = {10.1093/bioinformatics/bty267}
}

@article{che2018improved,
  title={Improved deep learning-based macromolecules structure classification from electron cryo-tomograms},
  author={Che, Chengqian and Lin, Ruogu and Zeng, Xiangrui and Elmaaroufi, Karim and Galeotti, John and Xu, Min},
  journal={Machine Vision and Applications},
  volume={29},
  number={8},
  pages={1227--1236},
  year={2018},
  publisher={Springer}
}

@article{zeng2018convolutional,
  title={A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation},
  author={Zeng, Xiangrui and Leung, Miguel Ricardo and Zeev-Ben-Mordehai, Tzviya and Xu, Min},
  journal={Journal of structural biology},
  volume={202},
  number={2},
  pages={150--160},
  year={2018},
  publisher={Elsevier}
}

@inproceedings{zhou2018feature,
  title={Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms},
  author={Zhou, Bo and Guo, Qiang and Wang, Kaiwen and Zeng, Xiangrui and Gao, Xin and Xu, Min},
  booktitle={2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  pages={2467--2473},
  year={2018},
  organization={IEEE}
}

@inproceedings{liu2018deep,
  title={Deep learning based supervised semantic segmentation of Electron Cryo-Subtomograms},
  author={Liu, Chang and Zeng, Xiangrui and Lin, Ruogu and Liang, Xiaodan and Freyberg, Zachary and Xing, Eric and Xu, Min},
  booktitle={2018 25th IEEE International Conference on Image Processing (ICIP)},
  pages={1578--1582},
  year={2018},
  organization={IEEE}
}

@inproceedings{guo2018model,
  title={Model compression for faster structural separation of macromolecules captured by Cellular Electron Cryo-Tomography},
  author={Guo, Jialiang and Zhou, Bo and Zeng, Xiangrui and Freyberg, Zachary and Xu, Min},
  booktitle={International Conference Image Analysis and Recognition},
  pages={144--152},
  year={2018},
  organization={Springer}
}

@article{xu2019novo,
  title={De Novo Structural Pattern Mining in Cellular Electron Cryotomograms},
  author={Xu, Min and Singla, Jitin and Tocheva, Elitza I and Chang, Yi-Wei and Stevens, Raymond C and Jensen, Grant J and Alber, Frank},
  journal={Structure},
  year={2019},
  volume={27},
  number={4},
  pages={679--691},
  publisher={Elsevier}
}

@article{doerr2019template,
  title= {Template-free visual proteomics},
  author= {Doerr, Allison},
  journal={Nature Methods},
  volume = {16},
  number = {4},
  pages = {285},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{li2019automatic,
  title={Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN},
  author={Li, Ran and Zeng, Xiangrui and Sigmund, Stephanie E and Lin, Ruogu and Zhou, Bo and Liu, Chang and Wang, Kaiwen and Jiang, Rui and Freyberg, Zachary and Lv, Hairong and Xu, Min},
  journal={BMC bioinformatics},
  volume={20},
  number={3},
  pages={132},
  year={2019},
  publisher={BioMed Central}
}

@inproceedings{luo2019deep,
  title={Deep learning-based strategy for macromolecules classification with imbalanced data from cellular electron cryotomography},
  author={Luo, Ziqian and Zeng, Xiangrui and Bao, Zhipeng and Xu, Min},
  booktitle={2019 International Joint Conference on Neural Networks (IJCNN)},
  pages={1--8},
  year={2019},
  organization={IEEE}
}

@article{han2019a,
  title={A joint method for marker-free alignment of tilt series in electron tomography},
  author={Han, Renmin and Bao, Zhipeng and Zeng, Xiangrui and Niu, Tongxin and Zhang, Fa and Xu, Min and Gao, Xin},
  journal={Bioinformatics},
  volume={35},
  number={14},
  pages={i249--i259},
  year={2019},
  publisher={Oxford University Press},
  doi = {10.1093/bioinformatics/btz323}
}

@article{lin2019adversarial,
  title={Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms},
  author={Lin, Ruogu and Zheng, Xiangrui and Kitani, Kris and Xu, Min},
  journal={Bioinformatics},
  volume={35},
  number={14},
  pages={i260--i268},
  year={2019},
  publisher={Oxford University Press},
  doi = {10.1093/bioinformatics/btz364}
}

@article{lu2019fine,
  title={Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization},
  author={L{\"u}, Yongchun and Zeng, Xiangrui and Zhao, Xiaofang and Li, Shirui and Li, Hua and Gao, Xin and Xu, Min},
  journal={BMC bioinformatics},
  volume={20},
  number={1},
  pages={1--13},
  year={2019},
  publisher={BioMed Central}
}

@inproceedings {gubins2019classification,
  booktitle = {Eurographics Workshop on 3D Object Retrieval},
  editor = {Biasotti, Silvia and Lavoué, Guillaume and Veltkamp, Remco},
  title = {{Classification in Cryo-Electron Tomograms}},
  author = {Gubins, Ilja and Schot, Gijs van der and Veltkamp, Remco C. and Förster, Friedrich and Du, Xuefeng and Zeng, Xiangrui and Zhu, Zhenxi and Chang, Lufan and Xu, Min and Moebel, Emmanuel and Martinez-Sanchez, Antonio and Kervrann, Charles and Lai, Tuan M. and Han, Xusi and Terashi, Genki and Kihara, Daisuke and Himes, Benjamin A. and Wan, Xiaohua and Zhang, Jingrong and Gao, Shan and Hao, Yu and Lv, Zhilong and Wan, Xiaohua and Yang, Zhidong and Ding, Zijun and Cui, Xuefeng and Zhang, Fa},
  year = {2019},
  publisher = {The Eurographics Association},
  ISSN = {1997-0471},
  ISBN = {978-3-03868-077-2},
  DOI = {10.2312/3dor.20191061}
}

@article{liu2019semi,
  title={Semi-supervised Macromolecule Structural Classification in Cellular Electron Cryo-Tomograms using 3D Autoencoding Classifier},
  author={Liu, Siyuan and Du, Xuefeng and Xi, Rong and Xu, Fuya and Zeng, Xiangrui and Zhou, Bo and Xu, Min},
  booktitle={British Machine Vision Conference (BMVC)},
  year={2019}
}

@article{du2019open,
  title={Open-set Recognition of Unseen Macromolecules in Cellular Electron Cryo-Tomograms by Soft Large Margin Centralized Cosine Loss},
  author={Du, Xuefeng and Zeng, Xiangrui and Zhou, Bo and Singh, Alex and Xu, Min},
  booktitle={British Machine Vision Conference (BMVC)},
  year={2019}
}

@inproceedings{wu2019regularized,
  title={Regularized Adversarial Training (RAT) for Robust Cellular Electron Cryo Tomograms Classification},
  author={Wu, Xindi and Mao, Yijun and Wang, Haohan and Zeng, Xiangrui and Gao, Xin and Xing, Eric, and Xu, Min},
  booktitle={2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  year={2019},
  organization={IEEE}
}

@inproceedings{che2019domain,
  title={Domain Randomization for Macromolecule Structure Classification and Segmentation in Electron Cyro-tomograms},
  author={Che, Chengqian and Xian, Zhou, and Zeng, Xiangrui and Gao, Xin and Xu, Min},
  booktitle={2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  year={2019},
  organization={IEEE}
}

@inproceedings{lu2020spark,
  title={Spark-based parallel calculation of 3D Fourier shell correlation for macromolecule structure local resolution estimation},
  author={Lu, Yongchun and Zeng, Xiangrui and Tian, Xinhui and Shi, Xiao and Wang, Hui and Zheng, Xiaohui and Liu, Xiaodong and Zhao, Xiaofang and Gao, Xin and Xu, Min},
  booktitle={2020 Asia Pacific Bioinformatics Conference (APBC)},
  year={2020}
}

@incollection{wu2019template,
  author      = {Wu, Xindi and Zeng, Xiangrui and Zhu, Zhenxi and Gao, Xin and Xu, Min},
  title       = {Template-Based and Template-Free Approaches in Cellular Cryo-Electron Tomography Structural Pattern Mining},
  editor      = {},
  booktitle   = {Computational Biology},
  publisher   = {Codon Publications},
  address     = {Australia},
  year        = 2019,
  pages       = {175-186},
  chapter     = 11,
}

@article{zeng2019aitom,
  title={AITom: Open-source AI platform for cryo-electron Tomography data analysis},
  author={Zeng, Xiangrui and Xu, Min},
  journal={arXiv preprint arXiv:1911.03044},
  year={2019}
}


@article{wang2019learn,
  title={Learn to segment single cells with deep distance estimator and deep cell detector},
  author={Wang, Weikang and Taft, David A and Chen, Yi-Jiun and Zhang, Jingyu and Wallace, Callen T and Xu, Min and Watkins, Simon C and Xing, Jianhua},
  journal={Computers in biology and medicine},
  volume={108},
  pages={133--141},
  year={2019},
  publisher={Elsevier}
}

@article{li2019machine,
  title={Machine Learning (ML)-Assisted Design and Fabrication for Solar Cells},
  author={Li, Fan and Peng, Xiaoqi and Wang, Zuo and Zhou, Yi and Wu, Yuxia and Jiang, Minlin and Xu, Min},
  journal={Energy \& Environmental Materials},
  volume={2},
  number={4},
  pages={280--291},
  year={2019},
  publisher={Wiley Online Library}
}

@inproceedings{wang2019ellipse,
  title={Ellipse Detection of Optic Disc-and-Cup Boundary in Fundus Images},
  author={Wang, Zeya and Dong, Nanqing and Rosario, Sean D and Xu, Min and Xie, Pengtao and Xing, Eric P},
  booktitle={2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)},
  pages={601--604},
  year={2019},
  organization={IEEE}
}



@inproceedings{dong2019neural,
  title={Neural Architecture Search for Adversarial Medical Image Segmentation},
  author={Dong, Nanqing and Xu, Min and Liang, Xiaodan and Jiang, Yiliang and Dai, Wei and Xing, Eric},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={828--836},
  year={2019},
  organization={Springer}
}

@inproceedings{xiao2019improving,
  title={Improving Lesion Segmentation for Diabetic Retinopathy Using Adversarial Learning},
  author={Xiao, Qiqi and Zou, Jiaxu and Yang, Muqiao and Gaudio, Alex and Kitani, Kris and Smailagic, Asim and Costa, Pedro and Xu, Min},
  booktitle={International Conference on Image Analysis and Recognition},
  pages={333--344},
  year={2019},
  organization={Springer}
}


@inproceedings{zeng2020gum,
  title={Gum-Net: Unsupervised Geometric Matching for Fast and Accurate 3D Subtomogram Image Alignment and Averaging},
  author={Zeng, Xiangrui and Xu, Min},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={},
  year={2020}
}

@article{chen2020pub,
  title={PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation},
  author={Chen, Feiyang and Jiang, Ying and Zeng, Xiangrui and Zhang, Jing and Gao, Xin and Xu, Min},
  journal={Algorithms},
  volume={13},
  number={126},
  year={2020},
  publisher={MDPI}
}

@inproceedings{gao2020dilated,
  title={Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography},
  author={Gao, Shan and Han, Renmin and Zeng, Xiangrui and Cui, Xuefeng and Liu, Zhiyong and Xu, Min and Zhang, Fa},
  booktitle={International Symposium on Bioinformatics Research and Applications},
  pages={82--94},
  year={2020},
  organization={Springer}
}

@article{shi2020a,
  title={A simulated annealing approach for resolution guided homogeneous cryo electron microscopy image selection},
  author={Shi, Jie and Zeng, Xiangrui and Jiang, Rui and Jiang, Tao and Xu, Min},
  journal={Quantitative Biology},
  volume={8},
  number={1},
  pages={51--63},
  year={2020},
  url = {http://journal.hep.com.cn/qb/EN/abstract/article_26354.shtml},
  doi = {10.1007/s40484-019-0191-8}
}


@article{gubins2020classification,
  title = {{SHREC’20 Benchmark: Classification in cryo-electron tomograms}},
  author = {Gubins, Ilja and Chaillet, Marten and van der Schot, Gijs and Veltkamp, Remco and Förster, Friedrich and Hao, Yu and Wan, Xiaohua and Cui, Xuefeng and Zhang, Fa and Moebel, Emmanuel and Wang, Xiao and Kihara, Daisuke and Zeng, Xiangrui and Xu, Min and Nguyen, Nguyen and White, Tommi and Bunyak, Filiz},
  year = {2020},
  journal = {Computers \& Graphics},
  publisher = {The Eurographics Association}
}

@article{liu2020a,
  title={A Unified Framework for Packing Deformable and Non-deformable Subcellular Structures in Crowded Cryo-electron Tomogram Simulation},
  author={Liu, Sinuo and Ban, Xiaojuan and Zeng, Xiangrui and Zhao, Fengnian and Gao, Yuan and Wu, Wenjie and Zhang, Hongpan and Chen, Feiyang and Hall, Thomas and Gao, Xin and Xu Min},
  journal={BMC Bioinformatics},
  year={2020},
  publisher={BioMed Central}
}

@article{yu2020few,
  title={Few Shot Domain Adaptation for in situ Macromolecule Structural Classification in Cryo-electron Tomograms},
  author={Yu, Liangyong and Li, Ran and Zeng, Xiangrui and Wang, Hongyi and Jin, Jie and Yang, Ge and Jiang, Rui and Xu Min},
  journal={Bioinformatics},
  year={2020},
  publisher={Oxford University Press}
}


@article{li2020few,
  title={Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms},
  author={Li, Ran and Yu, Liangyong and Zhou, Bo and Zeng, Xiangrui and Wang, Zhenyu and Yang, Xiaoyan and Zhang, Jing and Gao, Xin and Jiang, Rui and Xu Min},
  journal={PLOS Computational Biology},
  year={2020},
  publisher={Public Library of Science}
}

@article{zheng2020poly,
  title={Poly(A)-DG: a deep-learning-based domain generalization method to identify cross-species Ploy(A) signal without prior knowledge from target species.},
  author={Zheng, Yumin and Wang, Haohan and Zhang, Yang and Gao, Xin and Xu Min},
  journal={PLOS Computational Biology},
  year={2020},
  publisher={Public Library of Science}
}

@article{yang2020attpnet,
  title={AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis},
  author={Yang, Yufeng and Ma, Yixiao and Zhang, Jing and Gao, Xin and Xu, Min},
  journal={Sensors},
  volume={20},
  number={19},
  pages={5455},
  year={2020},
  publisher={Multidisciplinary Digital Publishing Institute}
}



@inproceedings{liu2020efficient,
  title={Efficient Cryo-Electron Tomogram Simulation of Macromolecular Crowding with Application to SARS-CoV-2},
  author={Liu, Sinuo and Ma, Yan and Ban, Xiaojuan and Zeng, Xiangrui and Nallapareddy, Vamsi and Chaudhari, Ajinkya and Xu, Min},
  booktitle={2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  pages={80--87},
  year={2020},
  organization={IEEE}
}


@article{zhou2020one,
  title={One-shot Learning with Attention-guided Segmentation in Cryo-Electron Tomography},
  author={Zhou, Bo and Yu, Haisu and Zeng, Xiangrui and Yang, Xiaoyan and Zhang, Jing and Xu, Min},
  journal={Frontiers in Molecular Biosciences},
  volume={7},
  pages={473},
  year={2021},
  publisher={Frontiers}
}

@article{dong2020towards,
  title={Towards Robust Medical Image Segmentation on Small-Scale Data with Incomplete Labels},
  author={Dong, Nanqing and Kampffmeyer, Michael and Liang, Xiaodan and Xu, Min and Voiculescu, Irina and Xing, Eric P},
  journal={arXiv preprint arXiv:2011.14164},
  year={2020}
}


@article{du2021active,
    author = {Du, Xuefeng and Wang, Haohan and Zhu, Zhenxi and Zeng, Xiangrui and Chang, Yi-Wei and Zhang, Jing and Xing, Eric and Xu, Min},
    title = "{Active Learning to Classify Macromolecular Structures in situ for Less Supervision in Cryo-Electron Tomography}",
    journal = {Bioinformatics},
    year = {2021},
    month = {02},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btab123},
    url = {https://doi.org/10.1093/bioinformatics/btab123},
    note = {btab123},
    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab123/36340627/btab123.pdf},
}


@ARTICLE{gao2021macromolecules,
  author={Gao, Shan and Han, Renmin and Zeng, Xiangrui and Liu, Zhiyong and Xu, Min and Zhang, Fa},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, 
  title={Macromolecules Structural Classification with a 3D Dilated Dense Network in Cryo-electron Tomography}, 
  year={2021},
  volume={},
  number={},
  pages={1-1},
  doi={10.1109/TCBB.2021.3065986}}



@article{yi2021disentangling,
  title={Disentangling semantic features of macromolecules in Cryo-Electron Tomography},
  author={Yi, Kai and Pang, Jianye and Zhang, Yungeng and Zeng, Xiangrui and Xu, Min},
  journal={arXiv preprint arXiv:2106.14192},
  year={2021}
}


@inproceedings{zeng2021unsupervised,
  title={Unsupervised Domain Alignment based Open Set Structural Recognition of Macromolecules Captured by Cryo-Electron Tomography},
  author={Zeng, Yuchen and Howe, Gregory and Zeng, Xiangrui and Zhang, Jing and Chang, Yi-Wei and Xu, Min},
  booktitle={2021 IEEE International Conference on Image Processing (ICIP)},
  year={2021},
  organization={IEEE}
}


@inproceedings{zeng2021end,
  title={End-to-end Robust Joint Unsupervised Image Alignment and Clustering},
  author={Zeng, Xiangrui and Howe, Gregory and Xu, Min},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
  pages={},
  year={2021}
}


@inproceedings{zhu2021weakly,
  title={Weakly Supervised 3D Semantic Segmentation Using Cross-Image Consensus and Inter-Voxel Affinity Relations},
  author={Zhu, Xiaoyu and Chen, Jeffery and Zeng, Xiangrui and Liang, Junwei and Li, Chengqi and Liu, Sinuo and Behpour, Sima and Xu, Min},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
  pages={},
  year={2021}
}


@inproceedings{cang2021scan,
  title={Scan-IT: Domain segmentation of spatial transcriptomics images by graph neural network},
  author={Cang, Zixuan and Ning, Xinyi and Nie, Annika and Xu, Min and Zhang, Jing},
  booktitle={British Machine Vision Conference (BMVC)},
  year={2021}
}

@article{bandyopadhyay2021cryo,
  title={Cryo-shift: Reducing domain shift in cryo-electron subtomograms with unsupervised domaina daptation and randomization},
  author={Bandyopadhyay, Hmrishav and Deng, Zihao and Ding, Leiting and Liu, Sinuo and Uddin, Mostofa and Zeng, Xiangrui and Behpour, Sima and Xu, Min},
  journal={Bioinformatics},
  year={2021},
  publisher={Oxford University Press},
  doi = {10.1093/bioinformatics/btab794}
}


@article{dong2021towards,
  title={Towards robust partially supervised multi-structure medical image segmentation on small-scale data},
  author={Dong, Nanqing and Kampffmeyer, Michael and Liang, Xiaodan and Xu, Min and Voiculescu, Irina and Xing, Eric},
  journal={Applied Soft Computing},
  pages={108074},
  year={2021},
  publisher={Elsevier}
}


@article{zhang2021deep,
  title={Deep learning predicts EBV status in gastric cancer based on spatial patterns of lymphocyte infiltration},
  author={Zhang, Baoyi and Yao, Kevin and Xu, Min and Wu, Jia and Cheng, Chao},
  journal={Cancers},
  year={2021},
  publisher={Multidisciplinary Digital Publishing Institute}
}


@inproceedings{wang2022boosting, 
  title={Boosting Active Learning via Improving Test Performance}, 
  author={Wang, Tianyang and Li, Xingjian and Yang, Pengkun and Hu, Guosheng and Zeng, Xiangrui and Huang, Siyu and Xu, Cheng-Zhong and Xu, Min}, 
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence (AAAI)}, 
  year={2022} 
}


@inproceedings{uddin2021practical,
  title={Practical Analysis of Macromolecule Identity from Cryo-electron Tomography Images using Deep Learning},
  author={Uddin, Mostofa Rafid and Ahmed, Ajmain Yasar and Khan, Kafi and Fatemi, Md Shahrar and Zeng, Xiangrui and Xu, Min},
  booktitle={2021 IEEE Applied Imagery Pattern Recognition Workshop (AIPR)},
  pages={1--9},
  year={2021},
  organization={IEEE}
}


@article{wu2022cryoetgan,
  title={CryoETGAN: Cryo-Electron Tomography Image Synthesis via Unpaired Image Translation},
  author={Wu, Xindi and Li, Chengkun and Zeng, Xiangrui and Wei, Haocheng and Deng, Hong-Wen and Zhang, Jing and Xu, Min},
  journal={Frontiers in Physiology},
  pages={128},
  year={2022},
  publisher={Frontiers}
}


@article{chharia2022deep,
  title={Deep-precognitive diagnosis: preventing future pandemics by novel disease detection With biologically-inspired conv-fuzzy network},
  author={Chharia, Aviral and Upadhyay, Rahul and Kumar, Vinay and Cheng, Chao and Zhang, Jing and Wang, Tianyang and Xu, Min},
  journal={IEEE Access},
  volume={10},
  pages={23167--23185},
  year={2022},
  publisher={IEEE}
}

@article{chandra2022prolificacy,
  title={Prolificacy Assessment of Spermatozoan via state-of-the-art Deep Learning Frameworks},
  author={Chandra, Satish and Gourisaria, Mahendra Kumar and Gm, Harshvardhan and Konar, Debanjan and Gao, Xin and Wang, Tianyang and Xu, Min},
  journal={IEEE Access},
  volume={10},
  pages={13715--13727},
  year={2022},
  publisher={IEEE}
}

@article{srinivasan2022insulock,
  title={InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification},
  author={Srinivasan, Shushrruth Sai and Gong, Yanwen and Xu, Siwei and Hwang, Ahyeon and Xu, Min and Girgenti, Matthew J and Zhang, Jing},
  journal={Genes},
  volume={13},
  number={4},
  pages={621},
  year={2022},
  publisher={MDPI}
}


@inproceedings{uddin2021practical,
  title={Practical Analysis of Macromolecule Identity from Cryo-electron Tomography Images using Deep Learning},
  author={Uddin, Mostofa Rafid and Ahmed, Ajmain Yasar and Khan, Kafi and Fatemi, Md Shahrar and Zeng, Xiangrui and Xu, Min},
  booktitle={2021 IEEE Applied Imagery Pattern Recognition Workshop (AIPR)},
  pages={1--9},
  year={2021},
  organization={IEEE}
}

@inproceedings{uddin2022harmony,
  title={Harmony: A Generic Unsupervised Approach for Disentangling Semantic Content From Parameterized Transformations},
  author={Uddin, Mostofa Rafid and Howe, Gregory and Zeng, Xiangrui and Xu, Min},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={20646--20655},
  year={2022}
}


@article{gao2022fscc,
  title={FSCC: Few-shot Learning for Macromolecule Classification based on Contrastive Learning and Distribution Calibration in Cryo-Electron Tomography},
  author={Gao, Shan and Zeng, Xiangrui and Xu, Min and Zhang, Fa},
  journal={Frontiers in Molecular Biosciences},
  pages={620},
  year={2022},
  publisher={Frontiers}
}


@inproceedings{wang2022deep,
  title={Deep active learning for cryo-electron tomography classification},
  author={Wang, Tianyang and Li, Bo and Zhang, Jing and Zeng, Xiangrui and Uddin, Mostofa Rafid and Wu, Wei and Xu, Min},
  booktitle={2022 IEEE International Conference on Image Processing (ICIP)},
  year={2022},
  organization={IEEE}
}

@inproceedings{zhu2022unsupervised,
  title={Unsupervised Multi-task Learning for 3D Subtomogram Image Alignment, Clustering and Segmentation},
  author={Zhu, Haoyi and Wang, Chuting and Wang, Yuanxin and Fan, Zhaoxin and Uddin, Mostofa Rafid and Gao, Xin and Zhang, Jing and Zeng, Xiangrui and Xu, Min},
  booktitle={2022 IEEE International Conference on Image Processing (ICIP)},
  year={2022},
  organization={IEEE}
}

@article{zeng2022structure,
author = {Zeng, Xiangrui and Lin, Ziqian and Uddin, Mostofa Rafid and Zhou, Bo and Cheng, Chao and Zhang, Jing and Freyberg, Zachary and Xu, Min},
title = {Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series},
journal = {Journal of Computational Biology},
volume = {0},
number = {0},
pages = {null},
year = {0},
doi = {10.1089/cmb.2021.0606},
    note ={PMID: 35862434},
URL = { https://doi.org/10.1089/cmb.2021.0606},
eprint = { https://doi.org/10.1089/cmb.2021.0606}
}


@article{gupta2022self,
  title={Self-supervised learning for macromolecular structure classification based on cryo-electron tomograms},
  author={Gupta, Tarun and He, Xuehai and Uddin, Mostofa Rafid and Zeng, Xiangrui and Zhou, Andrew and Zhang, Jing and Freyberg, Zachary and Xu, Min}
  journal={Frontiers in Physiology},
  year={2022},
  publisher={Frontiers}
}

@article{zeng2023high,
  title={High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering},
  author={Zeng, Xiangrui and Kahng, Anson and Xue, Liang and Mahamid, Julia and Chang, Yi-Wei and Xu, Min},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  volume={120},
  number={15},
  pages={e2213149120},
  year={2023}
}


@inproceedings{li2024deep,
  title={Deep active learning with noise stability},
  author={Li, Xingjian and Yang, Pengkun and Gu, Yangcheng and Zhan, Xueying and Wang, Tianyang and Xu, Min and Xu, Chengzhong},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  volume={38},
  number={12},
  pages={13655--13663},
  year={2024}
}

@article{jain2024knowledge,
  title={Knowledge transfer from macro-world to micro-world: enhancing 3D Cryo-ET classification through fine-tuning video-based deep models},
  author={Jain, Sabhay and Li, Xingjian and Xu, Min},
  journal={Bioinformatics},
  volume={40},
  number={7},
  pages={btae368},
  year={2024},
  publisher={Oxford University Press}
}


----------------------------------------------
% websites

@misc{xulab2016,
  author = {Xu, Min},
  title = {Open source softwares published at Xu lab},
  year = 2016,
  howpublished = "\url{http://www.cs.cmu.edu/~mxu1}",
  urldate = {2016-07-01}
}

@misc{xulab2016software,
  author = {Xu, Min},
  title = {Open source softwares published at Xu lab},
  year = 2016,
  howpublished = "\url{http://www.cs.cmu.edu/~mxu1/softwares/softwares.html}",
  urldate = {2016-07-01}
}

@misc{xulab2016project,
  author = {Xu, Min},
  title = {Open source projects published at Xu lab},
  year = 2016,
  howpublished = "\url{https://github.com/xulabs/projects}",
  urldate = {2016-07-01}
}


@misc{xulab2019aitom,
  author = {Xu, Min},
  title = {AITom library},
  year = 2019,
  howpublished = "\url{https://github.com/xulabs/aitom}",
  urldate = {2019-06-21}
}