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Zhong, D., Jiang, H., Zhou, C., Ahmed, A., Li, H., Wei, X., … Ge, M. (2023). The microbiota regulates hematopoietic stem and progenitor cell development by mediating inflammatory signals in the niche. Cell Reports, 42(2). doi:10.1016/j.celrep.2023.112116
Zhang, S., Hu, Y., Wu, Z., Zhou, X., Wu, T., Li, P., … Xue, J. (2023). Deficiency of Carbamoyl Phosphate Synthetase 1 Engenders Radioresistance in Hepatocellular Carcinoma via Deubiquitinating c-Myc. International Journal of Radiation Oncology*Biology*Physics, 115(5), 1244–1256. doi:10.1016/j.ijrobp.2022.11.022
Wang, A., Zhou, J., Wang, G., Zhang, B., Xin, H., & Zhou, H. (2023). Deep learning of endoscopic features for assessment of neoadjuvant therapy response in locally advanced rectal cancer. Asian Journal of Surgery. doi:10.1016/j.asjsur.2023.03.165
Pan, M.-H., Xin, H.-Y., Xia, C.-Q., & Shen, H.-B. (2023). Few-shot classification with task-adaptive semantic feature learning. Pattern Recognition, 141, 109594. doi:10.1016/j.patcog.2023.10959
Shan, Y., Zhang, Q., Guo, W., Wu, Y., Miao, Y., Xin, H., … Gu, J. (2022). TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics. Genomics, Proteomics & Bioinformatics. doi:10.1016/j.gpb.2022.11.012
Zhou, J., & Xin, H. (2022). Emerging artificial intelligence methods for fighting lung cancer: A survey. Clinical EHealth, 5, 19–34. doi:10.1016/j.ceh.2022.04.001
Gao, F., Huang, K., & Xing, Y. (2022). Artificial Intelligence in Omics. Genomics, Proteomics & Bioinformatics, 20(5), 811–813. doi:10.1016/j.gpb.2023.01.002
Yang, D., Zhou, J., Chen, R., Song, Y., Song, Z., Zhang, X., … Bai, C. (2022). Expert consensus on the metaverse in medicine. Clinical EHealth, 5, 1–9. doi:10.1016/j.ceh.2022.02.001
Zhou, J., Jing, B., Wang, Z., Xin, H., & Tong, H. (2021). Soda: Detecting covid-19 in chest x-rays with semi-supervised open set domain adaptation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(5), 2605–2612. doi:10.1109/TCBB.2021.3066331
Wu, R., Guo, W., Qiu, X., Wang, S., Sui, C., Lian, Q., … Chen, L. (2021). Comprehensive analysis of spatial architecture in primary liver cancer. Science Advances, 7(51), eabg3750. doi:10.1126/sciadv.abg3750
Wu, T., Luo, G., Lian, Q., Sui, C., Tang, J., Zhu, Y., … Chen, L. (2021). Discovery of a Carbamoyl Phosphate Synthetase 1–Deficient HCC Subtype With Therapeutic Potential Through Integrative Genomic and Experimental Analysis. Hepatology, 74(6), 3249–3268. doi:10.1002/hep.32088
Shu, H., Zhou, J., Lian, Q., Li, H., Zhao, D., Zeng, J., & Ma, J. (2021). Modeling gene regulatory networks using neural network architectures. Nature Computational Science, 1(7), 491–501. doi:10.1038/s43588-021-00099-8
Cai, J., Xu, Y., Zhang, W., Ding, S., Sun, Y., Lyu, J., … Zhou, F. (2021). A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. Briefings in Bioinformatics, 22(4), bbaa253. doi:10.1093/bib/bbaa253
Xin, H., Lian, Q., Jiang, Y., Luo, J., Wang, X., Erb, C., … Chen, W. (2020). GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biology, 21(1), 188. doi:10.1186/s13059-020-02084-2
Lian, Q., Xin, H., Ma, J., Konnikova, L., Chen, W., Gu, J., & Chen, K. (2020). Artificial-cell-type aware cell-type classification in CITE-seq. Bioinformatics, 36(Supplement_1), i542–i550. doi:10.1093/bioinformatics/btaa467
Wang, X., Sun, Z., Zhang, Y., Xu, Z., Xin, H., Huang, H., … Chen, W. (2020). BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data. Nucleic Acids Research, 48(11), 5814–5824. doi:10.1093/nar/gkaa314
Yan, Q., Weeks, D. E., Xin, H., Swaroop, A., Chew, E. Y., Huang, H., … Chen, W. (2020). Deep-learning-based prediction of late age-related macular degeneration progression. Nature Machine Intelligence, 2(2), 141–150. doi:10.1038/s42256-020-0154-9
Xin, H., Shao, M., & Kingsford, C. (2020). Context-aware seeds for read mapping. Algorithms for Molecular Biology, 15(1), 10. doi:10.1186/s13015-020-00172-3
Sun, Z., Chen, L., Xin, H., Jiang, Y., Huang, Q., Cillo, A. R., … Chen, W. (2019). A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies. Nature Communications, 10(1), 1649. doi:10.1038/s41467-019-09639-3
Jayaram, K. R., Gandhi, A., Xin, H., & Tao, S. (2019). Adaptively accelerating map-reduce/spark with GPUs: A case study. 2019 IEEE International Conference on Autonomic Computing (ICAC), 105–114. doi:10.1109/ICAC.2019.00022
Kim, J. S., Senol Cali, D., Xin, H., Lee, D., Ghose, S., Alser, M., … Mutlu, O. (2018). GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genomics, 19(2), 89. doi:10.1186/s12864-018-4460-0
Alser, M., Hassan, H., Xin, H., Ergin, O., Mutlu, O., & Alkan, C. (2017). GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinformatics, 33(21), 3355–3363. doi:10.1093/bioinformatics/btx342
Xin, H., Nahar, S., Zhu, R., Emmons, J., Pekhimenko, G., Kingsford, C., … Mutlu, O. (2016). Optimal seed solver: optimizing seed selection in read mapping. Bioinformatics, 32(11), 1632–1642. doi:10.1093/bioinformatics/btv670
Xin, H., Greth, J., Emmons, J., Pekhimenko, G., Kingsford, C., Alkan, C., & Mutlu, O. (2015). Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinformatics, 31(10), 1553–1560. doi:10.1093/bioinformatics/btu856
Seshadri, V., Yedkar, S., Xin, H., Mutlu, O., Gibbons, P. B., Kozuch, M. A., & Mowry, T. C. (2015). Mitigating Prefetcher-Caused Pollution Using Informed Caching Policies for Prefetched Blocks. ACM Transactions on Architecture and Code Optimization, 11(4), 1–22. doi:10.1145/2677956
Lee, D., Hormozdiari, F., Xin, H., Hach, F., Mutlu, O., & Alkan, C. (2015). Fast and accurate mapping of Complete Genomics reads. Methods, 79–80, 3–10. doi:10.1016/j.ymeth.2014.10.012
Pekhimenko, G., Seshadri, V., Kim, Y., Xin, H., Mutlu, O., Gibbons, P. B., … Mowry, T. C. (2013). Linearly compressed pages: a low-complexity, low-latency main memory compression framework. Proceedings of the 46th Annual IEEE/ACM International Symposium on Microarchitecture - MICRO-46, 172–184. doi:10.1145/2540708.2540724
Xin, H., Lee, D., Hormozdiari, F., Yedkar, S., Mutlu, O., & Alkan, C. (2013). Accelerating read mapping with FastHASH. BMC Genomics, 14(1), S13. doi:10.1186/1471-2164-14-S1-S13
Greathouse, J. L., Xin, H., Luo, Y., & Austin, T. (2012, March). A case for unlimited watchpoints. Proceedings of the Seventeenth International Conference on Architectural Support for Programming Languages and Operating Systems, 159–172. doi:10.1145/2150976.2150994