HX
Hongyi Xin
bioinformaticsq-bio.GNSingle-Cell AnalysisSoftwareAdenocarcinoma of Lungcs.CEDeep learningDeep LearningGene Expression ProfilingHigh-Throughput Nucleotide Sequencing
On Valency
published · living versionsW_92jh5vez·v1 · currentpublished
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
with Richard Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko +3
1 version
Preprints & journals
44 papers in the corpus · 2013–2026Benchmarking niche identification via domain segmentation for spatial transcriptomics data10.64898/2026.02.27.708202v3 · Wang, Y., Chen, Y., Yang, L. et al.2026 · 0 citationsbioRxiv
Rapid discovery of monoclonal antibodies via high-throughput single BCR affinity sequencing.42621736 · Hu, Mengzhu, Lian, Qiuyu, Cui, Xiaonan et al.2026 · 0 citationsNucleic acids research. 2026;54(15)
Benchmarking protein sequence and structure search methods for remote homology detection.42458582 · Liu, Yuan, Zhou, Yingquan, Huang, Yan et al.2026 · 1 citationGenome biology. 2026
Atlas of predicted protein complex structures across kingdoms.41882029 · Qi, Xianzhi, Ye, Cheng, Liang, Jianqiang et al.2026 · 5 citationsNature communications. 2026;17(1)
Population-Scale Advancing Interface Modeling Reveals How Bacterial Swarms Encode Future Spatial Architecture2602.01056v3 · Shengyou Duan, Zhaoyang Wang, Kaiyi Xiong et al.2026 · 0 citationsarXiv
Gene-First Identity Construction for Robust Cell Identification in Single-Cell Transcriptomics10.64898/2026.02.25.707869v2 · Yang, L., Huang, Z., Cai, J. et al.2026 · 0 citationsbioRxiv
Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis10.64898/2026.02.25.707866v2 · Cai, J., Wang, Y., Qiao, Y. et al.2026 · 0 citationsbioRxiv
VeloTrace Reconciles Divergent Velocity and Trajectory in Single-cell Transcriptomics with Deep Neural ODE10.64898/2026.04.09.717458v1 · Cheng, H., Qiao, Y., Feng, Y. et al.2026 · 0 citationsbioRxiv
A novel deep learning system for STEMI prognostic prediction from multi-sequence cardiac magnetic resonance.41314962 · Chen, Yifan, Jiang, Meng, Xia, Chao et al.2025 · 38 citationsScience bulletin. 2025;70(24):4241-4252
PLVAP mediates the regulation of the tumour microenvironment in early-stage lung adenocarcinoma.41431249 · Xie, Linshan, Sun, Mengting, Zheng, Yujie et al.2025 · 3 citationsClinical and translational medicine. 2025;15(12):e70532
Efficient trace reconstruction in DNA storage systems using bidirectional beam search.41280695 · Gu, Zhenhao, Xin, Hongyi, Sharma, Puru et al.2025 · 0 citationsiScience. 2025;28(11):113791
Simultaneously infer cell pseudotime, velocity field, and gene interaction from multi-branch scRNA-seq data with scPN.41229398 · Zhou, Zhen, Li, Jiachen, Xin, Hongyi et al.2025 · 1 citationNAR genomics and bioinformatics. 2025;7(4):lqaf144
PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation2510.07964v1 · Jiabei Cheng, Changxi Chi, Jingbo Zhou et al.2025 · 0 citationsarXiv
SODA: Detecting COVID-19 in Chest X-Rays With Semi-Supervised Open Set Domain Adaptation.33729944 · Zhou, Jieli, Jing, Baoyu, Wang, Zeya et al.2025 · 50 citationsIEEE/ACM transactions on computational biology and bioinformatics. 2022;19(5):2605-2612
Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search10.1101/2025.04.16.644694v2 · Gu, Z., Xin, H., Sharma, P. et al.2025 · 0 citationsbioRxiv
Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression.32285025 · Yan, Qi, Weeks, Daniel E, Xin, Hongyi et al.2025 · 153 citationsNature machine intelligence. 2020;2(2):141-150
Simultaneously Infer Cell Pseudotime,Velocity Field and Gene Interaction from Multi-Branch scRNA-seq Data with scPN2410.18394v1 · Zhen Zhou, Jiachen Li, Hongyi Xin et al.2024 · 1 citationarXiv
Large language model answers medical questions about standard pathology reports.39359921 · Wang, Anqi, Zhou, Jieli, Zhang, Peng et al.2024 · 13 citationsFrontiers in medicine. 2024;11:1402457
Context-aware seeds for read mapping.32489399 · Xin, Hongyi, Shao, Mingfu, Kingsford, Carl2024 · 5 citationsAlgorithms for molecular biology : AMB. 2020;15:10
Spatial transcriptomics reveals heterogeneity of histological subtypes between lepidic and acinar lung adenocarcinoma.38318637 · Xie, Linshan, Kong, Hui, Yu, Jinjie et al.2024 · 28 citationsClinical and translational medicine. 2024;14(2):e1573
CRCS: An automatic image processing pipeline for hormone level analysis of Cushing's disease.38159688 · Li, Haiyue, Xie, Jing, Song, Jialin et al.2024 · 2 citationsMethods (San Diego, Calif.). 2024;222:28-40
The microbiota regulates hematopoietic stem and progenitor cell development by mediating inflammatory signals in the niche.36795566 · Zhong, Dan, Jiang, Haowei, Zhou, Chengzhuo et al.2023 · 24 citationsCell reports. 2023;42(2):112116
Deep learning of endoscopic features for the assessment of neoadjuvant therapy response in locally advanced rectal cancer.37062601 · Wang, Anqi, Zhou, Jieli, Wang, Gang et al.2023 · 12 citationsAsian journal of surgery. 2023;46(9):3568-3574
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics.36549467 · Shan, Yiran, Zhang, Qian, Guo, Wenbo et al.2023 · 27 citationsGenomics, proteomics & bioinformatics. 2022;20(5):974-988
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics10.1101/2022.07.23.501220v1 · Shan, Y., Zhang, Q., Guo, W. et al.2022 · 27 citationsbioRxiv
GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing.32731885 · Xin, Hongyi, Lian, Qiuyu, Jiang, Yale et al.2021 · 90 citationsGenome biology. 2020;21(1):188
Artificial-cell-type aware cell-type classification in CITE-seq.32657383 · Lian, Qiuyu, Xin, Hongyi, Ma, Jianzhu et al.2021 · 16 citationsBioinformatics (Oxford, England). 2020;36(Suppl_1):i542-i550
GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping1604.01789v3 · Mohammed Alser, Hasan Hassan, Hongyi Xin et al.2016 · 115 citationsBioinformatics. Nov 1;33(21):3355-3363, 2017
BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data.32379315 · Wang, Xinjun, Sun, Zhe, Zhang, Yanfu et al.2020 · 108 citationsNucleic acids research. 2020;48(11):5814-5824
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies1711.01177v1 · Jeremie S. Kim, Damla Senol Cali, Hongyi Xin et al.2017 · 130 citationsBMC Genomics, 19 (Suppl 2):89, 2018
Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression10.1101/19006171v2 · Yan, Q., Weeks, D. E., Xin, H. et al.2019 · 153 citationsmedRxiv
Artificial-Cell-Type Aware Cell Type Classification in CITE-seq10.1101/2020.01.31.928010v2 · Lian, Q., Xin, H., Ma, J. et al.2020 · 16 citationsbioRxiv
Sample demultiplexing, multiplet detection, experiment planning and novel cell type verification in single cell sequencing10.1101/828483v1 · Xin, H., Yan, Q., Jiang, Y. et al.2019 · 2 citationsbioRxiv
Context-Aware Seeds for Read Mapping10.1101/643072v1 · Xin, H., Shao, M., Kingsford, C.2019 · 5 citationsbioRxiv
A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies.30967541 · Sun, Zhe, Chen, Li, Xin, Hongyi et al.2019 · 92 citationsNature communications. 2019;10(1):1649
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping1506.08235v1 · Hongyi Xin, Richard Zhu, Sunny Nahar et al.2015 · 43 citationsBioinformatics, Jun 1;32(11):1632-42, 2016on Valency
BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies10.1101/392662v1 · Sun, Z., Chen, L., Xin, H. et al.2018 · 0 citationsbioRxiv
GRIM-filter: fast seed filtering in read mapping using emerging memory technologies1708.04329v1 · Jeremie S Kim, Damla Senol, Hongyi Xin et al.2017 · 17 citationsarXiv
LEAP: A Generalization Of The Landau-Vishkin Algorithm With Custom Gap Penalties10.1101/133157v3 · Xin, H., Kim, J., Nahar, S. et al.2017 · 3 citationsbioRxiv
Fast and accurate mapping of Complete Genomics reads.25461772 · Lee, Donghyuk, Hormozdiari, Farhad, Xin, Hongyi et al.2016 · 9 citationsMethods (San Diego, Calif.). 2015;79-80:3-10
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.25577434 · Xin, Hongyi, Greth, John, Emmons, John et al.2015 · 98 citationsBioinformatics (Oxford, England). 2015;31(10):1553-60
Accelerating read mapping with FastHASH.23369189 · Xin, Hongyi, Lee, Donghyuk, Hormozdiari, Farhad et al.2013 · 154 citationsBMC genomics. 2013;14 Suppl 1:S13
Career total: 65 works. 44 are in this corpus.Showing the 42 most recent.
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