Faculty Directory

Hongyi Xin
Assistant professor
Office 436
Tel +86-21-34206765 Ext.4361
Email hongyi.xin@sjtu.edu.cn
Webpage https://xinhongyi.me


Ph.D. Computer Science, Carnegie Mellon University, Pittsburgh, United States (2018)
B.S.E. Computer Engineering, University of Michigan, Ann Arbor, United States (2011)
B.S.E. Electrical and Computer Engineering, Shanghai Jiao Tong University, Shanghai, China (2011)

Work Experience

2020-pres. Assistant Professor, UM-SJTU Joint Institute, Shanghai Jiao Tong University
2018-2020 Postdoctoral Associate, Pediatrics, University of Pittsburgh

 Research Interests

  • Bioinformatics: Single cell data analysis
  • Bioinformatics: Read mapping and DNA assembly algorithms
  • Novel computing architecture: DNA data storage

 Selected Publications

  • Hongyi Xin, Qiuyu Lian, Yale Jiang, Jiadi Luo, Xinjun Wang, Carla Erb, Xiaoyi Zhang, Elisa Heidrich-O’Hare, Qi Yan, Richard Duerr, Kong Chen, Wei Chen. “Sample demultiplexing, multiplet detection, experiment planning and novel cell type verification in single cell sequencing”, to be appear on Genome Biology.
  • Qiuyu Lian, Hongyi Xin (co-first), Jianzhu Ma, Lina Konnikova, Wei Chen, Jin Gu, Kong Chen. “Artificial-Cell-Type Aware Cell Type Classification in CITE-seq”, in Bioinformatics, Volume 36, Issue Supplement_1, July 2020.
  • Hongyi Xin, Mingfu Shao, Carl Kingsford. “Context-Aware Seeds for Read Mapping”, in Algorithms in Molecular Biology, 15, 10, May 2020.
  • Xinjun Wang, Zhe Sun, Yanfu Zhang, Zhongli Xu, Hongyi Xin, Heng Huang, Richard H Duerr, Kong Chen, Ying Ding, Wei Chen. “BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data”, in Nucleic Acids Research, gkaa314, May 2020.
  • Qi Yan, Daniel Weeks, Hongyi Xin, Anand Swaroop, Emily Chew, Heng Huang, Ying Ding, Wei Chen. “Deep-LearningBased Prediction of Late Age-Related Macular Degeneration Progression”, in Nature Machine Intelligence, 2, 141-150, February 2020.
  • KR Jayaram, Anshul Gandhi, Hongyi Xin, Shu Tao. “Adaptively Accelerating Map-Reduce/Spark with GPUs: A Case Study”, in Proceedings of the 16th The International Conference on Autonomic Computing (ICAC 2019), Umea, Sweden, June 2019.
  • Zhe Sun, Li Chen, Hongyi Xin, Qianhui Huang, Anthony Cillo, Tracy Tabib, Ying Ding, Jay Kolls, Tullia Bruno, Robert Lafyatis, Dario Vignali, Kong Chen, Ming Hu, and Wei Chen. “BAMM-SC: A Bayesian Mixture Model for Clustering Droplet-Based Single Cell Transcriptomic Data from Population Studies”, in Nature Communications, 10(1), Page 1649, 2019.
  • Jeremie Kim, Damla Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, O˘guz Ergin, Can Alkan, Onur Mutlu. “GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-inMemory Technologies”, in BMC Genomics, Volume 19, issue 2, May 2018.
  • Hongyi Xin, Jeremie Kim, Sunny Nahar, Can Alkan, Onur Mutlu. “LEAP: A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties”, in Proceedings of the 7th RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2017), Hong Kong, China, May 2017.
  • Mohammed Alser; Hasan Hassan; Hongyi Xin; O˘guz Ergin, Onur Mutlu, Can Alkan. “GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping”, in Oxford Bioinformatics, Volume 33 Issue 21, November 2017
  • Hongyi Xin, Sunny Nahar, Richard Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu. “Optimal Seed Solver: Optimizing Seed Selection in Read Mapping”, in Oxford Bioinformatics, Volume 32, Issue 11, May 2016.
  • Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu. “Shifted Hamming Distance: A Fast and Accurate SIMD-Friendly Filter for Local Alignment in Read Mapping”, in Oxford Bioinformatics, Volume 31 Issue 10, June 2015.
  • Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Can Alkan, Onur Mutlu. “Fast and Accurate Mapping of Complete Genomics Reads”, in Methods (Elsevier), Volume 79-80, June 2015.
  • Vivek Seshadri, Samihan Yedkar, Hongyi Xin, Onur Mutlu, Phillip B. Gibbons, Michael A. Kozuch, Todd Mowry. “Mitigating Prefetcher-Caused Pollution using Informed Caching Policies for Prefetched Blocks”, in ACMTransactions on Architecture and Code Optimization (TACO), Volume 11 Issue 4, January 2015.
  • Gennady Pekhimenko, Vivek Seshadri, Yoongu Kim, Hongyi Xin, Onur Mutlu, Todd Mowry. “Linearly Compressed Pages: A Low-complexity, low-latency main memory compression framework” in Proceedings of the 46th International Symposium on Microarchitecture (MICRO 2013), Davis, CA, USA, December 2013.
  • Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan. “Accelerating Read Mapping with FastHASH”, in BMC Genomics, Volume 14, January 2013.
  • Joseph L. Greathouse, Hongyi Xin, Yixin Luo, and Todd Austin. “A Case for Unlimited Watchpoints”, in Proceedings of the 17th International Conference on Architectural Support for Programming Languages and OperatingSystems (ASPLOS 2012), London, United Kingdom, March 2012.