Photo of Mingfu Shao

Mingfu Shao

Charles K. Etner Early Career Assistant Professor

Affiliation(s):

  • School of Electrical Engineering and Computer Science
  • Computer Science and Engineering
  • Huck Institutes of the Life Sciences

Research Areas:

Computational Science; Data Science and Artificial Intelligence; Theoretical Computer Science

 
 

 

Education

Publications

Journal Articles

  • Qimin Zhang and Mingfu Shao, 2023, "Transcript assembly and annotations: Bias and adjustment", PLOS Computational Biology, 19, (12), pp. e1011734
  • Ke Chen and Mingfu Shao, 2023, "Locality-sensitive bucketing functions for the edit distance", Algorithms for Molecular Biology, 18, (7)
  • Qimin Zhang, Qian Shi and Mingfu Shao, 2022, "Accurate assembly of multi-end RNA-seq data with Scallop2", Nature Computational Science, 2, pp. 148--152
  • Hongyi Xin, Mingfu Shao and Carl Kingsford, 2020, "Context-aware seeds for read mapping", Algorithms for Molecular Biology, 15, pp. 1--12
  • Laura H Tung, Mingfu Shao and Carl Kingsford, 2019, "Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads", Genome Biology, 20, (1), pp. 1--18
  • Mingfu Shao and Carl Kingsford, 2019, "Efficient heuristic for decomposing a flow with minimum number of paths", IEEE-ACM Transactions on Computational Biology and Bioinformatics, 16, (2), pp. 658--670
  • Cong Ma, Mingfu Shao and Carl Kingsford, 2018, "SQUID: transcriptomic structural variation detection from RNA-seq", Genome Biology, 19, (1), pp. 52
  • Mingfu Shao and Carl Kingsford, 2017, "Accurate assembly of transcripts through phase-preserving graph decomposition", Nature Biotechnology, 35, (12), pp. 1167--1169
  • Mingfu Shao and Bernard M.E. Moret, 2017, "On computing breakpoint distances for genomes with duplicate genes", Journal of Computational Biology, 26, (6), pp. 571--580
  • Mingfu Shao and Bernard M.E. Moret, 2016, "A fast and exact algorithm for the exemplar breakpoint distance", Journal of Computational Biology, 23, (5), pp. 337--346
  • Nishanth U. Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher and Bernard M.E. Moret, 2016, "A maximum-likelihood approach for building cell-type trees by lifting", BMC Genomics, 17, (Suppl 1), pp. 14
  • Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2015, "An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes", Journal of Computational Biology, 22, (5), pp. 425--435

Conference Proceedings

  • Xiang Li, Qian Shi, Ke Chen and Mingfu Shao, 2023, "Seeding with minimized subsequence", 39, (Supplement_1), pp. i232–i241
  • Ke Chen and Mingfu Shao, 2022, "Locality-sensitive bucketing functions for the edit distance", 242, pp. 22:1--22:14
  • Hongyi Xin, Mingfu Shao and Carl Kingsford, 2019, "Context-aware seeds for read mapping", 143, pp. 15:1--15:13
  • Mingfu Shao, Jianzhu Ma and Sheng Wang, 2017, "DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields", 33, (14), pp. i267--i273
  • Mingfu Shao and Bernard M.E. Moret, 2016, "On computing breakpoint distances for genomes with duplicate genes", 9649, pp. 189--203
  • Mingfu Shao and Bernard M.E. Moret, 2015, "Comparing genomes with rearrangements and segmental duplications", 31, (12), pp. i329--i338
  • Mingfu Shao and Bernard M.E. Moret, 2015, "A fast and exact algorithm for the exemplar breakpoint distance", 9029, pp. 309--322
  • Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2014, "An exact algorithm to compute the DCJ distance for genomes with duplicate genes", 8394, pp. 280--292
  • Mingfu Shao and Bernard M.E. Moret, 2014, "On the DCJ median problem", 8486, pp. 273--282
  • Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2013, "Sorting genomes with rearrangements and segmental duplications through trajectory graphs", 14, (Suppl 15), pp. S9
  • Mingfu Shao and Yu Lin, 2012, "Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion", 13, (Suppl 19), pp. S13
  • Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai-Cheng Li, Wei-Mou Zheng and Dongbo Bu, 2011, "Incorporating ab initio energy into threading approaches for protein structure prediction", 12, (Suppl 1), pp. S54
  • Yi Wei, Mingfu Shao, Jishuang Yang, Chao Wang, Shuai-Cheng Li and Dongbo Bu, 2010, "Approximating conserved regions of protein structures", 9, pp. 204--212
  • Leran Ma, Ke Chen and Mingfu Shao, , "On the maximal independent sets of k-mers with the edit distance"
  • Xiang Li and Mingfu Shao, , "On de novo bridging paired-end RNA-seq data"

Research Projects

Honors and Awards

Service

Service to Penn State:

Service to External Organizations:

 


 

About

The School of Electrical Engineering and Computer Science was created in the spring of 2015 to allow greater access to courses offered by both departments for undergraduate and graduate students in exciting collaborative research fields.

We offer B.S. degrees in electrical engineering, computer science, computer engineering and data science and graduate degrees (master's degrees and Ph.D.'s) in electrical engineering and computer science and engineering. EECS focuses on the convergence of technologies and disciplines to meet today’s industrial demands.

School of Electrical Engineering and Computer Science

The Pennsylvania State University

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Department of Electrical Engineering

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