Photo of Mingfu Shao

Mingfu Shao

Charles K. Etner Early Career Assistant Professor

Affiliation(s):

  • Computer Science and Engineering
  • School of Electrical Engineering and Computer Science

Research Areas:

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

 
 

 

Education

  • Ph D, Computer Science, EPFL, 2015

Publications

Journal Articles

  • Xiang Li, Qian Shi and Mingfu Shao, 2021, "On bridging paired-end RNA-seq data", bioRxiv
  • Qimin Zhang, Qian Shi and Mingfu Shao, 2021, "Scallop2 enables accurate assembly of multiple-end RNA-seq data", bioRxiv
  • Hong Xin, Mingfu Shao and Carl Kingsford, 2020, "Context-aware seeds for read mapping", Algorithms for Molecular Biology, 15, pp. 1--12
  • Hongyi Xin, Mingfu Shao and Carl Kingsford, 2020, "Context-aware seeds for read mapping", Algorithms for Molecular Biology, 15, pp. 1--12
  • Qian Shi and Mingfu Shao, 2020, "Coral accurately bridges paired-end RNA-seq reads alignment", bioRxiv
  • Mingfu Shao and Carl Kingsford, 2019, "Efficient heuristic for decomposing a flow with minimum number of paths", IEEE-ACM Transactions on Comput. Biol. and Bioinf., 16, pp. 658--670
  • 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
  • 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
  • Cong Ma, Mingfu Shao and Carl Kingsford, 2018, "SQUID: transcriptomic structural variation detection from RNA-seq", Genome Biology, 19, (1), pp. 52
  • 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, , "A fast and exact algorithm for the exemplar breakpoint distance", J. Comput. Biol., 23, (5), pp. 337--346
  • Nishanth U. Nair, Laura Hunter, Mingfu Shao, P. Grnarova, Yu Lin, P. Bucher and Bernard M.E. Moret, , "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, , "An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes", J. Comput. Biol., 22, (5), pp. 425--435
  • Mingfu Shao and Yu Lin, , "Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion", BMC Bioinformatics, 13, (Suppl 19), pp. S13
  • Mingfu Shao and Bernard M.E. Moret, , "Comparing genomes with rearrangements and segmental duplications", Bioinformatics, 31, (12), pp. i329--i338
  • Mingfu Shao, Jianzhu Ma and Sheng Wang, , "DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields", Bioinformatics, 33, (14), pp. i267--i273
  • Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai-Cheng Li, Wei-Mou Zheng and Dongbo Bu, , "Incorporating ab initio energy into threading approaches for protein structure prediction", BMC Bioinformatics, 12, (Suppl 1), pp. S54
  • Mingfu Shao and Bernard M.E. Moret, , "On computing breakpoint distances for genomes with duplicate genes", J. Comput. Biol., 26, (6), pp. 571--580
  • Mingfu Shao, Yu Lin and Bernard M.E. Moret, , "Sorting genomes with rearrangements and segmental duplications through trajectory graphs", BMC Bioinformatics, 14, (Suppl 15), pp. S9

Conference Proceedings

  • Hongyi Xin, Mingfu Shao and Carl Kingsford, 2019, "Context-aware seeds for read mapping", 143, pp. 15:1--15:13
  • 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, "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
  • 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

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

207 Electrical Engineering West

University Park, PA 16802

814-863-6740

Department of Computer Science and Engineering

814-865-9505

Department of Electrical Engineering

814-865-7667