Mingfu Shao Lane Fellow Computational Biology Department School of Computer Science Carnegie Mellon University Email: mingfu.shao # cs.cmu.edu Address: GHC 7401, 5000 Forbes Ave, Pittsburgh, PA 15213

About me

I finished my postdoc study at June 30, 2018. After that I joined Pennsylvania State University as an assistant professor. My current website is here.

I have been a Lane Fellow at CMU under the supervision of Prof. Carl Kingsford. I obtained my Ph.D. (Thesis: Models and Algorithms for Comparative Genomics) in July 2015 from École Polytechnique Fédérale de Lausanne (EPFL), Switzerland, under the supervision of Prof. Bernard M.E. Moret. Here is my CV.

My research interests lie in algorithm design and combinatorial optimization, and particularly their applications in computational biology. Currently I am working on transcriptome assembly, RNA-seq quantification, and cancer transcriptome analysis. I am also very interested in genome rearrangements, phylogeny reconstruction, and protein folding.

Softwares

• Scallop is an accurate reference-based transcriptome assembler. Software is available at github. Scallop has been published at Nature Biotechnology. A podcast about Scallop (thanks to Roman Cheplyaka for the interview) is available at both bioinformatics.chat and iTunes.


• GREDU (Genome REarrangements with DUplications) is a software package that implements fast and exact algorithms for the following five edit distance problems between pairwise genomes with duplicate genes:
  
  1. DCJ distance
  2. DCJ + segmental duplication distance
  3. exemplar breakpoint distance
  4. intermediate breakpoint distance
  5. maximum-matching breakpoint distance
  Released source code is at github. Reference manual is here.

Publications

• Ma, C., Shao, M., and Kingsford, C.
  "SQUID: transcriptomic structural variation detection from RNA-seq".
  Genome Biology, (accpted, to appear, 2018).


• Shao, M., and Kingsford, C.
  "Efficient heuristic for decomposing a flow with minimum number of paths".
  TCBB, (accepted, to appear, 2017).


• Shao, M., and Kingsford, C.
  "Accurate assembly of transcripts through phasing-preserving graph decomposition".
  Nature Biotechnology, 35(12):1167-1169 (2017)


• Shao, M., Ma, J., and Wang, S.
  "DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields".
  In Proc. 25rd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB'17), Bioinformatics, 33(14):i267-i273 (2017).


• Shao, M., and Moret, B.M.E.
  "On computing breakpoint distances for genomes with duplicate genes".
  J. Comput. Biol., 26(6):571-580 (2017).


• Shao, M., and Moret, B.M.E.
  "A fast and exact algorithm for the exemplar breakpoint distance".
  J. Comput. Biol., 23(5):337-346 (2016).


• Shao, M., and Moret, B.M.E.
  "On computing breakpoint distances for genomes with duplicate genes".
  In Proc. 20th Int'l Conf. Comput. Mol. Biol. (RECOMB'16), volume 9649 of Lecture Notes in Comp. Sci., 189-203, (2016).


• Nair, N.U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P., and Moret, B.M.E.
  "A maximum-likelihood approach for building cell-type trees by lifting".
  In Proc. 14th Asia Pacific Bioinf. Conf. (APBC'16), BMC Genomics, 17(Suppl 1):14 (2016).


• Shao, M., and Moret, B.M.E.
  "Comparing genomes with rearrangements and segmental duplications".
  In Proc. 23rd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB'15), Bioinformatics, 31(12):i329-i338 (2015).


• Shao, M., Lin, Y., and Moret, B.M.E.
  "An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes".
  J. Comput. Biol., 22(5):425-435 (2015).


• Shao, M., and Moret, B.M.E.
  "A fast and exact algorithm for the exemplar breakpoint distance".
  In Proc. 19th Int'l Conf. Comput. Mol. Bio. (RECOMB'15), volume 9029 of Lecture Notes in Comp. Sci., pages 309-322, (2015).


• Shao, M., and Moret, B.M.E.
  "On the DCJ median problem".
  In Proc. 25th Symp. on Combinatorial Pattern Matching (CPM'14), volume 8486 of Lecture Notes in Comp. Sci., 273-282, (2014).


• Shao, M., Lin, Y., and Moret, B.M.E.
  "An exact algorithm to compute the DCJ distance for genomes with duplicate genes".
  In Proc. 18th Int'l Conf. Comput. Mol. Bio. (RECOMB'14), volume 8394 of Lecture Notes in Comp. Sci., 282-290, (2014).


• Shao, M., Lin, Y., and Moret, B.M.E.
  "Sorting genomes with rearrangements and segmental duplications through trajectory graphs".
  In Proc. 11th RECOMB Workshop on Comparative Genomics (RECOMB-CG'13), BMC Bioinformatics 14(Suppl. 15):S9 (2013).


• Shao, M., and Lin, Y.
  "Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion".
  In Proc. 10th RECOMB Workshop on Comparative Genomics (RECOMB-CG'12), BMC Bioinformatics 13(Suppl. 19):S13 (2012).


• Shao, M., Wang, S., Wang, C., Yuan, X., Li, S.-C., Zheng, W.-M., and Bu, D.
  "Incorporating ab initio energy into threading approaches for protein structure prediction".
  In Proc. 9th Asia Pacific Bioinf. Conf. (APBC'11), BMC Bioinformatics 12(Suppl. 1):S54 (2011).


• Wei, Y., Shao, M., Yang, J., Wang, C., Li, S.-C., and Bu, D.
  "Approximating conserved regions of protein structures".
  In Proc. 9th Ann. Int’l Comput. Systems Bioinf. Conf (CSB'10), volume 9, pages 204-212 (2010).