Incorporating Ab Initio energy into threading approaches for protein structure prediction. - Mingfu Shao; Sheng Wang 001; Chao Wang; Xiongying Yuan; Shuai Li; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2011)

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. - Mingfu Shao; Yu Lin 001 (BMC Bioinform., 2012)

Sorting genomes with rearrangements and segmental duplications through trajectory graphs. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (BMC Bioinform., 2013)

On the DCJ Median Problem. - Mingfu Shao; Bernard M. E. Moret (CPM, 2014)

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2014)

Comparing genomes with rearrangements and segmental duplications. - Mingfu Shao; Bernard M. E. Moret (Bioinform., 2015)

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2015)

Models and Algorithms for Comparative Genomics. - Mingfu Shao (2015)

A maximum-likelihood approach for building cell-type trees by lifting. - Nishanth Ulhas Nair; Laura Hunter; Mingfu Shao; Paulina Grnarova; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (BMC Genom., 2016)

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. - Mingfu Shao; Bernard M. E. Moret (J. Comput. Biol., 2016)

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. - Mingfu Shao; Jianzhu Ma; Sheng Wang 001 (Bioinform., 2017)

On Computing Breakpoint Distances for Genomes with Duplicate Genes. - Mingfu Shao; Bernard M. E. Moret (J. Comput. Biol., 2017)

Theory and A Heuristic for the Minimum Path Flow Decomposition Problem. - Mingfu Shao; Carl Kingsford (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Context-aware seeds for read mapping. - Hongyi Xin; Mingfu Shao; Carl Kingsford (Algorithms Mol. Biol., 2020)

Accurate assembly of multi-end RNA-seq data with Scallop2. - Qimin Zhang; Qian Shi 006; Mingfu Shao (Nat. Comput. Sci., 2022)

On de novo Bridging Paired-end RNA-seq Data. - Xiang Li; Mingfu Shao (BCB, 2023)

On the Maximal Independent Sets of k-mers with the Edit Distance. - Leran Ma; Ke Chen 011; Mingfu Shao (BCB, 2023)

Seeding with minimized subsequence. - Xiang Li; Qian Shi 006; Ke Chen 011; Mingfu Shao (Bioinform., 2023)

On the Maximal Independent Sets of k-mers with the Edit Distance. - Leran Ma; Ke Chen 011; Mingfu Shao (CoRR, 2023)

Locality-sensitive bucketing functions for the edit distance. - Ke Chen 011; Mingfu Shao (Algorithms Mol. Biol., 2023)

Transcript assembly and annotations: Bias and adjustment. - Qimin Zhang; Mingfu Shao (PLoS Comput. Biol., 2023)

Accurate Assembly of Circular RNAs with TERRACE. - Tasfia Zahin; Qian Shi 006; Xiaofei Carl Zang; Mingfu Shao (RECOMB, 2024)

Accurate assembly of multiple RNA-seq samples with Aletsch. - Qian Shi 006; Qimin Zhang; Mingfu Shao (Bioinform., 2024)

Learning locality-sensitive bucketing functions. - Xin Yuan; Ke Chen 011; Xiang Li; Qian Shi 006; Mingfu Shao (Bioinform., 2024)

An Exact and Fast SAT Formulation for the DCJ Distance. - Aaryan M. Sarnaik; Ke Chen 011; Austin Diaz; Mingfu Shao (RECOMB, 2025)

Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. - Zhezheng Song; Tasfia Zahin; Xiang Li; Mingfu Shao (RECOMB, 2025)

Sequence Similarity Estimation by Random Subsequence Sketching. - Ke Chen 011; Vinamratha Pattar; Mingfu Shao (WABI, 2025)

Anchorage accurately assembles anchor-flanked synthetic long reads. - Xiaofei Carl Zang; Xiang Li; Kyle Metcalfe; Tuval Ben-Yehezkel; Ryan Kelley; Mingfu Shao (Algorithms Mol. Biol., 2025)