Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding. - Sing-Hoi Sze; Songjian Lu; Jianer Chen (WABI, 2004)

Greedy Localization and Color-Coding: Improved Matching and Packing Algorithms. - Yang Liu 002; Songjian Lu; Jianer Chen; Sing-Hoi Sze (IWPEC, 2006)

Improved Algorithms for Weighted and Unweighted Set Splitting Problems. - Jianer Chen; Songjian Lu (COCOON, 2007)

Directed Feedback Vertex Set Problem is FPT. - Jianer Chen; Yang Liu 002; Songjian Lu (Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs, 2007)

Improved algorithms for path, matching, and packing problems. - Jianer Chen; Songjian Lu; Sing-Hoi Sze; Fenghui Zhang (SODA, 2007)

Finding Pathway Structures in Protein Interaction Networks. - Songjian Lu; Fenghui Zhang; Jianer Chen; Sing-Hoi Sze (Algorithmica, 2007)

A fixed-parameter algorithm for the directed feedback vertex set problem. - Jianer Chen; Yang Liu 002; Songjian Lu; Barry O'Sullivan; Igor Razgon (J. ACM, 2008)

Improved algorithms for feedback vertex set problems. - Jianer Chen; Fedor V. Fomin; Yang Liu 002; Songjian Lu; Yngve Villanger (J. Comput. Syst. Sci., 2008)

Improved Deterministic Algorithms for Weighted Matching and Packing Problems. - Qilong Feng; Yang Liu 002; Songjian Lu; Jianxin Wang 001 (TAMC, 2009)

Improved Parameterized Set Splitting Algorithms: A Probabilistic Approach. - Jianer Chen; Songjian Lu (Algorithmica, 2009)

An Improved Parameterized Algorithm for the Minimum Node Multiway Cut Problem. - Jianer Chen; Yang Liu 002; Songjian Lu (Algorithmica, 2009)

A graph model and an exact algorithm for finding transcription factor modules. - Songjian Lu; Xinghua Lu 001 (BCB, 2011)

Improved deterministic algorithms for weighted matching and packing problems. - Jianer Chen; Qilong Feng; Yang Liu 002; Songjian Lu; Jianxin Wang 001 (Theor. Comput. Sci., 2011)

Iterative Expansion and Color Coding: An Improved Algorithm for 3D-Matching. - Jianer Chen; Yang Liu 002; Songjian Lu; Sing-Hoi Sze; Fenghui Zhang (ACM Trans. Algorithms, 2012)

Using graph model to find transcription factor modules: the hitting set problem and an exact algorithm. - Songjian Lu; Xinghua Lu 001 (Algorithms Mol. Biol., 2013)

An exact algorithm with the time complexity of $O^*(1.299^m)$ for the weighed mutually exclusive set cover problem - Songjian Lu; Xinghua Lu 001 (CoRR, 2013)

An exact algorithm for the weighed mutually exclusive maximum set cover problem. - Songjian Lu; Xinghua Lu 001 (CoRR, 2014)

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. - Songjian Lu; Kevin N. Lu; Shi-Yuan Cheng; Bo Hu; Xiaojun Ma; Nicholas Nystrom; Xinghua Lu 001 (PLoS Comput. Biol., 2015)

An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. - Songjian Lu; Gunasheil Mandava; Gaibo Yan; Xinghua Lu 001 (Algorithms Mol. Biol., 2016)

Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. - Xiao-Nan Fan 001; Shao-Wu Zhang 001; Song-Yao Zhang; Kunju Zhu; Songjian Lu (BMC Bioinform., 2019)

Integrating data and knowledge to identify functional modules of genes: a multilayer approach. - Lifan Liang; Vicky Chen; Kunju Zhu; Xiaonan Fan 001; Xinghua Lu 001; Songjian Lu (BMC Bioinform., 2019)

Noisy and Incomplete Boolean Matrix Factorizationvia Expectation Maximization. - Lifan Liang; Songjian Lu (CoRR, 2019)

Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. - Chunhui Cai; Gregory F. Cooper; Kevin N. Lu; Xiaojun Ma; Shuping Xu; Zhenlong Zhao; Xueer Chen; Yifan Xue; Adrian V. Lee; Nathan Clark; Vicky Chen; Songjian Lu; et al. (PLoS Comput. Biol., 2019)

BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization. - Lifan Liang; Kunju Zhu; Songjian Lu (Bioinform., 2020)

ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. - Lifan Liang; Kunju Zhu; Junyan Tao; Songjian Lu (PLoS Comput. Biol., 2021)