Daming Zhu

ORCID

Publication Activity (10 Years)

Years Active: 1994-2023
Publications (10 Years): 70

Top Venues

BIBM

Theor. Comput. Sci.

IEEE ACM Trans. Comput. Biol. Bioinform.

FAW

Publications

Xin Tong, Yixiao Yu, Ziyi Fang, Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu
Men Can't Always be Transformed into Mice: Decision Algorithms and Complexity for Sorting by Symmetric Reversals. CoRR (2023)
Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui
ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Chengcheng Sun, Haitao Jiang, Daming Zhu
Improved Approximation Algorithms for Sorting Unsigned Genomes by Reversals. BIBM (2023)
Huixiu Xu, Xin Tong, Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu
On Sorting by Flanked Transpositions. ISBRA (2023)
Yuyang Wang, Haitao Jiang, Haodi Feng, Daming Zhu
Minimize Maximum Coverage of Fragment Alignment Selection. BIBM (2023)
Shu Zhang, Qichen Wang, Daming Zhu, Haitao Jiang
Longest Order Conserved Repetition-free Subsequences. BIBM (2023)
Yanmin Liu, Xuan Zhang, Wei Zhao, Daming Zhu, Xuefeng Cui
De Novo Molecular Structure Generation from Mass Spectra. BIBM (2023)
Xin Tong, Yixiao Yu, Ziyi Fang, Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu
Cabbage Can't Always Be Transformed into Turnip: Decision Algorithms for Sorting by Symmetric Reversals. COCOON (2) (2023)
Jingjing Ma, Haitao Jiang, Daming Zhu, Runmin Yang
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Zhendong Liu, Dongyan Li, Xi Chen, Xinrong Lv, Daming Zhu, Xiaofeng Li
Predicting Algorithm of Transcription Factor Binding Sites Based on Weighted Multi-Grained Scanning. BIBM (2022)
Zhendong Liu, Xi Chen, Dongyan Li, Xinrong Lv, Daming Zhu, Xiaofeng Li
Prediction Algorithm of DNA Sites Based on Weighted Feature Matrix. BIBM (2022)
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
mzMD: visualization-oriented MS data storage and retrieval. Bioinform. 38 (8) (2022)
Shengjun Xie, Haodi Feng, Haitao Jiang, Daming Zhu
Approximation algorithms for sorting by bounded singleton moves. Theor. Comput. Sci. 917 (2022)
Tiantian Li, Daming Zhu, Haitao Jiang, Haodi Feng, Xuefeng Cui
Longest k-tuple Common Sub-Strings. BIBM (2022)
Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Yu Zhang, Chenchen Li, Haodi Feng, Daming Zhu
DLmeta: a deep learning method for metagenomic identification. BIBM (2022)
Jinsheng Shang, Qihong Jiao, Cheng Chen, Daming Zhu, Xuefeng Cui
Pretraining Transformers for TCR-pMHC Binding Prediction. BIBM (2022)
Yongfa Li, Xiaoqing Zuo, Daming Zhu, Wenhao Wu, Xu Yang, Shipeng Guo, Chao Shi, Cheng Huang, Fang Li, Xinyu Liu
Identification and Analysis of Landslides in the Ahai Reservoir Area of the Jinsha River Basin Using a Combination of DS-InSAR, Optical Images, and Field Surveys. Remote. Sens. 14 (24) (2022)
Jingjing Ma, Daming Zhu, Haitao Jiang, Binhai Zhu
On the solution bound of two-sided scaffold filling. Theor. Comput. Sci. 873 (2021)
Chenchen Li, Jin Zhao, Haodi Feng, Daming Zhu
TransCoord: Genome-guided Transcripts Assembly by Coordinating Candidate Paths into Two-phased Linear Programming. BIBM (2021)
Xingfu Li, Daming Zhu, Lusheng Wang
A 43-approximation algorithm for the Maximum Internal Spanning Tree Problem. J. Comput. Syst. Sci. 118 (2021)
Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu
SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data. J. Comput. Biol. 28 (8) (2021)
Shu Zhang, Daming Zhu, Haitao Jiang, Jiong Guo, Haodi Feng, Xiaowen Liu
Sorting a Permutation by Best Short Swaps. Algorithmica 83 (7) (2021)
Zongzhao Qiu, Qihong Jiao, Yuxiao Wang, Cheng Chen, Daming Zhu, Xuefeng Cui
rzMLP-DTA: gMLP network with ReZero for sequence-based drug-target affinity prediction. BIBM (2021)
Anhong Tian, Junsan Zhao, Bo-Hui Tang, Daming Zhu, Chengbiao Fu, Heigang Xiong
Study on the Pretreatment of Soil Hyperspectral and Na+ Ion Data under Different Degrees of Human Activity Stress by Fractional-Order Derivatives. Remote. Sens. 13 (19) (2021)
Peiyan Zhou, Haitao Jiang, Daming Zhu, Binhai Zhu
Approximation algorithms for the maximum vertex coverage problem on bounded degree graphs. Theor. Comput. Sci. 888 (2021)
Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui
Hydrogen bonds meet self-attention: all you need for protein structure embedding. BIBM (2021)
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
mzMD: A New Storage and Retrieval System for Mass Spectrometry Data. ICIC (3) (2021)
Anhong Tian, Junsan Zhao, Bo-Hui Tang, Daming Zhu, Chengbiao Fu, Heigang Xiong
Hyperspectral Prediction of Soil Total Salt Content by Different Disturbance Degree under a Fractional-Order Differential Model with Differing Spectral Transformations. Remote. Sens. 13 (21) (2021)
Chengbiao Fu, Anhong Tian, Daming Zhu, Junsan Zhao, Heigang Xiong
Estimation of Salinity Content in Different Saline-Alkali Zones Based on Machine Learning Model Using FOD Pretreatment Method. Remote. Sens. 13 (24) (2021)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads". IEEE ACM Trans. Comput. Biol. Bioinform. 17 (6) (2020)
Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu
SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data. ISBRA (2020)
Lianrong Pu, Daming Zhu, Haitao Jiang
A 1.375-approximation algorithm for unsigned translocation sorting. J. Comput. Syst. Sci. 113 (2020)
Hai Yang, Daming Zhu
Improved detection algorithm for copy number variations based on hidden Markov model. Multim. Tools Appl. 79 (13-14) (2020)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Lixin Liu, Haitao Jiang, Peiqiang Liu, Binhai Zhu, Daming Zhu
Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear Linear Programming-Rounding. J. Comput. Biol. 27 (2) (2020)
Huiqiang Jia, Haichao Wei, Daming Zhu, Jingjing Ma, Hai Yang, Ruizhi Wang, Xianzhong Feng
PASA: Identifying More Credible Structural Variants of Hedou12. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (5) (2020)
Hai Yang, Daming Zhu
Combinatorial Detection Algorithm for Copy Number Variations Using High-throughput Sequencing Reads. Int. J. Pattern Recognit. Artif. Intell. 33 (14) (2019)
Lixin Liu, Haitao Jiang, Peiqiang Liu, Binhai Zhu, Daming Zhu
Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear LP-Rounding. ISBRA (2019)
Shengjun Xie, Haodi Feng, Haitao Jiang, Junfeng Luan, Daming Zhu
An Approximation Algorithm for Sorting by Bounded Singleton Moves. COCOON (2019)
Zhendong Liu, Daming Zhu, Qionghai Dai
Improved predicting algorithm of RNA pseudoknotted structure. Int. J. Comput. Sci. Eng. 19 (1) (2019)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees. BMC Bioinform. (25) (2019)
Shanshan Zhai, Peng Zhang, Daming Zhu, Weitian Tong, Yao Xu, Guohui Lin
An approximation algorithm for genome sorting by reversals to recover all adjacencies. J. Comb. Optim. 37 (4) (2019)
Haitao Jiang, Jiong Guo, Daming Zhu, Binhai Zhu
A 2-Approximation Algorithm for the Complementary Maximal Strip Recovery Problem. CPM (2019)
Huiqiang Jia, Haichao Wei, Daming Zhu, Ruizhi Wang, Haodi Feng, Xiangzhong Feng
PASA: Identifying More Credible Structural Variants of Hedou12. ICIC (1) (2018)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees. ICIC (1) (2018)
Lianrong Pu, Yu Lin, Daming Zhu, Haitao Jiang
Can a breakpoint graph be decomposed into none other than 2-cycles? Theor. Comput. Sci. 734 (2018)
Hai Yang, Daming Zhu, Huiqiang Jia
Improved Indel Detection Algorithm Based on Split-Read and Read-Depth. ICIC (3) (2018)
Zhendong Liu, Daming Zhu, Qionghai Dai
Predicting Model and Algorithm in RNA Folding Structure Including Pseudoknots. Int. J. Pattern Recognit. Artif. Intell. 32 (10) (2018)
Shu Zhang, Daming Zhu, Haitao Jiang, Jingjing Ma, Jiong Guo, Haodi Feng
Can a permutation be sorted by best short swaps?. CPM (2018)
Shu Zhang, Ruizhi Wang, Daming Zhu, Haitao Jiang, Haodi Feng, Jiong Guo, Xiaowen Liu
The Longest Common Exemplar Subsequence Problem. BIBM (2018)
Daming Zhu, Sergey Bereg
Preface. Theor. Comput. Sci. 734 (2018)
Haitao Jiang, Letu Qingge, Daming Zhu, Binhai Zhu
A 2-approximation algorithm for the contig-based genomic scaffold filling problem. J. Bioinform. Comput. Biol. 16 (6) (2018)
Jingjing Ma, Haitao Jiang, Daming Zhu, Shu Zhang
A 1.4-Approximation Algorithm for Two-Sided Scaffold Filling. FAW (2017)
Runmin Yang, Daming Zhu, Qiang Kou, Poornima Bhat-Nakshatri, Harikrishna Nakshatri, Si Wu, Xiaowen Liu
A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry. BIBM (2017)
Aiyong Xian, Kaiyuan Zhu, Daming Zhu, Lianrong Pu, Hong Liu
Approximating Max NAE-k-SAT by anonymous local search. Theor. Comput. Sci. 657 (2017)
Aizhong Zhou, Haitao Jiang, Jiong Guo, Daming Zhu
A New Approximation Algorithm for the Maximum Stacking Base Pairs Problem from RNA Secondary Structures Prediction. COCOA (1) (2017)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads - (Extended Abstract). ISBRA (2017)
Jie Cheng, Daming Zhu, Binhai Zhu
Improved algorithms for intermediate dataset storage in a cloud-based dataflow. Theor. Comput. Sci. 657 (2017)
Nan Liu, Daming Zhu, Haitao Jiang, Binhai Zhu
A 1.5-Approximation Algorithm for Two-Sided Scaffold Filling. Algorithmica 74 (1) (2016)
Lianrong Pu, Daming Zhu, Haitao Jiang
A New Approximation Algorithm for Unsigned Translocation Sorting. WABI (2016)
Huiqiang Jia, Haicho Wei, Daming Zhu, Jingjing Ma, Hai Yang, Ruizhi Wang, Xianzhong Feng
Mining structural variants of Heduo12 using paired-end reads. BIBM (2016)
Haitao Jiang, Chenglin Fan, Boting Yang, Farong Zhong, Daming Zhu, Binhai Zhu
Genomic Scaffold Filling Revisited. CPM (2016)
Zhexue Wei, Daming Zhu, Lusheng Wang
A Dynamic Programming Algorithm For (1, 2)-Exemplar Breakpoint Distance. J. Comput. Biol. 22 (7) (2015)
Haitao Jiang, Jingjing Ma, Junfeng Luan, Daming Zhu
Approximation and Nonapproximability for the One-Sided Scaffold Filling Problem. COCOON (2015)
Aiyong Xian, Kaiyuan Zhu, Daming Zhu, Lianrong Pu
Local Search to Approximate Max NAE- k k -Sat Tightly. FAW (2015)
Zhendong Liu, Daming Zhu, Qionghai Dai
Predicting Algorithm of RNA Folding Structure with Pseudoknots. CIS (2015)
Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu
A factor-(1.408 + ε) approximation for sorting unsigned genomes by reciprocal translocations. Theor. Comput. Sci. 607 (2015)
Jie Cheng, Daming Zhu, Binhai Zhu
A New Algorithm for Intermediate Dataset Storage in a Cloud-Based Dataflow. FAW (2015)
Haitao Jiang, Guohui Lin, Weitian Tong, Daming Zhu, Binhai Zhu
Isomorphism and similarity for 2-generation pedigrees. BMC Bioinform. 16 (S-5) (2015)
Haitao Jiang, Haodi Feng, Daming Zhu
An 5/4-Approximation Algorithm for Sorting Permutations by Short Block Moves. ISAAC (2014)
Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu
A (1.408+ε)-Approximation Algorithm for Sorting Unsigned Genomes by Reciprocal Translocations. FAW (2014)
Zhexue Wei, Daming Zhu, Lusheng Wang
A parameterized algorithm for (1, 2)-exemplar breakpoint distance. BIBM (2014)
Xingfu Li, Daming Zhu
Approximating the Maximum Internal Spanning Tree Problem via a Maximum Path-Cycle Cover. ISAAC (2014)
Zhendong Liu, Daming Zhu, Hongwei Ma
Predicting scheme of RNA folding structure including pseudoknots. Int. J. Sens. Networks 16 (4) (2014)
Xingfu Li, Daming Zhu
A 4/3-approximation algorithm for finding a spanning tree to maximize its internal vertices. CoRR (2014)
Daming Zhu, Lusheng Wang
An Exact Algorithm for the Zero Exemplar Breakpoint Distance Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (6) (2013)
Meixia Qu, Ke Chen, Daming Zhu, Junfeng Luan
Implementing program extraction from CL1-proofs. CoRR (2013)
Nan Liu, Haitao Jiang, Daming Zhu, Binhai Zhu
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies. COCOON (2013)
Hong Liu, Daming Zhu
Parameterized complexity of control by voter selection in Maximin, Copeland, Borda, Bucklin, and Approval election systems. Theor. Comput. Sci. 498 (2013)
Zhendong Liu, Daming Zhu
New Heuristic Algorithm of RNA Structure Prediction Including Pseudoknots. J. Comput. 8 (2) (2013)
Zhendong Liu, Daming Zhu, Wei Cui, Nan Liu
An Approximation Scheme for RNA Folding Structure Prediction Including Pseudoknots. CIS (2013)
Nan Liu, Daming Zhu
The Algorithm for the Two-Sided Scaffold Filling Problem. TAMC (2013)
Hui Wang, Daming Zhu
The Duplication-Loss Problem: Novel Algorithms Based on k-NNI Local Search. BIFE (2013)
Zhexue Wei, Daming Zhu
A Dynamic Programming Algorithm for Unsigned (1, 2)-Exemplar Breakpoint Distance Problem with Span Constraint. BIFE (2013)
Xiao Yin, Daming Zhu
Sorting genomes by generalized translocations. Theor. Comput. Sci. 491 (2013)
Nan Liu, Haitao Jiang, Daming Zhu, Binhai Zhu
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Peng Zhang, Wenbo Zhao, Daming Zhu
Complexity and Approximation Results for the Min-Sum and Min-Max Disjoint Paths Problems. Comput. Informatics 32 (1) (2013)
Zhexue Wei, Daming Zhu
De Novo Peptide Sequencing Based on Vertex Contraction Algorithm. CSO (2012)
Meixia Qu, Junfeng Luan, Daming Zhu
On the toggling-branching recurrence of Computability Logic CoRR (2012)
Fei Guo, Shuai Cheng Li, Lusheng Wang, Daming Zhu
Protein-protein binding site identification by enumerating the configurations. BMC Bioinform. 13 (2012)
Haitao Jiang, Binhai Zhu, Daming Zhu, Hong Zhu
Minimum common string partition revisited. J. Comb. Optim. 23 (4) (2012)
Hong Liu, Peng Zhang, Daming Zhu
On Editing Graphs into 2-Club Clusters. FAW-AAIM (2012)
Haitao Jiang, Daming Zhu, Binhai Zhu
A (1+ε)-approximation algorithm for sorting by short block-moves. Theor. Comput. Sci. 439 (2012)
Peng Zhang, Daming Zhu, Junfeng Luan
An approximation algorithm for the Generalized k-Multicut problem. Discret. Appl. Math. 160 (7-8) (2012)
Xiaowen Lou, Daming Zhu
A new approximation algorithm for cut-and-paste sorting of unsigned circular permutations. J. Comput. Syst. Sci. 78 (4) (2012)
Haitao Jiang, Binhai Zhu, Daming Zhu
Algorithms for sorting unsigned linear genomes by the DCJ operations. Bioinform. 27 (3) (2011)
Daming Zhu, Shaohan Ma, Pingping Zhang
Tight Bounds on Local Search to Approximate the Maximum Satisfiability Problems. COCOON (2011)
Haitao Jiang, Daming Zhu
A 14/11-approximation algorithm for sorting by short block-moves. Sci. China Inf. Sci. 54 (2) (2011)
Ming Li, Ali Miri, Daming Zhu
Analysis of the Hamming Weight of the Extended wmbNAF. IACR Cryptol. ePrint Arch. 2011 (2011)

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Publication Activity (10 Years)

Top Topics

Top Venues

Daming Zhu