The Identification of Antisense Gene Pairs Through Available Software. - Mark J. Lawson; Liqing Zhang 002 (ISBRA, 2007)

Note on the Computation of Critical Effective Population Sizes. - Liqing Zhang 002; Layne T. Watson (J. Comput. Biol., 2007)

A Framework to Understand the Mechanism of Toxicity. - Wenhui Huang; Liqing Zhang 002 (ICIC (2), 2008)

Using Cost-Sensitive Learning to Determine Gene Conversions. - Mark J. Lawson; Lenwood S. Heath; Naren Ramakrishnan; Liqing Zhang 002 (ICIC (2), 2008)

A Holistic View of Evolutionary Rates in Paralogous and Orthologous Genes. - Deng Pan; Liqing Zhang 002 (ICIC (2), 2008)

Identifying disease associations via genome-wide association studies. - Wenhui Huang; Pengyuan Wang 005; Zhen Liu; Liqing Zhang 002 (BMC Bioinform., 2009)

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors. - Ashwin M. Aji; Liqing Zhang 002; Wu-chun Feng (CSE, 2010)

The Expected Fitness Cost of a Mutation Fixation under the One-Dimensional Fisher Model. - Liqing Zhang 002; Layne T. Watson (ISBRA, 2010)

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. - Guanqun Shi; Liqing Zhang 002; Tao Jiang 001 (BMC Bioinform., 2010)

A new functional association-based protein complex prediction. - Mingming Liu 006; Yanwei Huang; Liqing Zhang 002; David R. Bevan (BIBM Workshops, 2011)

A Network of SCOP Hidden Markov Models and Its Analysis. - Liqing Zhang 002; Layne T. Watson; Lenwood S. Heath (BMC Bioinform., 2011)

Status of Research on Insertion and Deletion Variations in the Human Population. - Liqing Zhang 002; Mingming Liu 006; Layne T. Watson (Models and Algorithms for Genome Evolution, 2013)

Improving bisulfite short-read mapping efficiency with hairpin-bisulfite data. - Jacob Porter; Ming-an Sun; Hehuang Xie; Liqing Zhang 002 (ICCABS, 2014)

Classification of Mutations by Functional Impact Type: Gain of Function, Loss of Function, and Switch of Function. - Mingming Liu 006; Layne T. Watson; Liqing Zhang 002 (ISBRA, 2014)

Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools. - Hong Tran; Jacob Porter; Ming-an Sun; Hehuang Xie; Liqing Zhang 002 (Adv. Bioinformatics, 2014)

Vindel: a simple pipeline for checking indel redundancy. - Zhiyi Li; Xiaowei Wu 003; Bin He; Liqing Zhang 002 (BMC Bioinform., 2014)

Quantitative prediction of the effect of genetic variation using hidden Markov models. - Mingming Liu 006; Layne T. Watson; Liqing Zhang 002 (BMC Bioinform., 2014)

PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. - Wei Chen 064; Xitong Zhang; Jordan Brooker; Hao Lin 001; Liqing Zhang 002; Kuo-Chen Chou (Bioinform., 2015)

HMMvar-func: a new method for predicting the functional outcome of genetic variants. - Mingming Liu 006; Layne T. Watson; Liqing Zhang 002 (BMC Bioinform., 2015)

Poster: Diagnosing and treating code-duplication problems in bioinformatics libraries. - Mohammad Shabbir Hasan; Saima Sultana Tithi; Eli Tilevich; Liqing Zhang 002 (ICCABS, 2016)

UPS-indel: A better approach for finding indel redundancy. - Mohammad Shabbir Hasan; Xiaowei Wu 003; Layne T. Watson; Zhiyi Li; Liqing Zhang 002 (ICCABS, 2016)

Analysis of whole genome sequence and genome-wide SNPs in highly inbred pigs. - Jinlong Huo; Wenmin Chen; Xiaowei Wu 003; Kuan Yang; Weirong Pan; Liqing Zhang 002; Yangzhi Zeng (ICCABS, 2017)

InfoTrim: A DNA read quality trimmer using entropy. - Jacob Porter; Liqing Zhang 002 (ICCABS, 2017)

Leaf image based cucumber disease recognition using sparse representation classification. - Shanwen Zhang; Xiaowei Wu 003; Zhuhong You; Liqing Zhang 002 (Comput. Electron. Agric., 2017)

Combining weighted adaptive CS-LBP and local linear discriminant projection for gait recognition. - Shanwen Zhang; Liqing Zhang 002 (Multim. Tools Appl., 2018)

A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples. - Gustavo A. Arango-Argoty; Lenwood S. Heath; Amy Pruden; Peter J. Vikesland; Liqing Zhang 002 (ICCABS, 2020)

ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. - Gustavo A. Arango-Argoty; G. K. P. Guron; Emily Garner; M. V. Riquelme; Lenwood S. Heath; Amy Pruden; Peter J. Vikesland; Liqing Zhang 002 (Bioinform., 2020)

Towards a Serverless Bioinformatics Cyberinfrastructure Pipeline. - Shunyu David Yao; Muhammad Ali Gulzar; Liqing Zhang 002; Ali Raza Butt (HiPS@HPDC, 2021)

AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. - Xiao Liang; Kyle Akers; Ishi Keenum; Lauren Wind; Suraj Gupta; Chaoqi Chen; Reem Aldaihani; Amy Pruden; Liqing Zhang 002; Katharine F. Knowlton; Kang Xia; Lenwood S. Heath (BMC Bioinform., 2021)

MetaMLP: A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples. - Gustavo A. Arango-Argoty; Lenwood S. Heath; Amy Pruden; Peter J. Vikesland; Liqing Zhang 002 (J. Comput. Biol., 2021)

LM-ARG: Identification & classification of antibiotic resistance genes leveraging pre-trained protein language models. - Shafayat Ahmed; Muhit Islam Emon; Nazifa Ahmed Moumi; Liqing Zhang 002 (BIBM, 2022)

Protein-Protein Interaction Network Analysis Reveals Distinct Patterns of Antibiotic Resistance Genes. - Nazifa Ahmed Moumi; Connor L. Brown; Peter J. Vikesland; Amy Pruden; Liqing Zhang 002 (BIBM, 2022)

Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models. - Sidhant Chandak; Liqing Zhang 002; Connor L. Brown; Lifu Huang (BioNLP@ACL, 2022)

FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data. - Saima Sultana Tithi; Frank O. Aylward; Roderick V. Jensen; Liqing Zhang 002 (J. Comput. Biol., 2023)

DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation. - Joung Min Choi; Ming Ji; Layne T. Watson; Liqing Zhang 002 (Bioinform., 2023)

DeePSP-GIN: identification and classification of phage structural proteins using predicted protein structure, pretrained protein language model, and graph isomorphism network. - Muhit Islam Emon; Badhan Das; Ashrith Reddy Thukkaraju; Liqing Zhang 002 (BCB, 2024)

Mastering Long-Tail Complexity on Graphs: Characterization, Learning, and Generalization. - Haohui Wang; Baoyu Jing; Kaize Ding; Yada Zhu; Wei Cheng 002; Si Zhang; Yonghui Fan; Liqing Zhang 002; Dawei Zhou 003 (KDD, 2024)