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DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

Liyuan Zhao 0 Fang Wei Jing Li 0 0 Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai , China Background: Epitope

Multi-omics profiling reveals microRNA-mediated insulin signaling networks

Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China Yang-Chi-Dung Lin, Hsi-Yuan Huang, Hsiao-Chin Hong, Jing Li & Hsien-Da Huang Warshel Institute ... for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China Yang-Chi-Dung Lin, Hsi-Yuan Huang, Hsiao-Chin Hong, Jing Li & Hsien-Da

Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks

Outstanding Young Scholars of Northwestern Polytechnical University. Author information Author notes Yuanke Zhong and Jing Li contributed equally to this work. Affiliations School of Computer Science ... Campus, Fenghe Campus, Xi’an, 710124, China Jing Li Centre of Multidisciplinary Convergence Computing, School of Computer Science, Northwestern Polytechnical University, 1 Dong Xiang Road, Xi’an, 710129

MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification

, Huazhong Agricultural University, Wuhan, 430070, China Ze Wang & Jing Li Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore Wing-Kin Sung Department of ... Scholar Ze Wang View author publications You can also search for this author in PubMed Google Scholar Jing Li View author publications You can also search for this author in PubMed Google Scholar

A novel algorithm based on bi-random walks to identify disease-related lncRNAs

Li AuthorsSearch for Jialu Hu in:PubMed • Google Scholar Search for Yiqun Gao in:PubMed • Google Scholar Search for Jing Li in:PubMed • Google Scholar Search for Yan Zheng in:PubMed • Google

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

, USAAngela H. Ting AuthorsSearch for Ke Hu in:PubMed • Google Scholar Search for Angela H. Ting in:PubMed • Google Scholar Search for Jing Li in:PubMed • Google Scholar Corresponding author Correspondence ... to Jing Li. Additional information Competing interests The authors declare that they have no competing interests. Authors’ contributions JL and AT initiated the study. KH implemented the system and

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

Background Bisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However...

A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study

in:PubMed • Google Scholar Search for William Yang in:PubMed • Google Scholar Search for Qingzhong Liu in:PubMed • Google Scholar Search for Jack Y Yang in:PubMed • Google Scholar Search for Jing Li

A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study

Background Combining information from different studies is an important and useful practice in bioinformatics, including genome-wide association study, rare variant data analysis and other set-based analyses. Many statistical methods have been proposed to combine p-values from independent studies. However, it is known that there is no uniformly most powerful test under all...

Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

Somatically-acquired translocations may serve as important markers for assessing the cause and nature of diseases like cancer. Algorithms to locate translocations may use next-generation sequencing (NGS) platform data. However, paired-end strategies do not accurately predict precise translocation breakpoints, and "split-read

Evaluation and integration of existing methods for computational prediction of allergens

in:PubMed • Google Scholar Search for Dabing Zhang in:PubMed • Google Scholar Search for Jing Li in:PubMed • Google Scholar Corresponding author Correspondence to Jing Li. Additional information

Evaluation and integration of existing methods for computational prediction of allergens

Background Allergy involves a series of complex reactions and factors that contribute to the development of the disease and triggering of the symptoms, including rhinitis, asthma, atopic eczema, skin sensitivity, even acute and fatal anaphylactic shock. Prediction and evaluation of the potential allergenicity is of importance for safety evaluation of foods and other environment...

Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

Matthew Hayes 0 Jing Li 0 0 Department of Electrical Engineering and Computer Science, Case Western Reserve University , 10900 Euclid Ave., Cleveland, OH , USA Background: Somatically-acquired

CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method

, Shanghai University, Shanghai, 200444, ChinaKai Wang, Hua Cheng, Meng Jiang, Ruili Feng, Jing Li & Tieqiao WenDepartment of Mathematics, College of Sciences, Shanghai University, Shanghai, 200444, ChinaFuyan ... • Google Scholar Search for Meng Jiang in:PubMed • Google Scholar Search for Ruili Feng in:PubMed • Google Scholar Search for Jing Li in:PubMed • Google Scholar Search for Tieqiao Wen in:PubMed • Google

CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method

Jing Li 0 Tieqiao Wen 0 0 Laboratory of Molecular Neurobiology, School of Life Sciences and Institute of Systems Biology, Shanghai University , Shanghai 200444 , China 1 Department of Mathematics

Accurate HLA type inference using a weighted similarity graph

Jing Li in:PubMed • Google Scholar Search for Tao Jiang in:PubMed • Google Scholar Corresponding authors Correspondence to Minzhu Xie or Tao Jiang. Additional information Competing interests The

Enabling proteomics-based identification of human cancer variations

Medicine, Nashville, TN, 37232, USADavid L Tabb & Daniel C Liebler AuthorsSearch for Jing Li in:PubMed • Google Scholar Search for Zeqiang Ma in:PubMed • Google Scholar Search for Robbert JC Slebos

A novel approach for haplotype-based association analysis using family data

?issue=S1. Author information AffiliationsElectrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, 44106, USAYixuan Chen, Xin Li & Jing Li AuthorsSearch ... for Yixuan Chen in:PubMed • Google Scholar Search for Xin Li in:PubMed • Google Scholar Search for Jing Li in:PubMed • Google Scholar Corresponding author Correspondence to Jing Li. Additional

Accurate HLA type inference using a weighted similarity graph

Background The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transplantations. Numerous studies have demonstrated that variation in HLA genes is associated with many autoimmune, inflammatory and infectious diseases. However...