1
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Liu L, Jia R, Hou R, Huang C. Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state. Methods 2024; 226:151-160. [PMID: 38670416 DOI: 10.1016/j.ymeth.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Chromatin loop is of crucial importance for the regulation of gene transcription. Cohesin is a type of chromatin-associated protein that mediates the interaction of chromatin through the loop extrusion. Cohesin-mediated chromatin interactions have strong cell-type specificity, posing a challenge for predicting chromatin loops. Existing computational methods perform poorly in predicting cell-type-specific chromatin loops. To address this issue, we propose a random forest model to predict cell-type-specific cohesin-mediated chromatin loops based on chromatin states identified by ChromHMM and the occupancy of related factors. Our results show that chromatin state is responsible for cell-type-specificity of loops. Using only chromatin states as features, the model achieved high accuracy in predicting cell-type-specific loops between two cell types and can be applied to different cell types. Furthermore, when chromatin states are combined with the occurrence frequency of CTCF, RAD21, YY1, and H3K27ac ChIP-seq peaks, more accurate prediction can be achieved. Our feature extraction method provides novel insights into predicting cell-type-specific chromatin loops and reveals the relationship between chromatin state and chromatin loop formation.
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Affiliation(s)
- Li Liu
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China.
| | - Ranran Jia
- Key Laboratory of Data Science and Intelligence Education, Hainan Normal University, Ministry of Education, Haikou 571158, China.
| | - Rui Hou
- College of Data Science and Application, Inner Mongolia University of Technology, Hohhot 010051, China.
| | - Chengbing Huang
- School of Computer Science and Technology, Aba Teachers University, Aba 623002, China.
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2
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Jiang J, Pei H, Li J, Li M, Zou Q, Lv Z. FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization. Brief Bioinform 2024; 25:bbae037. [PMID: 38366802 PMCID: PMC10939380 DOI: 10.1093/bib/bbae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/27/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024] Open
Abstract
Anti-coronavirus peptides (ACVPs) represent a relatively novel approach of inhibiting the adsorption and fusion of the virus with human cells. Several peptide-based inhibitors showed promise as potential therapeutic drug candidates. However, identifying such peptides in laboratory experiments is both costly and time consuming. Therefore, there is growing interest in using computational methods to predict ACVPs. Here, we describe a model for the prediction of ACVPs that is based on the combination of feature engineering (FE) optimization and deep representation learning. FEOpti-ACVP was pre-trained using two feature extraction frameworks. At the next step, several machine learning approaches were tested in to construct the final algorithm. The final version of FEOpti-ACVP outperformed existing methods used for ACVPs prediction and it has the potential to become a valuable tool in ACVP drug design. A user-friendly webserver of FEOpti-ACVP can be accessed at http://servers.aibiochem.net/soft/FEOpti-ACVP/.
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Affiliation(s)
- Jici Jiang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Hongdi Pei
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Jiayu Li
- College of Life Science, Sichuan University, Chengdu 610065, China
| | - Mingxin Li
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Zhibin Lv
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
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3
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Guo X, Guo Y, Chen H, Liu X, He P, Li W, Zhang MQ, Dai Q. Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection. Comput Biol Med 2023; 166:107550. [PMID: 37826950 DOI: 10.1016/j.compbiomed.2023.107550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Genomic islands are fragments of foreign DNA that are found in bacterial and archaeal genomes, and are typically associated with symbiosis or pathogenesis. While numerous genomic island detection methods have been proposed, there has been limited evaluation of the efficiency of the genome information processing and boundary recognition tools. In this study, we conducted a review of the statistical methods involved in genomic signatures, host signature extraction, informative signature selection, divergence measures, and boundary detection steps in genomic island prediction. We compared the performances of these methods on simulated experiments using alien fragments obtained from both artificial and real genomes. Our results indicate that among the nine genomic signatures evaluated, genomic signature frequency and full probability performed the best. However, their performance declined when normalized to their expectations and variances, such as Z-score and composition vector. Based on our experiments of the E. coli genome, we found that the confidence intervals of the window variances achieved the best performance in the signature extraction of the host, with the best confidence interval being 1.5-2 times the standard error. Ordered kurtosis was most effective in selecting informative signatures from a single genome, without requiring prior knowledge from other datasets. Among the three divergence measures evaluated, the two-sample t-test was the most successful, and a non-overlapping window with a small eye window (size 2) was best suited for identifying compositionally distinct regions. Finally, the maximum of the Markovian Jensen-Shannon divergence score, in terms of GC-content bias, was found to make boundary detection faster while maintaining a similar error rate.
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Affiliation(s)
- Xiangting Guo
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yichu Guo
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Hu Chen
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaoqing Liu
- College of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Pingan He
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Wenshu Li
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Michael Q Zhang
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA; Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, 100084, China
| | - Qi Dai
- Zhejiang Sci-Tech University, Hangzhou, 310018, China; Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA.
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4
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Wan H, Zhang Y, Huang S. Prediction of thermophilic protein using 2-D general series correlation pseudo amino acid features. Methods 2023; 218:141-148. [PMID: 37604248 DOI: 10.1016/j.ymeth.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/08/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023] Open
Abstract
The demand for thermophilic protein has been increasing in protein engineering recently. Many machine-learning methods for identifying thermophilic proteins have emerged during this period. However, most machine learning-based thermophilic protein identification studies have only focused on accuracy. The relationship between the features' meaning and the proteins' physicochemical properties has yet to be studied in depth. In this article, we focused on the relationship between the features and the thermal stability of thermophilic proteins. This method used 2-D general series correlation pseudo amino acid (SC-PseAAC-General) features and realized accuracy of 82.76% using the J48 classifier. In addition, this research found the presence of higher frequencies of glutamic acid in thermophilic proteins, which help thermophilic proteins maintain their thermal stability by forming hydrogen bonds and salt bridges that prevent denaturation at high temperatures.
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Affiliation(s)
- Hao Wan
- College of Life Science, Qingdao University, Qingdao 266071, China.
| | - Yanan Zhang
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Shibo Huang
- Beidahuang Industry Group General Hospital, Harbin 150001, China
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5
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Fan R, Ding Y, Zou Q, Yuan L. Multi-view local hyperplane nearest neighbor model based on independence criterion for identifying vesicular transport proteins. Int J Biol Macromol 2023; 247:125774. [PMID: 37437677 DOI: 10.1016/j.ijbiomac.2023.125774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Vesicular transport proteins participate in various biological processes and play a significant role in the movement of substances within cells. These proteins are associated with numerous human diseases, making their identification particularly important. In this study, we developed a novel strategy for accurately identifying vesicular transport proteins. We developed a novel multi-view classifier called graph-regularized k-local hyperplane distance nearest neighbor model (HSIC-GHKNN), which combines the Hilbert-Schmidt independence criterion (HSIC)-based multi-view learning method with a local hyperplane distance nearest-neighbor classifier. We first extracted protein evolution information using two feature extraction methods, pseudo-position-specific scoring matrix (PsePSSM) and AATP, and addressed dataset imbalance using the Edited Nearest Neighbors (ENN) algorithm. Subsequently, we employed a local hyperplane distance nearest-neighbor classifier for each view identification and added an HSIC term to maintain independence between views. We then assessed the performance of our identification strategy and analyzed the PsePSSM and AATP feature sets to determine the influencing factors of the classification results. The experimental results demonstrate that the accurate and Matthew correlation coefficients of our strategy on the independent test set are 85.8 % and 0.548, respectively. Our approach outperformed existing methods in most evaluation metrics. In addition, the proposed multi-view classification model can easily be applied to similar identification tasks.
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Affiliation(s)
- Rui Fan
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324000, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324000, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324000, China.
| | - Lei Yuan
- Department of Hepatobiliary Surgery, Quzhou People's Hospital, Quzhou, Zhejiang 324000, China.
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6
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Meng C, Pei Y, Zou Q, Yuan L. DP-AOP: A novel SVM-based antioxidant proteins identifier. Int J Biol Macromol 2023; 247:125499. [PMID: 37414318 DOI: 10.1016/j.ijbiomac.2023.125499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
The identification of antioxidant proteins is a challenging yet meaningful task, as they can protect against the damage caused by some free radicals. In addition to time-consuming, laborious, and expensive experimental identification methods, efficient identification of antioxidant proteins through machine learning algorithms has become increasingly common. In recent years, researchers have proposed models for identifying antioxidant proteins; unfortunately, although the accuracy of models is already high, their sensitivity is too low, indicating the possibility of overfitting in the model. Therefore, we developed a new model called DP-AOP for the recognition of antioxidant proteins. We used the SMOTE algorithm to balance the dataset, selected Wei's proposed feature extraction algorithm to obtain 473 dimensional feature vectors, and based on the sorting function in MRMD, scored and ranked each feature to obtain a feature set with contribution values ranging from high to low. To effectively reduce the feature dimension, we combined the dynamic programming idea to make the local eight features the optimal subset. After obtaining the 36 dimensional feature vectors, we finally selected 17 features through experimental analysis. The SVM classification algorithm was used to implement the model through the libsvm tool. The model achieved satisfactory performance, with an accuracy rate of 91.076 %, SN of 96.4 %, SP of 85.8 %, MCC of 82.6 %, and F1 core of 91.5 %. Furthermore, we built a free web server to facilitate researchers' subsequent unfolding studies of antioxidant protein recognition. The website is http://112.124.26.17:8003/#/.
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Affiliation(s)
- Chaolu Meng
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, China.
| | - Yue Pei
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, China.
| | - Lei Yuan
- Department of Hepatobiliary Surgery, Quzhou People's Hospital, China.
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7
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Deng Y, Ma S, Li J, Zheng B, Lv Z. Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides. Int J Mol Sci 2023; 24:10854. [PMID: 37446031 DOI: 10.3390/ijms241310854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Anticancer peptides (ACPs) represent a promising new therapeutic approach in cancer treatment. They can target cancer cells without affecting healthy tissues or altering normal physiological functions. Machine learning algorithms have increasingly been utilized for predicting peptide sequences with potential ACP effects. This study analyzed four benchmark datasets based on a well-established random forest (RF) algorithm. The peptide sequences were converted into 566 physicochemical features extracted from the amino acid index (AAindex) library, which were then subjected to feature selection using four methods: light gradient-boosting machine (LGBM), analysis of variance (ANOVA), chi-squared test (Chi2), and mutual information (MI). Presenting and merging the identified features using Venn diagrams, 19 key amino acid physicochemical properties were identified that can be used to predict the likelihood of a peptide sequence functioning as an ACP. The results were quantified by performance evaluation metrics to determine the accuracy of predictions. This study aims to enhance the efficiency of designing peptide sequences for cancer treatment.
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Affiliation(s)
- Yiting Deng
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Shuhan Ma
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Jiayu Li
- College of Life Science, Sichuan University, Chengdu 610065, China
| | - Bowen Zheng
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Zhibin Lv
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
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8
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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9
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Mathematical Modeling and Computational Prediction of High-Risk Types of Human Papillomaviruses. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1515810. [PMID: 35912141 PMCID: PMC9334084 DOI: 10.1155/2022/1515810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
Abstract
Cervical cancer is one of the main causes of cancer death all over the world. Most diseases such as cervical epithelial atypical hyperplasia and invasive cervical cancer are closely related to the continuous infection of high-risk types of human papillomavirus. Therefore, the high-risk types of human papillomavirus are the key to the prevention and treatment of cervical cancer. With the accumulation of high-throughput and clinical data, the use of systematic and quantitative methods for mathematical modeling and computational prediction has become more and more important. This paper summarizes the mathematical models and prediction methods of the risk types of human papillomavirus, especially around the key steps such as feature extraction, feature selection, and prediction algorithms. We summarized and discussed the advantages and disadvantages of existing algorithms, which provides a theoretical basis for follow-up research.
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10
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Liu X, Guo W, Cui S, Tang X, Zhao J, Zhang H, Mao B, Chen W. A Comprehensive Assessment of the Safety of Blautia producta DSM 2950. Microorganisms 2021; 9:microorganisms9050908. [PMID: 33922843 PMCID: PMC8146736 DOI: 10.3390/microorganisms9050908] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, Blautia has attracted attention for its role in ameliorating host diseases. In particular, Blautia producta DSM 2950 has been considered a potential probiotic due to its ability to mitigate inflammation in poly(I:C) induced HT-29 cells. Thus, to promote the development of indigenous intestinal microorganisms with potential probiotic function, we conducted a comprehensive experimental analysis of DSM 2950 to determine its safety. This comprised a study of its potential virulence genes, antibiotic resistance genes, genomic islands, antibiotic resistance, and hemolytic activity and a 14-day test of its acute oral toxicity in mice. The results indicated no toxin-related virulence genes in the DSM 2950 genome. Most of the genomic islands in DSM 2950 were related to metabolism, rather than virulence expression. DSM 2950 was sensitive to most of the tested antibiotics but was tolerant of treatment with kanamycin, neomycin, clindamycin, or ciprofloxacin, probably because it possessed the corresponding antibiotic resistance genes. Oral acute toxicity tests indicated that the consumption of DSM 2950 does not cause toxic side effects in mice. Overall, the safety profile of DSM 2950 confirmed that it could be a candidate probiotic for use in food and pharmaceutical preparations.
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Affiliation(s)
- Xuemei Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Weiling Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: (S.C.); (B.M.); Tel.: +86-510-8591-2155 (B.M.)
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: (S.C.); (B.M.); Tel.: +86-510-8591-2155 (B.M.)
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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