Literature DB >> 27151186

PHYPred: a tool for identifying bacteriophage enzymes and hydrolases.

Hui Ding1, Wuritu Yang1,2, Hua Tang3, Peng-Mian Feng4, Jian Huang1, Wei Chen5,6, Hao Lin7.   

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Year:  2016        PMID： 27151186      PMCID： PMC8193383          DOI： 10.1007/s12250-016-3740-6

Source DB:  PubMed          Journal:  Virol Sin        ISSN： 1995-820X            Impact factor:   4.327


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  14 in total

Review 1.  Machine learning approaches for the prediction of signal peptides and other protein sorting signals.

Authors:  H Nielsen; S Brunak; G von Heijne
Journal:  Protein Eng       Date:  1999-01

2.  iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.

Authors:  Hao Lin; En-Ze Deng; Hui Ding; Wei Chen; Kuo-Chen Chou
Journal:  Nucleic Acids Res       Date:  2014-10-31       Impact factor: 16.971

3.  iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition.

Authors:  Bin Liu; Longyun Fang; Ren Long; Xun Lan; Kuo-Chen Chou
Journal:  Bioinformatics       Date:  2015-10-17       Impact factor: 6.937

4.  Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition.

Authors:  Pan-Pan Zhu; Wen-Chao Li; Zhe-Jin Zhong; En-Ze Deng; Hui Ding; Wei Chen; Hao Lin
Journal:  Mol Biosyst       Date:  2014-12-01

5.  Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis.

Authors:  Hui Ding; Peng-Mian Feng; Wei Chen; Hao Lin
Journal:  Mol Biosyst       Date:  2014-08

6.  Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition.

Authors:  Hao Lin; Hui Ding; Feng-Biao Guo; An-Ying Zhang; Jian Huang
Journal:  Protein Pept Lett       Date:  2008       Impact factor: 1.890

7.  Artificial neural networks trained to detect viral and phage structural proteins.

Authors:  Victor Seguritan; Nelson Alves; Michael Arnoult; Amy Raymond; Don Lorimer; Alex B Burgin; Peter Salamon; Anca M Segall
Journal:  PLoS Comput Biol       Date:  2012-08-23       Impact factor: 4.475

8.  Naïve Bayes classifier with feature selection to identify phage virion proteins.

Authors:  Peng-Mian Feng; Hui Ding; Wei Chen; Hao Lin
Journal:  Comput Math Methods Med       Date:  2013-05-15       Impact factor: 2.238

9.  CD-HIT: accelerated for clustering the next-generation sequencing data.

Authors:  Limin Fu; Beifang Niu; Zhengwei Zhu; Sitao Wu; Weizhong Li
Journal:  Bioinformatics       Date:  2012-10-11       Impact factor: 6.937

10.  AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes.

Authors:  Hao Lin; Wei Chen; Hui Ding
Journal:  PLoS One       Date:  2013-10-09       Impact factor: 3.240
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  14 in total

Review 1.  Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies.

Authors:  Annegrete Visnapuu; Marie Van der Gucht; Jeroen Wagemans; Rob Lavigne
Journal:  Viruses       Date:  2022-05-16       Impact factor: 5.818

2.  Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy.

Authors:  Md Mehedi Hasan; Sho Tsukiyama; Jae Youl Cho; Hiroyuki Kurata; Md Ashad Alam; Xiaowen Liu; Balachandran Manavalan; Hong-Wen Deng
Journal:  Mol Ther       Date:  2022-05-06       Impact factor: 12.910

3.  Extremely-randomized-tree-based Prediction of N6-Methyladenosine Sites in Saccharomyces cerevisiae.

Authors:  Rajiv G Govindaraj; Sathiyamoorthy Subramaniyam; Balachandran Manavalan
Journal:  Curr Genomics       Date:  2020-01       Impact factor: 2.236

4.  i6mA-Fuse: improved and robust prediction of DNA 6 mA sites in the Rosaceae genome by fusing multiple feature representation.

Authors:  Md Mehedi Hasan; Balachandran Manavalan; Watshara Shoombuatong; Mst Shamima Khatun; Hiroyuki Kurata
Journal:  Plant Mol Biol       Date:  2020-03-05       Impact factor: 4.076

5.  Identification of Sub-Golgi protein localization by use of deep representation learning features.

Authors:  Zhibin Lv; Pingping Wang; Quan Zou; Qinghua Jiang
Journal:  Bioinformatics       Date:  2020-12-26       Impact factor: 6.937

6.  A novel feature ranking method for prediction of cancer stages using proteomics data.

Authors:  Ehsan Saghapour; Saeed Kermani; Mohammadreza Sehhati
Journal:  PLoS One       Date:  2017-09-21       Impact factor: 3.240

7.  Identification of Human Enzymes Using Amino Acid Composition and the Composition of k-Spaced Amino Acid Pairs.

Authors:  Lifu Zhang; Benzhi Dong; Zhixia Teng; Ying Zhang; Liran Juan
Journal:  Biomed Res Int       Date:  2020-05-22       Impact factor: 3.411

8.  HBPred: a tool to identify growth hormone-binding proteins.

Authors:  Hua Tang; Ya-Wei Zhao; Ping Zou; Chun-Mei Zhang; Rong Chen; Po Huang; Hao Lin
Journal:  Int J Biol Sci       Date:  2018-05-22       Impact factor: 6.580

9.  Identifying Phage Virion Proteins by Using Two-Step Feature Selection Methods.

Authors:  Jiu-Xin Tan; Fu-Ying Dao; Hao Lv; Peng-Mian Feng; Hui Ding
Journal:  Molecules       Date:  2018-08-10       Impact factor: 4.411

10.  A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features.

Authors:  Shohreh Ariaeenejad; Maryam Mousivand; Parinaz Moradi Dezfouli; Maryam Hashemi; Kaveh Kavousi; Ghasem Hosseini Salekdeh
Journal:  PLoS One       Date:  2018-10-22       Impact factor: 3.240
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