Molecular Computing and Bioinformatics

392 Pages·2019·39.796 MB·English

by  Xiangxiang Zeng, Alfonso Rodríguez-Patón Quan Zou

molecules
Molecular
Computing and
Bioinformatics
Edited by
Xiangxiang Zeng, Alfonso Rodríguez-Patón and Quan Zou
Printed Edition of the Special Issue Published in Molecules
www.mdpi.com/journal/molecules
Molecular Computing
and Bioinformatics

Molecular Computing
and Bioinformatics
SpecialIssueEditors
XiangxiangZeng
AlfonsoRodr´ıguez-Pato´n
QuanZou
MDPI•Basel•Beijing•Wuhan•Barcelona•Belgrade
Special Issue Editors
Xiangxiang Zeng Alfonso Rodr´ıguez-Pat´on
Xiamen University Universidad Politcnica de Madrid
China Spain
Quan Zou
University of Electronic Science and Technology of China
China
EditorialOffice
MDPI
St.Alban-Anlage66
4052Basel,Switzerland
ThisisareprintofarticlesfromtheSpecialIssuepublishedonlineintheopenaccessjournalMolecules
(ISSN 1420-3049) from 2018 to 2019 (available at: https://www.mdpi.com/journal/molecules/
specialissues/MolecularComputingBioinformatics)
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Contents
AbouttheSpecialIssueEditors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
XinLiang,WenZhu,ZhibinLvandQuanZou
MolecularComputingandBioinformatics
Reprintedfrom:Molecules2019,24,2358,doi:10.3390/molecules24132358. . . . . . . . . . . . . . 1
KeHan,MiaoWang,LeiZhangandChunyuWang
Application of Molecular Methods in the Identification of Ingredients in Chinese
HerbalMedicines
Reprintedfrom:Molecules2018,23,2728,doi:10.3390/molecules23102728. . . . . . . . . . . . . . 8
RuolanChen,XiangrongLiu,ShutingJin,JiaweiLinandJuanLiu
MachineLearningforDrug-TargetInteractionPrediction
Reprintedfrom:Molecules2018,23,2208,doi:10.3390/molecules23092208. . . . . . . . . . . . . . 21
Xiaoke Ping, Tengyue Wang, Na Lin, Feifei Di, Yangyang Li, Hongju Jian, Hao Wang,
Kun Lu, Jiana Li, Xinfu Xu and Liezhao Liu
Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress
in Brassica napus
Reprintedfrom:Molecules2019,24,1985,doi:10.3390/molecules24101985. . . . . . . . . . . . . . 36
ChristinaBaek,Sang-WooLee,Beom-JinLee,Dong-HyunKwakandByoung-TakZhang
EnzymaticWeightUpdateAlgorithmforDNA-BasedMolecularLearning
Reprintedfrom:Molecules2019,24,1409,doi:10.3390/molecules24071409. . . . . . . . . . . . . . 55
Therapeutic Effects of HIF-1α on Bone Formation around Implants in Diabetic Mice Using
Cell-PenetratingDNA-BindingProtein
Reprintedfrom:Molecules2019,24,760,doi:10.3390/molecules24040760 . . . . . . . . . . . . . . 73
PengmianFeng,ZhaochunXu,HuiYang,HaoLv,HuiDingandLiLiu
Identification of D Modification Sites by Integrating Heterogeneous Features in
Saccharomycescerevisiae
Reprintedfrom:Molecules2019,24,380,doi:10.3390/molecules24030380 . . . . . . . . . . . . . . 85
JingpuZhangandLeiDeng
IntegratingMultipleInteractionNetworksforGeneFunctionInference
Reprintedfrom:Molecules2019,24,30,doi:10.3390/molecules24010030 . . . . . . . . . . . . . . . 93
He Su, Yang Chu, Junqi Bai, Lu Gong, Juan Huang, Wen Xu, Jing Zhang, Xiaohui Qiu,
Jiang Xu and Zhihai Huang
Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng
and Eleven Flowering Plants
Reprintedfrom:Molecules2019,24,15,doi:10.3390/molecules24010015 . . . . . . . . . . . . . . . 108
BaofangHu,HongWang,LutongWangandWeihuaYuan
AdverseDrugReactionPredictionsUsingStackingDeepHeterogeneousInformationNetwork
EmbeddingApproach
Reprintedfrom:Molecules2018,23,3193,doi:10.3390/molecules23123193. . . . . . . . . . . . . . 125
v
LeiXu,GuangminLiang,ChangruiLiao,Gin-DenChenandChi-ChangChang
AnEfficientClassifierforAlzheimer’sDiseaseGenesIdentification
Reprintedfrom:Molecules2018,23,3140,doi:10.3390/molecules23123140. . . . . . . . . . . . . . 141
Haiqiong Luo, Wei Lan, Qingfeng Chen, Zhiqiang Wang, Zhixian Liu, Xiaofeng Yue and
LingzhiZhu
Inferring microRNA-Environmental Factor Interactions Based on Multiple Biological
InformationFusion
Reprintedfrom:Molecules2018,23,2439,doi:10.3390/molecules23102439. . . . . . . . . . . . . . 154
MingzheXu,ZhongmengZhao,XuanpingZhang,AiqingGao,ShuyanWuandJiayinWang
Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in
FusionStructures
Reprintedfrom:Molecules2018,23,2055,doi:10.3390/molecules23082055. . . . . . . . . . . . . . 165
V.Kalidasan,AdleenAzman,NarcisseJoseph,SureshKumar,RukmanAwangHamatand
VasanthaKumariNeela
PutativeIronAcquisitionSystemsinStenotrophomonasmaltophilia
Reprintedfrom:Molecules2018,23,2048,doi:10.3390/molecules23082048. . . . . . . . . . . . . . 185
ChunChen,Ming-HanLee,Ching-FengWengandMaxK.Leong
Theoretical Prediction of the Complex P-Glycoprotein Substrate Efflux Based on the Novel
HierarchicalSupportVectorRegressionScheme
Reprintedfrom:Molecules2018,23,1820,doi:10.3390/molecules23071820. . . . . . . . . . . . . . 204
XiujunZhang,HuiqinJiang,Jia-BaoLiuandZehuiShao
The Cartesian Product and Join Graphs on Edge-Version Atom-Bond Connectivity and
GeometricArithmeticIndices
Reprintedfrom:Molecules2018,23,1731,doi:10.3390/molecules23071731. . . . . . . . . . . . . . 229
XiaoliQiang,ZhengKou,GangFangandYanfengWang
Scoring Amino Acid Mutations to Predict Avian-to-Human Transmission of Avian
InfluenzaViruses
Reprintedfrom:Molecules2018,23,1584,doi:10.3390/molecules23071584. . . . . . . . . . . . . . 244
BuwenCao,ShuguangDeng,HuaQin,PingjianDing,ShaopengChenandGuanghuiLi
Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse
Protein–ProteinInteractionNetwork
Reprintedfrom:Molecules2018,23,1460,doi:10.3390/molecules23061460. . . . . . . . . . . . . . 256
JoannaMiskiewiczandMartaSzachniuk
DiscoveringStructuralMotifsinmiRNAPrecursorsfromtheViridiplantaeKingdom
Reprintedfrom:Molecules2018,23,1367,doi:10.3390/molecules23061367. . . . . . . . . . . . . . 266
YutingXing,ChengkunWu,XiYang,WeiWang,EnZhuandJianpingYin
ParaBTM:AParallelProcessingFrameworkforBiomedicalTextMiningonSupercomputers
Reprintedfrom:Molecules2018,23,1028,doi:10.3390/molecules23051028. . . . . . . . . . . . . . 280
Mohammed Zakariah, Shahanavaj Khan, Anis Ahmad Chaudhary, Christian Rolfo,
MohamedMaherBenIsmailandYousefAjamiAlotaibi
ToDeciphertheMycoplasmahominisProteinsTargetingintotheEndoplasmicReticulumand
TheirImplicationsinProstateCancerEtiologyUsingNext-GenerationSequencingData
Reprintedfrom:Molecules2018,23,994,doi:10.3390/molecules23050994 . . . . . . . . . . . . . . 291
vi
YinghanHong,ZhifengHao,GuizhenMai,HanHuangandArunKumarSangaiah
CausalDiscoveryCombiningK2withBrainStormOptimizationAlgorithm
Reprintedfrom:Molecules2018,23,1729,doi:10.3390/molecules23071729. . . . . . . . . . . . . . 303
JianyingYuan,DequanGuo,GexiangZhang,PrithwineelPaul,MingZhuandQiangYang
A Resolution-Free Parallel Algorithm for Image Edge Detection within the Framework of
EnzymaticNumericalPSystems
Reprintedfrom:Molecules2019,2019,1235,doi:10.3390/molecules24071235 . . . . . . . . . . . . 319
XunWang,PanZhengTongmaoMaandTaoSong
SmallUniversalBacteriaandPlasmidComputingSystems
Reprintedfrom:Molecules2018,23,1307,doi:10.3390/molecules23061307. . . . . . . . . . . . . . 335
WeixuanHanandChangjunZhou
8-BitAdderandSubtractorwithDomainLabelBasedonDNAStrandDisplacement
Reprintedfrom:Molecules2018,23,2989,doi:10.3390/molecules23112989. . . . . . . . . . . . . . 348
BinWang,YingjieXie,ShihuaZhou,XuedongZhengandChangjunZhou
CorrectingErrorsinImageEncryptionBasedonDNACoding
Reprintedfrom:Molecules2018,23,1878,doi:10.3390/molecules23081878. . . . . . . . . . . . . . 366
vii

About the Special Issue Editors
Xiangxiang Zeng is affiliated with the College of Information Science and Engineering, Hunan
University, Changsha, Hunan, China. He received a BSc degree in Automation from Hunan
University,China,in2005andaPhDdegreeinSystemEngineeringfromtheHuazhongUniversity
ofScienceandTechnology, China, in2011. From2011to2018, hewasanAssistantProfessorand
AssociateProfessorintheDepartmentofComputerScience,XiamenUniversity. Hismainresearch
interestsincludesystemsbiology,naturalcomputinganddatamining.
Alfonso Rodr´ıguez-Pato´n received a BSc degree in Electronic and Computational Specialty from
theUniversityofSantiagodeCompostela,Spain,in1992. HereceivedaPhDdegreeinComputer
Science from the Polytechnic University of Madrid, in 1999. He is an Associate Professor in the
FacultyofInformaticsatthePolytechnicUniversityofMadrid. Hismainresearchinterestsfocuson
theinterplaybetweencomputerscience,biology,andengineering.
Quan Zou received a PhD degree from the Harbin Institute of Technology, P.R. China, in 2009.
From2015to2018,hewasaProfessorofComputerScienceatTianjinUniversity.From2009to2015,
hewasanAssistantandAssociateProfessoratXiamenUniversity,P.R.China. Hisresearchisinthe
areasofbioinformatics,machinelearning,andparallelcomputing. Severalrelatedworkshavebeen
publishedbyScience,BriefingsinBioinformatics,andBioinformatics,amongothers.GoogleScholar
showsthatover100ofhispapershavebeencitedmorethan3,000times.
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