Kinectin 1 promotes the growth of triple-negative breast cancer via directly co-activating NF-kappaB/p65 and enhancing its transcriptional activity.

Gao L, Chen S, Hong M, Zhou W, Wang B, Qiu J, Xia J, Zhao P, Fu L, Wang J, Dai Y, Xie N, Yang Q, Huang HD, Gao X, Zou C.

Signal Transduct Target Ther. 2021 Jul 5;6(1):250. doi: 10.1038/s41392-021-00652-x. PMID: 34219129; PMCID: PMC8255318.


Assessing the Performance of Traveling-salesman based Automated Path Searching (TAPS) on Complex Biomolecular Systems.

Xi K, Hu Z, Wu Q, Wei M, Qian R, Zhu L.

J Chem Theory Comput. 2021 Jul 16. doi: 10.1021/acs.jctc.1c00182.


Circulating microRNAs Associated With Reversible Cerebral Vasoconstriction Syndrome.

Chen SP, Chang YA, Chou CH, Juan CC, Lee HC, Chen LK, Wu PC, Wang YF, Fuh JL, Lirng JF, Ducros A, Huang HD, Wang SJ.

Ann Neurol. 2021 Mar;89(3):459-473. doi: 10.1002/ana.25965.


Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism.

 Han Y, Zhuang Q, Sun B, Lv W, Wang S, Xiao Q, Pang B, Zhou Y, Wang F, Chi P, Wang Q, Li Z, Zhu L, Li F, Deng D, Chiang YC, Li Z, Ren R.

Nat Commun. 2021 Jan 19;12(1):449. doi: 10.1038/s41467-020-20675-2. PMID: 33469028; PMCID: PMC7815742.


Enantioselective Nickel-Catalyzed Hydrocyanative Desymmetrization of Norbornene Derivatives

Sun F, Wang T, Cheng GJ, Fang XJ

ACS Catalysis 2021 11 (12), 7578-7583. DOI: 10.1021/acscatal.1c01971


Exploring the Activation Process of the β2AR-Gs Complex.

Bai C, Wang J, Mondal D, Du Y, Ye RD, Warshel A.

J Am Chem Soc. 2021 Jul 28;143(29):11044-11051. doi: 10.1021/jacs.1c03696.


Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes.

 Xiao P, Yan W, Gou L, Zhong YN, Kong L, Wu C, Wen X, Yuan Y, Cao S, Qu C, Yang X, Yang CC, Xia A, Hu Z, Zhang Q, He YH, Zhang DL, Zhang C, Hou GH, Liu H, Zhu L, Fu P, Yang S, Rosenbaum DM, Sun JP, Du Y, Zhang L, Yu X, Shao Z.

Cell. 2021 Feb 18;184(4):943-956.e18. doi: 10.1016/j.cell.2021.01.028.


Ligand-Controlled Regiodivergent Nickel-Catalyzed Hydrocyanation of Silyl-Substituted 1,3-Diynes.

Sun F, Yang C, Ni J, Cheng GJ, Fang X.

Org Lett. 2021 May 21;23(10):4045-4050. doi: 10.1021/acs.orglett.1c01262.


MethHC 2.0: information repository of DNA methylation and gene expression in human cancer.

Huang HY, Li J, Tang Y, Huang YX, Chen YG, Xie YY, Zhou ZY, Chen XY, Ding SY, Luo MF, Jin CN, Zhao LS, Xu JT, Zhou Y, Lin YC, Hong HC, Zuo HL, Hu SY, Xu PY, Li X, Huang HD.

Nucleic Acids Res. 2021 Jan 8;49(D1):D1268-D1275. doi: 10.1093/nar/gkaa1104.


Roles of KLF4 and AMPK in the inhibition of glycolysis by pulsatile shear stress in endothelial cells.

Han Y, He M, Marin T, Shen H, Wang WT, Lee TY, Hong HC, Jiang ZL, Garland T Jr, Shyy JY, Gongol B, Chien S.

Proc Natl Acad Sci U S A. 2021 May 25;118(21):e2103982118. doi: 10.1073/pnas.2103982118.


Structure-guided modification of isoxazole-type FXR agonists: Identification of a potent and orally bioavailable FXR modulator.

Luo G, Lin X, Li Z, Xiao M, Li X, Zhang D, Xiang H.

Eur J Med Chem. 2021 Jan 1;209:112910. doi: 10.1016/j.ejmech.2020.112910.


The challenges and opportunities of traditional Chinese medicines against COVID-19: a way out from a network perspective.

Zuo HL, Lin YC, Huang HY, Wang X, Tang Y, Hu YJ, Kong XJ, Chen QJ, Zhang YZ, Hong HC, Li J, Hu SY, Huang HD.

Acta Pharmacol Sin. 2021 Jun;42(6):845-847. doi: 10.1038/s41401-021-00645-0.


A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra.

Wang HY, Chung CR, Wang Z, Li S, Chu BY, Horng JT, Lu JJ, Lee TY.

Brief Bioinform. 2021 May 20;22(3):bbaa138. doi: 10.1093/bib/bbaa138.


Antibacterial kaneoheoic acids A-F from a Hawaiian fungus Fusarium sp. FM701.

Uz Zaman KA, Wu X, Hu Z, Yoshida W, Hou S, Saito J, Avad KA, Hevener KE, Alumasa JN, Cao S.

Phytochemistry. 2021 Jan;181:112545. doi: 10.1016/j.phytochem.2020.112545.


AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches.

Pang Y, Yao L, Jhong JH, Wang Z, Lee TY.

Brief Bioinform. 2021 Jul 19:bbab263. doi: 10.1093/bib/bbab263.


Biomarker Identification through Multiomics Data Analysis of Prostate Cancer Prognostication Using a Deep Learning Model and Similarity Network Fusion.

Wang TH, Lee CY, Lee TY, Huang HD, Hsu JB, Chang TH.

Cancers (Basel). 2021 May 21;13(11):2528. doi: 10.3390/cancers13112528.


Dual Effects of Let-7b in the Early Stage of Hepatitis C Virus Infection.

Yeh YJ, Tseng CP, Hsu SD, Huang HY, Lai MMC, Huang HD, Cheng JC.

J Virol. 2021 Jan 28;95(4):e01800-20. doi: 10.1128/JVI.01800-20.


Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies.

Pang Y, Wang Z, Jhong JH, Lee TY.

Brief Bioinform. 2021 Mar 22;22(2):1085-1095. doi: 10.1093/bib/bbaa423.


Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in Staphylococcus aureus.

Wang Z, Wang HY, Chung CR, Horng JT, Lu JJ, Lee TY.

Brief Bioinform. 2021 Jul 20;22(4):bbaa293. doi: 10.1093/bib/bbaa293.


Oral microbial dysbiosis and its performance in predicting oral cancer.

Su SC, Chang LC, Huang HD, Peng CY, Chuang CY, Chen YT, Lu MY, Chiu YW, Chen PY, Yang SF.

Carcinogenesis. 2021 Feb 11;42(1):127-135. doi: 10.1093/carcin/bgaa062.


Secondary Metabolites from the Leather Coral-Derived Fungal Strain Xylaria sp. FM1005 and Their Glycoprotein IIb/IIIa Inhibitory Activity.

Zaman KAU, Park JH, DeVine L, Hu Z, Wu X, Kim HS, Cao S.

J Nat Prod. 2021 Feb 26;84(2):466-473. doi: 10.1021/acs.jnatprod.0c01330.


Synbiotics Alleviate the Gut Indole Load and Dysbiosis in Chronic Kidney Disease.

Yang CY, Chen TW, Lu WL, Liang SS, Huang HD, Tseng CP, Tarng DC.

Cells. 2021 Jan 9;10(1):114. doi: 10.3390/cells10010114.


The Use of Chinese Yang/Qi-Invigorating Tonic Botanical Drugs/Herbal Formulations in Ameliorating Chronic Kidney Disease by Enhancing Mitochondrial Function.

Tian J, Huang Y, Wu T, Huang HD, Ko KM, Zhu BT, Chen J.

Front Pharmacol. 2021 Jun 24;12:622498. doi: 10.3389/fphar.2021.622498.


UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.

Li Z, Chen S, Jhong JH, Pang Y, Huang KY, Li S, Lee TY.

Database (Oxford). 2021 Mar 8;2021:baab010. doi: 10.1093/database/baab010.


Adipose MSCs Suppress MCF7 and MDA-MB-231 Breast Cancer Metastasis and EMT Pathways Leading to Dormancy via Exosomal-miRNAs Following Co-Culture Interaction.

Mohd Ali N, Yeap SK, Ho WY, Boo L, Ky H, Satharasinghe DA, Tan SW, Cheong SK, Huang HD, Lan KC, Chiew MY, Ong HK.

Pharmaceuticals (Basel). 2020 Dec 24;14(1):8. doi: 10.3390/ph14010008.


Aspochalasin H1: A New Cyclic Aspochalasin from Hawaiian Plant-Associated Endophytic Fungus Aspergillus sp. FT1307.

Qader M, Zaman KHAU, Hu Z, Wang C, Wu X, Cao S.

Molecules. 2021 Jul 12;26(14):4239. doi: 10.3390/molecules26144239.


Computational exploration of copper catalyzed vinylogous aerobic oxidation of unsaturated compounds.

Wang T, Zhou Y, Xu Y, Cheng GJ.

Sci Rep. 2021 Jan 14;11(1):1304. doi: 10.1038/s41598-020-80188-2.


Fungal Epithiodiketopiperazines Carrying α,β-Polysulfide Bridges from Penicillium steckii YE, and Their Chemical Interconversion.

Jiang G, Zhang P, Ratnayake R, Yang G, Zhang Y, Zuo R, Powell M, Huguet-Tapia JC, Abboud KA, Dang LH, Teplitski M, Paul V, Xiao R, Ahammad KH, Zaman U, Hu Z, Cao S, Luesch H, Ding Y.

Chembiochem. 2021 Jan 15;22(2):416-422. doi: 10.1002/cbic.202000403.


Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides.

Wan Y, Wang Z, Lee TY.

BMC Bioinformatics. 2021 May 29;22(1):286. doi: 10.1186/s12859-021-03965-4.


Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations.

Chen YP, Tsai CF, Rekha PD, Ghate SD, Huang HY, Hsu YH, Liaw LL, Young CC.

Bot Stud. 2021 May 18;62(1):8. doi: 10.1186/s40529-021-00314-9.


A panel of eight microRNAs is a good predictive parameter for triple-negative breast cancer relapse.

Hong HC, Chuang CH, Huang WC, Weng SL, Chen CH, Chang KH, Liao KW, Huang HD.

Theranostics. 2020 Jul 9;10(19):8771-8789. doi: 10.7150/thno.46142.


Control of matrix stiffness promotes endodermal lineage specification by regulating SMAD2/3 via lncRNA LINC00458.

Chen YF, Li YJ, Chou CH, Chiew MY, Huang HD, Ho JH, Chien S, Lee OK.

Sci Adv. 2020 Feb 5;6(6):eaay0264. doi: 10.1126/sciadv.aay0264.


Cryo-EM structure of activated bile acids receptor TGR5 in complex with stimulatory G protein.

Chen G, Wang X, Ge Y, Ma L, Chen Q, Liu H, Du Y, Ye RD, Hu H, Ren R.

Signal Transduct Target Ther. 2020 Aug 3;5(1):142. doi: 10.1038/s41392-020-00262-z.


Diastereo- and Enantioselective Catalytic Radical Oxysulfonylation of Alkenes in β,γ-Unsaturated Ketoximes.

Xi-Tao Li, Ling Lv, Ting Wang, Qiang-Shuai Gu, Guo-Xing Xu, Zhong-Liang Li, Liu Ye, Xinhao Zhang, Gui-Juan Cheng, Xin-Yuan Liu.

Chem. 2020, Jul 6(7); 1692-1706. doi: 10.1016/j.chempr.2020.03.024


Direct C–H Arylation of Aldehydes by Merging Photocatalyzed Hydrogen Atom Transfer with Palladium Catalysis

Wang L, Wang T, Cheng GJ, Li XB, Wei JJ, Guo B, Zheng CJ, Chen GY, Ran CZ, Zheng C.

ACS Catalysis 2020 10 (14), 7543-7551. DOI: 10.1021/acscatal.0c02105


Directing-Group-Based Strategy Enabling Intermolecular Heck-Type Reaction of Cycloketone Oxime Esters and Unactivated Alkenes.

Deng Y, Zhao C, Zhou Y, Wang H, Li X, Cheng GJ, Fu J.

Org Lett. 2020 May 1;22(9):3524-3530. doi: 10.1021/acs.orglett.0c00963.


Discovery of an orally active VHL-recruiting PROTAC that achieves robust HMGCR degradation and potent hypolipidemic activity in vivo.

Luo G, Li Z, Lin X, Li X, Chen Y, Xi K, Xiao M, Wei H, Zhu L, Xiang H.

Acta Pharm Sin B. 2021 May;11(5):1300-1314. doi: 10.1016/j.apsb.2020.11.001.


Discovery of novel quinazoline derivatives as potent PI3Kδ inhibitors with high selectivity.

Teng Y, Li X, Ren S, Cheng Y, Xi K, Shen H, Ma W, Luo G, Xiang H.

Eur J Med Chem. 2020 Dec 15;208:112865. doi: 10.1016/j.ejmech.2020.112865.


MicroRNA-483 amelioration of experimental pulmonary hypertension.

Zhang J, He Y, Yan X, Chen S, He M, Lei Y, Zhang J, Gongol B, Gu M, Miao Y, Bai L, Cui X, Wang X, Zhang Y, Fan F, Li Z, Shen Y, Chou CH, Huang HD, Malhotra A, Rabinovitch M, Jing ZC, Shyy JY.

EMBO Mol Med. 2020 May 8;12(5):e11303. doi: 10.15252/emmm.201911303.


miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

Huang HY, Lin YC, Li J, Huang KY, Shrestha S, Hong HC, Tang Y, Chen YG, Jin CN, Yu Y, Xu JT, Li YM, Cai XX, Zhou ZY, Chen XH, Pei YY, Hu L, Su JJ, Cui SD, Wang F, Xie YY, Ding SY, Luo MF, Chou CH, Chang NW, Chen KW, Cheng YH, Wan XH, Hsu WL, Lee TY, Wei FX, Huang HD.

Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154. doi: 10.1093/nar/gkz896.


Ni-Catalyzed Isomerization-Hydrocyanation Tandem Reactions: Access to Linear Nitriles from Aliphatic Internal Olefins.

Gao J, Ni J, Yu R, Cheng GJ, Fang X.

Org Lett. 2021 Jan 15;23(2):486-490. doi: 10.1021/acs.orglett.0c04007.


Nickel-Catalyzed Cross-Electrophile Coupling Reactions for the Synthesis of gem-Difluorovinyl Arenes

Xiong BJ, Wang T, Sun HT, Li Y, Kramer S, Cheng GJ, Lian Z.

ACS Catalysis 2020 10 (22), 13616-13623. DOI: 10.1021/acscatal.0c03993


Nickel-Catalyzed Migratory Hydrocyanation of Internal Alkenes: Unexpected Diastereomeric-Ligand-Controlled Regiodivergence.

Gao J, Jiao M, Ni J, Yu R, Cheng GJ, Fang X.

Angew Chem Int Ed Engl. 2021 Jan 25;60(4):1883-1890. doi: 10.1002/anie.202011231.


SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites.

Kao HJ, Nguyen VN, Huang KY, Chang WC, Lee TY.

Genomics Proteomics Bioinformatics. 2020 Apr;18(2):208-219. doi: 10.1016/j.gpb.2018.10.010.


Characterization and Identification of Natural Antimicrobial Peptides on Different Organisms.

Chung CR, Jhong JH, Wang Z, Chen S, Wan Y, Horng JT, Lee TY.

Int J Mol Sci. 2020 Feb 2;21(3):986. doi: 10.3390/ijms21030986.


Highly Regio- and Stereoselective Ni-Catalyzed Hydrocyanation of 1,3-Enynes.

Sun F, Ni J, Cheng GJ, Fang X.

Chemistry. 2020 May 12;26(27):5956-5960. doi: 10.1002/chem.202000651.


Incorporating Deep Learning With Word Embedding to Identify Plant Ubiquitylation Sites.

Wang H, Wang Z, Li Z, Lee TY.

Front Cell Dev Biol. 2020 Sep 30;8:572195. doi: 10.3389/fcell.2020.572195.


Multi-omics profiling reveals microRNA-mediated insulin signaling networks.

Lin YC, Huang HY, Shrestha S, Chou CH, Chen YH, Chen CR, Hong HC, Li J, Chang YA, Chiew MY, Huang YR, Tu SJ, Sun TH, Weng SL, Tseng CP, Huang HD.

BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):389. doi: 10.1186/s12859-020-03678-0.


NF-κB Inhibitory and Antibacterial Helvolic and Fumagillin Derivatives from Aspergillus terreus.

Zaman KAU, Hu Z, Wu X, Hou S, Saito J, Kondratyuk TP, Pezzuto JM, Cao S.

J Nat Prod. 2020 Mar 27;83(3):730-737. doi: 10.1021/acs.jnatprod.9b01190.


Characterization and identification of lysine crotonylation sites based on machine learning method on both plant and mammalian.

Wang R, Wang Z, Wang H, Pang Y, Lee TY. 

Sci Rep. 2020 Nov 24;10(1):20447. doi: 10.1038/s41598-020-77173-0. 


Computational analysis for identification of the extracellular matrix molecules involved in endometrial cancer progression.

Yadav VK, Lee TY, Hsu JB, Huang HD, Yang WV, Chang TH.

PLoS One. 2020 Apr 21;15(4):e0231594. doi: 10.1371/journal.pone.0231594.


Mechanism for the Reactivation of the Peroxidase Activity of Human Cyclooxygenases: Investigation Using Phenol as a Reducing Cosubstrate

Yang CX, Li P, Ding XL, Sui HC, Rao S, Hsu CH, Leung WP, Cheng GJ, Wang P, Zhu BT.

Sci Rep.  
2020 Sep 16;10(1):15187. doi: 10.1038/s41598-020-71237-x.


Pilot Study to Establish a Novel Five-Gene Biomarker Panel for Predicting Lymph Node Metastasis in Patients With Early Stage Endometrial Cancer.

Huang CY, Liao KW, Chou CH, Shrestha S, Yang CD, Chiew MY, Huang HT, Hong HC, Huang SH, Chang TH, Huang HD.

Front Oncol. 2020 Jan 21;9:1508. doi: 10.3389/fonc.2019.01508.


SVAD: A genetic database curates non-ischemic sudden cardiac death-associated variants.

Huang WC, Huang HT, Chen PY, Wang WC, Ko TM, Shrestha S, Yang CD, Tai CS, Chiew MY, Chou YP, Hu YF, Huang HD.

PLoS One. 2020 Aug 19;15(8):e0237731. doi: 10.1371/journal.pone.0237731.


Tryptoquivalines W and X, two new compounds from a Hawaiian fungal strain and their biological activities.

Zaman KAU, Hu Z, Wu X, Cao S.

Tetrahedron Lett. 2020 Apr 2;61(14):151730. doi: 10.1016/j.tetlet.2020.151730.


Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication.

Lee TY, Huang KY, Chuang CH, Lee CY, Chang TH.

Comput Biol Chem. 2020 May 12;87:107277. doi: 10.1016/j.compbiolchem.2020.107277.


Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis.

Li WY, Huang SW, Wang SF, Liu HF, Chou CH, Wu SJ, Huang HD, Lu PL, Fann CSJ, Chen M, Chen YH, Chen YA.

J Microbiol Immunol Infect. 2020 Jan 27:S1684-1182(20)30002-5. doi: 10.1016/j.jmii.2019.12.002.


Membrane Protein-Regulated Networks across Human Cancers.

Lin CY, Lee CH, Chuang YH, Lee JY, Chiu YY, Wu Lee YH, Jong YJ, Hwang JK, Huang SH, Chen LC, Wu CH, Tu SH, Ho YS, Yang JM.

Nat Commun. 2019 Jul 16;10(1):3131. doi: 10.1038/s41467-019-10920-8.


Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications

He M, Huang TS, Li S, Hong HC, Chen Z, Martin M, Zhou X, Huang HY, Su SH, Zhang J, Wang WT, Kang J, Huang HD, Zhang J, Chien S, Shyy JY.

Arterioscler Thromb Vasc Biol. 2019 May;39(5):902-914. doi: 10.1161/ATVBAHA.118.312301.


Liver X Receptor/Retinoid X Receptor Pathway Plays a Regulatory Role in Pacing-Induced Cardiomyopathy.

Lin YS, Chang TH, Shi CS, Wang YZ, Ho WC, Huang HD, Chang ST, Pan KL, Chen MC.

J Am Heart Assoc. 2019 Jan 8;8(1):e009146. doi: 10.1161/JAHA.118.009146.


Mechanical stretch induces hair regeneration through the alternative activation of macrophages

Chu SY, Chou CH, Huang HD, Yen MH, Hong HC, Chao PH, Wang YH, Chen PY, Nian SX, Chen YR, Liou LY, Liu YC, Chen HM, Lin FM, Chang YT, Chen CC, Lee OK.

Nat Commun. 2019 Apr 3;10(1):1524. doi: 10.1038/s41467-019-09402-8.


Resistin Enhances Monocyte Chemoattractant Protein-1 Production in Human Synovial Fibroblasts and Facilitates Monocyte Migration

Chen WC, Wang SW, Lin CY, Tsai CH, Fong YC, Lin TY, Weng SL, Huang HD, Liao KW, Tang CH.

Cell Physiol Biochem. 2019;52(3):408-420. doi: 10.33594/000000029. Epub 2019 Mar 8.


dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.

Huang KY, Lee TY, Kao HJ, Ma CT, Lee CC, Lin TH, Chang WC, Huang HD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D298-D308. doi: 10.1093/nar/gky1074.


Characterization and Identification of Antimicrobial Peptides with Different Functional Activities

Chung CR Kuo TR, Wu LC Lee TY, Horng JT

Brief Bioinform. 2019 Jun 3. pii: bbz043. doi: 10.1093/bib/bbz043. [Epub ahead of print]


Increase Trichomonas vaginalis detection based on urine routine analysis through a machine learning approach

Wang HY, Hung CC, Chen CH, Lee TY, Huang KY, Ning HC, Lai NC, Tsai MH, Lu LC, Tseng YJ, Lu JJ.

Sci Rep. 2019 Aug 19;9(1):11074. doi: 10.1038/s41598-019-47361-8.


Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites

Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu , Shun-Long Weng and Tzong-Yi Lee

BMC Bioinformatics 2019, 19(Suppl 13):384.


Structural and functional characterization of β 2 ?glycoprotein I domain 1 in anti?melanoma cell migration

Leu SJ, Lee TY, Cheng SW, Tsai MY, Lin YS, Chiou TJ, Huang KY, Chiang AN.

Cancer Sci. 2019 Jun;110(6):1974-1986. doi: 10.1111/cas.14030. Epub 2019 May 15.


Identification of potential biomarkers related to glioma survival by gene expression profile analysis

Hsu JB1, Chang TH2, Lee GA1, Lee TY3,4,5, Chen CY6,7,8,9,10.

BMC Med Genomics. 2019 Mar 20;11(Suppl 7):34. doi: 10.1186/s12920-019-0479-6.


dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data

Jhong JH, Chi YH, Li WC, Lin TH, Huang KY, Lee TY.

Nucleic Acids Res. 2019 Jan 8;47(D1):D285-D297. doi: 10.1093/nar/gky1030.


PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1155-D1163. doi: 10.1093/nar/gky1081.


Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites

Huang KY, Kao HJ, Hsu JB, Weng SL, Lee TY.

BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):384. doi: 10.1186/s12859-018-2394-9.


TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules

Zhu L, Sheong FK Cao S1, Liu S, Unarta IC, Huang X.

J Chem Phys. 2019 Mar 28;150(12):124105. doi: 10.1063/1.5082633.


Relationships between residue Voronoi volume and sequence conservation in proteins.

Liu JW, Cheng CW, Lin YF, Chen SY, Hwang JK, Yen SC.

Biochim Biophys Acta Proteins Proteom. 2018 Feb;1866(2):379-386. doi: 10.1016/j.bbapap.2017.09.003. Epub 2017 Sep 11.


Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes

Cai Q, Qiao L, Wang M, He B, Lin FM, Palmquist J, Huang SD, Jin H.

Science. 2018 Jun 8;360(6393):1126-1129. doi: 10.1126/science.aar4142. Epub 2018 May 17.


A Three-MicroRNA Signature as a Potential Biomarker for the Early Detection of Oral Cancer

Chang YA, Weng SL, Yang SF, Chou CH, Huang WC, Tu SJ, Chang TH, Huang CN, Jong YJ, Huang HD.

Int J Mol Sci. 2018 Mar 7;19(3). pii: E758. doi: 10.3390/ijms19030758.


AMP-activated Protein Kinase Phosphorylation of Angiotensin-Converting Enzyme 2 in Endothelium Mitigates Pulmonary Hypertension

Zhang J, Dong J, Martin M, He M, Gongol B, Marin TL, Chen L, Shi X, Yin Y, Shang F, Wu Y, Huang HY, Zhang J, Zhang Y, Kang J, Moya EA, Huang HD, Powell FL, Chen Z, Thistlethwaite PA, Yuan ZY, Shyy JY.

Am J Respir Crit Care Med. 2018 Aug 15;198(4):509-520. doi: 10.1164/rccm.201712-2570OC.


Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs

Liu YC, Chiu YJ, Li JR, Sun CH, Liu CC, Huang HD.

BMC Genomics. 2018 Jan 19;19(Suppl 1):958. doi: 10.1186/s12864-017-4335-9.


CCN6-mediated MMP-9 activation enhances metastatic potential of human chondrosarcoma

Tzeng HE, Tang CH, Wu SH, Chen HT, Fong YC, Lu YC, Chen WC, Huang HD, Lin CY17, Wang SW.

Cell Death Dis. 2018 Sep 20;9(10):955. doi: 10.1038/s41419-018-1008-9.


Compositional and functional variations of oral microbiota associated with the mutational changes in oral cancer

Yang SF, Huang HD, Fan WL, Jong YJ, Chen MK, Huang CN, Chuang CY, Kuo YL, Chung WH, Su SC.

Oral Oncol. 2018 Feb;77:1-8. doi: 10.1016/j.oraloncology.2017.12.005. Epub 2017 Dec 9.


Extension of C-elegans lifespan using the center dot NO-delivery dinitrosyl iron complexes

Huang HW, Lin YH, Lin MH, Huang YR, Chou CH, Hong HC, Wang MR, Tseng YT, Liao PC, Chung MC, Ma YJ, Wu SC, Chuang YJ, Wang HD, Wang YM, Huang HD, Lu TT, Liaw WF.

J Biol Inorg Chem. 2018 Jul;23(5):775-784. doi: 10.1007/s00775-018-1569-1. Epub 2018 Jun 1.


Gut microbiome changes in overweight male adults following bowel preparation.

Chen HM, Chen CC, Chen CC, Wang SC, Wang CL, Huang CH, Liou JS, Liu TW, Peng HL, Lin FM, Liu CY, Weng SL, Cheng CJ, Hung YF, Liao CC, Huang HD.

BMC Genomics. 2018 Dec 31;19(Suppl 10):904. doi: 10.1186/s12864-018-5285-6.


Idi1 and Hmgcs2 Are Affected by Stretch in HL-1 Atrial Myocytes

Fang CY, Chen MC, Chang TH, Wu CC, Chang JP, Huang HD, Ho WC, Wang YZ, Pan KL, Lin YS, Huang YK, Chen CJ, Lee WC.

Int J Mol Sci. 2018 Dec 18;19(12). pii: E4094. doi: 10.3390/ijms19124094.


Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation

Kung WH, Lee CL Yang CD, Yu CF, Chiew MY, Chen FH, Huang HD.

Comput Biol Chem. 2018 Jun;74:368-378. doi: 10.1016/j.compbiolchem.2018.03.016. Epub 2018 Mar 13.


Integrated MicroRNA-mRNA Analysis Reveals miR-204 Inhibits Cell Proliferation in Gastric Cancer by Targeting CKS1B, CXCL1 and GPRC5A

Shrestha S, Yang CD, Hong HC, Chou CH, Tai CS, Chiew MY, Chen WL, Weng SL, Chen CC, Chang YA, Lee ML, Huang WY, Hsu SD, Chen YC, Huang HD.

Int J Mol Sci. 2017 Dec 28;19(1). pii: E87. doi: 10.3390/ijms19010087.


Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops.

Int J Mol Sci. 2018 Aug 9;19(8). pii: E2335. doi: 10.3390/ijms19082335.

Yang CD, Huang HY, Shrestha S, Chen YH, Huang HD, Tseng CP.


MicroRNA-224 down-regulates Glycine N-methyltransferase gene expression in Hepatocellular Carcinoma

Hung JH, Li CH, Yeh CH, Huang PC, Fang CC, Chen YF, Lee KJ, Chou CH, Cheng HY, Huang HD, Chen M, Tsai TF, Lin AM, Yen CH, Tsou AP, Tyan YC, Chen YA.

Sci Rep. 2018 Aug 16;8(1):12284. doi: 10.1038/s41598-018-30682-5.


miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, Huang WC, Sun TH, Tu SJ, Lee WH, Chiew MY, Tai CS, Wei TY, Tsai TR, Huang HT, Wang CY, Wu HY, Ho SY, Chen PR, Chuang CH, Hsieh PJ, Wu YS, Chen WL, Li MJ, Wu YC, Huang XY, Ng FL, Buddhakosai W, Huang PC, Lan KC, Huang CY, Weng SL, Cheng YN, Liang C, Hsu WL, Huang HD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D296-D302. doi: 10.1093/nar/gkx1067.


Mitral valve repair versus replacement in patients with ischemic mitral regurgitation

Lee ML, Chen TH, Huang HD, Hou SM.

J Thorac Dis. 2018 May;10(5):2820-2828. doi: 10.21037/jtd.2018.04.93.


Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

Liu YC, Hong HC, Yang CD, Lee WH, Huang HT, Huang HD.

BMC Genomics. 2018 May 9;19(Suppl 2):171. doi: 10.1186/s12864-018-4456-9.


PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

Tsai MJ, Wang JR, Yang CD, Kao KC, Huang WL, Huang HY, Tseng CP, Huang HD, Ho SY.

Sci Rep. 2018 Jan 17;8(1):951. doi: 10.1038/s41598-017-18648-5.


The aquatic animals' transcriptome resource for comparative functional analysis

Chou CH, Huang HY, Huang WC, Hsu SD, Hsiao CD, Liu CY, Chen YH, Liu YC, Huang WY, Lee ML, Chen YC, Huang HD.

BMC Genomics. 2018 May 9;19(Suppl 2):103. doi: 10.1186/s12864-018-4463-x.


Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes

Weng SL, Huang KY, Weng JT, Hung FY, Chang TH, Lee TY.

Brief Bioinform. 2018 Nov 27;19(6):1102-1114. doi: 10.1093/bib/bbx046.


Rapid Detection of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight: Using a Machine Learning Approach and Unbiased Validation

Wang HY, Chen CH, Lee TY, Horng JT, Liu TP, Tseng YJ, Lu JJ.

Front Microbiol. 2018 Oct 11;9:2393. doi: 10.3389/fmicb.2018.02393. eCollection 2018.


Machine learning-based method for obesity risk evaluation using single nucleotide polymorphisms derived from next-generation sequencing

Wang HY, Chang SC, Lin WY, Chen C5, Chiang SH, Huang KY, Chu BY, Lu JJ, Lee TY.

J Comput Biol. 2018 Dec;25(12):1347-1360. doi: 10.1089/cmb.2018.0002. Epub 2018 Sep 8.


Delineation of Condition Specific Cis- and Trans-acting Elements in Plant Promoters under Various Endo- and Exogenous Stimuli

Chow CN, Chiang-Hsieh YF, Chien CH, Zheng HQ, Lee TY, Wu NY, Tseng KC, Hou PF, Chang WC.

BMC Genomics. 2018 May 9;19(Suppl 2):85. doi: 10.1186/s12864-018-4469-4.


A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach

Wang HY, Lee TY, Tseng YJ, Liu TP, Huang KY, Chang YT, Chen CH, Lu JJ.

PLoS One. 2018 Mar 13;13(3):e0194289. doi: 10.1371/journal.pone.0194289. eCollection 2018.


Dual role of ethyl bromodifluoroacetate in the formation of fluorine-containing heteroaromatic compounds

Ma X, Mai S, Zhou Y, Cheng GJ, Song Q.

Chem Commun (Camb). 2018 Aug 21;54(65):8960-8963. doi: 10.1039/c8cc04298e. Epub 2018 Jun 22.


Molecular dynamics study of taxadiene synthase catalysis

Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W.

J Comput Chem. 2018 Jul 15;39(19):1215-1225. doi: 10.1002/jcc.25184. Epub 2018 Feb 15.


Computational Study of B(C6F5)3-Catalyzed Selective Deoxygenation of 1,2-Diols: Cyclic and Noncyclic Pathways

Gui-Juan Cheng, Nikolaos Drosos, Bill Morandi, and Walter Thiel

ACS Catal. 2018, 8, 1697−1702. doi: 10.1021/acscatal.7b04209.


3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

Siqin Cao, Lizhe Zhu and Xuhui Huang

MOLECULAR PHYSICS, 2017. doi: 10.1080/00268976.2017.1416195.


Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models

Unarta IC, Zhu L, Tse CKM, Cheung PP, Yu J, Huang X.

Curr Opin Struct Biol. 2018 Apr;49:54-62. doi: 10.1016/ Epub 2018 Feb 3.


Harnessing complexity in molecular self-assembly using computer simulations

Zeng X, Zhu L, Zheng X, Cecchini M, Huang X.

Phys Chem Chem Phys. 2018 Mar 7;20(10):6767-6776. doi: 10.1039/c7cp06181a.


Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

Mei L, Zhou Y, Zhu L, Liu C, Wu Z, Wang F, Hao G, Yu D, Yuan H, Cui Y.

Int J Mol Sci. 2018 Mar 20;19(3). pii: E916. doi: 10.3390/ijms19030916.


Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk

Bratkowski M, Unarta IC, Zhu L, Shubbar M, Huang X, Liu X.

J Biol Chem. 2018 Feb 2;293(5):1651-1665. doi: 10.1074/jbc.M117.811521. Epub 2017 Nov 20.


Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

Zeng X, Li ZW, Zheng X, Zhu L, Sun ZY, Lu ZY, Huang X.

Phys Chem Chem Phys. 2018 Apr 18;20(15):10030-10037. doi: 10.1039/c8cp00522b.