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.

https://www.ncbi.nlm.nih.gov/pubmed/31311925


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30917677


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30612502


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30944305


 

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.

https://www.cellphysiolbiochem.com/Articles/000029/


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30418626


 

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]

https://www.ncbi.nlm.nih.gov/pubmed/31155657


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/31423009


 

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. https://doi.org/10.1186/s12859-018-2394-9

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2394-9


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/31012976


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30894197


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30380085


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30395277


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30717647


 

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.

https://aip.scitation.org/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.

https://linkinghub.elsevier.com/retrieve/pii/S157096391730211X


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29773668


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29518940


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29570986


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29363420


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30237403


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29362114


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29858679


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30598081


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30567295


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29615312


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29283424


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30096859


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30115977


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29126174


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29997945


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29764361


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29343727


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29764375


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/28531277


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30364336


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/30204480


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29764390


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29534106


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29932181


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29450907


 

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.

https://pubs.acs.org/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.

https://www.tandfonline.com/doi/full/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/j.sbi.2018.01.002. Epub 2018 Feb 3.

https://www.ncbi.nlm.nih.gov/pubmed/29414512


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29479585


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29558421


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29158257


 

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.

https://www.ncbi.nlm.nih.gov/pubmed/29620122