Journal

Y.F. Yang, S.H. Yu, J.B. Liao, Y.H. Lin, “ Identification and validation of Novel Estrogen Biosynthesis Biomarkers in Sinonasal Inverted Papilloma ” International Journal of Medical Sciences, 2025, 22 (1),158-169

S.H. Yu, S.C. Chen, P.S. Wu, P.I. Kuo, T.A. Chen, H.Y. Lee, M.H. Lin, “ Quantification Quality Control Emerges as A Crucial Factor to Enhance Single Cell Proteomics Data Analysis ” Molecular & Cellular Proteomics, 2024, 100768

H. Lee*, S.H. Yu*, J.E. Shim and D. Yong, “ Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae ” mSystems, 2024, e00877-23 (Co-first author)

P.H. Wu, J. Lin, M.C. Kuo and S.H. Yu, “ The eQTL analysis to discover unique eGFR-related SNPs for the Taiwanese population ” Journal of Nephrology, 2023

P.S. Wu, S.H. Yu and M.H. Lin, “ Benchmarking dataset for optimizing differential expression analysis in label-free quantitative proteomic analysis ” Journal of Proteome Data and Methods, 2023, 5, 14

M.H. Lin, P.S. Wu, T.H. Wong, I.Y. Lin, J. Lin, J. Cox and S.H. Yu, “ Benchmarking differential expression, imputation and quantification methods for proteomics data ” Briefings in Bioinformatics, 2022, 23 (3), bbac138

K. Moon, M. Sim, C.H. Tai, K. Yoo, C. Merzbacher, S.H. Yu, D. Kim, J. Lee, K.U. Förstner, Q. Chen, S. Stibitz, L. Knipling and D. Hinton, “ Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic” Microbiology Spectrum, 2021, e0004421

S.H. Yu, P. Kyriakidou and J. Cox, “ Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ionbased quantification” Journal of Proteome Research, 2020, 19 (10), 3945-3954

S.H. Yu, D. Ferretti, J.P. Schessner, J.D. Rudolph, G.H.H. Borner and J. Cox, “ Expanding the Perseus software for omics data analysis with custom plugins” Current Protocols in Bioinformatics, 2020, 71 (1), e105

S.H. Yu, J. Vogel and K.U. Förstner, “ ANNOgesic: A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes” GigaScience, 2018, 7 (9), giy096

B. Remes, T. Rische-Grahl, K.M.H. Müller, K.U. Förstner, S.H. Yu, L. Weber, A. Jäger, V. Peuser and G. Klug, “An RpoHI-dependent response promotes outgrowth after extended stationary phase in the alphaproteobacterium Rhodobacter sphaeroides” Journal of bacteriology, 2017, 199 (14), e00249-17

J. Dingemans, P. Monsieurs, S.H. Yu, A. Crabbé, K.U. Förstner, A. Malfroot, P. Cornelis and R. Van Houdt, “Effect of shear stress on Pseudomonas aeruginosa isolated from the cystic fibrosis lung” MBio, 2016, 7 (4), e00813-16

S.W. Yeh, T.T. Huang, J.W. Liu, S.H. Yu, C.H. Shih, J.K. Hwang and J. Echave, “Local packing density is the main structural determinant of the rate of protein sequence evolution at site level” BioMed research international, 2014

S.W. Yeh, J.W. Liu, S.H. Yu, C.H. Shih, J.K. Hwang and J. Echave, “Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure” Molecular Biology and Evolution, 2013, 31 (1), 135-139

S.W. Huang, S.H. Yu, C.H. Shih, H.W. Guan, T.T. Huang and J.K. Hwang, “On the relationship between catalytic residues and their protein contact number” Current Protein and Peptide Science, 2011, 12 (6), 574-579

Y.L. Lai, S.C. Yen, S.H. Yu and J.K. Hwang, “pKNOT: the protein KNOT web server” Nucleic acids research, 2007, 35, W420-W424

C.H. Shih, S.W. Huang, S.C. Yen, Y.L. Lai, S.H. Yu and J.K. Hwang, “A simple way to compute protein dynamics without a mechanical model” PROTEINS: Structure, Function, and Bioinformatics, 2007, 68 (1), 34-38

Book Chapter

C.H. Tai, D. Hinton and S.H. Yu, “ Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic” Bacterial regulatory RNAs - Methods and Protocols, 2nd Edition, MIMB, volume 2741, 2024, p.p. 35-69,