Research

Research interests

• Next generation sequencing (NGS) data analysis

• Epigenetics and transcriptomics

• Genome annotation

• Comparative genomics

Publications

Journal article

1. Chew C, Brand OJ, Yamamura T, Lawless C, Morais MRPT, Zeef L, Lin IH, Howell G, Lui S, Lausecker F, Jagger C, Shaw TN, Krishnan S, McClure FA, Bridgeman H, Wemyss K, Konkel JE, Hussell T, Lennon R (2024). Kidney resident macrophages have distinct subsets and multifunctional roles. Matrix Biol. S0945-053X(24)00021-0. (PMID: 38331051; DOI)

2. Tachó-Piñot R, Stamper CT, King JI, Matei-Rascu V, Richardson E, Li Z, Roberts LB, Bassett JW, Melo-Gonzalez F, Fiancette R, Lin IH, Dent A, Harada Y, Finlay C, Mjösberg J, Withers DR, Hepworth MR (2023). Bcl6 is a subset defining transcription factor of Lymphoid Tissue inducer-like ILC3. Cell Rep. 42(11):113425 (PMID: 37950867; DOI)

3. Richardson R, Feigin CY, Bano-Otalora B, Johnson MR, Allen AE, Park J, McDowell RJ, Mereby SA, Lin IH, Lucas RJ, Mallarino R (2023) The genomic basis of temporal niche evolution in a diurnal rodent. Curr Biol. 33(15):3289-3298.e6. (PMID: 37480852; DOI)

4. Gregory G, Jones AP, Haley M, Hoyle C, Zeef L, Lin IH, Coope D, King A, Evans DG, Paszek P, Couper K, Brough D, Pathmanaban O (2023). The comparable tumour microenvironment in sporadic and NF2-schwannomatosis vestibular schwannoma. Brain Commun. 5(4):fcad197 (PMID: 37680691; DOI)

5. Gu NX, Guo YR, Lin SE, Wang YH, Lin IH, Chen YF, Yen Y (2023). Frizzled-7 modulates Goblet and Paneth cell fate and maintains the homeostasis in intestines. Development. 150(4):dev200932. (PMID: 36691900; DOI)

6. Chen WJ, Lin IH, Lee CW, Yoshioka K, Ono Y, Yan YT, Yen Y, Chen YF (2022). Ribonucleotide reductase M2B in the myofibers modulates stem cell fate in skeletal muscle. NPJ Regen Med. 7(1):37. (PMID: 35906243; DOI)

7. Huang WC, Tung CL, Yang YC, Lin IH, Ng XE, Tung YT (2022). Endurance exercise ameliorates Western diet–induced atherosclerosis through modulation of microbiota and its metabolites. Sci Rep. 12(1):3612. (PMID: 35256637; DOI)

8. Le TT, Hsieh CL, Lin IH, Chu CY, Do AD, Chen SH, Shigemura K, Kitagawa K, Fujisawa M, Liu MC, Chen KC, Sung SY (2022). The ADAM9/UBN2/AKR1C3 axis promotes resistance to androgen-deprivation in prostate cancer. Am J Cancer Res. 12(1):176-197. (PMID: 35141012)

9. Tung YT, Zeng JL, Ho ST, Xu JW, Lin IH, Wu JH (2022). Djulis Hull Improves Insulin Resistance and Modulates the Gut Microbiota in High-Fat Diet (HFD)-Induced Hyperglycaemia. Antioxidants (Basel). 11(1):45. (PMID: 35052549; DOI)

10. Barnes BM, Nelson L, Tighe A, Burghel GJ, Lin IH, Desai S, McGrail JC, Morgan RD, Taylor SS (2021). Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes. Genome Med. 13(1):140. (PMID: 34470661; DOI)

11. Huang YF, Chang CH, Chen PJ, Lin IH, Tsai YA, Chen CF, Wang YC, Huang WY, Tsai MS, Chen ML (2021). Prenatal Bisphenol A Exposure, DNA methylation, and Low Birth Weight: A Pilot Study in Taiwan. Int J Environ Res Public Health. 18(11):6144. (PMID: 34200176; DOI)

12. Chen WJ, Lin IH, Lee CW, Chen YF (2021).  Aged Skeletal Muscle Retains the Ability to Remodel Extracellular Matrix for Degradation of Collagen Deposition after Muscle Injury. Int J Mol Sci 22(4):2123. (PMID: 33672763; DOI)

13. Lee YL, Ito K, Pi WC, Lin IH, Chu CS, Malik S, Cheng IH, Chen WY, Roeder R (2021). Mediator subunit MED1 is required for E2A-PBX1–mediated oncogenic transcription and leukemic cell growth. Proc Natl Acad Sci U S A. 118(6):e1922864118. (PMID: 33542097; DOI)

14. Chu CY, Lee YC, Hsieh CH, Yeh CT, Chao TY, Chen PH, Lin IH, Hsieh TH, Shih JW, Cheng CH, Chang CC, Lin PS, Huang YL, Chen TM, Yen Y, Ann D, Kung HJ (2021). Genome-wide CRISPR/Cas9 knockout screening uncovers a novel inflammatory pathway critical for resistance to arginine-deprivation therapy. Theranostics. 11(8):3624-3641. (PMID: 33664852; DOI)

15. Lo YC, Chen KY, Chou HC, Lin IH, Chen CM (2021). Neonatal hyperoxia induces gut dysbiosis and behavioral changes in adolescent mice.  J Chin Med Assoc. 84(3):290-298. (PMID: 33496514; DOI)

16. Hsieh SY, Lian YZ, Lin IH, Yang YC, Tinkov A, Skalny A, Chao J (2021). Combined Lycium babarum polysaccharides and C-phycocyanin increase gastric Bifidobacterium relative abundance and protect against gastric ulcer caused by aspirin in rats. Nutr Metab (Lond). 18(1):4.  (PMID:  33407626; DOI)

17. Lian YZ, Lin IH, Yang YC, Chao J (2020). Gastroprotective effect of Lycium barbarum polysaccharides and C-phyocyanin in rats with ethanol-induced gastric ulcer. Int J Biol Macromol. 165(Pt A):1519-1528. (PMID: 33058973; DOI)

18. Olie CS, van der Wal E, Domagoj C, Maton L, de Greef JC, Lin IH, Chen YF, Kareem E, Penninger JM, Kessler BM, Raz V (2020). Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability. Sci Rep. 10(1):17621. (PMID: 33077830; DOI)

19. Lee HC, Lo YC, Yu SC, Tung TH, Lin IH, Huang SY (2020). Degree of lipid saturation affects depressive-like behaviour and gut microbiota in mice.  Int J Food Sci Nutr. 71(4):440-452. (PMID: 31645150; DOI)

20. Chen YF, Chou TY, Lin IH, Chen CG, Kao CH, Huang GJ, Chen LK, Wang PN, Lin CP, Tsai TF (2020). Upregulation of Cisd2 attenuates Alzheimer's related neuronal loss in mice.  J Pathol. 250(3):299-311. (PMID: 31837018; DOI)

21. Yang YC, Chang HW, Lin IH, Chien LN, Wu MJ, Liu YR, Chu P, Xie G, Dong F, W Jia, Chang V, Yen Y (2020). Long-term Proton Pump Inhibitor Administration Caused Physiological and Microbiota Changes in Rats. Sci Rep. 21;10(1):866. (PMID: 31964941; DOI)

22. Tung TH, Tung YT, Lin IH, Shih CK, Nguyen NTK, Shabrina A, Huang SY (2019). Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress. Biomolecules. 21;9(10). (PMID: 31546592)

23. Yang YN, Yang YSH, Lin IH, Chen YY, Lin HY, Wu CY, Su YT, Yang YJ, Yang SN, Suen JL (2019). Phthalate exposure alters gut microbiota composition and IgM vaccine response in human newborns. Food Chem Toxicol. 132:110700. (PMID: 31356917)

24. Chen YF, Lin IH, Guo YR, Chiu WJ, Wu MS, Jia W, Yen Y (2019). Rrm2b deletion causes mitochondrial metabolic defects in renal tubules. Sci Rep. 13;9(1):13238. (PMID: 31519977)

25. Lee HC, Yu SC, Lo YC, Lin IH, Tung TH, Huang SY (2019). A high linoleic acid diet exacerbates metabolic responses and gut microbiota dysbiosis in obese rats with diabetes mellitus. Food Funct. 10(2):786-798. (PMID: 30672576)

26. Lee WH, Chen LC, Lee CJ, Huang CC, Ho YS, Yang PS, Ho CT, Chang HL, Lin IH, Chang HW, Liu YR, Wu CH, Tu SH (2019). DNA primase polypeptide 1 (PRIM1) involves in estrogen-induced breast cancer formation through activation of the G2/M cell cycle checkpoint. Int J Cancer. 144(3):615-630. (PMID: 30097999)

27. Lin IH, Chang JL, Hua K, Huang WC, Hsu MT, Chen YF (2018). Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression. BMC Genet. 19(1):55. (PMID: 30089464)

28. Lin IH, Chen YF, Hsu MT (2017). Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver. PLoS One.12(1):e0170779. (PMID: 28125731)

29. Su CH, Lin IH, Tzeng TY, Hsieh WT, Hsu MT (2016). Regulation of IL-20 Expression by Estradiol through KMT2B-mediated Epigenetic Modification. PLoS One. 11(11):e0166090. (PMID: 27806114)

30. Su CH, Cheng C, Tzeng TY, Lin IH, Hsu MT (2016). An H2A Histone Isotype, H2ac, Associates with Telomere and Maintains Telomere Integrity. PLoS One. 11(5):e0156378. (PMID: 27228173)

31. Lee YL, Li YC, Su CH, Chiao CH, Lin IH, Hsu MT (2015). MAF1 represses CDKN1A through a Pol III-dependent mechanism. eLife. 4:e06283. (PMID: 26067234)

32. Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT (2015). Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes. PLoS One. 10(2):e0118453. (PMID: 25706888)

33. Wu PC, Lu JW, Yang JY, Lin IH, Ou DL, Lin YH, Chou KH, Huang WF, Wang WP, Huang YL, Hsu C, Lin LI, Lin YM, Shen CK, Tzeng TY (2014). H3K9 Histone Methyltransferase, KMT1E/SETDB1, Cooperates with the SMAD2/3 Pathway to Suppress Lung Cancer Metastasis. Cancer Res. 74(24):7333-43. (PMID: 25477335)

34. Lin IH, Hsu MT, Chang CH (2012). Protein domain repetition enriched in Streptococcal cell-surface proteins. Genomics. 100(6):370-9. (PMID: 22921469)

35. Liu YC, Lin IH, Chung WJ, Hu WS, Ng V, Lu CY, Huang TY, Shu HW, Hsiao KJ, Tsai SF, Chang CH, Lin CH (2012). Proteomics characterization of cytoplasmic and lipid-associated membrane proteins of human pathogen Mycoplasma fermentans M64. PLoS One. 7(4):e35304. (PMID: 22536369)

36. Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT (2011). Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence. PLoS ONE 6(5): e20519. (PMID: 21633709)

37. Liao WC, Ng V, Lin IH, Syu WJ, Liu TT, Chang CH (2011). T4-like Genome Organization of the Escherichia coli O157:H7 Lytic Phage AR1. J Virol. 85(13):6567-78. (PMID: 21507986)

38. Lai CJ, Chen SY, Lin IH, Chang CH, Wong HC (2009). Change of protein profiles in the induction of the viable but nonculturable state of Vibrio parahaemolyticus. Int J Food Microbiol. 135(2):118-24. (PMID: 19735955)

39. Lan SF, Huang CH, Chang CH, Liao WC, Lin IH, Jian WN, Wu YG, Chen SY, Wong HC (2009). Characterization of a New Plasmid-like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 strain. Appl Environ Microbiol. 75(9):2659-67. (PMID: 19286788)

Book chapter

1. Lin IH (2018) Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq). In: Brachypodium Genomics. Methods in Molecular Biology, Drs. Gaurav Sablok, Hikmet Budak, and Peter J. Ralph (Eds.), ISBN 978-1-4939-7278-4, Humana Press. (Available from: springer.com) (PMID:  29039015)

2. Lin IH, Hsu MT (2016). Analysis of microarray gene expression data of 10086 samples uncovers genes that sub-classify breast cancer intrinsic subtypes. In: Breast Cancer, Dr. Phuc Van Pham (Ed.), ISBN 978-953-51-4947-7, InTech. (Available from: intechopen.com)

3. Lin IH, Hsu MT (2015). Genome-Wide Gene Expression Analysis to Identify Epistatic Gene-Pairs Associated with Prognosis of Breast Cancer. In: A Concise Review of Molecular Pathology of Breast Cancer, Prof. Mehmet Gunduz (Ed.), ISBN: 978-953-51-2030-8, InTech. (Available from: intechopen.com)

Invited Talks

1. Research and clinical applications of next-generation sequencing technologies. Taipei Medical University (U-Town). July 19, 2019

2. Identification of Chinese colon cancer mutation landscape. Case Western Reserve University. May 23, 2019.

3. Long-term follow-up of gut microbiota in Taiwanese colorectal cancer patients. Taipei Medical University (Main Campus), January 12, 2019.

4. Microbial community structure and biodiversity assessment using next-generation sequencing technology. Academia Sinica, November 08, 2018

5. An overview of epigenomics and epigenome-wide analysis. Tri-Service General Hospital, National Defense Medical Center, April 12, 2018

6. Gut microbiome profiling using 16S rDNA sequencing. Taipei Medical University (Main Campus), November 18, 2017.

7. NGS workshop: Hands-on training in RNA-Seq data analysis. Academia Sinica, November 19, 2015. Online Resource

8. NRPB workshop: Hands-on training in methylation sequencing analysis. National Yang-Ming University, December 19, 2014. Online Resource

Conferences

1. Lin IH, Chang CH. (2009). Computational Analysis of Mycoplasma fermentans M64 Genome. BioSysBio Conference 2009. Cambridge, UK.

2. Liao WC, Lin IH, Tseng CH, Chang CH. (2007). Systematic Genomic Approach to Unique Gene Discovery: A Lactococcus lactis Example. 11th Bacteria Conference. Hsinchu, Taiwan.

3. Lin IH, Chen KB, Lin YH, Chang CH. (2006). Automated Prediction Of Bacterial Replication Origin (APBRO). 4th Asia Pacific Bioinformatics Conference. Taipei, Taiwan.

4. Chang YF, Chen CY, Chen HW, Lin IH, Luo WX, Yang CH, Lin YH, Chang CH. (2005). Bioinformatics analysis for genome design and synthetic biology. 5th Emerging Information Technology Conference. Taipei, Taiwan.

5. Lin IH, Chang CH. (2004). Comparative Analysis of Mycoplasmal Replication Origins. 8th Bacteria Conference. Hualien, Taiwan.