Pei-Yu Lin

Experiences

Research Assistant (RA)

Institute of Plant ans Microbial Biology, Academia Sinica

Nov 2019 - present (4 yr)

Taipei, Taiwan

• Adopted a novel method for fungal genomic research and reach 90% accuracy in essential gene prediction
• Analysed the NGS samples mostly ATAC-seq and RNA-seq
• Developed and maintain the programmes for bioinformatic analyses
• Wrote research reports and papers
• Gave lectures in the universities for graduated students about NGS analyses
• Maintained and managed the four servers and lab website
• Recruited new lab members and mentored undergraduate students

Bioinformatics

Biostatistics

Epigenetics

R

Python

Intern

Conservation centre, Taipei Zoo

Jul 2016 - Aug 2016 (2 mon)

Taipei, Taiwan

• Designed and implemented behavioural enrichment strategies for sun bears
• Wrote and present research reports

Ecology

Conservation

Behaviour

Bears

Zoology

Education

University of Aberdeen

MSc in Ecology and Conservation

Aug 2018 - Jun 2019

Influences of Social and Spacing System on the Subadult of Townsend’s Vole (Microtus townsendii)

Fu Jen Catholic University

BSc in Life Science

Sep 2014 - Jun 2018

Olfactory Cues to Elicit Aggressive Response of Two Gall-forming Aphids in Hormaphidinae

Fungal Genomics

Main project | Nov 2019 - Present

Predict fungal essential gene through core gene identification
Predict biosynthesis gene clusters based on essential genes

Collaboration | May 2021 - Present

Identify actin biosynthesis-related of Antrodia cinnamon

Fungi

Genomics

Core genes

Essential genes

BGC

Maize (Epi)genomics

Jun 2022 - Present

Validate a new maize ATAC-seq protocol

Collaboration | Jun 2021 - Present

Find maize ufo1 related DEG

ATAC-seq

RNA-seq

Zea Maize

Methylation Analyses

Dec 2021 - Present

Construct a tool for calculating methtylaion heterogeneity

OCt 2022 - Present

Improve a tool for methylation analyses

Methylation heterogeneity

Mathematical model

Biodiversity framework

0000-0003-0255-5467

Google Scholar

*co-first author

Publications

JW. A. Hsieh*, PY. Lin*, CT. Wang, YJ. Lee, P. Chang, R. JH. Lu, PY. Chen and CJ. R. Wang (2024) Establishing an optimized ATAC-seq protocol for the maize Frontiers in Plant Science, Sec. Plant Genetics, Epigenetics and Chromosome Biology, Volume 15, https://doi.org/10.3389/fpls.2024.1370618

PY. Lin* YT. S. Chang, YC. Hunag and PY. Chen (2023) There’s More to It: Uncovering Genomewide DNA Methylation Heterogeneity Epigenetics & Chromatin, https://doi.org/10.1186/s13072-023-00521-7

HT Lee, PY. Lin and PY. Chen (2023) There’s More to It: Uncovering Genomewide DNA Methylation Heterogeneity Epigenomics, https://doi.org/10.2217/epi-2023-0228

R. JH. Lu*, PY. Lin*, MR. Yen*, BH. Wu and PY. Chen (2023) MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation Botanical studies, https://doi.org/10.1186/s40529-022-00366-5

PY. Lin and PY. Chen (2021) Review of: Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction. Qeios, https://doi.org/10.32388/14X8U9

Book chapter

PY. Lin, KL. Chen, GJ. Lin, SC. Huang and PY. Chen (2024) Bioinformatics Analysis of DNA Methylation. Methods in Molecular Biology, Accepted

CY. L. Sheu*, YC. Huang*, PY. Lin , GJ. Lin and PY. Chen (2024) Bioinformatics of Epigenetic Data Generated from Next-Generation Sequencing, chapter 4. Elsevier in Translational Epigenetics, 3 edition, ISBN: 9780443218125

Conferences

2023 - Jul : Identification of Core Genes in Fungal Genomes Assisting the Discovery of Essential Genes. oral session presented at 2023 MSA Annual Meeting: Elevating Mycology, Flagstaff, Arizona, USA
2022 - Jul : Estimating Genome-wide DNA Methylation Heterogeneity with Methylation Patterns. oral session presented at The 31th South Taiwan Statistic Conference, Taichung, Taiwan
2021 - Dec : 500 Fungal Genomes: Predicting Essential Genes through Core Genes by Network Statistics. poster session presented at Academic Advisory Committee Meeting, online
2021 - Nov : A network-based method for predicting fungal essential genes through identification of core genes. oral presented at Annual Meeting of Taiwan Mycological Society, online
2021 - Oct : A network-based method for predicting fungal essential genes through identification of core genes. oral presented at The 30th South Taiwan Statistic Conference, Kaohsiung, Taiwan
2021 - Jul : 500 Fungal Genomes: Finding Essential Genes based on Core Genes Prediction. poster session presented at Botany 2021 Virtual, online
2021 - Apr : Finding Potential Drug Targets of Pathogenic Fungi by Fungal Essential Genes Through Core Genes Prediction. poster session presented at Annual Meeting of Taiwan Agronomy Society, Chiayi, Taiwan
2020 - Oct : FunCore: A Database for Fungal Core Genes. poster and short talk session presented at Annual Meeting of Taiwan Mycological Society, Taipei, Taiwan
2020 - Jul : FunCore: A Database for Fungal Core Genes. poster session presented at Annual Meeting of Mycological Society of America, online
2018 - Mar : Olfactory Cues to Elicit Aggressive Response of Two Gall-forming Aphids in Hormaphidinae. poster session presented at Seventh International Symposium on Cecidology, Nantou, Taiwan
2017 - Jan : Behavioural Enrichment Strategies of Sun Bear (Helarctos malayanus) in Taipei Zoo. poster session presented at 2017 Congress of Animal Behavior and Ecology, Kaohsiung, Taiwan