Yu-Feng Huang, Ph.D / 黃鈺峰

E-mail: yfhuang{at}csie{dot}ntu{dot}edu{dot}tw; yfhuang{at}gmail{dot}com

Research social network
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Introduction

Yu-Feng Huang obtained his Ph.D. in 2010 from the Department of Computer Science and Information Engineering at National Taiwan University, specializing in protein binding residue prediction. Following graduation, he continued his research in protein-DNA and protein-RNA binding site prediction as a Postdoctoral Researcher under his doctoral advisor.

In 2011, Yu-Feng joined Academia Sinica as a Postdoctoral Researcher in the laboratory of Dr. Kuo-Ping Chiu. He later transitioned to TOP Science Biotechnologies Inc. in 2021, a company founded by Dr. Chiu, where he continued his work as a Postdoctoral Researcher.

In July 2021, he joined ACT Genomics Inc. as a Senior Bioinformatics Engineer. His career progression at ACT Genomics was rapid: in July 2022, he was promoted to Manager of the Department of Applied Artificial Intelligence, and following a departmental reorganization in September 2022, he became Manager of the Department of Bioinformatics Innovation. By August 2023, he was promoted to Associate Director of the Division of Bioinformatics.

Demonstrating a strong commitment to innovation, Yu-Feng assumed the role of Innovation Project Lead in May 2024, focusing on the development of cutting-edge products. Most recently, in September 2024, he took on the position of Team Lead of the Bioinformatics Development Department, where he is responsible for delivering LDTS-grade pipelines to support assay development.

Research Interests

• Big data analysis for next-generation sequencing (NGS)
  Applications by using next-generation sequencing for biomarker identification, gene assembly, gene expression, cancer research, etc.
• Bioinformatics/computational biology
  Applying information technology on solving biological problems from data collection including sequence, structure and interaction analysis.
• Data mining and machine learning
  Improving machine learning and data mining techniques and applying on applications including bioinformatics. medical informatics or next-generation sequencing.

Professional Skills

As a cross-disciplinary bioinformatics expert and software architect, I focus on building advanced, production-grade genomic analysis workflows that bridge research and clinical diagnostics. My approach combines scientific rigor with modern software engineering practices, ensuring scalability, accuracy, and regulatory compliance in NGS-based precision oncology.

Bioinformatics Leadership & Genomic Data Science

• Architect end-to-end NGS pipelines for detecting SNVs, INDELs, CNVs, MSI, LGRs, and gene fusions using hybrid capture technology or cutting-edge biotechnology
• Lead clinical pipeline development under CAP/ISO compliance frameworks with full IQ/OQ/PQ implementation
• Specialize in assay performance evaluation, probe capture efficiency, and quality metrics such as Fold 80 Base Penalty
• Implement statistical modeling for somatic variant calling, including LoD/LoB estimation, PoN construction, and outlier filtering

Software Development & DevOps Engineering

• Design and maintain scalable bioinformatics workflows using Nextflow DSL2, shell scripting, and LSF-based cluster scheduling
• Develop Python-based tools for fusion detection, MNV simulation, variant parsing, and coverage QC
• Deploy pipelines on Kubernetes (K8s) environments using Docker for containerized, reproducible execution
• Adopt industry best practices in version control (Git/Git LFS) and project tracking (Jira, Markdown documentation)

I am committed to delivering precision bioinformatics solutions that are scientifically sound, operationally efficient, and clinically impactful.

Education

• Advanced Training, Bioinformatics and Comparative Genome Analysis 2010, Institut Pasteur Paris (2010.7.5 ~ 2010.7.17)
  Topics: Genomes databases, comparisons, visualizations and alignments; Phylogenetics analyses; Orthologs prediction and classification; Next generation sequencing
• D.Sc. Computer Science and Information Engineering, National Taiwan University (2003.9 ~ 2010.1)
  Advisors: Dr. Yen-Jen Oyang and Dr. Chien-Kang Huang
  Dissertation: A study of prediction of protein binding residues
• M.Sc. Computer Science, National Chung Cheng University (1999.9 ~ 2001.6)
  Advisor: Dr. Sun Wu
  Thesis:Personalized Information Subscription and Search
• B.Sc. Computer Science and Engineering, Yuan Ze University (1995.9 ~ 1999.6)

Experience

• 2024.09 ~, Team Lead, Bioinformatics Development Department
  ACT Genomics Inc.
• 2024.05 ~ 2024.08, Innovation Project Lead
  ACT Genomics Inc.
• 2023.08 ~ 2024.04, Associate Director
  Division of Bioinformatics, ACT Genomics Inc.
• 2022.09 ~ 2023.07, Manager
  Department of Bioinformatics Innovation, Division of Bioinformatics, ACT Genomics Inc.
• 2022.07 ~ 2022.08, Manager
  Department of Applied Artificial Intelligence, Division of Software Service, ACT Genomics Inc.
• 2021.07 ~ 2022.06, Senior Bioinformatics Engineer
  Division of Bioinformatics and Artificial Intelligence, ACT Genomics Inc.
• 2021.08 ~ 2022.01, Adjunct Assistant Professor
  Deaprtment of Computer Science and Engineering, Yuan-Ze University
• 2021.02 ~ 2021.06, Postdoctoral Researcher
  TOP Science Biotechnologies Inc.
• 2011.10 ~ 2021.01, Postdoctoral Researcher
  Genomics Research Center, Academia Sinica
  Topic: NGS-driven genome data analysis
• 2010.02 ~ 2011.07, Postdoctoral Researcher
  Department of Computer Science & Information Engineering, National Taiwan University
  Topic: binding residues prediction for protein energy function design
• 2005.06 ~ 2011.07, System Administrator
  Core Facility, Center for Systems Biology, National Taiwan University
  
• 2005 ~ 2010 System developer
  NTU Biotech Summer Courses online registration system development, Center for Biotechnology, National Taiwan University
• 2008.09 ~ 2009.06, Adjunct Lecturer
  Department of Information Management, Hwa Hsia Institute of Technology
• 2006.06 ~ 2006.12, Co-system developer
  Mutual Found Performance Evaluation, Taiwan, Department of Finance, National Taiwan University
• 2004.08 ~ 2006.07, Full-Time Teaching Assistant / System Administrator
  Workstation Laboratory, Department of Computer Science and Information Engineering, National Taiwan University
• 2002.09 ~ 2004.02, Adjunct Lecturer
  Department of Electronic Engineering, Hwa Hsia Institute of Technology

Honors and Awards

• Marquis Who’s Who in the World listee: 2011, 2014~2015, 2017~2020
• GRC Outstanding Performance Awards, Postdoctoral: 2013, 2018
• Marquis Who’s Who in the World Top 3% listee: 2018~2019
• Yu-Feng Huang, Chia-Chen Chang, Chien-Kang Huang, “Residue Environment Property Explorations on DNA-binding Proteins,” Best Poster Award (2008), Asia Pacific Bioinformatics Conference (APBC2008), Kyoto, Japan, January 14-17 2008.
• John Yu-Feng Huang, Chi-Jun Sheu, Tian-Wei Hsu, Chien-Kang Huang, “Mining Conserved Local Structure from Functional Hierarchical Classification via Local Structure Comparison,” Good Paper Award (2006), Computer Society of the Republic of China.

Academic Service

• Reviewer for Wellcome Data Note, 2024~2025.
• Reviewer for Frontiers in Genetics, 2023.
• Reviewer for Genes and Genomics, 2017.
• Reviewer for Evolutionary Bioinformatics, Libertas Academica, 2014~2017.
• Reviewer for Cancer Informatics, Libertas Academica, 2015~2017.
• Reviewer for Briefings in Bioinformatics, Oxford University Press, 2011~2013.
• Reviewer for a special issue of BMC Bioinformatics for ISBRA (International Symposium on Bioinformatics Research and Applications, 2011), 2011.

Patents

• 2016/09/30 Issued: Taiwan, IA0001/ACA0096TW. Kuo Ping Chiu, Yu-Shin Nai and Yu-Feng Huang. Methods for full-length amplification of double-stranded linear nucleic acids of unknown sequences (未知序列之雙股線性核酸之全長增幅方法). [URL]
• DNA sample non-selective amplification. Try TOP-PCR!!

Publication

• Journal Papers
  1. Yu-Yun Kuo, Ju-Chun Chang, Yi-Hsuan Li, Yu-Feng Huang, Tzong-Yuan Wu, Yu-Shin Nai, "The Complete Mitochondrial Genome and Phylogenetic Analysis of Rhagastis binoculata (Matsumura, 1909) (Lepidoptera: Sphingidae)," Genes, 2024. [doi]
  2. Yao-Chia Liu, Tzu-Han Chen, Yu-Feng Huang, Chang-Lin Chen, Yu-Shin Nai, "Investigation of the fall armyworm Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome," Journal of Invertebrate Pathology, 2023. [doi]
  3. Yi-Hsuan Li, Ju-Chun Chang, Ming-Ren Yen, Yu-Feng Huang, Tzu-Han Chen, Li-Hung Chen, Yu-Shin Nai, "Whole-genome DNA methylome analysis of different developmental stages of the entomopathogenic fungus Beauveria bassiana NCHU-157 by nanopore sequencing," Frontiers in Genetics. 2023. [doi]
  4. Yi-Hsuan Li Zih-Ting Chang, Ming-Ren Yen, Yu-Feng Huang, Tzu-Han Chen, Ju-Chun Chang, Ming-Cheng Wu, Yu-Liang Yang, Yue-Wen Chen, Yu-Shin Nai, "Transcriptome of Nosema ceranae and Upregulated Microsporidia Genes during Its Infection of Western Honey Bee (Apis mellifera)," Insects. 2022. [doi]
  5. Yu-Feng Huang, Hakan Bozdoğan, Tzu-Han Chen, Chia-Chieh Hsieh, Yu-Shin Nai, "The complete mitochondrial genome of Attacus atlas formosanus Villiard, 1969 (Lepidoptera: Saturniidae)," Mitochondrial DNA Part B: Resources, 2022 [doi]
  6. Zih-Ting Chang, Yu-Feng Huang, Yue-Wen Chen, Ming-Ren Yen, Po-Ya Hsu, Tzu-Han Chen, Yi-Hsuan Li, Kuo-Ping Chiu, Yu-Shin Nai, "Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae," Nature Scientific Reports, 2021. [doi]
  7. Yi-Hsuan Li, Yu-Feng Huang, Tzu-Han Chen, Shin-Shan Wu, Hsin-Chieh Tang, Chung-Yi Hsiao, Lung-Chun Huang, Ju-Chun Chang, Kuo-Ping Chiu , Yu-Shin Nai, “Comparison of gut microbiota of healthy and diseased walking sticks, Phasmotaenia lanyuhensis," Archives of Insect Biochemistry and Physiology, 2020. [doi]
  8. Mohit K. Midha, Yu-Feng Huang, Hsiao-Hsiang Yang, Tan-Chi Fan, Nai-Chuan Chang, Tzu-Han Chen, Yu-Tai Wang, Wen-Hung Kuo, King-Jen Chang, Chen-Yang Shen, Alice L. Yu, Kuo-Ping Chiu, Chien-Jen Chen, “Comprehensive cohort analysis of mutational spectrum in early-onset breast cancer patients," Cancers, 2020. [doi]
  9. Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo-Ping Chiu, Yu-Shin Nai, “Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features," BMC Genomics, 2019. [doi]
  10. Yih-Shien Chiang, Yu-Feng Huang, Mohit K. Midha, Tzu-Han Chen, Hsin-Chieh Shiau, Kuo-Ping Chiu, “Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions," PLOS ONE, 2018. [doi]
  11. Ju-Chun Chang, Zih-Ting Chang, Yu-Feng Huang, Se Jin Lee, Jae Su Kim, Yu-Shin Nai, “Characterization and functional assay of apsup (Lyxy105) from Lymantria xylina multiple nucleopolyhedrovirus (LyxyMNPV)," Virus Genes, 2018. [doi]
  12. Yu-Feng Huang, Yen-Ju Chen, Tan-Chi Fan, Nai-Chuan Chang, Yi-Jie Chen, Mohit K. Midha, Tzu-Han Chen, Hsiao-Hsiang Yang, Yu-Tai Wang, Alice L. Yu and Kuo-Ping Chiu, “Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females," BMC Medical Genomics, 2018. [doi]
  13. Yu-Shin Nai, Tzu-Han Chen, Yu-Feng Huang, Mohit K. Midha, Hsin-Chieh Shiau, Chen-Yang Shen, Chien-Jen Chen, Alice L. Yu and Kuo Ping Chiu, “T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids," Nature Scientific Reports, 2017. [doi]
  14. Yu-Feng Huang, Mohit Midha, Tzu-Han Chen, Yu-Tai Wang, David Glenn Smith, Kurtis Jai-Chyi Pei, Kuo Ping Chiu, “Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy," PLOS ONE, 2015. [doi]
  15. Hung-Ju Hsu, Kuo Hao Lee, Jhih-Wei Jian, Hung-Ju Chang, Chung-Ming Yu, Yu-Ching Lee, Ing-Chien Chen, Hung-Pin Peng, Chih Yuan Wu, Yu-Feng Huang, Chih-Yun Shao, Kuo Ping Chiu, An-Suei Yang, “Antibody Variable Domain Interface and Framework Sequence Requirements for Stability and Function by High-Throughput Experiments," Structure, 2014. [doi]
  16. Yen-Ju Chen, Mike W. C. Thang, Yu-Tzu Chan, Yu-Feng Huang, Nianhan Ma, Alice L. Yu, Chung-Yi Wu, Miao-Lin Hu, Kuo Ping Chiu, “Global Assessment of Antrodia cinnamomea-Induced MicroRNA Alterations in Hepatocarcinoma Cells," PLOS ONE, 2013. [doi]
  17. Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen, Kuo Ping Chiu, “Palindromic sequence impedes sequencing-by-ligation mechanism," BMC Systems Biology 2012, 6(Suppl 2):S10 [doi]
  18. Yi-Zhong Weng, Darby Tien-Hao Chang, Yu-Feng Huang, Chih-Wei Lin, “A study on the flexibility of enzyme active sites," BMC Bioinformatics, 12(Suppl 1):S32 (Supplement for the Ninth Asia Pacific Bioinformatics Conference, APBC2011), 2011. [doi]
  19. Yu-Feng Huang, Li-Yuan Chiu, Chun-Chin Huang, Chien-Kang Huang, “Predicting RNA-binding residues from evolutionary information and sequence conservation," BMC Genomics, 11(Suppl 4):S2 (Supplement for International Conference on Bioinformatics, InCoB2010), 2010. [doi]
  20. Yu-Cheng Liu, Shien-Ching Hwang, Yu-Feng Huang, Win-Li Lin, Yen-Jen Oyang, Chien-Kang Huang, “SEQUENCE-BASED PREDICTION OF PROTEIN B-FACTORS WITH DUAL SUPERVIZED LEARNING MODELS," Biomedical Engineering: Applications, Basis and Communications, 2010. [doi]
  21. Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, and Darby Tien-Hao Chang, “Introducing sequence-order constraint into prediction of protein binding sites with automatically extracted templates," International Journal of Biological and Life Sciences 5:4 2009. [doi]
  22. Yu-Feng Huang, Chun-Chin Huang, Yu-Cheng Liu, Yen-Jen Oyang, Chien-Kang Huang, “DNA-binding Residues and Binding Mode Prediction with Binding-Mechanism Concerned Models," BMC Genomics, 10(Suppl 3):S23 (Supplement for International Conference on Bioinformatics, InCoB2009), 2009. [doi]
  23. Wen-Yi Chu, Yu-Feng Huang, Chun-Chin Huang, Yi-Sheng Cheng, Chien-Kang Huang, Yen-Jen Oyang, “ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors," Nucleic Acids Research, Web Server Issue, 2009. [doi]
  24. Yu-Feng Huang, Chia-Chen Chang, Chien-Kang Huang, “Massive Protein Structural Property Explorations using New Indexing Mechanism," Lecture Notes in Computer Science, 2007(4802). [doi]
• Book Chapter
  1. Yu-Shin Nai, Yu-Feng Huang, Tzu-Han Chen, Kuo-Ping Chiu, Chung-Hsiung Wang, “Determination of Nucleopolyhedrovirus’ Taxonomic Position,” Book chapter, Biological Control of Pest and Vector Insects, InTech, 2017. [doi]
• NCBI GenBank accession
  1. Rhagastis binoculata mitochondrion: OQ812083 [URL]
  2. Taiwan macaque (Macaca cyclopis) mitochondrion: KM023192, NC_027449 [URL]
  3. Troides aeacus nucleopolyhedrovirus (TraeNPV): MH077961 [URL]
  4. Early on-set breast cancer sequencing, Taiwan population: PRJNA574486 [URL]
  5. RNA-Seq of deformed wing virus (DWV) infection on honey bee larvae: PRJNA669279 [URL]
  6. Attacus atlas formosanus mitochondrion: MZ098706 [URL]
• Conference Papers
  1. Yi-Hsuan Li, Yu-Feng Huang, Tzu-Han Chen, Shin-Shan Wu, Hsin-Chieh Tang, Chung-Yi Hsiao, Lung-Chun Huang, Ju-Chun Chang, Kuo-Ping Chiu and Yu-Shin Nai, “Comparison of gut microbiota of healthy and unhealthy diseased walking sticks, Phasmotaenia lanyuhensis” Annual Meeting of Taiwan Entomological Society, Taipei, Taiwan, October 16-18, 2020.
  2. Yu-Feng Huang, Chun-Chin Huang, Yu-Cheng Liu, Yen-Jen Oyang, Chien-Kang Huang, “DNA-binding Residues and Binding Mode Prediction with Binding-Mechanism Concerned Models, “International Conference on Bioinformatics (InCoB2009), Singapore, September 7-11, 2009.
  3. Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang, “Introducing sequence-order constraint into prediction of protein binding sites with automatically extracted templates,” International Conference on Bioinformatics and Bioengineering (ICBB2009), Tokyo, Japan, May 27-29, 2009.
  4. Yu-Feng Huang, Chia-Jui Yang, Yi-Wei Yang, Chien-Kang Huang, “Spatial Encoding Scheme for Protein Supporting Structure Discovery,” The 9th IEEE International Conference on Bioinformatics and Bioengineering (BIBE2009), Taichung, Taiwan, June 22-24, 2009.
  5. Yu-Feng Huang, Chia-Jui Yang, Yi-Wei Yang, Chun-Chin Huang, Chien-Kang Huang, “Protein Supporting Structure Discovery by Rigid Structure Identification via One-dimensional Structural Signature,” IEEE International Conference on Bioinformatics and Biomedicine (BIBM2008), Philadelphia, USA, November 3-5, 2008.
  6. Yu-Feng Huang, Chia-Chen Chang, and Chien-Kang Huang, “Massive Protein Structural Property Explorations using New Indexing Mechanism,” First International Workshop on Conceptual Modeling for Life Sciences Applications (CMLSA 2007), Auckland, New Zealand, November 5-9, 2007.
  7. Yhi Shiau, Jia-Nan Wang, Yu-Feng Huang, Chien-Kang Huang, “Heuristic Strategy for Geometric Hashing based Protein Structure Comparison of Ellipsoidal Representation,” The IEEE International Conference on Bioinformatics and Biomedicine (BIBM2007), Silicon Valley, USA, November 2-4, 2007.
  8. Yu-Feng Huang, Yu-Shin Lin, Tian-Wei Hsu, Chien-Kang Huang, “Mining Conserved Structures of Enzymes from Functional Hierarchical Classification,” The IEEE International Conference on Bioinformatics and Bioengineering (BIBE2007), Boston, USA, October 14-17, 2007.
  9. Yhi Shiau, Yu-Feng Huang, Chien-Kang Huang, “A Study on Local Structure Representation and Local Conserved Structure Discovery,” International Conference of Machine Learning and Cybernetics (ICMLC2007), Hong Kong, Chain, August 19-22, 2007.
  10. John Yu-Feng Huang, Chi-Jun Sheu, Tian-Wei Hsu, Chien-Kang Huang, “Mining Conserved Local Structure from Functional Hierarchical Classification via Local Structure Comparison,” In Proc. of International Computer Symposiums (ICS2006), Taiwan, December 4-6, 2006.
• Conference Posters
  1. Yu-Feng Huang, Chi-Jun Sheu, Tian-Wei Hsu, Chia-Jui Yang, Chien-Kang Huang, “Using Protein Local Structure Comparison Approach to Discover Local conservation for enzyme family,” International Conference on Bioinformatics (InCoB2009), Singapore, September 7-11, 2009.
  2. Yu-Cheng Liu, Win-Li Lin, Shien-Ching Hwang, Yu-Feng Huang, Chien-Kang Huang, Yen-Jen Oyang, “A Sequence-based Dual-model Predictor of protein B-factors,” International Conference on Bioinformatics (InCoB2009), Singapore, September 7-11, 2009.
  3. Yu-Feng Huang, Chia-Jui Yang, Chun-Chin Huang, Chien-Kang Huang, Chun-Yi Huang, Li-Yuan Chiu, Pei-Chun Ko, Chiun-Yao Chiang, Detecting protein structure flexibility via rigid structure identification, Asia Pacific Bioinformatics Conference (APBC2009), Beijing, China, January 13-16, 2009.
  4. Yu-Feng Huang, Chia-Chen Chang, Chien-Kang Huang, “Residue Environment Property Explorations on DNA-binding Proteins,” Asia Pacific Bioinformatics Conference (APBC2008), Kyoto, Japan, January 14-17, 2008.
  5. Yhi Shiau, Jia-Nan Wang, Yu-Feng Huang, Chien-Kang Huang, “Geometric Hashing Based Heuristic Strategy for Protein Structure Comparison,” The 6th Annual International Conference on Computational Systems Bioinformatics CSB2007, August 13-17, 2007.