PROFILE

I’m currently an assistant professor at Division of Data Science, The University of Suwon. My research area focuses on bioinformatics to develop AI-based bio-medical tools for analyzing high throughput next generation sequencing data from various organisms, such as, rice, Arabidopsis, mouse and human.

  • Assistant professor at Division of Data Science and Director of DS&ML Center, The University of Suwon

  • Location : 1012, Building of Global Business, The University of Suwon, 17, Wauan-gil, Bongdam-eup, Hwaseong-si, Gyeonggi-do 18323, Republic of Korea
  • TEL : +82-31-229-8762
  • E-mail : hongryulahn@gmail.com

EDUCATIONS

2012.9. – 2019.2. Ph.D. in Computer Science and Engineering, Seoul National University, Seoul, South Korea
[Ph. D. Dissertation] Clustering-Based Integrated Analysis of Time-Series Gene Expression Data to Identify Stress-Responsive Genes

2005.3. - 2012.2. BS in Computer Science and Engineering, Seoul National University, Seoul, South Korea

EXPERIENCES

2021.3. – present. Director of DS&ML Center, The University of Suwon, Hwaseong-si, Gyeonggi-do, South Korea

2020.3. – present. Assistant Professor at Division of Data Science, The University of Suwon, Hwaseong-si, Gyeonggi-do, South Korea

2019.9. – 2020.2. Research Fellow at BK21+ Program, Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea

2019.3. – 2019.9. Research Fellow at Bioinformatics Institute, Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea

2012.3. – 2012.8. Research Intern. Bio-MAX/N-Bio institute, Seoul National University, Seoul, South Korea

2008.1. – 2009.12. Military service at ROK army, South Korea

RESEARCHES

2020.03.01. – present. Development of graph convolutional neural network model using transcriptome data for treatment for lung squamous cell carcinoma.

2015.01.15. – 2017.12.31. Development of environmental stress responsive genes via genomic expression profiling using integrative bioinformatics analyses.

2014.11.01. – 2020.02.29. Development of high performance analysis technologies and open platforms for the integrated analysis of genomics data.

2012.07.01. – 2017.06.30. Development of Enabling Software Technology for Mining Big Data in Natural Science(Bio-informatics).

2012.05.01. – 2014.12.31. Development of abiotic stress related genes for global GM crops via genomics and epigenomics.

PUBLICATIONS

International Articles (Journal Papers / Conference Proceedings)

Ahn H (First), Jung I, Chae H, Oh M, Kim I, Kim S*. "IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data" 2021 IEEE International Conference on Big Data (Big Data), 2021 Dec 15, [link]

Jung J, Hwang Y, Ahn H, Lee S*, Yoo S*. "Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes" International Journal of Molecular Sciences [SCIE journal, IF:5.924, JCR: top 23%], 2021 Oct 15, [link]

Kang H, Ahn H (Joint-First), Jo K, Oh M, Kim S*. "mirTime: Identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering". Bioinformatics [SCI journal, IF:4.531, JCR: top 6%], 2021 Jun 1. [link]

Pak M, Jung D, Moon JH, Ahn H, Hur B, Lee S, Kim S*. "Network Propagation for the Analysis of Multi-omics Data" Recent Advances in Biological Network Analysis, 2021 Jan 13. [link]

Jo HY, Lee Y, Ahn H, Han HJ, Kwon A, Kim BY, Ha HY, Kim SC, Kim JH, Kim YO, Kim S, Koo SK*, Park MH*. "Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation" Scientific Reports [SCI(E) journal, IF:3.998, JCR: top 24%], 2020 Oct 29. [link]

Hoang NV, Choe G, Zheng Y, Fandiño ACA, Sung I, Hur J, Kamran M, Park C, Kim H, Ahn H , Kim S, Fei Z, Lee JY*. "Identification of Conserved Gene-Regulatory Networks that Integrate Environmental Sensing and Growth in the Root Cambium" Current Biology [SCI journal, IF:9.601, JCR: top 4%], 2020 Aug 3. [link]

Lee CJ, Ahn H, Jeong D, Park M, Moon JH, Kim S*. "Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer". BMC Medical Genomics [SCIE journal, IF:2.568, JCR: top 53%], 2020 Feb 24. [link]

Kang D, Ahn H (Joint-First), Lee S, Lee CJ, Hur J, Jung W*, Kim S*. "StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in Arabidopsis". BMC Genomics [SCIE journal, IF:3.501, JCR: top 30%], 2019 Dec 20. [link]

Ahn H (First), Jung I, Chae H, Kang D, Jung W*, Kim S*. "HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis". BMC Bioinformatics [SCIE journal, IF:2.511, JCR: top 15%], 2019 Dec 2. [link]

Ahn H (Joint-First), Jo K, Jung D, Pak M, Hur J, Jung W*, Kim S*. "PropaNet: time-varying condition-specific transcriptional network construction by network propagation". Frontiers in Plant Science [SCIE journal, IF:4.106, JCR: top 9%], 2019 Jun 14. [link]

Ahn H (Joint-First), Son S, Kim S*. "DeepFunNet: Deep learning for gene functional similarity network construction". In The 6th IEEE International Conference on Big Data and Smart Computing (BigComp), 2019 Feb 27. [link]

Kang D, Ahn H (Joint-First), Lee S, Lee CJ, Hur J, Jung W*, Kim S*. "Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data". In The 2018 International Conference on Bioinformatics and Biomedicine (BIBM), 2018 Dec 3. [link]

Ahn H (First), Jung I, Chae H, Kang D, Jung W, Kim S*. "HTRgene: Integrating multiple heterogeneous time-series data to investigate cold and heat stress response signaling genes in Arabidopsis". In The 2018 International Conference on Bioinformatics and Biomedicine (BIBM), 2018 Dec 3. [link]

Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S*. "TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes". Bioinformatics [SCI journal, IF:4.531, JCR: top 6%], 2017 Dec 1. [link]

Ahn H (First), Jung I, Shin SJ, Park J, Rhee S, Kim JK, Jung W, Kwon HB*, Kim S*. "Transcriptional network analysis reveals drought resistance specific biological mechanisms underlying AP2/ERF transgenic rice species". Frontiers in Plant Science [SCIE journal, IF:4.106, JCR: top 9%], 2017 Jun 15. [link]

Ahn H (First), Chae H, Jung W, Kim S*. "Integration of heterogeneous time series gene expression data by clustering on time dimension". In The 4th IEEE International Conference on Big Data and Smart Computing (BigComp), 2017 Mar 20. [link]

Jung I, Ahn H, Shin SJ, Kim JK, Kwon HB, Jung W, Kim S*. "Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice". BMC Systems Biology [SCI journal, IF:2.048, JCR: top 37%], 2016 Dec 23. [link]

Shin SJ, Ahn H, Jung I, Rhee S, Kim S, Kwon HB*. "Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L". Genes & Genomics [SCIE journal, IF:0.759], 2016 Oct 23. [link]

Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee J, Ryu H*, Kim S*. "Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice". BMC Medical Genomics [SCIE journal, IF:2.568, JCR: top 53%], 2016 Aug 12. [link]

Kim KY, Hwang YJ, Jung MK, Choe J, Kim Y, Kim S, Lee CJ, Ahn H, Lee J, Kowall NW, Kim YK, Kim JI, Lee SB, Ryu H*. "A multifunctional protein EWS regulates the expression of Drosha and microRNAs". Cell Death and Differentiation [SCI journal, IF: 8.086, JCR: top 9%], 2014 Jan. [link]

* : Correspondence

International Conference Presentations

Ahn H*. "Network Propagation Embedded Deep Neural Network for Disorder Gene Prediction". The 28th International Conference on Intelligent Systems for Molecular Biology (ISMB), Virtual Conference, 2020 Jul 14.

Lee CJ, Ahn H, Jeong D, Park M, Moon JH, Kim S*. "Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer". The 30th International Conference on Genome Informatics (GIW), Sydney, Australia, 2019 Dec 11.

Ahn H (Joint-First), Son S, Kim S*. "DeepFunNet: Deep learning for gene functional similarity network construction". The 6th IEEE International Conference on Big Data and Smart Computing (BigComp), Kyoto, Japan, 2019 Mar 2.

Kang D, Ahn H (Joint-First), Lee S, Lee CJ, Hur J, Jung W*, Kim S*. "Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data". The 2018 International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018 Dec 4.

Ahn H (First), Jung I, Chae H, Kang D, Jung W, Kim S*. "HTRgene: Integrating multiple heterogeneous time-series data to investigate cold and heat stress response signaling genes in Arabidopsis". The 2018 International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018 Dec 4.

Kang H, Ahn H (Joint-First), Jo K, Oh M, Kim S*. "mirTime: Identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering". The 29th International Conference on Genome Informatics (GIW), Yunnan, China, 2018 Dec 3.

Ahn H (First), Chae H, Jung W, Kim S*. "Integration of heterogeneous time series gene expression data by clustering on time dimension". The 4th IEEE International Conference on Big Data and Smart Computing (BigComp), Jeju, Korea, 2017 Feb 14.

Jung I, Ahn H, Shin SJ, Kim JK, Kwon HB, Jung W, Kim S*. "Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice". The 27th International Conference on Genome Informatics (GIW), Shanghai, China, 2016 Oct 4.

Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S*. "TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes". The 27th International Conference on Genome Informatics (GIW), Shanghai, China, 2016 Oct 3.

Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee J, Ryu H*, Kim S*. "Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of EWS KO mice". The 5th Translational Bioinformatics Conference (TBC), Tokyo, Japan, 2015 Nov 7.

* : Correspondence

Domestic Articles

김승원, 김용하, 이슬희, 최지현, 안홍렬*, "유전자 발현 데이터의 비모수 리샘플링 스케일러 개발", 한국정보과학회 한국정보과학회 학술발표논문집, Vol.2021, pp.1912-1914.

김현태, 한채은, 김예지, 안홍렬*, "유전자 발현량 데이터에서의 부츠스트랩 가중치 앙상블 특성 선택 기법", 한국정보과학회 한국정보과학회 학술발표논문집, Vol.2021, pp.1945-1947.

김혁주, 방채영, 이동수, 안홍렬*, "딥러닝 모델에서 증강 데이터를 활용한 선행 학습", 한국정보과학회 한국정보과학회 학술발표논문집, Vol.2021, pp.1969-1971.

강동원, 안홍렬, 이상선, 정우석, 김선*. "시계열 유전자 발현 데이터의 스트레스 특이 반응 유전자 검출 및 스트레스 예측 알고리즘 개발", 한국정보과학회 2018 한국컴퓨터종합학술대회 논문집, Vol.2018, pp.1063-1065.

손승현, 안홍렬, 김선*. "딥러닝을 통한 유전자 온톨로지 거리의 추론", 한국정보과학회 2017 한국소프트웨어종합학술대회 논문집, Vol.2017, pp.954-956.

정인욱, 김장욱, 안홍렬, 김진현, 허지혜, 유재련, 김선*, 정우석*, "Analysis of differentially expressed genes of Korean ginseng grown under ambient heat", 한국작물학회 학술발표대회 논문집, Vol.2017, p.276. 2017 Oct.

강동원, 안홍렬, 정우석, 김선*. "이질적 시계열 유전자 발현 데이터의 통합 분석 문제의 정의 및 애기장대에서의 저온 스트레스 반응 유전자 검출 알고리즘 개발", 한국정보과학회 2015년 동계학술발표회 논문집, Vol.2015, No.12, pp.648-650.

* : Correspondence