Dr. Jeongbin Park

(last updated: Dec 18, 2024)

(The latest version of this CV is available at: https://jeongbinpark.com/cv)

Address:	Room #413, Kyung-Ahm Engineering Building, Busandaehak-ro 49, Mulgeum-eup, Yangsan-si, 50612 Republic of Korea
email:	jeongbin.park at pusan.ac.kr
Tel.:	+82-51-510-8597

EDUCATION

2016 - 2020	Dr. rer. nat. (Ph. D. equivalent) in Biology, Heidelberg University, Germany
2012 - 2014	M. Sc. in Physics, Seoul National University, Korea
2008 - 2012	B. Sc. in Physics, Pusan National University, Korea

WORK EXPERIENCE

2022 - Present	Assistant Professor, School of Biomedical Convergence Engineering, Pusan National University
2020 - 2022	Postdoctoral Researcher, Division of Computational Genomics and System Genetics, German Cancer Research Center (DKFZ) (Advisor: Prof. Oliver Stegle)
2018 - 2020	Researcher (PhD student), Digital Health Center, Berlin Institute of Health (BIH) / Charité (Advisor: Prof. Roland Eils)
2016 - 2018	Researcher (PhD student), Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) (Advisor: Prof. Roland Eils)
2015 - 2016	Research Collaboration, Molecular Genome Engineering Laboratory, Hanyang University (Research collaborator: Prof. Sangsu Bae)
2014 - 2015	Research Collaboration, Genome Engineering Laboratory, Seoul National University (Research collaborator: Dr. Sangsu Bae)
2012 - 2014	Researcher (MSc student), Single Molecule Biophysics Laboratory, Seoul National University (Advisor: Prof. Sungchul Hohng)

SERVICE

Scientific Community:

Korean Society for Bioinformatics (KSBI), Public Affairs Committee Member, 2023 / Academic Affairs Committee Member, 2024
Korea Genome Organization (KOGO), Information and Computing Committee Member, 2023-2024

Ad-hoc Journal Reviewer:

Bioinformatics, eLife, Communications Biology, NAR: Genomics and Bioinformatics, Scientific Reports, BMC Genomics, Journal of Open Source Software (JOSS)

Book Translation:

A Byte of Python (Korean Translation): An online Python guidebook originally written by Swaroop C H. Free access at https://github.com/pjb7687/byte_of_python/.

Open Source Contribution:

GNU Data Language (GDL): Ported GDL (https://github.com/gnudatalanguage/gdl/) on Windows (contributed mainly in 2014 - 2015). From 2021, serving as release manager of the project.

TEACHING

At PNU:

“Bioinformatics”, “UNIX Fundamentals”, “Introduction to Biomedical Informatics”, “Object-oriented Programming”, “Web Programming”, School of Biomedical Convergence Engineering, Pusan National University
“Statistical Genomics”, “Clinical and Genomic Informatics”, Graduate School of Genomic Data Science, Pusan National University

Before PNU:

Invited lecture “Spatial transcriptomics” at “Single cell RNA-seq data analysis with R” (sponsored by the ELIXIR EXCELERATE project). CSC, Espoo, Finland. 29 May 2019.
Student supervision, 3 student research interns (including 1 co-supervision), Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Germany. Jul 2016 - Feb 2018.
“Methoden der Bioinformatik - Python” (lecture assistant), Faculty of Biosciences, Heidelberg University, WS 2016 and WS 2017.
“Physics Laboratory” (teaching assistant), Department of Physics, Seoul National University, SS 2012.

CONFERENCE PROCEEDINGS

Martina K Zowada, Stephan M Tirier, Sebastian M Dieter, Teresa Krieger, Ava Oberlack, Robert L Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R Ball, “Transcriptional heterogeneity identifies functional states of tumor-initiating cell differentiation in human colorectal cancer”, Cancer Research 80 (16 Supplement), Abstract nr. 1491 (2020).

Cristina Lopez, Rabea Wagener, Kortine Kleinheinz, Julia Bausinger, Sietse M Aukema, Inga Nagel, Umut H Toprak, Julian Seufert, Janine Altmueller, Holger Thiele, Christof Schneider, Julia Kolarova, Jeongbin Park, Daniel Huebschmann, Eva M Murga Penas, Hans G Drexler, Andishe Attarbaschi, Randi Hovland, Eigil Kjeldsen, Michael Kneba, Udo Kontny, Laurence de Leval, Peter Nuernberg, Ilske Oschlies, David Oscier, Brigitte Schlegelberger, Stephan Stilgenbauer, Wilhelm Woessmann, Matthias Schlesner, Birgit Burkhardt, Wolfram Klapper, Elaine S Jaffe, Ralf Kueppers, Reiner Siebert, “IG-MYC-positive leukemia and lymphoma with precursor B-cell phenotype are genetically and epigenetically distinct from Burkitt lymphomas”, British Journal of Haematology 182 (S1), 19-21, Abstract nr. 23 (2018).

Alain Coulais, Marc Schellens, Gilles Duvert, Jeongbin Park, Orion Poplawski, Sylwester Arabas, Stephane Erard, Benjamin Laurent, Mathieu Pinter, Nodar Kasradze, Mouadh Ayad, “Scaling GDL for multi-cores to process Planck HFI beams Monte Carlo on HPC”, Astronomical Data Analysis Software and Systems XXIII 485, 331 (2014). [cited: 1]

PUBLICATIONS

Hanyi Choi, Hyunjae Shin, Chan Yong Kim, Jeongbin Park, Hyeran Kim, “Highly efficient CRISPR/Cas9-RNP mediated CaPAD1 editing in protoplasts of three pepper (Capsicum annuum L.) cultivars”, Plant Signaling & Behavior 19 (1), 2383822 (2024).

Taein Kim, Seul Lee, Yejin Kwak, Min‐Soo Choi, Jeongbin Park, Sung Ju Hwang, Sang‐Gyu Kim, “READRetro: natural product biosynthesis predicting with retrieval‐augmented dual‐view retrosynthesis”, New Phytologist 243 (6), 2512-2527 (2024). [cited: 5]

Jaewoo Mo^#, Junseong Bae^#, Jahanzeb Saqib, Dohyun Hwang, Yunjung Jin, Beomsu Park, Jeongbin Park^*, Junil Kim^*, “Current computational methods for spatial transcriptomics in cancer biology”, Advances in Cancer Research 163, 71-106 (2024).

Yujin Kim, Minwoo Jeong, In Gyeong Koh, Chanhee Kim, Hyeji Lee, Jae Hyun Kim, Ronald Yurko, Il Bin Kim, Jeongbin Park, Donna M Werling, Stephan J Sanders, Joon-Yong An, “CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data”, Briefings in Bioinformatics 25 (4), bbae323 (2024). [cited: 1]

Ocima Kamboj, Jeongbin Park, Oliver Stegle, Fred A Hamprecht, “From spots to cells: Cell segmentation in spatial transcriptomics with BOMS”, bioRxiv, 2024.09. 21.614281 (2024).

Teng-Feng Li, Arthur Lang, Paul Rothhaar, Oliver Gruenvogel, Ombretta Colasanti, Santa Mariela Olivera Ugarte, Jannik Traut, Antonio Piras, Nelson Acosta-Rivero, Vladimir Goncalves Magalhaes, Emely Springer, Andreas Betz, Hao-En Huang, Jeongbin Park, Ruiyue Qiu, Gnimah Eva Gnouamozi, Ann-Kathrin Mehnert, Viet Loan Dao Thi, Stephan Urban, Martina Muckenthaler, Matthias Schlesner, Dirk Wohlleber, Marco Binder, Ralf Bartenschlager, Andreas Pichlmair, Volker Lohmann, “RBM39 shapes innate immunity through transcriptional and splicing control of IRF3 and other key factors”, bioRxiv, 2023.10. 13.562221 (2023). [cited: 2]

Yun Zhang^#, Jeremy A Miller^#, Jeongbin Park^#, Boudewijn P Lelieveldt, Brian Long, Tamim Abdelaal, Brian D Aevermann, Tommaso Biancalani, Charles Comiter, Oleh Dzyubachyk, Jeroen Eggermont, Christoffer Mattsson Langseth, Viktor Petukhov, Gabriele Scalia, Eeshit Dhaval Vaishnav, Yilin Zhao, Ed S Lein, Richard H Scheuermann, “Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain”, Scientific Reports 13 (1), 9567 (2023). [cited: 18]

Jeongbin Park, Nagarajan Paramasivam, “PyOncoPrint: a python package for plotting OncoPrints”, Genomics & Informatics 21 (1), e14 (2023).

Brian Long, Jeremy Miller, The SpaceTx Consortium, “SpaceTx: A Roadmap for Benchmarking Spatial Transcriptomics Exploration of the Brain”, arXiv, 2301.08436 (2023). [cited: 16]

Jeongbin Park, Gilles Duvert, Alain Coulais, Gregory V Jung, Sylwester Arabas, Brian Barker, Takeshi Enomoto, Sylvain Flinois, Oliver Gressel, Tomas Hillberg, Thibault Huillet, Jan Kohnert, Orion Poplawski, Eloi Rozier de Linage, Remi A Solås, Luke Stagner, Ole Streicher, James Tappin, Thierry Thomas, Jingwei Wang, Christian Wimmer, “GNU Data Language 1.0: a free/libre and open-source drop-in replacement for IDL/PV-WAVE”, Journal of Open Source Software 7 (80), 4633 (2022). [cited: 3]

Jeongbin Park^#, Wonyl Choi^#, Sebastian Tiesmeyer, Brian Long, Lars E Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils, Naveed Ishaque, “Cell segmentation-free inference of cell types from in situ transcriptomics data”, Nature Communications 12, 3545 (2021). [cited: 109]

Martina K Zowada, Stephan M Tirier, Sebastian M Dieter, Teresa G Krieger, Ava Oberlack, Robert Lorenz Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R Ball, “Functional states in tumor-initiating cell differentiation in human colorectal cancer”, Cancers 13 (5), 1097 (2021). [cited: 11]

Teresa G Krieger, Stephan M Tirier, Jeongbin Park, Katharina Jechow, Tanja Eisemann, Heike Peterziel, Peter Angel, Roland Eils, Christian Conrad, “Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics”, Neuro-oncology, noaa091 (2020). [cited: 110]

Andres Quintero, Daniel Hübschmann, Nils Kurzawa, Sebastian Steinhauser, Philipp Rentzsch, Stephen Krämer, Carolin Andresen, Jeongbin Park, Roland Eils, Matthias Schlesner, Carl Herrmann, “ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets”, Biology Methods and Protocols 5 (1), bpaa022 (2020). [cited: 18]

Stephan M Tirier, Jeongbin Park, Friedrich Preußer, Lisa Amrhein, Zuguang Gu, Simon Steiger, Jan-Philipp Mallm, Teresa Krieger, Marcel Waschow, Björn Eismann, Marta Gut, Ivo G Gut, Karsten Rippe, Matthias Schlesner, Fabian Theis, Christiane Fuchs, Claudia R Ball, Hanno Glimm, Roland Eils, Christian Conrad, “pheno-seq–linking visual features and gene expression in 3D cell culture systems”, Scientific Reports 9, 12367 (2019). [cited: 24]

Gue-Ho Hwang^#, Jeongbin Park^#, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Eunchong Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim, Sangsu Bae, “Web-based design and analysis tools for CRISPR base editing”, BMC Bioinformatics 19, 542 (2018). [cited: 180]