논문
연구실에서 발표한 논문, 프리프린트, 오픈소스 도구를 소개합니다.
연구실 구성원은 굵은 글씨로 표시됩니다. # 공동 제1저자 · * 교신저자. 인용수는 Google Scholar 기준입니다.
2026
Universal conditional knockout approach to multiple species, from fish to human induced pluripotent stem cells
Jung-Hwa Choi, Jihoon Moon, Youngchul Oh, Thomas M Klompstra, Yujin Kim, Gayoung Baek, Yejin Kwak, Yeongjun Kim, Sangmin Lee, Sujin Park, Jeongmin Ha, Ohbin Kwon, Young Ki Choi, Jeong Hun Kim, Ji-Hyun Lee, Jeongbin Park, Jong Kyoung Kim, Dong Ho Woo, Ki-Jun Yoon, Bon-Kyoung Koo, Heetak Lee
Nucleic Acids Research 54(9):gkag480 link
Reproducible and shareable bioinformatics pipelines from natural-language prompts Preprint
Hyeon-Min Kim, Hwayeon Jeong, Abyot Melkamu Mekonnen, Yeongjun Kim, Youngchul Oh, Heetak Lee, Cheulhee Jung, Jeongbin Park
bioRxiv:2026.05. 28.719125 link
Lung Microphysiological System Validates Novel Cell Therapy for Acute Respiratory Distress Syndrome
Bokyong Kim#, So‐Hui Kim#, Jieun Kim, Eun‐Young Eo, Hyung‐Jun Kim, Jae Ho Lee, Choon‐Taek Lee, Taeho Kong, Su Kyoung Seo, Seunghee Lee, Jeongbin Park*, Young‐Jae Cho*
Advanced Biology 10(1):e00225 · 2 citations link
2025
Towards a transparent and reproducible AI-assisted research paper writing
Jeongbin Park
Genomics & Informatics 23(1):26 · 4 citations link
READRetro web: A user-friendly platform for predicting plant natural product biosynthesis
Yejin Kwak, Taein Kim, Sang-Gyu Kim, Jeongbin Park
Molecules and Cells 48(8):100235 · 3 citations link
From spots to cells: Cell segmentation in spatial transcriptomics with BOMS
Ocima Kamboj, Jeongbin Park, Oliver Stegle, Fred A Hamprecht
PloS one 20(6):e0311458 · 1 citations link
The mitochondrial genome data of the Capsicum annuum cv. Dempsey (Solanaceae)
Seona Yun, Junseong Bae, Jeongbin Park, Hyeran Kim
Data in Brief:111640 · 1 citations link
Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications
Abyot Melkamu Mekonnen#, Kang Seong#, Hyeran Kim, Jeongbin Park
Nucleic Acids Research:gkaf389 · 11 citations
RBM39 shapes innate immunity by controlling the expression of key factors of the interferon response
Teng-Feng Li, Paul Rothhaar, Arthur Lang, Oliver Grünvogel, Ombretta Colasanti, Santa Mariela Olivera Ugarte, Jannik Traut, Antonio Piras, Nelson Acosta-Rivero, Vladimir Gonçalves Magalhães, 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
Frontiers in immunology 16:1568056 · 3 citations link
Inhibiting EZH2 complements steroid effects in Duchenne muscular dystrophy
Eun Young Jeon, Yejin Kwak, Hyeji Kang, Se Young Jin, Soojin Park, Ryeo Gyeong Kim, Dayoung Ko, Jae-Kyung Won, Anna Cho, Inkyung Jung, Chul-Hwan Lee, Jeongbin Park, Hyun-Young Kim, Jong-Hee Chae, Murim Choi
Science Advances 11(11):eadr4443 · 4 citations link
2024
Highly efficient CRISPR/Cas9-RNP mediated CaPAD1 editing in protoplasts of three pepper (Capsicum annuum L.) cultivars
Hanyi Choi, Hyunjae Shin, Chan Yong Kim, Jeongbin Park, Hyeran Kim
Plant Signaling & Behavior 19(1):2383822 · 9 citations link
READRetro: natural product biosynthesis predicting with retrieval‐augmented dual‐view retrosynthesis
Taein Kim, Seul Lee, Yejin Kwak, Min‐Soo Choi, Jeongbin Park, Sung Ju Hwang, Sang‐Gyu Kim
New Phytologist 243(6):2512-2527 · 28 citations link
Current computational methods for spatial transcriptomics in cancer biology
Jaewoo Mo#, Junseong Bae#, Jahanzeb Saqib, Dohyun Hwang, Yunjung Jin, Beomsu Park, Jeongbin Park*, Junil Kim*
Advances in Cancer Research 163:71-106 link
CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data
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
Briefings in Bioinformatics 25(4):bbae323 · 15 citations
2023
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
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
Scientific Reports 13(1):9567 · 28 citations link
PyOncoPrint: a python package for plotting OncoPrints
Jeongbin Park*, Nagarajan Paramasivam
Genomics & Informatics 21(1):e14 · 4 citations link
SpaceTx: A Roadmap for Benchmarking Spatial Transcriptomics Exploration of the Brain Preprint
Brian Long, Jeremy Miller, The SpaceTx Consortium
arXiv:2301.08436 · 19 citations link
2022
GNU Data Language 1.0: a free/libre and open-source drop-in replacement for IDL/PV-WAVE Software
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
Journal of Open Source Software 7(80):4633 · 9 citations link
2021
Cell segmentation-free inference of cell types from in situ transcriptomics data
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
Nature Communications 12:3545 · 156 citations link
Functional states in tumor-initiating cell differentiation in human colorectal cancer
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
Cancers 13(5):1097 · 18 citations link
2020
Transcriptional heterogeneity identifies functional states of tumor-initiating cell differentiation in human colorectal cancer
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
Cancer Research 80(16 Supplement):Abstract nr. 1491 link
Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics
Teresa G Krieger, Stephan M Tirier, Jeongbin Park, Katharina Jechow, Tanja Eisemann, Heike Peterziel, Peter Angel, Roland Eils, Christian Conrad
Neuro-oncology:noaa091 · 170 citations link
ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets
Andres Quintero, Daniel Hübschmann, Nils Kurzawa, Sebastian Steinhauser, Philipp Rentzsch, Stephen Krämer, Carolin Andresen, Jeongbin Park, Roland Eils, Matthias Schlesner, Carl Herrmann
Biology Methods and Protocols 5(1):bpaa022 · 21 citations link
2019
pheno-seq–linking visual features and gene expression in 3D cell culture systems
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
Scientific Reports 9:12367 · 27 citations link
2018
Web-based design and analysis tools for CRISPR base editing
Gue-Ho Hwang#, Jeongbin Park#, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Eunchong Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim, Sangsu Bae
BMC Bioinformatics 19:542 · 238 citations link
IG-MYC+ neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas
Rabea Wagener, Cristina López, Kortine Kleinheinz, Julia Bausinger, Sietse M Aukema, Inga Nagel, Umut H Toprak, Julian Seufert, Janine Altmüller, Holger Thiele, Christof Schneider, Julia Kolarova, Jeongbin Park, Daniel Hübschmann, Eva M Murga Penas, Hans G Drexler, Andishe Attarbaschi, Randi Hovland, Eigil Kjeldsen, Michael Kneba, Udo Kontny, Laurence De Leval, Peter Nürnberg, Ilske Oschlies, David Oscier, Brigitte Schlegelberger, Stephan Stilgenbauer, Wilhelm Wössmann, Matthias Schlesner, Birgit Burkhardt, Wolfram Klapper, Elaine S Jaffe, Ralf Küppers, Reiner Siebert
Blood 132(21):2280-2285 · 90 citations link
IG-MYC-positive leukemia and lymphoma with precursor B-cell phenotype are genetically and epigenetically distinct from Burkitt lymphomas
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
British Journal of Haematology 182(S1):19-21, Abstract nr. 23 link
HTSlib-js: developer toolkit for a client-side JavaScript interface for HTSlib Preprint
Jeongbin Park#, Liam H Childs#, Matthias Schlesner, Roland Eils
bioRxiv:397935 · 1 citations link
Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”
Sang-Tae Kim#, Jeongbin Park#, Daesik Kim, Kyoungmi Kim, Sangsu Bae, Matthias Schlesner, Jin-Soo Kim
Nature Methods 15(4):239-240 · 49 citations link
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1
Jeongbin Park, Sangsu Bae
Bioinformatics 34(6):1077-1079 · 39 citations link
Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin
Manuel Rodríguez-Paredes, Felix Bormann, Günter Raddatz, Julian Gutekunst, Carlota Lucena-Porcel, Florian Köhler, Elisabeth Wurzer, Katrin Schmidt, Stefan Gallinat, Horst Wenck, Joachim Röwert-Huber, Evgeniya Denisova, Lars Feuerbach, Jeongbin Park, Benedikt Brors, Esther Herpel, Ingo Nindl, Thomas G Hofmann, Marc Winnefeld, Frank Lyko
Nature Communications 9:577 · 97 citations link
2017
RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia
Daniel B Lipka, Tania Witte, Reka Toth, Jing Yang, Manuel Wiesenfarth, Peter Nöllke, Alexandra Fischer, David Brocks, Zuguang Gu, Jeongbin Park, Brigitte Strahm, Marcin Wlodarski, Ayami Yoshimi, Rainer Claus, Michael Lübbert, Hauke Busch, Melanie Boerries, Mark Hartmann, Maximilian Schönung, Umut Kilik, Jens Langstein, Justyna A Wierzbinska, Caroline Pabst, Swati Garg, Albert Catalá, Barbara De Moerloose, Michael Dworzak, Henrik Hasle, Franco Locatelli, Riccardo Masetti, Markus Schmugge, Owen Smith, Jan Stary, Marek Ussowicz, Marry M Van Den Heuvel-Eibrink, Yassen Assenov, Matthias Schlesner, Charlotte Niemeyer, Christian Flotho, Christoph Plass
Nature Communications 8:2126 · 143 citations link
Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Julia Jabs, Franziska M Zickgraf, Jeongbin Park, Steve Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut H Toprak, Marc A Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin Sprick, Roland Eils, Christian Conrad
Molecular Systems Biology 13:955 · 250 citations link
Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers Preprint
Daniel Hüebschmann, Nils Kurzawa, Sebastian Steinhauser, Philipp Rentzsch, Stephen Krämer, Carolin Andresen, Jeongbin Park, Roland Eils, Matthias Schlesner, Carl Herrmann
bioRxiv:199547 · 8 citations link
CRISPR/Cas9-mediated gene knockout screens and target identification via whole-genome sequencing uncover host genes required for picornavirus infection
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Journal of Biological Chemistry 292(25):10664-10671 · 53 citations link
Digenome-seq web tool for profiling CRISPR specificity
Jeongbin Park, Liam Childs, Daesik Kim, Gue-Ho Hwang, Sunghyun Kim, Sang-Tae Kim, Jin-Soo Kim, Sangsu Bae
Nature Methods 14(6):548-549 · 54 citations link
Cas-analyzer: an online tool for assessing genome editing results using NGS data
Jeongbin Park, Kayeong Lim, Jin-Soo Kim, Sangsu Bae
Bioinformatics 33(2):286-288 · 478 citations link
2016
Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9
Jeongbin Park, Jin-Soo Kim, Sangsu Bae
Bioinformatics 32(13):2017-2023 · 64 citations link
Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq
Daesik Kim, Sojung Kim, Sunghyun Kim, Jeongbin Park, Jin-Soo Kim
Genome Research 26(3):406-415 · 269 citations link
2015
Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites
Jeongbin Park, Sangsu Bae, Jin-Soo Kim
Bioinformatics 31(24):4014-4016 · 576 citations link
Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells
Daesik Kim, Sangsu Bae, Jeongbin Park, Eunji Kim, Seokjoong Kim, Hye Ryeong Yu, Jinha Hwang, Jong-Il Kim, Jin-Soo Kim
Nature Methods 12(3):237-243 · 1256 citations link
2014
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
Sangsu Bae#, Jeongbin Park#, Jin-Soo Kim
Bioinformatics 30(10):1473-1475 · 2656 citations link
Scaling GDL for multi-cores to process Planck HFI beams Monte Carlo on HPC
Alain Coulais, Marc Schellens, Gilles Duvert, Jeongbin Park, Orion Poplawski, Sylwester Arabas, Stephane Erard, Benjamin Laurent, Mathieu Pinter, Nodar Kasradze, Mouadh Ayad
Astronomical Data Analysis Software and Systems XXIII 485:331 · 1 citations link
Protein conformational dynamics dictate the binding affinity for a ligand
Moon-Hyeong Seo, Jeongbin Park, Eunkyung Kim, Sungchul Hohng, Hak-Sung Kim
Nature Communications 5:3724 · 198 citations link