PUBLICATONS
18. Linbu Liao*, Patrick CN Martin*, Hyobin Kim, Sanaz Panahandeh, Kyoung Jae Won, Data enhancement in the age of spatial biology, under review. (* co-first authors)
17. Martina Zoccheddu, Mattias N. D. Svensson, Paramita Dutta, Myungja Ro, Yizhou Wang, Hyobin Kim, Zbigniew Mikulski, Katarzyna Dobaczewska, Francesca Ingegnoli, Angela Denn, Roberto Caporali, Pietro Simone Randelli, David A McBride, Wang Zhipin, Jason Moore, Nisarg J. Shah, Kyoung Jae Won, Ferhat Ay, Nunzio Bottini, Conversion of Th17 into exTh17 sustains rheumatoid-like IL-17-independent inflammatory arthritis, under review.
16. Esha Madan, Antonio Palma, Davide Accardi, Sara Belião, Denise Camacho, Maria Peixoto, Antonio Beltran, Eduardo Moreno, Vignesh Vudatha, Jose Trevino, Jochen Wilhelm, Isabelle Dreier, Michail Yekelchyk, Thais Araujo, Elena Garre, Anna Gustafsson, Goran Landberg, Lena Neufeld, Eilam Yeini, Ronit Satchi-Fainaro, Hans Rolfsnes, Rolf Bjerkvig, Frits Thorsen, Hyobin Kim, Patrick Martin, Kyoung-Jae Won, Amit Kumar, Praveen Bhoopathi, Paul Fisher, Linbu Liao, Kartik Gupta, Sahil Chaudhary, Masaki Nagane, Kalpana Dorayappan, Selvendiran Karuppaiyah, Kedar Natarajan, Periannan Kuppusamy, Isabel Correia, Cláudia da Silva, Arsenio Fialho, Hongjun Wang, Max Wicha, David Sidransky, Steven Grossman, Ronny Drapkin, Denise Connolly, Andrew Godwin, Robert Winn, Maximillian Ackermann, Alexandar Tzankov, Christopher Pelham, Tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells, under review.
15. Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim, Amit Kumar, Praveen Bhoopathi, Robert Winn, Jose Trevino, Paul Fisher, Cord Herbert Brakebusch, Rajan Gogna, Kyoung Jae Won, SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution, under review. [Link]
14. [Journal] Hyobin Kim*, Amit Kumar*, Cecilia Lövkvist, António M. Palma, Patrick Martin, Junil Kim, Praveen Bhoopathi, Jose Trevino, Paul Fisher, Esha Madan, Rajan Gogna#, and Kyoung Jae Won#, CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data, Molecular Systems Biology, 19(11), e11670, 2023. (* co-first authors, # co-corresponding authors) [Link] This paper was selected as a journal cover paper.
13. [Journal] Patrick C.N. Martin, Hyobin Kim, Cecilia Lövkvist, Byung-Woo Hong, and Kyoung Jae Won, Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis, Molecular Systems Biology, 18(9), e11080, 2022. [Link]
12.[Journal] Raphael Reuten#, Sina Zendehroud, Monica Nicolau, Lutz Fleischhauer, Anu Laitala, Stefanie Kiderlen, Denise Nikodemus, Lena Wullkopf, Sebastian Rune Nielsen, Sarah McNeilly, Carina Prein, Maria Rafaeva, Erwin Schoof, Benjamin Furtwängler, Bo T. Porse, Hyobin Kim, Kyoung Jae Won, Stefanie Sudhop, Kamilla Westarp Zornhagen, Frank Suhr, Eleni Maniati, Oliver M. T. Pearce, Manuel Koch, Lene Broeng Oddershede, Tom van Agtmael, Chris D. Madsen, Alejandro E. Mayorca-Guiliani, Wilhelm Bloch, Roland R. Netz, Hauke Clausen-Schaumann, Janine T. Erler#, Basement membrane stiffness determines metastasis formation, Nature Materials, 20, pp.892–903, 2021. (# co-corresponding authors) [Link]
11. [Proceedings] Octavio Zapata, Hyobin Kim, and Carlos Gershenson, On two information-theoretic measures of random fuzzy networks, Proceedings of the 2020 Conference on Artificial Life (ALIFE 2020), MIT Press, pp.623-625, 2020. [Link]
10. [Journal] Hyobin Kim, Stalin Muñoz, Pamela Osuna, and Carlos Gershenson, Antifragility predicts the robustness and evolvability of biological networks through multi-class classification with a convolutional neural network, Entropy, 22(9), 986, 2020. [Link]
9. [Proceedings] Hyobin Kim, Farnaz Zamani Esfahlani, Samuel Heiserman, Nasim Nezamoddini, and Hiroki Sayama, Instability of multilayer networks induced by inter-layer coupling, Proceedings of the 2019 IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2019 -- IEEE ALIFE 2019), December 6-9, 2019, Xiamen, China. [Link]
8. [Journal] Luis A. Escobar, Hyobin Kim, and Carlos Gershenson, Effects of anti-modularity and multiscale influence in random Boolean networks, Complexity, Volume 2019, Article ID 8209146, 2019. [Link]
7. [Journal] Hyobin Kim, Omar K. Pineda, and Carlos Gershenson, A multilayer structure facilitates the production of antifragile systems in Boolean network models, Complexity, Volume 2019, Article ID 2783217, 2019. [Link]
6. [Journal] Omar K. Pineda*, Hyobin Kim*, and Carlos Gershenson, A novel antifragility measure based on satisfaction and its application to random and biological Boolean networks, Complexity, Volume 2019, Article ID 3728621, 2019. (* co-first authors) [Link]
5. [Proceedings] Hyobin Kim and Hiroki Sayama, Robustness and evolvability of multilayer gene regulatory networks, Proceedings of the 2018 Conference on Artificial Life (ALIFE 2018), MIT Press, pp.546-547, 2018. [Link]
4. [Journal] Hyobin Kim and Hiroki Sayama, How criticality of gene regulatory networks affects the resulting morphogenesis under genetic perturbations, Artificial Life, 24(2), pp. 85-105, 2018. [Link]
3. [Journal] Hyobin Kim and Hiroki Sayama, The role of criticality of gene regulatory networks in morphogenesis, IEEE Transactions on Cognitive and Developmental Systems, 12(3), pp. 390-400, 2020 (physical print date). [Link]
2. [Proceedings] Hyobin Kim and Hiroki Sayama, Criticality of gene regulatory networks and the resulting morphogenesis, Proceedings of the Fourteenth European Conference on Artificial Life (ECAL 2017), MIT Press, pp. 245-246, 2017. [Link]
1. [Proceedings] Hyobin Kim and Hiroki Sayama, The relationship between microscopic and collective properties in gene regulatory network-based morphogenetic systems, Proceedings of the Artificial Life Conference 2016 (ALIFE XV), MIT Press, pp.370-371, 2016. [Link]
PRESENTATIONS
28. Hyobin Kim, CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data, a lightning talk, 2nd Spatial Biology Symposium, March 07, 2024, Cedars-Sinai Medical Center, CA, USA.
27. Hyobin Kim, CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data, an invited seminar talk, BRIC, January 03, 2024, Republic of Korea. [Link1], [Link2]
26. Patrick Martin, Wenqi Wang, Hyobin Kim, Kyoung Jae Won, Mapping spatial assays when tissue architecture doesn't match, presented as a talk at the GIW ISCB-Asia 2023, November 18-21, 2023, Lee Kong Chian School of Medicine Novena campus, Singapore.
25. Patrick Martin, Wenqi Wang, Hyobin Kim, Kyoung Jae Won, Mapping spatial assays when tissue architecture doesn't match, presented as a poster at the Cell Symposia 2023, August 28-30, 2023, Paradise Point Resort, San Diego, CA, USA.
24. Hyobin Kim, Amit Kumar, Cecilia Lövkvist, António M. Palma, Patrick Martin, Junil Kim, Praveen Bhoopathi, Jose Trevino, Paul Fisher, Esha Madan, Rajan Gogna, and Kyoung Jae Won, Studying cell-cell communicaiton mediated by cell contact, presented as a poster at the Cell Symposia 2023, August 28-30, 2023, Paradise Point Resort, San Diego, CA, USA.
23. Linbu Liao, Esha Madan, Hyobin Kim, Rajan Gogna and Kyoung Jae Won, SC2Spa: a deep learning based apporach to map transcriptome to spatial origins at cellular resolution, presented as a poster at the ISMB/ECCB 2023, July 23-27, 2023, Centre de Congres de Lyon, Lyon, France.
22. Patrick Martin, Wenqi Wang, Hyobin Kim, and Kyoung Jae Won, Exploring tissue structure across spatial omic modalities with Vesalius, presented as a poster at the ISMB/ECCB 2023, July 23-27, 2023, Centre de Congres de Lyon, Lyon, France.
21. Hyobin Kim, Detecting cell contact-dependent gene expression from spatial transcriptomics data (PART I), Single cell RNA-sequencing pipeline (PART II), an invited seminar talk, Seoul National University, August 26, 2022, Seoul, Republic of Korea.
20. Hyobin Kim, Detecting cell contact-dependent gene expression from spatial transcriptomics data, an invited seminar talk, Soongsil University, August 25, 2022, Seoul, Republic of Korea.
19. Linbu Liao, Hyobin Kim, and Kyoung Jae Won, SC2Spa: Mapping transcriptome to spatial locations at cellular resolution, presented as a poster at the Single Cell Biology Conference, Wellcome Genome Campus, June 06-08, 2022, Hinxton, Cambridge, UK.
18. Patrick C.N. Martin, Hyobin Kim, Cecilia Lövkvist, Byung-Woo Hong, and Kyoung Jae Won, Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis, presented as a poster at the Single Cell Biology Conference, Wellcome Genome Campus, June 06-08, 2022, Hinxton, Cambridge, UK.
17. Hyobin Kim, Cecilia Lövkvist, Patrick Martin, Junil Kim and Kyoung Jae Won, Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data, presented as a poster at the Single Cell Biology Conference, Wellcome Genome Campus, June 06-08, 2022, Hinxton, Cambridge, UK.
16. Hyobin Kim, Towards spatial transcriptomics: a cell is known by the company it keeps (PART II), a seminar talk at the HeaDS (Center for Health Data Science) seminar, University of Copenhagen, April 21, 2022, Copenhagen, Denmark.
15. Hyobin Kim, Why you should know your neighbors: effect of neighbors on gene expression, a seminar talk at the BRIC (Biotech Research & Innovation Center) seminar, University of Copenhagen, November 24, 2021, Copenhagen, Denmark.
14. Hyobin Kim, Cecilia Lövkvist, and Kyoung Jae Won, Exploring neighboring cell dependent gene expression using spatial transcriptomics, presented as a poster at the Swedish Bioinformatics Workshop (SWB), Lund University, October 20-21, 2021, Lund, Sweden.
13. Linbu Liao, Hyobin Kim, Cecilia Lövkvist, and Kyoung Jae Won, Deep learning-based spatial inference by mapping single cell transcriptomic data to spatial transcriptomic data, presented as a poster at the Swedish Bioinformatics Workshop (SWB), Lund University, October 20-21, 2021, Lund, Sweden.
12. Hyobin Kim, My postdoc story, an invited talk at the CoCo Faculty-Student Mixer, SUNY at Binghamton, April 14, 2021, Binghamton, NY.
11. Darío Alatorre, Roger Cremades, Carlos Gershenson, Hyobin Kim and José L. Mateos, Antifragility of food trade networks: preliminar results, presented as a talk at the NetSci4SDGs (Network Science for the Sustainable Development Goals) -- NetSci 2020 Satellite Symposium, September 20, 2020, Virtual conference (due to COVID-19).
10. Hyobin Kim, Stalin Muñoz, Pamela Osuna, and Carlos Gershenson, Prediction of robustness and evolvability of biological networks based on antifragility, presented as a poster at the BiotICC (Biology through Information Coding and Communication Theory) workshop, January 21-22, 2020, Alexandria, VA.
9. Hyobin Kim, Stalin Muñoz, Pamela Osuna, and Carlos Gershenson, Prediction of robustness and evolvability of biological networks based on antifragility, presented as a poster at the 2019 Conference on Complex Systems (CCS 2019), September 30-October 4, 2019, Nanyang Technological University, Singapore.
8. Hyobin Kim, Omar K. Pineda, and Carlos Gershenson, Antifragility and a multilayer structure in Boolean network models, presented as a talk at the 2019 Conference on Complex Systems (CCS 2019), September 30-October 4, 2019, Nanyang Technological University, Singapore. [Link]
7. Hyobin Kim and Carlos Gershenson, Robustness and evolvability of multilayer gene regulatory networks (updated version of the proceedings of ALIFE 2018), presented as a poster at la 3a Semana de la Complejidad (3rd Week of Complexity), National Autonomous University of Mexico (UNAM), November 26-28, 2018, Mexico City, Mexico.
6. Hyobin Kim, The role of criticality of gene regulatory networks on emergent properties of biological systems, a seminar talk at the Seminario Proyectos Posdoctorales (Seminar on Postdoctoral Projects), Center for Complexity Sciences (C3), National Autonomous University of Mexico (UNAM), August 20, 2018, Mexico City, Mexico. [Link1], [Link2], [Link3]
5. Hyobin Kim, The role of criticality of gene regulatory networks on emergent properties of biological systems, dissertation defense & a seminar talk at the CoCo Seminar, SUNY at Binghamton, April 18, 2018, Binghamton, NY. [Link]
4. Hyobin Kim and Hiroki Sayama, Criticality of gene regulatory networks and robustness of morphogenesis against perturbations, presented as a talk at the Seventh Morphogenetic Engineering Workshop (MEW), September 4, 2017, Lyon, France. [Link]
3. Hyobin Kim, Farnaz Zamani Esfahlani, Samuel Heiserman, Nasim Nezamoddini, and Hiroki Sayama, Instability of multilayer networks induced by inter-layer coupling, presented as a talk at the 2016 Conference on Complex Systems (CCS 2016), September 19-22, 2016, Amsterdam, the Netherlands. [Link]
2. Hyobin Kim and Hiroki Sayama, RBN-based morphogenetic systems with spring-mass-damper kinetics, presented as a talk at the Sixth Morphogenetic Engineering Workshop (MEW), July 4, 2016, Cancun, Mexico. [Link]
1. Hyo-Bin Kim, Sung Hoon Jung, and Kwang-Hyun Cho, Self-organization facilitates the evolution of biological networks, presented as a poster at the 11th International Conference on Systems Biology (ICSB 2010), October 11-14, 2010, Edinburgh, Scotland, UK.
DOCTORAL DISSERTATION
Hyobin Kim, The Role of Criticality of Gene Regulatory Networks on Emergent Properties of Biological Systems, Ph.D. Dissertation, Department of Systems Science and Industrial Engineering, Thomas J. Watson School of Engineering and Applied Science, SUNY at Binghamton, May 2018. [Link]
MASTER'S THESIS
Hyo-Bin Kim, The Role of Self-Organization in the Evolution of Bio-Molecular Interaction Networks, M.Sc. Thesis, Department of Bio and Brain Engineering, College of Engineering, KAIST, February 2011. (written in Korean) [Link]