Publications

For a full list see: Google Scholar
^# Co-first authors; ^* Co-corresponding authors

Selected papers

1. Mapping spatially-resolved transcriptomes in systemic sclerosis
   Zhijian Li, Aleix Rius Rigau, Wenjie Xie, Xiaohang Shao, Yi-Nan Li, Alexandru Emil Matei, Hejian Zou, Luca Pinello, Jorg H.W. Distler^*, Rui He^*, Minrui Liang^*
   Biorxiv (2025).

2. Deaminase-mediated chromatin accessibility profiling with single-allele resolution
   Tian Yu^#, Zhijian Li^#, Ellie Gibbs^#, Reina Iwase, Matthew J Francoeur, Quang vinh Phan, Jing Zhao, Jane Rosin, Phillip A Cole, Luca Pinello^*, Richard I Sherwood^*
   Biorxiv (2024).

3. Single cell multi-omics of fibrotic kidney reveal epigenetic regulation of antioxidation and apoptosis within proximal tubule
   Zhejun Chen, Liqing Ye, Minyan Zhu, Cong Xia, Junfen Fan, Hongbo Chen, Zhijian Li^*, Shan Mou^*.
   Cellular and Molecular Life Sciences 81, 1-16 (2024).

4. Benchmarking computational methods to identify spatially variable genes and peaks
   Zhijian Li^#, Zain M.Patel^#, Dongyuan Song, Guanao Yan, Jingyi Jessica Li, Luca Pinello.
   Biorxiv (2023).

5. RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
   Zhijian Li^#*, Chao-Chung Kuo^#, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo Gade Gusmao, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa^*.
   BMC Bioinformatics 24, 79 (2023).

6. scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference
   Zhijian Li, James S Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa.
   Bioinformatics Advances, (2023).

7. Spatial multi-omic map of human myocardial infarction
   Christoph Kuppe^#, Ricardo O. Ramirez Flores^#, Zhijian Li^#, Sikander Hayat, Rebecca T. Levinson, Xian Liao, Monica T. Hannani, Jovan Tanevski, Florian Wünnemann, James S. Nagai, Maurice Halder, David Schumacher, Sylvia Menzel, Gideon Schäfer, Konrad Hoeft, Mingbo Cheng, Susanne Ziegler, Xiaoting Zhang, Fabian Peisker, Nadine Kaesler, Turgay Saritas, Yaoxian Xu, Astrid Kassner, Jan Gummert, Michiel Morshuis, Junedh Amrute, Rogier J. A. Veltrop, Peter Boor, Karin Klingel, Linda W. Van Laake, Aryan Vink, Remco M. Hoogenboezem, Eric M. J. Bindels, Leon Schurgers, Susanne Sattler, Denis Schapiro, Rebekka K. Schneider, Kory Lavine, Hendrik Milting^*, Ivan G. Costa^*, Julio Saez-Rodriguez^*, Rafael Kramann^*.
   Nature 608, 766–777 (2022).

8. Chromatin-accessibility estimation of single-cell ATAC-seq data with scOpen
   Zhijian Li^#, Christoph Kuppe^#, Susanne Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, Martin Zenke, Rafael Kramann^*, Ivan G. Costa^*.
   Nature Communications 12, (2021).

9. Identification of transcription factor binding sites using ATAC-seq
   Zhijian Li, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa.
   Genome Biology 20, (2019).

10. Improving the JADE Algorithm by Clustering Successful Parameters
    Zhijian Li, Jinglei Guo, Shengxiang Yang.
    International Journal of Wireless and Mobile Computing (2016).

Contributed papers

1. CREB determines the expression of ST2 in Tregs and mediates the balance between type 1 and type 2 immune responses
   Sudheendra Hebbar Subramanyam, Judit Hriczko, Thomas Look, Tannaz Goodarzi, Tim Clarner, Eva Verjans, Svenja Boell, Christopher Neullens, Ivan Costa, Zhijian Li, Lin Gan, Bernd Denecke, Angela Schippers, Stefan Floess, Jochen Huehn, Edgar Schmitt, Tobias Bopp, Hermann Wasmuth, Ron Winograd, Rudi Beyaert, Bart Lambrecht, Peter Boor, Martin Zenke, Norbert Wagner, Kim Ohl, Klaus Tenbrock
   Biorxiv (2024).

2. PHLOWER-Single cell trajectory analysis using Decomposition of the Hodge Laplacian
   Mingbo Cheng, Jitske Jansen, Katharina Reimer, James Shiniti Nagai, Zhijian Li, Paul Kiessling, Martin Grasshoff, Christoph Kuppe, Michael Schaub, Rafael Kramann, Ivan Gesteira Costa Filho
   Biorxiv (2024).

3. Deciphering the impact of genomic variation on function
   IGVF Consortium.
   Nature (2024).

4. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification
   Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I. Love, Guillaume Lettre, David B. Ascher, Christopher A. Cassa, Richard I. Sherwood, Luca Pinello. Nature Genetics (2024).

5. A lncRNA identifies IRF8 enhancer in feedback control of DC development
   Huaming Xu, Zhijian Li, Chao-Chung Kuo, Katrin Götz, Thomas Look, Marcelo AS de Toledo, Kristin Seré, Ivan G Costa, Martin Zenke.
   eLife (2023).

6. Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease
   Yaoxian Xu^#, Christoph Kuppe^#, Javier Perales-Patón, Sikander Hayat, Jennifer Kranz, Ali T. Abdallah, James Nagai, Zhijian Li, Fabian Peisker, Turgay Saritas, Maurice Halder, Sylvia Menzel, Konrad Hoeft, Annegien Kenter, Hyojin Kim, Claudia R. C. van Roeyen, Michael Lehrke, Julia Moellmann, Thimoteus Speer, Eva M. Buhl, Remco Hoogenboezem, Peter Boor, Jitske Jansen, Cordula Knopp, Ingo Kurth, Bart Smeets, Eric Bindels, Marlies E. J. Reinders, Carla Baan, Joost Gribnau, Ewout J. Hoorn, Joachim Steffens, Tobias B. Huber, Ivan Costa, Jürgen Floege, Rebekka K. Schneider, Julio Saez-Rodriguez, Benjamin S. Freedman, Rafael Kramann.
   Nature Genetics 54, 1690–1701 (2022).

7. MOJITOO: a fast and universal method for integration of multimodal single cell data
   Mingbo Cheng, Zhijian Li, Ivan G Costa.
   Bioinformatics (2022).

8. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation
   Sandra Heller, Zhijian Li, Qiong Lin, Ryan Geusz, Markus Breunig, Meike Hohwieler, Xi Zhang, Gopika G. Nair, Thomas Seufferlein, Matthias Hebrok, Maike Sander, Cécile Julier, Alexander Kleger^*, Ivan G. Costa^*.
   Communications Biology 4, (2021).

9. Mutations and variants of ONECUT1 in diabetes
   Anne Philippi^#, Sandra Heller^#, Ivan G. Costa^#, Valérie Senée^#, Markus Breunig, Zhijian Li, Gino Kwon, Ronan Russell, Anett Illing, Qiong Lin, Meike Hohwieler, Anne Degavre, Pierre Zalloua, Stefan Liebau, Michael Schuster, Johannes Krumm, Xi Zhang, Ryan Geusz, Jacqueline R. Benthuysen, Allen Wang, Joshua Chiou, Kyle Gaulton, Heike Neubauer, Eric Simon, Thomas Klein, Martin Wagner, Gopika Nair, Céline Besse, Claire Dandine-Roulland, Robert Olaso, Jean-François Deleuze, Bernhard Kuster, Matthias Hebrok, Thomas Seufferlein, Maike Sander, Bernhard O. Boehm, Franz Oswald, Marc Nicolino^*, Cécile Julier^*, Alexander Kleger^*.
   Nature Medicine 27, 1928–1940 (2021).

10. Accelerating differential evolution based on a subset-to-subset survivor selection operator
    Jinglei Guo, Zhijian Li, Shengxiang Yang.
    Soft Computing (2019).

11. Dissipative differential evolution with self-adaptive control parameters
    Jinglei Guo, Zhijian Li, Wei Xie, Hui Wang.
    IEEE Congress on Evolutionary Computation (2015).