Colab logo Computational Omics Laboratory (Colab)

Publications

A chronological list of peer-reviewed papers and preprints. Lab members are shown in bold; * marks corresponding authors; # marks co-first authors.

Full publication list also available on Google Scholar.

Preprints

  1. Mapping disease critical spatially variable gene programs by integrating spatial transcriptomics with human genetics Preprint

    Hanbyul Lee, Haochen Sun, Xuewei Cao, Berke Karaahmet, Zhijian Li, Hans-Ulrich Klein, Mariko Taga, Gao Wang, Philip L. De Jager, David A. Bennett, Luca Pinello, Xin Jin, Rahul Mazumder, Kushal K. Dey

    bioRxiv

  2. Chemokine Landscapes of the Tumor Microenvironment Preprint

    Lukas M Altenburger, Aditya Patil, Jakob Jobst, Raphael Kfuri-Rubens, Taylor T Chrisikos, Kazuhiro Taguchi, Meredith F Ellis, Nicolas Roehrle, Murat Tekguc, Zhijian Li, Ryuji Morizane, Luca Pinello, Fabian Theis, Andrew D Luster, Orr Ashenberg, Ramnik J Xavier, Lloyd Bod, Rod A Rahimi, Gary Reynolds, Thorsten R Mempel

    bioRxiv

  3. Deaminase-mediated chromatin accessibility profiling with single-allele resolution Preprint

    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

2026

  1. EPInformer: scalable and integrative prediction of gene expression from promoter–enhancer sequences with multimodal epigenomic profiles

    Jiecong Lin, Zhijian Li, Yajie Zhao, Ruibang Luo, Luca Pinello

    Nature Communications 17, 3975 (2026).

2025

  1. Defining and benchmarking open problems in single-cell analysis

    Malte D. Luecken, Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt, Daniel C. Strobl, Nikolay S. Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael E. Vinyard, D. S. Magruder, Michaela F. Mueller, Alma Andersson, Emma Dann, Qian Qin, Dominik J. Otto, Michal Klein, Olga Borisovna Botvinnik, Louise Deconinck, Kai Waldrant, Sai Nirmayi Yasa, Artur Szałata, Andrew Benz, Zhijian Li, Open Problems Jamboree Members, Jonathan M. Bloom, Angela Oliveira Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian J. Theis & Smita Krishnaswamy

    Nature Biotechnology 43, 1035-1040 (2025).

  2. Systematic benchmarking of computational methods to identify spatially variable genes

    Zhijian Li#, Zain M.Patel#, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan, Jingyi Jessica Li, Luca Pinello.

    Genome Biology 26, 285 (2025).

  3. Spatial multiomics decipher fibroblast–macrophage dynamics in systemic sclerosis

    Zhijian Li, Aleix Rius Rigau, Wenjie Xie, Linlin Huang, Wenjing Ye, Yi-Nan Li, Alexandru-Emil Matei, Christina Bergmann, Xiaohang Shao, Hejian Zou, Jiucun Wang, Luca Pinello, Jörg H W Distler, Rui He, Minrui Liang

    Annals of the Rheumatic Diseases 84, 1231-1245 (2025).

  4. PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories

    Mingbo Cheng, Jitske Jansen, Katharina C. Reimer, Vincent P. Grande, James S. Nagai, Zhijian Li, Paul Kießling, Martin Grasshoff, Christoph Kuppe, Michael T. Schaub, Rafael Kramann & Ivan G. Costa

    Nature Methods 22, 2328-2336 (2025).

  5. CREB regulates Foxp3+ST-2+ TREGS with enhanced IL-10 production

    Sudheendra Hebbar Subramanyam, Judit Turyne Hriczko, Saskia Schulz, Thomas Look, Tannaz Goodarzi, Tim Clarner, Miriam Scheld, Markus Kipp, 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, Martin Zenke, Norbert Wagner, Kim Ohl, Klaus Tenbrock

    Frontiers in Immunology 16, 1601008 (2025).

2024

  1. Deciphering the impact of genomic variation on function

    IGVF Consortium

    Nature 633, 47-57 (2024).

  2. 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, 56 (2024).

  3. 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, Vineel Bhat, Guillaume Lettre, David B. Ascher, Christopher A. Cassa, Richard I. Sherwood & Luca Pinello

    Nature Genetics 56, 925-937 (2024).

2023

  1. scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference

    Zhijian Li, James S Nagai, Christoph Kuppe, Rafael Kramann Ivan G Costa

    Bioinformatics Advances 3, vbad003 (2023).

  2. 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).

  3. A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation

    Huaming Xu, Zhijian Li, Chao-Chung Kuo, Katrin Götz, Thomas Look, Marcelo AS de Toledo, Kristin Seré, Ivan G Costa, Martin Zenke

    eLife 12, e83342 (2023).

2022

  1. 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).

  2. MOJITOO: a fast and universal method for integration of multimodal single-cell data

    Mingbo Cheng, Zhijian Li, Ivan G Costa

    Bioinformatics 38, i282-i289 (2022).

  3. 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).

2021

  1. Chromatin-accessibility estimation from 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, 6386 (2021).

  2. 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, 1298 (2021).

  3. 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).

2019

  1. 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, 45 (2019).

  2. Accelerating differential evolution based on a subset-to-subset survivor selection operator

    Jinglei Guo, Zhijian Li, Shengxiang Yang

    Soft Computing 23, 4113-4130 (2019).