Publications

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

Selected papers

• RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
  Z Li^#*, CC Kuo^#, F Ticconi, M Shaigan, E G Gusmao, M Allhoff, M Manolov, M Zenke, I G Costa^*.
  BMC Bioinformatics (2023).

• scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference
  Z Li, J Nagai, C Kuppe, R Kramann, IG Costa.
  Bioinformatics Advances (2023).

• Spatial multi-omic map of human myocardial infarction
  C Kuppe^#, ROR Flores^#, Z Li^#, S Hayat, RT Levinson, X Liao, MT Hannani, J Tanevski, F Wünnemann, J Nagai, M Halder, D Schumacher, S Menzel, G Schäfer, K Hoeft, M Cheng, S Ziegler, X Zhang, F Peisker, N Kaesler, T Saritas, Y Xu, A Kassner, J Gummert, M Morshuis, J Amrute, RJA Veltrop, P Boor, K Klingel, LW Van Laake, A Vink, RM Hoogenboezem, EMJ Bindels, L Schurgers, S Sattler, D Schapiro, RK Schneider, K Lavine, H Milting^*, IG Costa^*, J Saez-Rodriguez^* and R Kramann^*.
  Nature (2022).

• Chromatin-accessibility estimation of single-cell ATAC-seq data with scOpen
  Z Li^#, C Kuppe^#, S Ziegler, M Cheng, N Kabgani, S Menzel, M Zenke, R Kramann^*, IG Costa^*.
  Nature Communications (2021).

• Identification of transcription factor binding sites using ATAC-seq
  Z Li, MH Schulz, T Look, M Begemann, M Zenke, I G Costa.
  Genome Biology (2019).

• Improving the JADE Algorithm by Clustering Successful Parameters
  Z Li, J Guo, S Yang.
  International Journal of Wireless and Mobile Computing (2016).

Contributed papers

• A lncRNA identifies IRF8 enhancer in feedback control of DC development
  H Xu, Z Li, CC Kuo, K Götz, T Look, MAS de Toledo, K Seré, IG Costa, M Zenke.
  eLife (2023).

• Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease
  Y Xu^#, C Kuppe^#, JP Patón, S Hayat, J Kranz, AT Abdallah, J Nagai, Z Li, F Peisker, T Saritas, M Halder, S Menzel, K Hoeft, A Kenter, H Kim, C van Roeyen, M Lehrke, J Moellmann, T Speer, EM Buhl, R Hoogenboezem, P Boor, J Jansen, C Knopp, I Kurth, B Smeets, E Bindels, M Reinders, C Baan, J Gribnau, E Hoorn, J Steffens, T Huber, IG Costa, J Floege, RK Schneider, J Saez-Rodriguez, BS Freedman^*, R Kramann^*.
  Nature Genetics (2022).

• MOJITOO: a fast and universal method for integration of multimodal single cell data
  M Cheng, Z Li, IG Costa.
  Bioinformatics (2022).

• Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation
  S Heller, Z Li, Q Lin, R Geusz, M Breunig, M Hohwieler, X Zhang, G Nair, T Seufferlein, M Hebrok, M Sander, C Julier, A Kleger^*, IG Costa^*.
  Communications Biology (2021).

• Mutations and variants of ONECUT1 in diabetes
  A Philippi^#, S Heller^#, IG Costa^#, V Senée^#, M Breunig, Z Li, G Kwon, R Russell, A Illing, Q Lin, M Hohwieler, A Degavre, P Zalloua, S Liebau, M Schuster, J Krumm, X Zhang, R Geusz, JR Benthuysen, A Wang, J Chiou, K Gaulton, H Neubauer, E Simon, T Klein, M Wagner, G Nair, C Besse, CD Roulland, R Olaso, J Deleuze, B Kuster, M Hebrok, T Seufferlein, M Sander, BO Boehm, F Oswald, M Nicolino^*, C Julier^*, A Kleger^*.
  Nature Medicine (2021).

• Accelerating differential evolution based on a subset-to-subset survivor selection operator
  J Guo, Z Li, S Yang.
  Soft Computing (2019).

• Dissipative differential evolution with self-adaptive control parameters
  J Guo, Z Li, W Xie, H Wang.
  IEEE Congress on Evolutionary Computation (2015).