Publications of Z Bao

Cheng, L.; Wang, N.; Bao, Z.; Zhou, Q.; Guarracino, A.; Yang, Y.; Wang, P.; Zhang, Z.; Tang, D.; Zhang, P. et al.; Wu, Y.; Zhou, Y.; Zheng, Y.; Hu, Y.; Liang, Q.; Ma, Z.; Lassois, L.; Zhang, C.; Lucas, W.; Garrison, E.; Stein, N.; Städler, T.; Zhou, Y.; Huang, S.: Leveraging a phased pangenome for haplotype design of hybrid potato. Nature Epub ahead (2025)

Xian, W.; Bezrukov, I.; Bao, Z.; Vorbrugg, S.; Gautam, A.; Weigel, D.: TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data. Molecular Biology and Evolution 42 (1), msae247 (2025)

Vorbrugg, S.; Bezrukov, I.; Bao, Z.; Weigel, D.: Gretl: Variation GRaph Evaluation TooLkit. Bioinformatics 41 (1), btae755 (2024)

Garrison, E.; Guarracino, A.; Heumos, S.; Villani, F.; Bao, Z.; Tattini, T.; Hagmann, J.; Vorbrugg, S.; Marco-Sola, S.; Kubica, C. et al.; Ashbrook, G.; Thorell, K.; Rusholme-Pilcher, R.; Liti, G.; Rudbeck, E.; Golicz, A.; Nahnsen, S.; Yang, Z.; Mwaniki, M.; Nobrega, F.; Wu, Y.; Chen, H.; de Ligt, J.; Sudmant, P.; Huang, S.; Weigel, D.; Soranzo, N.; Colonna, V.; Williams, R.; Prins, P.: Building pangenome graphs. Nature Methods 21 (11), pp. 2008 - 2012 (2024)

Koren, S.; Bao, Z.; Guarracino, A.; Ou, S.; Goodwin, S.; Jenike, K.; Lucas, J.; McNulty, B.; Park, J.; Rautiainen, M. et al.; Rhie, A.; Roelofs, D.; Schneiders, H.; Vrijenhoek, I.; Nijbroek, K.; Nordesjo, O.; Nurk, S.; Vella, M.; Lawrence, K.; Ware, D.; Schatz, M.; Garrison, E.; Huang, S.; McCombie, W.; Miga, K.; Wittenberg, A.; Phillippy, A.: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Genome Research 34 (11), pp. 1919 - 1930 (2024)

Huang, G.; Bao, Z.; Feng, L.; Zhai, J.; Wendel, J.; Cao, X.; Zhu, Y.: A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nature Genetics 56 (9), pp. 1953 - 1963 (2024)

Tao, Y.; Xian, W.; Bao, Z.; Rabanal, F.; Movilli, A.; Lanz, C.; Shirsekar, G.; Weigel, D.: Atlas of telomeric repeat diversity in Arabidopsis thaliana. Genome Biology: Biology for the Post-Genomic Era 25 (1), 244 (2024)

Wu, Y.; Li, D.; Hu, Y.; Li, H.; Ramstein, G.; Zhou, S.; Zhang, X.; Bao, Z.; Zhang, Y.; Song, B. et al.; Zhou, Y.; Zhou, Y.; Gagnon, E.; Särkinen, T.; Knapp, S.; Zhang, C.; Städler, T.; Buckler, E.; Huang, S.: Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186 (11), pp. 2313 - 2328 (2023)

Bao, Z.; Rabanal, F.; Guarracino, A.; Vorbrugg, S.; Xian, W.; Movilli, A.; Teasdale, L.; Murray, K.; Shirsekar, G.; Tao, Y. et al.; Lucke, M.; Garrison, E.; Weigel, D.: Understanding mutational processes from Arabidopsis pangeome graphs. In 34th International Conference on Arabidopsis Research (ICAR 2024), C12-2, p. 156. 34th International Conference on Arabidopsis Research (ICAR 2024), San Diego, CA, USA, July 15, 2024 - July 19, 2024. (2024)

Ou, S.; Bousios, A.; Bao, Z.: Comprehensive annotation of transposable elements in the TAIR12 Arabidopsis genome. In 34th International Conference on Arabidopsis Research (ICAR 2024), C23-4, p. 246. 34th International Conference on Arabidopsis Research (ICAR 2024), San Diego, CA, USA, July 15, 2024 - July 19, 2024. (2024)

Bao, Z.: Understanding the mutational process with Arabidopsis pangenome graphs. In PhD Students’ Symposium 2024. PhD Students’ Symposium 2024, Tübingen, Germany, June 19, 2024 - June 20, 2024. (2024)

Ou, S.; Bousios, A.; Bao, Z.: Comprehensive Annotation of Transposable Elements in the T2T TAIR12 Arabidopsis Genome. In Plant and Animal Genome 31 Conference (PAG 2024). Plant and Animal Genome 31 Conference (PAG 2024), San Diego, CA, USA, January 12, 2024 - January 17, 2024. (2024)

Ou, S.; Liao, H.; Lu, T.; Bao, Z.; Heringer, P.; Dainat, J.; Deng, C.; Rashid, U.: EDTA2: De Novo Transposon Annotation in Diverse TE Landscapes. In Plant and Animal Genome 31 Conference (PAG 2024). Plant and Animal Genome 31 Conference (PAG 2024), San Diego, CA, USA, January 12, 2024 - January 17, 2024. (2024)

Bao, Z.; Vorbrugg, S.; Huang, S.; Weigel, D.: Benchmarking graph building pipeline on plant genome assemblies. In 33rd International Conference on Arabidopsis Research (ICAR 2023), WS02-05. 33rd International Conference on Arabidopsis Research (ICAR 2023), Chiba, Japan, June 05, 2023 - June 06, 2023. (2023)

Xian, W.; Bao, Z.; Vorbrugg, S.; Tao, Y.; Movilli, A.; Bezrukov, I.; Weigel, D.: The structure of mitochondrial genomes is associated with geography in Arabidopsis thaliana. (submitted)

The 1001 Genomes Plus Consortium; Alonso-Blanco, C.; Ashkenazy, H.; Baduel, P.; Bao, Z.; Becker, C.; Caillieux, E.; Colot, V.; Crosbie, D.; De Oliveira, L. et al.; Fitz, J.; Fritschi, K.; Grigoreva, E.; Guo, Y.; Habring, A.; Henderson, I.; Hou, X.-H.; Hu, Y.; Igolkina, A.; Kang, M.; Kemen, E.; Kersey, P.; Kornienko, A.; Lian, Q.; Liu, H.; Liu, J.; Lucke, M.; Mayjonade, B.; Mercier, R.; Mollá Morales, A.; Movilli, A.; Murray, K.; Naish, M.; Nordborg, M.; Rabanal, F.; Roux, F.; Schandry, N.; Schneeberger, K.; Schwab, R.; Shirsekar, G.; Sushko, S.; Tao, Y.; Teasdale, L.; Vorbrugg, S.; Weigel, D.; Xian, W.: The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research. (submitted)

Vorbrugg, S.; Bezrukov, I.; Bao, Z.; Xian, W.; Weigel, D.: Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes. (submitted)

Xian, W.; Bezrukov, I.; Bao, Z.; Vorbrugg, S.; Gautam, A.; Weigel, D.: TIPP_plastid: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data. (submitted)