The Bee lab

Evolution and Ecology:

1. S. Liu*, M. Westbury, N. Dussex, K. Mitchel, M. Sinding, P. Heintzman, D. Duchêne, J. Kapp, J. Seth, et al., 2021. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family, Cell, 184, 1-12

2. T. Valk, P. Patrícia, D. David, B. Anders, O. Jonas, H. Stefanie, X. Georgios, et al. 2021. Million-Year-Old DNA Sheds Light on the Genomic History of Mammoths. Nature 591 (7849): 265–69. 

3. C. Yang, Y. Zheng, S. Tan, G. Meng, W. Rao, C. Yang, D. Bourne, ……, and S. Liu*. 2020. Efficient COI Barcoding Using High Throughput Single-End 400 Bp Sequencing. BMC Genomics 21 (1): 862. 

4. Z. Nolen, Y. Burcin, I. Iker, S. Liu, G. Clara, B. Daniel, M. Frieder, T. Gilbert, and R. Pereira. 2020. Historical Isolation Facilitates Species Radiation by Sexual Selection: Insights from Chorthippus Grasshoppers. Molecular Ecology, no. October: 4985–5002. 

5. Y. Ji, X. Li, T. Ji, J. Tang, L. Qiu, J. Hu, J. Dong, et al. 2020. Gene Reuse Facilitates Rapid Radiation and Independent Adaptation to Diverse Habitats in the Asian Honeybee. Science Advances 6 (51). 

6. A. Margaryan, M. Sinding, S. Liu, F. Vieira, Y. Chan, S. Nathan, Y. Moodley, M. Bruford, and M. Gilbert. 2020. Recent Mitochondrial Lineage Extinction in the Critically Endangered Javan Rhinoceros. Zoological Journal of the Linnean Society, March, 1–12. 

7. Y. Zhang, Y. Zhong, Y. Hong, Y. Xue, D. Li, C. Zhou, and S. Liu*. 2019. RAD-Seq data advance captive-based conservation of wild Bactrian camels (Camelus ferus). Conservation Genetics 20: 817-824.

8. E. Cappellini, F. Welker, L. Pandolfi, J. Ramos-Madrigal, D. Samodova, P. L Rüther, A. K Fotakis, et al. 2019. Early Pleistocene Enamel Proteome from Dmanisi Resolves Stephanorhinus Phylogeny. Nature 574 (7776): 103–7. 

9. S. Liu#, C. Yang#, C. Zhou#, and X. Zhou*. 2017. Filling reference gaps via assembling DNA barcodes using high-throughput sequencing – moving toward barcoding the world. GigaScience 6(12): 1-8.

10. F. Mitterboeck#, S. Liu#, S. Adamowicz, J. Fu, R. Zhang, W. Song, K. Meusemann, and X. Zhou*. 2017. Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes. GigaScience 6(10): 1-14.

11. S. Liu, X. Wang, L. Xie, M. Tan, Z. Li, X. Su, H. Zhang, et al. 2016. Mitochondrial capture enriches mito-DNA 100-fold, enabling PCR-free mitogenomics biodiversity analysis. Molecular Ecology Resources16: 470-479

12. B. Misof*, S. Liu, K. Meusemann, R. Peters, A. Donath, C. Mayer, P. B. Frandsen, et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science 346 (6210)

Bioinformatics:

1. D. Lang#, S. Zhang#, P. Ren, F. Liang, Z. Sun, G. Meng, Y. Tan, ……. and S. Liu*. 2020. Comparison of the Two Up-to-Date Sequencing Technologies for Genome Assembly: HiFi Reads of Pacific Biosciences Sequel II System and Ultralong Reads of Oxford Nanopore. GigaScience 9 (12): 1–7.

2. J. Hu, J. Fan, Z. Sun, and S. Liu*. 2019. NextPolish: a fast and efficient genome polishing tool for long read assembly. Bioinformatics 36(7): 2253-2255.

3. G. Meng, Y. Li, C. Yang and S. Liu*. 2019. MitoZ: A toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research 47(11): e63

4. Y. Xie#, G. Wu#, J. Tang#, R. Luo, J. Patterson, S. Liu, W. Huang, et al. 2014. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30(12): 1660-1666.

5. S. Liu, Y. Li, J. Lu, X. Su, M. Tang, R. Zhang, L. Zhou, et al. 2013. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology and Evolution 4: 1142-1150.