All Stories

  1. MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps

    Article • Briefings in Bioinformatics, May 2026, Oxford University Press (OUP)

    Cai Li

  2. Germline de novo mutation rate of the highly heterozygous amphioxus genome

    Article • Molecular Biology and Evolution, January 2026, Oxford University Press (OUP)

    Cai Li

  3. Direct detection of meiotic recombination events in the highly heterozygous amphioxus genome

    Article • July 2025, Cold Spring Harbor Laboratory Press

    Cai Li

  4. A generalizable deep learning framework for inferring fine-scale germline mutation rate maps

    Article • Nature Machine Intelligence, December 2022, Springer Science + Business Media

    Cai Li

  5. Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

    Article • Nature Communications, March 2020, Springer Science + Business Media

    Professor Nicholas Luscombe, Cai Li

  6. The Genomic Footprints of the Fall and Recovery of the Crested Ibis

    Article • Current Biology, January 2019, Elsevier

    Cai Li

  7. Nucleosome positioning stability is a significant modulator of germline mutation rate variation across the human genome:

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Cai Li

  8. The origin of new transcription start sites and how they evolve over time

    Article • Genome Research, April 2018, Cold Spring Harbor Laboratory Press

    Cai Li

  9. Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Professor Nicholas Luscombe, Cai Li

  10. Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

    Article • Nature Communications, February 2017, Springer Science + Business Media

    Cai Li

  11. The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

    Article • GigaScience, September 2016, Oxford University Press (OUP)

    Cai Li

  12. Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida

    Article • Molecular Biology and Evolution, July 2015, Oxford University Press (OUP)

    Cai Li

  13. Genomic signatures of evolutionary transitions from solitary to group living

    Article • Science, May 2015, American Association for the Advancement of Science

    Cai Li

  14. Improving the ostrich genome assembly using optical mapping data

    Article • GigaScience, May 2015, Oxford University Press (OUP)

    Cai Li

  15. Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

    Article • Current Biology, May 2015, Elsevier

    Cai Li

  16. A genomic comparison of two termites with different social complexity

    Article • Frontiers in Genetics, March 2015, Frontiers

    Cai Li

  17. Phylogenomic analyses data of the avian phylogenomics project

    Article • GigaScience, February 2015, Oxford University Press (OUP)

    Cai Li, Edward L Braun

  18. Avianbase: a community resource for bird genomics

    Article • Genome Biology, January 2015, Springer Science + Business Media

    Cai Li

  19. Comparative genomics reveals insights into avian genome evolution and adaptation

    Article • Science, December 2014, American Association for the Advancement of Science

    Cai Li, Edward L Braun, Dr Jacqueline Smith

  20. Whole-genome analyses resolve early branches in the tree of life of modern birds

    Article • Science, December 2014, American Association for the Advancement of Science

    Cai Li, Edward L Braun, Dr Sankar Subramanian

  21. Comparative genomic data of the Avian Phylogenomics Project

    Article • GigaScience, December 2014, Oxford University Press (OUP)

    Cai Li

  22. Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles

    Article • BMC Evolutionary Biology, December 2014, Springer Science + Business Media

    Cai Li

  23. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

    Article • GigaScience, December 2014, Oxford University Press (OUP)

    Cai Li, Dr Sankar Subramanian

  24. Complementary symbiont contributions to plant decomposition in a fungus-farming termite

    Article • Proceedings of the National Academy of Sciences, September 2014, Proceedings of the National Academy of Sciences

    Cai Li

  25. Molecular traces of alternative social organization in a termite genome

    Article • Nature Communications, May 2014, Nature

    Cai Li

  26. The Genome of the Clonal Raider Ant Cerapachys biroi

    Article • Current Biology, February 2014, Elsevier

    Cai Li

  27. Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

    Article • Science, January 2013, American Association for the Advancement of Science

    Cai Li

  28. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

    Article • Genome Biology, January 2013, Springer Science + Business Media

    Cai Li

  29. Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes

    Article • BMC Veterinary Research, January 2012, Springer Science + Business Media

    Cai Li

  30. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

    Article • Genome Research, June 2011, Cold Spring Harbor Laboratory Press

    Dr Yannick Wurm, Cai Li

  31. Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

    Article • Science, August 2010, American Association for the Advancement of Science

    Cai Li