Research Interests
Our main goal is to understand how genome regulation and genome evolution interplay with each other. Evolutionary changes in the genome can affect diverse cellular behaviors, including how genomic transactions (e.g. transcription, replication, DNA repair) are regulated. In turn, existing genomic regulatory systems can impact how and where genetic mutations occur, as well as evolutionary fates of mutations. Genome regulation and genome evolution have been and are being heavily investigated by thriving functional genomic and evolutionary genomic approaches, respectively. However, the two fundamental biological processes are usually investigated independently of each other and the intricate interplay between them remains poorly understood. Investigating this interplay is essential for understanding many biological phenomena which can not be adequately explained by looking at only one of the two aspects. By harnessing various omics data generated by high-throughput methods, we aim to perform integrative analysis to address related questions, with a strong emphasis on computational and quantitative biology. See more details at our group website //caililab.org.
Publications
Selected work (*co-first author; #corresponding author; bold, lab member):
Fang Y*, Deng S*, Li C#. A generalizable deep learning framework for inferring fine-scale germline mutation rate maps. Nature Machine Intelligence 2022;4(12):1209-23. Link
Chia M*, Li C*, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biology 2021;22(1):34. Link
Li C#, Luscombe NM. Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome. Nature Communications. 2020;11(1):1363. Link
Li C#, Lenhard B, Luscombe NM. Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Genome Research. 2018;28(5):676-88.Link
Seki R*, Li C*, Fang Q, Hayashi S, Egawa S, Hu J, et al. Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nature Communications. 2017;8:14229. Link
Zhang G*, Li C*, Li Q, Li B, Larkin DM, Lee C, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346(6215):1311-20. Link
Terrapon N*, Li C*, Robertson HM, Ji L, Meng X, Booth W, et al. Molecular traces of alternative social organization in a termite genome. Nature Communications. 2014;5:3636. Link
Li C*, Zhang Y*, Li J*, Kong L*, Hu H, Pan H, et al. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. GigaScience. 2014;3(1):27. Link
Kocher SD*, Li C*, Yang W, Tan H, Yi SV, Yang X, et al. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology. 2013;14(12):R142. Link
Yan G*, Zhang G*, Fang X*, Zhang Y*, Li C*, Ling F*, et al. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nature Biotechnology. 2011;29(11):1019. Link
Nygaard S*, Zhang G*, Schiøtt M*, Li C*, Wurm Y, Hu H, et al. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Research. 2011;21(8):1339-48. Link
See the full list at Google Scholar //scholar.google.com/citations?hl=en&user=tJ1YzXIAAAAJ&view_op=list_works&sortby=pubdate
