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Braun J, Neme R, Feng Y, et al. (2023) SDRAP for annotating scrambled or rearranged genomes. Nar Genomics and Bioinformatics. 5: lqad096 |
Feng Y, Neme R, Beh LY, et al. (2022) Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. Elife. 11 |
Feng Y, Landweber LF. (2021) Transposon debris in ciliate genomes. Plos Biology. 19: e3001354 |
Miller RV, Neme R, Clay DM, et al. (2021) Transcribed germline-limited coding sequences in Oxytricha trifallax. G3 (Bethesda, Md.) |
Feng Y, Beh LY, Chang WJ, et al. (2020) SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping. Genome Biology and Evolution |
Yerlici VT, Lu MW, Hoge CR, et al. (2019) Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Research |
Beh LY, Debelouchina GT, Clay DM, et al. (2019) Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization. Cell |
Burns J, Kukushkin D, Chen X, et al. (2016) Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax. Journal of Theoretical Biology |
Schaap P, Barrantes I, Minx P, et al. (2015) The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-component and Metazoan-type Tyrosine Kinase Signaling. Genome Biology and Evolution |
Burns J, Kukushkin D, Lindblad K, et al. (2015) |