Recent publications

Ni, J.; Hao, Y.; Jimenez-Marin, B.; Ali, F.; Pan, J.; Wang, Y.; Deng, Z.; Gout, J.-F.; Zhang, Y.; Lynch, M.; Long, H. 2025. Whole-genome duplications revealed by macronuclear genomes of five rare species of the model ciliates Paramecium. SCIENCE CHINA Life Sciences (Accepted)

Pan, J.; Wang, Y.; Li, C.; Zhang, S.; Ye, Z.; Ni, J.; Li, H.; Li, Y.; Yue, H.; Ruan, C.; Zhao, D.; Jiang, Y.; Wu, X.; Shen, X.; Zufall, R.A.; Zhang, Y.; Li, W.; Lynch, M.; Long, H. 2024. Molecular basis of phenotypic plasticity in a marine ciliate. The ISME Journal 18: wrae136 [Pan et al. ISME J 2024.pdf]

Li, H.; Wu, K.; Feng, Y.; Gao, C.; Wang, Y.; Zhang, Y.; Pan, J.; Shen, X.; Zufall, R.A.; Zhang, Y.; Zhang, W.; Sun, J.; Ye, Z.;  Li, W.; Lynch, M.; Long, H. 2024. Integrative analyses on the ciliates Colpoda illuminate the life history evolution of soil microorganisms. mSystems 9: e01379-23 [Li et al. mSystems 2024.pdf]

Zhang, Y.; Li, H.; Wang, Y.; Nie, M.; Zhang, K.; Pan, J.; Zhang, Y.; Ye, Z.; Zufall, R.; Lynch, M.; Long, H. 2024. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 9: e01161-23 [Zhang et al. mSystems 2024.pdf]

Long, H.; Johri, P.; Gout, J.F.; Ni, J.; Hao, Y.; Licknack, T.; Wang, Y.; Pan, J.; Berenice Jiménez-Marín; Lynch, M. 2023. Paramecium genetics, genomics and evolution. Annual Review of Genetics 57: 391-410 [Long et al. ARG 2023.pdf]

Lynch, M.; Ali, F.; Lin, T.; Wang, Y.; Ni, J.; Long, H. 2023 The divergence of mutation rates and spectra across the Tree of Life. EMBO Reports e57561 [Lynch et al. EMBO Reports 2023.pdf]

Ni, J.; Pan, J.; Wang, Y.; Chen, T.; Feng, X.; Li, Y.; Lin, T.; Lynch, M.; Long, H.; Li, W. 2023. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Marine Life Science and Technology 5:564-572. [Ni et al. MLST 2023.pdf]

Wu, K.; Li, H.; Cui, X.; Feng, R.; Chen, W.; Jiang, Y.; Tang, C.; Wang, Y.; Shen, X.; Liu, Y.; Lynch, M.; Long, H. 2022. Mutagenesis and resistance development of bacteria challenged by silver nanoparticles. Antimicrobial Agents and Chemotherapy [Wu et al. AAC 2022.pdf]

Pan, J.; Li, W.; Ni, J.; Wu, K.; Konigsberg, I.; Rivera, C.; Tincher, C.; Gregory, C.; Zhou, X.; Doak, T.; Lee, H.; Wang, Y.; Gao, X.; Lynch, M.; Long, H. 2022. Rates of mutations and transcript errors in the foodborne pathogen Salmonella enterica subsp. enterica. Molecular Biology and Evolution 39(4): msac081[Pan et al. MBE 2022.pdf]

Long, H.; Miller, S.F.; Williams, E.; Lynch, M. 2018. Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria. Molecular Biology and Evolution 35(10):2414-2421. [Long et al Mol Biol Evol 2018.pdf]    

Long, H.; Sung, W.; Kucukyildirim,S.; Williams,E.; Miller, S.;Guo, W.; Patterson, C.; Gregory, C.; Strauss, C.; Stone, C.; Berne, C.; Kysela, D.; Shoemaker, W.; Muscarella, M.; Luo, H.; Lennon, J.; Brun, Y.; Lynch, M. 2018. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology and Evolution 2: 237-240. [Long et al Nat Ecol Evol 2018.pdf]

Long, H.; Miller, S.F.; Strauss, C.; Zhao, C.; Cheng, L.; Ye, Z.; Griffin, K.; Te, R.; Lee, H.; Chen, C.; Lynch, M. 2016. Antibiotic treatment enhances the genome-wide mutation rate of target cells. PNAS 113(18): E2498-E2505. [Long et al. PNAS 2016.pdf]

Long, H.; Kucukyildirim#, S.; Sung, W.; Williams, E.; Lee, H.; Ackerman, M.; Doak, T.; Tang, H.; Lynch, M. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Molecular Biology and Evolution 32(9): 2383-2392. [Long et al. MBE 2015.pdf]