My Bibliography

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Angelova MT, Feng Y, Villano DJ, Aslan E, Lu MW, Estève PO, Sen S, Jack WE, Pradhan S, Landweber LF. A PIWI protein-dependent DNA N6-adenine methylation pathway in Oxytricha protects genomic sequences from deletion. bioRxiv. 2026 Jan 11;. doi: 10.64898/2026.01.06.698049. PubMed PMID: 41542652; PubMed Central PMCID: PMC12803261.

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Walker MWG, Akematsu T, Aslan E, Villano DJ, Fried HS, Lan H, Sternberg SH, Landweber LF. Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement. Nucleic Acids Res. 2025 Jul 8;53(13). doi: 10.1093/nar/gkaf577. PubMed PMID: 40637233; PubMed Central PMCID: PMC12242761.

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Walker MWG, Akematsu T, Aslan E, Villano DJ, Fried HS, Lan H, Sternberg SH, Landweber LF. Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement. bioRxiv. 2025 Mar 18;. doi: 10.1101/2025.03.17.643836. PubMed PMID: 40166331; PubMed Central PMCID: PMC11956929.

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Villano DJ, Prahlad M, Singhal A, Sanbonmatsu KY, Landweber LF. Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax. bioRxiv. 2025 Jan 2;. doi: 10.1101/2024.12.31.630814. PubMed PMID: 39803579; PubMed Central PMCID: PMC11722245.

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Braun J, Neme R, Feng Y, Landweber LF, Jonoska N. SDRAP for annotating scrambled or rearranged genomes. NAR Genom Bioinform. 2023 Dec;5(4):lqad096. doi: 10.1093/nargab/lqad096. eCollection 2023 Dec. PubMed PMID: 37942284; PubMed Central PMCID: PMC10629285.

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Lu MW, Beh LY, Yerlici VT, Fang W, Kulej K, Garcia BA, Landweber LF. Exploration of the Nuclear Proteomes in the Ciliate Oxytricha trifallax. Microorganisms. 2023 Jan 30;11(2). doi: 10.3390/microorganisms11020343. PubMed PMID: 36838311; PubMed Central PMCID: PMC9958989.

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Feng Y, Neme R, Beh LY, Chen X, Braun J, Lu MW, Landweber LF. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. Elife. 2022 Nov 24;11. doi: 10.7554/eLife.82979. PubMed PMID: 36421078; PubMed Central PMCID: PMC9797194.

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Li X, Guo S, Cui Y, Zhang Z, Luo X, Angelova MT, Landweber LF, Wang Y, Wu TP. NT-seq: a chemical-based sequencing method for genomic methylome profiling. Genome Biol. 2022 May 30;23(1):122. doi: 10.1186/s13059-022-02689-9. PubMed PMID: 35637459; PubMed Central PMCID: PMC9150344.

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Feng Y, Neme R, Beh LY, Chen X, Braun J, Lu M, Landweber LF. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. [preprint]. 2022 May. Available from: https://www.biorxiv.org/content/10.1101/2022.05.09.490778v1. doi: 10.1101/2022.05.09.490778.

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Feng Y, Landweber LF. Transposon debris in ciliate genomes. PLoS Biol. 2021 Aug;19(8):e3001354. doi: 10.1371/journal.pbio.3001354. eCollection 2021 Aug. PubMed PMID: 34428213; PubMed Central PMCID: PMC8384191.

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Miller RV, Neme R, Clay DM, Pathmanathan JS, Lu MW, Yerlici VT, Khurana JS, Landweber LF. Transcribed germline-limited coding sequences in Oxytricha trifallax. G3 (Bethesda). 2021 Jun 17;11(6). doi: 10.1093/g3journal/jkab092. PubMed PMID: 33772542; PubMed Central PMCID: PMC8495736.

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Feng Y, Beh LY, Chang WJ, Landweber LF. SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping. Genome Biol Evol. 2020 Oct 1;12(10):1711-1718. doi: 10.1093/gbe/evaa147. PubMed PMID: 32790832; PubMed Central PMCID: PMC7586852.

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Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF. Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics. 2019 Dec 30;20(1):1037. doi: 10.1186/s12864-019-6189-9. PubMed PMID: 31888453; PubMed Central PMCID: PMC6937825.

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Yerlici VT, Lu MW, Hoge CR, Miller RV, Neme R, Khurana JS, Bracht JR, Landweber LF. Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Res. 2019 Oct 10;47(18):9741-9760. doi: 10.1093/nar/gkz725. PubMed PMID: 31504770; PubMed Central PMCID: PMC6765146.

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Clay DM, Kim H, Landweber LF. Transformation with Artificial Chromosomes in Oxytricha trifallax and Their Applications. G3 (Bethesda). 2019 Oct 7;9(10):3119-3127. doi: 10.1534/g3.119.400298. PubMed PMID: 31506318; PubMed Central PMCID: PMC6778790.

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Clay DM, Yerlici VT, Villano DJ, Landweber LF. Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax. G3 (Bethesda). 2019 Oct 7;9(10):3105-3118. doi: 10.1534/g3.118.200930. PubMed PMID: 31506317; PubMed Central PMCID: PMC6778801.

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Braun J, Nabergall L, Neme R, Landweber LF, Saito M, Jonoska N. Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax. G3 (Bethesda). 2018 May 4;8(5):1669-1674. doi: 10.1534/g3.118.200176. PubMed PMID: 29545465; PubMed Central PMCID: PMC5940158.

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Khurana JS, Clay DM, Moreira S, Wang X, Landweber LF. Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. RNA. 2018 Jan;24(1):18-29. doi: 10.1261/rna.061333.117. Epub 2017 Oct 27. PubMed PMID: 29079634; PubMed Central PMCID: PMC5733567.

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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol. 2017 Jun 29;15(1):55. doi: 10.1186/s12915-017-0391-5. PubMed PMID: 28662661; PubMed Central PMCID: PMC5492503.

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Lindblad KA, Bracht JR, Williams AE, Landweber LF. Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 2017 Aug;23(8):1200-1208. doi: 10.1261/rna.058511.116. Epub 2017 Apr 27. PubMed PMID: 28450531; PubMed Central PMCID: PMC5513065.

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Bracht JR, Wang X, Shetty K, Chen X, Uttarotai GJ, Callihan EC, McCloud SS, Clay DM, Wang J, Nowacki M, Landweber LF. Chromosome fusions triggered by noncoding RNA. RNA Biol. 2017 May 4;14(5):620-631. doi: 10.1080/15476286.2016.1195940. Epub 2016 Jun 7. PubMed PMID: 27267579; PubMed Central PMCID: PMC5449082.

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Chen X, Landweber LF. Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha. Mob DNA. 2016;7:2. doi: 10.1186/s13100-016-0057-9. eCollection 2016. PubMed PMID: 26811739; PubMed Central PMCID: PMC4724952.

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Goldman AD, Beatty JT, Landweber LF. The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. J Mol Evol. 2016 Jan;82(1):17-26. doi: 10.1007/s00239-015-9722-8. Epub 2016 Jan 5. PubMed PMID: 26733481; PubMed Central PMCID: PMC4709378.

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Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, Landweber LF, Maric C, Miller D, Noegel AA, Peace R, Pierron G, Sasaki T, Schallenberg-Rüdinger M, Schleicher M, Singh R, Spaller T, Storey KB, Suzuki T, Tomlinson C, Tyson JJ, Warren WC, Werner ER, Werner-Felmayer G, Wilson RK, Winckler T, Gott JM, Glöckner G, Marwan W. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biol Evol. 2015 Nov 27;8(1):109-25. doi: 10.1093/gbe/evv237. PubMed PMID: 26615215; PubMed Central PMCID: PMC4758236.

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Burns J, Kukushkin D, Lindblad K, Chen X, Jonoska N, Landweber LF. : a database of ciliate genome rearrangements. Nucleic Acids Res. 2016 Jan 4;44(D1):D703-9. doi: 10.1093/nar/gkv1190. Epub 2015 Nov 19. PubMed PMID: 26586804; PubMed Central PMCID: PMC4702850.

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Chen X, Jung S, Beh LY, Eddy SR, Landweber LF. Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates. Genome Biol Evol. 2015 Sep 2;7(10):2859-70. doi: 10.1093/gbe/evv172. PubMed PMID: 26338187; PubMed Central PMCID: PMC4684698.

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Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res. 2015 Nov;25(11):1727-38. doi: 10.1101/gr.188516.114. Epub 2015 Sep 1. PubMed PMID: 26330564; PubMed Central PMCID: PMC4617968.

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Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G. Where Next for Genetics and Genomics?. PLoS Biol. 2015 Jul;13(7):e1002216. doi: 10.1371/journal.pbio.1002216. eCollection 2015 Jul. PubMed PMID: 26225775; PubMed Central PMCID: PMC4520474.

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Yerlici VT, Landweber LF. Programmed Genome Rearrangements in the Ciliate Oxytricha. Microbiol Spectr. 2014 Dec;2(6). doi: 10.1128/microbiolspec.MDNA3-0025-2014. Review. PubMed PMID: 26104449; PubMed Central PMCID: PMC4480583.

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Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell. 2014 Aug 28;158(5):1187-1198. doi: 10.1016/j.cell.2014.07.034. PubMed PMID: 25171416; PubMed Central PMCID: PMC4199391.

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Khurana JS, Wang X, Chen X, Perlman DH, Landweber LF. Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. Genetics. 2014 Jul;197(3):839-49. doi: 10.1534/genetics.114.163279. Epub 2014 May 1. PubMed PMID: 24793090; PubMed Central PMCID: PMC4096365.

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Vogt A, Goldman AD, Mochizuki K, Landweber LF. Transposon domestication versus mutualism in ciliate genome rearrangements. PLoS Genet. 2013;9(8):e1003659. doi: 10.1371/journal.pgen.1003659. Epub 2013 Aug 1. Review. PubMed PMID: 23935529; PubMed Central PMCID: PMC3731211.

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Koonin EV, Landweber LF, Lipman DJ. Biology Direct: celebrating 7 years of open, published peer review. Biol Direct. 2013 Apr 30;8:11. doi: 10.1186/1745-6150-8-11. PubMed PMID: 23631729; PubMed Central PMCID: PMC3651295.

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Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. Genomes on the edge: programmed genome instability in ciliates. Cell. 2013 Jan 31;152(3):406-16. doi: 10.1016/j.cell.2013.01.005. Review. PubMed PMID: 23374338; PubMed Central PMCID: PMC3725814.

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Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol. 2013;11(1):e1001473. doi: 10.1371/journal.pbio.1001473. Epub 2013 Jan 29. PubMed PMID: 23382650; PubMed Central PMCID: PMC3558436.

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Fang W, Wei Y, Kang Y, Landweber LF. Detection of a common chimeric transcript between human chromosomes 7 and 16. Biol Direct. 2012 Dec 29;7:49. doi: 10.1186/1745-6150-7-49. PubMed PMID: 23273016; PubMed Central PMCID: PMC3538553.

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Fang W, Landweber LF. RNA-mediated genome rearrangement: hypotheses and evidence. Bioessays. 2013 Feb;35(2):84-7. doi: 10.1002/bies.201200140. Epub 2012 Dec 20. PubMed PMID: 23281134; PubMed Central PMCID: PMC3821980.

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Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell. 2012 Dec 7;151(6):1243-55. doi: 10.1016/j.cell.2012.10.045. PubMed PMID: 23217708; PubMed Central PMCID: PMC3678556.

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Goldman AD, Bernhard TM, Dolzhenko E, Landweber LF. LUCApedia: a database for the study of ancient life. Nucleic Acids Res. 2013 Jan;41(Database issue):D1079-82. doi: 10.1093/nar/gks1217. Epub 2012 Nov 27. PubMed PMID: 23193296; PubMed Central PMCID: PMC3531223.

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Bracht JR, Perlman DH, Landweber LF. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biol. 2012 Oct 17;13(10):R99. doi: 10.1186/gb-2012-13-10-r99. PubMed PMID: 23075511; PubMed Central PMCID: PMC3491425.

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Goldman AD, Landweber LF. Oxytricha as a modern analog of ancient genome evolution. Trends Genet. 2012 Aug;28(8):382-8. doi: 10.1016/j.tig.2012.03.010. Epub 2012 May 21. Review. PubMed PMID: 22622227; PubMed Central PMCID: PMC3401270.

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Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, Herrick G, Landweber LF. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. Protist. 2012 Jul;163(4):643-57. doi: 10.1016/j.protis.2011.12.006. Epub 2012 Feb 9. PubMed PMID: 22325790; PubMed Central PMCID: PMC3433844.

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Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet. 2011;12:367-89. doi: 10.1146/annurev-genom-082410-101420. Review. PubMed PMID: 21801022; PubMed Central PMCID: PMC3518427.

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Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF. The Oxytricha trifallax mitochondrial genome. Genome Biol Evol. 2012;4(2):136-54. doi: 10.1093/gbe/evr136. Epub 2011 Dec 16. PubMed PMID: 22179582; PubMed Central PMCID: PMC3318907.

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Zhou Y, Wubneh H, Schwarz C, Landweber LF. A chimeric chromosome in the ciliate oxytricha resulting from duplication. J Mol Evol. 2011 Oct;73(3-4):70-3. doi: 10.1007/s00239-011-9464-1. Epub 2011 Oct 22. PubMed PMID: 22037698; PubMed Central PMCID: PMC3494457.

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Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, Eddy SR. Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes. Nucleic Acids Res. 2011 Sep 1;39(17):7529-47. doi: 10.1093/nar/gkr501. Epub 2011 Jun 28. PubMed PMID: 21715380; PubMed Central PMCID: PMC3177221.

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Nowacki M, Haye JE, Fang W, Vijayan V, Landweber LF. RNA-mediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22140-4. doi: 10.1073/pnas.1012236107. Epub 2010 Nov 15. PubMed PMID: 21078984; PubMed Central PMCID: PMC3009799.

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Nowacki M, Landweber LF. Epigenetic inheritance in ciliates. Curr Opin Microbiol. 2009 Dec;12(6):638-43. doi: 10.1016/j.mib.2009.09.012. Epub 2009 Oct 31. Review. PubMed PMID: 19879799; PubMed Central PMCID: PMC2868311.

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Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, Landweber LF. A functional role for transposases in a large eukaryotic genome. Science. 2009 May 15;324(5929):935-8. doi: 10.1126/science.1170023. Epub 2009 Apr 16. PubMed PMID: 19372392; PubMed Central PMCID: PMC3491810.

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Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon-van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA. Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics. 2008 Dec 5;9:587. doi: 10.1186/1471-2164-9-587. PubMed PMID: 19061489; PubMed Central PMCID: PMC2633312.