Publications
SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping.
Feng Y, Beh LY, Chang WJ, Landweber LF.
Genome Biol Evol. 2020 Oct 1;12(10):1711-1718. doi: 10.1093/gbe/evaa147.
Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms.
Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF.
BMC Genomics. 2019 Dec 30;20(1):1037. doi: 10.1186/s12864-019-6189-9.
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.
Yerlici VT, Lu MW, Hoge CR, Miller RV, Neme R, Khurana JS, Bracht JR, Landweber LF.
Nucleic Acids Res. 2019 Oct 10;47(18):9741-9760. doi: 10.1093/nar/gkz725.
Transformation with Artificial Chromosomes in Oxytricha trifallax and Their Applications.
Clay DM, Kim H, Landweber LF.
G3 (Bethesda). 2019 Oct 7;9(10):3119-3127. doi: 10.1534/g3.119.400298.
Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax.
Clay DM, Yerlici VT, Villano DJ, Landweber LF.
G3 (Bethesda). 2019 Oct 7;9(10):3105-3118. doi: 10.1534/g3.118.200930.
Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.
Beh LY, Debelouchina GT, Clay DM, Thompson RE, Lindblad KA, Hutton ER, Bracht JR, Sebra RP, Muir TW, Landweber LF.
Cell. 2019 Jun 13;177(7):1781-1796.e25. doi: 10.1016/j.cell.2019.04.028. Epub 2019 May 16.
Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax.
Braun J, Nabergall L, Neme R, Landweber LF, Saito M, Jonoska N.
G3 (Bethesda). 2018 May 4;8(5):1669-1674. doi: 10.1534/g3.118.200176.
Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha.
Khurana JS, Clay DM, Moreira S, Wang X, Landweber LF.
RNA. 2018 Jan;24(1):18-29. doi: 10.1261/rna.061333.117. Epub 2017 Oct 27.
Non-model model organisms.
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.
BMC Biol. 2017 Jun 29;15(1):55. doi: 10.1186/s12915-017-0391-5.
Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development.
Lindblad KA, Bracht JR, Williams AE, Landweber LF.
RNA. 2017 Aug;23(8):1200-1208. doi: 10.1261/rna.058511.116. Epub 2017 Apr 27.
Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax.
Burns J, Kukushkin D, Chen X, Landweber LF, Saito M, Jonoska N.
J Theor Biol. 2016 Dec 7;410:171-180. doi: 10.1016/j.jtbi.2016.08.038. Epub 2016 Sep 2.
What Is a Genome?
Goldman AD, Landweber LF.
PLoS Genet. 2016 Jul 21;12(7):e1006181. doi: 10.1371/journal.pgen.1006181. eCollection 2016 Jul. Review.
Chromosome fusions triggered by noncoding RNA.
Bracht JR, Wang X, Shetty K, Chen X, Uttarotai GJ, Callihan EC, McCloud SS, Clay DM, Wang J, Nowacki M, Landweber LF.
RNA Biol. 2017 May 4;14(5):620-631. doi: 10.1080/15476286.2016.1195940. Epub 2016 Jun 7.
Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha.
Chen X, Landweber LF.
Mob DNA. 2016 Jan 25;7:2. doi: 10.1186/s13100-016-0057-9. eCollection 2016.
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism.
Goldman AD, Beatty JT, Landweber LF.
J Mol Evol. 2016 Jan;82(1):17-26. doi: 10.1007/s00239-015-9722-8. Epub 2016 Jan 5.
The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.
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.
Genome Biol Evol. 2015 Nov 27;8(1):109-25. doi: 10.1093/gbe/evv237.
mds_ies_db: a database of ciliate genome rearrangements.
Burns J, Kukushkin D, Lindblad K, Chen X, Jonoska N, Landweber LF.
Nucleic Acids Res. 2016 Jan 4;44(D1):D703-9. doi: 10.1093/nar/gkv1190. Epub 2015 Nov 19.
Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.
Chen X, Jung S, Beh LY, Eddy SR, Landweber LF.
Genome Biol Evol. 2015 Sep 2;7(10):2859-70. doi: 10.1093/gbe/evv172.
DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.
Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF.
Genome Res. 2015 Nov;25(11):1727-38. doi: 10.1101/gr.188516.114. Epub 2015 Sep 1.
Where Next for Genetics and Genomics?
Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G.
PLoS Biol. 2015 Jul 30;13(7):e1002216. doi: 10.1371/journal.pbio.1002216. eCollection 2015 Jul.
Programmed Genome Rearrangements in the Ciliate Oxytricha.
Yerlici VT, Landweber LF.
Microbiol Spectr. 2014 Dec;2(6). doi: 10.1128/microbiolspec.MDNA3-0025-2014. Review.
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF.
Cell. 2014 Aug 28;158(5):1187-1198. doi: 10.1016/j.cell.2014.07.034.
Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax.
Khurana JS, Wang X, Chen X, Perlman DH, Landweber LF.
Genetics. 2014 Jul;197(3):839-49. doi: 10.1534/genetics.114.163279. Epub 2014 May 1.
Transposon domestication versus mutualism in ciliate genome rearrangements.
Vogt A, Goldman AD, Mochizuki K, Landweber LF.
PLoS Genet. 2013;9(8):e1003659. doi: 10.1371/journal.pgen.1003659. Epub 2013 Aug 1. Review.
Biology Direct: celebrating 7 years of open, published peer review.
Koonin EV, Landweber LF, Lipman DJ.
Biol Direct. 2013 Apr 30;8:11. doi: 10.1186/1745-6150-8-11. No abstract available.
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.
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.
PLoS Biol. 2013;11(1):e1001473. doi: 10.1371/journal.pbio.1001473. Epub 2013 Jan 29.
Genomes on the edge: programmed genome instability in ciliates.
Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF.
Cell. 2013 Jan 31;152(3):406-16. doi: 10.1016/j.cell.2013.01.005. Review.