RESEARCH ARTICLES ( ª = AU graduate student, = AU undergraduate student)

Asrat TMª, Cho W, Liu FA, Shapiro SM, Bracht JR, Zestos AG. Direct Detection of DNA and RNA on Carbon Fiber Microelectrodes Using Fast-Scan Cyclic Voltammetry. (2021) ACS Omega, 6, 10, 6571–6581


Kaufmann J., Asalone KCª, Corizzo R., Saldanha C., Bracht JR., Japkowicz N. (2020) One-Class Ensembles for Rare Genomic Sequences Identification. In: Appice A., Tsoumakas G., Manolopoulos Y., Matwin S. (eds) Discovery Science. DS 2020. Lecture Notes in Computer Science, vol 12323. Springer, Cham.


Asalone KCª, Ryan Kª, Yamadi Mª, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR*. Regional sequence expansion or collapse in heterozygous genome assemblies. (2020) PLoS computational biology 16 (7), e1008104. (*corresponding)


Cordero, A.D.; Callihan, E.C.; Said, R.ª; Alowais, Y.ª; Paffhausen, E.S.; Bracht, J.R*. Epigenetic Regulation of Neuregulin-1 Tunes White Adipose Stem Cell Differentiation. Cells 2020, 9, 1148. (*corresponding)


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 20, 1037 (2019)


Weinstein DJª, Allen Sª, Lau M, Erasmus M, Asalone KCª, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR*. The genome of a subterrestrial nematode reveals adaptations to heat. Nat Commun 10, 5268 (2019) (*Corresponding.)


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 Research (2019). gkz725,


Guerin M, Weinstein DJª, Bracht JR*. Stress-adapted Mollusca and Nematoda exhibit convergently expanded Hsp70 and AIG1 gene families. J Mol Evol (2019) 87: 289. (*Corresponding.)

NOTE:   Guerin, Weinstein, and Bracht 2019 was nominated for the 2019 Zuckerlandl prize for best paper of the year: Liberles DA. 2019 Zuckerkandl Prize. J Mol Evol. 2020 Mar;88(2):121.


Beh LY, Debelouchina GT, Clay DM, Thompson RE, Lindblad KA, Hutton ER, Bracht JR, Sebra RP, Muir TW, Landweber LF.  Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization. Cell. 2019 June 13.

Nelson MMª, Waldron CL†, Bracht JR*. Rapid molecular detection of macrolide resistance. BMC Infectious Diseases. 2019 Feb 12;19(1):144. (*Corresponding.)


Asalone KCª, Nelson, MMª, Bracht JR*. Novel sequence discovery by subtractive genomics. J. Vis. Exp. (143), e58877, doi:10.3791/58877 (2019). (*Corresponding.)


Paffhausen ES†1, Alowais Yª1, Chao CW†, Callihan EC, Creswell K, Bracht, JR*. Discovery of a stem-like multipotent cell fate. American Journal of Stem Cells. 2018 June 10 ;7(2):25-37. (1= co-first authors. * corresponding.)


Biederman MKª, Nelson MMª, Asalone KCª, Pedersen ALª, Saldanha CJ, Bracht JR*. Discovery of the first germline-restricted gene by subtractive transcriptomic analysis in the zebra finch Taeniopygia guttata. Current Biology. 2018 May 21;28(10):1620-1627. (*Corresponding.)


Lindblad KA1, Bracht, JR1, 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. (1 Equal contribution.)


Beh LY, Debelouchina GT, Lindblad KA, Kulej K, Hutton ER, Bracht JR, Sebra RP, Garcia BA, Muir TW, Landweber LF.  Synthesis of a eukaryotic chromosome reveals a role for N6-methyladenine in nucleosome organization. bioRxiv, 184929. 2017 Jan. 1.


Bracht JR1*, Wang X1*, Shetty K, Chen X, Uttarotai Gª, Callihan E, McCloud S, Clay D, Wang J, Nowacki M, Landweber LF*. Chromosome fusions triggered by noncoding RNA. RNA Biology. 2016 Jun 7:1-12.  (1 Equal contribution. * Corresponding.)


Chen X1, Bracht JR1, Goldman A, Swart E, Dolzhenko E, Swart E, Clay D, Perlman DH, Doak TG, Stuart A, Amemiya C, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell. 2014 Aug 28:158(5):1187-98. (1 Equal contribution.)


Swart E, Bracht JR, Magrini V, Minx P,Chen X, Zhou Y, Khurana J, Goldman AD, Nowacki M, Schotanus K, et al. The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with over 16,000 Tiny Chromosomes. PLoS Biology. 2013 Jan 29;11(1).


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):1243-1255.


Bracht JR*, Perlman DH, Landweber LF*. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biology. 2012 Oct 17;13(10):R99 (*corresponding.)


Bracht JR1, Van Wynsberghe PM1, Mondol V, Pasquinelli AE. Regulation of lin-4 miRNA expression, organismal growth and development by a conserved RNA binding protein in C. elegans. Dev Biol. 2010 Dec 15;348(2):210-21.  (1 Equal contribution.)


Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 2005 Aug 26;122(4):553-563


Bracht J1, Hunter S1, Eachus R, Weeks P, Pasquinelli AE. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA. 2004 10:1586-1594. (1 Equal contribution.)


REVIEW ARTICLES & BOOK CHAPTERS ( ª = AU graduate student, † = AU undergraduate student)

Bracht JR, Vieira-Potter VJ, De Souza Santos R, Oz OK, Palmer BF, Clegg DJ. The role of estrogens in the adipose tissue milieu. Ann. N.Y. Acad. Sci., 1461: 127-143. (2019). Refereed. Cover image.

Bruun, K1. Schermer E1. Sivendra A1, Valaik E1, Wise RB1. Said Rª, Bracht JR. Therapeutic applications of adipose-derived stem cells in cardiovascular disease. American Journal of Stem Cells. 2018;7(4):94-103. (1 Equal contribution.). Refereed.


Bracht JR*. RNA-mediated somatic genome rearrangement in ciliates. Somatic Genome Variation in Animals, Plants, and Microorganisms. Edited by Xiu-Qing Li. Wiley-Blackwell, Hoboken, NJ, 2017. Ch. 8, pp 167-198. (* corresponding.)


Bracht JR*, Ferraro EM, Bracht KA. How do cysts know when to hatch? The role of ecological communication in awakening latent life. Biocommunication of Ciliates. Edited by Guenther Witzany and Mariusz Nowacki. Springer. 2016 97:119. (* corresponding.)


Bracht JR. Beyond transcriptional silencing: Is cytosine methylation a widely conserved eukaryotic DNA elimination mechanism? BioEssays. April 2014 36(4):346-52. Refereed.


Goldman, A. D., Stein, E. M., Bracht, J. R. and L. F. Landweber. Programmed Genome Processing in Ciliates. Discrete and Topological Models in Molecular Biology. Natural Computing Series. Edited by N. Jonoska and M. Saito. Springer Berlin Heidelberg. 2014 273-287.


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):406-416. Refereed.


Pasquinelli AE*, Hunter SE, Bracht J. MicroRNAs: A Developing Story. Curr Opin Genet Dev. April 2005 15:200-205 (*corresponding.) Refereed.