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Transcriptional interference by small transcripts in proximal promoter regions.

Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA.

Nucleic Acids Res. 2018 Feb 16;46(3):1069-1088. doi: 10.1093/nar/gkx1242.


De-novo emergence of SINE retroposons during the early evolution of passerine birds.

Suh A, Bachg S, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J.

Mob DNA. 2017 Dec 14;8:21. doi: 10.1186/s13100-017-0104-1. eCollection 2017.


Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions.

Schmitz J, Noll A, Raabe CA, Churakov G, Voss R, Kiefmann M, Rozhdestvensky T, Brosius J, Baertsch R, Clawson H, Roos C, Zimin A, Minx P, Montague MJ, Wilson RK, Warren WC.

Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997.


BC1 RNA motifs required for dendritic transport in vivo.

Robeck T, Skryabin BV, Rozhdestvensky TS, Skryabin AB, Brosius J.

Sci Rep. 2016 Jun 28;6:28300. doi: 10.1038/srep28300.


Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice.

Rozhdestvensky TS, Robeck T, Galiveti CR, Raabe CA, Seeger B, Wolters A, Gubar LV, Brosius J, Skryabin BV.

Sci Rep. 2016 Feb 5;6:20398. doi: 10.1038/srep20398.


What is an RNA? A top layer for RNA classification.

Brosius J, Raabe CA.

RNA Biol. 2016;13(2):140-4. doi: 10.1080/15476286.2015.1128064.


Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora).

Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J.

Mol Biol Evol. 2015 Dec;32(12):3194-204. doi: 10.1093/molbev/msv188. Epub 2015 Sep 3.


Corrigendum: Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids.

Hartig G, Churakov G, Warren WC, Brosius J, Makałowski W, Schmitz J.

Sci Rep. 2015 Jul 28;5:12590. doi: 10.1038/srep12590. No abstract available.


Evidence for a Novel Mechanism of Influenza Virus-Induced Type I Interferon Expression by a Defective RNA-Encoded Protein.

Boergeling Y, Rozhdestvensky TS, Schmolke M, Resa-Infante P, Robeck T, Randau G, Wolff T, Gabriel G, Brosius J, Ludwig S.

PLoS Pathog. 2015 May 29;11(5):e1004924. doi: 10.1371/journal.ppat.1004924. eCollection 2015 May.


The changing spectrum of surgically treated cystic neoplasms of the pancreas.

Plichta JK, Brosius JA, Pappas SG, Abood GJ, Aranha GV.

HPB Surg. 2015;2015:791704. doi: 10.1155/2015/791704. Epub 2015 Mar 30.


Does every transcript originate from a gene?

Raabe CA, Brosius J.

Ann N Y Acad Sci. 2015 Apr;1341:136-48. doi: 10.1111/nyas.12741.


Ancient traces of tailless retropseudogenes in therian genomes.

Noll A, Raabe CA, Churakov G, Brosius J, Schmitz J.

Genome Biol Evol. 2015 Feb 26;7(3):889-900. doi: 10.1093/gbe/evv040.


An alternative method for the calculation of joint probability distributions. Application to the expectation of the triplet invariant.

Brosius J.

Acta Crystallogr A Found Adv. 2015 Jan;71(Pt 1):76-81. doi: 10.1107/S2053273314023560. Epub 2015 Jan 1.


Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

Suh A, Churakov G, Ramakodi MP, Platt RN 2nd, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J.

Genome Biol Evol. 2014 Dec 11;7(1):205-17. doi: 10.1093/gbe/evu256.


GPAC-genome presence/absence compiler: a web application to comparatively visualize multiple genome-level changes.

Noll A, Grundmann N, Churakov G, Brosius J, Makałowski W, Schmitz J.

Mol Biol Evol. 2015 Jan;32(1):275-86. doi: 10.1093/molbev/msu276. Epub 2014 Sep 25.


The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function.

Brosius J.

Cold Spring Harb Perspect Biol. 2014 Jul 31;6(12):a016089. doi: 10.1101/cshperspect.a016089. Review.


Biases in small RNA deep sequencing data.

Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS.

Nucleic Acids Res. 2014 Feb;42(3):1414-26. doi: 10.1093/nar/gkt1021. Epub 2013 Nov 5. Review.


Alternative processing as evolutionary mechanism for the origin of novel nonprotein coding RNAs.

Mo D, Raabe CA, Reinhardt R, Brosius J, Rozhdestvensky TS.

Genome Biol Evol. 2013;5(11):2061-71. doi: 10.1093/gbe/evt155.


The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses.

Suh A, Brosius J, Schmitz J, Kriegs JO.

Nat Commun. 2013;4:1791. doi: 10.1038/ncomms2798.


Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids.

Hartig G, Churakov G, Warren WC, Brosius J, Makałowski W, Schmitz J.

Sci Rep. 2013;3:1756. doi: 10.1038/srep01756. Erratum in: Sci Rep. 2015;5:12590.


Ancestry of the Australian termitivorous numbat.

Zemann A, Churakov G, Donnellan S, Grützner F, Zhao F, Brosius J, Schmitz J.

Mol Biol Evol. 2013 May;30(5):1041-5. doi: 10.1093/molbev/mst032. Epub 2013 Feb 21.


Genomic impact of eukaryotic transposable elements.

Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J.

Mob DNA. 2012 Nov 21;3(1):19. doi: 10.1186/1759-8753-3-19.


A universal method for the study of CR1 retroposons in nonmodel bird genomes.

Suh A, Kriegs JO, Donnellan S, Brosius J, Schmitz J.

Mol Biol Evol. 2012 Oct;29(10):2899-903. Epub 2012 Apr 20.


Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era.

Matzke A, Churakov G, Berkes P, Arms EM, Kelsey D, Brosius J, Kriegs JO, Schmitz J.

Mol Biol Evol. 2012 Jun;29(6):1497-501. doi: 10.1093/molbev/msr319. Epub 2012 Jan 3.


Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds.

Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, Brosius J, Kriegs JO, Schmitz J.

Nat Commun. 2011 Aug 23;2:443. doi: 10.1038/ncomms1448.


Exonization of transposed elements: A challenge and opportunity for evolution.

Schmitz J, Brosius J.

Biochimie. 2011 Nov;93(11):1928-34. doi: 10.1016/j.biochi.2011.07.014. Epub 2011 Jul 26. Review.


Retroposon insertions and the chronology of avian sex chromosome evolution.

Suh A, Kriegs JO, Brosius J, Schmitz J.

Mol Biol Evol. 2011 Nov;28(11):2993-7. doi: 10.1093/molbev/msr147. Epub 2011 Jun 1.


The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome.

Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS.

RNA. 2011 Jul;17(7):1357-66. doi: 10.1261/rna.2682311. Epub 2011 May 24.


A novel web-based TinT application and the chronology of the Primate Alu retroposon activity.

Churakov G, Grundmann N, Kuritzin A, Brosius J, Makałowski W, Schmitz J.

BMC Evol Biol. 2010 Dec 2;10:376. doi: 10.1186/1471-2148-10-376.


Acknowledging conservation trade-offs and embracing complexity.

Hirsch PD, Adams WM, Brosius JP, Zia A, Bariola N, Dammert JL.

Conserv Biol. 2011 Apr;25(2):259-64. doi: 10.1111/j.1523-1739.2010.01608.x. Epub 2010 Nov 17.


Tracking marsupial evolution using archaic genomic retroposon insertions.

Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, Schmitz J.

PLoS Biol. 2010 Jul 27;8(7):e1000436. doi: 10.1371/journal.pbio.1000436.


Retroposon insertions provide insights into deep lagomorph evolution.

Kriegs JO, Zemann A, Churakov G, Matzke A, Ohme M, Zischler H, Brosius J, Kryger U, Schmitz J.

Mol Biol Evol. 2010 Dec;27(12):2678-81. doi: 10.1093/molbev/msq162. Epub 2010 Jun 28.


Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi.

Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS.

Nucleic Acids Res. 2010 Sep;38(17):5893-908. doi: 10.1093/nar/gkq281. Epub 2010 May 11.


Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype.

Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J, Rozhdestvensky TS, Peters G, von Eiff C, Becker K.

J Mol Med (Berl). 2010 Jun;88(6):565-75. doi: 10.1007/s00109-010-0597-2. Epub 2010 Feb 12.


Rodent evolution: back to the root.

Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J.

Mol Biol Evol. 2010 Jun;27(6):1315-26. doi: 10.1093/molbev/msq019. Epub 2010 Jan 25.


Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR.

Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z.

RNA. 2010 Feb;16(2):450-61. doi: 10.1261/rna.1755810. Epub 2009 Dec 29.


A global view of the nonprotein-coding transcriptome in Plasmodium falciparum.

Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS.

Nucleic Acids Res. 2010 Jan;38(2):608-17. doi: 10.1093/nar/gkp895. Epub 2009 Oct 28.


The fragmented gene.

Brosius J.

Ann N Y Acad Sci. 2009 Oct;1178:186-93. doi: 10.1111/j.1749-6632.2009.05004.x. Review.


Mosaic retroposon insertion patterns in placental mammals.

Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J.

Genome Res. 2009 May;19(5):868-75. doi: 10.1101/gr.090647.108. Epub 2009 Mar 4.


Retrocopy contributions to the evolution of the human genome.

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J.

BMC Genomics. 2008 Oct 8;9:466. doi: 10.1186/1471-2164-9-466.


Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes.

Volff JN, Brosius J.

Genome Dyn. 2007;3:175-90. doi: 10.1159/000107611. Review.


A statistical interpretation of the triplet and quartet invariant in P1. A theoretical discussion.

Brosius J.

Acta Crystallogr A. 2008 Sep;64(Pt 5):571-86. doi: 10.1107/S0108767308016966. Epub 2008 Aug 14.


The quartet revisited.

Brosius J.

Acta Crystallogr A. 2008 Sep;64(Pt 5):564-70. doi: 10.1107/S0108767308016978. Epub 2008 Aug 14.


The triplet invariant revisited.

Brosius J.

Acta Crystallogr A. 2008 Sep;64(Pt 5):560-3. doi: 10.1107/S010876730801698X. Epub 2008 Aug 14.


Beyond DNA: RNA editing and steps toward Alu exonization in primates.

Möller-Krull M, Zemann A, Roos C, Brosius J, Schmitz J.

J Mol Biol. 2008 Oct 10;382(3):601-9. doi: 10.1016/j.jmb.2008.07.014. Epub 2008 Jul 16.


Seeing (and doing) conservation through cultural lenses.

Peterson RB, Russell D, West P, Brosius JP.

Environ Manage. 2010 Jan;45(1):5-18. doi: 10.1007/s00267-008-9135-1. Epub 2008 Jul 1.


Reply to Bagni: On BC1 RNA and the fragile X mental retardation protein.

Iacoangeli A, Rozhdestvensky TS, Dolzhanskaya N, Tournier B, Schütt J, Brosius J, Denman RB, Khandjian EW, Kindler S, Tiedge H.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):E29. doi: 10.1073/pnas.0803737105. Epub 2008 May 29. No abstract available.


Genome analysis of the platypus reveals unique signatures of evolution.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.

Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added].


Retroposed SNOfall--a mammalian-wide comparison of platypus snoRNAs.

Schmitz J, Zemann A, Churakov G, Kuhl H, Grützner F, Reinhardt R, Brosius J.

Genome Res. 2008 Jun;18(6):1005-10. doi: 10.1101/gr.7177908. Epub 2008 May 7.


On BC1 RNA and the fragile X mental retardation protein.

Iacoangeli A, Rozhdestvensky TS, Dolzhanskaya N, Tournier B, Schütt J, Brosius J, Denman RB, Khandjian EW, Kindler S, Tiedge H.

Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):734-9. doi: 10.1073/pnas.0710991105. Epub 2008 Jan 9.

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