Genome Regulation
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1. Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA. Transcriptional interference by small transcripts in proximal promoter regions. Nucleic Acids Res. 2018 Feb 16;46(3):1069-1088. doi: 10.1093/nar/gkx1242. PubMed PMID: 29309647; PubMed Central PMCID: PMC5815073.
2. 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. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997. PubMed PMID: 27708261; PubMed Central PMCID: PMC5059674.
3. 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. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997. PubMed PMID: 27708261; PubMed Central PMCID: PMC5059674.
4. Rozhdestvensky TS, Robeck T, Galiveti CR, Raabe CA, Seeger B, Wolters A, Gubar LV, Brosius J, Skryabin BV. Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice. Sci Rep. 2016 Feb 5;6:20398. doi: 10.1038/srep20398. PubMed PMID: 26848093; PubMed Central PMCID: PMC4742849.
5. Noll A, Raabe CA, Churakov G, Brosius J, Schmitz J. Ancient traces of tailless retropseudogenes in therian genomes. Genome Biol Evol. 2015 Feb 26;7(3):889-900. doi: 10.1093/gbe/evv040. PubMed PMID: 25724209; PubMed Central PMCID: PMC5322556.
6. Galiveti CR, Raabe CA, Konthur Z, Rozhdestvensky TS. Differential regulation of non-protein coding RNAs from Prader-Willi Syndrome locus. Sci Rep. 2014 Sep 23;4:6445. doi: 10.1038/srep06445. PubMed PMID: 25246219; PubMed Central PMCID: PMC4171697.
7. Mo D, Raabe CA, Reinhardt R, Brosius J, Rozhdestvensky TS. Alternative processing as evolutionary mechanism for the origin of novel nonprotein coding RNAs. Genome Biol Evol. 2013;5(11):2061-71. doi: 10.1093/gbe/evt155. PubMed PMID: 24132753; PubMed Central PMCID: PMC3845636.
8. Camacho-Vanegas O, Camacho SC, Till J, Miranda-Lorenzo I, Terzo E, Ramirez MC, Schramm V, Cordovano G, Watts G, Mehta S, Kimonis V, Hoch B, Philibert KD, Raabe CA, Bishop DF, Glucksman MJ, Martignetti JA. Primate genome gain and loss: a bone dysplasia, muscular dystrophy, and bone cancer syndrome resulting from mutated retroviral-derived MTAP transcripts. Am J Hum Genet. 2012 Apr 6;90(4):614-27. doi: 10.1016/j.ajhg.2012.02.024. Epub 2012 Mar 29. PubMed PMID: 22464254; PubMed Central PMCID: PMC3322221.
9. Khayrullina GA, Raabe CA, Hoe CH, Becker K, Reinhardt R, Tang TH, Rozhdestvensky TS, Kopylov AM. Transcription analysis and small non-protein coding RNAs associated with bacterial ribosomal protein operons. Curr Med Chem. 2012;19(30):5187-98. PubMed PMID: 22680642.
10. Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS. Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res. 2010 Sep;38(17):5893-908. doi: 10.1093/nar/gkq281. Epub 2010 May 11. PubMed PMID: 20460466; PubMed Central PMCID: PMC2943607.
11. 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. A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res. 2010 Jan;38(2):608-17. doi: 10.1093/nar/gkp895. Epub 2009 Oct 28. PubMed PMID: 19864253; PubMed Central PMCID: PMC2811010.
12. Khanam T, Raabe CA, Kiefmann M, Handel S, Skryabin BV, Brosius J. Can ID repetitive elements serve as cis-acting dendritic targeting elements? An in vivo study. PLoS One. 2007 Sep 26;2(9):e961. PubMed PMID: 17896001; PubMed Central PMCID: PMC1978531.
13. Kanniappan P, Ahmed SA, Rajasekaram G, Marimuthu C, Ch'ng ES, Lee LP, Raabe CA, Rozhdestvensky TS, Tang TH. RNomic identification and evaluation of npcTB_6715, a non-protein-coding RNA gene as a potential biomarker for the detection of Mycobacterium tuberculosis. J Cell Mol Med. 2017 Oct;21(10):2276-2283. doi: 10.1111/jcmm.13148. Epub 2017 Jul 29. PubMed PMID: 28756649; PubMed Central PMCID: PMC5618688.
14. Janice J, Pande A, Weiner J, Lin CF, Makałowski W. U12-type spliceosomal introns of Insecta. Int J Biol Sci. 2012;8(3):344-52. doi: 10.7150/ijbs.3933. Epub 2012 Feb 17. PubMed PMID: 22393306; PubMed Central PMCID: PMC3291851.
15. Dröge J, Pande A, Englander EW, Makałowski W. Comparative genomics of neuroglobin reveals its early origins. PLoS One. 2012;7(10):e47972. doi:10.1371/journal.pone.0047972. Epub 2012 Oct 25. PubMed PMID: 23133533; PubMed Central PMCID: PMC3485006.
16. Kathum OA, Schräder T, Anhlan D, Nordhoff C, Liedmann S, Pande A, Mellmann A, Ehrhardt C, Wixler V, Ludwig S. Phosphorylation of influenza A virus NS1 protein at threonine 49 suppresses its interferon antagonistic activity. Cell Microbiol. 2016 Jun;18(6):784-91. doi: 10.1111/cmi.12559. Epub 2016 Jan 27. PubMed PMID:26687707; PubMed Central PMCID: PMC5066752.
17. Sharma R, Sharma PR, Choudhary ML, Pande A, Khatri GS. Cytoplasmic expression of mature glycylglycine endopeptidase lysostaphin with an amino terminal hexa-histidine in a soluble and catalytically active form in Escherichia coli. Protein Expr Purif. 2006 Jan;45(1):206-15. Epub 2005 Aug 19. PubMed PMID:16181789.
Review articles:
---------
1. Kuehnl A, Musiol A, Raabe CA, Rescher U. Emerging functions as host cell factors - an encyclopedia of annexin-pathogen interactions. Biol Chem. 2016 Oct 1;397(10):949-59. doi: 10.1515/hsz-2016-0183. Review. PubMed PMID: 27366904.
2. Brosius J, Raabe CA. What is an RNA? A top layer for RNA classification. RNA Biol. 2016;13(2):140-4. doi: 10.1080/15476286.2015.1128064. PubMed PMID: 26818079; PubMed Central PMCID: PMC4829331.
3. Raabe CA, Brosius J. Does every transcript originate from a gene? Ann N Y Acad Sci. 2015 Apr;1341:136-48. doi: 10.1111/nyas.12741. PubMed PMID: 25847549.
4. Hoe CH, Raabe CA, Rozhdestvensky TS, Tang TH. Bacterial sRNAs: regulation in stress. Int J Med Microbiol. 2013 Jul;303(5):217-29. doi: 10.1016/j.ijmm.2013.04.002. Epub 2013 Apr 11. Review. PubMed PMID: 23660175.
5. Makałowski W, Pande A, Gotea V, Makałowska I. Transposable elements and their identification. Methods Mol Biol. 2012;855:337-59. doi:10.1007/978-1-61779-582-4_12. Review. PubMed PMID: 22407715.
Next Generation Sequencing:
----------------------------
1. Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS. The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. RNA. 2011 Jul;17(7):1357-66. doi: 10.1261/rna.2682311. Epub 2011 May 24. PubMed PMID: 21610211; PubMed Central PMCID: PMC3138571
2. Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res. 2014 Feb;42(3):1414-26. doi: 10.1093/nar/gkt1021. Epub 2013 Nov 5. Review. PubMed PMID: 24198247; PubMed Central PMCID: PMC3919602
------------------
1. Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA. Transcriptional interference by small transcripts in proximal promoter regions. Nucleic Acids Res. 2018 Feb 16;46(3):1069-1088. doi: 10.1093/nar/gkx1242. PubMed PMID: 29309647; PubMed Central PMCID: PMC5815073.
2. 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. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997. PubMed PMID: 27708261; PubMed Central PMCID: PMC5059674.
3. 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. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997. PubMed PMID: 27708261; PubMed Central PMCID: PMC5059674.
4. Rozhdestvensky TS, Robeck T, Galiveti CR, Raabe CA, Seeger B, Wolters A, Gubar LV, Brosius J, Skryabin BV. Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice. Sci Rep. 2016 Feb 5;6:20398. doi: 10.1038/srep20398. PubMed PMID: 26848093; PubMed Central PMCID: PMC4742849.
5. Noll A, Raabe CA, Churakov G, Brosius J, Schmitz J. Ancient traces of tailless retropseudogenes in therian genomes. Genome Biol Evol. 2015 Feb 26;7(3):889-900. doi: 10.1093/gbe/evv040. PubMed PMID: 25724209; PubMed Central PMCID: PMC5322556.
6. Galiveti CR, Raabe CA, Konthur Z, Rozhdestvensky TS. Differential regulation of non-protein coding RNAs from Prader-Willi Syndrome locus. Sci Rep. 2014 Sep 23;4:6445. doi: 10.1038/srep06445. PubMed PMID: 25246219; PubMed Central PMCID: PMC4171697.
7. Mo D, Raabe CA, Reinhardt R, Brosius J, Rozhdestvensky TS. Alternative processing as evolutionary mechanism for the origin of novel nonprotein coding RNAs. Genome Biol Evol. 2013;5(11):2061-71. doi: 10.1093/gbe/evt155. PubMed PMID: 24132753; PubMed Central PMCID: PMC3845636.
8. Camacho-Vanegas O, Camacho SC, Till J, Miranda-Lorenzo I, Terzo E, Ramirez MC, Schramm V, Cordovano G, Watts G, Mehta S, Kimonis V, Hoch B, Philibert KD, Raabe CA, Bishop DF, Glucksman MJ, Martignetti JA. Primate genome gain and loss: a bone dysplasia, muscular dystrophy, and bone cancer syndrome resulting from mutated retroviral-derived MTAP transcripts. Am J Hum Genet. 2012 Apr 6;90(4):614-27. doi: 10.1016/j.ajhg.2012.02.024. Epub 2012 Mar 29. PubMed PMID: 22464254; PubMed Central PMCID: PMC3322221.
9. Khayrullina GA, Raabe CA, Hoe CH, Becker K, Reinhardt R, Tang TH, Rozhdestvensky TS, Kopylov AM. Transcription analysis and small non-protein coding RNAs associated with bacterial ribosomal protein operons. Curr Med Chem. 2012;19(30):5187-98. PubMed PMID: 22680642.
10. Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS. Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res. 2010 Sep;38(17):5893-908. doi: 10.1093/nar/gkq281. Epub 2010 May 11. PubMed PMID: 20460466; PubMed Central PMCID: PMC2943607.
11. 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. A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res. 2010 Jan;38(2):608-17. doi: 10.1093/nar/gkp895. Epub 2009 Oct 28. PubMed PMID: 19864253; PubMed Central PMCID: PMC2811010.
12. Khanam T, Raabe CA, Kiefmann M, Handel S, Skryabin BV, Brosius J. Can ID repetitive elements serve as cis-acting dendritic targeting elements? An in vivo study. PLoS One. 2007 Sep 26;2(9):e961. PubMed PMID: 17896001; PubMed Central PMCID: PMC1978531.
13. Kanniappan P, Ahmed SA, Rajasekaram G, Marimuthu C, Ch'ng ES, Lee LP, Raabe CA, Rozhdestvensky TS, Tang TH. RNomic identification and evaluation of npcTB_6715, a non-protein-coding RNA gene as a potential biomarker for the detection of Mycobacterium tuberculosis. J Cell Mol Med. 2017 Oct;21(10):2276-2283. doi: 10.1111/jcmm.13148. Epub 2017 Jul 29. PubMed PMID: 28756649; PubMed Central PMCID: PMC5618688.
14. Janice J, Pande A, Weiner J, Lin CF, Makałowski W. U12-type spliceosomal introns of Insecta. Int J Biol Sci. 2012;8(3):344-52. doi: 10.7150/ijbs.3933. Epub 2012 Feb 17. PubMed PMID: 22393306; PubMed Central PMCID: PMC3291851.
15. Dröge J, Pande A, Englander EW, Makałowski W. Comparative genomics of neuroglobin reveals its early origins. PLoS One. 2012;7(10):e47972. doi:10.1371/journal.pone.0047972. Epub 2012 Oct 25. PubMed PMID: 23133533; PubMed Central PMCID: PMC3485006.
16. Kathum OA, Schräder T, Anhlan D, Nordhoff C, Liedmann S, Pande A, Mellmann A, Ehrhardt C, Wixler V, Ludwig S. Phosphorylation of influenza A virus NS1 protein at threonine 49 suppresses its interferon antagonistic activity. Cell Microbiol. 2016 Jun;18(6):784-91. doi: 10.1111/cmi.12559. Epub 2016 Jan 27. PubMed PMID:26687707; PubMed Central PMCID: PMC5066752.
17. Sharma R, Sharma PR, Choudhary ML, Pande A, Khatri GS. Cytoplasmic expression of mature glycylglycine endopeptidase lysostaphin with an amino terminal hexa-histidine in a soluble and catalytically active form in Escherichia coli. Protein Expr Purif. 2006 Jan;45(1):206-15. Epub 2005 Aug 19. PubMed PMID:16181789.
Review articles:
---------
1. Kuehnl A, Musiol A, Raabe CA, Rescher U. Emerging functions as host cell factors - an encyclopedia of annexin-pathogen interactions. Biol Chem. 2016 Oct 1;397(10):949-59. doi: 10.1515/hsz-2016-0183. Review. PubMed PMID: 27366904.
2. Brosius J, Raabe CA. What is an RNA? A top layer for RNA classification. RNA Biol. 2016;13(2):140-4. doi: 10.1080/15476286.2015.1128064. PubMed PMID: 26818079; PubMed Central PMCID: PMC4829331.
3. Raabe CA, Brosius J. Does every transcript originate from a gene? Ann N Y Acad Sci. 2015 Apr;1341:136-48. doi: 10.1111/nyas.12741. PubMed PMID: 25847549.
4. Hoe CH, Raabe CA, Rozhdestvensky TS, Tang TH. Bacterial sRNAs: regulation in stress. Int J Med Microbiol. 2013 Jul;303(5):217-29. doi: 10.1016/j.ijmm.2013.04.002. Epub 2013 Apr 11. Review. PubMed PMID: 23660175.
5. Makałowski W, Pande A, Gotea V, Makałowska I. Transposable elements and their identification. Methods Mol Biol. 2012;855:337-59. doi:10.1007/978-1-61779-582-4_12. Review. PubMed PMID: 22407715.
Next Generation Sequencing:
----------------------------
1. Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS. The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. RNA. 2011 Jul;17(7):1357-66. doi: 10.1261/rna.2682311. Epub 2011 May 24. PubMed PMID: 21610211; PubMed Central PMCID: PMC3138571
2. Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res. 2014 Feb;42(3):1414-26. doi: 10.1093/nar/gkt1021. Epub 2013 Nov 5. Review. PubMed PMID: 24198247; PubMed Central PMCID: PMC3919602