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Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
Helder I Nakaya, Paulo P Amaral, Rodrigo Louro, André Lopes, Angela A Fachel, Yuri B Moreira, Tarik A El-Jundi, Aline M da Silva, Eduardo M Reis, Sergio Verjovski-Almeida
Genome Biol. 2007; 8(3): R43. Published online 2007 March 26. doi: 10.1186/gb-2007-8-3-r43
PMCID:
PMC1868932
Abstract Full Text PDF–1.8M Supplementary Material
 Is Cited by the Following 26 Articles in this Archive:
Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer
Ana C Tahira, Márcia S Kubrusly, Michele F Faria, Bianca Dazzani, Rogério S Fonseca, Vinicius Maracaja-Coutinho, Sergio Verjovski-Almeida, Marcel CC Machado, Eduardo M Reis
Mol Cancer. 2011; 10: 141. Published online 2011 November 13. doi: 10.1186/1476-4598-10-141
PMCID:
PMC3225313
Abstract Full Text PDF–2.7M Supplementary Material
Intronic L1 Retrotransposons and Nested Genes Cause Transcriptional Interference by Inducing Intron Retention, Exonization and Cryptic Polyadenylation
Kristel Kaer, Jelena Branovets, Anni Hallikma, Pilvi Nigumann, Mart Speek
PLoS One. 2011; 6(10): e26099. Published online 2011 October 13. doi: 10.1371/journal.pone.0026099
PMCID:
PMC3192792
Abstract Full Text PDF–2.6M Supplementary Material
Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript
Dominic Rose, Peter F. Stadler
Front Genet. 2011; 2: 69. Published online 2011 October 5. doi: 10.3389/fgene.2011.00069
PMCID:
PMC3268622
Abstract Full Text PDF–1.9M
The Reality of Pervasive Transcription
Michael B. Clark, Paulo P. Amaral, Felix J. Schlesinger, Marcel E. Dinger, Ryan J. Taft, John L. Rinn, Chris P. Ponting, Peter F. Stadler, Kevin V. Morris, Antonin Morillon, Joel S. Rozowsky, Mark B. Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, Thomas R. Gingeras, John S. Mattick
PLoS Biol. 2011 July; 9(7): e1000625. Published online 2011 July 12. doi: 10.1371/journal.pbio.1000625
PMCID:
PMC3134446
Full Text PDF–256K Supplementary Material
The sequence, structure and evolutionary features of HOTAIR in mammals
Sha He, Shiping Liu, Hao Zhu
BMC Evol Biol. 2011; 11: 102. Published online 2011 April 16. doi: 10.1186/1471-2148-11-102
PMCID:
PMC3103462
Abstract Full Text PDF–752K Supplementary Material
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
Philipp Kapranov, Georges St Laurent, Tal Raz, Fatih Ozsolak, C Patrick Reynolds, Poul HB Sorensen, Gregory Reaman, Patrice Milos, Robert J Arceci, John F Thompson, Timothy J Triche
BMC Biol. 2010; 8: 149. Published online 2010 December 21. doi: 10.1186/1741-7007-8-149
Correction in:
BMC Biol. 2011; 9: 86.
PMCID:
PMC3022773
Abstract Full Text PDF–1.2M Supplementary Material Correction
lncRNAdb: a reference database for long noncoding RNAs
Paulo P. Amaral, Michael B. Clark, Dennis K. Gascoigne, Marcel E. Dinger, John S. Mattick
Nucleic Acids Res. 2011 January; 39(Database issue): D146–D151. Published online 2010 November 25. doi: 10.1093/nar/gkq1138
PMCID:
PMC3013714
Abstract Full Text PDF–3.0M
Critical association of ncRNA with introns
David Rearick, Ashwin Prakash, Andrew McSweeny, Samuel S. Shepard, Larisa Fedorova, Alexei Fedorov
Nucleic Acids Res. 2011 March; 39(6): 2357–2366. Published online 2010 November 10. doi: 10.1093/nar/gkq1080
PMCID:
PMC3064772
Abstract Full Text PDF–1.5M Supplementary Material
Novel Primate-Specific Genes, RMEL 1, 2 and 3, with Highly Restricted Expression in Melanoma, Assessed by New Data Mining Tool
Josane F. Sousa, Raul Torrieri, Rodrigo R. Silva, Cristiano G. Pereira, Valeria Valente, Erico Torrieri, Kamila C. Peronni, Waleska Martins, Nair Muto, Guilherme Francisco, Carla Abdo Brohem, Carlos G. Carlotti, Jr., Silvya S. Maria-Engler, Roger Chammas, Enilza M. Espreafico
PLoS One. 2010; 5(10): e13510. Published online 2010 October 20. doi: 10.1371/journal.pone.0013510
PMCID:
PMC2958148
Abstract Full Text PDF–5.2M Supplementary Material
Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts
Mariana O Baratti, Yuri B Moreira, Fabiola Traina, Fernando F Costa, Sergio Verjovski-Almeida, Sara T Olalla-Saad
BMC Med Genomics. 2010; 3: 30. Published online 2010 July 15. doi: 10.1186/1755-8794-3-30
PMCID:
PMC2914047
Abstract Full Text PDF–3.7M Supplementary Material
Characterization of the RNA content of chromatin
Tanmoy Mondal, Markus Rasmussen, Gaurav Kumar Pandey, Anders Isaksson, Chandrasekhar Kanduri
Genome Res. 2010 July; 20(7): 899–907. doi: 10.1101/gr.103473.109
PMCID:
PMC2892091
Abstract Full Text PDF–700K
Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer
Nuankanya Sathira, Riu Yamashita, Kousuke Tanimoto, Akinori Kanai, Takako Arauchi, Soutaro Kanematsu, Kenta Nakai, Yutaka Suzuki, Sumio Sugano
DNA Res. 2010 June; 17(3): 169–183. Published online 2010 April 17. doi: 10.1093/dnares/dsq007
PMCID:
PMC2885271
Abstract Full Text PDF–472K Supplementary Material
In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines
Daniel Klevebring, Magnus Bjursell, Olof Emanuelsson, Joakim Lundeberg
PLoS One. 2010; 5(3): e9762. Published online 2010 March 25. doi: 10.1371/journal.pone.0009762
PMCID:
PMC2845605
Abstract Full Text PDF–722K Supplementary Material
Gene Expression Profile of Mesenchymal Stem Cells from Paired Umbilical Cord Units: Cord is Different from Blood
Mariane Secco, Yuri B. Moreira, Eder Zucconi, Natassia M. Vieira, Tatiana Jazedje, Alysson R. Muotri, Oswaldo K. Okamoto, Sergio Verjovski-Almeida, Mayana Zatz
Stem Cell Rev. 2009 December; 5(4): 387–401. Published online 2009 November 7. doi: 10.1007/s12015-009-9098-5
PMCID:
PMC2803263
Abstract Full Text PDF–540K Supplementary Material
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
Paulo P. Amaral, Christine Neyt, Simon J. Wilkins, Marjan E. Askarian-Amiri, Susan M. Sunkin, Andrew C. Perkins, John S. Mattick
RNA. 2009 November; 15(11): 2013–2027. doi: 10.1261/rna.1705309
PMCID:
PMC2764477
Abstract Full Text PDF–1.0M
Annotating non-coding transcription using functional genomics strategies
Alistair R. R. Forrest, Rehab F. Abdelhamid, Piero Carninci
Brief Funct Genomic Proteomic. 2009 November; 8(6): 437–443. Published online 2009 October 14. doi: 10.1093/bfgp/elp041
PMCID:
PMC2762128
Abstract Full Text PDF–95K
Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus
Richard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry
Int J Biol Sci. 2009; 5(6): 558–569. Published online 2009 September 1.
PMCID:
PMC2737716
Abstract Full Text PDF–683K
Apprehending multicellularity: regulatory networks, genomics and evolution
L. Aravind, Vivek Anantharaman, Thiago M. Venancio
Birth Defects Res C Embryo Today. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: Birth Defects Res C Embryo Today. 2009 June; 87(2): 143–164. doi: 10.1002/bdrc.20153
PMCID:
PMC2754411
Abstract Full Text PDF–1.2M
No-match ORESTES explored as tumor markers
Barbara P. Mello, Eduardo F. Abrantes, César H. Torres, Ariane Machado-Lima, Rogério da Silva Fonseca, Dirce M. Carraro, Ricardo R. Brentani, Luiz F. L. Reis, Helena Brentani
Nucleic Acids Res. 2009 May; 37(8): 2607–2617. Published online 2009 May. doi: 10.1093/nar/gkp074
PMCID:
PMC2677862
Abstract Full Text PDF–494K Supplementary Material
New Genomic Structure for Prostate Cancer Specific Gene PCA3 within BMCC1: Implications for Prostate Cancer Detection and Progression
Raymond A. Clarke, Zhongming Zhao, An-Yuan Guo, Kathrein Roper, Linda Teng, Zhi-Ming Fang, Hema Samaratunga, Martin F. Lavin, Robert A. Gardiner
PLoS ONE. 2009; 4(3): e4995. Published online 2009 March 25. doi: 10.1371/journal.pone.0004995
PMCID:
PMC2655648
Abstract Full Text PDF–697K Supplementary Material
Influence of the TSH Receptor Gene on Susceptibility to Graves' Disease and Graves' Ophthalmopathy
Xiaoming Yin, Rauf Latif, Rebecca Bahn, Yaron Tomer, Terry F. Davies
Thyroid. 2008 November; 18(11): 1201–1206. doi: 10.1089/thy.2008.0098
PMCID:
PMC2857451
Abstract Full Text PDF–83K
Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism
Vincenzo Calvanese, Meera Mallya, R Duncan Campbell, Begoña Aguado
BMC Mol Biol. 2008; 9: 81. Published online 2008 September 25. doi: 10.1186/1471-2199-9-81
PMCID:
PMC2562388
Abstract Full Text PDF–941K
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
Marcel E. Dinger, Paulo P. Amaral, Tim R. Mercer, Ken C. Pang, Stephen J. Bruce, Brooke B. Gardiner, Marjan E. Askarian-Amiri, Kelin Ru, Giulia Soldà, Cas Simons, Susan M. Sunkin, Mark L. Crowe, Sean M. Grimmond, Andrew C. Perkins, John S. Mattick
Genome Res. 2008 September; 18(9): 1433–1445. doi: 10.1101/gr.078378.108
PMCID:
PMC2527704
Abstract Full Text PDF–910K
Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs
Aristotelis Tsirigos, Isidore Rigoutsos
Nucleic Acids Res. 2008 June; 36(10): 3484–3493. Published online 2008 June. doi: 10.1093/nar/gkn155
PMCID:
PMC2425492
Abstract Full Text PDF–3.9M Supplementary Material
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
Yi-Fei Huang, Deng-Ke Niu
BMC Evol Biol. 2008; 8: 154. Published online 2008 May 20. doi: 10.1186/1471-2148-8-154
PMCID:
PMC2424036
Abstract Full Text PDF–355K Supplementary Material
Specific expression of long noncoding RNAs in the mouse brain
Tim R. Mercer, Marcel E. Dinger, Susan M. Sunkin, Mark F. Mehler, John S. Mattick
Proc Natl Acad Sci U S A. 2008 January 15; 105(2): 716–721. Published online 2008 January 9. doi: 10.1073/pnas.0706729105
PMCID:
PMC2206602
Abstract Full Text PDF–806K Supplementary Material
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