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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson, Minoru SH Ko
Genome Biol. 2005; 6(7): R61. Published online 2005 June 30. doi: 10.1186/gb-2005-6-7-r61
PMCID:
PMC1175992
Abstract Full Text PDF–303K Supplementary Material
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 Is Cited by the Following 34 Articles in this Archive:
Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells
Tetsuya Hirata, Tomokazu Amano, Yuhki Nakatake, Misa Amano, Yulan Piao, Hien G. Hoang, Minoru S. H. Ko
Sci Rep. 2012; 2: 208. Published online 2012 January 4. doi: 10.1038/srep00208
PMCID:
PMC3250575
Full Text PDF–11M Supplementary Material
Generation of mouse ES cell lines engineered for the forced induction of transcription factors
Lina S. Correa-Cerro, Yulan Piao, Alexei A. Sharov, Akira Nishiyama, Jean S. Cadet, Hong Yu, Lioudmila V. Sharova, Li Xin, Hien G. Hoang, Marshall Thomas, Yong Qian, Dawood B. Dudekula, Emily Meyers, Bernard Y. Binder, Gregory Mowrer, Uwem Bassey, Dan L. Longo, David Schlessinger, Minoru S. H. Ko
Sci Rep. 2011; 1: 167. Published online 2011 November 23. doi: 10.1038/srep00167
PMCID:
PMC3240988
Abstract Full Text PDF–3.7M Supplementary Material
Stage-Specific Germ-Cell Marker Genes Are Expressed in All Mouse Pluripotent Cell Types and Emerge Early during Induced Pluripotency
Xingbo Xu, D. V. Krishna Pantakani, Sandra Lührig, Xiaoying Tan, Tatjana Khromov, Jessica Nolte, Ralf Dressel, Ulrich Zechner, Wolfgang Engel
PLoS One. 2011; 6(7): e22413. Published online 2011 July 25. doi: 10.1371/journal.pone.0022413
PMCID:
PMC3143132
Abstract Full Text PDF–2.3M Supplementary Material
Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity
Deng-Ke Niu, Yu-Fei Yang
Biol Direct. 2011; 6: 24. Published online 2011 May 18. doi: 10.1186/1745-6150-6-24
PMCID:
PMC3118952
Abstract Full Text PDF–334K
The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution
Nikolay G. Kolev, Joseph B. Franklin, Shai Carmi, Huafang Shi, Shulamit Michaeli, Christian Tschudi
PLoS Pathog. 2010 September; 6(9): e1001090. Published online 2010 September 9. doi: 10.1371/journal.ppat.1001090
PMCID:
PMC2936537
Abstract Full Text PDF–2.3M Supplementary Material
Parallel gateways to pluripotency: open chromatin in stem cells and development
Fong Ming Koh, Michael Sachs, Marcela Guzman-Ayala, Miguel Ramalho-Santos
Curr Opin Genet Dev. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Curr Opin Genet Dev. 2010 October; 20(5): 492–499. Published online 2010 July 2. doi: 10.1016/j.gde.2010.06.002
PMCID:
PMC2943036
Abstract Full Text PDF–528K
Strand-specific deep sequencing of the transcriptome
Ana P. Vivancos, Marc Güell, Juliane C. Dohm, Luis Serrano, Heinz Himmelbauer
Genome Res. 2010 July; 20(7): 989–999. doi: 10.1101/gr.094318.109
PMCID:
PMC2892100
Abstract Full Text PDF–1.3M
A Role for Borg5 during Trophectoderm Differentiation
Queenie P. Vong, Zhonghua Liu, Jae Gyu Yoo, Rong Chen, Wen Xie, Alexei A. Sharov, Chen-ming Fan, Chengyu Liu, Minoru S. H. Ko, Yixian Zheng
Stem Cells. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Stem Cells. 2010 June; 28(6): 1030–1038. doi: 10.1002/stem.428
PMCID:
PMC2957878
Abstract Full Text PDF–1.5M Supplementary Material
Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript
Maurice A. Canham, Alexei A. Sharov, Minoru S. H. Ko, Joshua M. Brickman
PLoS Biol. 2010 May; 8(5): e1000379. Published online 2010 May 25. doi: 10.1371/journal.pbio.1000379
PMCID:
PMC2876051
Abstract Full Text PDF–1.4M Supplementary Material
Gene expression profiling of mouse embryos with microarrays
Alexei A. Sharov, Yulan Piao, Minoru S. H. Ko
Methods Enzymol. Author manuscript; available in PMC 2011 September 4.
Published in final edited form as: Methods Enzymol. 2010; 477: 511–541. doi: 10.1016/S0076-6879(10)77025-7
PMCID:
PMC3166619
Abstract Full Text PDF–3.3M
Pharmacology of epigenetics in brain disorders
Pritika Narayan, Mike Dragunow
Br J Pharmacol. 2010 January; 159(2): 285–303. Published online 2009 December 15. doi: 10.1111/j.1476-5381.2009.00526.x
PMCID:
PMC2825351
Abstract Full Text PDF–423K
Absolute quantification of microRNAs by using a universal reference
Ute Bissels, Stefan Wild, Stefan Tomiuk, Angela Holste, Markus Hafner, Thomas Tuschl, Andreas Bosio
RNA. 2009 December; 15(12): 2375–2384. doi: 10.1261/rna.1754109
PMCID:
PMC2779673
Abstract Full Text PDF–766K
Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency
Kai N Stölting, Gerrit Gort, Christian Wüst, Anthony B Wilson
BMC Genomics. 2009; 10: 565. Published online 2009 November 30. doi: 10.1186/1471-2164-10-565
PMCID:
PMC2797533
Abstract Full Text PDF–3.3M Supplementary Material
Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors
Akira Nishiyama, Li Xin, Alexei A. Sharov, Marshall Thomas, Gregory Mowrer, Emily Meyers, Yulan Piao, Samir Mehta, Sarah Yee, Yuhki Nakatake, Carole Stagg, Lioudmila Sharova, Lina S. Correa-Cerro, Uwem Bassey, Hien Hoang, Eugene Kim, Richard Tapnio, Yong Qian, Dawood Dudekula, Michal Zalzman, Manxiang Li, Geppino Falco, Hsih-Te Yang, Sung-Lim Lee, Manuela Monti, Ilaria Stanghellini, Md. Nurul Islam, Ramaiah Nagaraja, Ilya Goldberg, Weidong Wang, Dan L. Longo, David Schlessinger, Minoru S. H. Ko
Cell Stem Cell. Author manuscript; available in PMC 2010 October 2.
Published in final edited form as: Cell Stem Cell. 2009 October 2; 5(4): 420–433. doi: 10.1016/j.stem.2009.07.012
PMCID:
PMC2770715
Abstract Full Text PDF–2.6M Supplementary Material
Stochastic noise in splicing machinery
Eugene Melamud, John Moult
Nucleic Acids Res. 2009 August; 37(14): 4873–4886. Published online 2009 August. doi: 10.1093/nar/gkp471
PMCID:
PMC2724286
Abstract Full Text PDF–1.6M Supplementary Material
Defining Developmental Potency and Cell Lineage Trajectories by Expression Profiling of Differentiating Mouse Embryonic Stem Cells
Kazuhiro Aiba, Timur Nedorezov, Yulan Piao, Akira Nishiyama, Ryo Matoba, Lioudmila V. Sharova, Alexei A. Sharov, Shinya Yamanaka, Hitoshi Niwa, Minoru S. H. Ko
DNA Res. 2009 February; 16(1): 73–80. Published online 2008 December 26. doi: 10.1093/dnares/dsn035
PMCID:
PMC2644347
Abstract Full Text PDF–314K Supplementary Material
Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs
Fumihito Miura, Noriko Kawaguchi, Mikio Yoshida, Chihiro Uematsu, Keiji Kito, Yoshiyuki Sakaki, Takashi Ito
BMC Genomics. 2008; 9: 574. Published online 2008 November 29. doi: 10.1186/1471-2164-9-574
PMCID:
PMC2612024
Abstract Full Text PDF–904K Supplementary Material
Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells
Lioudmila V. Sharova, Alexei A. Sharov, Timur Nedorezov, Yulan Piao, Nabeebi Shaik, Minoru S.H. Ko
DNA Res. 2009 February; 16(1): 45–58. Published online 2008 November 11. doi: 10.1093/dnares/dsn030
PMCID:
PMC2644350
Abstract Full Text PDF–549K Supplementary Material
Essential Role of Chromatin Remodeling Protein Bptf in Early Mouse Embryos and Embryonic Stem Cells
Joseph Landry, Alexei A. Sharov, Yulan Piao, Lioudmila V. Sharova, Hua Xiao, Eileen Southon, Jennifer Matta, Lino Tessarollo, Ying E. Zhang, Minoru S. H. Ko, Michael R. Kuehn, Terry P. Yamaguchi, Carl Wu
PLoS Genet. 2008 October; 4(10): e1000241. Published online 2008 October 31. doi: 10.1371/journal.pgen.1000241
PMCID:
PMC2570622
Abstract Full Text PDF–512K Supplementary Material
Maintenance of undifferentiated mouse embryonic stem cells in suspension by the serum- and feeder-free defined culture condition
Yukiiko Tsuji, Naoko Yoshimura, Hitomi Aoki, Alexei A. Sharov, Minoru S.H. Ko, Tsutomu Motohashi, Takahiro Kunisada
Dev Dyn. Author manuscript; available in PMC 2008 October 3.
Published in final edited form as: Dev Dyn. 2008 August; 237(8): 2129–2138. doi: 10.1002/dvdy.21617
PMCID:
PMC2559871
Abstract Full Text PDF–2.9M Supplementary Material
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data
Alexei A Sharov, Shinji Masui, Lioudmila V Sharova, Yulan Piao, Kazuhiro Aiba, Ryo Matoba, Li Xin, Hitoshi Niwa, Minoru SH Ko
BMC Genomics. 2008; 9: 269. Published online 2008 June 3. doi: 10.1186/1471-2164-9-269
PMCID:
PMC2424064
Abstract Full Text PDF–621K Supplementary Material
Effects of aging and calorie restriction on the global gene expression profiles of mouse testis and ovary
Alexei A Sharov, Geppino Falco, Yulan Piao, Suresh Poosala, Kevin G Becker, Alan B Zonderman, Dan L Longo, David Schlessinger, Minoru SH Ko
BMC Biol. 2008; 6: 24. Published online 2008 June 3. doi: 10.1186/1741-7007-6-24
PMCID:
PMC2426674
Abstract Full Text PDF–649K Supplementary Material
Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells
Tatiana Subkhankulova, Michael J Gilchrist, Frederick J Livesey
BMC Genomics. 2008; 9: 268. Published online 2008 June 3. doi: 10.1186/1471-2164-9-268
PMCID:
PMC2429916
Abstract Full Text PDF–455K Supplementary Material
Validation of oligoarrays for quantitative exploration of the transcriptome
Vigdis Nygaard, Fang Liu, Marit Holden, Winston P Kuo, Jeff Trimarchi, Lucila Ohno-Machado, Connie L Cepko, Arnoldo Frigessi, Ingrid K Glad, Mark A van de Wiel, Eivind Hovig, Heidi Lyng
BMC Genomics. 2008; 9: 258. Published online 2008 May 30. doi: 10.1186/1471-2164-9-258
PMCID:
PMC2430212
Abstract Full Text PDF–810K 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
Coupled Global and Targeted Proteomics of Human Embryonic Stem Cells during Induced Differentiation
Anastasia K. Yocum, Theresa E. Gratsch, Nancy Leff, John R. Strahler, Christie L. Hunter, Angela K. Walker, George Michailidis, Gilbert S. Omenn, K. Sue O'Shea, Philip C. Andrews
Mol Cell Proteomics. 2008 April; 7(4): 750–767. doi: 10.1074/mcp.M700399-MCP200
PMCID:
PMC2401335
Abstract Full Text Supplementary Material
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells
Zhijiang Yan, Zhong Wang, Lioudmila Sharova, Alexei A. Sharov, Chen Ling, Yulan Piao, Kazuhiro Aiba, Ryo Matoba, Weidong Wang, Minoru S.H. Ko
Stem Cells. Author manuscript; available in PMC 2008 June 3.
Published in final edited form as: Stem Cells. 2008 May; 26(5): 1155–1165. Published online 2008 March 6. doi: 10.1634/stemcells.2007-0846
PMCID:
PMC2409195
Abstract Full Text PDF–1.6M Supplementary Material
MicroRNAs (miRNAs) in Neurodegenerative Diseases
Peter T. Nelson, Wang-Xia Wang, Bernard W. Rajeev
Brain Pathol. Author manuscript; available in PMC 2010 April 26.
Published in final edited form as: Brain Pathol. 2008 January; 18(1): 130–138. doi: 10.1111/j.1750-3639.2007.00120.x
PMCID:
PMC2859437
Abstract Full Text PDF–941K
The Signal Sequence Coding Region Promotes Nuclear Export of mRNA
Alexander F Palazzo, Michael Springer, Yoko Shibata, Chung-Sheng Lee, Anusha P Dias, Tom A Rapoport
PLoS Biol. 2007 December; 5(12): e322. Published online 2007 December 4. doi: 10.1371/journal.pbio.0050322
PMCID:
PMC2100149
Abstract Full Text PDF–844K Supplementary Material
An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells
Mark G. Carter, Carole A. Stagg, Geppino Falco, Toshiyuki Yoshikawa, Uwem C. Bassey, Kazuhiro Aiba, Lioudmila V. Sharova, Nabeebi Shaik, Minoru S.H. Ko
Gene Expr Patterns. Author manuscript; available in PMC 2009 February 1.
Published in final edited form as: Gene Expr Patterns. 2008 February; 8(3): 181–198. Published online 2007 November 4. doi: 10.1016/j.gep.2007.10.009
PMCID:
PMC2238805
Abstract Full Text PDF–4.3M Supplementary Material
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