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BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, III, Andrew I Su
Genome Biol. 2009; 10(11): R130. Published online 2009 November 17. doi: 10.1186/gb-2009-10-11-r130
PMCID:
PMC3091323
Abstract Full Text PDF–1.1M Supplementary Material
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 Is Cited by the Following 55 Articles in this Archive:
5-alpha-reductase type I (SRD5A1) is up-regulated in non-small cell lung cancer but does not impact proliferation, cell cycle distribution or apoptosis
Friedrich G Kapp, Anette Sommer, Thomas Kiefer, Gottfried Dölken, Bernard Haendler
Cancer Cell Int. 2012; 12: 1. Published online 2012 January 18. doi: 10.1186/1475-2867-12-1
PMCID:
PMC3269976
Abstract Full Text PDF–794K Supplementary Material
Identifying Single Copy Orthologs in Metazoa
Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork
PLoS Comput Biol. 2011 December; 7(12): e1002269. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002269
PMCID:
PMC3228760
Abstract Full Text PDF–1.3M 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
PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer
Luca Magnani, Elizabeth B. Ballantyne, Xiaoyang Zhang, Mathieu Lupien
PLoS Genet. 2011 November; 7(11): e1002368. Published online 2011 November 17. doi: 10.1371/journal.pgen.1002368
PMCID:
PMC3219601
Abstract Full Text PDF–1.0M Supplementary Material
WikiPathways: building research communities on biological pathways
Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. Evelo, Alexander R. Pico
Nucleic Acids Res. 2012 January; 40(D1): D1301–D1307. Published online 2011 November 16. doi: 10.1093/nar/gkr1074
PMCID:
PMC3245032
Abstract Full Text PDF–2.7M
Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs
Janet M Young, Ralf M Luche, Barbara J Trask
BMC Genomics. 2011; 12: 561. Published online 2011 November 15. doi: 10.1186/1471-2164-12-561
PMCID:
PMC3247239
Abstract Full Text PDF–816K Supplementary Material
Gene Expression Profile Change and Associated Physiological and Pathological Effects in Mouse Liver Induced by Fasting and Refeeding
Fang Zhang, Xiang Xu, Ben Zhou, Zhishui He, Qiwei Zhai
PLoS One. 2011; 6(11): e27553. Published online 2011 November 9. doi: 10.1371/journal.pone.0027553
PMCID:
PMC3212576
Abstract Full Text PDF–1.1M Supplementary Material
Novel Common Integration Sites Targeted by Mouse Mammary Tumor Virus Insertion in Mammary Tumors Have Oncogenic Activity
Hyoung H. Kim, A. Pieter J. van den Heuvel, John W. Schmidt, Susan R. Ross
PLoS One. 2011; 6(11): e27425. Published online 2011 November 7. doi: 10.1371/journal.pone.0027425
PMCID:
PMC3210173
Abstract Full Text PDF–725K
Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity
Frederic Koch, Jean-Christophe Andrau
Transcription. 2011 Nov-Dec; 2(6): 263–268. Published online 2011 November 1. doi: 10.4161/trns.2.6.18747
PMCID:
PMC3265787
Abstract Full Text PDF–2.4M
Thousands of Rab GTPases for the Cell Biologist
Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-Cadete, Miguel C. Seabra, José B. Pereira-Leal
PLoS Comput Biol. 2011 October; 7(10): e1002217. Published online 2011 October 13. doi: 10.1371/journal.pcbi.1002217
PMCID:
PMC3192815
Abstract Full Text PDF–1.4M Supplementary Material
Plexin-B2 Negatively Regulates Macrophage Motility, Rac, and Cdc42 Activation
Kelly E. Roney, Brian P. O'Connor, Haitao Wen, Eda K. Holl, Elizabeth H. Guthrie, Beckley K. Davis, Stephen W. Jones, Sushmita Jha, Lisa Sharek, Rafael Garcia-Mata, James E. Bear, Jenny P.-Y. Ting
PLoS One. 2011; 6(9): e24795. Published online 2011 September 23. doi: 10.1371/journal.pone.0024795
PMCID:
PMC3179467
Abstract Full Text PDF–1.0M Supplementary Material
Identification of Novel Pax8 Targets in FRTL-5 Thyroid Cells by Gene Silencing and Expression Microarray Analysis
Tina Di Palma, Anna Conti, Tiziana de Cristofaro, Serena Scala, Lucio Nitsch, Mariastella Zannini
PLoS One. 2011; 6(9): e25162. Published online 2011 September 23. doi: 10.1371/journal.pone.0025162
PMCID:
PMC3179481
Abstract Full Text PDF–1.5M Supplementary Material
A promoter DNA demethylation landscape of human hematopoietic differentiation
Vincenzo Calvanese, Agustín F. Fernández, Rocío G. Urdinguio, Beatriz Suárez-Alvarez, Cristina Mangas, Vicente Pérez-García, Clara Bueno, Rosa Montes, Verónica Ramos-Mejía, Pablo Martínez-Camblor, Cecilia Ferrero, Yassen Assenov, Christoph Bock, Pablo Menendez, Ana Clara Carrera, Carlos Lopez-Larrea, Mario F. Fraga
Nucleic Acids Res. 2012 January; 40(1): 116–131. Published online 2011 September 10. doi: 10.1093/nar/gkr685
PMCID:
PMC3245917
Abstract Full Text PDF–5.9M Supplementary Material
dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells
Jana Nejepinska, Radek Malik, Jody Filkowski, Matyas Flemr, Witold Filipowicz, Petr Svoboda
Nucleic Acids Res. 2012 January; 40(1): 399–413. Published online 2011 September 8. doi: 10.1093/nar/gkr702
PMCID:
PMC3245926
Abstract Full Text PDF–13M Supplementary Material
Co-Regulation of Histone-Modifying Enzymes in Cancer
Abul B. M. M. K. Islam, William F. Richter, Laura A. Jacobs, Nuria Lopez-Bigas, Elizaveta V. Benevolenskaya
PLoS One. 2011; 6(8): e24023. Published online 2011 August 23. doi: 10.1371/journal.pone.0024023
PMCID:
PMC3160334
Abstract Full Text PDF–1.6M Supplementary Material
Molecular Analysis of the Retinoic Acid Induced 1 Gene (RAI1) in Patients with Suspected Smith-Magenis Syndrome without the 17p11.2 Deletion
Thierry Vilboux, Carla Ciccone, Jan K. Blancato, Gerald F. Cox, Charu Deshpande, Wendy J. Introne, William A. Gahl, Ann C. M. Smith, Marjan Huizing
PLoS One. 2011; 6(8): e22861. Published online 2011 August 8. doi: 10.1371/journal.pone.0022861
PMCID:
PMC3152558
Abstract Full Text PDF–683K Supplementary Material
Genetic Loci Associated with Plasma Phospholipid n-3 Fatty Acids: A Meta-Analysis of Genome-Wide Association Studies from the CHARGE Consortium
Rozenn N. Lemaitre, Toshiko Tanaka, Weihong Tang, Ani Manichaikul, Millennia Foy, Edmond K. Kabagambe, Jennifer A. Nettleton, Irena B. King, Lu-Chen Weng, Sayanti Bhattacharya, Stefania Bandinelli, Joshua C. Bis, Stephen S. Rich, David R. Jacobs, Jr., Antonio Cherubini, Barbara McKnight, Shuang Liang, Xiangjun Gu, Kenneth Rice, Cathy C. Laurie, Thomas Lumley, Brian L. Browning, Bruce M. Psaty, Yii-Der I. Chen, Yechiel Friedlander, Luc Djousse, Jason H. Y. Wu, David S. Siscovick, André G. Uitterlinden, Donna K. Arnett, Luigi Ferrucci, Myriam Fornage, Michael Y. Tsai, Dariush Mozaffarian, Lyn M. Steffen
PLoS Genet. 2011 July; 7(7): e1002193. Published online 2011 July 28. doi: 10.1371/journal.pgen.1002193
PMCID:
PMC3145614
Abstract Full Text PDF–998K Supplementary Material
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin Dewey, Sündüz Keleş
PLoS Comput Biol. 2011 July; 7(7): e1002111. Published online 2011 July 14. doi: 10.1371/journal.pcbi.1002111
PMCID:
PMC3136429
Abstract Full Text PDF–709K Supplementary Material
Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response
Carsten Münk, Andreas F.R. Sommer, Renate König
Viruses. 2011 July; 3(7): 1112–1130. Published online 2011 July 11. doi: 10.3390/v3071112
PMCID:
PMC3185791
Abstract Full Text PDF–290K
Mechanisms of translational regulation by a human eIF5-mimic protein
Chingakham Ranjit Singh, Ryosuke Watanabe, Donghui Zhou, Martin D. Jennings, Akira Fukao, Bumjun Lee, Yuka Ikeda, John A. Chiorini, Susan G. Campbell, Mark P. Ashe, Toshinobu Fujiwara, Ronald C. Wek, Graham D. Pavitt, Katsura Asano
Nucleic Acids Res. 2011 October; 39(19): 8314–8328. Published online 2011 July 9. doi: 10.1093/nar/gkr339
PMCID:
PMC3201852
Abstract Full Text PDF–7.3M Supplementary Material
The evolutionary history of the catenin gene family during metazoan evolution
Zi-Ming Zhao, Albert B Reynolds, Eric A Gaucher
BMC Evol Biol. 2011; 11: 198. Published online 2011 July 8. doi: 10.1186/1471-2148-11-198
PMCID:
PMC3141441
Abstract Full Text PDF–2.0M Supplementary Material
Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis
Soha N. Yazbek, David A. Buchner, Jonathan M. Geisinger, Lindsay C. Burrage, Sabrina H. Spiezio, Gabriel E. Zentner, Chang-Wen Hsieh, Peter C. Scacheri, Colleen M. Croniger, Joseph H. Nadeau
Genome Res. 2011 July; 21(7): 1065–1073. doi: 10.1101/gr.120741.111
PMCID:
PMC3129249
Abstract Full Text PDF–392K
MTF-1-Mediated Repression of the Zinc Transporter Zip10 Is Alleviated by Zinc Restriction
Louis A. Lichten, Moon-Suhn Ryu, Liang Guo, Jennifer Embury, Robert J. Cousins
PLoS One. 2011; 6(6): e21526. Published online 2011 June 27. doi: 10.1371/journal.pone.0021526
PMCID:
PMC3124522
Abstract Full Text PDF–1.3M Supplementary Material
Systemic Signature of the Lung Response to Respiratory Syncytial Virus Infection
Jeroen L. A. Pennings, Annemieke Schuurhof, Hennie M. Hodemaekers, Annemarie Buisman, Lia C. G. H. de Rond, Myra N. Widjojoatmodjo, Willem Luytjes, Jan L. L. Kimpen, Louis Bont, Riny Janssen
PLoS One. 2011; 6(6): e21461. Published online 2011 June 24. doi: 10.1371/journal.pone.0021461
PMCID:
PMC3123345
Abstract Full Text PDF–342K
Tissue-specific Distribution and Dynamic Changes of 5-Hydroxymethylcytosine in Mammalian Genomes
Shannon Morey Kinney, Hang Gyeong Chin, Romualdas Vaisvila, Jurate Bitinaite, Yu Zheng, Pierre-Olivier Estève, Suhua Feng, Hume Stroud, Steven E. Jacobsen, Sriharsa Pradhan
J Biol Chem. 2011 July 15; 286(28): 24685–24693. Published online 2011 May 24. doi: 10.1074/jbc.M110.217083
PMCID:
PMC3137044
Abstract Full Text Supplementary Material
Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures
Rudi Alberts, Lu Lu, Robert W Williams, Klaus Schughart
Respir Res. 2011; 12(1): 61. Published online 2011 May 2. doi: 10.1186/1465-9921-12-61
Correction in:
Respir Res. 2012; 13(1): 5.
PMCID:
PMC3105947
Abstract Full Text PDF–9.6M Correction
Characterization of the genomic structure and function of regions influencing renin and angiogenesis in the SS rat
Timothy J. Stodola, Micheline M. de Resende, Allison B. Sarkis, Daniela N. Didier, Howard J. Jacob, Norbert Huebner, Oliver Hummel, Kathrin Saar, Carol Moreno, Andrew S. Greene
Physiol Genomics. 2011 July; 43(13): 808–817. Published online 2011 April 26. doi: 10.1152/physiolgenomics.00171.2010
PMCID:
PMC3132840
Abstract Full Text
Replication of TCF4 through Association and Linkage Studies in Late-Onset Fuchs Endothelial Corneal Dystrophy
Yi-Ju Li, Mollie A. Minear, Jacqueline Rimmler, Bei Zhao, Elmer Balajonda, Michael A. Hauser, R. Rand Allingham, Allen O. Eghrari, S. Amer Riazuddin, Nicholas Katsanis, John D. Gottsch, Simon G. Gregory, Gordon K. Klintworth, Natalie A. Afshari
PLoS One. 2011; 6(4): e18044. Published online 2011 April 20. doi: 10.1371/journal.pone.0018044
PMCID:
PMC3080358
Abstract Full Text PDF–224K
A Flow Cytometry-Based Screen of Nuclear Envelope Transmembrane Proteins Identifies NET4/Tmem53 as Involved in Stress-Dependent Cell Cycle Withdrawal
Nadia Korfali, Vlastimil Srsen, Martin Waterfall, Dzmitry G. Batrakou, Vanja Pekovic, Christopher J. Hutchison, Eric C. Schirmer
PLoS One. 2011; 6(4): e18762. Published online 2011 April 14. doi: 10.1371/journal.pone.0018762
PMCID:
PMC3077400
Abstract Full Text PDF–1.2M
Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening
Jeroen L. A. Pennings, Wendy Rodenburg, Sandra Imholz, Maria P. H. Koster, Conny T. M. van Oostrom, Timo M. Breit, Peter C. J. I. Schielen, Annemieke de Vries
PLoS One. 2011; 6(4): e18866. Published online 2011 April 14. doi: 10.1371/journal.pone.0018866
PMCID:
PMC3077415
Abstract Full Text PDF–338K Supplementary Material
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