My NCBISign In
GoMiner: a resource for biological interpretation of genomic and proteomic data
Barry R Zeeberg, Weimin Feng, Geoffrey Wang, May D Wang, Anthony T Fojo, Margot Sunshine, Sudarshan Narasimhan, David W Kane, William C Reinhold, Samir Lababidi, Kimberly J Bussey, Joseph Riss, J Carl Barrett, John N Weinstein
Genome Biol. 2003; 4(4): R28. Published online 2003 March 25. doi: 10.1186/gb-2003-4-4-r28
PMCID:
PMC154579
Abstract Full Text PDF–1.0M

Is Cited by the Following 266 Articles in this Archive:

Differential Gene Expression in the EphA4 Knockout Spinal Cord and Analysis of the Inflammatory Response Following Spinal Cord Injury
Kathryn M. Munro, Victoria M. Perreau, Ann M. Turnley
PLoS One. 2012; 7(5): e37635. Published online 2012 May 22. doi: 10.1371/journal.pone.0037635
PMCID:
PMC3358264
Abstract Full Text PDF–3.6M Supplementary Material
Hypocotyl Transcriptome Reveals Auxin Regulation of Growth-Promoting Genes through GA-Dependent and -Independent Pathways
Elisabeth J. Chapman, Kathleen Greenham, Cristina Castillejo, Ryan Sartor, Agniezska Bialy, Tai-ping Sun, Mark Estelle
PLoS One. 2012; 7(5): e36210. Published online 2012 May 9. doi: 10.1371/journal.pone.0036210
PMCID:
PMC3348943
Abstract Full Text PDF–1.1M Supplementary Material
The Impact of Recent Alcohol Use on Genome Wide DNA Methylation Signatures
Robert A. Philibert, Jeffrey M. Plume, Frederick X. Gibbons, Gene H. Brody, Steven R. H. Beach
Front Genet. 2012; 3: 54. Published online 2012 April 10. doi: 10.3389/fgene.2012.00054
PMCID:
PMC3322340
Abstract Full Text PDF–268K
Functional Annotation of Hierarchical Modularity
Kanchana Padmanabhan, Kuangyu Wang, Nagiza F. Samatova
PLoS One. 2012; 7(4): e33744. Published online 2012 April 4. doi: 10.1371/journal.pone.0033744
PMCID:
PMC3319548
Abstract Full Text PDF–664K Supplementary Material
Upregulation of miR-142-3p in Peripheral Blood Mononuclear Cells of Operationally Tolerant Patients with a Renal Transplant
Richard Danger, Annaïck Pallier, Magali Giral, Marc Martínez-Llordella, Juan José Lozano, Nicolas Degauque, Alberto Sanchez-Fueyo, Jean-Paul Soulillou, Sophie Brouard
J Am Soc Nephrol. 2012 April; 23(4): 597–606. doi: 10.1681/ASN.2011060543
PMCID:
PMC3312506
Free in PMC on 2013/04/01
Molecular Characterisation of Transport Mechanisms at the Developing Mouse Blood–CSF Interface: A Transcriptome Approach
Shane A. Liddelow, Sally Temple, Kjeld Møllgård, Renate Gehwolf, Andrea Wagner, Hannelore Bauer, Hans-Christian Bauer, Timothy N. Phoenix, Katarzyna M. Dziegielewska, Norman R. Saunders
PLoS One. 2012; 7(3): e33554. Published online 2012 March 21. doi: 10.1371/journal.pone.0033554
PMCID:
PMC3310074
Abstract Full Text PDF–2.3M Supplementary Material
The cerebrospinal fluid proteome in HIV infection: change associated with disease severity
Thomas E Angel, Jon M Jacobs, Serena S Spudich, Marina A Gritsenko, Dietmar Fuchs, Teri Liegler, Henrik Zetterberg, David G Camp, II, Richard W Price, Richard D Smith
Clin Proteomics. 2012; 9(1): 3. Published online 2012 March 20. doi: 10.1186/1559-0275-9-3
PMCID:
PMC3353874
Abstract Full Text PDF–4.5M Supplementary Material
Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership
Ernesto Iacucci, Hans H. Zingg, Theodore J. Perkins
Front Genet. 2012; 3: 24. Prepublished online 2011 November 19. Published online 2012 February 23. doi: 10.3389/fgene.2012.00024
PMCID:
PMC3284693
Abstract Full Text PDF–1.8M
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Purvesh Khatri, Marina Sirota, Atul J. Butte
PLoS Comput Biol. 2012 February; 8(2): e1002375. Published online 2012 February 23. doi: 10.1371/journal.pcbi.1002375
PMCID:
PMC3285573
Abstract Full Text PDF–663K Supplementary Material
Annotator: Post-processing Software for generating function-based signatures from quantitative mass spectrometry
Juliesta E. Sylvester, Tyler S. Bray, Stephen J. Kron
J Proteome Res. Author manuscript; available in PMC 2013 March 2.
Published in final edited form as: J Proteome Res. 2012 March 2; 11(3): 1521–1536. Published online 2012 February 3. doi: 10.1021/pr200460s
PMCID:
PMC3292622
Free in PMC on 2013/03/02
Functional Categories Associated with Clusters of Genes That Are Co-Expressed across the NCI-60 Cancer Cell Lines
Barry R. Zeeberg, William Reinhold, René Snajder, Gerhard G. Thallinger, John N. Weinstein, Kurt W. Kohn, Yves Pommier
PLoS One. 2012; 7(1): e30317. Published online 2012 January 24. doi: 10.1371/journal.pone.0030317
PMCID:
PMC3265467
Abstract Full Text PDF–637K Supplementary Material
Global kinetic analysis of proteolysis via quantitative targeted proteomics
Nicholas J. Agard, Sami Mahrus, Jonathan C. Trinidad, Aenoch Lynn, Alma L. Burlingame, James A. Wells
Proc Natl Acad Sci U S A. 2012 February 7; 109(6): 1913-1918. Published online 2012 January 23. doi: 10.1073/pnas.1117158109
PMCID:
PMC3277568
Free in PMC on 2012/08/07
A searchable cross-platform gene expression database reveals connections between drug treatments and disease
Gareth Williams
BMC Genomics. 2012; 13: 12. Published online 2012 January 10. doi: 10.1186/1471-2164-13-12
PMCID:
PMC3305579
Abstract Full Text PDF–1.4M Supplementary Material
Perturbation of FliL Interferes with Proteus mirabilis Swarmer Cell Gene Expression and Differentiation
Kathleen Cusick, Yi-Ying Lee, Brian Youchak, Robert Belas
J Bacteriol. 2012 January; 194(2): 437–447. doi: 10.1128/JB.05998-11
PMCID:
PMC3256649
Free in PMC on 2012/07/01
Maximizing biomarker discovery by minimizing gene signatures
Chang Chang, Junwei Wang, Chen Zhao, Jennifer Fostel, Weida Tong, Pierre R Bushel, Youping Deng, Lajos Pusztai, W Fraser Symmans, Tieliu Shi
BMC Genomics. 2011; 12(Suppl 5): S6. Published online 2011 December 23. doi: 10.1186/1471-2164-12-S5-S6
PMCID:
PMC3287502
Abstract Full Text PDF–811K Supplementary Material
Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals Epigenetic Control of Cisplatin Resistance in Ovarian Cancer Cell
Wei Yu, Chengmeng Jin, Xiaoyan Lou, Xu Han, Lisha Li, Yinghua He, Hongyu Zhang, Kelong Ma, Jingde Zhu, Lihua Cheng, Biaoyang Lin
PLoS One. 2011; 6(12): e29450. Published online 2011 December 22. doi: 10.1371/journal.pone.0029450
PMCID:
PMC3245283
Abstract Full Text PDF–704K Supplementary Material
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data
Benjamin Linard, Ngoc Hoan Nguyen, Francisco Prosdocimi, Olivier Poch, Julie D. Thompson
Evol Bioinform Online. 2012; 8: 61–77. Published online 2011 December 21. doi: 10.4137/EBO.S8814
PMCID:
PMC3256995
Abstract Full Text PDF–4.4M Supplementary Material
Modeling the Transcriptional Consequences of Epidermal Growth Factor Receptor Ablation in Ras-Initiated Squamous Cancer
Lisa Nolan Wright, Andrew Ryscavage, Glenn Merlino, Stuart H. Yuspa
Clin Cancer Res. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Clin Cancer Res. 2012 January 1; 18(1): 170–183. Published online 2011 November 8. doi: 10.1158/1078-0432.CCR-11-1349
PMCID:
PMC3251736
Free in PMC on 2013/01/01
In Vivo Functional and Transcriptional Profiling of Bone Marrow Stem Cells after Transplantation into Ischemic Myocardium
Ahmad Y. Sheikh, Bruno C. Huber, Kazim H. Narsinh, Joshua M. Spin, Koen van der Bogt, Patricia E. de Almeida, Katherine J. Ransohoff, Daniel L. Kraft, Giovanni Fajardo, Diego Ardigo, Julia Ransohoff, Daniel Bernstein, Michael P. Fischbein, Robert C. Robbins, Joseph C. Wu
Arterioscler Thromb Vasc Biol. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Arterioscler Thromb Vasc Biol. 2012 January; 32(1): 92–102. Published online 2011 October 27. doi: 10.1161/ATVBAHA.111.238618
PMCID:
PMC3241895
Free in PMC on 2013/01/01
Novel Proteomic Tools Reveal Essential Roles of SRP and Importance of Proper Membrane Protein Biogenesis
Dawei Zhang, Michael J. Sweredoski, Robert L. J. Graham, Sonja Hess, Shu–ou Shan
Mol Cell Proteomics. 2012 February; 11(2): M111.011585. Published online 2011 October 26. doi: 10.1074/mcp.M111.011585
PMCID:
PMC3277757
Free in PMC on 2013/02/01
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae
Ke Jin, Jingjing Li, Frederick S. Vizeacoumar, Zhijian Li, Renqiang Min, Lee Zamparo, Franco J. Vizeacoumar, Alessandro Datti, Brenda Andrews, Charles Boone, Zhaolei Zhang
Nucleic Acids Res. 2012 January; 40(D1): D687–D694. Published online 2011 October 18. doi: 10.1093/nar/gkr827
PMCID:
PMC3245137
Abstract Full Text PDF–6.3M
Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells
Peter C. Hollenhorst, Mary W. Ferris, Megan A. Hull, Heejoon Chae, Sun Kim, Barbara J. Graves
Genes Dev. 2011 October 15; 25(20): 2147–2157. doi: 10.1101/gad.17546311
PMCID:
PMC3205585
Abstract Full Text PDF–912K
High-Throughput Analysis of Promoter Occupancy Reveals New Targets for Arx, a Gene Mutated in Mental Retardation and Interneuronopathies
Marie-Lise Quillé, Solenne Carat, Sylvia Quéméner-Redon, Edouard Hirchaud, Daniel Baron, Caroline Benech, Jeanne Guihot, Morgane Placet, Olivier Mignen, Claude Férec, Rémi Houlgatte, Gaëlle Friocourt
PLoS One. 2011; 6(9): e25181. Published online 2011 September 22. doi: 10.1371/journal.pone.0025181
PMCID:
PMC3178625
Abstract Full Text PDF–1.1M Supplementary Material
Analysis of the dynamics of limb transcriptomes during mouse development
Istvan Gyurján, Bernhard Sonderegger, Felix Naef, Denis Duboule
BMC Dev Biol. 2011; 11: 47. Published online 2011 July 29. doi: 10.1186/1471-213X-11-47
PMCID:
PMC3160909
Abstract Full Text PDF–791K Supplementary Material
mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
PLoS One. 2011; 6(7): e18337. Published online 2011 July 8. doi: 10.1371/journal.pone.0018337
PMCID:
PMC3132743
Abstract Full Text PDF–928K Supplementary Material
Evolutionary plasticity of segmentation clock networks
Aurélie J. Krol, Daniela Roellig, Mary-Lee Dequéant, Olivier Tassy, Earl Glynn, Gaye Hattem, Arcady Mushegian, Andrew C. Oates, Olivier Pourquié
Development. 2011 July 1; 138(13): 2783–2792. doi: 10.1242/dev.063834
PMCID:
PMC3109603
Abstract Full Text Supplementary Material
Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development
Martin Ehler, Vinodh N Rajapakse, Barry R Zeeberg, Brian P Brooks, Jacob Brown, Wojciech Czaja, Robert F Bonner
BMC Proc. 2011; 5(Suppl 2): S3. Published online 2011 May 28. doi: 10.1186/1753-6561-5-S2-S3
PMCID:
PMC3090761
Abstract Full Text PDF–1.8M
TAFFEL: Independent Enrichment Analysis of gene sets
Mitja I Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä-Herttuala, Juha E Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong, Petri Pehkonen
BMC Bioinformatics. 2011; 12: 171. Published online 2011 May 19. doi: 10.1186/1471-2105-12-171
PMCID:
PMC3120704
Abstract Full Text PDF–1.2M Supplementary Material
The Involvement of SMILE/TMTC3 in Endoplasmic Reticulum Stress Response
Maud Racapé, Jean-Paul Duong Van Huyen, Richard Danger, Magali Giral, Françoise Bleicher, Yohann Foucher, Annaïck Pallier, Paul Pilet, Petra Tafelmeyer, Joanna Ashton-Chess, Emilie Dugast, Ségolène Pettré, Béatrice Charreau, Jean-Paul Soulillou, Sophie Brouard
PLoS One. 2011; 6(5): e19321. Published online 2011 May 16. doi: 10.1371/journal.pone.0019321
PMCID:
PMC3095597
Abstract Full Text PDF–1.2M Supplementary Material
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps
Christian Perez-Llamas, Nuria Lopez-Bigas
PLoS One. 2011; 6(5): e19541. Published online 2011 May 13. doi: 10.1371/journal.pone.0019541
PMCID:
PMC3094337
Abstract Full Text PDF–1.3M Supplementary Material
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