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Reactome: a knowledge base of biologic pathways and processes
Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein
Genome Biol. 2007; 8(3): R39. Published online 2007 March 16. doi: 10.1186/gb-2007-8-3-r39
Correction in:
Genome Biol. 2009; 10(2): 402.
PMCID:
PMC1868929
Abstract Full Text PDF–1.0M Supplementary Material Correction
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 Is Cited by the Following 123 Articles in this Archive:
Preservation of Ranking Order in the Expression of Human Housekeeping Genes
Grace T. W. Shaw, Edward S. C. Shih, Chun-Houh Chen, Ming-Jing Hwang
PLoS One. 2011; 6(12): e29314. Published online 2011 December 22. doi: 10.1371/journal.pone.0029314
PMCID:
PMC3245260
Abstract Full Text PDF–680K Supplementary Material
INOH: ontology-based highly structured database of signal transduction pathways
Satoko Yamamoto, Noriko Sakai, Hiromi Nakamura, Hiroshi Fukagawa, Ken Fukuda, Toshihisa Takagi
Database (Oxford) 2011; 2011: bar052. Published online 2011 November 25. doi: 10.1093/database/bar052
PMCID:
PMC3225078
Abstract Full Text PDF–1.6M
The Reactome BioMart
Robin A. Haw, David Croft, Christina K. Yung, Nelson Ndegwa, Peter D'Eustachio, Henning Hermjakob, Lincoln D. Stein
Database (Oxford) 2011; 2011: bar031. Published online 2011 October 17. doi: 10.1093/database/bar031
PMCID:
PMC3197281
Abstract Full Text PDF–724K
The representation of protein complexes in the Protein Ontology (PRO)
Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu
BMC Bioinformatics. 2011; 12: 371. Published online 2011 September 19. doi: 10.1186/1471-2105-12-371
PMCID:
PMC3189193
Abstract Full Text PDF–1.1M
Analysis of VEGF-A Regulated Gene Expression in Endothelial Cells to Identify Genes Linked to Angiogenesis
Corban G. Rivera, Sofie Mellberg, Lena Claesson-Welsh, Joel S. Bader, Aleksander S. Popel
PLoS One. 2011; 6(9): e24887. Published online 2011 September 13. doi: 10.1371/journal.pone.0024887
PMCID:
PMC3172305
Abstract Full Text PDF–655K Supplementary Material
Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Jitao David Zhang, Cindy Koerner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Sahin, Stefan Wiemann, Ulrich Tschulena
PLoS One. 2011; 6(7): e22176. Published online 2011 July 13. doi: 10.1371/journal.pone.0022176
PMCID:
PMC3135613
Abstract Full Text PDF–489K Supplementary Material
Differential Effects of Krill Oil and Fish Oil on the Hepatic Transcriptome in Mice
Lena Burri, Kjetil Berge, Karin Wibrand, Rolf K. Berge, Jamie L. Barger
Front Genet. 2011; 2: 45. Prepublished online 2011 April 11. Published online 2011 July 12. doi: 10.3389/fgene.2011.00045
PMCID:
PMC3268598
Abstract Full Text PDF–961K
Fenfluramine-induced gene dysregulation in human pulmonary artery smooth muscle and endothelial cells
Weijuan Yao, Wenbo Mu, Amy Zeifman, Michelle Lofti, Carmelle V. Remillard, Ayako Makino, David L. Perkins, Joe G. Garcia, Jason X. J. Yuan, Wei Zhang
Pulm Circ. 2011 Jul-Sep; 1(3): 405–418. doi: 10.4103/2045-8932.87310
PMCID:
PMC3224433
Abstract Full Text
Integrated Bio-Entity Network: A System for Biological Knowledge Discovery
Lindsey Bell, Rajesh Chowdhary, Jun S. Liu, Xufeng Niu, Jinfeng Zhang
PLoS One. 2011; 6(6): e21474. Published online 2011 June 27. doi: 10.1371/journal.pone.0021474
PMCID:
PMC3124513
Abstract Full Text PDF–472K Supplementary Material
In Silico Gene Prioritization by Integrating Multiple Data Sources
Yixuan Chen, Wenhui Wang, Yingyao Zhou, Robert Shields, Sumit K. Chanda, Robert C. Elston, Jing Li
PLoS One. 2011; 6(6): e21137. Published online 2011 June 24. doi: 10.1371/journal.pone.0021137
PMCID:
PMC3123338
Abstract Full Text PDF–826K Supplementary Material
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data
Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron
BMC Bioinformatics. 2011; 12: 249. Published online 2011 June 21. doi: 10.1186/1471-2105-12-249
PMCID:
PMC3236061
Abstract Full Text PDF–3.8M Supplementary Material
Systematic Approaches towards the Development of Host-Directed Antiviral Therapeutics
Andrew Prussia, Pahk Thepchatri, James P. Snyder, Richard K. Plemper
Int J Mol Sci. 2011; 12(6): 4027–4052. Published online 2011 June 15. doi: 10.3390/ijms12064027
PMCID:
PMC3131607
Abstract Full Text PDF–729K Supplementary Material
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways
Luca Beltrame, Enrica Calura, Razvan R. Popovici, Lisa Rizzetto, Damariz Rivero Guedez, Michele Donato, Chiara Romualdi, Sorin Draghici, Duccio Cavalieri
Bioinformatics. 2011 August 1; 27(15): 2127–2133. Published online 2011 June 7. doi: 10.1093/bioinformatics/btr339
PMCID:
PMC3137220
Abstract Full Text PDF–152K Supplementary Material
BioProfiling.de: analytical web portal for high-throughput cell biology
Alexey V. Antonov
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W323–W327. Published online 2011 May 23. doi: 10.1093/nar/gkr372
PMCID:
PMC3125774
Abstract Full Text PDF–215K
Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins
Corban G. Rivera, Joel S. Bader, Aleksander S. Popel
Ann Biomed Eng. Author manuscript; available in PMC 2011 August 4.
Published in final edited form as: Ann Biomed Eng. 2011 August; 39(8): 2213–2222. Published online 2011 May 18. doi: 10.1007/s10439-011-0325-2
PMCID:
PMC3150481
Abstract Full Text PDF–445K
Knowledge-Driven Multi-Locus Analysis Reveals Gene-Gene Interactions Influencing HDL Cholesterol Level in Two Independent EMR-Linked Biobanks
Stephen D. Turner, Richard L. Berg, James G. Linneman, Peggy L. Peissig, Dana C. Crawford, Joshua C. Denny, Dan M. Roden, Catherine A. McCarty, Marylyn D. Ritchie, Russell A. Wilke
PLoS One. 2011; 6(5): e19586. Published online 2011 May 11. doi: 10.1371/journal.pone.0019586
PMCID:
PMC3092760
Abstract Full Text PDF–359K Supplementary Material
Cancer computational biology
Zohar Yakhini, Igor Jurisica
BMC Bioinformatics. 2011; 12: 120. Published online 2011 April 26. doi: 10.1186/1471-2105-12-120
PMCID:
PMC3111371
Full Text PDF–753K
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format
Ryan L Webb, Avi Ma'ayan
Source Code Biol Med. 2011; 6: 5. Published online 2011 March 21. doi: 10.1186/1751-0473-6-5
PMCID:
PMC3071313
Abstract Full Text PDF–345K
NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs
Elize A. Shirdel, Wing Xie, Tak W. Mak, Igor Jurisica
PLoS One. 2011; 6(2): e17429. Published online 2011 February 25. doi: 10.1371/journal.pone.0017429
PMCID:
PMC3045450
Abstract Full Text PDF–2.0M Supplementary Material
ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web
Geoffrey Fucile, David Di Biase, Hardeep Nahal, Garon La, Shokoufeh Khodabandeh, Yani Chen, Kante Easley, Dinesh Christendat, Lawrence Kelley, Nicholas J. Provart
PLoS One. 2011; 6(1): e15237. Published online 2011 January 10. doi: 10.1371/journal.pone.0015237
PMCID:
PMC3018417
Abstract Full Text PDF–1.1M Supplementary Material
De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits
Shuang Chen, Pengcheng Yang, Feng Jiang, Yuanyuan Wei, Zongyuan Ma, Le Kang
PLoS One. 2010; 5(12): e15633. Published online 2010 December 30. doi: 10.1371/journal.pone.0015633
PMCID:
PMC3012706
Abstract Full Text PDF–1.4M Supplementary Material
Bioinformatics Analysis of Macrophages Exposed to Porphyromonas gingivalis: Implications in Acute vs. Chronic Infections
Wen-Han Yu, Han Hu, Qingde Zhou, Yu Xia, Salomon Amar
PLoS One. 2010; 5(12): e15613. Published online 2010 December 23. doi: 10.1371/journal.pone.0015613
PMCID:
PMC3009741
Abstract Full Text PDF–298K Supplementary Material
The annotation and the usage of scientific databases could be improved with public issue tracker software
Giovanni Marco Dall'Olio, Jaume Bertranpetit, Hafid Laayouni
Database (Oxford) 2010; 2010: baq035. Published online 2010 December 23. doi: 10.1093/database/baq035
PMCID:
PMC3011984
Abstract Full Text PDF–88K
The Morningside Initiative: Collaborative Development of a Knowledge Repository to Accelerate Adoption of Clinical Decision Support
Robert Greenes, Meryl Bloomrosen, Nancy E. Brown-Connolly, Clayton Curtis, Don E Detmer, Robert Enberg, Douglas Fridsma, Emory Fry, Mary K Goldstein, Peter Haug, Nathan Hulse, Tonya Hongsermeier, Saverio Maviglia, Craig W Robbins, Hemant Shah
Open Med Inform J. 2010; 4: 278–290. Published online 2010 December 14. doi: 10.2174/1874431101004010278
PMCID:
PMC3097479
Abstract Full Text PDF–1004K
Systematic integration of experimental data and models in systems biology
Peter Li, Joseph O Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick Dunn, Farid Khan, Naglis Malys, Hanan L Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David S Broomhead, Carole A Goble, Simon J Gaskell, Douglas B Kell, Hans V Westerhoff, Pedro Mendes, Norman W Paton
BMC Bioinformatics. 2010; 11: 582. Published online 2010 November 29. doi: 10.1186/1471-2105-11-582
PMCID:
PMC3008707
Abstract Full Text PDF–468K Supplementary Material
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
Yves Sucaet, Eve Syrkin Wurtele
BMC Res Notes. 2010; 3: 312. Published online 2010 November 18. doi: 10.1186/1756-0500-3-312
PMCID:
PMC2998519
Abstract Full Text PDF–1.3M Supplementary Material
Concept and application of a computational vaccinology workflow
Johannes Söllner, Andreas Heinzel, Georg Summer, Raul Fechete, Laszlo Stipkovits, Susan Szathmary, Bernd Mayer
Immunome Res. 2010; 6(Suppl 2): S7. Published online 2010 November 3. doi: 10.1186/1745-7580-6-S2-S7
PMCID:
PMC2981879
Abstract Full Text PDF–1.5M
Human and chicken TLR pathways: manual curation and computer-based orthology analysis
Marc Gillespie, Veronica Shamovsky, Peter D’Eustachio
Mamm Genome. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Mamm Genome. 2011 February; 22(1-2): 130–138. Published online 2010 October 30. doi: 10.1007/s00335-010-9296-0
PMCID:
PMC3035812
Abstract Full Text PDF–129K
Literature-based discovery of diabetes- and ROS-related targets
Junguk Hur, Kelli A Sullivan, Adam D Schuyler, Yu Hong, Manjusha Pande, David J States, H V Jagadish, Eva L Feldman
BMC Med Genomics. 2010; 3: 49. Published online 2010 October 27. doi: 10.1186/1755-8794-3-49
PMCID:
PMC2988702
Abstract Full Text PDF–1016K Supplementary Material
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
Jennifer I Deegan (née Clark), Emily C Dimmer, Christopher J Mungall
BMC Bioinformatics. 2010; 11: 530. Published online 2010 October 25. doi: 10.1186/1471-2105-11-530
PMCID:
PMC3098089
Abstract Full Text PDF–1.2M
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