My NCBISign In
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

Is Cited by the Following 133 Articles in this Archive:

Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs
Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross KK Leung, Xiang-Sun Zhang, Stephen KW Tsui, Luonan Chen
BMC Bioinformatics. 2012; 13(Suppl 7): S6. Published online 2012 May 8. doi: 10.1186/1471-2105-13-S7-S6
PMCID:
PMC3348046
Abstract Full Text PDF–803K Supplementary Material
Automatic Filtering and Substantiation of Drug Safety Signals
Anna Bauer-Mehren, Erik M. van Mullingen, Paul Avillach, María del Carmen Carrascosa, Ricard Garcia-Serna, Janet Piñero, Bharat Singh, Pedro Lopes, José L. Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura I. Furlong
PLoS Comput Biol. 2012 April; 8(4): e1002457. Published online 2012 April 5. doi: 10.1371/journal.pcbi.1002457
Correction in:
PLoS Comput Biol. 2012 May; 8(5): 10.1371/annotation/695450aa-95a0-491d-804d-470cbfa861e8.
PMCID:
PMC3320573
Abstract Full Text PDF–480K Supplementary Material Correction
Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing
Kimberly A. Dittmar, Peng Jiang, Juw Won Park, Karine Amirikian, Ji Wan, Shihao Shen, Yi Xing, Russell P. Carstens
Mol Cell Biol. 2012 April; 32(8): 1468–1482. doi: 10.1128/MCB.06536-11
PMCID:
PMC3318588
Free in PMC on 2012/10/01
Identifying Neighborhoods of Coordinated Gene Expression and Metabolite Profiles
Timothy Hancock, Nicolas Wicker, Ichigaku Takigawa, Hiroshi Mamitsuka
PLoS One. 2012; 7(2): e31345. Published online 2012 February 15. doi: 10.1371/journal.pone.0031345
PMCID:
PMC3280297
Abstract Full Text PDF–871K Supplementary Material
IMID: integrated molecular interaction database
Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang
Bioinformatics. 2012 March 1; 28(5): 747–749. Published online 2012 January 11. doi: 10.1093/bioinformatics/bts010
PMCID:
PMC3289914
Free in PMC on 2013/03/01
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Akhil Kumar, Patrick F Suthers, Costas D Maranas
BMC Bioinformatics. 2012; 13: 6. Published online 2012 January 10. doi: 10.1186/1471-2105-13-6
PMCID:
PMC3277463
Abstract Full Text PDF–1.1M
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
Insight into Bacterial Virulence Mechanisms against Host Immune Response via the Yersinia pestis-Human Protein-Protein Interaction Network
Huiying Yang, Yuehua Ke, Jian Wang, Yafang Tan, Sebenzile K. Myeni, Dong Li, Qinghai Shi, Yanfeng Yan, Hui Chen, Zhaobiao Guo, Yanzhi Yuan, Xiaoming Yang, Ruifu Yang, Zongmin Du
Infect Immun. 2011 November; 79(11): 4413–4424. doi: 10.1128/IAI.05622-11
PMCID:
PMC3257920
Abstract Full Text PDF–3.0M Supplementary Material
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
A Physical Interaction Network of Dengue Virus and Human Proteins
Sudip Khadka, Abbey D. Vangeloff, Chaoying Zhang, Prasad Siddavatam, Nicholas S. Heaton, Ling Wang, Ranjan Sengupta, Sudhir Sahasrabudhe, Glenn Randall, Michael Gribskov, Richard J. Kuhn, Rushika Perera, Douglas J. LaCount
Mol Cell Proteomics. 2011 December; 10(12): M111.012187. Published online 2011 September 12. doi: 10.1074/mcp.M111.012187
PMCID:
PMC3237087
Free in PMC on 2012/12/01
A network-based gene-weighting approach for pathway analysis
Zhaoyuan Fang, Weidong Tian, Hongbin Ji
Cell Res. 2012 March; 22(3): 565–580. Published online 2011 September 6. doi: 10.1038/cr.2011.149
PMCID:
PMC3292304
Free in PMC on 2013/03/01
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
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database
Giovanni Marco Dall'Olio, Bijay Jassal, Ludovica Montanucci, Pascal Gagneux, Jaume Bertranpetit, Hafid Laayouni
Glycobiology. 2011 November; 21(11): 1395–1400. Published online 2011 January 2. doi: 10.1093/glycob/cwq215
PMCID:
PMC3191915
Free in PMC on 2012/11/01
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