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Reactome enhanced pathway visualization

Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews (+8 others)
2017 Bioinformatics  
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate
more » ... navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications. Results: For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects. Availability and implementation: http://reactome.
doi:10.1093/bioinformatics/btx441 pmid:29077811 pmcid:PMC5860170 fatcat:ypdq4ibaandhnbs6ysoegcgab4

The Reactome pathway Knowledgebase

Antonio Fabregat, Konstantinos Sidiropoulos, Phani Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon McKay, Lisa Matthews, Bruce May (+10 others)
2015 Nucleic Acids Research  
The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations--an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation
more » ... logues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.
doi:10.1093/nar/gkv1351 pmid:26656494 pmcid:PMC4702931 fatcat:ikxhcsslzrfeziyzq2p6qadvay

Colony stimulating factor-1 receptor is a central component of the foreign body response to biomaterial implants in rodents and non-human primates

Joshua C. Doloff, Omid Veiseh, Arturo J. Vegas, Hok Hei Tam, Shady Farah, Minglin Ma, Jie Li, Andrew Bader, Alan Chiu, Atieh Sadraei, Stephanie Aresta-Dasilva, Marissa Griffin (+13 others)
2017 Nature Materials  
doi:10.1038/nmat4866 pmid:28319612 pmcid:PMC5445003 fatcat:pclswq65pvcxrgcysvymezhybu

Page 128 of POWER Vol. 83, Issue 1 [page]

1939 POWER  
Marissa, Ill. GEORGE BLUM  ...  E R WEBBER Simplex, Duplex, Complex?  ... 

Brown-Sequard syndrome from herniation of a thoracic disc

C. D. Witiw, M. F. Shamji
2014 CMAJ - Canadian Medical Association Journal  
Acknowledgement: The authors thank Marissa Webber for providing the illustration in Figure 1D .  ... 
doi:10.1503/cmaj.140117 pmid:25157052 pmcid:PMC4259774 fatcat:c5dsvnah6fgchgmok3czrx2ftm

Acknowledgments [chapter]

2020 Art for People's Sake  
Siddha Webber); and to Chicago' s students and teachers, their curiosity and imagination, and their struggles for equity and justice.  ...  In connection with research and programs there that nourished this book, I wish to thank Marissa Baker, Natalie Battles, Sammie Dortch, Skyla Hearn, Faheem Majeed, Charles Miles, Maséqua Myers, Clinton  ... 
doi:10.1515/9781478002468-002 fatcat:zznssjkn6fhwbpuhjev7au4la4

Page 5025 of Psychological Abstracts Vol. 88, Issue 12 [page]

2001 Psychological Abstracts  
., 37569 Adamson, Lynne, 38156 Adams-Webber, J.  ...  Javier, 37105 Amato, Paul R., 36521 Ambo, Hideo, 36892 Amdur, Marissa, 35548 Ameli, Rezvan, 36159 Amend, D., 36024 Ameratunga, Shanthi, 38727 American Psychological Asso, 38169 Amiaz, Revital, 37810 Amir  ... 

Issue Information ‐ TOC

2022 Nations and Nationalism  
(Marx 1970 (Marx [1844]] : 333); • in the case of online references that do not include a publication date, the reference should be as follows: (Webber online) • op.cit., ibid., idem. etc. should not be  ...  From cyberfascism to terrorism: challenges of American Jewish return migrants in the Israel On 4chan/pol/ culture and the transnational production of Defense Forces memetic violence HANS SIEBERS AND MARISSA  ... 
doi:10.1111/nana.12744 fatcat:nvnmhqnoingr5c76jlzi2nwcoa

A survey of Canadian cancer patients' perspectives on the characteristics and treatment of breakthrough pain

Gillian Bedard, Philippa Hawley, Liying Zhang, Marissa Slaven, Pierre Gagnon, Stuart Bisland, Margaret Bennett, Francois Tardif, Edward Chow
2013 Supportive Care in Cancer  
In a study by Webber et al., it was found that patients often had difficulty in describing their pain to their physician, as they were unable to find the right words to accurately describe it.  ... 
doi:10.1007/s00520-013-1817-4 pmid:23636647 fatcat:5idj5qi7zbhxve6zhkxgnyy37m

Supplemental Material for Proceedings of the American Psychological Association for the Legislative Year 2013: Minutes of the Annual Meeting of the Council of Representatives, February 22–24, 2013, Washington, DC, and July 31 and August 2, 2013, Honolulu, Hawaii, and Minutes of the February, June, April, July/August, and December 2013 Meetings of the Board of Directors

2014 American Psychologist  
Webber, Brittany Lauren Weber, Iris Weber, Paola B. Weber, Stephanie Marie Webster, Rebecca Dian Weeks, Molly Stroud Wegner, Kristin M.  ...  Floro, Marissa C. Floyd, Ligia Ivonne Follman, Leslie Fonck, Rene Forest, Mary Formisano, Felicia D. Fox, Rachel Anne Franklin, Bridgette Taflinski, Leida Taggart, Jeff Takkash, Ali M.  ... 
doi:10.1037/a0036645.supp fatcat:y3of2yg6qvfv5fbsnzrmeudkxq

Obesity in Youth with Type 1 Diabetes in Germany, Austria, and the United States

Stephanie N. DuBose, Julia M. Hermann, William V. Tamborlane, Roy W. Beck, Axel Dost, Linda A. DiMeglio, Karl Otfried Schwab, Reinhard W. Holl, Sabine E. Hofer, David M. Maahs, Steven Willi, Terri Lipman (+384 others)
2015 Journal of Pediatrics  
Objective To examine the current extent of the obesity problem in 2 large pediatric clinical registries in the US and Europe and to examine the hypotheses that increased body mass index (BMI) z-scores (BMIz) are associated with greater hemoglobin A1c (HbA1c) and increased frequency of severe hypoglycemia in youth with type 1 diabetes (T1D). Study design International (World Health Organization) and national (Centers for Disease Control and Prevention/ German Health Interview and Examination
more » ... ey for Children and Adolescents) BMI references were used to calculate BMIz in participants (age 2-<18 years and $1 year duration of T1D) enrolled in the T1D Exchange (n = 11 435) and the Diabetes Prospective Follow-up (n = 21 501). Associations between BMIz and HbA1c and severe hypoglycemia were assessed. Results Participants in both registries had median BMI values that were greater than international and their respective national reference values. BMIz was significantly greater in the T1D Exchange vs the Diabetes Prospective Follow-up (P < .001). After stratification by age-group, no differences in BMI between registries existed for children 2-5 years, but differences were confirmed for 6-to 9-, 10-to 13-, and 14-to 17-year age groups (all P < .001). Greater BMIz were significantly related to greater HbA1c levels and more frequent occurrence of severe hypoglycemia across the registries, although these associations may not be clinically relevant. Conclusions Excessive weight is a common problem in children with T1D in Germany and Austria and, especially, in the US. Our data suggest that obesity contributes to the challenges in achieving optimal glycemic control in children and adolescents with T1D. (J Pediatr 2015;-:---).
doi:10.1016/j.jpeds.2015.05.046 pmid:26164381 fatcat:taz7bav7wffjrj7fmcque43ta4

Subjective effects to marijuana associated with marijuana use in community and clinical subjects

Joanna S. Zeiger, Brett C. Haberstick, Robin P. Corley, Marissa A. Ehringer, Thomas J. Crowley, John K. Hewitt, Christian J. Hopfer, Michael C. Stallings, Susan E. Young, Soo Hyun Rhee
2010 Drug and Alcohol Dependence  
The scales are formed by taking pairs of items with the highest correlation and including other items that fit into the scale until there is no further improvement (Webber and Huxley, 2007) .  ... 
doi:10.1016/j.drugalcdep.2009.12.026 pmid:20149559 pmcid:PMC3000695 fatcat:fz5i4oqlj5cobhdfgb4zf4asde

Subjective effects for alcohol, tobacco, and marijuana association with cross-drug outcomes

Joanna S. Zeiger, Brett C. Haberstick, Robin P. Corley, Marissa A. Ehringer, Thomas J. Crowley, John K. Hewitt, Christian J. Hopfer, Michael C. Stallings, Susan E. Young, Soo Hyun Rhee
2012 Drug and Alcohol Dependence  
Scales from MSA are formed by taking pairs of items with the highest correlation and including other items until there is no further improvement (Webber and Huxley, 2007) .  ... 
doi:10.1016/j.drugalcdep.2012.02.014 pmid:22445481 pmcid:PMC3729264 fatcat:2dgp5x2b5bahhpiaoeau6ssnte

Supplemental Material for Proceedings of the American Psychological Association for the Legislative Year 2014 : Minutes of the Annual Meeting of the Council of Representatives, February 21–23, 2014, Washington, DC, and August 6 and August 8, 2014, Washington, DC, and Minutes of the February, June, August, and December 2014 Meetings of the Board of Directors

2015 American Psychologist  
Tsuda, Lily Tuazon, Anna Cristina Angeles Tung, Wai Ming Phyllis Tunis, Marissa S. Turner, Charles Wayne Turner, Darrel B.  ...  Floro, Marissa C. Foreman, Cia French, Alexis N. Fullick, Julia M. Fullmer Yetter, Brooke Furtaw, Paul C. Macias, Salvador Maciel, Duan Lee Magana, Marichu G.  ... 
doi:10.1037/a0039369.supp fatcat:uawfjspuybevrgatrvaitctbde

Maine Sea Grant Annual Report 2016 MAINE SEA GRANT Annual Report to the Vice President for Research

Catherine Schmitt, C Bartlett
2017 unpublished
Bigelow-Colby Semester Program Program Development (Webber) Tyler Lewtan Colby College Unknown Program Development (Webber) Albertha Ladina Colby College Unknown Program Development (Webber)  ...  ) Vanessa Van Deusen Barnard College Unknown Program Development (Webber) Mahellelah Shauer Humboldt University Bigelow REU Program Program Development (Webber) Emily Geske Colby College  ... 
fatcat:4ovvzrw5bnbyvekv22mdf2gh3q
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