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CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.

F1000Research

Ono K, Muetze T, Kolishovski G, Shannon P, Demchak B.
PMID: 26672762
F1000Res. 2015 Aug 05;4:478. doi: 10.12688/f1000research.6767.1. eCollection 2015.

As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated...

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Ono K, Muetze T, Kolishovski G, et al. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res. 2015;4:478doi: 10.12688/f1000research.6767.1.
Ono, K., Muetze, T., Kolishovski, G., Shannon, P., & Demchak, B. (2015). CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Research, 4478. https://doi.org/10.12688/f1000research.6767.1
Ono, Keiichiro, et al. "CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API." F1000Research vol. 4 (2015): 478. doi: https://doi.org/10.12688/f1000research.6767.1
Ono K, Muetze T, Kolishovski G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res. 2015 Aug 05;4:478. doi: 10.12688/f1000research.6767.1. eCollection 2015. PMID: 26672762; PMCID: PMC4670004.
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Social Network: a Cytoscape app for visualizing co-authorship networks.

F1000Research

Kofia V, Isserlin R, Buchan AM, Bader GD.
PMID: 26949516
F1000Res. 2015 Aug 05;4:481. doi: 10.12688/f1000research.6804.3. eCollection 2015.

Networks that represent connections between individuals can be valuable analytic tools. The Social Network Cytoscape app is capable of creating a visual summary of connected individuals automatically. It does this by representing relationships as networks where each node denotes...

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Kofia V, Isserlin R, Buchan AM, et al. Social Network: a Cytoscape app for visualizing co-authorship networks. F1000Res. 2015;4:481doi: 10.12688/f1000research.6804.3.
Kofia, V., Isserlin, R., Buchan, A. M., & Bader, G. D. (2015). Social Network: a Cytoscape app for visualizing co-authorship networks. F1000Research, 4481. https://doi.org/10.12688/f1000research.6804.3
Kofia, Victor, et al. "Social Network: a Cytoscape app for visualizing co-authorship networks." F1000Research vol. 4 (2015): 481. doi: https://doi.org/10.12688/f1000research.6804.3
Kofia V, Isserlin R, Buchan AM, Bader GD. Social Network: a Cytoscape app for visualizing co-authorship networks. F1000Res. 2015 Aug 05;4:481. doi: 10.12688/f1000research.6804.3. eCollection 2015. PMID: 26949516; PMCID: PMC4760270.
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Journal of integrative bioinformatics

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D.
PMID: 28187405
J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to...

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Schreiber F, Bader GD, Gleeson P, et al. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J Integr Bioinform. 2016;13(3):289doi: 10.2390/biecoll-jib-2016-289.
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Le Novère, N., Myers, C., Nickerson, D., Sommer, B., & Walthemath, D. (2016). Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. Journal of integrative bioinformatics, 13(3), 289. https://doi.org/10.2390/biecoll-jib-2016-289
Schreiber, Falk, et al. "Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016." Journal of integrative bioinformatics vol. 13,3 (2016): 289. doi: https://doi.org/10.2390/biecoll-jib-2016-289
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289. PMID: 28187405; PMCID: PMC5431574.
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A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression.

F1000Research

Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J.
PMID: 29487738
F1000Res. 2017 Jun 06;6:784. doi: 10.12688/f1000research.11616.2. eCollection 2017.

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this task has required dedicated bioinformatics support...

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Carlin D, Kosnicki K, Garamszegi S, et al. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017;6:784doi: 10.12688/f1000research.11616.2.
Carlin, D., Kosnicki, K., Garamszegi, S., Ideker, T., Thorvaldsdóttir, H., Reich, M., & Mesirov, J. (2017). A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research, 6784. https://doi.org/10.12688/f1000research.11616.2
Carlin, Daniel, et al. "A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression." F1000Research vol. 6 (2017): 784. doi: https://doi.org/10.12688/f1000research.11616.2
Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017 Jun 06;6:784. doi: 10.12688/f1000research.11616.2. eCollection 2017. PMID: 29487738; PMCID: PMC5806050.
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Strategies for Network GWAS Evaluated Using Classroom Crowd Science.

Cell systems

Fong SH, Carlin DE, Ozturk K, Ideker T.
PMID: 31022372
Cell Syst. 2019 Apr 24;8(4):275-280. doi: 10.1016/j.cels.2019.03.013.

Biological networks can substantially boost power to identify disease genes in genome-wide association studies. To explore different network GWAS methods, we challenged students of a UC San Diego graduate level bioinformatics course, Network Biology and Biomedicine, to explore and...

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Fong SH, Carlin DE, Ozturk K. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019;8(4):275-280doi: 10.1016/j.cels.2019.03.013.
Fong, S. H., Carlin, D. E., Ozturk, K., & Ideker, T. (2019). Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell systems, 8(4), 275-280. https://doi.org/10.1016/j.cels.2019.03.013
Fong, Samson H, et al. "Strategies for Network GWAS Evaluated Using Classroom Crowd Science." Cell systems vol. 8,4 (2019): 275-280. doi: https://doi.org/10.1016/j.cels.2019.03.013
Fong SH, Carlin DE, Ozturk K, Ideker T. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 Apr 24;8(4):275-280. doi: 10.1016/j.cels.2019.03.013. PMID: 31022372; PMCID: PMC6764759.
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A convergent molecular network underlying autism and congenital heart disease.

Cell systems

Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T.
PMID: 34411509
Cell Syst. 2021 Nov 17;12(11):1094-1107.e6. doi: 10.1016/j.cels.2021.07.009. Epub 2021 Aug 18.

Patients with neurodevelopmental disorders, including autism, have an elevated incidence of congenital heart disease, but the extent to which these conditions share molecular mechanisms remains unknown. Here, we use network genetics to identify a convergent molecular network underlying autism...

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Rosenthal SB, Willsey HR, Xu Y, et al. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. 2021;12(11):1094-1107.e6doi: 10.1016/j.cels.2021.07.009.
Rosenthal, S. B., Willsey, H. R., Xu, Y., Mei, Y., Dea, J., Wang, S., Curtis, C., Sempou, E., Khokha, M. K., Chi, N. C., Willsey, A. J., Fisch, K. M., & Ideker, T. (2021). A convergent molecular network underlying autism and congenital heart disease. Cell systems, 12(11), 1094-1107.e6. https://doi.org/10.1016/j.cels.2021.07.009
Rosenthal, Sara Brin, et al. "A convergent molecular network underlying autism and congenital heart disease." Cell systems vol. 12,11 (2021): 1094-1107.e6. doi: https://doi.org/10.1016/j.cels.2021.07.009
Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. 2021 Nov 17;12(11):1094-1107.e6. doi: 10.1016/j.cels.2021.07.009. Epub 2021 Aug 18. PMID: 34411509; PMCID: PMC8602730.
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CyAnimator: Simple Animations of Cytoscape Networks.

F1000Research

Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE.
PMID: 26937268
F1000Res. 2015 Aug 05;4:482. doi: 10.12688/f1000research.6852.2. eCollection 2015.

CyAnimator (http://apps.cytoscape.org/apps/cyanimator) is a Cytoscape app that provides a tool for simple animations of Cytoscape networks. The tool allows you to take a series of snapshots (CyAnimator calls them frames) of Cytoscape networks. For example, the first frame might...

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Morris JH, Vijay D, Federowicz S, et al. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015;4:482doi: 10.12688/f1000research.6852.2.
Morris, J. H., Vijay, D., Federowicz, S., Pico, A. R., & Ferrin, T. E. (2015). CyAnimator: Simple Animations of Cytoscape Networks. F1000Research, 4482. https://doi.org/10.12688/f1000research.6852.2
Morris, John H, et al. "CyAnimator: Simple Animations of Cytoscape Networks." F1000Research vol. 4 (2015): 482. doi: https://doi.org/10.12688/f1000research.6852.2
Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015 Aug 05;4:482. doi: 10.12688/f1000research.6852.2. eCollection 2015. PMID: 26937268; PMCID: PMC4752027.
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HOX gene complement and expression in the planarian Schmidtea mediterranea.

EvoDevo

Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ.
PMID: 27034770
Evodevo. 2016 Mar 30;7:7. doi: 10.1186/s13227-016-0044-8. eCollection 2016.

BACKGROUND: Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial...

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Currie KW, Brown DD, Zhu S, et al. HOX gene complement and expression in the planarian Schmidtea mediterranea. Evodevo. 2016;7:7doi: 10.1186/s13227-016-0044-8.
Currie, K. W., Brown, D. D., Zhu, S., Xu, C., Voisin, V., Bader, G. D., & Pearson, B. J. (2016). HOX gene complement and expression in the planarian Schmidtea mediterranea. EvoDevo, 77. https://doi.org/10.1186/s13227-016-0044-8
Currie, Ko W, et al. "HOX gene complement and expression in the planarian Schmidtea mediterranea." EvoDevo vol. 7 (2016): 7. doi: https://doi.org/10.1186/s13227-016-0044-8
Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ. HOX gene complement and expression in the planarian Schmidtea mediterranea. Evodevo. 2016 Mar 30;7:7. doi: 10.1186/s13227-016-0044-8. eCollection 2016. PMID: 27034770; PMCID: PMC4815179.
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miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.

Cancer cell

Lechman ER, Gentner B, Ng SWK, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JCY, Naldini L, Dick JE.
PMID: 27070706
Cancer Cell. 2016 Apr 11;29(4):602-606. doi: 10.1016/j.ccell.2016.03.015.

No abstract available.

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Lechman ER, Gentner B, Ng SWK, et al. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell. 2016;29(4):602-606doi: 10.1016/j.ccell.2016.03.015.
Lechman, E. R., Gentner, B., Ng, S. W. K., Schoof, E. M., van Galen, P., Kennedy, J. A., Nucera, S., Ciceri, F., Kaufmann, K. B., Takayama, N., Dobson, S. M., Trotman-Grant, A., Krivdova, G., Elzinga, J., Mitchell, A., Nilsson, B., Hermans, K. G., Eppert, K., Marke, R., Isserlin, R., Voisin, V., Bader, G. D., Zandstra, P. W., Golub, T. R., Ebert, B. L., Lu, J., Minden, M., Wang, J. C. Y., Naldini, L., & Dick, J. E. (2016). miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer cell, 29(4), 602-606. https://doi.org/10.1016/j.ccell.2016.03.015
Lechman, Eric R, et al. "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." Cancer cell vol. 29,4 (2016): 602-606. doi: https://doi.org/10.1016/j.ccell.2016.03.015
Lechman ER, Gentner B, Ng SWK, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JCY, Naldini L, Dick JE. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell. 2016 Apr 11;29(4):602-606. doi: 10.1016/j.ccell.2016.03.015. PMID: 27070706; PMCID: PMC5628169.
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Inferring interaction type in gene regulatory networks using co-expression data.

Algorithms for molecular biology : AMB

Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Goliaei B, Bader GD.
PMID: 26157474
Algorithms Mol Biol. 2015 Jul 08;10:23. doi: 10.1186/s13015-015-0054-4. eCollection 2015.

BACKGROUND: Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulatory interactions from genomics data, such as gene expression profiles; however, these...

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Khosravi P, Gazestani VH, Pirhaji L, et al. Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol Biol. 2015;10:23doi: 10.1186/s13015-015-0054-4.
Khosravi, P., Gazestani, V. H., Pirhaji, L., Law, B., Sadeghi, M., Goliaei, B., & Bader, G. D. (2015). Inferring interaction type in gene regulatory networks using co-expression data. Algorithms for molecular biology : AMB, 1023. https://doi.org/10.1186/s13015-015-0054-4
Khosravi, Pegah, et al. "Inferring interaction type in gene regulatory networks using co-expression data." Algorithms for molecular biology : AMB vol. 10 (2015): 23. doi: https://doi.org/10.1186/s13015-015-0054-4
Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Goliaei B, Bader GD. Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol Biol. 2015 Jul 08;10:23. doi: 10.1186/s13015-015-0054-4. eCollection 2015. PMID: 26157474; PMCID: PMC4495944.
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WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.

Source code for biology and medicine

Oesper L, Merico D, Isserlin R, Bader GD.
PMID: 21473782
Source Code Biol Med. 2011 Apr 07;6:7. doi: 10.1186/1751-0473-6-7.

BACKGROUND: When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations...

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Oesper L, Merico D, Isserlin R, et al. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med. 2011;6:7doi: 10.1186/1751-0473-6-7.
Oesper, L., Merico, D., Isserlin, R., & Bader, G. D. (2011). WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source code for biology and medicine, 67. https://doi.org/10.1186/1751-0473-6-7
Oesper, Layla, et al. "WordCloud: a Cytoscape plugin to create a visual semantic summary of networks." Source code for biology and medicine vol. 6 (2011): 7. doi: https://doi.org/10.1186/1751-0473-6-7
Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med. 2011 Apr 07;6:7. doi: 10.1186/1751-0473-6-7. PMID: 21473782; PMCID: PMC3083346.
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Porting and using PanGIA for Cytoscape 3: challenges and solutions.

F1000Research

Welker D, Demchak B.
PMID: 25075307
F1000Res. 2014 Jul 01;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.

Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which...

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Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Res. 2014;3:150doi: 10.12688/f1000research.4546.1.
Welker, D., & Demchak, B. (2014). Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Research, 3150. https://doi.org/10.12688/f1000research.4546.1
Welker, David, and Demchak, Barry. "Porting and using PanGIA for Cytoscape 3: challenges and solutions." F1000Research vol. 3 (2014): 150. doi: https://doi.org/10.12688/f1000research.4546.1
Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Res. 2014 Jul 01;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014. PMID: 25075307; PMCID: PMC4103495.
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Showing 25 to 36 of 61 entries