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On the Robustness of Graph-Based Clustering to Random Network Alterations.

Molecular & cellular proteomics : MCP

Stacey RG, Skinnider MA, Foster LJ.
PMID: 33592499
Mol Cell Proteomics. 2020 Nov 24;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24.

Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as...

Cite
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2020;20:100002doi: 10.1074/mcp.RA120.002275.
Stacey, R. G., Skinnider, M. A., & Foster, L. J. (2020). On the Robustness of Graph-Based Clustering to Random Network Alterations. Molecular & cellular proteomics : MCP, 20100002. https://doi.org/10.1074/mcp.RA120.002275
Stacey, R Greg, et al. "On the Robustness of Graph-Based Clustering to Random Network Alterations." Molecular & cellular proteomics : MCP vol. 20 (2020): 100002. doi: https://doi.org/10.1074/mcp.RA120.002275
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2020 Nov 24;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24. PMID: 33592499; PMCID: PMC7896145.
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An atlas of protein-protein interactions across mouse tissues.

Cell

Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ.
PMID: 34214469
Cell. 2021 Jul 22;184(15):4073-4089.e17. doi: 10.1016/j.cell.2021.06.003. Epub 2021 Jul 01.

Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here,...

Cite
Skinnider MA, Scott NE, Prudova A, et al. An atlas of protein-protein interactions across mouse tissues. Cell. 2021;184(15):4073-4089.e17doi: 10.1016/j.cell.2021.06.003.
Skinnider, M. A., Scott, N. E., Prudova, A., Kerr, C. H., Stoynov, N., Stacey, R. G., Chan, Q. W. T., Rattray, D., Gsponer, J., & Foster, L. J. (2021). An atlas of protein-protein interactions across mouse tissues. Cell, 184(15), 4073-4089.e17. https://doi.org/10.1016/j.cell.2021.06.003
Skinnider, Michael A, et al. "An atlas of protein-protein interactions across mouse tissues." Cell vol. 184,15 (2021): 4073-4089.e17. doi: https://doi.org/10.1016/j.cell.2021.06.003
Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell. 2021 Jul 22;184(15):4073-4089.e17. doi: 10.1016/j.cell.2021.06.003. Epub 2021 Jul 01. PMID: 34214469.
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On the Robustness of Graph-Based Clustering to Random Network Alterations.

Molecular & cellular proteomics : MCP

Stacey RG, Skinnider MA, Foster LJ.
PMID: 33592499
Mol Cell Proteomics. 2021;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24.

Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as...

Cite
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2020;20:100002doi: 10.1074/mcp.RA120.002275.
Stacey, R. G., Skinnider, M. A., & Foster, L. J. (2021). On the Robustness of Graph-Based Clustering to Random Network Alterations. Molecular & cellular proteomics : MCP, 20100002. https://doi.org/10.1074/mcp.RA120.002275
Stacey, R Greg, et al. "On the Robustness of Graph-Based Clustering to Random Network Alterations." Molecular & cellular proteomics : MCP vol. 20 (2021): 100002. doi: https://doi.org/10.1074/mcp.RA120.002275
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2021;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24. PMID: 33592499; PMCID: PMC7896145.
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Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury.

Molecular & cellular proteomics : MCP

Skinnider MA, Rogalski J, Tigchelaar S, Manouchehri N, Prudova A, Jackson AM, Nielsen K, Jeong J, Chaudhary S, Shortt K, Gallagher-Kurtzke Y, So K, Fong A, Gupta R, Okon EB, Rizzuto MA, Dong K, Streijger F, Belanger L, Ritchie L, Tsang A, Christie S, Mac-Thiong JM, Bailey C, Ailon T, Charest-Morin R, Dea N, Wilson JR, Dhall S, Paquette S, Street J, Fisher CG, Dvorak MF, Shannon C, Borchers C, Balshaw R, Foster LJ, Kwon BK.
PMID: 34129941
Mol Cell Proteomics. 2021 Jun 12;20:100096. doi: 10.1016/j.mcpro.2021.100096. Epub 2021 Jun 12.

Despite the emergence of promising therapeutic approaches in preclinical studies, the failure of large-scale clinical trials leaves clinicians without effective treatments for acute spinal cord injury (SCI). These trials are hindered by their reliance on detailed neurological examinations to...

Cite
Skinnider MA, Rogalski J, Tigchelaar S, et al. Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Mol Cell Proteomics. 2021;20:100096doi: 10.1016/j.mcpro.2021.100096.
Skinnider, M. A., Rogalski, J., Tigchelaar, S., Manouchehri, N., Prudova, A., Jackson, A. M., Nielsen, K., Jeong, J., Chaudhary, S., Shortt, K., Gallagher-Kurtzke, Y., So, K., Fong, A., Gupta, R., Okon, E. B., Rizzuto, M. A., Dong, K., Streijger, F., Belanger, L., Ritchie, L., Tsang, A., Christie, S., Mac-Thiong, J. M., Bailey, C., Ailon, T., Charest-Morin, R., Dea, N., Wilson, J. R., Dhall, S., Paquette, S., Street, J., Fisher, C. G., Dvorak, M. F., Shannon, C., Borchers, C., Balshaw, R., Foster, L. J., & Kwon, B. K. (2021). Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Molecular & cellular proteomics : MCP, 20100096. https://doi.org/10.1016/j.mcpro.2021.100096
Skinnider, Michael A, et al. "Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury." Molecular & cellular proteomics : MCP vol. 20 (2021): 100096. doi: https://doi.org/10.1016/j.mcpro.2021.100096
Skinnider MA, Rogalski J, Tigchelaar S, Manouchehri N, Prudova A, Jackson AM, Nielsen K, Jeong J, Chaudhary S, Shortt K, Gallagher-Kurtzke Y, So K, Fong A, Gupta R, Okon EB, Rizzuto MA, Dong K, Streijger F, Belanger L, Ritchie L, Tsang A, Christie S, Mac-Thiong JM, Bailey C, Ailon T, Charest-Morin R, Dea N, Wilson JR, Dhall S, Paquette S, Street J, Fisher CG, Dvorak MF, Shannon C, Borchers C, Balshaw R, Foster LJ, Kwon BK. Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Mol Cell Proteomics. 2021 Jun 12;20:100096. doi: 10.1016/j.mcpro.2021.100096. Epub 2021 Jun 12. PMID: 34129941; PMCID: PMC8260874.
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Adrenalitis and anasarca in idiopathic multicentric Castleman's disease.

Lancet (London, England)

Chen LYC, Skinnider BF, Wilson D, Fajgenbaum DC.
PMID: 33965090
Lancet. 2021 May 08;397(10286):1749. doi: 10.1016/S0140-6736(21)00674-7.

No abstract available.

Cite
Chen LYC, Skinnider BF, Wilson D, et al. Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet. 2021;397(10286):1749doi: 10.1016/S0140-6736(21)00674-7.
Chen, L. Y. C., Skinnider, B. F., Wilson, D., & Fajgenbaum, D. C. (2021). Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet (London, England), 397(10286), 1749. https://doi.org/10.1016/S0140-6736(21)00674-7
Chen, Luke Y C, et al. "Adrenalitis and anasarca in idiopathic multicentric Castleman's disease." Lancet (London, England) vol. 397,10286 (2021): 1749. doi: https://doi.org/10.1016/S0140-6736(21)00674-7
Chen LYC, Skinnider BF, Wilson D, Fajgenbaum DC. Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet. 2021 May 08;397(10286):1749. doi: 10.1016/S0140-6736(21)00674-7. PMID: 33965090.
Copy Download .nbib Format: NLM
On the Robustness of Graph-Based Clustering to Random Network Alterations.

Molecular & cellular proteomics : MCP

Stacey RG, Skinnider MA, Foster LJ.
PMID: 33592499
Mol Cell Proteomics. 2021;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24.

Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as...

Cite
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2020;20:100002doi: 10.1074/mcp.RA120.002275.
Stacey, R. G., Skinnider, M. A., & Foster, L. J. (2021). On the Robustness of Graph-Based Clustering to Random Network Alterations. Molecular & cellular proteomics : MCP, 20100002. https://doi.org/10.1074/mcp.RA120.002275
Stacey, R Greg, et al. "On the Robustness of Graph-Based Clustering to Random Network Alterations." Molecular & cellular proteomics : MCP vol. 20 (2021): 100002. doi: https://doi.org/10.1074/mcp.RA120.002275
Stacey RG, Skinnider MA, Foster LJ. On the Robustness of Graph-Based Clustering to Random Network Alterations. Mol Cell Proteomics. 2021;20:100002. doi: 10.1074/mcp.RA120.002275. Epub 2020 Nov 24. PMID: 33592499; PMCID: PMC7896145.
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Post-radiation epithelioid angiosarcoma of the urinary bladder and prostate.

Canadian Urological Association journal = Journal de l'Association des urologues du Canada

Wang G, Black PC, Skinnider BF, Hayes MM, Jones EC.
PMID: 27790305
Can Urol Assoc J. 2016 May-Jun;10(5):E197-E200. doi: 10.5489/cuaj.3220. Epub 2016 May 12.

Angiosarcoma of the lower urinary tract is exceedingly rare. A minority of cases are associated with local radiotherapy. Epithelioid angiosarcoma is a variant of angiosarcoma composed of large rounded epithelioid endothelial cells that are positive for cytokeratin on immunostaining....

Cite
Wang G, Black PC, Skinnider BF, et al. Post-radiation epithelioid angiosarcoma of the urinary bladder and prostate. Can Urol Assoc J. 2016;10(5):E197-E200doi: 10.5489/cuaj.3220.
Wang, G., Black, P. C., Skinnider, B. F., Hayes, M. M., & Jones, E. C. (2016). Post-radiation epithelioid angiosarcoma of the urinary bladder and prostate. Canadian Urological Association journal = Journal de l'Association des urologues du Canada, 10(5), E197-E200. https://doi.org/10.5489/cuaj.3220
Wang, Gang, et al. "Post-radiation epithelioid angiosarcoma of the urinary bladder and prostate." Canadian Urological Association journal = Journal de l'Association des urologues du Canada vol. 10,5 (2016): E197-E200. doi: https://doi.org/10.5489/cuaj.3220
Wang G, Black PC, Skinnider BF, Hayes MM, Jones EC. Post-radiation epithelioid angiosarcoma of the urinary bladder and prostate. Can Urol Assoc J. 2016 May-Jun;10(5):E197-E200. doi: 10.5489/cuaj.3220. Epub 2016 May 12. PMID: 27790305; PMCID: PMC5065413.
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An atlas of protein-protein interactions across mouse tissues.

Cell

Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ.
PMID: 34214469
Cell. 2021 Jul 22;184(15):4073-4089.e17. doi: 10.1016/j.cell.2021.06.003. Epub 2021 Jul 01.

Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here,...

Cite
Skinnider MA, Scott NE, Prudova A, et al. An atlas of protein-protein interactions across mouse tissues. Cell. 2021;184(15):4073-4089.e17doi: 10.1016/j.cell.2021.06.003.
Skinnider, M. A., Scott, N. E., Prudova, A., Kerr, C. H., Stoynov, N., Stacey, R. G., Chan, Q. W. T., Rattray, D., Gsponer, J., & Foster, L. J. (2021). An atlas of protein-protein interactions across mouse tissues. Cell, 184(15), 4073-4089.e17. https://doi.org/10.1016/j.cell.2021.06.003
Skinnider, Michael A, et al. "An atlas of protein-protein interactions across mouse tissues." Cell vol. 184,15 (2021): 4073-4089.e17. doi: https://doi.org/10.1016/j.cell.2021.06.003
Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell. 2021 Jul 22;184(15):4073-4089.e17. doi: 10.1016/j.cell.2021.06.003. Epub 2021 Jul 01. PMID: 34214469.
Copy Download .nbib Format: NLM
Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury.

Molecular & cellular proteomics : MCP

Skinnider MA, Rogalski J, Tigchelaar S, Manouchehri N, Prudova A, Jackson AM, Nielsen K, Jeong J, Chaudhary S, Shortt K, Gallagher-Kurtzke Y, So K, Fong A, Gupta R, Okon EB, Rizzuto MA, Dong K, Streijger F, Belanger L, Ritchie L, Tsang A, Christie S, Mac-Thiong JM, Bailey C, Ailon T, Charest-Morin R, Dea N, Wilson JR, Dhall S, Paquette S, Street J, Fisher CG, Dvorak MF, Shannon C, Borchers C, Balshaw R, Foster LJ, Kwon BK.
PMID: 34129941
Mol Cell Proteomics. 2021;20:100096. doi: 10.1016/j.mcpro.2021.100096. Epub 2021 Jun 12.

Despite the emergence of promising therapeutic approaches in preclinical studies, the failure of large-scale clinical trials leaves clinicians without effective treatments for acute spinal cord injury (SCI). These trials are hindered by their reliance on detailed neurological examinations to...

Cite
Skinnider MA, Rogalski J, Tigchelaar S, et al. Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Mol Cell Proteomics. 2021;20:100096doi: 10.1016/j.mcpro.2021.100096.
Skinnider, M. A., Rogalski, J., Tigchelaar, S., Manouchehri, N., Prudova, A., Jackson, A. M., Nielsen, K., Jeong, J., Chaudhary, S., Shortt, K., Gallagher-Kurtzke, Y., So, K., Fong, A., Gupta, R., Okon, E. B., Rizzuto, M. A., Dong, K., Streijger, F., Belanger, L., Ritchie, L., Tsang, A., Christie, S., Mac-Thiong, J. M., Bailey, C., Ailon, T., Charest-Morin, R., Dea, N., Wilson, J. R., Dhall, S., Paquette, S., Street, J., Fisher, C. G., Dvorak, M. F., Shannon, C., Borchers, C., Balshaw, R., Foster, L. J., & Kwon, B. K. (2021). Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Molecular & cellular proteomics : MCP, 20100096. https://doi.org/10.1016/j.mcpro.2021.100096
Skinnider, Michael A, et al. "Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury." Molecular & cellular proteomics : MCP vol. 20 (2021): 100096. doi: https://doi.org/10.1016/j.mcpro.2021.100096
Skinnider MA, Rogalski J, Tigchelaar S, Manouchehri N, Prudova A, Jackson AM, Nielsen K, Jeong J, Chaudhary S, Shortt K, Gallagher-Kurtzke Y, So K, Fong A, Gupta R, Okon EB, Rizzuto MA, Dong K, Streijger F, Belanger L, Ritchie L, Tsang A, Christie S, Mac-Thiong JM, Bailey C, Ailon T, Charest-Morin R, Dea N, Wilson JR, Dhall S, Paquette S, Street J, Fisher CG, Dvorak MF, Shannon C, Borchers C, Balshaw R, Foster LJ, Kwon BK. Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury. Mol Cell Proteomics. 2021;20:100096. doi: 10.1016/j.mcpro.2021.100096. Epub 2021 Jun 12. PMID: 34129941; PMCID: PMC8260874.
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Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

Journal of cheminformatics

Skinnider MA, Dejong CA, Franczak BC, McNicholas PD, Magarvey NA.
PMID: 29086195
J Cheminform. 2017 Aug 16;9(1):46. doi: 10.1186/s13321-017-0234-y.

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of...

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Skinnider MA, Dejong CA, Franczak BC, et al. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. J Cheminform. 2017;9(1):46doi: 10.1186/s13321-017-0234-y.
Skinnider, M. A., Dejong, C. A., Franczak, B. C., McNicholas, P. D., & Magarvey, N. A. (2017). Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. Journal of cheminformatics, 9(1), 46. https://doi.org/10.1186/s13321-017-0234-y
Skinnider, Michael A, et al. "Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm." Journal of cheminformatics vol. 9,1 (2017): 46. doi: https://doi.org/10.1186/s13321-017-0234-y
Skinnider MA, Dejong CA, Franczak BC, McNicholas PD, Magarvey NA. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. J Cheminform. 2017 Aug 16;9(1):46. doi: 10.1186/s13321-017-0234-y. PMID: 29086195; PMCID: PMC5559407.
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PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data.

Bioinformatics (Oxford, England)

Skinnider MA, Cai C, Stacey RG, Foster LJ.
PMID: 33471077
Bioinformatics. 2021 Jan 20; doi: 10.1093/bioinformatics/btab022. Epub 2021 Jan 20.

SUMMARY: We present PrInCE, an R/Bioconductor package that employs a machine-learning approach to infer protein-protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in...

Cite
Skinnider MA, Cai C, Stacey RG, et al. PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab022.
Skinnider, M. A., Cai, C., Stacey, R. G., & Foster, L. J. (2021). PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab022
Skinnider, Michael A, et al. "PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab022
Skinnider MA, Cai C, Stacey RG, Foster LJ. PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. Bioinformatics. 2021 Jan 20; doi: 10.1093/bioinformatics/btab022. Epub 2021 Jan 20. PMID: 33471077.
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Adrenalitis and anasarca in idiopathic multicentric Castleman's disease.

Lancet (London, England)

Chen LYC, Skinnider BF, Wilson D, Fajgenbaum DC.
PMID: 33965090
Lancet. 2021 May 08;397(10286):1749. doi: 10.1016/S0140-6736(21)00674-7.

No abstract available.

Cite
Chen LYC, Skinnider BF, Wilson D, et al. Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet. 2021;397(10286):1749doi: 10.1016/S0140-6736(21)00674-7.
Chen, L. Y. C., Skinnider, B. F., Wilson, D., & Fajgenbaum, D. C. (2021). Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet (London, England), 397(10286), 1749. https://doi.org/10.1016/S0140-6736(21)00674-7
Chen, Luke Y C, et al. "Adrenalitis and anasarca in idiopathic multicentric Castleman's disease." Lancet (London, England) vol. 397,10286 (2021): 1749. doi: https://doi.org/10.1016/S0140-6736(21)00674-7
Chen LYC, Skinnider BF, Wilson D, Fajgenbaum DC. Adrenalitis and anasarca in idiopathic multicentric Castleman's disease. Lancet. 2021 May 08;397(10286):1749. doi: 10.1016/S0140-6736(21)00674-7. PMID: 33965090.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 16 entries