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Recommendations for the packaging and containerizing of bioinformatics software.

F1000Research

Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y.
PMID: 31543945
F1000Res. 2018 Jun 14;7. doi: 10.12688/f1000research.15140.2. eCollection 2018.

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis...

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Gruening B, Sallou O, Moreno P, et al. Recommendations for the packaging and containerizing of bioinformatics software. F1000Res. 2018;7doi: 10.12688/f1000research.15140.2.
Gruening, B., Sallou, O., Moreno, P., da Veiga Leprevost, F., Ménager, H., Søndergaard, D., Röst, H., Sachsenberg, T., O'Connor, B., Madeira, F., Dominguez Del Angel, V., Crusoe, M. R., Varma, S., Blankenberg, D., Jimenez, R. C., & Perez-Riverol, Y. (2018). Recommendations for the packaging and containerizing of bioinformatics software. F1000Research, 7. https://doi.org/10.12688/f1000research.15140.2
Gruening, Bjorn, et al. "Recommendations for the packaging and containerizing of bioinformatics software." F1000Research vol. 7 (2018). doi: https://doi.org/10.12688/f1000research.15140.2
Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y. Recommendations for the packaging and containerizing of bioinformatics software. F1000Res. 2018 Jun 14;7. doi: 10.12688/f1000research.15140.2. eCollection 2018. PMID: 31543945; PMCID: PMC6738188.
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PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.

Molecular & cellular proteomics : MCP

Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI.
PMID: 33568339
Mol Cell Proteomics. 2021;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub 2020 Dec 11.

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift...

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Geiszler DJ, Kong AT, Avtonomov DM, et al. PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Mol Cell Proteomics. 2020;20:100018doi: 10.1074/mcp.TIR120.002216.
Geiszler, D. J., Kong, A. T., Avtonomov, D. M., Yu, F., Leprevost, F. D. V., & Nesvizhskii, A. I. (2021). PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Molecular & cellular proteomics : MCP, 20100018. https://doi.org/10.1074/mcp.TIR120.002216
Geiszler, Daniel J, et al. "PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results." Molecular & cellular proteomics : MCP vol. 20 (2021): 100018. doi: https://doi.org/10.1074/mcp.TIR120.002216
Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI. PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Mol Cell Proteomics. 2021;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub 2020 Dec 11. PMID: 33568339; PMCID: PMC7950090.
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Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.

Journal of proteome research

Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y.
PMID: 33393786
J Proteome Res. 2021 Feb 05;20(2):1178-1189. doi: 10.1021/acs.jproteome.0c00359. Epub 2021 Jan 04.

When the JCVI-syn3.0 genome was designed and implemented in 2016 as the minimal genome of a free-living organism, approximately one-third of the 438 protein-coding genes had no known function. Subsequent refinement into JCVI-syn3A led to inclusion of 16 additional...

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Zhang C, Zheng W, Cheng M, et al. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. J Proteome Res. 2021;20(2):1178-1189doi: 10.1021/acs.jproteome.0c00359.
Zhang, C., Zheng, W., Cheng, M., Omenn, G. S., Freddolino, P. L., & Zhang, Y. (2021). Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of proteome research, 20(2), 1178-1189. https://doi.org/10.1021/acs.jproteome.0c00359
Zhang, Chengxin, et al. "Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome." Journal of proteome research vol. 20,2 (2021): 1178-1189. doi: https://doi.org/10.1021/acs.jproteome.0c00359
Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. J Proteome Res. 2021 Feb 05;20(2):1178-1189. doi: 10.1021/acs.jproteome.0c00359. Epub 2021 Jan 04. PMID: 33393786; PMCID: PMC7867644.
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IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.

Molecular & cellular proteomics : MCP

Yu F, Haynes SE, Nesvizhskii AI.
PMID: 33813065
Mol Cell Proteomics. 2021 Apr 02;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02.

Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem...

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Yu F, Haynes SE, Nesvizhskii AI. IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics. 2021;20:100077doi: 10.1016/j.mcpro.2021.100077.
Yu, F., Haynes, S. E., & Nesvizhskii, A. I. (2021). IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Molecular & cellular proteomics : MCP, 20100077. https://doi.org/10.1016/j.mcpro.2021.100077
Yu, Fengchao, et al. "IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs." Molecular & cellular proteomics : MCP vol. 20 (2021): 100077. doi: https://doi.org/10.1016/j.mcpro.2021.100077
Yu F, Haynes SE, Nesvizhskii AI. IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics. 2021 Apr 02;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02. PMID: 33813065; PMCID: PMC8131922.
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Philosopher: a versatile toolkit for shotgun proteomics data analysis.

Nature methods

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
PMID: 32669682
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y.

No abstract available.

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da Veiga Leprevost F, Haynes SE, Avtonomov DM, et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020;17(9):869-870doi: 10.1038/s41592-020-0912-y.
da Veiga Leprevost, F., Haynes, S. E., Avtonomov, D. M., Chang, H. Y., Shanmugam, A. K., Mellacheruvu, D., Kong, A. T., & Nesvizhskii, A. I. (2020). Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nature methods, 17(9), 869-870. https://doi.org/10.1038/s41592-020-0912-y
da Veiga Leprevost, Felipe, et al. "Philosopher: a versatile toolkit for shotgun proteomics data analysis." Nature methods vol. 17,9 (2020): 869-870. doi: https://doi.org/10.1038/s41592-020-0912-y
da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.
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Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma.

Hepatology communications

Alcedo KP, Guerrero A, Basrur V, Fu D, Richardson ML, McLane JS, Tsou CC, Nesvizhskii AI, Welling TH, Lebrilla CB, Otey CA, Kim HJ, Omary MB, Snider NT.
PMID: 31592495
Hepatol Commun. 2019 Aug 09;3(10):1400-1414. doi: 10.1002/hep4.1410. eCollection 2019 Oct.

CD73, a cell-surface

Cite
Alcedo KP, Guerrero A, Basrur V, et al. Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma. Hepatol Commun. 2019;3(10):1400-1414doi: 10.1002/hep4.1410.
Alcedo, K. P., Guerrero, A., Basrur, V., Fu, D., Richardson, M. L., McLane, J. S., Tsou, C. C., Nesvizhskii, A. I., Welling, T. H., Lebrilla, C. B., Otey, C. A., Kim, H. J., Omary, M. B., & Snider, N. T. (2019). Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma. Hepatology communications, 3(10), 1400-1414. https://doi.org/10.1002/hep4.1410
Alcedo, Karel P, et al. "Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma." Hepatology communications vol. 3,10 (2019): 1400-1414. doi: https://doi.org/10.1002/hep4.1410
Alcedo KP, Guerrero A, Basrur V, Fu D, Richardson ML, McLane JS, Tsou CC, Nesvizhskii AI, Welling TH, Lebrilla CB, Otey CA, Kim HJ, Omary MB, Snider NT. Tumor-Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma. Hepatol Commun. 2019 Aug 09;3(10):1400-1414. doi: 10.1002/hep4.1410. eCollection 2019 Oct. PMID: 31592495; PMCID: PMC6771166.
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IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.

Molecular & cellular proteomics : MCP

Yu F, Haynes SE, Nesvizhskii AI.
PMID: 33813065
Mol Cell Proteomics. 2021;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02.

Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem...

Cite
Yu F, Haynes SE, Nesvizhskii AI. IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics. 2021;20:100077doi: 10.1016/j.mcpro.2021.100077.
Yu, F., Haynes, S. E., & Nesvizhskii, A. I. (2021). IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Molecular & cellular proteomics : MCP, 20100077. https://doi.org/10.1016/j.mcpro.2021.100077
Yu, Fengchao, et al. "IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs." Molecular & cellular proteomics : MCP vol. 20 (2021): 100077. doi: https://doi.org/10.1016/j.mcpro.2021.100077
Yu F, Haynes SE, Nesvizhskii AI. IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics. 2021;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 02. PMID: 33813065; PMCID: PMC8131922.
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Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks.

Nature communications

Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B.
PMID: 34857745
Nat Commun. 2021 Dec 02;12(1):7036. doi: 10.1038/s41467-021-27280-x.

The molecular nanoscale organization of the surfaceome is a fundamental regulator of cellular signaling in health and disease. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would unlock theranostic opportunities to target...

Cite
Müller M, Gräbnitz F, Barandun N, et al. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nat Commun. 2021;12(1):7036doi: 10.1038/s41467-021-27280-x.
Müller, M., Gräbnitz, F., Barandun, N., Shen, Y., Wendt, F., Steiner, S. N., Severin, Y., Vetterli, S. U., Mondal, M., Prudent, J. R., Hofmann, R., van Oostrum, M., Sarott, R. C., Nesvizhskii, A. I., Carreira, E. M., Bode, J. W., Snijder, B., Robinson, J. A., Loessner, M. J., Oxenius, A., & Wollscheid, B. (2021). Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nature communications, 12(1), 7036. https://doi.org/10.1038/s41467-021-27280-x
Müller, Maik, et al. "Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks." Nature communications vol. 12,1 (2021): 7036. doi: https://doi.org/10.1038/s41467-021-27280-x
Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nat Commun. 2021 Dec 02;12(1):7036. doi: 10.1038/s41467-021-27280-x. PMID: 34857745; PMCID: PMC8639842.
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Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cell

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H.
PMID: 34534465
Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal...

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Cao L, Huang C, Cui Zhou D, et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184(19):5031-5052.e26doi: 10.1016/j.cell.2021.08.023.
Cao, L., Huang, C., Cui Zhou, D., Hu, Y., Lih, T. M., Savage, S. R., Krug, K., Clark, D. J., Schnaubelt, M., Chen, L., da Veiga Leprevost, F., Eguez, R. V., Yang, W., Pan, J., Wen, B., Dou, Y., Jiang, W., Liao, Y., Shi, Z., Terekhanova, N. V., Cao, S., Lu, R. J., Li, Y., Liu, R., Zhu, H., Ronning, P., Wu, Y., Wyczalkowski, M. A., Easwaran, H., Danilova, L., Mer, A. S., Yoo, S., Wang, J. M., Liu, W., Haibe-Kains, B., Thiagarajan, M., Jewell, S. D., Hostetter, G., Newton, C. J., Li, Q. K., Roehrl, M. H., Fenyö, D., Wang, P., Nesvizhskii, A. I., Mani, D. R., Omenn, G. S., Boja, E. S., Mesri, M., Robles, A. I., Rodriguez, H., Bathe, O. F., Chan, D. W., Hruban, R. H., Ding, L., Zhang, B., Zhang, H. (2021). Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell, 184(19), 5031-5052.e26. https://doi.org/10.1016/j.cell.2021.08.023
Cao, Liwei, et al. "Proteogenomic characterization of pancreatic ductal adenocarcinoma." Cell vol. 184,19 (2021): 5031-5052.e26. doi: https://doi.org/10.1016/j.cell.2021.08.023
Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. PMID: 34534465; PMCID: PMC8654574.
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Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years.

Molecular & cellular proteomics : MCP

Omenn GS.
PMID: 33640492
Mol Cell Proteomics. 2021;20:100062. doi: 10.1016/j.mcpro.2021.100062. Epub 2021 Feb 26.

We celebrate the 10th anniversary of the launch of the HUPO Human Proteome Project (HPP) and its major milestone of confident detection of at least one protein from each of 90% of the predicted protein-coding genes, based on the...

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Omenn GS. Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Mol Cell Proteomics. 2021;20:100062doi: 10.1016/j.mcpro.2021.100062.
Omenn, G. S. (2021). Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Molecular & cellular proteomics : MCP, 20100062. https://doi.org/10.1016/j.mcpro.2021.100062
Omenn, Gilbert S. "Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years." Molecular & cellular proteomics : MCP vol. 20 (2021): 100062. doi: https://doi.org/10.1016/j.mcpro.2021.100062
Omenn GS. Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Mol Cell Proteomics. 2021;20:100062. doi: 10.1016/j.mcpro.2021.100062. Epub 2021 Feb 26. PMID: 33640492; PMCID: PMC8058560.
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Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks.

Nature communications

Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B.
PMID: 34857745
Nat Commun. 2021 Dec 02;12(1):7036. doi: 10.1038/s41467-021-27280-x.

The molecular nanoscale organization of the surfaceome is a fundamental regulator of cellular signaling in health and disease. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would unlock theranostic opportunities to target...

Cite
Müller M, Gräbnitz F, Barandun N, et al. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nat Commun. 2021;12(1):7036doi: 10.1038/s41467-021-27280-x.
Müller, M., Gräbnitz, F., Barandun, N., Shen, Y., Wendt, F., Steiner, S. N., Severin, Y., Vetterli, S. U., Mondal, M., Prudent, J. R., Hofmann, R., van Oostrum, M., Sarott, R. C., Nesvizhskii, A. I., Carreira, E. M., Bode, J. W., Snijder, B., Robinson, J. A., Loessner, M. J., Oxenius, A., & Wollscheid, B. (2021). Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nature communications, 12(1), 7036. https://doi.org/10.1038/s41467-021-27280-x
Müller, Maik, et al. "Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks." Nature communications vol. 12,1 (2021): 7036. doi: https://doi.org/10.1038/s41467-021-27280-x
Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nat Commun. 2021 Dec 02;12(1):7036. doi: 10.1038/s41467-021-27280-x. PMID: 34857745; PMCID: PMC8639842.
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Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response.

Proceedings of the National Academy of Sciences of the United States of America

Zhang Y, Narayanan SP, Mannan R, Raskind G, Wang X, Vats P, Su F, Hosseini N, Cao X, Kumar-Sinha C, Ellison SJ, Giordano TJ, Morgan TM, Pitchiaya S, Alva A, Mehra R, Cieslik M, Dhanasekaran SM, Chinnaiyan AM.
PMID: 34099557
Proc Natl Acad Sci U S A. 2021 Jun 15;118(24). doi: 10.1073/pnas.2103240118.

Diverse subtypes of renal cell carcinomas (RCCs) display a wide spectrum of histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical behavior. Delineating the cells of origin for different RCC subtypes will provide mechanistic insights into their diverse pathobiology....

Cite
Zhang Y, Narayanan SP, Mannan R, et al. Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response. Proc Natl Acad Sci U S A. 2021;118(24)doi: 10.1073/pnas.2103240118.
Zhang, Y., Narayanan, S. P., Mannan, R., Raskind, G., Wang, X., Vats, P., Su, F., Hosseini, N., Cao, X., Kumar-Sinha, C., Ellison, S. J., Giordano, T. J., Morgan, T. M., Pitchiaya, S., Alva, A., Mehra, R., Cieslik, M., Dhanasekaran, S. M., & Chinnaiyan, A. M. (2021). Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response. Proceedings of the National Academy of Sciences of the United States of America, 118(24), . https://doi.org/10.1073/pnas.2103240118
Zhang, Yuping, et al. "Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response." Proceedings of the National Academy of Sciences of the United States of America vol. 118,24 (2021). doi: https://doi.org/10.1073/pnas.2103240118
Zhang Y, Narayanan SP, Mannan R, Raskind G, Wang X, Vats P, Su F, Hosseini N, Cao X, Kumar-Sinha C, Ellison SJ, Giordano TJ, Morgan TM, Pitchiaya S, Alva A, Mehra R, Cieslik M, Dhanasekaran SM, Chinnaiyan AM. Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response. Proc Natl Acad Sci U S A. 2021 Jun 15;118(24). doi: 10.1073/pnas.2103240118. PMID: 34099557; PMCID: PMC8214680.
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