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Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk.

International journal of cancer

Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H.
PMID: 31577861
Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31.

Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple...

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Dai J, Huang M, Amos CI, et al. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2019;146(10):2855-2864doi: 10.1002/ijc.32698.
Dai, J., Huang, M., Amos, C. I., Hung, R. J., Tardon, A., Andrew, A., Chen, C., Christiani, D. C., Albanes, D., Rennert, G., Fan, J., Goodman, G., Liu, G., Field, J. K., Grankvist, K., Kiemeney, L. A., Le Marchand, L., Schabath, M. B., Johansson, M., Aldrich, M. C., Johansson, M., Caporaso, N., Lazarus, P., Lam, S., Bojesen, S. E., Arnold, S., Landi, M. T., Risch, A., Wichmann, H. E., Bickeboller, H., Brennan, P., Shete, S., Melander, O., Brunnstrom, H., Zienolddiny, S., Woll, P., Stevens, V., Hu, Z., & Shen, H. (2020). Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. International journal of cancer, 146(10), 2855-2864. https://doi.org/10.1002/ijc.32698
Dai, Juncheng, et al. "Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk." International journal of cancer vol. 146,10 (2020): 2855-2864. doi: https://doi.org/10.1002/ijc.32698
Dai J, Huang M, Amos CI, Hung RJ, Tardon A, Andrew A, Chen C, Christiani DC, Albanes D, Rennert G, Fan J, Goodman G, Liu G, Field JK, Grankvist K, Kiemeney LA, Le Marchand L, Schabath MB, Johansson M, Aldrich MC, Johansson M, Caporaso N, Lazarus P, Lam S, Bojesen SE, Arnold S, Landi MT, Risch A, Wichmann HE, Bickeboller H, Brennan P, Shete S, Melander O, Brunnstrom H, Zienolddiny S, Woll P, Stevens V, Hu Z, Shen H. Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. Int J Cancer. 2020 May 15;146(10):2855-2864. doi: 10.1002/ijc.32698. Epub 2019 Oct 31. PMID: 31577861; PMCID: PMC7101262.
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Critical role of Shp2 in tumor growth involving regulation of c-Myc.

Genes & cancer

Ren Y, Chen Z, Chen L, Fang B, Win-Piazza H, Haura E, Koomen JM, Wu J.
PMID: 21442024
Genes Cancer. 2010 Oct;1(10):994-1007. doi: 10.1177/1947601910395582.

Activating mutants of Shp2 protein tyrosine phosphatase, encoded by the PTPN11 gene, are linked to leukemia. In solid tumors, however, PTPN11 mutations occur at low frequencies while the wildtype Shp2 is activated by protein tyrosine kinases (PTKs) in cancer...

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Ren Y, Chen Z, Chen L, et al. Critical role of Shp2 in tumor growth involving regulation of c-Myc. Genes Cancer. 2010;1(10):994-1007doi: 10.1177/1947601910395582.
Ren, Y., Chen, Z., Chen, L., Fang, B., Win-Piazza, H., Haura, E., Koomen, J. M., & Wu, J. (2010). Critical role of Shp2 in tumor growth involving regulation of c-Myc. Genes & cancer, 1(10), 994-1007. https://doi.org/10.1177/1947601910395582
Ren, Yuan, et al. "Critical role of Shp2 in tumor growth involving regulation of c-Myc." Genes & cancer vol. 1,10 (2010): 994-1007. doi: https://doi.org/10.1177/1947601910395582
Ren Y, Chen Z, Chen L, Fang B, Win-Piazza H, Haura E, Koomen JM, Wu J. Critical role of Shp2 in tumor growth involving regulation of c-Myc. Genes Cancer. 2010 Oct;1(10):994-1007. doi: 10.1177/1947601910395582. PMID: 21442024; PMCID: PMC3063420.
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Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development.

Oncotarget

Li Y, Xiao X, Bossé Y, Gorlova O, Gorlov I, Han Y, Byun J, Leighl N, Johansen JS, Barnett M, Chen C, Goodman G, Cox A, Taylor F, Woll P, Wichmann HE, Manz J, Muley T, Risch A, Rosenberger A, Han J, Siminovitch K, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Houlston R, Artigas MS, Grankvist K, Johansson M, Shepherd FA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Liu G, Bojesen SE, Wu X, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Bertazzi PA, Pesatori AC, Christiani DC, Caporaso N, Johansson M, McKay JD, Brennan P, Hung RJ, Amos CI.
PMID: 30956756
Oncotarget. 2019 Mar 05;10(19):1760-1774. doi: 10.18632/oncotarget.26678. eCollection 2019 Mar 05.

The development of cancer is driven by the accumulation of many oncogenesis-related genetic alterations and tumorigenesis is triggered by complex networks of involved genes rather than independent actions. To explore the epistasis existing among oncogenesis-related genes in lung cancer...

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Li Y, Xiao X, Bossé Y, et al. Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development. Oncotarget. 2019;10(19):1760-1774doi: 10.18632/oncotarget.26678.
Li, Y., Xiao, X., Bossé, Y., Gorlova, O., Gorlov, I., Han, Y., Byun, J., Leighl, N., Johansen, J. S., Barnett, M., Chen, C., Goodman, G., Cox, A., Taylor, F., Woll, P., Wichmann, H. E., Manz, J., Muley, T., Risch, A., Rosenberger, A., Han, J., Siminovitch, K., Arnold, S. M., Haura, E. B., Bolca, C., Holcatova, I., Janout, V., Kontic, M., Lissowska, J., Mukeria, A., Ognjanovic, S., Orlowski, T. M., Scelo, G., Swiatkowska, B., Zaridze, D., Bakke, P., Skaug, V., Zienolddiny, S., Duell, E. J., Butler, L. M., Houlston, R., Artigas, M. S., Grankvist, K., Johansson, M., Shepherd, F. A., Marcus, M. W., Brunnström, H., Manjer, J., Melander, O., Muller, D. C., Overvad, K., Trichopoulou, A., Tumino, R., Liu, G., Bojesen, S. E., Wu, X., Le Marchand, L., Albanes, D., Bickeböller, H., Aldrich, M. C., Bush, W. S., Tardon, A., Rennert, G., Teare, M. D., Field, J. K., Kiemeney, L. A., Lazarus, P., Haugen, A., Lam, S., Schabath, M. B., Andrew, A. S., Bertazzi, P. A., Pesatori, A. C., Christiani, D. C., Caporaso, N., Johansson, M., McKay, J. D., Brennan, P., Hung, R. J., & Amos, C. I. (2019). Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development. Oncotarget, 10(19), 1760-1774. https://doi.org/10.18632/oncotarget.26678
Li, Yafang, et al. "Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development." Oncotarget vol. 10,19 (2019): 1760-1774. doi: https://doi.org/10.18632/oncotarget.26678
Li Y, Xiao X, Bossé Y, Gorlova O, Gorlov I, Han Y, Byun J, Leighl N, Johansen JS, Barnett M, Chen C, Goodman G, Cox A, Taylor F, Woll P, Wichmann HE, Manz J, Muley T, Risch A, Rosenberger A, Han J, Siminovitch K, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Houlston R, Artigas MS, Grankvist K, Johansson M, Shepherd FA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Liu G, Bojesen SE, Wu X, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Bertazzi PA, Pesatori AC, Christiani DC, Caporaso N, Johansson M, McKay JD, Brennan P, Hung RJ, Amos CI. Genetic interaction analysis among oncogenesis-related genes revealed novel genes and networks in lung cancer development. Oncotarget. 2019 Mar 05;10(19):1760-1774. doi: 10.18632/oncotarget.26678. eCollection 2019 Mar 05. PMID: 30956756; PMCID: PMC6442994.
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Integrating omics technologies to study pulmonary physiology and pathology at the systems level.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

Pathak RR, Davé V.
PMID: 24802001
Cell Physiol Biochem. 2014;33(5):1239-60. doi: 10.1159/000358693. Epub 2014 Apr 28.

Assimilation and integration of "omics" technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular...

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Pathak RR, Davé V. Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cell Physiol Biochem. 2014;33(5):1239-60doi: 10.1159/000358693.
Pathak, R. R., & Davé, V. (2014). Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 33(5), 1239-60. https://doi.org/10.1159/000358693
Pathak, Ravi Ramesh, and Davé, Vrushank. "Integrating omics technologies to study pulmonary physiology and pathology at the systems level." Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology vol. 33,5 (2014): 1239-60. doi: https://doi.org/10.1159/000358693
Pathak RR, Davé V. Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cell Physiol Biochem. 2014;33(5):1239-60. doi: 10.1159/000358693. Epub 2014 Apr 28. PMID: 24802001; PMCID: PMC4396816.
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Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer.

Proteomes

Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB.
PMID: 28154798
Proteomes. 2016 Apr 27;4(2):16. doi: 10.3390/proteomes4020016. eCollection 2016 Jun.

One way cancer cells can escape from targeted agents is through their ability to evade drug effects by rapidly rewiring signaling networks. Many protein classes, such as kinases and metabolic enzymes, are regulated by ATP binding and hydrolysis. We...

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Kim JY, Stewart PA, Borne AL, et al. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016;4(2):16doi: 10.3390/proteomes4020016.
Kim, J. Y., Stewart, P. A., Borne, A. L., Fang, B., Welsh, E. A., Chen, Y. A., Eschrich, S. A., Koomen, J. M., & Haura, E. B. (2016). Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes, 4(2), 16. https://doi.org/10.3390/proteomes4020016
Kim, Jae-Young, et al. "Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer." Proteomes vol. 4,2 (2016): 16. doi: https://doi.org/10.3390/proteomes4020016
Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Apr 27;4(2):16. doi: 10.3390/proteomes4020016. eCollection 2016 Jun. PMID: 28154798; PMCID: PMC5217344.
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Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures.

International journal of genomics

Berglund AE, Welsh EA, Eschrich SA.
PMID: 28265563
Int J Genomics. 2017;2017:2354564. doi: 10.1155/2017/2354564. Epub 2017 Feb 06.

UNIQUENESS: the general direction of the data being examined can drive most of the observed signal. Robustness: if a gene signature is designed to measure a single biological effect, then this signal should be sufficiently strong and distinct compared...

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Berglund AE, Welsh EA, Eschrich SA. Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. Int J Genomics. 2017;2017:2354564doi: 10.1155/2017/2354564.
Berglund, A. E., Welsh, E. A., & Eschrich, S. A. (2017). Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. International journal of genomics, 20172354564. https://doi.org/10.1155/2017/2354564
Berglund, Anders E, et al. "Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures." International journal of genomics vol. 2017 (2017): 2354564. doi: https://doi.org/10.1155/2017/2354564
Berglund AE, Welsh EA, Eschrich SA. Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. Int J Genomics. 2017;2017:2354564. doi: 10.1155/2017/2354564. Epub 2017 Feb 06. PMID: 28265563; PMCID: PMC5317117.
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Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes.

Journal of integrated OMICS

Haura EB, Sacco R, Li J, Müller AC, Grebien F, Superti-Furga G, Bennett KL.
PMID: 24077984
J Integr OMICS. 2012 May;2(1):55-68. doi: 10.5584/jiomics.v2i1.81.

In this study we show that via stable, retroviral-expression of tagged EGFR del (L747-S752 deletion mutant) in the PC9 lung cancer cell line and stable doxycycline-inducible expression of tagged Grb2 using a Flp-mediated recombination HEK293 cell system, the SH-TAP...

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Haura EB, Sacco R, Li J, et al. Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. J Integr OMICS. 2012;2(1):55-68doi: 10.5584/jiomics.v2i1.81.
Haura, E. B., Sacco, R., Li, J., Müller, A. C., Grebien, F., Superti-Furga, G., & Bennett, K. L. (2012). Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. Journal of integrated OMICS, 2(1), 55-68. https://doi.org/10.5584/jiomics.v2i1.81
Haura, Eric B, et al. "Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes." Journal of integrated OMICS vol. 2,1 (2012): 55-68. doi: https://doi.org/10.5584/jiomics.v2i1.81
Haura EB, Sacco R, Li J, Müller AC, Grebien F, Superti-Furga G, Bennett KL. Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. J Integr OMICS. 2012 May;2(1):55-68. doi: 10.5584/jiomics.v2i1.81. PMID: 24077984; PMCID: PMC3785125.
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Computational methods and opportunities for phosphorylation network medicine.

Translational cancer research

Chen YA, Eschrich SA.
PMID: 25530950
Transl Cancer Res. 2014 Jun 01;3(3):266-278.

Protein phosphorylation, one of the most ubiquitous post-translational modifications (PTM) of proteins, is known to play an essential role in cell signaling and regulation. With the increasing understanding of the complexity and redundancy of cell signaling, there is a...

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Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res. 2014;3(3):266-278
Chen, Y. A., & Eschrich, S. A. (2014). Computational methods and opportunities for phosphorylation network medicine. Translational cancer research, 3(3), 266-278.
Chen, Yian Ann, and Eschrich, Steven A. "Computational methods and opportunities for phosphorylation network medicine." Translational cancer research vol. 3,3 (2014): 266-278.
Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res. 2014 Jun 01;3(3):266-278. PMID: 25530950; PMCID: PMC4271781.
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Indoleamine 2,3-dioxygenase activity and clinical outcome following induction chemotherapy and concurrent chemoradiation in Stage III non-small cell lung cancer.

Oncoimmunology

Creelan BC, Antonia S, Bepler G, Garrett TJ, Simon GR, Soliman HH.
PMID: 23802083
Oncoimmunology. 2013 Mar 01;2(3):e23428. doi: 10.4161/onci.23428.

Indoleamine 2,3-dioxygenase (IDO) has recently been proposed to account for tumor-induced immunosuppression by influencing the conversion of tryptophan (Trp) into kynurenine (Kyn). The objective of our study was to correlate IDO activity with disease outcome in non-small cell lung...

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Creelan BC, Antonia S, Bepler G, et al. Indoleamine 2,3-dioxygenase activity and clinical outcome following induction chemotherapy and concurrent chemoradiation in Stage III non-small cell lung cancer. Oncoimmunology. 2013;2(3):e23428doi: 10.4161/onci.23428.
Creelan, B. C., Antonia, S., Bepler, G., Garrett, T. J., Simon, G. R., & Soliman, H. H. (2013). Indoleamine 2,3-dioxygenase activity and clinical outcome following induction chemotherapy and concurrent chemoradiation in Stage III non-small cell lung cancer. Oncoimmunology, 2(3), e23428. https://doi.org/10.4161/onci.23428
Creelan, Ben C, et al. "Indoleamine 2,3-dioxygenase activity and clinical outcome following induction chemotherapy and concurrent chemoradiation in Stage III non-small cell lung cancer." Oncoimmunology vol. 2,3 (2013): e23428. doi: https://doi.org/10.4161/onci.23428
Creelan BC, Antonia S, Bepler G, Garrett TJ, Simon GR, Soliman HH. Indoleamine 2,3-dioxygenase activity and clinical outcome following induction chemotherapy and concurrent chemoradiation in Stage III non-small cell lung cancer. Oncoimmunology. 2013 Mar 01;2(3):e23428. doi: 10.4161/onci.23428. PMID: 23802083; PMCID: PMC3661168.
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Cell-surface marker discovery for lung cancer.

Oncotarget

Cohen AS, Khalil FK, Welsh EA, Schabath MB, Enkemann SA, Davis A, Zhou JM, Boulware DC, Kim J, Haura EB, Morse DL.
PMID: 29371917
Oncotarget. 2017 Dec 07;8(69):113373-113402. doi: 10.18632/oncotarget.23009. eCollection 2017 Dec 26.

Lung cancer is the leading cause of cancer deaths in the United States. Novel lung cancer targeted therapeutic and molecular imaging agents are needed to improve outcomes and enable personalized care. Since these agents typically cannot cross the plasma...

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Cohen AS, Khalil FK, Welsh EA, et al. Cell-surface marker discovery for lung cancer. Oncotarget. 2017;8(69):113373-113402doi: 10.18632/oncotarget.23009.
Cohen, A. S., Khalil, F. K., Welsh, E. A., Schabath, M. B., Enkemann, S. A., Davis, A., Zhou, J. M., Boulware, D. C., Kim, J., Haura, E. B., & Morse, D. L. (2017). Cell-surface marker discovery for lung cancer. Oncotarget, 8(69), 113373-113402. https://doi.org/10.18632/oncotarget.23009
Cohen, Allison S, et al. "Cell-surface marker discovery for lung cancer." Oncotarget vol. 8,69 (2017): 113373-113402. doi: https://doi.org/10.18632/oncotarget.23009
Cohen AS, Khalil FK, Welsh EA, Schabath MB, Enkemann SA, Davis A, Zhou JM, Boulware DC, Kim J, Haura EB, Morse DL. Cell-surface marker discovery for lung cancer. Oncotarget. 2017 Dec 07;8(69):113373-113402. doi: 10.18632/oncotarget.23009. eCollection 2017 Dec 26. PMID: 29371917; PMCID: PMC5768334.
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