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Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method.

Cancer informatics

Ryu S, Gallis B, Goo YA, Shaffer SA, Radulovic D, Goodlett DR.
PMID: 19259412
Cancer Inform. 2008;6:243-55. doi: 10.4137/cin.s385. Epub 2008 Apr 17.

Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing...

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Ryu S, Gallis B, Goo YA, et al. Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform. 2008;6:243-55doi: 10.4137/cin.s385.
Ryu, S., Gallis, B., Goo, Y. A., Shaffer, S. A., Radulovic, D., & Goodlett, D. R. (2008). Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer informatics, 6243-55. https://doi.org/10.4137/cin.s385
Ryu, Soyoung, et al. "Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method." Cancer informatics vol. 6 (2008): 243-55. doi: https://doi.org/10.4137/cin.s385
Ryu S, Gallis B, Goo YA, Shaffer SA, Radulovic D, Goodlett DR. Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform. 2008;6:243-55. doi: 10.4137/cin.s385. Epub 2008 Apr 17. PMID: 19259412; PMCID: PMC2623286.
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Proteomics on Fixed Tissue Specimens - A Review.

Current proteomics

Reimel BA, Pan S, May DH, Shaffer SA, Goodlett DR, McIntosh MW, Yerian LM, Bronner MP, Chen R, Brentnall TA.
PMID: 19829741
Curr Proteomics. 2009 Apr 01;6(1):63-69. doi: 10.2174/157016409787847420.

The vast majority of clinical tissue samples are formalin-fixed and paraffin-preserved. This type of preservation has been considered an obstacle to protein extraction from these tissues. However, these are the very tissue samples that have associated patient histories, diagnoses...

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Reimel BA, Pan S, May DH, et al. Proteomics on Fixed Tissue Specimens - A Review. Curr Proteomics. 2009;6(1):63-69doi: 10.2174/157016409787847420.
Reimel, B. A., Pan, S., May, D. H., Shaffer, S. A., Goodlett, D. R., McIntosh, M. W., Yerian, L. M., Bronner, M. P., Chen, R., & Brentnall, T. A. (2009). Proteomics on Fixed Tissue Specimens - A Review. Current proteomics, 6(1), 63-69. https://doi.org/10.2174/157016409787847420
Reimel, Beth Ann, et al. "Proteomics on Fixed Tissue Specimens - A Review." Current proteomics vol. 6,1 (2009): 63-69. doi: https://doi.org/10.2174/157016409787847420
Reimel BA, Pan S, May DH, Shaffer SA, Goodlett DR, McIntosh MW, Yerian LM, Bronner MP, Chen R, Brentnall TA. Proteomics on Fixed Tissue Specimens - A Review. Curr Proteomics. 2009 Apr 01;6(1):63-69. doi: 10.2174/157016409787847420. PMID: 19829741; PMCID: PMC2760948.
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Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software.

Proteomics. Clinical applications

Goo YA, Li Z, Pajkovic N, Shaffer S, Taylor G, Chen J, Campbell D, Arnstein L, Goodlett DR, van Breemen RB.
PMID: 20740054
Proteomics Clin Appl. 2007 May 01;1(5):513-523. doi: 10.1002/prca.200600511.

Lycopene, the red pigment of tomatoes, is a carotenoid with potent antioxidant properties. Although lycopene might function as a prostate cancer chemoprevention agent, little is known about its effects at the cellular level. To define general changes induced by...

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Goo YA, Li Z, Pajkovic N, et al. Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics Clin Appl. 2007;1(5):513-523doi: 10.1002/prca.200600511.
Goo, Y. A., Li, Z., Pajkovic, N., Shaffer, S., Taylor, G., Chen, J., Campbell, D., Arnstein, L., Goodlett, D. R., & van Breemen, R. B. (2007). Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics. Clinical applications, 1(5), 513-523. https://doi.org/10.1002/prca.200600511
Goo, Young Ah, et al. "Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software." Proteomics. Clinical applications vol. 1,5 (2007): 513-523. doi: https://doi.org/10.1002/prca.200600511
Goo YA, Li Z, Pajkovic N, Shaffer S, Taylor G, Chen J, Campbell D, Arnstein L, Goodlett DR, van Breemen RB. Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics Clin Appl. 2007 May 01;1(5):513-523. doi: 10.1002/prca.200600511. PMID: 20740054; PMCID: PMC2926987.
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A comparison of two classes of methods for estimating false discovery rates in microarray studies.

Scientifica

Hansen E, Kerr KF.
PMID: 24278709
Scientifica (Cairo). 2012;2012:519394. doi: 10.6064/2012/519394. Epub 2012 Jul 08.

The goal of many microarray studies is to identify genes that are differentially expressed between two classes or populations. Many data analysts choose to estimate the false discovery rate (FDR) associated with the list of genes declared differentially expressed....

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Hansen E, Kerr KF. A comparison of two classes of methods for estimating false discovery rates in microarray studies. Scientifica (Cairo). 2012;2012:519394doi: 10.6064/2012/519394.
Hansen, E., & Kerr, K. F. (2012). A comparison of two classes of methods for estimating false discovery rates in microarray studies. Scientifica, 2012519394. https://doi.org/10.6064/2012/519394
Hansen, Emily, and Kerr, Kathleen F. "A comparison of two classes of methods for estimating false discovery rates in microarray studies." Scientifica vol. 2012 (2012): 519394. doi: https://doi.org/10.6064/2012/519394
Hansen E, Kerr KF. A comparison of two classes of methods for estimating false discovery rates in microarray studies. Scientifica (Cairo). 2012;2012:519394. doi: 10.6064/2012/519394. Epub 2012 Jul 08. PMID: 24278709; PMCID: PMC3820438.
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Genotype and age at Parkinson disease diagnosis.

International journal of molecular epidemiology and genetics

Searles Nielsen S, Bammler TK, Gallagher LG, Farin FM, Longstreth W, Franklin GM, Swanson PD, Checkoway H.
PMID: 23565323
Int J Mol Epidemiol Genet. 2013;4(1):61-9. Epub 2013 Mar 18.

Parkinson disease (PD) is a degenerative movement disorder that results from the destruction of dopaminergic neurons in the midbrain substantia nigra. Both genetic and environmental factors contribute to PD risk, and likely to age at diagnosis. Among 258 newly...

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Searles Nielsen S, Bammler TK, Gallagher LG, et al. Genotype and age at Parkinson disease diagnosis. Int J Mol Epidemiol Genet. 2013;4(1):61-9
Searles Nielsen, S., Bammler, T. K., Gallagher, L. G., Farin, F. M., Longstreth, W., Franklin, G. M., Swanson, P. D., & Checkoway, H. (2013). Genotype and age at Parkinson disease diagnosis. International journal of molecular epidemiology and genetics, 4(1), 61-9.
Searles Nielsen, Susan, et al. "Genotype and age at Parkinson disease diagnosis." International journal of molecular epidemiology and genetics vol. 4,1 (2013): 61-9.
Searles Nielsen S, Bammler TK, Gallagher LG, Farin FM, Longstreth W, Franklin GM, Swanson PD, Checkoway H. Genotype and age at Parkinson disease diagnosis. Int J Mol Epidemiol Genet. 2013;4(1):61-9. Epub 2013 Mar 18. PMID: 23565323; PMCID: PMC3612455.
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The effect of nicotinamide on gene expression in a traumatic brain injury model.

Frontiers in neuroscience

Anderson GD, Peterson TC, Farin FM, Bammler TK, Beyer RP, Kantor ED, Hoane MR.
PMID: 23550224
Front Neurosci. 2013 Feb 26;7:21. doi: 10.3389/fnins.2013.00021. eCollection 2013.

Microarray-based transcriptional profiling was used to determine the effect of nicotinamide on gene expression in an experimental traumatic brain injury (TBI) model. Ingenuity Pathway Analysis (IPA) was used to evaluate the effect on relevant functional categories and canonical pathways....

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Anderson GD, Peterson TC, Farin FM, et al. The effect of nicotinamide on gene expression in a traumatic brain injury model. Front Neurosci. 2013;7:21doi: 10.3389/fnins.2013.00021.
Anderson, G. D., Peterson, T. C., Farin, F. M., Bammler, T. K., Beyer, R. P., Kantor, E. D., & Hoane, M. R. (2013). The effect of nicotinamide on gene expression in a traumatic brain injury model. Frontiers in neuroscience, 721. https://doi.org/10.3389/fnins.2013.00021
Anderson, G D, et al. "The effect of nicotinamide on gene expression in a traumatic brain injury model." Frontiers in neuroscience vol. 7 (2013): 21. doi: https://doi.org/10.3389/fnins.2013.00021
Anderson GD, Peterson TC, Farin FM, Bammler TK, Beyer RP, Kantor ED, Hoane MR. The effect of nicotinamide on gene expression in a traumatic brain injury model. Front Neurosci. 2013 Feb 26;7:21. doi: 10.3389/fnins.2013.00021. eCollection 2013. PMID: 23550224; PMCID: PMC3581799.
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Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function.

Clinical and translational science

Fohner AE, Dalton R, Skagen K, Jackson K, Claw KG, Hopkins SE, Robinson R, Khan BA, Prasad B, Schuetz EG, Nickerson DA, Thornton TA, Dillard DA, Boyer BB, Thummel KE, Woodahl EL.
PMID: 33503331
Clin Transl Sci. 2021 Jul;14(4):1292-1302. doi: 10.1111/cts.12970. Epub 2021 Jan 27.

The frequencies of genetic variants in the CYP3A4 and CYP3A5 genes differ greatly across global populations, leading to profound differences in the metabolic activity of these enzymes and resulting drug metabolism rates, with important consequences for therapeutic safety and...

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Fohner AE, Dalton R, Skagen K, et al. Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function. Clin Transl Sci. 2021;14(4):1292-1302doi: 10.1111/cts.12970.
Fohner, A. E., Dalton, R., Skagen, K., Jackson, K., Claw, K. G., Hopkins, S. E., Robinson, R., Khan, B. A., Prasad, B., Schuetz, E. G., Nickerson, D. A., Thornton, T. A., Dillard, D. A., Boyer, B. B., Thummel, K. E., & Woodahl, E. L. (2021). Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function. Clinical and translational science, 14(4), 1292-1302. https://doi.org/10.1111/cts.12970
Fohner, Alison E, et al. "Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function." Clinical and translational science vol. 14,4 (2021): 1292-1302. doi: https://doi.org/10.1111/cts.12970
Fohner AE, Dalton R, Skagen K, Jackson K, Claw KG, Hopkins SE, Robinson R, Khan BA, Prasad B, Schuetz EG, Nickerson DA, Thornton TA, Dillard DA, Boyer BB, Thummel KE, Woodahl EL. Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function. Clin Transl Sci. 2021 Jul;14(4):1292-1302. doi: 10.1111/cts.12970. Epub 2021 Jan 27. PMID: 33503331; PMCID: PMC8301563.
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Prenatal urinary metabolites of polycyclic aromatic hydrocarbons and toddler cognition, language, and behavior.

Environment international

Wallace ER, Ni Y, Loftus CT, Sullivan A, Masterson E, Szpiro AA, Day DB, Robinson M, Kannan K, Tylavsky FA, Sathyanarayana S, Bush NR, LeWinn KZ, Karr CJ.
PMID: 34902794
Environ Int. 2022 Jan 15;159:107039. doi: 10.1016/j.envint.2021.107039. Epub 2021 Dec 11.

BACKGROUND: Animal and epidemiological studies suggest that prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) may negatively impact toddler neurodevelopment.METHODS: We investigated this association in 835 mother-child pairs from CANDLE, a diverse pregnancy cohort in the mid-South region of the...

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Wallace ER, Ni Y, Loftus CT, et al. Prenatal urinary metabolites of polycyclic aromatic hydrocarbons and toddler cognition, language, and behavior. Environ Int. 2021;159:107039doi: 10.1016/j.envint.2021.107039.
Wallace, E. R., Ni, Y., Loftus, C. T., Sullivan, A., Masterson, E., Szpiro, A. A., Day, D. B., Robinson, M., Kannan, K., Tylavsky, F. A., Sathyanarayana, S., Bush, N. R., LeWinn, K. Z., & Karr, C. J. (2022). Prenatal urinary metabolites of polycyclic aromatic hydrocarbons and toddler cognition, language, and behavior. Environment international, 159107039. https://doi.org/10.1016/j.envint.2021.107039
Wallace, Erin R, et al. "Prenatal urinary metabolites of polycyclic aromatic hydrocarbons and toddler cognition, language, and behavior." Environment international vol. 159 (2022): 107039. doi: https://doi.org/10.1016/j.envint.2021.107039
Wallace ER, Ni Y, Loftus CT, Sullivan A, Masterson E, Szpiro AA, Day DB, Robinson M, Kannan K, Tylavsky FA, Sathyanarayana S, Bush NR, LeWinn KZ, Karr CJ. Prenatal urinary metabolites of polycyclic aromatic hydrocarbons and toddler cognition, language, and behavior. Environ Int. 2022 Jan 15;159:107039. doi: 10.1016/j.envint.2021.107039. Epub 2021 Dec 11. PMID: 34902794; PMCID: PMC8748410.
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Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers.

Toxicological sciences : an official journal of the Society of Toxicology

Lim JJ, Dutta M, Dempsey JL, Lehmler HJ, MacDonald J, Bammler T, Walker C, Kavanagh TJ, Gu H, Mani S, Cui JY.
PMID: 34453844
Toxicol Sci. 2021 Oct 27;184(1):83-103. doi: 10.1093/toxsci/kfab104.

Recent evidence suggests that complex diseases can result from early life exposure to environmental toxicants. Polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) and remain a continuing risk to human health despite being banned...

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Lim JJ, Dutta M, Dempsey JL, et al. Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers. Toxicol Sci. 2021;184(1):83-103doi: 10.1093/toxsci/kfab104.
Lim, J. J., Dutta, M., Dempsey, J. L., Lehmler, H. J., MacDonald, J., Bammler, T., Walker, C., Kavanagh, T. J., Gu, H., Mani, S., & Cui, J. Y. (2021). Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers. Toxicological sciences : an official journal of the Society of Toxicology, 184(1), 83-103. https://doi.org/10.1093/toxsci/kfab104
Lim, Joe Jongpyo, et al. "Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers." Toxicological sciences : an official journal of the Society of Toxicology vol. 184,1 (2021): 83-103. doi: https://doi.org/10.1093/toxsci/kfab104
Lim JJ, Dutta M, Dempsey JL, Lehmler HJ, MacDonald J, Bammler T, Walker C, Kavanagh TJ, Gu H, Mani S, Cui JY. Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers. Toxicol Sci. 2021 Oct 27;184(1):83-103. doi: 10.1093/toxsci/kfab104. PMID: 34453844; PMCID: PMC8557404.
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Publicly available low-cost sensor measurements for PM.

Environment international

Bi J, Carmona N, Blanco MN, Gassett AJ, Seto E, Szpiro AA, Larson TV, Sampson PD, Kaufman JD, Sheppard L.
PMID: 34601393
Environ Int. 2022 Jan;158:106897. doi: 10.1016/j.envint.2021.106897. Epub 2021 Sep 30.

High-resolution, high-quality exposure modeling is critical for assessing the health effects of ambient PM

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Bi J, Carmona N, Blanco MN, et al. Publicly available low-cost sensor measurements for PM. Environ Int. 2021;158:106897doi: 10.1016/j.envint.2021.106897.
Bi, J., Carmona, N., Blanco, M. N., Gassett, A. J., Seto, E., Szpiro, A. A., Larson, T. V., Sampson, P. D., Kaufman, J. D., & Sheppard, L. (2022). Publicly available low-cost sensor measurements for PM. Environment international, 158106897. https://doi.org/10.1016/j.envint.2021.106897
Bi, Jianzhao, et al. "Publicly available low-cost sensor measurements for PM." Environment international vol. 158 (2022): 106897. doi: https://doi.org/10.1016/j.envint.2021.106897
Bi J, Carmona N, Blanco MN, Gassett AJ, Seto E, Szpiro AA, Larson TV, Sampson PD, Kaufman JD, Sheppard L. Publicly available low-cost sensor measurements for PM. Environ Int. 2022 Jan;158:106897. doi: 10.1016/j.envint.2021.106897. Epub 2021 Sep 30. PMID: 34601393.
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Quantum Dot Cellular Uptake and Toxicity in the Developing Brain: Implications for Use as Imaging Probes.

Nanoscale advances

Zhang M, Bishop BP, Thompson NL, Hildahl K, Dang B, Mironchuk O, Chen N, Aoki R, Holmberg VC, Nance E.
PMID: 31867563
Nanoscale Adv. 2019 Sep 01;1(9):3424-3442. doi: 10.1039/C9NA00334G. Epub 2019 Jul 30.

Nanometer-sized luminescent semiconductor quantum dots (QDs) have been utilized as imaging and therapeutic agents in a variety of disease settings, including diseases of the central nervous system. QDs have several advantages over traditional fluorescent probes including their small size...

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Zhang M, Bishop BP, Thompson NL, et al. Quantum Dot Cellular Uptake and Toxicity in the Developing Brain: Implications for Use as Imaging Probes. Nanoscale Adv. 2019;1(9):3424-3442doi: 10.1039/C9NA00334G.
Zhang, M., Bishop, B. P., Thompson, N. L., Hildahl, K., Dang, B., Mironchuk, O., Chen, N., Aoki, R., Holmberg, V. C., & Nance, E. (2019). Quantum Dot Cellular Uptake and Toxicity in the Developing Brain: Implications for Use as Imaging Probes. Nanoscale advances, 1(9), 3424-3442. https://doi.org/10.1039/C9NA00334G
Zhang, Mengying, et al. "Quantum Dot Cellular Uptake and Toxicity in the Developing Brain: Implications for Use as Imaging Probes." Nanoscale advances vol. 1,9 (2019): 3424-3442. doi: https://doi.org/10.1039/C9NA00334G
Zhang M, Bishop BP, Thompson NL, Hildahl K, Dang B, Mironchuk O, Chen N, Aoki R, Holmberg VC, Nance E. Quantum Dot Cellular Uptake and Toxicity in the Developing Brain: Implications for Use as Imaging Probes. Nanoscale Adv. 2019 Sep 01;1(9):3424-3442. doi: 10.1039/C9NA00334G. Epub 2019 Jul 30. PMID: 31867563; PMCID: PMC6924642.
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Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model.

Communications biology

Zhang A, Matsushita M, Zhang L, Wang H, Shi X, Gu H, Xia Z, Cui JY.
PMID: 34912029
Commun Biol. 2021 Dec 15;4(1):1398. doi: 10.1038/s42003-021-02898-1.

The human Apolipoprotein E4 (ApoE4) variant is the strongest known genetic risk factor for Alzheimer's disease (AD). Cadmium (Cd) has been shown to impair learning and memory at a greater extent in humanized ApoE4 knock-in (ApoE4-KI) mice as compared...

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Zhang A, Matsushita M, Zhang L, et al. Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model. Commun Biol. 2021;4(1):1398doi: 10.1038/s42003-021-02898-1.
Zhang, A., Matsushita, M., Zhang, L., Wang, H., Shi, X., Gu, H., Xia, Z., & Cui, J. Y. (2021). Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model. Communications biology, 4(1), 1398. https://doi.org/10.1038/s42003-021-02898-1
Zhang, Angela, et al. "Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model." Communications biology vol. 4,1 (2021): 1398. doi: https://doi.org/10.1038/s42003-021-02898-1
Zhang A, Matsushita M, Zhang L, Wang H, Shi X, Gu H, Xia Z, Cui JY. Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model. Commun Biol. 2021 Dec 15;4(1):1398. doi: 10.1038/s42003-021-02898-1. PMID: 34912029.
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Showing 1 to 12 of 75 entries