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Introducing the systems biology of cell state regulation section of Physiological Genomics.

Physiological genomics

Coller HA.
PMID: 23632415
Physiol Genomics. 2013 Jun 03;45(11):407-8. doi: 10.1152/physiolgenomics.00052.2013. Epub 2013 Apr 30.

No abstract available.

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Coller HA. Introducing the systems biology of cell state regulation section of Physiological Genomics. Physiol Genomics. 2013;45(11):407-8doi: 10.1152/physiolgenomics.00052.2013.
Coller, H. A. (2013). Introducing the systems biology of cell state regulation section of Physiological Genomics. Physiological genomics, 45(11), 407-8. https://doi.org/10.1152/physiolgenomics.00052.2013
Coller, Hilary A. "Introducing the systems biology of cell state regulation section of Physiological Genomics." Physiological genomics vol. 45,11 (2013): 407-8. doi: https://doi.org/10.1152/physiolgenomics.00052.2013
Coller HA. Introducing the systems biology of cell state regulation section of Physiological Genomics. Physiol Genomics. 2013 Jun 03;45(11):407-8. doi: 10.1152/physiolgenomics.00052.2013. Epub 2013 Apr 30. PMID: 23632415.
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The .

Physiological genomics

Chesney KL, Men H, Hankins MA, Bryda EC.
PMID: 33818130
Physiol Genomics. 2021 Jun 01;53(6):269-281. doi: 10.1152/physiolgenomics.00114.2020. Epub 2021 Apr 05.

No abstract available.

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Chesney KL, Men H, Hankins MA, et al. The . Physiol Genomics. 2021;53(6):269-281doi: 10.1152/physiolgenomics.00114.2020.
Chesney, K. L., Men, H., Hankins, M. A., & Bryda, E. C. (2021). The . Physiological genomics, 53(6), 269-281. https://doi.org/10.1152/physiolgenomics.00114.2020
Chesney, Kari L, et al. "The ." Physiological genomics vol. 53,6 (2021): 269-281. doi: https://doi.org/10.1152/physiolgenomics.00114.2020
Chesney KL, Men H, Hankins MA, Bryda EC. The . Physiol Genomics. 2021 Jun 01;53(6):269-281. doi: 10.1152/physiolgenomics.00114.2020. Epub 2021 Apr 05. PMID: 33818130; PMCID: PMC8285577.
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Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration.

Physiological genomics

Parrish A, Srivastava A, Juskeviciute E, Hoek JB, Vadigepalli R, Keramitsoglou KM.
PMID: 34796728
Physiol Genomics. 2021 Nov 19; doi: 10.1152/physiolgenomics.00113.2021. Epub 2021 Nov 19.

Impaired liver regeneration has been considered as a hallmark of progression of alcohol-associated liver disease. Our previous studies demonstrated that in vivo inhibition of the microRNA (miRNA) miR21 can restore regenerative capacity of the liver in chronic ethanol-fed animals....

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Parrish A, Srivastava A, Juskeviciute E, et al. Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration. Physiol Genomics. 2021;doi: 10.1152/physiolgenomics.00113.2021.
Parrish, A., Srivastava, A., Juskeviciute, E., Hoek, J. B., Vadigepalli, R., & Keramitsoglou, K. M. (2021). Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration. Physiological genomics, . https://doi.org/10.1152/physiolgenomics.00113.2021
Parrish, Austin, et al. "Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration." Physiological genomics vol. (2021). doi: https://doi.org/10.1152/physiolgenomics.00113.2021
Parrish A, Srivastava A, Juskeviciute E, Hoek JB, Vadigepalli R, Keramitsoglou KM. Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration. Physiol Genomics. 2021 Nov 19; doi: 10.1152/physiolgenomics.00113.2021. Epub 2021 Nov 19. PMID: 34796728.
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Epistemological issues in omics and high-dimensional biology: give the people what they want.

Physiological genomics

Mehta TS, Zakharkin SO, Gadbury GL, Allison DB.
PMID: 16968808
Physiol Genomics. 2006 Dec 13;28(1):24-32. doi: 10.1152/physiolgenomics.00095.2006. Epub 2006 Sep 12.

Gene expression microarrays have been the vanguard of new analytic approaches in high-dimensional biology. Draft sequences of several genomes coupled with new technologies allow study of the influences and responses of entire genomes rather than isolated genes. This has...

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Mehta TS, Zakharkin SO, Gadbury GL, et al. Epistemological issues in omics and high-dimensional biology: give the people what they want. Physiol Genomics. 2006;28(1):24-32doi: 10.1152/physiolgenomics.00095.2006.
Mehta, T. S., Zakharkin, S. O., Gadbury, G. L., & Allison, D. B. (2006). Epistemological issues in omics and high-dimensional biology: give the people what they want. Physiological genomics, 28(1), 24-32. https://doi.org/10.1152/physiolgenomics.00095.2006
Mehta, Tapan S, et al. "Epistemological issues in omics and high-dimensional biology: give the people what they want." Physiological genomics vol. 28,1 (2006): 24-32. doi: https://doi.org/10.1152/physiolgenomics.00095.2006
Mehta TS, Zakharkin SO, Gadbury GL, Allison DB. Epistemological issues in omics and high-dimensional biology: give the people what they want. Physiol Genomics. 2006 Dec 13;28(1):24-32. doi: 10.1152/physiolgenomics.00095.2006. Epub 2006 Sep 12. PMID: 16968808.
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Comparative impact of dietary carbohydrates on the liver transcriptome in two strains of mice.

Physiological genomics

Chi Y, Youn DY, Xiaoli AM, Liu L, Qiu Y, Kurland IJ, Pessin JB, Yang F, Pessin JE.
PMID: 34643091
Physiol Genomics. 2021 Nov 01;53(11):456-472. doi: 10.1152/physiolgenomics.00053.2021. Epub 2021 Oct 13.

Excessive long-term consumption of dietary carbohydrates, including glucose, sucrose, or fructose, has been shown to have significant impact on genome-wide gene expression, which likely results from changes in metabolic substrate flux. However, there has been no comprehensive study on...

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Chi Y, Youn DY, Xiaoli AM, et al. Comparative impact of dietary carbohydrates on the liver transcriptome in two strains of mice. Physiol Genomics. 2021;53(11):456-472doi: 10.1152/physiolgenomics.00053.2021.
Chi, Y., Youn, D. Y., Xiaoli, A. M., Liu, L., Qiu, Y., Kurland, I. J., Pessin, J. B., Yang, F., & Pessin, J. E. (2021). Comparative impact of dietary carbohydrates on the liver transcriptome in two strains of mice. Physiological genomics, 53(11), 456-472. https://doi.org/10.1152/physiolgenomics.00053.2021
Chi, Yuling, et al. "Comparative impact of dietary carbohydrates on the liver transcriptome in two strains of mice." Physiological genomics vol. 53,11 (2021): 456-472. doi: https://doi.org/10.1152/physiolgenomics.00053.2021
Chi Y, Youn DY, Xiaoli AM, Liu L, Qiu Y, Kurland IJ, Pessin JB, Yang F, Pessin JE. Comparative impact of dietary carbohydrates on the liver transcriptome in two strains of mice. Physiol Genomics. 2021 Nov 01;53(11):456-472. doi: 10.1152/physiolgenomics.00053.2021. Epub 2021 Oct 13. PMID: 34643091; PMCID: PMC8616594.
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Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows.

Physiological genomics

Tsuchiya Y, Chiba E, Sugino T, Kawashima K, Kushibiki S, Kizaki K, Kim YH, Sato S.
PMID: 34097531
Physiol Genomics. 2021 Jul 01;53(7):285-294. doi: 10.1152/physiolgenomics.00048.2021. Epub 2021 Jun 07.

We investigated changes in rumen fermentation, peripheral blood metabolites and hormones, and hepatic transcriptomic dynamics in Holstein cows with and those without subacute ruminal acidosis (SARA) during the periparturient period. Sixteen multiparous Holstein cows were categorized in the SARA...

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Tsuchiya Y, Chiba E, Sugino T, et al. Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows. Physiol Genomics. 2021;53(7):285-294doi: 10.1152/physiolgenomics.00048.2021.
Tsuchiya, Y., Chiba, E., Sugino, T., Kawashima, K., Kushibiki, S., Kizaki, K., Kim, Y. H., & Sato, S. (2021). Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows. Physiological genomics, 53(7), 285-294. https://doi.org/10.1152/physiolgenomics.00048.2021
Tsuchiya, Yoshiyuki, et al. "Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows." Physiological genomics vol. 53,7 (2021): 285-294. doi: https://doi.org/10.1152/physiolgenomics.00048.2021
Tsuchiya Y, Chiba E, Sugino T, Kawashima K, Kushibiki S, Kizaki K, Kim YH, Sato S. Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows. Physiol Genomics. 2021 Jul 01;53(7):285-294. doi: 10.1152/physiolgenomics.00048.2021. Epub 2021 Jun 07. PMID: 34097531.
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Circulating extracellular DNA is in association with continuous metabolic syndrome score in healthy adolescents.

Physiological genomics

Celec P, Janovičová Ĺ, Gurecká R, Koborová I, Gardlík R, Šebeková K.
PMID: 34097532
Physiol Genomics. 2021 Jul 01;53(7):309-318. doi: 10.1152/physiolgenomics.00029.2021. Epub 2021 Jun 07.

Obesity is associated with chronic low-grade inflammation that eventually leads to metabolic complications. Extracellular DNA (ecDNA) is a damage-associated molecular pattern. Extracellular mitochondrial DNA can activate innate immunity. We hypothesized that ecDNA, especially of mitochondrial origin, could be associated...

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Celec P, Janovičová Ĺ, Gurecká R, et al. Circulating extracellular DNA is in association with continuous metabolic syndrome score in healthy adolescents. Physiol Genomics. 2021;53(7):309-318doi: 10.1152/physiolgenomics.00029.2021.
Celec, P., Janovičová, �. �., Gurecká, R., Koborová, I., Gardlík, R., & Šebeková, K. (2021). Circulating extracellular DNA is in association with continuous metabolic syndrome score in healthy adolescents. Physiological genomics, 53(7), 309-318. https://doi.org/10.1152/physiolgenomics.00029.2021
Celec, Peter, et al. "Circulating extracellular DNA is in association with continuous metabolic syndrome score in healthy adolescents." Physiological genomics vol. 53,7 (2021): 309-318. doi: https://doi.org/10.1152/physiolgenomics.00029.2021
Celec P, Janovičová Ĺ, Gurecká R, Koborová I, Gardlík R, Šebeková K. Circulating extracellular DNA is in association with continuous metabolic syndrome score in healthy adolescents. Physiol Genomics. 2021 Jul 01;53(7):309-318. doi: 10.1152/physiolgenomics.00029.2021. Epub 2021 Jun 07. PMID: 34097532.
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Age-dependent transcriptional alterations in cardiac endothelial cells.

Physiological genomics

Emechebe U, Nelson JW, Alkayed NJ, Kaul S, Adey AC, Barnes AP.
PMID: 34097533
Physiol Genomics. 2021 Jul 01;53(7):295-308. doi: 10.1152/physiolgenomics.00037.2021. Epub 2021 Jun 07.

Aging is a significant risk factor for cardiovascular disease. Despite the fact that endothelial cells play critical roles in cardiovascular function and disease, the molecular impact of aging on this cell population in many organ systems remains unknown. In...

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Emechebe U, Nelson JW, Alkayed NJ, et al. Age-dependent transcriptional alterations in cardiac endothelial cells. Physiol Genomics. 2021;53(7):295-308doi: 10.1152/physiolgenomics.00037.2021.
Emechebe, U., Nelson, J. W., Alkayed, N. J., Kaul, S., Adey, A. C., & Barnes, A. P. (2021). Age-dependent transcriptional alterations in cardiac endothelial cells. Physiological genomics, 53(7), 295-308. https://doi.org/10.1152/physiolgenomics.00037.2021
Emechebe, Uchenna, et al. "Age-dependent transcriptional alterations in cardiac endothelial cells." Physiological genomics vol. 53,7 (2021): 295-308. doi: https://doi.org/10.1152/physiolgenomics.00037.2021
Emechebe U, Nelson JW, Alkayed NJ, Kaul S, Adey AC, Barnes AP. Age-dependent transcriptional alterations in cardiac endothelial cells. Physiol Genomics. 2021 Jul 01;53(7):295-308. doi: 10.1152/physiolgenomics.00037.2021. Epub 2021 Jun 07. PMID: 34097533; PMCID: PMC8321782.
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Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating females: a pilot study.

Physiological genomics

MacGregor KA, Rodriguez-Sanchez N, Di Virgilio TG, Barwell ND, Gallagher IJ, Moran CN.
PMID: 34796732
Physiol Genomics. 2022 Jan 01;54(1):1-10. doi: 10.1152/physiolgenomics.00088.2021. Epub 2021 Nov 19.

Cyclical changes in hormone profiles across the menstrual cycle are associated with alterations in metabolic control. MicroRNAs (miRNAs) contribute to regulating metabolic control, including adipose tissue metabolism. How fluctuations in hormonal profiles across the menstrual cycle affect adipose tissue...

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MacGregor KA, Rodriguez-Sanchez N, Di Virgilio TG, et al. Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating females: a pilot study. Physiol Genomics. 2021;54(1):1-10doi: 10.1152/physiolgenomics.00088.2021.
MacGregor, K. A., Rodriguez-Sanchez, N., Di Virgilio, T. G., Barwell, N. D., Gallagher, I. J., & Moran, C. N. (2022). Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating females: a pilot study. Physiological genomics, 54(1), 1-10. https://doi.org/10.1152/physiolgenomics.00088.2021
MacGregor, Kirstin A, et al. "Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating females: a pilot study." Physiological genomics vol. 54,1 (2022): 1-10. doi: https://doi.org/10.1152/physiolgenomics.00088.2021
MacGregor KA, Rodriguez-Sanchez N, Di Virgilio TG, Barwell ND, Gallagher IJ, Moran CN. Changes in adipose tissue microRNA expression across the menstrual cycle in regularly menstruating females: a pilot study. Physiol Genomics. 2022 Jan 01;54(1):1-10. doi: 10.1152/physiolgenomics.00088.2021. Epub 2021 Nov 19. PMID: 34796732.
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Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content.

Physiological genomics

Czernik PJ, Golonka RM, Chakraborty S, Yeoh BS, Abokor AA, Saha P, Yeo JY, Mell B, Cheng X, Baroi S, Tian Y, Patterson AD, Joe B, Vijay-Kumar M, Lecka-Czernik B.
PMID: 34714176
Physiol Genomics. 2021 Dec 01;53(12):518-533. doi: 10.1152/physiolgenomics.00017.2021. Epub 2021 Oct 29.

Integration of microbiota in a host begins at birth and progresses during adolescence, forming a multidirectional system of physiological interactions. Here, we present an instantaneous effect of natural, bacterial gut colonization on the acceleration of longitudinal and radial bone...

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Czernik PJ, Golonka RM, Chakraborty S, et al. Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content. Physiol Genomics. 2021;53(12):518-533doi: 10.1152/physiolgenomics.00017.2021.
Czernik, P. J., Golonka, R. M., Chakraborty, S., Yeoh, B. S., Abokor, A. A., Saha, P., Yeo, J. Y., Mell, B., Cheng, X., Baroi, S., Tian, Y., Patterson, A. D., Joe, B., Vijay-Kumar, M., & Lecka-Czernik, B. (2021). Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content. Physiological genomics, 53(12), 518-533. https://doi.org/10.1152/physiolgenomics.00017.2021
Czernik, Piotr J, et al. "Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content." Physiological genomics vol. 53,12 (2021): 518-533. doi: https://doi.org/10.1152/physiolgenomics.00017.2021
Czernik PJ, Golonka RM, Chakraborty S, Yeoh BS, Abokor AA, Saha P, Yeo JY, Mell B, Cheng X, Baroi S, Tian Y, Patterson AD, Joe B, Vijay-Kumar M, Lecka-Czernik B. Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content. Physiol Genomics. 2021 Dec 01;53(12):518-533. doi: 10.1152/physiolgenomics.00017.2021. Epub 2021 Oct 29. PMID: 34714176.
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MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378.

Physiological genomics

Tang Y, Shah TA, Yurkow EJ, Rogers MB.
PMID: 32956022
Physiol Genomics. 2020 Sep 21; doi: 10.1152/physiolgenomics.00074.2020. Epub 2020 Sep 21.

Our goal was to elucidate microRNAs (miRNAs) that may repress the excess bone morphogenetic protein (BMP) signaling observed during pathological calcification in the Klotho mouse model of kidney disease. We hypothesized that restoring healthy levels of miRNAs that post-transcriptionally...

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Tang Y, Shah TA, Yurkow EJ, et al. MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378. Physiol Genomics. 2020;doi: 10.1152/physiolgenomics.00074.2020.
Tang, Y., Shah, T. A., Yurkow, E. J., & Rogers, M. B. (2020). MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378. Physiological genomics, . https://doi.org/10.1152/physiolgenomics.00074.2020
Tang, Ying, et al. "MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378." Physiological genomics vol. (2020). doi: https://doi.org/10.1152/physiolgenomics.00074.2020
Tang Y, Shah TA, Yurkow EJ, Rogers MB. MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378. Physiol Genomics. 2020 Sep 21; doi: 10.1152/physiolgenomics.00074.2020. Epub 2020 Sep 21. PMID: 32956022.
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Corrigendum.

Physiological genomics

[No authors listed]
PMID: 27994048
Physiol Genomics. 2016 Dec 01;48(12):961. doi: 10.1152/physiolgenomics.zh7-4153-corr.2016.

No abstract available.

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Corrigendum. Physiol Genomics. 2016;48(12):961doi: 10.1152/physiolgenomics.zh7-4153-corr.2016.
(2016). Corrigendum. Physiological genomics, 48(12), 961. https://doi.org/10.1152/physiolgenomics.zh7-4153-corr.2016
"Corrigendum." Physiological genomics vol. 48,12 (2016): 961. doi: https://doi.org/10.1152/physiolgenomics.zh7-4153-corr.2016
Corrigendum. Physiol Genomics. 2016 Dec 01;48(12):961. doi: 10.1152/physiolgenomics.zh7-4153-corr.2016. PMID: 27994048; PMCID: PMC5206386.
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