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ORE identifies extreme expression effects enriched for rare variants.

Bioinformatics (Oxford, England)

Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD.
PMID: 30903145
Bioinformatics. 2019 Oct 15;35(20):3906-3912. doi: 10.1093/bioinformatics/btz202.

MOTIVATION: Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying...

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Richter F, Hoffman GE, Manheimer KB, et al. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics. 2019;35(20):3906-3912doi: 10.1093/bioinformatics/btz202.
Richter, F., Hoffman, G. E., Manheimer, K. B., Patel, N., Sharp, A. J., McKean, D., Morton, S. U., DePalma, S., Gorham, J., Kitaygorodksy, A., Porter, G. A., Giardini, A., Shen, Y., Chung, W. K., Seidman, J. G., Seidman, C. E., Schadt, E. E., & Gelb, B. D. (2019). ORE identifies extreme expression effects enriched for rare variants. Bioinformatics (Oxford, England), 35(20), 3906-3912. https://doi.org/10.1093/bioinformatics/btz202
Richter, F, et al. "ORE identifies extreme expression effects enriched for rare variants." Bioinformatics (Oxford, England) vol. 35,20 (2019): 3906-3912. doi: https://doi.org/10.1093/bioinformatics/btz202
Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics. 2019 Oct 15;35(20):3906-3912. doi: 10.1093/bioinformatics/btz202. PMID: 30903145; PMCID: PMC6792115.
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Genomic frontiers in congenital heart disease.

Nature reviews. Cardiology

Morton SU, Quiat D, Seidman JG, Seidman CE.
PMID: 34272501
Nat Rev Cardiol. 2022 Jan;19(1):26-42. doi: 10.1038/s41569-021-00587-4. Epub 2021 Jul 16.

The application of next-generation sequencing to study congenital heart disease (CHD) is increasingly providing new insights into the causes and mechanisms of this prevalent birth anomaly. Whole-exome sequencing analysis identifies damaging gene variants altering single or contiguous nucleotides that...

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Morton SU, Quiat D, Seidman JG, et al. Genomic frontiers in congenital heart disease. Nat Rev Cardiol. 2021;19(1):26-42doi: 10.1038/s41569-021-00587-4.
Morton, S. U., Quiat, D., Seidman, J. G., & Seidman, C. E. (2022). Genomic frontiers in congenital heart disease. Nature reviews. Cardiology, 19(1), 26-42. https://doi.org/10.1038/s41569-021-00587-4
Morton, Sarah U, et al. "Genomic frontiers in congenital heart disease." Nature reviews. Cardiology vol. 19,1 (2022): 26-42. doi: https://doi.org/10.1038/s41569-021-00587-4
Morton SU, Quiat D, Seidman JG, Seidman CE. Genomic frontiers in congenital heart disease. Nat Rev Cardiol. 2022 Jan;19(1):26-42. doi: 10.1038/s41569-021-00587-4. Epub 2021 Jul 16. PMID: 34272501.
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Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy.

Cardiovascular research

Huang ZP, Ding Y, Chen J, Wu G, Kataoka M, Hu Y, Yang JH, Liu J, Drakos SG, Selzman CH, Kyselovic J, Qu LH, Dos Remedios CG, Pu WT, Wang DZ.
PMID: 27557636
Cardiovasc Res. 2016 Nov 01;112(2):543-554. doi: 10.1093/cvr/cvw201.

AIMS: Ischemic cardiomyopathy (ICM) resulting from myocardial infarction is a major cause of heart failure (HF). Recently, thousands of long non-coding RNAs (lncRNAs) have been discovered and implicated in a variety of biological processes. However, the role of most...

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Huang ZP, Ding Y, Chen J, et al. Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy. Cardiovasc Res. 2016;112(2):543-554doi: 10.1093/cvr/cvw201.
Huang, Z. P., Ding, Y., Chen, J., Wu, G., Kataoka, M., Hu, Y., Yang, J. H., Liu, J., Drakos, S. G., Selzman, C. H., Kyselovic, J., Qu, L. H., Dos Remedios, C. G., Pu, W. T., & Wang, D. Z. (2016). Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy. Cardiovascular research, 112(2), 543-554. https://doi.org/10.1093/cvr/cvw201
Huang, Zhan-Peng, et al. "Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy." Cardiovascular research vol. 112,2 (2016): 543-554. doi: https://doi.org/10.1093/cvr/cvw201
Huang ZP, Ding Y, Chen J, Wu G, Kataoka M, Hu Y, Yang JH, Liu J, Drakos SG, Selzman CH, Kyselovic J, Qu LH, Dos Remedios CG, Pu WT, Wang DZ. Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy. Cardiovasc Res. 2016 Nov 01;112(2):543-554. doi: 10.1093/cvr/cvw201. PMID: 27557636; PMCID: PMC5079274.
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Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice.

Genome medicine

Haigh JL, Adhikari A, Copping NA, Stradleigh T, Wade AA, Catta-Preta R, Su-Feher L, Zdilar I, Morse S, Fenton TA, Nguyen A, Quintero D, Agezew S, Sramek M, Kreun EJ, Carter J, Gompers A, Lambert JT, Canales CP, Pennacchio LA, Visel A, Dickel DE, Silverman JL, Nord AS.
PMID: 33910599
Genome Med. 2021 Apr 26;13(1):69. doi: 10.1186/s13073-021-00884-0.

BACKGROUND: Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the NaMETHODS: To determine the functional role of one of these potentially...

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Haigh JL, Adhikari A, Copping NA, et al. Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice. Genome Med. 2021;13(1):69doi: 10.1186/s13073-021-00884-0.
Haigh, J. L., Adhikari, A., Copping, N. A., Stradleigh, T., Wade, A. A., Catta-Preta, R., Su-Feher, L., Zdilar, I., Morse, S., Fenton, T. A., Nguyen, A., Quintero, D., Agezew, S., Sramek, M., Kreun, E. J., Carter, J., Gompers, A., Lambert, J. T., Canales, C. P., Pennacchio, L. A., Visel, A., Dickel, D. E., Silverman, J. L., & Nord, A. S. (2021). Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice. Genome medicine, 13(1), 69. https://doi.org/10.1186/s13073-021-00884-0
Haigh, Jessica L, et al. "Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice." Genome medicine vol. 13,1 (2021): 69. doi: https://doi.org/10.1186/s13073-021-00884-0
Haigh JL, Adhikari A, Copping NA, Stradleigh T, Wade AA, Catta-Preta R, Su-Feher L, Zdilar I, Morse S, Fenton TA, Nguyen A, Quintero D, Agezew S, Sramek M, Kreun EJ, Carter J, Gompers A, Lambert JT, Canales CP, Pennacchio LA, Visel A, Dickel DE, Silverman JL, Nord AS. Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice. Genome Med. 2021 Apr 26;13(1):69. doi: 10.1186/s13073-021-00884-0. PMID: 33910599; PMCID: PMC8080386.
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Showing 1 to 4 of 4 entries