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Showing 1 to 12 of 58 entries
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Efficient population-scale variant analysis and prioritization with VAPr.

Bioinformatics (Oxford, England)

Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM.
PMID: 29659724
Bioinformatics. 2018 Aug 15;34(16):2843-2845. doi: 10.1093/bioinformatics/bty192.

SUMMARY: With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package Variant Analysis and Prioritization (VAPr). VAPr leverages...

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Birmingham A, Mark AM, Mazzaferro C, et al. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018;34(16):2843-2845doi: 10.1093/bioinformatics/bty192.
Birmingham, A., Mark, A. M., Mazzaferro, C., Xu, G., & Fisch, K. M. (2018). Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics (Oxford, England), 34(16), 2843-2845. https://doi.org/10.1093/bioinformatics/bty192
Birmingham, Amanda, et al. "Efficient population-scale variant analysis and prioritization with VAPr." Bioinformatics (Oxford, England) vol. 34,16 (2018): 2843-2845. doi: https://doi.org/10.1093/bioinformatics/bty192
Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 Aug 15;34(16):2843-2845. doi: 10.1093/bioinformatics/bty192. PMID: 29659724; PMCID: PMC6084604.
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Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine.

Genetics in medicine : official journal of the American College of Medical Genetics

Esplin ED, Haverfield E, Yang S, Aradhya S, Nussbaum RL.
PMID: 30245515
Genet Med. 2019 May;21(5):1250-1251. doi: 10.1038/s41436-018-0302-3. Epub 2018 Sep 24.

No abstract available.

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Esplin ED, Haverfield E, Yang S, et al. Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine. Genet Med. 2018;21(5):1250-1251doi: 10.1038/s41436-018-0302-3.
Esplin, E. D., Haverfield, E., Yang, S., Aradhya, S., & Nussbaum, R. L. (2019). Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine. Genetics in medicine : official journal of the American College of Medical Genetics, 21(5), 1250-1251. https://doi.org/10.1038/s41436-018-0302-3
Esplin, Edward D, et al. "Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine." Genetics in medicine : official journal of the American College of Medical Genetics vol. 21,5 (2019): 1250-1251. doi: https://doi.org/10.1038/s41436-018-0302-3
Esplin ED, Haverfield E, Yang S, Aradhya S, Nussbaum RL. Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine. Genet Med. 2019 May;21(5):1250-1251. doi: 10.1038/s41436-018-0302-3. Epub 2018 Sep 24. PMID: 30245515.
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Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease.

Circulation. Genomic and precision medicine

Paige SL, Saha P, Priest JR.
PMID: 29555674
Circ Genom Precis Med. 2018 Mar;11(3):e002097. doi: 10.1161/CIRCGEN.118.002097.

No abstract available.

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Paige SL, Saha P, Priest JR. Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease. Circ Genom Precis Med. 2018;11(3):e002097doi: 10.1161/CIRCGEN.118.002097.
Paige, S. L., Saha, P., & Priest, J. R. (2018). Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease. Circulation. Genomic and precision medicine, 11(3), e002097. https://doi.org/10.1161/CIRCGEN.118.002097
Paige, Sharon L, et al. "Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease." Circulation. Genomic and precision medicine vol. 11,3 (2018): e002097. doi: https://doi.org/10.1161/CIRCGEN.118.002097
Paige SL, Saha P, Priest JR. Beyond Gene Panels: Whole Exome Sequencing for Diagnosis of Congenital Heart Disease. Circ Genom Precis Med. 2018 Mar;11(3):e002097. doi: 10.1161/CIRCGEN.118.002097. PMID: 29555674; PMCID: PMC6049807.
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When ".

Cold Spring Harbor molecular case studies

Cassa CA, Akle S, Jordan DM, Rosenfeld JA.
PMID: 28487880
Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099.

The expanding use of genomic sequencing promises to improve clinical diagnostics and to drive the discovery of new disease genes. Candidate genes are increasingly being identified through recurrent cases (e.g., two or more independent cases ["

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Cassa CA, Akle S, Jordan DM, et al. When ". Cold Spring Harb Mol Case Stud. 2017;3(3):a001099doi: 10.1101/mcs.a001099.
Cassa, C. A., Akle, S., Jordan, D. M., & Rosenfeld, J. A. (2017). When ". Cold Spring Harbor molecular case studies, 3(3), a001099. https://doi.org/10.1101/mcs.a001099
Cassa, Christopher A, et al. "When "." Cold Spring Harbor molecular case studies vol. 3,3 (2017): a001099. doi: https://doi.org/10.1101/mcs.a001099
Cassa CA, Akle S, Jordan DM, Rosenfeld JA. When ". Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099. PMID: 28487880; PMCID: PMC5411689.
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The Impact of Whole-Exome Sequencing on Kidney Disease Ontology: The Tip of the Iceberg?.

American journal of kidney diseases : the official journal of the National Kidney Foundation

Geara AS, Kallish S, Hogan JJ.
PMID: 31027884
Am J Kidney Dis. 2019 Aug;74(2):281-283. doi: 10.1053/j.ajkd.2019.03.413. Epub 2019 Apr 23.

No abstract available.

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Geara AS, Kallish S, Hogan JJ. The Impact of Whole-Exome Sequencing on Kidney Disease Ontology: The Tip of the Iceberg?. Am J Kidney Dis. 2019;74(2):281-283doi: 10.1053/j.ajkd.2019.03.413.
Geara, A. S., Kallish, S., & Hogan, J. J. (2019). The Impact of Whole-Exome Sequencing on Kidney Disease Ontology: The Tip of the Iceberg?. American journal of kidney diseases : the official journal of the National Kidney Foundation, 74(2), 281-283. https://doi.org/10.1053/j.ajkd.2019.03.413
Geara, Abdallah S, et al. "The Impact of Whole-Exome Sequencing on Kidney Disease Ontology: The Tip of the Iceberg?." American journal of kidney diseases : the official journal of the National Kidney Foundation vol. 74,2 (2019): 281-283. doi: https://doi.org/10.1053/j.ajkd.2019.03.413
Geara AS, Kallish S, Hogan JJ. The Impact of Whole-Exome Sequencing on Kidney Disease Ontology: The Tip of the Iceberg?. Am J Kidney Dis. 2019 Aug;74(2):281-283. doi: 10.1053/j.ajkd.2019.03.413. Epub 2019 Apr 23. PMID: 31027884.
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PLD3 and spinocerebellar ataxia.

Brain : a journal of neurology

Gonzalez AC, Stroobants S, Reisdorf P, Gavin AL, Nemazee D, Schwudke D, D'Hooge R, Saftig P, Damme M.
PMID: 30312375
Brain. 2018 Nov 01;141(11):e78. doi: 10.1093/brain/awy258.

No abstract available.

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Gonzalez AC, Stroobants S, Reisdorf P, et al. PLD3 and spinocerebellar ataxia. Brain. 2018;141(11):e78doi: 10.1093/brain/awy258.
Gonzalez, A. C., Stroobants, S., Reisdorf, P., Gavin, A. L., Nemazee, D., Schwudke, D., D'Hooge, R., Saftig, P., & Damme, M. (2018). PLD3 and spinocerebellar ataxia. Brain : a journal of neurology, 141(11), e78. https://doi.org/10.1093/brain/awy258
Gonzalez, Adriana Carolina, et al. "PLD3 and spinocerebellar ataxia." Brain : a journal of neurology vol. 141,11 (2018): e78. doi: https://doi.org/10.1093/brain/awy258
Gonzalez AC, Stroobants S, Reisdorf P, Gavin AL, Nemazee D, Schwudke D, D'Hooge R, Saftig P, Damme M. PLD3 and spinocerebellar ataxia. Brain. 2018 Nov 01;141(11):e78. doi: 10.1093/brain/awy258. PMID: 30312375; PMCID: PMC6202572.
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Reply: PLD3 and spinocerebellar ataxia.

Brain : a journal of neurology

Ma KY, Verbeek DS.
PMID: 30312384
Brain. 2018 Nov 01;141(11):e79. doi: 10.1093/brain/awy259.

No abstract available.

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Ma KY, Verbeek DS. Reply: PLD3 and spinocerebellar ataxia. Brain. 2018;141(11):e79doi: 10.1093/brain/awy259.
Ma, K. Y., & Verbeek, D. S. (2018). Reply: PLD3 and spinocerebellar ataxia. Brain : a journal of neurology, 141(11), e79. https://doi.org/10.1093/brain/awy259
Ma, Kai Yu, and Verbeek, Dineke S. "Reply: PLD3 and spinocerebellar ataxia." Brain : a journal of neurology vol. 141,11 (2018): e79. doi: https://doi.org/10.1093/brain/awy259
Ma KY, Verbeek DS. Reply: PLD3 and spinocerebellar ataxia. Brain. 2018 Nov 01;141(11):e79. doi: 10.1093/brain/awy259. PMID: 30312384.
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Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis.

Genetics in medicine : official journal of the American College of Medical Genetics

Alaimo JT, Glinton KE, Liu N, Xiao J, Yang Y, Reid Sutton V, Elsea SH.
PMID: 32439973
Genet Med. 2020 Sep;22(9):1560-1566. doi: 10.1038/s41436-020-0827-0. Epub 2020 May 22.

PURPOSE: A primary barrier to improving exome sequencing diagnostic rates is the interpretation of variants of uncertain clinical significance. We aimed to determine the contribution of integrated untargeted metabolomics in the analysis of exome sequencing data by retrospective analysis...

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Alaimo JT, Glinton KE, Liu N, et al. Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis. Genet Med. 2020;22(9):1560-1566doi: 10.1038/s41436-020-0827-0.
Alaimo, J. T., Glinton, K. E., Liu, N., Xiao, J., Yang, Y., Reid Sutton, V., & Elsea, S. H. (2020). Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis. Genetics in medicine : official journal of the American College of Medical Genetics, 22(9), 1560-1566. https://doi.org/10.1038/s41436-020-0827-0
Alaimo, Joseph T, et al. "Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis." Genetics in medicine : official journal of the American College of Medical Genetics vol. 22,9 (2020): 1560-1566. doi: https://doi.org/10.1038/s41436-020-0827-0
Alaimo JT, Glinton KE, Liu N, Xiao J, Yang Y, Reid Sutton V, Elsea SH. Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis. Genet Med. 2020 Sep;22(9):1560-1566. doi: 10.1038/s41436-020-0827-0. Epub 2020 May 22. PMID: 32439973; PMCID: PMC7483344.
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Exploring the biological role of postzygotic and germinal de novo mutations in ASD.

Scientific reports

Alonso-Gonzalez A, Calaza M, Amigo J, González-Peñas J, Martínez-Regueiro R, Fernández-Prieto M, Parellada M, Arango C, Rodriguez-Fontenla C, Carracedo A.
PMID: 33431980
Sci Rep. 2021 Jan 11;11(1):319. doi: 10.1038/s41598-020-79412-w.

De novo mutations (DNMs), including germinal and postzygotic mutations (PZMs), are a strong source of causality for Autism Spectrum Disorder (ASD). However, the biological processes involved behind them remain unexplored. Our aim was to detect DNMs (germinal and PZMs)...

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Alonso-Gonzalez A, Calaza M, Amigo J, et al. Exploring the biological role of postzygotic and germinal de novo mutations in ASD. Sci Rep. 2021;11(1):319doi: 10.1038/s41598-020-79412-w.
Alonso-Gonzalez, A., Calaza, M., Amigo, J., González-Peñas, J., Martínez-Regueiro, R., Fernández-Prieto, M., Parellada, M., Arango, C., Rodriguez-Fontenla, C., & Carracedo, A. (2021). Exploring the biological role of postzygotic and germinal de novo mutations in ASD. Scientific reports, 11(1), 319. https://doi.org/10.1038/s41598-020-79412-w
Alonso-Gonzalez, A, et al. "Exploring the biological role of postzygotic and germinal de novo mutations in ASD." Scientific reports vol. 11,1 (2021): 319. doi: https://doi.org/10.1038/s41598-020-79412-w
Alonso-Gonzalez A, Calaza M, Amigo J, González-Peñas J, Martínez-Regueiro R, Fernández-Prieto M, Parellada M, Arango C, Rodriguez-Fontenla C, Carracedo A. Exploring the biological role of postzygotic and germinal de novo mutations in ASD. Sci Rep. 2021 Jan 11;11(1):319. doi: 10.1038/s41598-020-79412-w. PMID: 33431980; PMCID: PMC7801448.
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Benchmarking germline CNV calling tools from exome sequencing data.

Scientific reports

Gordeeva V, Sharova E, Babalyan K, Sultanov R, Govorun VM, Arapidi G.
PMID: 34257369
Sci Rep. 2021 Jul 13;11(1):14416. doi: 10.1038/s41598-021-93878-2.

Whole-exome sequencing is an attractive alternative to microarray analysis because of the low cost and potential ability to detect copy number variations (CNV) of various sizes (from 1-2 exons to several Mb). Previous comparison of the most popular CNV...

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Gordeeva V, Sharova E, Babalyan K, et al. Benchmarking germline CNV calling tools from exome sequencing data. Sci Rep. 2021;11(1):14416doi: 10.1038/s41598-021-93878-2.
Gordeeva, V., Sharova, E., Babalyan, K., Sultanov, R., Govorun, V. M., & Arapidi, G. (2021). Benchmarking germline CNV calling tools from exome sequencing data. Scientific reports, 11(1), 14416. https://doi.org/10.1038/s41598-021-93878-2
Gordeeva, Veronika, et al. "Benchmarking germline CNV calling tools from exome sequencing data." Scientific reports vol. 11,1 (2021): 14416. doi: https://doi.org/10.1038/s41598-021-93878-2
Gordeeva V, Sharova E, Babalyan K, Sultanov R, Govorun VM, Arapidi G. Benchmarking germline CNV calling tools from exome sequencing data. Sci Rep. 2021 Jul 13;11(1):14416. doi: 10.1038/s41598-021-93878-2. PMID: 34257369; PMCID: PMC8277855.
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Response to Esplin et al.

Genetics in medicine : official journal of the American College of Medical Genetics

Biesecker LG.
PMID: 30283096
Genet Med. 2019 May;21(5):1252-1253. doi: 10.1038/s41436-018-0303-2. Epub 2018 Oct 04.

No abstract available.

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Biesecker LG. Response to Esplin et al. Genet Med. 2018;21(5):1252-1253doi: 10.1038/s41436-018-0303-2.
Biesecker, L. G. (2019). Response to Esplin et al. Genetics in medicine : official journal of the American College of Medical Genetics, 21(5), 1252-1253. https://doi.org/10.1038/s41436-018-0303-2
Biesecker, Leslie G. "Response to Esplin et al." Genetics in medicine : official journal of the American College of Medical Genetics vol. 21,5 (2019): 1252-1253. doi: https://doi.org/10.1038/s41436-018-0303-2
Biesecker LG. Response to Esplin et al. Genet Med. 2019 May;21(5):1252-1253. doi: 10.1038/s41436-018-0303-2. Epub 2018 Oct 04. PMID: 30283096.
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CRCDA--Comprehensive resources for cancer NGS data analysis.

Database : the journal of biological databases and curation

Thangam M, Gopal RK.
PMID: 26450948
Database (Oxford). 2015 Oct 08;2015. doi: 10.1093/database/bav092. Print 2015.

Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS...

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Thangam M, Gopal RK. CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford). 2015;2015doi: 10.1093/database/bav092.
Thangam, M., & Gopal, R. K. (2015). CRCDA--Comprehensive resources for cancer NGS data analysis. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav092
Thangam, Manonanthini, and Gopal, Ramesh Kumar. "CRCDA--Comprehensive resources for cancer NGS data analysis." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav092
Thangam M, Gopal RK. CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford). 2015 Oct 08;2015. doi: 10.1093/database/bav092. Print 2015. PMID: 26450948; PMCID: PMC4597977.
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Showing 1 to 12 of 58 entries