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Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing.

Cold Spring Harbor molecular case studies

Rehm H.
PMID: 30275005
Cold Spring Harb Mol Case Stud. 2018 Oct 01;4(5). doi: 10.1101/mcs.a003467. Print 2018 Oct.

No abstract available.

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Rehm H. Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing. Cold Spring Harb Mol Case Stud. 2018;4(5)doi: 10.1101/mcs.a003467.
Rehm, H. (2018). Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing. Cold Spring Harbor molecular case studies, 4(5), . https://doi.org/10.1101/mcs.a003467
Rehm, Heidi. "Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing." Cold Spring Harbor molecular case studies vol. 4,5 (2018). doi: https://doi.org/10.1101/mcs.a003467
Rehm H. Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing. Cold Spring Harb Mol Case Stud. 2018 Oct 01;4(5). doi: 10.1101/mcs.a003467. Print 2018 Oct. PMID: 30275005; PMCID: PMC6169822.
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Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa.

BMC genomics

Cobo-Simón M, Tamames J.
PMID: 28662636
BMC Genomics. 2017 Jun 29;18(1):499. doi: 10.1186/s12864-017-3888-y.

BACKGROUND: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount...

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Cobo-Simón M, Tamames J. Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics. 2017;18(1):499doi: 10.1186/s12864-017-3888-y.
Cobo-Simón, M., & Tamames, J. (2017). Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC genomics, 18(1), 499. https://doi.org/10.1186/s12864-017-3888-y
Cobo-Simón, Marta, and Tamames, Javier. "Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa." BMC genomics vol. 18,1 (2017): 499. doi: https://doi.org/10.1186/s12864-017-3888-y
Cobo-Simón M, Tamames J. Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics. 2017 Jun 29;18(1):499. doi: 10.1186/s12864-017-3888-y. PMID: 28662636; PMCID: PMC5492924.
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Gene expression profile analysis of ventilator-associated pneumonia.

Molecular medicine reports

Xu X, Yuan B, Liang Q, Huang H, Yin X, Sheng X, Nie N, Fang H.
PMID: 26459786
Mol Med Rep. 2015 Nov;12(5):7455-62. doi: 10.3892/mmr.2015.4389. Epub 2015 Sep 29.

Based on the gene expression profile of patients with ventilator-associated pneumonia (VAP) and patients not affected by the disease, the present study aimed to enhance the current understanding of VAP development using bioinformatics methods. The expression profile GSE30385 was...

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Xu X, Yuan B, Liang Q, et al. Gene expression profile analysis of ventilator-associated pneumonia. Mol Med Rep. 2015;12(5):7455-62doi: 10.3892/mmr.2015.4389.
Xu, X., Yuan, B., Liang, Q., Huang, H., Yin, X., Sheng, X., Nie, N., & Fang, H. (2015). Gene expression profile analysis of ventilator-associated pneumonia. Molecular medicine reports, 12(5), 7455-62. https://doi.org/10.3892/mmr.2015.4389
Xu, Xiaoli, et al. "Gene expression profile analysis of ventilator-associated pneumonia." Molecular medicine reports vol. 12,5 (2015): 7455-62. doi: https://doi.org/10.3892/mmr.2015.4389
Xu X, Yuan B, Liang Q, Huang H, Yin X, Sheng X, Nie N, Fang H. Gene expression profile analysis of ventilator-associated pneumonia. Mol Med Rep. 2015 Nov;12(5):7455-62. doi: 10.3892/mmr.2015.4389. Epub 2015 Sep 29. PMID: 26459786; PMCID: PMC4626132.
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Identification of potential gene targets in systemic vasculitis using DNA microarray analysis.

Molecular medicine reports

Feng Y, Zheng M, Gan S, Zhang L, Wan Z, Zhang Y, Qian Q, Tang J.
PMID: 28440408
Mol Med Rep. 2017 Jun;15(6):3665-3673. doi: 10.3892/mmr.2017.6455. Epub 2017 Apr 11.

The present study aimed to identify the involvement of critical genes in systemic vasculitis, to gain an improved understanding of the molecular circuity and to investigate novel potential gene targets for systemic vasculitis treatment. The dual‑color cDNA microarray data...

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Feng Y, Zheng M, Gan S, et al. Identification of potential gene targets in systemic vasculitis using DNA microarray analysis. Mol Med Rep. 2017;15(6):3665-3673doi: 10.3892/mmr.2017.6455.
Feng, Y., Zheng, M., Gan, S., Zhang, L., Wan, Z., Zhang, Y., Qian, Q., & Tang, J. (2017). Identification of potential gene targets in systemic vasculitis using DNA microarray analysis. Molecular medicine reports, 15(6), 3665-3673. https://doi.org/10.3892/mmr.2017.6455
Feng, Yiwen, et al. "Identification of potential gene targets in systemic vasculitis using DNA microarray analysis." Molecular medicine reports vol. 15,6 (2017): 3665-3673. doi: https://doi.org/10.3892/mmr.2017.6455
Feng Y, Zheng M, Gan S, Zhang L, Wan Z, Zhang Y, Qian Q, Tang J. Identification of potential gene targets in systemic vasculitis using DNA microarray analysis. Mol Med Rep. 2017 Jun;15(6):3665-3673. doi: 10.3892/mmr.2017.6455. Epub 2017 Apr 11. PMID: 28440408; PMCID: PMC5436278.
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The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.

Nucleic acids research

Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS.
PMID: 14681416
Nucleic Acids Res. 2004 Jan 01;32:D293-5. doi: 10.1093/nar/gkh108.

The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous...

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Sundararaj S, Guo A, Habibi-Nazhad B, et al. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004;32:D293-5doi: 10.1093/nar/gkh108.
Sundararaj, S., Guo, A., Habibi-Nazhad, B., Rouani, M., Stothard, P., Ellison, M., & Wishart, D. S. (2004). The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic acids research, 32D293-5. https://doi.org/10.1093/nar/gkh108
Sundararaj, Shan, et al. "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli." Nucleic acids research vol. 32 (2004): D293-5. doi: https://doi.org/10.1093/nar/gkh108
Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004 Jan 01;32:D293-5. doi: 10.1093/nar/gkh108. PMID: 14681416; PMCID: PMC308842.
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Toward better governance of human genomic data.

Nature genetics

O'Doherty KC, Shabani M, Dove ES, Bentzen HB, Borry P, Burgess MM, Chalmers D, De Vries J, Eckstein L, Fullerton SM, Juengst E, Kato K, Kaye J, Knoppers BM, Koenig BA, Manson SM, McGrail KM, McGuire AL, Meslin EM, Nicol D, Prainsack B, Terry SF, Thorogood A, Burke W.
PMID: 33414545
Nat Genet. 2021 Jan;53(1):2-8. doi: 10.1038/s41588-020-00742-6.

No abstract available.

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O'Doherty KC, Shabani M, Dove ES, et al. Toward better governance of human genomic data. Nat Genet. 2021;53(1):2-8doi: 10.1038/s41588-020-00742-6.
O'Doherty, K. C., Shabani, M., Dove, E. S., Bentzen, H. B., Borry, P., Burgess, M. M., Chalmers, D., De Vries, J., Eckstein, L., Fullerton, S. M., Juengst, E., Kato, K., Kaye, J., Knoppers, B. M., Koenig, B. A., Manson, S. M., McGrail, K. M., McGuire, A. L., Meslin, E. M., Nicol, D., Prainsack, B., Terry, S. F., Thorogood, A., & Burke, W. (2021). Toward better governance of human genomic data. Nature genetics, 53(1), 2-8. https://doi.org/10.1038/s41588-020-00742-6
O'Doherty, Kieran C, et al. "Toward better governance of human genomic data." Nature genetics vol. 53,1 (2021): 2-8. doi: https://doi.org/10.1038/s41588-020-00742-6
O'Doherty KC, Shabani M, Dove ES, Bentzen HB, Borry P, Burgess MM, Chalmers D, De Vries J, Eckstein L, Fullerton SM, Juengst E, Kato K, Kaye J, Knoppers BM, Koenig BA, Manson SM, McGrail KM, McGuire AL, Meslin EM, Nicol D, Prainsack B, Terry SF, Thorogood A, Burke W. Toward better governance of human genomic data. Nat Genet. 2021 Jan;53(1):2-8. doi: 10.1038/s41588-020-00742-6. PMID: 33414545; PMCID: PMC8450011.
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Nebula: ultra-efficient mapping-free structural variant genotyper.

Nucleic acids research

Khorsand P, Hormozdiari F.
PMID: 33503255
Nucleic Acids Res. 2021 May 07;49(8):e47. doi: 10.1093/nar/gkab025.

Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task...

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Khorsand P, Hormozdiari F. Nebula: ultra-efficient mapping-free structural variant genotyper. Nucleic Acids Res. 2021;49(8):e47doi: 10.1093/nar/gkab025.
Khorsand, P., & Hormozdiari, F. (2021). Nebula: ultra-efficient mapping-free structural variant genotyper. Nucleic acids research, 49(8), e47. https://doi.org/10.1093/nar/gkab025
Khorsand, Parsoa, and Hormozdiari, Fereydoun. "Nebula: ultra-efficient mapping-free structural variant genotyper." Nucleic acids research vol. 49,8 (2021): e47. doi: https://doi.org/10.1093/nar/gkab025
Khorsand P, Hormozdiari F. Nebula: ultra-efficient mapping-free structural variant genotyper. Nucleic Acids Res. 2021 May 07;49(8):e47. doi: 10.1093/nar/gkab025. PMID: 33503255; PMCID: PMC8096284.
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The variant call format provides efficient and robust storage of GWAS summary statistics.

Genome biology

Lyon MS, Andrews SJ, Elsworth B, Gaunt TR, Hemani G, Marcora E.
PMID: 33441155
Genome Biol. 2021 Jan 13;22(1):32. doi: 10.1186/s13059-020-02248-0.

GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically...

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Lyon MS, Andrews SJ, Elsworth B, et al. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol. 2021;22(1):32doi: 10.1186/s13059-020-02248-0.
Lyon, M. S., Andrews, S. J., Elsworth, B., Gaunt, T. R., Hemani, G., & Marcora, E. (2021). The variant call format provides efficient and robust storage of GWAS summary statistics. Genome biology, 22(1), 32. https://doi.org/10.1186/s13059-020-02248-0
Lyon, Matthew S, et al. "The variant call format provides efficient and robust storage of GWAS summary statistics." Genome biology vol. 22,1 (2021): 32. doi: https://doi.org/10.1186/s13059-020-02248-0
Lyon MS, Andrews SJ, Elsworth B, Gaunt TR, Hemani G, Marcora E. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol. 2021 Jan 13;22(1):32. doi: 10.1186/s13059-020-02248-0. PMID: 33441155; PMCID: PMC7805039.
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Automated generation of gene summaries at the Alliance of Genome Resources.

Database : the journal of biological databases and curation

Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, Genome Resources TAO.
PMID: 32559296
Database (Oxford). 2020 Jan 01;2020. doi: 10.1093/database/baaa037.

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult...

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Kishore R, Arnaboldi V, Van Slyke CE, et al. Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford). 2020;2020doi: 10.1093/database/baaa037.
Kishore, R., Arnaboldi, V., Van Slyke, C. E., Chan, J., Nash, R. S., Urbano, J. M., Dolan, M. E., Engel, S. R., Shimoyama, M., Sternberg, P. W., & Genome Resources, T. A. O. (2020). Automated generation of gene summaries at the Alliance of Genome Resources. Database : the journal of biological databases and curation, 2020. https://doi.org/10.1093/database/baaa037
Kishore, Ranjana, et al. "Automated generation of gene summaries at the Alliance of Genome Resources." Database : the journal of biological databases and curation vol. 2020 (2020). doi: https://doi.org/10.1093/database/baaa037
Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, Genome Resources TAO. Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford). 2020 Jan 01;2020. doi: 10.1093/database/baaa037. PMID: 32559296; PMCID: PMC7304461.
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EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures.

British journal of cancer

Vasaikar SV, Deshmukh AP, den Hollander P, Addanki S, Kuburich NA, Kudaravalli S, Joseph R, Chang JT, Soundararajan R, Mani SA.
PMID: 33299129
Br J Cancer. 2021 Jan;124(1):259-269. doi: 10.1038/s41416-020-01178-9. Epub 2020 Dec 10.

BACKGROUND: The epithelial-mesenchymal transition (EMT) enables dissociation of tumour cells from the primary tumour mass, invasion through the extracellular matrix, intravasation into blood vessels and colonisation of distant organs. Cells that revert to the epithelial state via the mesenchymal-epithelial...

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Vasaikar SV, Deshmukh AP, den Hollander P, et al. EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures. Br J Cancer. 2020;124(1):259-269doi: 10.1038/s41416-020-01178-9.
Vasaikar, S. V., Deshmukh, A. P., den Hollander, P., Addanki, S., Kuburich, N. A., Kudaravalli, S., Joseph, R., Chang, J. T., Soundararajan, R., & Mani, S. A. (2021). EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures. British journal of cancer, 124(1), 259-269. https://doi.org/10.1038/s41416-020-01178-9
Vasaikar, Suhas V, et al. "EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures." British journal of cancer vol. 124,1 (2021): 259-269. doi: https://doi.org/10.1038/s41416-020-01178-9
Vasaikar SV, Deshmukh AP, den Hollander P, Addanki S, Kuburich NA, Kudaravalli S, Joseph R, Chang JT, Soundararajan R, Mani SA. EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures. Br J Cancer. 2021 Jan;124(1):259-269. doi: 10.1038/s41416-020-01178-9. Epub 2020 Dec 10. PMID: 33299129; PMCID: PMC7782839.
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Toward a fine-scale population health monitoring system.

Cell

Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, Torre D, Moscati A, Wojcik GL, Shemirani R, Beckmann ND, Cohain A, Sorokin EP, Park DS, Ambite JL, Ellis S, Auton A, Bottinger EP, Cho JH, Loos RJF, Abul-Husn NS, Zaitlen NA, Gignoux CR, Kenny EE.
PMID: 33861964
Cell. 2021 Apr 15;184(8):2068-2083.e11. doi: 10.1016/j.cell.2021.03.034.

Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations....

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Belbin GM, Cullina S, Wenric S, et al. Toward a fine-scale population health monitoring system. Cell. 2021;184(8):2068-2083.e11doi: 10.1016/j.cell.2021.03.034.
Belbin, G. M., Cullina, S., Wenric, S., Soper, E. R., Glicksberg, B. S., Torre, D., Moscati, A., Wojcik, G. L., Shemirani, R., Beckmann, N. D., Cohain, A., Sorokin, E. P., Park, D. S., Ambite, J. L., Ellis, S., Auton, A., Bottinger, E. P., Cho, J. H., Loos, R. J. F., Abul-Husn, N. S., Zaitlen, N. A., Gignoux, C. R., & Kenny, E. E. (2021). Toward a fine-scale population health monitoring system. Cell, 184(8), 2068-2083.e11. https://doi.org/10.1016/j.cell.2021.03.034
Belbin, Gillian M, et al. "Toward a fine-scale population health monitoring system." Cell vol. 184,8 (2021): 2068-2083.e11. doi: https://doi.org/10.1016/j.cell.2021.03.034
Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, Torre D, Moscati A, Wojcik GL, Shemirani R, Beckmann ND, Cohain A, Sorokin EP, Park DS, Ambite JL, Ellis S, Auton A, Bottinger EP, Cho JH, Loos RJF, Abul-Husn NS, Zaitlen NA, Gignoux CR, Kenny EE. Toward a fine-scale population health monitoring system. Cell. 2021 Apr 15;184(8):2068-2083.e11. doi: 10.1016/j.cell.2021.03.034. PMID: 33861964.
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Showing 445 to 455 of 455 entries