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Showing 1 to 12 of 18 entries
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Preprocessing and downstream analysis of microarray DNA copy number profiles.

Briefings in bioinformatics

van de Wiel MA, Picard F, van Wieringen WN, Ylstra B.
PMID: 20172948
Brief Bioinform. 2011 Jan;12(1):10-21. doi: 10.1093/bib/bbq004. Epub 2010 Feb 19.

Analysis of DNA copy number profiles requires methods tailored to the specific nature of these data. The number of available data analysis methods has grown enormously in the last 5 years. We discuss the typical characteristics of DNA copy...

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van de Wiel MA, Picard F, van Wieringen WN, et al. Preprocessing and downstream analysis of microarray DNA copy number profiles. Brief Bioinform. 2010;12(1):10-21doi: 10.1093/bib/bbq004.
van de Wiel, M. A., Picard, F., van Wieringen, W. N., & Ylstra, B. (2011). Preprocessing and downstream analysis of microarray DNA copy number profiles. Briefings in bioinformatics, 12(1), 10-21. https://doi.org/10.1093/bib/bbq004
van de Wiel, Mark A, et al. "Preprocessing and downstream analysis of microarray DNA copy number profiles." Briefings in bioinformatics vol. 12,1 (2011): 10-21. doi: https://doi.org/10.1093/bib/bbq004
van de Wiel MA, Picard F, van Wieringen WN, Ylstra B. Preprocessing and downstream analysis of microarray DNA copy number profiles. Brief Bioinform. 2011 Jan;12(1):10-21. doi: 10.1093/bib/bbq004. Epub 2010 Feb 19. PMID: 20172948.
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A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns.

BMC bioinformatics

Gambin T, Walczak K.
PMID: 19208168
BMC Bioinformatics. 2009 Jan 30;10:S64. doi: 10.1186/1471-2105-10-S1-S64.

BACKGROUND: Classification using aCGH data is an important and insufficiently investigated problem in bioinformatics. In this paper we propose a new classification method of DNA copy number data based on the concept of limited Jumping Emerging Patterns. We present...

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Gambin T, Walczak K. A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns. BMC Bioinformatics. 2009;10:S64doi: 10.1186/1471-2105-10-S1-S64.
Gambin, T., & Walczak, K. (2009). A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns. BMC bioinformatics, 10S64. https://doi.org/10.1186/1471-2105-10-S1-S64
Gambin, Tomasz, and Walczak, Krzysztof. "A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns." BMC bioinformatics vol. 10 (2009): S64. doi: https://doi.org/10.1186/1471-2105-10-S1-S64
Gambin T, Walczak K. A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns. BMC Bioinformatics. 2009 Jan 30;10:S64. doi: 10.1186/1471-2105-10-S1-S64. PMID: 19208168; PMCID: PMC2648754.
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CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.

Bioinformatics (Oxford, England)

van Houte BP, Binsl TW, Hettling H, Heringa J.
PMID: 20418341
Bioinformatics. 2010 May 15;26(10):1366-7. doi: 10.1093/bioinformatics/btq155. Epub 2010 Apr 23.

SUMMARY: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations...

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van Houte BP, Binsl TW, Hettling H, et al. CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. Bioinformatics. 2010;26(10):1366-7doi: 10.1093/bioinformatics/btq155.
van Houte, B. P., Binsl, T. W., Hettling, H., & Heringa, J. (2010). CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. Bioinformatics (Oxford, England), 26(10), 1366-7. https://doi.org/10.1093/bioinformatics/btq155
van Houte, Bart P P, et al. "CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs." Bioinformatics (Oxford, England) vol. 26,10 (2010): 1366-7. doi: https://doi.org/10.1093/bioinformatics/btq155
van Houte BP, Binsl TW, Hettling H, Heringa J. CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. Bioinformatics. 2010 May 15;26(10):1366-7. doi: 10.1093/bioinformatics/btq155. Epub 2010 Apr 23. PMID: 20418341.
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[Upper G.I. cancer: the esophagus and stomach. II. The current status of comprehensive gene analysis of esophageal cancer].

Gan to kagaku ryoho. Cancer & chemotherapy

Shuto A, Tanaka F, Mimori K, Fujita H, Shirouzu K, Mori M.
PMID: 19798826
Gan To Kagaku Ryoho. 2009 Sep;36(9):1435-41.

No abstract available.

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Shuto A, Tanaka F, Mimori K, et al. [Upper G.I. cancer: the esophagus and stomach. II. The current status of comprehensive gene analysis of esophageal cancer]. Gan To Kagaku Ryoho. 2009;36(9):1435-41
Shuto, A., Tanaka, F., Mimori, K., Fujita, H., Shirouzu, K., & Mori, M. (2009). [Upper G.I. cancer: the esophagus and stomach. II. The current status of comprehensive gene analysis of esophageal cancer]. Gan to kagaku ryoho. Cancer & chemotherapy, 36(9), 1435-41.
Shuto, Asaya, et al. "[Upper G.I. cancer: the esophagus and stomach. II. The current status of comprehensive gene analysis of esophageal cancer]." Gan to kagaku ryoho. Cancer & chemotherapy vol. 36,9 (2009): 1435-41.
Shuto A, Tanaka F, Mimori K, Fujita H, Shirouzu K, Mori M. [Upper G.I. cancer: the esophagus and stomach. II. The current status of comprehensive gene analysis of esophageal cancer]. Gan To Kagaku Ryoho. 2009 Sep;36(9):1435-41. Japanese. PMID: 19798826.
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Developmental psychopathology: the role of structural variation in the genome.

Development and psychopathology

Gill M.
PMID: 23062300
Dev Psychopathol. 2012 Nov;24(4):1319-34. doi: 10.1017/S0954579412000739.

A wide range of developmental disorders present with characteristic psychopathologies and behaviors, with diagnoses including, inter alia, cognitive disorders and learning disabilities, epilepsies, autism, and schizophrenia. Each, to varying extent, has a genetic component to etiology and is associated...

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Gill M. Developmental psychopathology: the role of structural variation in the genome. Dev Psychopathol. 2012;24(4):1319-34doi: 10.1017/S0954579412000739.
Gill, M. (2012). Developmental psychopathology: the role of structural variation in the genome. Development and psychopathology, 24(4), 1319-34. https://doi.org/10.1017/S0954579412000739
Gill, Michael. "Developmental psychopathology: the role of structural variation in the genome." Development and psychopathology vol. 24,4 (2012): 1319-34. doi: https://doi.org/10.1017/S0954579412000739
Gill M. Developmental psychopathology: the role of structural variation in the genome. Dev Psychopathol. 2012 Nov;24(4):1319-34. doi: 10.1017/S0954579412000739. PMID: 23062300.
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Chromothripsis Detection and Characterization Using the CTLPScanner Web Server.

Methods in molecular biology (Clifton, N.J.)

Yang J, Liu B, Cai H.
PMID: 29564830
Methods Mol Biol. 2018;1769:265-278. doi: 10.1007/978-1-4939-7780-2_17.

Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate...

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Yang J, Liu B, Cai H. Chromothripsis Detection and Characterization Using the CTLPScanner Web Server. Methods Mol Biol. 2018;1769:265-278doi: 10.1007/978-1-4939-7780-2_17.
Yang, J., Liu, B., & Cai, H. (2018). Chromothripsis Detection and Characterization Using the CTLPScanner Web Server. Methods in molecular biology (Clifton, N.J.), 1769265-278. https://doi.org/10.1007/978-1-4939-7780-2_17
Yang, Jian, et al. "Chromothripsis Detection and Characterization Using the CTLPScanner Web Server." Methods in molecular biology (Clifton, N.J.) vol. 1769 (2018): 265-278. doi: https://doi.org/10.1007/978-1-4939-7780-2_17
Yang J, Liu B, Cai H. Chromothripsis Detection and Characterization Using the CTLPScanner Web Server. Methods Mol Biol. 2018;1769:265-278. doi: 10.1007/978-1-4939-7780-2_17. PMID: 29564830.
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Enhancer chip: detecting human copy number variations in regulatory elements.

PloS one

Savarese M, Piluso G, Orteschi D, Di Fruscio G, Dionisi M, Blanco Fdel V, Torella A, Giugliano T, Iacomino M, Zollino M, Neri G, Nigro V.
PMID: 23284961
PLoS One. 2012;7(12):e52264. doi: 10.1371/journal.pone.0052264. Epub 2012 Dec 20.

Critical functional properties are embedded in the non-coding portion of the human genome. Recent successful studies have shown that variations in distant-acting gene enhancer sequences can contribute to disease. In fact, various disorders, such as thalassaemias, preaxial polydactyly or...

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Savarese M, Piluso G, Orteschi D, et al. Enhancer chip: detecting human copy number variations in regulatory elements. PLoS One. 2012;7(12):e52264doi: 10.1371/journal.pone.0052264.
Savarese, M., Piluso, G., Orteschi, D., Di Fruscio, G., Dionisi, M., Blanco, F. d. e. l. . V., Torella, A., Giugliano, T., Iacomino, M., Zollino, M., Neri, G., & Nigro, V. (2012). Enhancer chip: detecting human copy number variations in regulatory elements. PloS one, 7(12), e52264. https://doi.org/10.1371/journal.pone.0052264
Savarese, Marco, et al. "Enhancer chip: detecting human copy number variations in regulatory elements." PloS one vol. 7,12 (2012): e52264. doi: https://doi.org/10.1371/journal.pone.0052264
Savarese M, Piluso G, Orteschi D, Di Fruscio G, Dionisi M, Blanco Fdel V, Torella A, Giugliano T, Iacomino M, Zollino M, Neri G, Nigro V. Enhancer chip: detecting human copy number variations in regulatory elements. PLoS One. 2012;7(12):e52264. doi: 10.1371/journal.pone.0052264. Epub 2012 Dec 20. PMID: 23284961; PMCID: PMC3527541.
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Application of array-based comparative genome hybridization in children with developmental delay or mental retardation.

Pediatrics and neonatology

Liang JS, Shimojima K, Yamamoto T.
PMID: 19166117
Pediatr Neonatol. 2008 Dec;49(6):213-7. doi: 10.1016/S1875-9572(09)60013-9.

Children with developmental delay or mental retardation (DD/MR) are commonly encountered in child neurology clinics, and establishing an etiologic diagnosis is a challenge for child neurologists. Among the etiologies, chromosomal imbalance is one of the most important causes. However,...

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Liang JS, Shimojima K, Yamamoto T. Application of array-based comparative genome hybridization in children with developmental delay or mental retardation. Pediatr Neonatol. 2008;49(6):213-7doi: 10.1016/S1875-9572(09)60013-9.
Liang, J. S., Shimojima, K., & Yamamoto, T. (2008). Application of array-based comparative genome hybridization in children with developmental delay or mental retardation. Pediatrics and neonatology, 49(6), 213-7. https://doi.org/10.1016/S1875-9572(09)60013-9
Liang, Jao-Shwann, et al. "Application of array-based comparative genome hybridization in children with developmental delay or mental retardation." Pediatrics and neonatology vol. 49,6 (2008): 213-7. doi: https://doi.org/10.1016/S1875-9572(09)60013-9
Liang JS, Shimojima K, Yamamoto T. Application of array-based comparative genome hybridization in children with developmental delay or mental retardation. Pediatr Neonatol. 2008 Dec;49(6):213-7. doi: 10.1016/S1875-9572(09)60013-9. PMID: 19166117.
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rCGH: a comprehensive array-based genomic profile platform for precision medicine.

Bioinformatics (Oxford, England)

Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.
PMID: 26708336
Bioinformatics. 2016 May 01;32(9):1402-4. doi: 10.1093/bioinformatics/btv718. Epub 2015 Dec 26.

UNLABELLED: We present rCGH, a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine. rCGH supports the major microarray platforms, ensures a full traceability and facilitates profiles interpretation and decision-making through...

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Commo F, Guinney J, Ferté C, et al. rCGH: a comprehensive array-based genomic profile platform for precision medicine. Bioinformatics. 2015;32(9):1402-4doi: 10.1093/bioinformatics/btv718.
Commo, F., Guinney, J., Ferté, C., Bot, B., Lefebvre, C., Soria, J. C., & André, F. (2016). rCGH: a comprehensive array-based genomic profile platform for precision medicine. Bioinformatics (Oxford, England), 32(9), 1402-4. https://doi.org/10.1093/bioinformatics/btv718
Commo, Frederic, et al. "rCGH: a comprehensive array-based genomic profile platform for precision medicine." Bioinformatics (Oxford, England) vol. 32,9 (2016): 1402-4. doi: https://doi.org/10.1093/bioinformatics/btv718
Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F. rCGH: a comprehensive array-based genomic profile platform for precision medicine. Bioinformatics. 2016 May 01;32(9):1402-4. doi: 10.1093/bioinformatics/btv718. Epub 2015 Dec 26. PMID: 26708336; PMCID: PMC4848396.
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[Diagnosis of Wolf-Hirschhorn syndrome by array-comparative genomic hybridization in an infant].

Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics

Que LP, Liang LY, Meng Z, Luo XY, Ou RQ, Hou LL.
PMID: 25523581
Zhongguo Dang Dai Er Ke Za Zhi. 2014 Dec;16(12):1277-8.

No abstract available.

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Que LP, Liang LY, Meng Z, et al. [Diagnosis of Wolf-Hirschhorn syndrome by array-comparative genomic hybridization in an infant]. Zhongguo Dang Dai Er Ke Za Zhi. 2014;16(12):1277-8
Que, L. P., Liang, L. Y., Meng, Z., Luo, X. Y., Ou, R. Q., & Hou, L. L. (2014). [Diagnosis of Wolf-Hirschhorn syndrome by array-comparative genomic hybridization in an infant]. Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics, 16(12), 1277-8.
Que, Li-Ping, et al. "[Diagnosis of Wolf-Hirschhorn syndrome by array-comparative genomic hybridization in an infant]." Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics vol. 16,12 (2014): 1277-8.
Que LP, Liang LY, Meng Z, Luo XY, Ou RQ, Hou LL. [Diagnosis of Wolf-Hirschhorn syndrome by array-comparative genomic hybridization in an infant]. Zhongguo Dang Dai Er Ke Za Zhi. 2014 Dec;16(12):1277-8. Chinese. PMID: 25523581.
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SNP genotyping with the next generation of CGH microarray.

MLO: medical laboratory observer

Burton R.
PMID: 24180067
MLO Med Lab Obs. 2013 Jul;45(7):8, 10, 12 passim.

Enabling the simultaneous detection of CNV and copy-neutral aberrations within one test, the combined aCGH and SNP array has the potential to vastly improve both workflow efficiency and productivity within the cytogenetics research laboratory. The applications of the combined...

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Burton R. SNP genotyping with the next generation of CGH microarray. MLO Med Lab Obs. 2013;45(7):8, 10, 12 passim
Burton, R. (2013). SNP genotyping with the next generation of CGH microarray. MLO: medical laboratory observer, 45(7), 8, 10, 12 passim.
Burton, Ruth. "SNP genotyping with the next generation of CGH microarray." MLO: medical laboratory observer vol. 45,7 (2013): 8, 10, 12 passim.
Burton R. SNP genotyping with the next generation of CGH microarray. MLO Med Lab Obs. 2013 Jul;45(7):8, 10, 12 passim. PMID: 24180067.
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Array-CGH: importance in the study of developmental delays in pediatrics.

Revista de neurologia

Pinheiro MI, Silva C, Lourenço L, Gonçalves D, Dória S, Guardiano M, Leão M.
PMID: 32729108
Rev Neurol. 2020 Sep 01;71(5):171-176. doi: 10.33588/rn.7105.2020211.

INTRODUCTION: Global developmental delay (GDD) is an intellectual and adaptive impairment in infants under 5 years of age who fail to meet expected developmental milestones. Intellectual disability is characterized by limitation in intellectual function and adaptive behavior, with onset...

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Pinheiro MI, Silva C, Lourenço L, et al. Relevancia de los arrays de hibridación genómica comparada en el estudio de los retrasos del desarrollo en pediatría. Array-CGH: importance in the study of developmental delays in pediatrics. Rev Neurol. 2020;71(5):171-176doi: 10.33588/rn.7105.2020211.
Pinheiro, M. I., Silva, C., Lourenço, L., Gonçalves, D., Dória, S., Guardiano, M., & Leão, M. (2020). Relevancia de los arrays de hibridación genómica comparada en el estudio de los retrasos del desarrollo en pediatría. Array-CGH: importance in the study of developmental delays in pediatrics. Revista de neurologia, 71(5), 171-176. https://doi.org/10.33588/rn.7105.2020211
Pinheiro, M I, et al. "Relevancia de los arrays de hibridación genómica comparada en el estudio de los retrasos del desarrollo en pediatría." Array-CGH: importance in the study of developmental delays in pediatrics. Revista de neurologia vol. 71,5 (2020): 171-176. doi: https://doi.org/10.33588/rn.7105.2020211
Pinheiro MI, Silva C, Lourenço L, Gonçalves D, Dória S, Guardiano M, Leão M. Relevancia de los arrays de hibridación genómica comparada en el estudio de los retrasos del desarrollo en pediatría. Array-CGH: importance in the study of developmental delays in pediatrics. Rev Neurol. 2020 Sep 01;71(5):171-176. doi: 10.33588/rn.7105.2020211. Spanish. PMID: 32729108.
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Showing 1 to 12 of 18 entries