bib copy number variations (2005)

Bibliography on copy number variations (2005)

front page
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
90s
80s
glossary
links
programs

Patrick G Buckley, Caroline Jarbo, Uwe Menzel, Tiit Mathiesen, Carol Scott, Simon G Gregory, Cordelia F Langford, Jan P Dumanski (2005), "Comprehensive DNA copy number profiling of meningioma using a chromosome 1 tiling path microarray identifies novel candidate tumor suppressor loci", Cancer Research, 65:2653-2661.
[abstract]
PG Buckley, KK Mantripragada, A Piotrowski, T Diaz de Stahl, JP Dumanski (2005), "Copy-number polymorphisms: mining the tip of an iceberg", Trends in Genetics, 21(6):315-317.
[PDF]
Bert BA De Vries, Rolph Pfundt, Martijn Leisink, David A Koolen, Lisenka ELM Vissers, Irene M Janssen, Simon van Reijmersdal, Willy M Nillesen, Erik HLPG Huys, Nicole de Leeuw, Dominique Smeets, Erik A Sistermans, Ton Feuth, Conny MA van Ravenswaaij-Arts, Ad Geurts van Kessel, Eric FPM Schoenmakers, Han G Brunner, Joris A Veltman (2005), "Diagnostic genome profiling in mental retardation", American Journal of Human Genetics, 77(4):606-616.
[html]
P Dhami, A Coffey, S Abbs, J Vermeesch, J Dumanski, K Woodward, R Andrews, C Langford, D Vetrie (2005), "Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome", American Journal of Human Genetics, 76(5):750-762
J Hicks, L Muthuswamy, A Krasnitz, N Navin, M Riggs, V Grubor, D Esposito, J Alexander, J Troge, M Wigler, S Maner, P Lundin, A Zetterberg (2005), "High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors", Cold Spring Harb Symposium on Quantitative Biology, 70:51-63.
L Hsu, SG Self, D Grove, T Randolph, K Wang, JJ Delrow, L Loo, P Porter (2005), "Denoising array-based comparative genomic hybridization data using wavelets", Biostatistics, 6:211-226.
Tao Huang , Baolin Wu, Paul Lizardi, and Hongyu Zhao (2005), "Detection of DNA copy number alterations using penalized least squares regression", Bioinformatics, 21(20):3811-3817.
[abstract] [program]
V Jobanputra, J Sebat, J Troge, W Chung, K Anyane-Yeboa, M Wigler, D Warburton (2005), "Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements", Genetics in Medicine, 7(2):111-118.
G Jonsson, T L Naylor, J Vallon-Christersson, J Staaf, J Huang, M R Ward, J D Greshock, L Luts, H Olsson, N Rahman, M Stratton, M Ringnér, A Borg, BL Weber (2005), "Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization", Cancer Research, 65(17):7612-7621.
[abstract]
Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward, Calum MacAulay (2005), "A stepwise framework for the normalization of array CGH data", BMC Bioinformatics, 6:274
[abstract]
YL Lai, HY Zhao (2005), "A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data", Computational Biology and Chemistry, 29:90-98.
Weil R Lai, Mark D Johnson, Raju Kucherlapati, and Peter J Park (2005), "Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data", Bioinformatics, 21(19):3763-3770.
[abstract]
Ole Christian Lingjærde, Lars O. Baumbusch, Knut Liestøl, Ingrid K. Glad, and Anne-Lise Børresen-Dale (2005), "CGH-Explorer: a program for analysis of array-CGH data", Bioinformatics, 21(6):821-822.
[abstract]
Adam A Margolin, Joel Greshock, Tara L Naylor, Yael Mosse, John M Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, and Barbara L. Weber (2005), "CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data", Bioinformatics, 21(15):3308-3311.
[abstract]
Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele (2005), "arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays", BMC Bioinformatics, 6:124.
[abstract]
Y Nannya, M Sanada, K Nakazaki, N Hosoya, L Wang, A Hangaishi, M Kurokawa, S Chiba, DK Bailey, GC Kennedy, S Ogawa (2005), "A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays", Cancer Research, 65(14):6071-6079.
[abstract]
Tera L Newman, Eray Tuzun, V Anne Morrison, Karen E Hayden, Mario Ventura, Sean D McGrath, Mariano Rocchi, Evan E Eichler (2005), "A genome-wide survey of structural variation between human and chimpanzee", Genome Research, 15:1344-1356.
[abstract]
F Picard, S Robin, M Lavielle, C Vaisse, J Daudin (2005), "A statistical approach for array CGH data analysis", BMC Bioinformatics, 6:27.
Daniel Pinkel, Donna G Albertson (2005), "Array comparative genomic hybridization and its applications in cancer", Nature Genetics, 37(supp):S11-S17.
[PDF]
Thomas S Price, Regina Regan, Richard Mott, Åsa Hedman, Ben Honey, Rachael J Daniels, Lee Smith, Andy Greenfield, Ana Tiganescu, Veronica Buckle, Nicki Ventress, Helena Ayyub, Anita Salhan, Susana Pedraza-Diaz, John Broxholme, Jiannis Ragoussis, Douglas R Higgs, Jonathan Flint, Samantha J L Knight (2005), "SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data", Nucleic Acids Research, 33:3455-3464.
[abstract]
Falk Schubert, Bernhard Tausch, Stefan Joos, Roland Eils (2005), "CGH-Profiler: Data mining based on genomic aberration profiles", BMC Bioinformatics, 6:188.
[abstract]
A Sharp, D Locke, S McGrath, Z Cheng, J Bailey, R Vallente, L Pertz, R Clark, S Schwartz, R Segraves (2005), "Segmental duplications and copy-number variation in the human genome", American Journal of Human Genetics, 77(1):78-88.
[html]
Eray Tuzun, Andrew J Sharp, Jeffrey A Bailey, Rajinder Kaul, V Anne Morrison, Lisa M Pertz, Eric Haugen, Hillary Hayden, Donna Albertson, Daniel Pinkel, Maynard V Olson, Evan E Eichler (2005), "Fine-scale structural variation of the human genome", Nature Genetics, 37:727-732.
[abstract]
Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege, Dhinoth Kumar Bangarusamy, Jos Jonkers, Gerrit A Meijer, Carlos Caldas, Bauke Ylstra (2006), "Human and mouse oligonucleotide-based array CGH", Nucleic Acids Research, 33(22):e192-e192.
[abstract]
GJ Van Ommen (2005), "Frequency of new copy number variation in humans" (commentary), Nature Genetics, 37(4):333-334.
Joris R Vermeesch, Cindy Melotte, Guy Froyen, Steven Van Vooren, Binita Dutta, Nicole Maas, Stefan Vermeulen, Björn Menten, Frank Speleman, Bart De Moor, Paul Van Hummelen, Peter Marynen, Jean-Pierre Fryns, Koen Devriendt (2005), "Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis", Journal of Histochemistry & Cytochemistry, 53(3):413-422.
[abstract]
P Wang, Y Kim, J Pollack, B Narasimhan, R Tibishirani (2005), "A method for calling gains and losses in array CGH data", Biostatistics, 6:45-58.
[abstract]
H Willenbrock and J Fridlyand (2005), "A comparison study: applying segmentation to array CGH data for downstream analyses", Bioinformatics, 21(22):4084-4091.
[abstract]
NR Zhang (2005), Change-Point Detection And Sequence Alignment: Statistical Problems of Genomics (Ph.D Thesis, Stanford University)
[PDF]

		Bibliography on copy number variations (2005)
	front page 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 90s 80s glossary links programs	Patrick G Buckley, Caroline Jarbo, Uwe Menzel, Tiit Mathiesen, Carol Scott, Simon G Gregory, Cordelia F Langford, Jan P Dumanski (2005), "Comprehensive DNA copy number profiling of meningioma using a chromosome 1 tiling path microarray identifies novel candidate tumor suppressor loci", Cancer Research, 65:2653-2661. [abstract] PG Buckley, KK Mantripragada, A Piotrowski, T Diaz de Stahl, JP Dumanski (2005), "Copy-number polymorphisms: mining the tip of an iceberg", Trends in Genetics, 21(6):315-317. [PDF] Bert BA De Vries, Rolph Pfundt, Martijn Leisink, David A Koolen, Lisenka ELM Vissers, Irene M Janssen, Simon van Reijmersdal, Willy M Nillesen, Erik HLPG Huys, Nicole de Leeuw, Dominique Smeets, Erik A Sistermans, Ton Feuth, Conny MA van Ravenswaaij-Arts, Ad Geurts van Kessel, Eric FPM Schoenmakers, Han G Brunner, Joris A Veltman (2005), "Diagnostic genome profiling in mental retardation", American Journal of Human Genetics, 77(4):606-616. [html] P Dhami, A Coffey, S Abbs, J Vermeesch, J Dumanski, K Woodward, R Andrews, C Langford, D Vetrie (2005), "Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome", American Journal of Human Genetics, 76(5):750-762 J Hicks, L Muthuswamy, A Krasnitz, N Navin, M Riggs, V Grubor, D Esposito, J Alexander, J Troge, M Wigler, S Maner, P Lundin, A Zetterberg (2005), "High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors", Cold Spring Harb Symposium on Quantitative Biology, 70:51-63. L Hsu, SG Self, D Grove, T Randolph, K Wang, JJ Delrow, L Loo, P Porter (2005), "Denoising array-based comparative genomic hybridization data using wavelets", Biostatistics, 6:211-226. Tao Huang , Baolin Wu, Paul Lizardi, and Hongyu Zhao (2005), "Detection of DNA copy number alterations using penalized least squares regression", Bioinformatics, 21(20):3811-3817. [abstract] [program] V Jobanputra, J Sebat, J Troge, W Chung, K Anyane-Yeboa, M Wigler, D Warburton (2005), "Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements", Genetics in Medicine, 7(2):111-118. G Jonsson, T L Naylor, J Vallon-Christersson, J Staaf, J Huang, M R Ward, J D Greshock, L Luts, H Olsson, N Rahman, M Stratton, M Ringnér, A Borg, BL Weber (2005), "Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization", Cancer Research, 65(17):7612-7621. [abstract] Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward, Calum MacAulay (2005), "A stepwise framework for the normalization of array CGH data", BMC Bioinformatics, 6:274 [abstract] YL Lai, HY Zhao (2005), "A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data", Computational Biology and Chemistry, 29:90-98. Weil R Lai, Mark D Johnson, Raju Kucherlapati, and Peter J Park (2005), "Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data", Bioinformatics, 21(19):3763-3770. [abstract] Ole Christian Lingjærde, Lars O. Baumbusch, Knut Liestøl, Ingrid K. Glad, and Anne-Lise Børresen-Dale (2005), "CGH-Explorer: a program for analysis of array-CGH data", Bioinformatics, 21(6):821-822. [abstract] Adam A Margolin, Joel Greshock, Tara L Naylor, Yael Mosse, John M Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, and Barbara L. Weber (2005), "CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data", Bioinformatics, 21(15):3308-3311. [abstract] Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele (2005), "arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays", BMC Bioinformatics, 6:124. [abstract] Y Nannya, M Sanada, K Nakazaki, N Hosoya, L Wang, A Hangaishi, M Kurokawa, S Chiba, DK Bailey, GC Kennedy, S Ogawa (2005), "A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays", Cancer Research, 65(14):6071-6079. [abstract] Tera L Newman, Eray Tuzun, V Anne Morrison, Karen E Hayden, Mario Ventura, Sean D McGrath, Mariano Rocchi, Evan E Eichler (2005), "A genome-wide survey of structural variation between human and chimpanzee", Genome Research, 15:1344-1356. [abstract] F Picard, S Robin, M Lavielle, C Vaisse, J Daudin (2005), "A statistical approach for array CGH data analysis", BMC Bioinformatics, 6:27. Daniel Pinkel, Donna G Albertson (2005), "Array comparative genomic hybridization and its applications in cancer", Nature Genetics, 37(supp):S11-S17. [PDF] Thomas S Price, Regina Regan, Richard Mott, Åsa Hedman, Ben Honey, Rachael J Daniels, Lee Smith, Andy Greenfield, Ana Tiganescu, Veronica Buckle, Nicki Ventress, Helena Ayyub, Anita Salhan, Susana Pedraza-Diaz, John Broxholme, Jiannis Ragoussis, Douglas R Higgs, Jonathan Flint, Samantha J L Knight (2005), "SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data", Nucleic Acids Research, 33:3455-3464. [abstract] Falk Schubert, Bernhard Tausch, Stefan Joos, Roland Eils (2005), "CGH-Profiler: Data mining based on genomic aberration profiles", BMC Bioinformatics, 6:188. [abstract] A Sharp, D Locke, S McGrath, Z Cheng, J Bailey, R Vallente, L Pertz, R Clark, S Schwartz, R Segraves (2005), "Segmental duplications and copy-number variation in the human genome", American Journal of Human Genetics, 77(1):78-88. [html] Eray Tuzun, Andrew J Sharp, Jeffrey A Bailey, Rajinder Kaul, V Anne Morrison, Lisa M Pertz, Eric Haugen, Hillary Hayden, Donna Albertson, Daniel Pinkel, Maynard V Olson, Evan E Eichler (2005), "Fine-scale structural variation of the human genome", Nature Genetics, 37:727-732. [abstract] Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege, Dhinoth Kumar Bangarusamy, Jos Jonkers, Gerrit A Meijer, Carlos Caldas, Bauke Ylstra (2006), "Human and mouse oligonucleotide-based array CGH", Nucleic Acids Research, 33(22):e192-e192. [abstract] GJ Van Ommen (2005), "Frequency of new copy number variation in humans" (commentary), Nature Genetics, 37(4):333-334. Joris R Vermeesch, Cindy Melotte, Guy Froyen, Steven Van Vooren, Binita Dutta, Nicole Maas, Stefan Vermeulen, Björn Menten, Frank Speleman, Bart De Moor, Paul Van Hummelen, Peter Marynen, Jean-Pierre Fryns, Koen Devriendt (2005), "Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis", Journal of Histochemistry & Cytochemistry, 53(3):413-422. [abstract] P Wang, Y Kim, J Pollack, B Narasimhan, R Tibishirani (2005), "A method for calling gains and losses in array CGH data", Biostatistics, 6:45-58. [abstract] H Willenbrock and J Fridlyand (2005), "A comparison study: applying segmentation to array CGH data for downstream analyses", Bioinformatics, 21(22):4084-4091. [abstract] NR Zhang (2005), Change-Point Detection And Sequence Alignment: Statistical Problems of Genomics (Ph.D Thesis, Stanford University) [PDF]