Template:Publications - Revision history

Christoph: /* Citations */

2016-01-01T02:06:58Z

‎Citations

Christoph at 00:43, 13 July 2012

2012-07-13T00:43:56Z

Christoph at 16:38, 7 November 2010

2010-11-07T16:38:52Z

Christoph at 21:27, 3 August 2010

2010-08-03T21:27:17Z

Christoph at 04:10, 4 March 2009

2009-03-04T04:10:14Z

Christoph at 01:26, 25 December 2008

2008-12-25T01:26:59Z

Christoph at 06:19, 4 January 2008

2008-01-04T06:19:50Z

Christoph at 03:04, 18 October 2007

2007-10-18T03:04:24Z

Christoph at 03:47, 21 August 2007

2007-08-21T03:47:42Z

Christoph at 21:45, 15 June 2007

2007-06-15T21:45:18Z

@@ Line 9: / Line 9: @@
 ===Citations===
-''Note: The following is an incomplete lists.''
+''Note: The following is an incomplete list.''
 #Edwards SF, Siritoc M, Krahec R, Sinden RR (2009). "A Z-DNA sequence reduces slipped-strand structure formation in the myotonic dystrophy type 2 (CCTG).(CAGG) repeat". ''PNAS, 106(9):3270-327''. {{doi|10.1073/pnas.0807699106}}
 #Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. {{doi|10.1016/j.ymeth.2008.09.007}}

@@ Line 1: / Line 1: @@
-#Frank Zucker, '''P. Christoph Champ''', and Ethan A. Merritt (2010). Validation of crystallographic models containing TLS or other descriptions of anisotropy. ''Acta Cryst., D66:889-900''. {{doi|10.1107/S0907444910020421}}
+#Frank Zucker, '''P. Christoph Champ''', and Ethan A. Merritt (2010). "Validation of crystallographic models containing TLS or other descriptions of anisotropy". ''Acta Cryst., D66:889-900''. {{doi|10.1107/S0907444910020421}}
-#'''P. Christoph Champ''' and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. ''Nucleic Acids Research (Web Issue)''. {{doi|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]
+#'''P. Christoph Champ''' and Carlos J. Camacho (2007). "FastContact: a free energy scoring tool for protein-protein complex structures". ''Nucleic Acids Research (Web Issue)''. {{doi|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]
-#'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]
+#'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). "Genome update: purine strand bias in 280 bacterial chromosomes". [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]
-#Carlos J. Camacho, Ma H, and '''P. Christoph Champ''' (2006). Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. [http://www3.interscience.wiley.com/cgi-bin/abstract/112467717/ABSTRACT?CRETRY=1&SRETRY=0 ''Proteins, 63(4):868-77] {{doi|10.1002/prot.20932}}''. [[http://www.hubmed.org/display.cgi?uids=16506242 HubMed]]
+#Carlos J. Camacho, Ma H, and '''P. Christoph Champ''' (2006). "Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions". [http://www3.interscience.wiley.com/cgi-bin/abstract/112467717/ABSTRACT?CRETRY=1&SRETRY=0 ''Proteins, 63(4):868-77] {{doi|10.1002/prot.20932}}''. [[http://www.hubmed.org/display.cgi?uids=16506242 HubMed]]
-#'''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510] {{doi|10.1093/nar/gkh988}}''. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here])
+#'''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). "Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation". [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510] {{doi|10.1093/nar/gkh988}}''. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here])
 ===Acknowledgments===
-*Camacho CJ, Zhang C (2005). FastContact: rapid estimate of contact and binding free energies. ''Bioinformatics, 21(10):2534-2536; {{doi|10.1093/bioinformatics/bti322}}''.
+*Camacho CJ, Zhang C (2005). "FastContact: rapid estimate of contact and binding free energies". ''Bioinformatics, 21(10):2534-2536; {{doi|10.1093/bioinformatics/bti322}}''.
 ===Citations===

@@ Line 1: / Line 1: @@
-*Frank Zucker, '''P. Christoph Champ''', and Ethan A. Merritt (2010). Validation of crystallographic models containing TLS or other descriptions of anisotropy. ''Acta Cryst., D66:889-900''. {{doi|10.1107/S0907444910020421}}
+#Frank Zucker, '''P. Christoph Champ''', and Ethan A. Merritt (2010). Validation of crystallographic models containing TLS or other descriptions of anisotropy. ''Acta Cryst., D66:889-900''. {{doi|10.1107/S0907444910020421}}
-*'''P. Christoph Champ''' and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. ''Nucleic Acids Research (Web Issue)''. {{doi|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]
+#'''P. Christoph Champ''' and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. ''Nucleic Acids Research (Web Issue)''. {{doi|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]
-*'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]
+#'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]
-*Carlos J. Camacho, Ma H, and '''P. Christoph Champ''' (2006). Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. [http://www3.interscience.wiley.com/cgi-bin/abstract/112467717/ABSTRACT?CRETRY=1&SRETRY=0 ''Proteins, 63(4):868-77] {{doi|10.1002/prot.20932}}''. [[http://www.hubmed.org/display.cgi?uids=16506242 HubMed]]
+#Carlos J. Camacho, Ma H, and '''P. Christoph Champ''' (2006). Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. [http://www3.interscience.wiley.com/cgi-bin/abstract/112467717/ABSTRACT?CRETRY=1&SRETRY=0 ''Proteins, 63(4):868-77] {{doi|10.1002/prot.20932}}''. [[http://www.hubmed.org/display.cgi?uids=16506242 HubMed]]
-*'''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510] {{doi|10.1093/nar/gkh988}}''. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here])
+#'''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510] {{doi|10.1093/nar/gkh988}}''. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here])
-:<u>Citations</u>:
-::&rarr; Edwards SF, Siritoc M, Krahec R, Sinden RR (2009). "A Z-DNA sequence reduces slipped-strand structure formation in the myotonic dystrophy type 2 (CCTG).(CAGG) repeat". ''PNAS, 106(9):3270-327''. {{doi|10.1073/pnas.0807699106}}
+===Acknowledgments===
-::&rarr; Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. {{doi|10.1016/j.ymeth.2008.09.007}}
+*Camacho CJ, Zhang C (2005). FastContact: rapid estimate of contact and binding free energies. ''Bioinformatics, 21(10):2534-2536; {{doi|10.1093/bioinformatics/bti322}}''.
-::&rarr; Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007). "A high-resolution atlas of nucleosome occupancy in yeast". ''Nature Genetics, 39:1235:1244''. {{doi|10.1038/ng2117}}
-::&rarr; Kulisha VV, Heng L, Dröge P (2007). "Z-DNA-induced super-transport of energy within genomes". ''Physica A: Statistical Mechanics and its Applications, 384(2):733-738''. {{doi|10.1016/j.physa.2007.06.023}}
+===Citations===
-::&rarr; Kouzine F, Levens D (2007). "Supercoil-driven DNA structures regulate genetic transactions". ''Frontiers in Bioscience, 12:4409-4423''.
+''Note: The following is an incomplete lists.''
-::&rarr; Khuu P, Sandor M, DeYoung J, Ho PS (2007). "Phylogenomic analysis of the emergence of GC-rich transcription elements". ''PNAS, 104(42):16528-16533''. {{doi|10.1073/pnas.0707203104}}
+#Edwards SF, Siritoc M, Krahec R, Sinden RR (2009). "A Z-DNA sequence reduces slipped-strand structure formation in the myotonic dystrophy type 2 (CCTG).(CAGG) repeat". ''PNAS, 106(9):3270-327''. {{doi|10.1073/pnas.0807699106}}
-::&rarr; Yoshida N, Amanai M, Fukui T, Kajikawa E, Brahmajosyula M, Iwahori A, Nakano Y, Shoji S, Diebold J, Hessel H, Huss R, Perry ACF (2007). "Broad, ectopic expression of the sperm protein PLCZ1 induces parthenogenesis and ovarian tumours in mice". ''Development, 134:3941-3952''. {{doi|10.1242/10.1242/dev.007930}}
+#Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. {{doi|10.1016/j.ymeth.2008.09.007}}
-::&rarr; Lorenzen S, Zhang Y (2007). Identification of near-native structures by clustering protein docking conformations. ''Proteins: Structure, Function, and Bioinformatics, 68(1):187-194; {{doi|10.1002/prot.21442}}''.
+#Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007). "A high-resolution atlas of nucleosome occupancy in yeast". ''Nature Genetics, 39:1235:1244''. {{doi|10.1038/ng2117}}
-::&rarr; Mobley DL, Dumont É, Chodera JD, Dill KA (2007). "Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent". ''J Phys Chem B, 111(9):2242-2254''. {{doi|10.1021/jp0667442}}
+#Kulisha VV, Heng L, Dröge P (2007). "Z-DNA-induced super-transport of energy within genomes". ''Physica A: Statistical Mechanics and its Applications, 384(2):733-738''. {{doi|10.1016/j.physa.2007.06.023}}
-::&rarr; Panpan Z, Lijuan W, Wenyuan Q (2006). The junction between B-DNA and Z-DNA. ''Chemistry, 69(11):822-825''.
+#Kouzine F, Levens D (2007). "Supercoil-driven DNA structures regulate genetic transactions". ''Frontiers in Bioscience, 12:4409-4423''.
-::&rarr; Bala Gupta V, Hegde, ML, Jagnnathan Rao KS (2006). Role of Protein Conformational Dynamics and DNA Integrity in Relevance to Neuronal Cell Death in Neurodegeneration. ''Current Alzheimer Research, 3(4):297-309(13); {{doi|10.2174/156720506778249452}}''.
+#Khuu P, Sandor M, DeYoung J, Ho PS (2007). "Phylogenomic analysis of the emergence of GC-rich transcription elements". ''PNAS, 104(42):16528-16533''. {{doi|10.1073/pnas.0707203104}}
-::&rarr; Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG (2006). Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. ''J Human Genetics, 120(4):519-526''; {{doi|10.1007/s00439-006-0222-1}}''.
+#Yoshida N, Amanai M, Fukui T, Kajikawa E, Brahmajosyula M, Iwahori A, Nakano Y, Shoji S, Diebold J, Hessel H, Huss R, Perry ACF (2007). "Broad, ectopic expression of the sperm protein PLCZ1 induces parthenogenesis and ovarian tumours in mice". ''Development, 134:3941-3952''. {{doi|10.1242/10.1242/dev.007930}}
-::&rarr; Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M (2006). Effect of Sequence-Directed Nucleosome Disruption on Cell-Type-Specific Repression by &alpha;2/Mcm1 in the Yeast Genome. ''Eukaryotic Cell, 5(11):1925-1933''. {{doi|10.1128/EC.00105-06}}
+#Lorenzen S, Zhang Y (2007). Identification of near-native structures by clustering protein docking conformations. ''Proteins: Structure, Function, and Bioinformatics, 68(1):187-194; {{doi|10.1002/prot.21442}}''.
-::&rarr; Kastenholz MA, Schwartz TU, Hunenberger PH (2006). The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. ''Biophys J, 91:2976-2990''.
+#Mobley DL, Dumont É, Chodera JD, Dill KA (2007). "Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent". ''J Phys Chem B, 111(9):2242-2254''. {{doi|10.1021/jp0667442}}
-::&rarr; Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. ''Mol Cell Biol, 26(7):2550-9''.
+#Panpan Z, Lijuan W, Wenyuan Q (2006). The junction between B-DNA and Z-DNA. ''Chemistry, 69(11):822-825''.
-::&rarr; Quyen DV, Kim KK, Kim YG (2006). Sequence-dependent kinetic behavior of protein-induced B- to Z-DNA transition. ''Bulletin of the Korean Chemical Society, 27(7):1071-1074''.
+#Bala Gupta V, Hegde, ML, Jagnnathan Rao KS (2006). Role of Protein Conformational Dynamics and DNA Integrity in Relevance to Neuronal Cell Death in Neurodegeneration. ''Current Alzheimer Research, 3(4):297-309(13); {{doi|10.2174/156720506778249452}}''.
-::&rarr; Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. ''Nature, 437:1183-1186''.
+#Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG (2006). Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. ''J Human Genetics, 120(4):519-526''; {{doi|10.1007/s00439-006-0222-1}}''.
-::&rarr; Kwon JA, Rich A (2005). Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. ''Proc Natl Acad Sci USA, 102:12759-12764''.
+#Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M (2006). Effect of Sequence-Directed Nucleosome Disruption on Cell-Type-Specific Repression by &alpha;2/Mcm1 in the Yeast Genome. ''Eukaryotic Cell, 5(11):1925-1933''. {{doi|10.1128/EC.00105-06}}
-: <u>Acknowledgments</u>:
+#Kastenholz MA, Schwartz TU, Hunenberger PH (2006). The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. ''Biophys J, 91:2976-2990''.
-::&rarr; Camacho CJ, Zhang C (2005). FastContact: rapid estimate of contact and binding free energies. ''Bioinformatics, 21(10):2534-2536; {{doi|10.1093/bioinformatics/bti322}}''.<noinclude>
+#Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. ''Mol Cell Biol, 26(7):2550-9''.
 ==BibTeX==

← Older revision		Revision as of 21:27, 3 August 2010
Line 1:		Line 1:
		+	*Frank Zucker, '''P. Christoph Champ''', and Ethan A. Merritt (2010). Validation of crystallographic models containing TLS or other descriptions of anisotropy. ''Acta Cryst., D66:889-900''. {{doi\|10.1107/S0907444910020421}}
	*'''P. Christoph Champ''' and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. ''Nucleic Acids Research (Web Issue)''. {{doi\|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]		*'''P. Christoph Champ''' and Carlos J. Camacho (2007). FastContact: a free energy scoring tool for protein-protein complex structures. ''Nucleic Acids Research (Web Issue)''. {{doi\|10.1093/nar/gkm326}}. [[http://www.hubmed.org/display.cgi?uids=17537824 HubMed]]
	*'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi\|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]		*'''P. Christoph Champ''', Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583] {{doi\|10.1099/mic.0.28637-0}}''. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]

@@ Line 4: / Line 4: @@
 *'''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510] {{doi|10.1093/nar/gkh988}}''. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here])
 :<u>Citations</u>:
 ::&rarr; Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. {{doi|10.1016/j.ymeth.2008.09.007}}
 ::&rarr; Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007). "A high-resolution atlas of nucleosome occupancy in yeast". ''Nature Genetics, 39:1235:1244''. {{doi|10.1038/ng2117}}