A sequence-based survey of the complex structural organization of tumor genomes (2008)
Raphael, Benjamin J, Volik, Stanislav, Yu, Peng, Wu, Chunxiao, Huang, Guiqing, Linardopoulou, Elena V, ...
Abstract Background The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which...
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene (2007)
Ward, Robert D., Cho, MinChul, Camper, S. A., Davis, Shannon W., Raetzman, Lori T., Smith, Timothy P. L., ...
Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and...
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons (2007)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Abstract Background Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis -regulatory elements based on constrained sequence evolution. However, these...
Primate-specific evolution of an LDLR enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Background Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. Results In this...
Primate-Specific Evolution of an LDLR Enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study, we...
Detection of Weakly Conserved Ancestral Mammalian Regulatory Sequences by Primate Comparisons (2006)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M., Boffelli, Dario
Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis-regulatory elements based on constrained sequence evolution. However, these methods fail to detect...
Decoding the fine-scale structure of a breast cancer genome and transcriptome (2006)
Volik, Stanislav, Raphael, Benjamin J., Huang, Guiqing, Stratton, Michael R., Bignel, Graham, Murnane, John, ...
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is...
Chimeric Plastid Proteome in the Florida "Red Tide" Dinoflagellate Karenia brevis (2006)
Nosenko, Tetyana, Lidie, Kristy L., Van Dolah, Frances M., Lindquist, Erika, Cheng, Jan-Fang, ...
Current understanding of the plastid proteome comes almost exclusively from studies of plants and red algae. The proteome in these taxa has a relatively simple origin via integration of proteins from...
Decoding the fine-scale structure of a breast cancer genome and transcriptome (2006)
Volik, Stanislav, Raphael, Benjamin J., Huang, Guiqing, Stratton, Michael R., Bignel, Graham, Murnane, John, ...
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is...
Chimeric Plastid Proteome in the Florida "Red Tide" Dinoflagellate Karenia brevis (2006)
Nosenko, Tetyana, Lidie, Kristy L., Van Dolah, Frances M., Lindquist, Erika, Cheng, Jan-Fang, ...
Current understanding of the plastid proteome comes almost exclusively from studies of plants and red algae. The proteome in these taxa has a relatively simple origin via integration of proteins from...
Primate-specific evolution of an LDLR enhancer (2005)
Wang, Qian-Fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Liang-Hao Ding, Masato Shingyoji, Fanqing Chen, Jeng-Jong Hwang, Sandeep Burma, Clarissa Lee, ...
Ding, L-H., Shingyoji, M., Chen, F., Hwang, J-J., Burma, S., Lee, C., Cheng, J-F. and Chen, D. J. Gene Expression Profiles of Normal Human Fibroblasts after Exposure to Ionizing Radiation: A...
Xiao, Yanjing, Hughes, Austin L, Ando, Junko, Matsuda, Yoichi, Cheng, Jan-Fang, Skinner-Noble, Donald, ...
Abstract Background Defensins comprise a large family of cationic antimicrobial peptides that are characterized by the presence of a conserved cysteine-rich defensin motif. Based on the spacing...
The complete sequence of human chromosome 5 (2004)
Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, ...
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Qian-fei Wang, Xin Liu, Ze Peng, Ronald M. Krauss, David L, John L. V, ...
Copyright © 2004 Oxford University Press Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons (2003)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Convergent evolution in primates and an insectivore (2003)
Boffelli, Dario, Cheng, Jan-Fang, Rubin, Edward M.
The cardiovascular risk factor apolipoprotein(a) (apo(a)) has a puzzling distribution among mammals, its presence being limited to a subset of primates and a member of the insectivore lineage, the...
Jaju, Rina J., Fidler, Carrie, Haas, Oskar A., Strickson, Amanda J., Watkins, Fiona, Clark, Kevin, ...
The recurrent translocation t(5;11)(q35;p15.5) associated with a 5q deletion, del(5q), has been reported in childhood acute myeloid leukemia (AML). We report the cloning of the translocation...
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters (2001)
Wu, Qiang, Zhang, Theresa, Cheng, Jan-Fang, Kim, Youngwook, Grimwood, Jane, Schmutz, Jeremy, ...
Evolutionarily Conserved Sequences on Human Chromosome 21 (2001)
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Frazer, Kelly A., Ueda, Yukihiko, Zhu, Yiwen, Gifford, Vincent R., Garofalo, Maria R., Mohandas, Narla, ...
Structural and transcriptional analysis of a human subtelomeric repeat (1991)
Cheng, Jan-Fang, Smith, Cassandra L., Cantor, Charles R.
A human subtelomeric repeat (designated as the HST repeat) has been Isolated and characterized from a yeast artificial chromosome containing one human telomere. This repeat is located immediately...
Isolation and characterization of a human telomere (1989)
Cheng, Jan-Fang, Smith, Cassandra L., Cantor, Charles R.
A method is described that allows cloning of human telomeres in S. cerevisiae by joining human telomeric restriction fragments to yeast artificial chromosome halves. The resulting chimeric...
A previously undetected pseudogene in the human alpha globin gene cluster (1986)
Hardison, Ross C., Sawada, Dcuhisa, Cheng, Jan-Fang, James Shen, Che-Kun, Schmid, Carl W.
The sequence of the DNA between two pseudogenes in the human α-like globin gene cluster has been determined. Comparison of this sequence with sequences from other α-like globin gene clusters...
Genomic interval engineering of mice identifies a novel modulator of triglyceride production
Zhu, Yiwen, Jong, Miek C., Frazer, Kelly A., Gong, Elaine, Krauss, Ronald M., Cheng, Jan-Fang, ...
To accelerate the biological annotation of novel genes discovered in sequenced regions of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such...
Santamarina-Fojo, Silvia, Peterson, Katherine, Knapper, Catherine, Qiu, Yang, Freeman, Lita, Cheng, Jan-Fang, ...
The ABCA1 gene, a member of the ATP-binding cassette A (ABCA1) transporter superfamily, encodes a membrane protein that facilitates the cellular efflux of cholesterol and phospholipids. Mutations in...
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters
Wu, Qiang, Zhang, Theresa, Cheng, Jan-Fang, Kim, Youngwook, Grimwood, Jane, Schmutz, Jeremy, ...
The genomic organization of the human protocadherin α, β, and γ gene clusters (designated Pcdhα [gene symbol PCDHA], Pcdhβ [PCDHB], and Pcdhγ [PCDHG]) is remarkably similar to that of...
Evolutionarily Conserved Sequences on Human Chromosome 21
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide...
Xiao, Yanjing, Hughes, Austin L, Ando, Junko, Matsuda, Yoichi, Cheng, Jan-Fang, Skinner-Noble, Donald, ...
Hughes, Jim R., Cheng, Jan-Fang, Ventress, Nicki, Prabhakar, Shyam, Clark, Kevin, Anguita, Eduardo, ...
An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple,...
Decoding the fine-scale structure of a breast cancer genome and transcriptome
Volik, Stanislav, Raphael, Benjamin J., Huang, Guiqing, Stratton, Michael R., Bignel, Graham, Murnane, John, ...
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is...
Genomic interval engineering of mice identifies a novel modulator of triglyceride production
Zhu, Yiwen, Jong, Miek C., Frazer, Kelly A., Gong, Elaine, Krauss, Ronald M., Cheng, Jan-Fang, ...
To accelerate the biological annotation of novel genes discovered in sequenced regions of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such...
Santamarina-Fojo, Silvia, Peterson, Katherine, Knapper, Catherine, Qiu, Yang, Freeman, Lita, Cheng, Jan-Fang, ...
The ABCA1 gene, a member of the ATP-binding cassette A (ABCA1) transporter superfamily, encodes a membrane protein that facilitates the cellular efflux of cholesterol and phospholipids. Mutations in...
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters
Wu, Qiang, Zhang, Theresa, Cheng, Jan-Fang, Kim, Youngwook, Grimwood, Jane, Schmutz, Jeremy, ...
The genomic organization of the human protocadherin α, β, and γ gene clusters (designated Pcdhα [gene symbol PCDHA], Pcdhβ [PCDHB], and Pcdhγ [PCDHG]) is remarkably similar to that of...
Evolutionarily Conserved Sequences on Human Chromosome 21
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide...
Xiao, Yanjing, Hughes, Austin L, Ando, Junko, Matsuda, Yoichi, Cheng, Jan-Fang, Skinner-Noble, Donald, ...
Hughes, Jim R., Cheng, Jan-Fang, Ventress, Nicki, Prabhakar, Shyam, Clark, Kevin, Anguita, Eduardo, ...
An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple,...
Decoding the fine-scale structure of a breast cancer genome and transcriptome
Volik, Stanislav, Raphael, Benjamin J., Huang, Guiqing, Stratton, Michael R., Bignel, Graham, Murnane, John, ...
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is...
Primate-specific evolution of an LDLR enhancer
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Intra-primate genome comparisons identify functional modules that are undetected by comparisons with non-mammalian genomes.
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene
Ward, Robert D., Davis, Shannon W., Cho, MinChul, Esposito, Constance, Lyons, Robert H., Cheng, Jan-Fang, ...
Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and...
A sequence-based survey of the complex structural organization of tumor genomes
Raphael, Benjamin J, Volik, Stanislav, Yu, Peng, Wu, Chunxiao, Huang, Guiqing, Linardopoulou, Elena V, ...
Tumors and cancer cell lines were surveyed with end-sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some...
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer
Nottingham, Wade T., Jarratt, Andrew, Burgess, Matthew, Speck, Caroline L., Cheng, Jan-Fang, Prabhakar, Shyam, ...
The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major...
Assembling the Marine Metagenome, One Cell at a Time
Woyke, Tanja, Xie, Gary, Copeland, Alex, González, José M., Han, Cliff, Kiss, Hajnalka, ...
The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of...
Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy
Zhang, Zhen, Alpert, Deanne, Francis, Richard, Chatterjee, Bishwanath, Yu, Qing, Tansey, Terry, ...
Forward genetic screens with ENU (N-ethyl-N-nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU- induced...