Genomes and Genes
Affiliation: University of Maryland
- Direct detection of potassium cations bound to G-quadruplex structures by solid-state 39K NMR at 19.6 TGang Wu
Department of Chemistry, Queen s University, Kingston, Ontario, Canada K7L 3N6
J Am Chem Soc 125:7182-3. 2003..Solid-state 39K NMR spectra for hydrated K salts of adenosine 2'-monophosphate and adenosine 5'-diphosphate are also reported...
- Integrative analyses of posttranscriptional regulation in the yeast Saccharomyces cerevisiae using transcriptomic and proteomic dataGang Wu
Department of Molecular Micriobiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
Curr Microbiol 57:18-22. 2008..Taken together, all posttranscriptional biological properties contributed to 33.15% of the total variation of mRNA-protein correlation...
- The effects of differential gene expression on coding sequence features: analysis by one-way ANOVAGang Wu
Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, MD 21250, USA
Biochem Biophys Res Commun 358:1108-13. 2007..This analysis also demonstrates that one-way ANOVA is a powerful and simple method to explore the influence of gene expression on CDS features...
- Simplified gene synthesis: a one-step approach to PCR-based gene constructionGang Wu
Applied Molecular Biology Laboratory, Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
J Biotechnol 124:496-503. 2006..Overall, the simplified gene synthesis provides an easier and more efficient approach to gene synthesis, providing a further step towards the future goal of generalized automation for this process...
- The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expressionGang Wu
Department of Biological Sciences, University of Maryland at Baltimore County, 21250, USA
Protein Expr Purif 47:441-5. 2006..The Synthetic Gene Designer, together with on-line tutorials and the forum, is available at ...
- SGDB: a database of synthetic genes re-designed for optimizing protein over-expressionGang Wu
Department of Biological Sciences, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21229, USA
Nucleic Acids Res 35:D76-9. 2007..evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27...
- Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundanceGang Wu
Department of Biological Sciences, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
Biochem Biophys Res Commun 344:114-21. 2006..This result demonstrates that upstream regulatory motifs and coding sequence information contribute to the overall mRNA expression in a combinatorial rather than an additive manner...
- The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expressionIwona Pawlikowska
Departments of Biostatistics, St Jude Children s Research Hospital, Memphis, TN, USA, Institue of Mathematics, University of Silesia, Katowice, Poland, Department of Computational Biology and Department of Oncology, St Jude Children s Research Hospital, Memphis, TN, USA
Bioinformatics 30:1400-8. 2014..MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia...
- Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analysesElisabetta Kuhn
Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
J Natl Cancer Inst 104:1503-13. 2012..However, the molecular pathogenesis of uterine serous carcinoma is largely unknown. We analyzed the genomes of uterine serous carcinoma samples to better understand the molecular genetic characteristics of this cancer...
- Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulenceGang Wu
Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
Antonie Van Leeuwenhoek 89:135-46. 2006..The results provided the first estimates of global gene expression patterns in N. farcinica, which will be useful in guiding experimental design for further investigations...
- Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinomaIe Ming Shih
Departments of Pathology, Oncology and Gynecology Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, Baltimore, MD 21231, USA
Mod Pathol 24:638-45. 2011..005). In summary, our data suggest that amplification at the ch19p13.2 NACC1 locus, leading to NAC1 overexpression, is one of the molecular genetic alterations associated with early tumor recurrence in ovarian cancer...
- Analysis of myostatin gene structure, expression and function in zebrafishCheng Xu
Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA
J Exp Biol 206:4067-79. 2003..Together, these data demonstrate that Myostatin plays an inhibitory role in hyperplastic muscle growth in zebrafish...
- Optimal encoding rules for synthetic genes: the need for a community effortGang Wu
Mol Syst Biol 3:134. 2007
- Event-specific qualitative and quantitative PCR detection methods for transgenic rapeseed hybrids MS1xRF1 and MS1xRF2Yuhua Wu
Institute of Oil Crops Research, Chinese Academy of Agricultural Sciences, No 2 Xudong 2nd Road, Wuhan, 430062, China
J Agric Food Chem 55:8380-9. 2007....
- Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining methodXiaomeng Wu
Bioinformatics Research Group, Department of Computing Science, University of Alberta Edmonton, Alberta, Canada
Int J Bioinform Res Appl 2:219-48. 2006..The final phylogenies were built by an improved clustered Neighbour-Joining method. The generated phylogenetic trees are highly consistent with taxonomy hierarchy and previous studies, with some biologically interesting disagreements...
- Zero erucic acid trait of rapeseed (Brassica napus L.) results from a deletion of four base pairs in the fatty acid elongase 1 geneGang Wu
Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Hubei, 430062, People s Republic of China
Theor Appl Genet 116:491-9. 2008..The four base pair deletion proved to be a mutation responsible for the low erucic acid trait in rapeseed and independent from the point mutation reported by Han et al. (Plant Mol Biol 46:229-239, 2001)...
- Secreted human apolipoprotein(a) kringle IV-10 and kringle V inhibit angiogenesis and xenografted tumor growthLe Shen
Department of Biochemistry and Molecular Biology, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, PR China
Biol Chem 389:135-41. 2008..01) against the control tumor cells. From these results, we conclude that human apolipoprotein(a) carboxyl-terminal kringle IV-10-kringle V fusion protein is an effective inhibitor of angiogenesis and angiogenesis-dependent tumor growth...
- Event-specific qualitative and quantitative polymerase chain reaction methods for detection of genetically modified rapeseed Ms8xRf3 based on the right border junctionsGang Wu
Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, No 2 Xudong 2nd Rd, Wuhan 430062, People s Republic of China
J AOAC Int 91:143-51. 2008..5 initial template copies for the Ms8 event and 50 copies for the Rf3 event. Quantitiative detection methods were established, with the absolute quantification limit being approximately 25 initial template copies...
- A solid-state 23Na NMR study of monovalent cation binding to double-stranded DNA at low relative humidityAlan Wong
Department of Chemistry, Queen s University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
Magn Reson Chem 46:308-15. 2008..The reported experimental results on relative ion-binding affinity for the DNA backbone may be used for testing theoretical treatment of cation-phosphate interactions in DNA...
- Direct NMR detection of alkali metal ions bound to G-quadruplex DNARamsey Ida
Department of Chemistry, Queen s University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
J Am Chem Soc 130:3590-602. 2008..Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA...
- Event-specific qualitative and quantitative PCR methods for the detection of genetically modified rapeseed Oxy-235Gang Wu
Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, No 2 Xudong 2nd Road, Wuhan, 430062, China
Transgenic Res 17:851-62. 2008..The real-time PCR systems so established were examined with two mixed rapeseed samples with known Oxy-235 contents and found to obtain the expected results...
- Cloning of fatty acid elongase1 gene and molecular identification of A and C genome in Brassica speciesYuhua Wu
Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
Sci China C Life Sci 50:343-9. 2007..rapa from B. oleracea and between the A and C genome of B. napus. In addition, the FAE1 genes could be used as marker genes to detect the pollen flow of B. napus, thus providing an alternative method for risk assessment of gene flow...
- Cloning and characterization of cholesteryl ester transfer transfer protein isolated from the tree shrewWuwei Zeng
Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
Chin Med J (Engl) 116:928-31. 2003..To obtain the nucleotide sequence and deduced amino acid sequence of cholesteryl ester transfer protein (CETP) cDNA from the tree shrew (Tupaia glis)...
- [Analysis of lecithin-cholesterol acyltransferase cDNA and protein sequence from tree shrew]Jian Zhang
National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS, PUMC, Beijing 100005, China
Zhongguo Yi Xue Ke Xue Yuan Xue Bao 24:149-55. 2002..To acquire cDNA sequence of lecithin-cholesterol acyltransferase (LCAT) from tree shrew and analyze the sequence structure...
- Glycogen phosphorylase sequences from the amitochondriate protists, Trichomonas vaginalis, Mastigamoeba balamuthi, Entamoeba histolytica and Giardia intestinalisGang Wu
The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
J Eukaryot Microbiol 50:366-72. 2003..Protist phosphorylases, as their prokaryotic and plant counterparts, are probably not regulated by phosphorylation...
- Rice dwarf phytoreovirus segment S6-encoded nonstructural protein has a cell-to-cell movement functionYi Li
Peking Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
J Virol 78:5382-9. 2004..S6 thus encodes a protein with characteristics identical to those of other viral proteins required for the cell-to-cell movement of their genome and therefore is likely required for the cell-to-cell movement of RDV...
- Disodium guanosine 5'-monophosphate self-associates into nanoscale cylinders at pH 8: a combined diffusion NMR spectroscopy and dynamic light scattering studyAlan Wong
Department of Chemistry, Queen s University, 90 Queen s Crescent, Kingston, Ontario, Canada K7L 3N6
J Am Chem Soc 127:6990-8. 2005..We observed a linear relationship between the axial ratio of the 5'-GMP cylinders and the Na(2)(5'-GMP) concentration for both types of 5'-GMP aggregates, which suggests a common stacking mechanism for monomers and G-quartets...
- Tissue factor as a link between wounding and tissue repairJiang Chen
University of Heidelberg, Department of Medicine I, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
Diabetes 54:2143-54. 2005..These data establish TF expression as an important link between the early inflammatory response to cutaneous wounding and reparative processes...
- Direct NMR detection of the "invisible" alkali metal cations tightly bound to G-quadruplex structuresAlan Wong
Department of Chemistry, Queen s University, Kingston, Ont, Canada K7L 3N6
Biochem Biophys Res Commun 337:363-6. 2005..Our finding that it is possible to directly observe these alkali metal cations by NMR spectroscopy provides a new tool for studying cation binding affinity and dynamics in G-quadruplex DNA...
- Identification of lipid binding and lipoprotein lipase activation domains of human apoAVGuotao Sun
Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
Chem Phys Lipids 143:22-8. 2006..While, the LPL activation function of apoAV remarkably impaired after deletion of residues 192-238. These findings suggested that the domain (192-238) is absolutely necessary for apoAV in lipid binding and lipoprotein lipase activation...
- Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorialDaniel G Lee
Department of Molecular Biology, Massachusetts General Hospital, Cambridge Street, Boston, Massachusetts 02114, USA
Genome Biol 7:R90. 2006..We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, and compared it with a previously sequenced (and less pathogenic) strain, PAO1, to identify novel virulence genes...
- Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: Involvement of an ancient horizontal gene transferJohannes C Scholten
Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochem Biophys Res Commun 352:48-54. 2007..vulgaris. This report provides novel insights into the origin and evolution of bacterial genes linked to the lifestyle change of D. vulgaris from a syntrophic to a sulfate-reducing lifestyle...
- Quartet-based phylogeny reconstruction with answer set programmingGang Wu
Department of Computing Science, University of Alberta, Edmonton, Canada
IEEE/ACM Trans Comput Biol Bioinform 4:139-52. 2007..The experimental results on a number of simulated data sets suggest that the new representation, combined with answer set programming, presents a unique perspective to the MQC problem...