Yan LiuSummaryAffiliation: Carnegie Mellon University Country: USA Publications
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Publications
Comparison of probabilistic combination methods for protein secondary structure predictionYan Liu
Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA
Bioinformatics 20:3099-107. 2004..In particular, conditional random fields (CRFs) moderately improve the predictions for helices and, more importantly, for beta sheets, which are the major bottleneck for protein secondary structure prediction...- Protein fold recognition using segmentation conditional random fields (SCRFs)Yan Liu
School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
J Comput Biol 13:394-406. 2006..Applying our prediction model to the Uniprot Database, we identify previously unknown potential beta-helices... - A platform for accurate mass and time analyses of mass spectrometry dataDamon May
Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
J Proteome Res 6:2685-94. 2007..The analysis workflow, referred to as msInspect/AMT, extends and combines existing open-source platforms for LC-MS/MS (CPAS) and LC-MS (msInspect) data analysis and is available in an unrestricted open-source distribution... - Synthesis, inhibitory activities, and QSAR study of xanthone derivatives as alpha-glucosidase inhibitorsYan Liu
School of Chemistry and Chemical Engineering, Sun Yat Sen University, Guangzhou 510275, PR China
Bioorg Med Chem 16:7185-92. 2008..The accuracy and predictive power of the proposed QSAR model were verified by LOO validation, Y-randomization, and test group validation with newly synthesized xanthone derivatives... - Synthesis of xanthone derivatives with extended pi-systems as alpha-glucosidase inhibitors: insight into the probable binding modeYan Liu
School of Chemistry and Chemical Engineering, Sun Yat Sen University, Guangzhou 510275, PR China
Bioorg Med Chem 15:2810-4. 2007..The present results suggest that pi-pi stacking effect and H-bonding make substantial contributions to elicit the inhibitory activities of this general class of inhibitors... - Modular self-assembly of DNA lattices with tunable periodicityYan Liu
Department of Chemistry and Biochemistry and Arizona Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
Small 1:327-30. 2005 - Preparation of neoglycolipids with ring-closed cores via chemoselective oxime-ligation for microarray analysis of carbohydrate-protein interactionsYan Liu
The Glycosciences Laboratory, Imperial College London, Harrow Middlesex, UK
Methods Enzymol 415:326-40. 2006..Thus, AO-NGLs have broadened the applicability of NGLs as probes in studies of carbohydrate-protein interactions... - Biodegradable PLGA microspheres as a sustained release system for a new luteinizing hormone-releasing hormone (LHRH) antagonistLina Du
Department of Pharmaceutical Chemistry, Beijing Institute of Pharmacology and Toxicology
Chem Pharm Bull (Tokyo) 54:1259-65. 2006..In conclusion, the PLGA microspheres could be a well sustained release system for LXT-101... - SNP genotyping by multiplex amplification and microarrays assay for forensic applicationLi Li
Institute of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
Forensic Sci Int 162:74-9. 2006..02 x 10(-15). The average exclusion probabilities in duos and in trios were 0.9894 and 0.9992, respectively. It may be concluded that the 59 SNPs loci yield the same power in forensic identification as CODIS STRs currently used... - DNA tile based self-assembly: building complex nanoarchitecturesChenxiang Lin
Department of Chemistry and Biochemistry and The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
Chemphyschem 7:1641-7. 2006..Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed... - Preparation of a novel composite particles and its application in the fluorescent detection of proteinsHong-Qi Chen
College of Chemistry and Material Science, Anhui Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu, 241000, People's Republic of China
Anal Bioanal Chem 385:1457-61. 2006..0 microg.ml(-1) with the detection limit of 35 ng.ml(-1) for Human gamma-IgG . The method has been applied to the determination of the total protein in human serum samples collected from the hospital and the results are satisfactory... - Developments in ambulatory electrocardiographyValérie Eveloy
Department of Mechanical Engineering, Petroleum Institute, United Arab Emirates
Biomed Instrum Technol 40:238-45. 2006..The engineering challenges associated with ambulatory electrocardiography are discussed, and technological improvement areas that are the focus of current research effort are reviewed... - EST-based identification of genes expressed in brain and spinal cord of Gekko japonicus, a species demonstrating intrinsic capacity of spinal cord regenerationYan Liu
Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001, China
J Mol Neurosci 29:21-8. 2006.... - Self-assembled peptide nanoarrays: an approach to studying protein-protein interactionsBerea A R Williams
Department of Chemistry and Biochemistry, Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5201, USA
Angew Chem Int Ed Engl 46:3051-4. 2007 - Numerical calculation of the sound field focused by acoustic lens with an arbitrary axisymmetric sound speed distributionXiang Hong Yan
College of Physics, Science, and Technology, China University of Petroleum, Dongying, Shandong, China
IEEE Trans Ultrason Ferroelectr Freq Control 54:823-9. 2007..The larger the coefficient of the SSD, the larger the focused beam width and the larger focal region, but the divergent angle is almost the same... - Discovery of nonsteroidal glucocorticoid receptor ligands based on 6-indole-1,2,3,4-tetrahydroquinolinesSteven L Roach
Discovery Research, Ligand Pharmaceuticals, 10275 Science Center Drive, San Diego, CA 92121, USA
Bioorg Med Chem Lett 18:3504-8. 2008..5nM) and 100- to 1000-fold selectivity over MR, PR, and AR while showing activity in an E-selectin repression assay... - Patterning metallic nanoparticles by DNA scaffoldsRahul Chhabra
Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
Adv Exp Med Biol 620:107-16. 2007..In this review, we will summarize the progress in organizing metallic nanoparticles templated by DNA scaffolds into one and two dimensional architectures... - Structure-activity relationships of C6-uridine derivatives targeting plasmodia orotidine monophosphate decarboxylaseAngelica M Bello
Center for Molecular Design and Preformulations and Division of Cell and Molecular Biology, Toronto General Research Institute University Health Network, MaRS TMDT, Toronto, ON, Canada
J Med Chem 51:439-48. 2008..falciparum ODCase. 6-Methyluridine exhibited weak antimalarial activity against P. falciparum 3D7 isolate. 6- N-Methylamino and 6- N, N-dimethylamino uridine derivatives exhibited moderate antimalarial activities... - Reduction of skin stretch induced motion artifacts in electrocardiogram monitoring using adaptive filteringYan Liu
Center for Adv. Life Cycle Eng, Maryland Univ, College Park, MD 20742, USA
Conf Proc IEEE Eng Med Biol Soc 1:6045-8. 2006..The results demonstrate that this device and method can significantly reduce skin strain induced ECG artifacts... - The zebrafish fleer gene encodes an essential regulator of cilia tubulin polyglutamylationNarendra Pathak
Nephrology Division, Massachusetts General Hospital, Charlestown, MA 02129, USA
Mol Biol Cell 18:4353-64. 2007..These results are the first in vivo evidence that tubulin polyglutamylation is required for vertebrate cilia motility and structure, and, when compromised, results in failed ciliogenesis... - Prediction of second malignant neoplasm incidence in a large cohort of long-term survivors of childhood cancersIrina Dinu
Department of Public Health Sciences, School of Public Health, University of Alberta, Edmonton, Alberta, Canada
Pediatr Blood Cancer 50:1026-31. 2008..The ability to predict adverse-event occurrences accurately in long-term survivors of childhood cancer is of high importance in late effects research, both clinically and methodologically... - Neoglycolipid probes prepared via oxime ligation for microarray analysis of oligosaccharide-protein interactionsYan Liu
Glycosciences Laboratory, Imperial College London, Northwick Park and St Mark s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
Chem Biol 14:847-59. 2007.... - Study of pellet formation of filamentous fungi Rhizopus oryzae using a multiple logistic regression modelYan Liu
Department of Biological Systems Engineering and Center for Bioenergy and Bioproducts, Washington State University, L J Smith 213, Pullman, Washington 99163, USA
Biotechnol Bioeng 99:117-28. 2008..Model building and diagnostics were obtained using the Statistical Analysis System (SAS 9.0) program. The model developed in this study can be used to predict the pellet formation of other R. oryzae strains as well... - Identification of a novel peptide ligand of human vascular endothelia growth factor receptor 3 for targeted tumour diagnosis and therapyXin Qin
Biotechnology Center of The Fourth Military Medical University, and State Key Laboratory of Cancer Biology, 17 Chang le West Road, 710032 Xi an, People s Republic of China
J Biochem 142:79-85. 2007..In addition, the flow cytometry assay and immunofluorescence showed that the FITC labelled P1 could bind to VEGFR-3 positive carcinoma cells with specificity. Our study suggests that P1 may be a homing peptide for treatment of tumours... - Bis[(para-methoxy)benzyl] phosphonate prodrugs with improved stability and enhanced cell penetrationQun Dang
Department of Chemistry, Metabasis Therapeutics, Inc, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA
Bioorg Med Chem Lett 17:3412-6. 2007..BisPMB NMPA esters (4b and 4c) with significantly improved aqueous stability were identified that also resulted in increased intracellular levels of NMPA following prodrug incubation with primary rat hepatocytes... - [Effect of three different curcumin pigmens on the prdiferation of vascular smooth muscle cells by ox-LDL and the expression of LDL-R]Yan Liu
Zhejiang Traditional Medical College, Hangzhou 310009, China
Zhongguo Zhong Yao Za Zhi 31:500-3. 2006.... - Synthesis and pharmacological activities of xanthone derivatives as alpha-glucosidase inhibitorsYan Liu
School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, PR China
Bioorg Med Chem 14:5683-90. 2006..Among them, polyhydroxylxanthones exhibited the highest activities and thus may be exploitable as a lead compound for the development of potent alpha-glucosidase inhibitors... - Electrochemical impedance behavior of DNA biosensor based on colloidal Ag and bilayer two-dimensional sol-gel as matricesYingzi Fu
Chongqing Key Laboratory of Analytical Chemistry, College of Chemistry and Chemical Engineering, Southwest China Normal University, Chongqing 400700, PR China
J Biochem Biophys Methods 62:163-74. 2005..0 x 10(-9) M at 3sigma. In addition, the experiment results indicate that oligonucleotide immobilized on this way exhibits a good sensitivity and selectivity, high stability and a long-term maintenance of bioactivity... - [Amplification and sequencing of the gene coding for mucin-like protein from Schistosoma japonicum]Yan Liu
Department of Parasitology, College of Basic Medicine, Nanhua University, Hengyang 421001, China
Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 22:167-9. 2004..mansoni and S. japonicum. CONCLUSION: The amplified fragment is consistent to the predicted one, providing a basis for cloning and further study on DNA immunization... - Bayesian analysis of risk factors for anovulationYan Liu
Department of Epidemiology and Preventive Medicine, School of Medicine, University of California, Davis, CA 95616, USA
Stat Med 23:1901-19. 2004..Our results indicated that increasing physical activity was associated with a significantly increased risk of anovulation; and smokers had a potentially, but not statistically significant, increased occurrence of anovulation... - Highly-efficient DNA photocleavers with long wavelength absorptions: thio-heterocyclic fused naphthalimides containing aminoalkyl side chainsXuhong Qian
State Key Laboratory of Fine Chemicals, Dalian University of Technology, PO Box 40, 158 Zhongshan Road, Dalian 116012, China
Bioorg Med Chem Lett 14:2665-8. 2004..They could photodamage supercoiled pBR322 DNA from form I (closed) to II (nicked) at a concentration as low as 0.5 microM and to form III (linear) at a concentration of 50 microM. A possible mechanism of superoxide anion was provided... - Screening of augmenter of liver regeneration-binding proteins by yeast-two hybrid techniqueJun Cheng
Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing 100039, China
Hepatobiliary Pancreat Dis Int 2:81-4. 2003..To investigate the biological function of augmenter of liver regeneration (ALR), we used yeast-two hybrid technique to detect proteins in hepatocytes interacting with ALR... - Cloning and expression of the gene of augmenter of liver regeneration in yeast cellsJun Cheng
Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing 100039, China
Hepatobiliary Pancreat Dis Int 1:87-91. 2002..To study the function of augmenter of liver regeneration (ALR) as a regulatory factor that specifically stimulates hepatic cell regeneration, we constructed yeast expressive vector of ALR and expressed it in yeast cells... - Application of statistically-based experimental designs for the optimization of nisin production from wheyChuanbin Liu
Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164-6120, USA
Biotechnol Lett 25:877-82. 2003..067 g l(-1) for yeast extract, 0.569 g l(-1) for KH2PO4, and 0.572 g l(-1) for MgSO4. The validity of the optimal conditions was verified by a separate experiment... - Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzymeKathryn W Underwood
Department of Biological Chemistry, Wyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140, USA
Structure 11:627-36. 2003..However, phosphorylation of MK2 41-364 by p38 restores the V(max) and K(m) for peptide substrate to values comparable to those seen in p38-activated MK2 41-400, suggesting a mechanism for regulation of enzyme activity... - Monitoring the synthetic reaction of a polyamide/peptide conjugate using electrospray ionization mass spectrometryChangjin Zhu
Key Laboratory for Bioorganic Phosphorus Chemistry of Ministry of Education, Department of Chemistry, School of Life Science and Engineering, Tsinghua University, Beijing 100084, China
Rapid Commun Mass Spectrom 17:825-31. 2003..Consequently, the reaction could be monitored successfully and the synthetic route optimized... - Organizational diversity among distinct glycoprotein endoplasmic reticulum-associated degradation programsChristopher M Cabral
Department of Pathology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
Mol Biol Cell 13:2639-50. 2002..How the processing of a mutant protein, rather than the mutation itself, can contribute to disease pathogenesis, is discussed... - Alpha1-antitrypsin as model to assess glycan function in endoplasmic reticulumDaniel Termine
Department of Pathology, Baylor College of Medicine, Houston, TX 77030-3498, USA
Methods 35:348-53. 2005..The conceptual framework, and associated techniques, can serve as a roadmap for the investigation of other mutated glycoproteins, many of which can contribute to disease... - Programmable DNA self-assemblies for nanoscale organization of ligands and proteinsSung Ha Park
Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
Nano Lett 5:729-33. 2005.... - The ETS protein MEF is regulated by phosphorylation-dependent proteolysis via the protein-ubiquitin ligase SCFSkp2Yan Liu
Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 575, New York, NY 10021, USA
Mol Cell Biol 26:3114-23. 2006..The tight regulation of MEF levels during the cell cycle contributes to its effects on regulating cell cycle entry and cell proliferation... - Prediction of chromatographic relative retention time of polychlorinated biphenyls from the molecular electronegativity distance vectorShu Shen Liu
State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing, P R China
J Sep Sci 29:296-301. 2006..99 except two models... - Novel fluorescent markers for hypoxic cells of naphthalimides with two heterocyclic side chains for bioreductive bindingYan Liu
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
Bioorg Med Chem 14:2935-41. 2006..A2 and A4 showed a very large differential fluorescence between hypoxic and oxic cells (V79 cells) in vitro and are promising candidate markers for hypoxic cells... - Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domainCharles Reichman
Department of Biochemistry and Molecular Biology, UMDNJ New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
Oncogene 24:8187-99. 2005..Our data provide insight into the role of highly conserved residues in the Crk-SH3-C, suggesting a mechanism for how the linker and the Crk-SH3-C function in the transactivation of the Abl tyrosine kinase... - Selectivity of inferior temporal neurons for realistic pictures predicted by algorithms for image database navigationSarah Allred
Department of Physiology and Biophysics, University of Washington, Seattle, 98195, USA
J Neurophysiol 94:4068-81. 2005.... - Screening of hepatocyte proteins binding to complete S protein of hepatitis B virus by yeast-two hybrid systemGui-Qin Bai
Department of Obstetrics and Gynecology of First Hospital, Xi'an Jiaotong University, Jiankang Road 1, Xi'an 710061, Shaanxi Province, China
World J Gastroenterol 11:3899-904. 2005..CONCLUSION: The yeast-two hybrid system is an effective method for identifying hepatocyte proteins interacting with complete S protein of HBV. The complete S protein may bind to different proteins i.e., its multiple functions in vivo... - An approach to studying lung cancer-related proteins in human bloodTing Xiao
Department of Etiology and Carcinogenesis, Cancer Institute (Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
Mol Cell Proteomics 4:1480-6. 2005..This pilot approach may lead to the identification of novel protein markers in blood and provide a new method of identifying tumor biomarker profiles for guiding both early detection and therapy of human cancer... - Effects of nutrient supplements on simultaneous fermentation of nisin and lactic acid from cull potatoesChuanbin Liu
Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164-6120, USA
Appl Biochem Biotechnol 121:475-83. 2005..The conditions for nisin biosynthesis and lactic acid coproduction by L. lactis subsp. lactis in a cull potato-based medium were subsequently optimized using a statistically based experimental design... - [Mutation on the 4th and 5th extrons of COCH gene in Meniere's disease]Yan Sun
Department of Otorhinopharyngolaryngy and Head-neck Surgery, Affiliated Tongren Hospital, Capital Medical University, Beijing 100730, China
Zhonghua Yi Xue Za Zhi 85:345-7. 2005 - [Identification and analysis of a mouse gene homologous to human hepatitis B virus pre-S1 protein-binding protein using the bioinformatics method]Jun Cheng
Institute of Infectious Diseases, Ditan Hospital, Beijing 100011, China
Zhonghua Gan Zang Bing Za Zhi 13:241-4. 2005..To clone and identify the mouse gene homologous to human hepatitis B virus (HBV) pre-S1 protein-binding protein (PS1BP)... - Gab3, a new DOS/Gab family member, facilitates macrophage differentiationIngrid Wolf
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
Mol Cell Biol 22:231-44. 2002..These results suggest that Gab3 is important for macrophage differentiation and that differentiation requires the early phosphorylation of Gab2 followed by induction and subsequent phosphorylation of Gab3...