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| 1 | YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research显示文摘We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. | Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams | 2015 | Genomics, Proteomics & Bioinformatics2015，13，1： | 3 |
| 2 | Further aspects of design for distal extension removable partial dentures based on the Kennedy classification显示文摘 | Benur Z Shifman A Aviv I | 1999 | J Oral Rehabil1999，26，： | 1 |
| 3 | 'Just Call Me A donai': A Case Study of Ethnic Humor and Immigrant Assimilation 显示文摘 | Limor Shifman Elihu Katz | 2005 | American SoeiologicM Review2005，，5： | 1 |
| 4 | Further aspects of design fordistal extension removable partial dentures based on the Kennedyclassification显示文摘 | Ben-Ur Z Shifman A Aviv I | 1999 | J Oral Rehabil1999，26，2： | 1 |
| 5 | A highly significant association between a COMT haplotype and schizophrenia显示文摘 | Shifman S Bronstein M Sternfeld M | 2001 | Am J Hum Genet2001，71，： | 1 |
| 6 | COMT: a common susceptibility gene in bipolar disorder and schizophrenia显示文摘 | Shifman S Bronstein M Sternfeld M | 2004 | Am J Med Genet2004，128，： | 1 |
| 7 | Further aspects of design for distal extension removable partial dentures based on the kennedy classification 显示文摘 | Benur Z Shifman A Aviv I | 1999 | J Oral Rehabil1999，26，2： | 1 |
| 8 | Stress levels for well-fitting implant superstructures as a function of tightening force levels, tightening sequence, and different operators显示文摘 | Gross M Shifman A | 2001 | J Prosthet Dent2001，86，1： | 1 |
| 9 | On the of spatio-temporal wavelet expansions for transient analysis of wire antennas and scatters显示文摘 | SHIFMAN Y LEVIATAN Y | 2004 | IEEE Transactions on Antennas and Propagation2004，52，9： | 1 |
| 10 | The Genetic Variation of RELN Expression in Schizophrenia and Bipolar Disorder显示文摘 | Galit Ovadia Sagiv Shifman | | 0，，05： | 1 |
| 11 | The mandibular first premolar as an abutment for distal-extension removable partial dentures: a modified clasp assembly design显示文摘 | Shifman A Ben-Ur Z | 2000 | Br Dent J2000，1188，5： | 1 |
| 12 | Hypothyroidism-induced myocardi- al damage and heart failure:an overlooked entity 显示文摘 | Shuvy M Shifman OE Nusair S | 2009 | Cardiovasc Pathol2009，18，3： | 1 |
| 13 | Peginterferon alfa - 2a and fibavirin for 16 or 24 weeks in HCV genotype 2 or 3 显示文摘 | Shifman ML Suter F Bacon BR | 2007 | N Engl J Med2007，357，2： | 1 |
| 14 | A critical evaluation of the manual/visual differential leukocyte counting method显示文摘 | Koepke JA Dotson MA Shifman MA | 1985 | Blood Cells1985，11，2： | 1 |
| 15 | Acetylcholinesterase/ paraoxonase interactions increase the risk of insecticide-induced Parkinsonrs disease显示文摘 | Benmoyal SL Vander T Shifman S | 2005 | FASEB J2005，19，6： | 1 |
| 16 | A critical evaluation of the manual/visual differential leukocyte counting method显示文摘 | Koepke JA Dotson MA Shifman MA | 1985 | Blood Cells1985，11，2： | 1 |
| 17 | QCD and resonance physics: theoretical foundations 显示文摘 | Shifman M A Vainshtein A I Zakharov V I | 1979 | Nucl Phys B1979，147，： | 1 |
| 18 | QCD and resonance physics, applications显示文摘 | Shifman M A Vainshtein A I Zakharov V I | 1979 | Nucl Phys B1979，147，： | 1 |
| 19 | The labial endodontic access:a rational treatment approach in anterior teeth显示文摘 | Madjar D Kusner W Shifman A | 1989 | J Prosthet Dent1989，61，3： | 1 |
| 20 | A survey of the 22q11 microdeletion in a large cohort of schizophrenia patients显示文摘 | Horowitz A Shifman S Rivlin N | 2005 | Schizophr Res2005，73，23： | 1 |
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