Bridging the Gap from Research Bench to Patient Bedside

The contribution made by our multidisciplinary team of associates can be seen in the body of scientific literature where our team members have been cited.  Below is a listing of publications where our Biotechnology Core associates are listed as authors (highlighted).

• Fletcher, C.M., Coyne, M.J., Villa, O.F., Chatzidaki-Livanis, M. & Comstock, L.E., A general O-glycosylation system important for the physiology of a major human intestinal symbiont. Cell 137, 321-331. 2009.
• Fletcher, C.M., Coyne, M.J., Bentley, D.L., Villa, O.F. & Comstock, L.E., Phase variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem. Proc. Natl. Acad. Sci. USA 104, 2413-2418. 2007.
• Lin, Y., Fletcher, C.M., Zhou, J., Allis, C.D. & Wagner, G., Solution structure of the catalytic domain of GCN5 histone acetyltransferase bound to coenzyme A. Nature 400, 86-89. 1999.
• Fletcher, C.M., Pestova, T.V., Hellen, C.U. & Wagner, G., Structure and interactions of the translation initiation factor eIF1. EMBO J. 18, 2631-2637. 1999.
• Fletcher, C.M. & Wagner, G., The interaction of eIF4E with 4E-BP1 is an induced fit to a completely disordered protein. Protein Sci. 7, 1639-1642. 1998.
• Fletcher, C.M., McGuire, A.M., Gingras, A.C., Li, H., Matsuo, H., Sonenberg, N. & Wagner, G., 4E binding proteins inhibit the translation factor eIF4E without folded structure. Biochemistry 37, 9-15. 1998.
• Wallach., and R. Lilien., “The Protein-Small-Molecule Database: A Non-Redundant Structural Resource for the Analysis of Protein-Ligand Binding.” Bioinformatics, 25(5):615-20., 2009.
• Georgiev, R. Lilien, B. Donald., “The Minimized Dead-End Elimination Criterion and its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles”, Journal of Computational Chemistry, 29(10):1527-42., 2008.
• M. Gorczynski, J. Grembecka, Y. Zhou, Y. Kong, L. Roudaia, M. Douvas, M. Newman, I. Bielnicka, G. Baber, T. Corpora, J. Shi, M. Sridharan, R. Lilien, B. Donald, N. Speck, M. Brown, J. Bushweller., “Allosteric Inhibition of the Protein-Protein Interaction between the Leukemia-Associated Proteins Runx1 and CBFB”., Chemistry & Biology, 14(10):1186-97., 2007.
• B. Stevens, R.H. Lilien, I. Georgiev, B.R. Donald, A.C. Anderson., “Redesigning the PheA Domain of Gramicidin Synthetase Leads to a New Understanding of the Enzyme’s Mechanism and Selectivity.” Biochemistry, 45(51):15495-15504., 2006.
• Georgiev, R.H. Lilien, B.R. Donald., “Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End Elimination, with Application to Protein Design.”, Bioinformatics, 22(14):e174-183., 2006.
• R.R. Mettu, R.H. Lilien, B.R. Donald.,“High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data.” Bioinformatics, 21(1):i292-i301., 2005.
• R.H. Lilien, B.W. Stevens, A.C. Anderson, B.R. Donald., “A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme:., Journal of Computational Biology, 12(6-7):740-761., 2005.
• R.H. Lilien, C. Bailey-Kellogg, A.C. Anderson, B.R. Donald., “A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry”., Acta Crystallographica D: Biological Crystallography, 60:1057-1067., 2004.
• R.E. Gillilan, R.H. Lilien., “Optimization and Dynamics of Protein-Protein Complexes Using B-Splines”., Journal of Computational Chemistry, 25(13):1630-1646., 2004.
• C.J. Langmead, A.K. Yan, R. Lilien, L. Wang, B.R. Donald., “A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments”., Journal of Computational Biology, 11:277-298., 2004.
• R.H. O’Neil, R.H. Lilien, B.R. Donald, R.M. Stroud, A.C. Anderson., “Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme dihydrofolate reductase-thymidylate synthase”., Journal of Biological Chemistry, 278(52):52980-52987., 2003.
• R.H. O’Neil, R.H. Lilien, B.R. Donald, R.M. Stroud, A.C. Anderson., “The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme”., Journal of Eukaryotic Microbiology, Supplement to Volume 50:555-556., 2003.
• L.D. Lilien, R.H. Lilien, S. Setrakian., “Hemopericardium and Cardiac Tamponade as Presenting Findings of Dexamethasone-Induced Hypertrophic Cardiomyopathy Complicated by Transmural Myocardial Infarction”.,  Pediatric Cardiology, 24:280-283., 2003.
• R.H. Lilien, H. Farid, B.R. Donald., “Probabilistic Disease Classification of Expression Dependent Proteomic Data from Mass Spectrometry of Human Serum”., Journal of Computational Biology, 10(6):925-946., 2003.
• Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z, “Single-molecule DNA sequencing of a viral genome”,  Science. 2008 Apr 4;320(5872):106-9.
• Zheng, Xie, N. Srividya, T. Sosnick, T. Pan, and N. F. Scherer., “Single Molecule Studies Highlight Conformational Heterogeneity in the Early Folding Steps of a Large Ribozyme”, Proc. Natl. Acad. Sci, 101, 534-539 (2004).
• Glenna J. Smith, Xiaohui Qu, Zheng Xie, Jelena Pesic, Tobin R. Sosnick, Tao Pan, and Norbert F. Scherer, “A large collapse-state RNA can exhibit simple exponential single molecule dynamics”,  JMB 378 941-951 (2008).