Derda, Ratmir - University of Alberta - Department of Chemistry

个人简介

Ratmir Derda received his B.Sci. in Physics from Moscow Institute of Physics and Technology in 2001 and Ph.D. in Chemistry from the University of Wisconsin-Madison in 2008, under the supervision of Laura L. Kiessling. From 2008 to 2011, he was a postdoctoral researcher at Harvard University working under the supervision of George M. Whitesides and and Donald E. Ingber. He is currently Assistant Professor at the Department of Chemistry and Principal Investigator at the Alberta Glycomics Centre and SENTINEL Bioactive Paper Network. His recent awards include Young Investigator Award from Boulder Peptide Society (2014), University of Alberta Award for Outstanding Mentorship in Undergraduate Research & Creative Activities (2014) and Canadian Rising Star in Global Health award from Grand Challenges Canada (2011)

研究领域

Research Vision: My lab works at the interface of chemistry and biology. Our general areas of interest are: Genetically-encoded libraries of small molecules for ligand discovery is enabled by our ability to synthesize million to billion-scale libraries of small molecules from genetically-encoded peptide libraries. (1) We use these libraries for development of inhibitors for therapeutically-important proteins and non-druggable proteins, with specific emphasis on proteins that recognize complex carbohydrates. (2) Our lab uses genetically-encoded libraries to develop materials that control differentiation of cells (see iCID). (3) We are interested in fundamental principles that govern selection and evolution of molecular interaction in complex selection landscapes. This knowledge will help us design ligands and probes for targets in a complex setting (receptors on the surface of the whole cell, disease-associated proteins circulating in serum, etc) Immobilized Chemical Inducers of Differentiation (iCID) and asymmetric cell division: In living organisms, it is often the location of the molecules, not their overall concentration, that determines the cell fate. My lab develops multiple approaches for controlling spatial gradients of biomolecules in cells and differentiation of cells during cell division (aka, asymmetric division). Specifically, we investigate the differentiation events that govern tumor development and control dynamic equilibrium between tumor-initiating cancer stem cells (CSC) and non-stem cancer cells (NSCC). Diagnostics: The Derda group is interested in developing diagnostic platforms for the point-of-care detection of bacteria, antimicrobial susceptibility or drug-resistance of cells and detection of disease biomarkers in serum.

近期论文

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S. Ng, E. Y. Lin, et al “Genetically-encoded Fragment-based Discovery of Glycopeptide Ligands for Carbohydrate-binding Proteins”, in review K. F. Tjhung, F. Deiss, J. Tran, Y. Chou, R. Derda*, “Intra-domain phage display (ID-PhD) of peptides and mini-domain proteins censored from canonical pIII phage display“, 2015 Frontiers Microbiology, doi: 10.3389/fmicb.2015.00340 (Book chapter) W. L. Matochko, R. Derda*, “Next-Generation Sequencing of Phage-Displayed Peptide Libraries“, Methods in Molecular Biology, Volume 1248, 2015, pp 249-266 (Book chapter) S. Ng, K. F., Tjhung, B. M. Paschal, C. J. Noren, R. Derda*, “Chemical Posttranslational Modification of Phage-Displayed Peptides“, Methods in Molecular Biology, Volume 1248, 2015, pp 155-172 (Book) Ratmir Derda (Editor): Peptide Libraries: Methods and Protocols (Springer), 2015, Vol. 1248. ISBN 978-1-4939-2020-4. Preface: Peptide Libraries on the Chemistry-Biology Interface. This Book is dedicated to the memory of Carlos Barbas the IIIrd Ratmir Derda, Jesse Gitaka, Thomas M. Kariuki, Catherine M. Klapperich, Charles R. Mace, Ashok A. Kumar, Marya Lieberman, Jacqueline Linnes, Joerg Jores, Johnson Nasimolo, Joseph Ndung’u, Evans Taracha, Abigail Weaver, Douglas B. Weibel, and Paul Yager “Enabling the development and deployment of next generation point of care diagnostics”, accepted, 2015, PLoS Neglected and Tropical Diseases M. Pan, L. Rosenfeld, M. Kim, M. Xu, E. Y. Lin, R. Derda and S. K. Y. Tang “Fluorinated Pickering Emulsions Impede Interfacial Transport and Form Rigid Interface for the Growth of Anchorage-Dependent Cells” ACS Appl. Mater. Interfaces, 2014, dx.doi.org/10.1021/am506443e S. Burnham, J. Hu, H. Anany, L. Brovko, F. Deiss, R. Derda, M. W. Griffiths*, “Towards rapid on-site phage-mediated detection of generic Escherichia coli in water using luminescent and visual readout“. Anal Bioanal Chem., 2014, 406, (23), 5685-5693Mansel_TOC P Kitov, D F Vinals , S Ng , K F Tjhung , and R Derda “Rapid, Hydrolytically Stable Modification of Aldehyde-terminated Proteins and Phage Libraries”, J. Am. Chem. Soc., 2014, 136, 8149–8152. K. F. Tjhung, S. Burnham, H. Anany, M. W. Griffiths and R. Derda “Rapid enumeration of phage in monodisperse emulsions“, Anal. Chem., 2014, 86, 5642–5648. F Deiss, W L Matochko, N Govindasamy, E Y Lin and R Derda “Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays”, Angewandte Chemie, 2014, 53, 6374–6377. (featured as ‘Hot Article’ and on back cover) B. Mosadegh, B. E. Dabiri, M. R. Lockett, R. Derda, P. Campbell, K. K. Parker, G. M. Whitesides “Three-Dimensional Paper-Based Model for Cardiac Ischemia“, Adv. Healthcare Mater., 2014, 3, 1036–1043. T Lin, Y Chen, L Rosenfeld, R Derda, SKY Tang “Review and Analysis of Performance Metrics of Microfluidic Droplet Systems for Diagnostics and High Throughput Screening Applications” Microfluidics and NanoFluidics, 2014, 16, (5), 921-939 MR Jafari, Lu Deng, S Ng, W Matochko, K Tjhung, A Zeberof, A Elias, John S. Klassen, R Derda* “Discovery of light-responsive ligands through screening of light-responsive genetically-encoded library“, ACS Chem. Biol., 2014, 9, 443–450 (front cover) F Deiss, MF Huacca, J Bal, K Tjhung, R Derda “Antimicrobial susceptibility assays in paper-based portable culture devices“, Lab Chip, 2014, 14, 167-171, (back cover, and featured as HOT article) W Matochko, SC Li, SKY Tang, R Derda * “Prospective identification of parasite sequences in phage display screens“ Nuc. Acid. Res., 2014, 42, (3), 1784-1798.TOC? L Liu, N Jalili, A Baergen, S Ng, J Bailey, R Derda, JS Klassen* “Energetics of Fluorine Bonding in Protein-Fatty Acid Complexes. Insights from Gas-Phase Measurements“, Journal of The American Society for Mass Spectrometry, 2014, 25, (5), 751-757 BM Scott, WL Matochko, RF Gierczak, V Bhakta, R Derda, WP Sheffield* “Phage display of the serpin alpha-1 proteinase inhibitor randomized at consecutive residues in the reactive centre loop and biopanned with or without thrombin“, PLoS One, 2014, 9, (1), e84491 A Zeberoff, R Derda, AL. Elias* “Remote activation of a microactuator using a frequency specific photo-responsive gold nanoparticle composite“, J. Micromech. Miroeng., 2013, 23, 125022 W Matochko, R Derda “Error analysis of deep sequencing of phage libraries: Peptides censored in sequencing” Comput Math Methods Med. (Phage Display Bioinformatics Issue), 2013, Vol. 2013, Article ID 491612