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Ratmir Derda - Publications

Affiliations: 
Chemistry University of Alberta, Edmonton, Alberta, Canada 
Area:
drug discovery
Website:
http://www.chem.ualberta.ca/~derda/people/RatmirDerda.html
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59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Wong JY, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chemical Science. 12: 9694-9703. PMID 34349940 DOI: 10.1039/d1sc01916c  0.693
2021 Ekanayake AI, Sobze L, Kelich P, Youk J, Bennett NJ, Mukherjee R, Bhardwaj A, Wuest F, Vukovic L, Derda R. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. Journal of the American Chemical Society. PMID 33784084 DOI: 10.1021/jacs.1c01186  0.676
2019 Derda R, Ng S. Genetically encoded fragment-based discovery. Current Opinion in Chemical Biology. 50: 128-137. PMID 31051435 DOI: 10.1016/J.Cbpa.2019.03.014  0.384
2018 Derda R, Jafari MR. Synthetic Cross-linking of Peptides: Molecular Linchpins for Peptide Cyclization. Protein and Peptide Letters. PMID 30457043 DOI: 10.2174/0929866525666181120090650  0.338
2018 Ng S, Bennett NJ, Schulze J, Gao N, Rademacher C, Derda R. Genetically-encoded fragment-based discovery of glycopeptide ligands for DC-SIGN. Bioorganic & Medicinal Chemistry. PMID 30344001 DOI: 10.1016/J.Bmc.2018.08.036  0.333
2018 Ning L, He B, Zhou P, Derda R, Huang J. Molecular Design of Peptide-Fc Fusion Drugs. Current Drug Metabolism. PMID 30129406 DOI: 10.2174/1389200219666180821095355  0.333
2018 Jafari MR, Yu H, Wickware JM, Lin YS, Derda R. Light-responsive bicyclic peptides. Organic & Biomolecular Chemistry. PMID 30067270 DOI: 10.1039/C7Ob03178E  0.357
2018 He B, Derda R, Dzisoo AM, Huang J. Development and Application of Computational Methods in Phage Display Technology. Current Medicinal Chemistry. PMID 29956612 DOI: 10.2174/0929867325666180629123117  0.318
2018 He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing. Scientific Reports. 8: 1214. PMID 29352178 DOI: 10.1038/S41598-018-19439-2  0.307
2018 Vinals DF, Kitov PI, Tu Z, Zou C, Cairo CW, Lin HC, Derda R. Selection of galectin-3 ligands derived from genetically encoded glycopeptide libraries Peptide Science. 111: e24097. DOI: 10.1002/Pep2.24097  0.577
2017 Akgun B, Li C, Hao Y, Lambkin G, Derda R, Hall DG. Synergic 'Click' Boronate/Thiosemicarbazone System for Fast and Irreversible Bioorthogonal Conjugation in Live Cells. Journal of the American Chemical Society. PMID 28891646 DOI: 10.1021/Jacs.7B08693  0.343
2017 Triana V, Derda R. Tandem Wittig/Diels-Alder diversification of genetically encoded peptide libraries. Organic & Biomolecular Chemistry. PMID 28880027 DOI: 10.1039/C7Ob01635B  0.32
2016 Kalhor-Monfared S, Jafari MR, Patterson JT, Kitov PI, Dwyer JJ, Nuss JM, Derda R. Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone. Chemical Science. 7: 3785-3790. PMID 30155020 DOI: 10.1039/C5Sc03856A  0.356
2016 Camci-Unal G, Laromaine A, Hong E, Derda R, Whitesides GM. Biomineralization Guided by Paper Templates. Scientific Reports. 6: 27693. PMID 27277575 DOI: 10.1038/Srep27693  0.648
2016 Deiss F, Yang Y, Matochko WL, Derda R. Heat-enhanced peptide synthesis on Teflon-patterned paper. Organic & Biomolecular Chemistry. PMID 27184468 DOI: 10.1039/C6Ob00898D  0.342
2016 Ng S, Derda R. Phage-displayed macrocyclic glycopeptide libraries. Organic & Biomolecular Chemistry. PMID 26889738 DOI: 10.1039/C5Ob02646F  0.366
2016 Jafari MR, Lakusta J, Lundgren RJ, Derda R. Allene Functionalized Azobenzene Linker Enables Rapid and Light-Responsive Peptide Macrocyclization. Bioconjugate Chemistry. PMID 26849798 DOI: 10.1021/Acs.Bioconjchem.6B00026  0.359
2016 Lin E, Sikand A, Wickware J, Hao Y, Derda R. Peptide microarray patterning for controlling and monitoring cell growth. Acta Biomaterialia. PMID 26805426 DOI: 10.1016/J.Actbio.2016.01.028  0.46
2016 Deiss F, Yang Y, Derda R. Parallel Syntheses of Peptides on Teflon-Patterned Paper Arrays (SyntArrays). Methods in Molecular Biology (Clifton, N.J.). 1368: 249-71. PMID 26614081 DOI: 10.1007/978-1-4939-3136-1_18  0.371
2015 Tjhung KF, Kitov PI, Ng S, Kitova EN, Deng L, Klassen JS, Derda R. Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries. Journal of the American Chemical Society. PMID 26683999 DOI: 10.1021/Jacs.5B10390  0.367
2015 Derda R, Gitaka J, Klapperich CM, Mace CR, Kumar AA, Lieberman M, Linnes JC, Jores J, Nasimolo J, Ndung'u J, Taracha E, Weaver A, Weibel DB, Kariuki TM, Yager P. Enabling the Development and Deployment of Next Generation Point-of-Care Diagnostics. Plos Neglected Tropical Diseases. 9: e0003676. PMID 25973602 DOI: 10.1371/Journal.Pntd.0003676  0.698
2015 Tjhung KF, Deiss F, Tran J, Chou Y, Derda R. Intra-domain phage display (ID-PhD) of peptides and protein mini-domains censored from canonical pIII phage display. Frontiers in Microbiology. 6: 340. PMID 25972845 DOI: 10.3389/Fmicb.2015.00340  0.301
2015 Ng S, Lin E, Kitov PI, Tjhung KF, Gerlits OO, Deng L, Kasper B, Sood A, Paschal BM, Zhang P, Ling CC, Klassen JS, Noren CJ, Mahal LK, Woods RJ, ... ... Derda R, et al. Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins. Journal of the American Chemical Society. 137: 5248-51. PMID 25860443 DOI: 10.1021/Ja511237N  0.348
2015 Derda R. Preface. Peptide libraries. Methods in Molecular Biology (Clifton, N.J.). 1248: vii-xii. PMID 25759871 DOI: 10.1007/978-1-4939-2020-4  0.339
2015 Matochko WL, Derda R. Next-generation sequencing of phage-displayed peptide libraries. Methods in Molecular Biology (Clifton, N.J.). 1248: 249-66. PMID 25616338 DOI: 10.1007/978-1-4939-2020-4_17  0.349
2015 Ng S, Tjhung KF, Paschal BM, Noren CJ, Derda R. Chemical posttranslational modification of phage-displayed peptides. Methods in Molecular Biology (Clifton, N.J.). 1248: 155-72. PMID 25616332 DOI: 10.1007/978-1-4939-2020-4_11  0.39
2014 Pan M, Rosenfeld L, Kim M, Xu M, Lin E, Derda R, Tang SK. Fluorinated pickering emulsions impede interfacial transport and form rigid interface for the growth of anchorage-dependent cells. Acs Applied Materials & Interfaces. 6: 21446-53. PMID 25347285 DOI: 10.1021/Am506443E  0.343
2014 Deiss F, Matochko WL, Govindasamy N, Lin EY, Derda R. Flow-through synthesis on Teflon-patterned paper to produce peptide arrays for cell-based assays. Angewandte Chemie (International Ed. in English). 53: 6374-7. PMID 24729420 DOI: 10.1002/Anie.201402037  0.412
2014 Mosadegh B, Dabiri BE, Lockett MR, Derda R, Campbell P, Parker KK, Whitesides GM. Three-dimensional paper-based model for cardiac ischemia. Advanced Healthcare Materials. 3: 1036-43. PMID 24574054 DOI: 10.1002/Adhm.201300575  0.713
2014 Scott BM, Matochko WL, Gierczak RF, Bhakta V, Derda R, Sheffield WP. 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. 9: e84491. PMID 24427287 DOI: 10.1371/Journal.Pone.0084491  0.307
2014 Matochko WL, Cory Li S, Tang SK, Derda R. Prospective identification of parasitic sequences in phage display screens. Nucleic Acids Research. 42: 1784-98. PMID 24217917 DOI: 10.1093/Nar/Gkt1104  0.33
2014 Jafari MR, Deng L, Kitov PI, Ng S, Matochko WL, Tjhung KF, Zeberoff A, Elias A, Klassen JS, Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. Acs Chemical Biology. 9: 443-50. PMID 24195775 DOI: 10.1021/Cb4006722  0.304
2014 Rosenfeld L, Lin T, Derda R, Tang SKY. Review and analysis of performance metrics of droplet microfluidics systems Microfluidics and Nanofluidics. 16: 921-939. DOI: 10.1007/S10404-013-1310-X  0.32
2014 Deiss F, Matochko WL, Govindasamy N, Lin EY, Derda R. Back Cover: Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays (Angew. Chem. Int. Ed. 25/2014) Angewandte Chemie International Edition. 53: 6570-6570. DOI: 10.1002/Anie.201404171  0.362
2014 Deiss F, Matochko WL, Govindasamy N, Lin EY, Derda R. Rücktitelbild: Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays (Angew. Chem. 25/2014) Angewandte Chemie. 126: 6688-6688. DOI: 10.1002/Ange.201404171  0.367
2013 Huang J, Derda R, Huang Y. Phage display informatics. Computational and Mathematical Methods in Medicine. 2013: 698395. PMID 24454540 DOI: 10.1155/2013/698395  0.355
2013 Deiss F, Mazzeo A, Hong E, Ingber DE, Derda R, Whitesides GM. Platform for high-throughput testing of the effect of soluble compounds on 3D cell cultures. Analytical Chemistry. 85: 8085-94. PMID 23952342 DOI: 10.1021/Ac400161J  0.752
2013 Derda R, Lockett MR, Tang SK, Fuller RC, Maxwell EJ, Breiten B, Cuddemi CA, Ozdogan A, Whitesides GM. Filter-based assay for Escherichia coli in aqueous samples using bacteriophage-based amplification. Analytical Chemistry. 85: 7213-20. PMID 23848541 DOI: 10.1021/Ac400961B  0.655
2013 Deiss F, Mazzeo A, Hong E, Ingber DE, Derda R, Whitesides GM. Cells in gels in paper in a new device Assay and Drug Development Technologies. 11: 512-514. DOI: 10.1089/Adt.2013.1109.Lr  0.485
2012 Funes-Huacca M, Wu A, Szepesvari E, Rajendran P, Kwan-Wong N, Razgulin A, Shen Y, Kagira J, Campbell R, Derda R. Portable self-contained cultures for phage and bacteria made of paper and tape. Lab On a Chip. 12: 4269-78. PMID 22895550 DOI: 10.1039/C2Lc40391A  0.308
2012 Matochko WL, Chu K, Jin B, Lee SW, Whitesides GM, Derda R. Deep sequencing analysis of phage libraries using Illumina platform. Methods (San Diego, Calif.). 58: 47-55. PMID 22819855 DOI: 10.1016/J.Ymeth.2012.07.006  0.462
2012 Matochko WL, Ng S, Jafari MR, Romaniuk J, Tang SK, Derda R. Uniform amplification of phage display libraries in monodisperse emulsions. Methods (San Diego, Calif.). 58: 18-27. PMID 22819853 DOI: 10.1016/J.Ymeth.2012.07.012  0.38
2012 Ng S, Jafari MR, Matochko WL, Derda R. Quantitative synthesis of genetically encoded glycopeptide libraries displayed on M13 phage. Acs Chemical Biology. 7: 1482-7. PMID 22725642 DOI: 10.1021/Cb300187T  0.379
2012 Mace CR, Akbulut O, Kumar AA, Shapiro ND, Derda R, Patton MR, Whitesides GM. Aqueous multiphase systems of polymers and surfactants provide self-assembling step-gradients in density. Journal of the American Chemical Society. 134: 9094-7. PMID 22594904 DOI: 10.1021/Ja303183Z  0.731
2012 Ng S, Jafari MR, Derda R. Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry. Acs Chemical Biology. 7: 123-38. PMID 21988453 DOI: 10.1021/Cb200342H  0.333
2011 Mammoto T, Mammoto A, Torisawa YS, Tat T, Gibbs A, Derda R, Mannix R, de Bruijn M, Yung CW, Huh D, Ingber DE. Mechanochemical control of mesenchymal condensation and embryonic tooth organ formation. Developmental Cell. 21: 758-69. PMID 21924961 DOI: 10.1016/J.Devcel.2011.07.006  0.511
2011 Derda R, Bracher PJ. YouTube or you lose: Grand Challenges Canada explores whether scientists are ready for Web-based grant competitions. Acs Chemical Biology. 6: 771-4. PMID 21851129 DOI: 10.1021/Cb200239T  0.68
2011 Li L, Klim JR, Derda R, Courtney AH, Kiessling LL. Spatial control of cell fate using synthetic surfaces to potentiate TGF-beta signaling. Proceedings of the National Academy of Sciences of the United States of America. 108: 11745-50. PMID 21719709 DOI: 10.1073/Pnas.1101454108  0.709
2011 Derda R, Tang SK, Laromaine A, Mosadegh B, Hong E, Mwangi M, Mammoto A, Ingber DE, Whitesides GM. Multizone paper platform for 3D cell cultures. Plos One. 6: e18940. PMID 21573103 DOI: 10.1371/Journal.Pone.0018940  0.588
2011 Tang SK, Derda R, Mazzeo AD, Whitesides GM. Reconfigurable self-assembly of mesoscale optical components at a liquid-liquid interface. Advanced Materials (Deerfield Beach, Fla.). 23: 2413-8. PMID 21491514 DOI: 10.1002/Adma.201100067  0.689
2011 Tang SK, Derda R, Quan Q, Lončar M, Whitesides GM. Continuously tunable microdroplet-laser in a microfluidic channel. Optics Express. 19: 2204-15. PMID 21369038 DOI: 10.1364/Oe.19.002204  0.354
2011 Derda R, Tang SK, Li SC, Ng S, Matochko W, Jafari MR. Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules (Basel, Switzerland). 16: 1776-803. PMID 21339712 DOI: 10.3390/Molecules16021776  0.389
2010 Norville JE, Derda R, Gupta S, Drinkwater KA, Belcher AM, Leschziner AE, Knight TF. Introduction of customized inserts for s-treamlined assembly and optimization of BioBrick synthetic genetic circuits. Journal of Biological Engineering. 4: 17. PMID 21172029 DOI: 10.1186/1754-1611-4-17  0.31
2010 Derda R, Tang SK, Whitesides GM. Uniform amplification of phage with different growth characteristics in individual compartments consisting of monodisperse droplets. Angewandte Chemie (International Ed. in English). 49: 5301-4. PMID 20583018 DOI: 10.1002/Anie.201001143  0.442
2010 Derda R, Musah S, Orner BP, Klim JR, Li L, Kiessling LL. High-throughput discovery of synthetic surfaces that support proliferation of pluripotent cells. Journal of the American Chemical Society. 132: 1289-95. PMID 20067240 DOI: 10.1021/Ja906089G  0.72
2009 Derda R, Laromaine A, Mammoto A, Tang SK, Mammoto T, Ingber DE, Whitesides GM. Paper-supported 3D cell culture for tissue-based bioassays. Proceedings of the National Academy of Sciences of the United States of America. 106: 18457-62. PMID 19846768 DOI: 10.1073/Pnas.0910666106  0.592
2007 Derda R, Wherritt DJ, Kiessling LL. Solid-phase synthesis of alkanethiols for the preparation of self-assembled monolayers. Langmuir : the Acs Journal of Surfaces and Colloids. 23: 11164-7. PMID 17880250 DOI: 10.1021/La701386V  0.557
2007 Derda R, Li L, Orner BP, Lewis RL, Thomson JA, Kiessling LL. Defined substrates for human embryonic stem cell growth identified from surface arrays. Acs Chemical Biology. 2: 347-55. PMID 17480050 DOI: 10.1021/Cb700032U  0.77
2004 Orner BP, Derda R, Lewis RL, Thomson JA, Kiessling LL. Arrays for the combinatorial exploration of cell adhesion. Journal of the American Chemical Society. 126: 10808-9. PMID 15339142 DOI: 10.1021/Ja0474291  0.765
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