Ratmir Derda - Publications

Chemistry University of Alberta, Edmonton, Alberta, Canada 
drug discovery

77 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  1
2021 Sojitra M, Sarkar S, Maghera J, Rodrigues E, Carpenter EJ, Seth S, Ferrer Vinals D, Bennett NJ, Reddy R, Khalil A, Xue X, Bell MR, Zheng RB, Zhang P, Nycholat C, ... ... Derda R, et al. Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage. Nature Chemical Biology. PMID 33958792 DOI: 10.1038/s41589-021-00788-5  1
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  1
2020 Scott BM, Matochko WL, Gierczak RF, Bhakta V, Derda R, Sheffield WP. Correction: 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. 15: e0238969. PMID 32913368 DOI: 10.1371/journal.pone.0238969  1
2019 Kitova EN, Han L, Vinals DF, Kitov PI, Derda R, Klassen JS. Influence of Labeling on the Glycan Affinities and Specificities of Glycan-Binding Proteins. A Case Study Involving a C-terminal Fragment of Human Galectin 3. Glycobiology. PMID 31529034 DOI: 10.1093/Glycob/Cwz076  1
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  1
2018 Kamijo Y, Derda R. Freeze-Float Selection of Ice Nucleators. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 30509075 DOI: 10.1021/Acs.Langmuir.8B02902  0.01
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  1
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  1
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  1
2018 Jafari MR, Yu H, Wickware JM, Lin YS, Derda R. Light-responsive bicyclic peptides. Organic & Biomolecular Chemistry. PMID 30067270 DOI: 10.1039/C7Ob03178E  1
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  1
2018 He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J. Biopanning data bank 2018: hugging next generation phage display. Database : the Journal of Biological Databases and Curation. 2018. PMID 29688378 DOI: 10.1093/Database/Bay032  1
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  1
2017 Chou Y, Kitova EN, Joe M, Brunton R, Lowary TL, Klassen JS, Derda R. Genetically-encoded fragment-based discovery (GE-FBD) of glycopeptide ligands with differential selectivity for antibodies related to mycobacterial infections. Organic & Biomolecular Chemistry. PMID 29255817 DOI: 10.1039/C7Ob02783D  1
2017 Chou Y, Kitova EN, Joe M, Brunton R, Lowary TL, Klassen JS, Derda R. Genetically-encoded fragment-based discovery (GE-FBD) of glycopeptide ligands with differential selectivity for antibodies related to mycobacterial infections. Organic & Biomolecular Chemistry. PMID 29255817 DOI: 10.1039/c7ob02783d  1
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  1
2017 Triana V, Derda R. Tandem Wittig/Diels-Alder diversification of genetically encoded peptide libraries. Organic & Biomolecular Chemistry. PMID 28880027 DOI: 10.1039/C7Ob01635B  0.01
2017 Adini A, Adini I, Chi ZL, Derda R, Birsner AE, Matthews BD, D'Amato RJ. A novel strategy to enhance angiogenesis in vivo using the small VEGF-binding peptide PR1P. Angiogenesis. PMID 28397127 DOI: 10.1007/S10456-017-9556-7  0.01
2017 Anany H, Chou Y, Cucic S, Derda R, Evoy S, Griffiths MW. From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophages. Annual Review of Food Science and Technology. PMID 28125341 DOI: 10.1146/Annurev-Food-041715-033235  1
2016 Rakonjac J, Das B, Derda R. Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology. Frontiers in Microbiology. 7: 2109. PMID 28066406 DOI: 10.3389/Fmicb.2016.02109  0.01
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  1
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  1
2016 Ng S, Derda R. Phage-displayed macrocyclic glycopeptide libraries. Organic & Biomolecular Chemistry. PMID 26889738 DOI: 10.1039/C5Ob02646F  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Subbiah SK, Derda R, Newman R, Berard T, Marsden R. Geomechanics solution for UGS: Prevent costly events and maximise profits through 3D coupled model Petroleum Abstracts. 55: 91.  1
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  1
2014 Burnham S, Hu J, Anany H, Brovko L, Deiss F, Derda R, Griffiths MW. Towards rapid on-site phage-mediated detection of generic Escherichia coli in water using luminescent and visual readout. Analytical and Bioanalytical Chemistry. 406: 5685-93. PMID 24969469 DOI: 10.1007/S00216-014-7985-3  1
2014 Tjhung KF, Burnham S, Anany H, Griffiths MW, Derda R. Rapid enumeration of phage in monodisperse emulsions. Analytical Chemistry. 86: 5642-8. PMID 24892245 DOI: 10.1021/Ac500244G  1
2014 Kitov PI, Vinals DF, Ng S, Tjhung KF, Derda R. Rapid, hydrolytically stable modification of aldehyde-terminated proteins and phage libraries. Journal of the American Chemical Society. 136: 8149-52. PMID 24848432 DOI: 10.1021/Ja5023909  1
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  1
2014 Liu L, Jalili N, Baergen A, Ng S, Bailey J, Derda R, Klassen JS. Fluorine bonding enhances the energetics of protein-lipid binding in the gas phase. Journal of the American Society For Mass Spectrometry. 25: 751-7. PMID 24658801 DOI: 10.1007/S13361-014-0837-8  1
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  1
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  1
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  1
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  1
2014 Deiss F, Funes-Huacca ME, Bal J, Tjhung KF, Derda R. Antimicrobial susceptibility assays in paper-based portable culture devices. Lab On a Chip. 14: 167-71. PMID 24185315 DOI: 10.1039/C3Lc50887K  1
2014 Scott BM, Matochko WL, Gierczak RF, Bhakta V, Derda R, Sheffield WP. Schematic diagrams of construction of phage display library and biopanning strategy. Plos One. DOI: 10.1371/Journal.Pone.0084491.G001  1
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  1
2014 Subbiah S, Knezevic RN, Derda R, Serrao J. Taking full advantage of the "safe mud window" Eage Workshop On Geomechanics in the Oil and Gas Industry. 146-149.  1
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  1
2013 Matochko WL, Derda R. Error analysis of deep sequencing of phage libraries: peptides censored in sequencing. Computational and Mathematical Methods in Medicine. 2013: 491612. PMID 24416071 DOI: 10.1155/2013/491612  1
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  1
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  1
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  1
2013 Zeberoff A, Derda R, Elias AL. Remote activation of a microactuator using a frequency specific photo-responsive gold nanoparticle composite Journal of Micromechanics and Microengineering. 23. DOI: 10.1088/0960-1317/23/12/125022  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Tang SKY, Derda R, Quan Q, Loncar M, Whitesides GM. Microdroplet optical cavity sensors 15th International Conference On Miniaturized Systems For Chemistry and Life Sciences 2011, Microtas 2011. 1: 702-703.  1
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  1
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  1
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  1
2010 Tang SKY, Derda R, Quan Q, Loncar M, Whitesides GM. Continuously tunable dye laser using dissolving drops in microchannels Aiche Annual Meeting, Conference Proceedings 1
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  1
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  1
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  1
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  1
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