Publications

2017

33. H. Anany, Y. Chou, S. Cucic, S. Evoy, R. Derda, MW Griffiths*, “From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophage“, Annu. Rev. Food Sci. Tech., 2017, 8 (in press).

2016

32.  F. Deiss,# Y. Yang,# W. L. Matochko, R. Derda*  Heat-enhanced peptide synthesis on Teflon-patterned paper“, Org. Biolmol. Chem. 2016, 14, 5148-5156

Access the recommendation on F1000PrimeDerda_Figure 1

31.  S. Kalhor-Monfared,   M. R. Jafari,   J. T. Patterson,   P. I. Kitov,   J. J. Dwyer,   J. J. Nuss and R. Derda  “Rapid Biocompatible Macrocyclization of Peptides with Decafluoro-diphenylsulfoneChem. Sci., 2016, 7, 3785-3790.

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30.  S. Ng and R Derda*  “Phage-displayed Macrocyclic Glycopeptide LibrariesOrg. Biomol. Chem., 2016, 14, 5539-5545

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29. F. Deiss, Y. Yang, R. Derda* Parallel Syntheses of Peptides on Teflon-Patterned Paper Arrays (SyntArrays). (book chapter) Methods. Mol. Biol. 2016, 1368, 249-71

28.  M. R. Jafari, J. Lakusta, R. J. Lundgren, and R Derda*  “Allene Functionalized Azobenzene Linker Enables Rapid and Light-Responsive Peptide MacrocyclizationBioconj. Chem., 2016, 27, 509–514

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27.  E. Lin, A. Sikhand, J. Wickware, Y. Hao and R Derda*  “Peptide Microarray Patterning for Controlling and Monitoring Cell GrowthActa Biomater., 2016, 34, 53–59

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26.  KF Tjhung, S. Ng, PI Kitov, EN Kitova, L Deng, JS Klassen, and R Derda*  “Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries“, J. Am. Chem. Soc., 2016, 138, 32–35.
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2015

25. S. Ng, E. Y. Lin, PI Kitov, KF Tjhung, OO Gerlits, L Deng, B Kasper, A Sood, BM Paschal, P Zhang, CC Ling, JS Klassen, CJ Noren, LK Mahal, RJ Woods, L Coates, and R Derda*  “Genetically-encoded Fragment-based Discovery of Glycopeptide Ligands for Carbohydrate-binding Proteins“, J. Am. Chem. Soc., 2015, 137, 5248–5251

Highlight in “Carbohydrates: Inhibitors in an Instant“ Nature Chemical Biology Practical Fragments: Fragments Ontology

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24. 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 Front. Microbiol. 6:340.

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23. 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“, 2015, PLoS Negl Trop Dis 9(5): e0003676

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22C. (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

22B. (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

22A. (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

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2014

21. 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 CellsACS Appl. Mater. Interfaces, 2014, 6, 21446–21453
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20. 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

19. 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.

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18. 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.

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17. 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)

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Highlighted in Chemical and Engineering News : “Peptide Synthesis: Nonstick barriers help build arrays for screening”

16. 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 ApplicationsMicrofluidics and NanoFluidics2014, 16, (5), 921-939

15. 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)

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14. 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)

See our article highlighted in Chemistry World, on CHEMIE.de information portals (bionity.com, analytica-world.com), and in here

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13. 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?

12. L Liu, N Jalili, A Baergen, S Ng, J Bailey, R Derda, JS Klassen* “Fluorine Bonding Enhances the Energetics of Protein-Lipid Binding in the Gas Phase“, Journal of The American Society for Mass Spectrometry, 2014, 25, (5), 751-757

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11. 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

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2013

10. 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

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9. W Matochko, R Derda Error analysis of deep sequencing of phage libraries: Peptides censored in sequencingComput Math Methods Med. (Phage Display Bioinformatics Issue), 2013, Vol. 2013, Article ID 491612TOC-CompMatMethods

8. F Deiss, A Mazzeo, E Hong, DE Ingber, R Derda,* GM Whitesides* “A Platform for High-Throughput Testing of the Effect of Soluble Compounds on 3D Cell CulturesAnal. Chem., 2013, 85, 8085–8094

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2012

7. MF Huacca, A Wu, E Szepesvari, P Rajendran, N Kwan-Wong, A Razgulin, Y Shen, J Kagira, R Campbell, R Derda* “Portable cultures for phage and bacteria made of paper and tapeLab Chip2012, 12, 4269-4278. Lab on a Chip Top 10% article

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6. S Ng, MR Jafari, W Matochko, R Derda* “Quantitative Synthesis of Genetically Encoded Glycopeptide Libraries Displayed on M13 PhageACS Chem. Biol.2012, 7 (9), 1482–1487. Cover Story of September Issue

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5. W Matochko, K Chu, B Jin, SW Lee, G Whitesides, R Derda* “Deep sequencing analysis of phage libraries using Illumina“, Methods2012, 58 (1), 47–55

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4. W Matochko, S Ng, MR Jafari, J Romaniuk, SKY Tang, R Derda* “Uniform amplification of phage display libraries in monodisperse emulsions“, Methods2012, 58 (1), 18-27.

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3. S Ng, MR Jafari, R Derda* “Bacteriophages and Viruses as a Support for Organic Synthesis and Combinatorial Chemistry“, ACS Chem. Biol., 2012, 7, 123.

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2. Derda R, Bracher PJ “YouTube or You Lose: Grand Challenges Canada Explores Whether Scientists Are Ready for Web-Based Grant Competitions” ACS Chem. Biol,20116(8), 771-774

1. Derda R, Tang SKY, Li SC, Ng S, Matochko WL, Jafari MR. “Diversity of Phage-Displayed Libraries of Peptides During Panning and Amplification” Molecules 201116, 1776-1803

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Graduate and Postdoctoral Work

 

15. R Derda, MR. Lockett, SKY Tang, RC Fuller, EJ Maxwell, B Breiten, CA Cuddemi, A Ozdogan, GM Whitesides “Filter-Based Assay for Escherichia coli in Aqueous Samples Using Bacteriophage-Based AmplificationAnal. Chem., 2013, 85 , 7213–7220

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14. C Mace, O Akbulut, A Kuma, N Shapiro, R Derda, M Patton, GM Whitesides* “Aqueous Multiphase Systems of Polymers and Surfactants Provide Self-Assembling Step-Gradients in Density“ J. Am. Chem. Soc., 2012, 134, pp 9094–9097

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13. 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.
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12. Tang SKY, Derda R, Quan Q, Loncar M, Whitesides GM “Continuously Tunable Droplet-based Optical Microcavities” Optics Express 2011, 19, 2204. This article was selected for publication in the Virtual Journal for Biomedical Optics, Volume 6, Issue 2, 2011.

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11. Derda R, Tang SKY, Laromaine A, Mosadegh B, Hong E, Mwangi M, Mammoto A, Ingber DE, Whitesides GM “Multizone paper platform for 3D cell cultures PLoS One2011, 6, e18940. Highlighted in Biotechniques: “Will paper cell cultures catch fire?”

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10. Tang SKY, Derda R, Mazzeo AD, Whitesides GM, “Reconfigurable Self-Assembly of Mesoscale Optical Components at a Liquid-Liquid Interface”, Adv. Mater.2011, 23, 2413.

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9. Li L, Klim JR, Derda R, Courtney AH, Kiessling LL, “Spatial control of cell fate using synthetic surfaces to potentiate TGF-beta  signaling Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 11745. Highlighted in C&E News 2011, 89, 6.

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8. Mammoto T, Mammoto A, Tat T, Gibbs A, Derda R, Mannix R, Bruijn M, Yung CW, Huh D, Ingber DE, “Mechanochemical Control of Mesenchymal Condensation and Embryonic Tooth Organ Formation” Dev. Cell 2011, 21, 758

7. Derda R, Tang SKY, Whitesides GM “Uniform Amplification of Phage with Different Growth Characteristics in Individual Compartments Consisting of Monodisperse DropletsAngew. Chem. Intl. Ed. 2010 49(31), 5301–5304. Highlighted in Faculty of 1000 Biology

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6. Derda R, Musah S, Orner BP, Klim JR, Li L, Kiessling LL “High-throughput Discovery of Synthetic Surfaces that Support Proliferation of Pluripotent Cells J. Am. Chem. Soc. 2010, 132, 1289. Highlighted in Faculty of 1000 Biology

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5. Norville JE, Derda R, Gupta S, Drinkwater KA, Belcher AM, Leschziner AE, Knight TFJr. “Introduction of customized inserts for streamlined assembly and optimization of BioBrick synthetic genetic circuits” J. Biol. Eng. 2010, 4, 17.

4. Derda R, Laromaine A, Mammoto A, Tang SKY, Mammoto T, Donald Ingber, Whitesides GM “Paper-Supported Three-Dimensional Cell Culture for Tissue-Based Bioassays” Proc. Natl. Acad. Sci. 2009, 106, 18457. Highlighted in Faculty of 1000 Biology, Faculty of 1000 Medicine and Nature Methods 2009, 6, 865.

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3. Derda R, Ligyin Li, Orner BP, Lewis RL, Thomson JA, Kiessling LL “Defined Substrates for Human Embryonic Stem Cell Growth Identified from Surface ArraysACS Chem. Biol. 2007, 2, 347

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2. Derda R, Wherritt DJ, Kiessling LL “Solid-phase Synthesis of Alkanethiols for the Preparation of Self-Assembled Monolayers on Gold” Langmuir 2007, 23, 11164.

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1. Orner BP, Derda R, Lewis RL, Thomson JA, Kiessling LL “The Design and Fabrication of Arrays for the Combinatorial Exploration of Cell Adherence” J. Am. Chem. Soc. 2004, 126, 10808-10809; The article was highlighted in Chemical and Engineering News 2004, 82, 21.

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