52. Guilherme M. Lima, Alexey Atrazhev, Susmita Sarkar, Mirat Sojitra, Revathi Reddy, Matthew S. Macauley, Gisele Monteiro*, and Ratmir Derda* “DNA-Encoded Multivalent Display of Protein Tetramers on Phage: Synthesis and In Vivo Applications” BioRxiv. Preprint 2021 doi:

51. Jeffrey Wong, Raja Mukherjee, Olena Bilyk, Jiayuan Miao, Vivian Triana Guzman, Mark Miskoizie, Yu-Shan Lin, Antoine Henninot, John J. Dwyer, Serhii Kharchenko, Anna Iampolska, Dmitriy Volochnyuk, Lynne M. Postovit, Ratmir Derda* “Genetically-Encoded Discovery of Proteolytically Stable Bicyclic Inhibitors of Morphogen NODAL“, ChemRxiv. Preprint 2021 DOI  

Article Twitter Feed: @RatmirDerda


50. Arunika Ekanayake, Lena Sobze, Jihea Youk, Nicholas J. Bennett, Raja Mukherjee, Atul Bhardwaj, Frank Wuest, Ratmir Derda, “Genetically Encoded Fragment-Based Discovery (GE-FBD) from Phage-Displayed Macrocyclic Libraries with Genetically-Encoded Unnatural Pharmacophores ChemRxiv. Preprint., 2020 DOI: 10.26434/chemrxiv.12644225.v1

Article Twitter Feed: @RatmirDerda, @Derdalab

49. Mirat SojitraSusmita SarkarJasmine MagheraEmily RodriguesEric J. CarpenterShaurya SethDaniel Ferrer VinalsNicholas J. BennettRevathi ReddyAmira Khalil, Xiaochao XueMichael BellRuixiang Blake ZhengPing ZhangChang Chun Ling, Todd L. LowaryJames C. PaulsonMatthew S. Macauley, Ratmir Derda* “Genetically Encoded, Multivalent Liquid Glycan Array (LiGA)“, BioRXiv, 2020, DOI: 10.1101/2020.03.24.997536  SI available at BioRXiv and

Article Twitter Feed: @RatmirDerda @derda_lab, @MITglycobio, @CarolynBertozzi, @ChemicalBiology


48. Elena N Kitova, Ling Han, Daniel F Vinals, Pavel I Kitov, Ratmir Derda, John S Klassen*, “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, 2019, 30, 49-57.

47.  Ratmir Derda* and Simon Ng “Genetically-Encoded Fragment-Based Discovery (GE-FBD)”, Current Opinion in Chemical Biology, 2019, 50, 128. 

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46. Yuki Kamijo and Ratmir Derda*“Freeze-Float Selection of Ice NucleatorsLangmuir, 2019, 35 (2), 359–364


45. Daniel Ferrer Vinals, Pavel I. Kitov, Zhijay Tu, Chunxia Zou, Christopher W. Cairo, Hans Chun-Hung Lin, Ratmir Derda* “Selection of galectin-3 ligands derived from genetically encoded glycopeptide libraries“, Peptide Sci., 2019, 111, e24097 


44. Bifang He, AM Dzisoo, Ratmir Derda, Jian Huang*. “Development and Application of Computational Methods in Phage Display Technology”, Curr. Med. Chem., 2019, 26, 7672.

43. L Ning, B He, P Zhou, R Derda, J Huang, Molecular Design of Peptide-Fc fusion DrugsCurr. Drug Metabolism, 2019,  20(3), 203-208.


42. Ratmir Derda and Mohammad R Jafari, “Synthetic Cross-linking of Peptides:  Molecular Linchpins for Peptide Cyclization”, Prot. Pep. Lett., 2018DOI : 10.2174/0929866525666181120090650


41.  Simon Ng, Nicholas James Bennett, Jessica Schulze, Nan Gao, Christoph Rademacher, Ratmir Derda* Genetically-encoded Fragment-based Discovery of Glycopeptide Ligands for DC-SIGN“, Bioorg. & Med. Chem., 2018, 26(19), 5368-5377.

Graphical Abstract

40. Mohammad R. Jafari,  Hongtao Yu,  Jessica M. Wickware,  Yu-Shan Lin  and  Ratmir Derda*, “Light Responsive Bicyclic PeptidesOrg. Biomol. Chem., 2018,16, 7588-7594.

Highlighted on RSC blog: “Creating a platform for the development of photoswitchable ligand libraries

TOC_OBC2018OBC Cover 2018

39. Bifang He, Lixu Jiang, Yaocong Duan, Guoshi Chai, Yewei Fang, Juanjuan Kang, Min Yu, Ning Li, Zhongjie Tang, Pengcheng Yao, Pengcheng Wu, Ratmir Derda, Jian Huang, “Biopanning data bank 2018: hugging next generation phage display“, Database, 2018, bay032. DOI: 10.1093/database/bay032

38. B. He, K. F. Tjhung, N. J. Bennett, Y. Chou, A. Rau, J. Huang, R. Derda*, “Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep SequencingNat. Sci. Reports.2018, 8, 1214


37. Y. Chou, E. N. Kitova , M. Joe, R. Brunton, T. L. Lowary, J. S. Klassen, R. Derda*, “Genetically-encoded fragment-based discovery (GE-FBD) of glycopeptide ligands with differential selectivity for antibodies related to mycobacterial infections“, Org. Biomol. Chem, 2018, 16, 223 – 227



36. B. Akgun, C. Li, Y. Hao, G. Lambkin, R. Derda, D. Hall*, “Synergic ‘Click’ Boronate/Thiosemicarbazone System for Fast and Irreversible Bioorthogonal Conjugation in Live Cells” J. Am. Chem. Soc.2017, 139, 14285–14291


35. V. Triana, R. Derda*, “Tandem Wittig / Diels-Alder Diversification of Genetically Encoded Peptide Libraries“, Org. Biomol. Chem.2017, 15, 7869-7877


34. A Adini, I Adini, Z Chi, R Derda, AE Birsner, BD Matthews, RJ D’Amato*, “A novel strategy to enhance angiogenesis in vivo using the small VEGF-binding peptide PR1P“, Angiogenesis2017, 20, 399–408.


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, 305-329.

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32.  K. F. Tjhung, S. Ng, P. I. Kitov, E. N. Kitova, L. Deng, J. S. Klassen, and R. Derda*  “Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries“, J. Am. Chem. Soc.2016, 138, 32–35.


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.


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


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


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 download PDF

Graphical Abstract

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

Access the recommendation on F1000Prime

Derda_Figure 1


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 2015, 11, 381, and Practical Fragments: Fragments Ontology


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.


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


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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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

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.


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.


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) Download PDF


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)

Derda TOC Picture

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 information portals (,, and in here


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?

data pages: illumina processing scripts, raw data files

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


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



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


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



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


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


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


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.


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.



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


Graduate and Postdoctoral Work


16. Gulden Camci-Unal, Anna Laromaine, Estrella Hong, Ratmir Derda, and George M. Whitesides*, “Biomineralization Guided by Paper Templates“, Sci. Rep., 2016, 6016; 6: 27693.

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


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


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.
template draft_1

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.


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?”


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.


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.


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


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


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.


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


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.


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.