Kejia Yan is developing chemical strategies for the synthesis of genetically-encoded libraries and uses them to answer fundamental questions in chemical reactivity.

Jeffrey is employing genetically-encoded chemical libraries to identify early drug leads that inhibit anti-tumor protein Nodal

test

Mirat is working on genetically-encoded chemical libraries, discovery of instructive biomaterials and Liquid Glycan Array (LiGA) technology

Publication from Derda Lab:

1. Mirat Sojitra, Susmita Sarkar, Jasmine Maghera, Emily Rodrigues, Eric J. Carpenter, Shaurya Seth, Daniel Ferrer Vinals, Nicholas J. Bennett, Revathi Reddy, Amira Khalil, Xiaochao Xue, Michael Bell, Ruixiang Blake Zheng, Ping Zhang, Chang Chun Ling, Todd L. Lowary, James C. Paulson, Matthew S. Macauley, Ratmir Derda* “Genetically Encoded, Multivalent Liquid Glycan Array (LiGA)“, BioRXiv, 2020, DOI: 10.1101/2020.03.24.997536

Revathi is working on genetically-encoded Liquid Glycan Array (LiGA) technology and its application in serological tests. Her awards include: Bronze medal at the International Genetically Engineered Machine (iGEM) competition in Boston for the project “Engineering E.coli for ammonia assimilation from public urinals”. As the Communications Officer of the Glyconet Trainee Association, Revathi moderates and writes for the CuriOSEity blog [1] [2] [3]. She also develops resources for the Synthetic Biology community by creating digital content [4] and organizing science communication training programs [5]

Tracy is working on chemo-enzymetic synthesis of complex glycans and their application in genetically-encoded Liquid Glycan Array (LiGA) technology

Arunika is developing new genetically encoded chemical spaces and uses them to discover new classes reversible covalent inhibitors of proteins

Publications from Derda Lab

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

Alexei is developing new classes of phage vectors to enable display, discovery and detection that is impossible with state-of-the-art display systems

Eric employs Bioinformatics and Machine Learning technologies to understand and predict interactions between proteins and glycans.

Publication from Derda Lab:

1. Mirat Sojitra, Susmita Sarkar, Jasmine Maghera, Emily Rodrigues, Eric J. Carpenter, Shaurya Seth, Daniel Ferrer Vinals, Nicholas J. Bennett, Revathi Reddy, Amira Khalil, Xiaochao Xue, Michael Bell, Ruixiang Blake Zheng, Ping Zhang, Chang Chun Ling, Todd L. Lowary, James C. Paulson, Matthew S. Macauley, Ratmir Derda* “Genetically Encoded, Multivalent Liquid Glycan Array (LiGA)“, BioRXiv, 2020, DOI: 10.1101/2020.03.24.997536

Sharyar employs Machine Learning technologies to analyze genetically-encoded discovery of ligands and chemical reactions

Shaurya (Shau) is developing deep neural network and other machine learning technologies to understand protein glycan interations. Shau’s awards include 2020 URI Fellowship from University of Alberta.

Noel is semploying machine learning technologies to understand protein glycan interations.

Lena is working on synthesis of macrocyclic and bicycle peptides via late-stage functionalization of unprotected natural peptides.

Publications from Derda Lab

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

Elizabeth is using parallel phage culture and expansion to build the foundation of the Liquid Glycan Array (LiGA) technology

SVEKY (a.k.a. Ser-Val-Glu-Lys-Tyr) joined Derda Lab in June 2017 as a 3 months old puppy and quickly rose through the ranks to become the CCO of Derda Lab. She has been named after a peptide sequence SVEKNDQKTYHA featured in numerous publications from Derda Lab:

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

2. 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

3. S Ng, MR Jafari, W Matochko, R Derda* “Quantitative Synthesis of Genetically Encoded Glycopeptide Libraries Displayed on M13 Phage” ACS Chem. Biol., 2012, 7 (9), 1482–1487

4. 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.

5. 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

Welcome to Centennial Centre for Interdisciplinary Science (CCIS), home of Derda Lab

SVEKY in the office working on water quality detection

SVEKY says “Always wear eye protection when working in the lab”

SVEKY, the CCO: hard day at work..

SVEKY measuring its melting point

Zanib Pannu and  Yi Meng Wang, joined the lab in October 2017 and worked on project that aims to identify ice-nucleating bacteria and peptides. The team participated in 2018 Sanofi Biogenius Canada competition at the University of Alberta in April, 2018.

Jesse Lee joined the project for a few months in summer 2018 and helped developing emulsion-based screening for ice nucleators

Simran Dhillon, Siddhant Gautam, and Xibu (Denny) Zhang joined the lab in October 2016 and worked on project that aims to identify ice-suppressing peptides. The team participated in 2017 Sanofi Biogenius Canada competition at the University of Calgary on April 13th, 2017.

Andre Truksa joined the project in May 2017

High School students Rifah Chowdhury, Preet Lat joined Derda Lab as research volunteers in Fall 2014 and they worked on development of portable diagnostics for detection of antibiotics resistant bacteria.

In Fall 2015 to Fall 2016, Rifah Chowdhury, Preet Lat and two new high school students Garrett Corkey and Hallie Trono volunteer in the Derda Lab in a research project that aimed to identify materials that trigger freezing of supercooled water.

In 2017 Rifah Chowdhury and  Preet Lat graduate from high school and joined University of Alberta for their undergraduate studies. Preet continues her research volunteer position in Derda group working on phage-based selection of ice nucleation agents.

Fall 2013 to Spring 2015, Patricia Yan and Amy Li, high school students from Harry Ainlay High School, volunteer in the Derda Lab. They were involved in the development of the electrochemical detection of bacteria in paper-based culture devices. Patricia Yan and Amy Li were the winners of the  Sanofi BioGenius Canada competition in 2015 (1st and 2nd place at the All-Alberta competition!) and they represented Alberta in all-Canadian Sanofi BioGenius competition.

Jessica and Falak joined the group in 2012 and worked on portable bacteria culture devices. In 2014, Jessica worked on paper based culture of cancer cells. In 2014, Jessica was a winner of Sanofi BioGenius Canada all-Alberta competition and represented Alberta on All-Canadian Sanofi BioGenius competition. Jessica started her undergraduate degree at the university of Alberta in 2014 and she continued her undergraduate research project in Derda Lab. From 2014 to 2017, she supervised research projects of over 10 high school students.

Fall 2011 to Summer 2012, four high school students–Ally Wu, Eszter Szepesvari, Pavitra Rajendran, Nicholas Kwan-Wong–were involved in development of portable diagnostic devices for developing countries. They were co-authors on the manuscript in Lab on a Chip:

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 tape” Lab Chip, 2012, 12, 4269-4278

Ally, Eszter, Pavitra, and Nick continue their undergraduate degree at the University of Alberta.