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Designing our future

Part of the Technical University of Denmark and DTU Bioengineering, the Digital Biotechnology Lab is a junior research group within the Tropical Pharmacology Lab. We are passionate about harnessing the power of modern technology to innovate the biotechnological landscape and develop real world solutions for the benefit of society. We focus on discovering and understanding protein-based binders, such as antibodies, nanobodies, and DARPins, using display technologies, and use of big data and artificial intelligence to achieve these goals. Importantly this includes the pursuit of fundamental questions, such as unravelling the core rule set that dictates binder-target interactions, as well as translational endeavours, such as discovering cost-effective therapeutics against infectious and neglected tropical diseases, such as snakebite envenoming.

 
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FOCUS AREAS

Fundamental

What dictates cross-reactivity of antibodies? Many variables are at play in antibody-target interactions. At the Digital Biotechnology Lab we are trying to understand which ones matter the most, and whether we can use that knowledge to discover more cross-reactive binders. For that purpose, we generate large, multifaceted datasets and employ structural modelling (e.g., AlphaFold2), as well as mapping the antibody-target interface. With the insights we gain and the data generated in the process we train machine learning algorithms to aid binder discovery and development.

 

Translational

Monoclonal antibodies have been developed into ‘blockbuster drugs’ and are predicted to reach a market value of 300 billion USD in 2025. Yet, whilst their high specificity and affinity for target antigens make them highly beneficial for many indications, different tools are required when multiple targets need to be neutralised. This is the case with animal venoms that comprise multitudes of similar and dissimilar toxins, but also for mutating diseases, such as cancer and infectious diseases. In such cases, it is beneficial, if not essential, to use broadly-neutralising antibodies that are able to target multiple similar antigens, do not easily lose their efficacy when faced with rapid target mutation, and are easy to manufacture. Thus, at the Digital Biotechnology Lab we use display technologies to discover broadly-neutralising antibodies and antibody alternatives such as DARPins and nanobodies against animal and plant toxins.

Entrepreneurship

At the Digital Biotechnology Lab, we leverage scientific advances to solve the world’s problems. For this reason, significant emphasis is put on evaluating new ideas and findings in an entrepreneurial context. To date, two commercial projects, Sweathut Therapeutics and Immunite, have received soft funding and are being development further.

 

THE DIGITAL BIOTECHNOLOGY LAB TEAM

Get to Know Us

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TIMOTHY P JENKINS

Assistant Professor

Tim completed his BSc in Zoology & Ecology at the James Cook University in Australia. He subsequently completed his PhD in host-parasite-microbiome interactions at the University of Cambridge and joined DTU as a H.C. Ørsted / Marie Skłodowska-Curie Actions postdoctoral fellow. He was appointed Assistant Professor upon completion of his 2-year postdoc.

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THOMAS FRYER

Affiliated Postdoc

Thomas is establishing high-throughput yeast display guided antibody discovery pipelines.

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ESPERANZA RIVERA-DE-TORRE

Affiliated Postdoc

Esperanza is leading the development and expression of complex consensus proteins

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JAMES ROONEY

Visiting PhD student

During his time at DBL James will recombinantly express several proteins, with putative antimicrobial activity, identified in the excretory-secretory products from gastrointestinal helminths.

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VLAD ROSCA

MSc Special Project

In his special project, Vlad is conducting machine learning guided protein hallucination for de novo therapeutic design

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NILS HOFMANN

MSc Special Project

Nils is establishing a high-throughput analysis pipeline for NGS data from phage display during his special project

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JESPER KILDEMAND

MSc Special Project

Jesper is working on a broad sprectrum allergy treatment based on designed allergens.

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LAURA CHRISTINE ASTRUPGAARD

BSc Special Project

Laura is using her special project to express recombinant spider toxins

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BRUNA CAVEION

Guest Researcher

Bruna is using her computer science background to establish a tool for the de novo protein hallucination of therapeutics

ALUMNI

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ANDREAS SIXTEN HALLSTEIN RYGAARD, BSc

Development of Cross-Reactive Designed Ankyrin Repeat Proteins binders toward Phospholipases A2 for Recombinant Snake Antivenom

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EMILIE MARIA SØLLING HENRIKSEN, MSc

Phage display guided discovery of designed ankyrin repeat proteins against Indian snake venom toxins

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CHARLOTTE RISAGER CHRISTENSEN, BSc

Phage display guided discovery of designed ankyrin repeat proteins against a small plant toxin

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GÁBOR DÁNYI, MSc

High-throughput synthesis and characterization of single-chain variable fragments for in silico antibody discovery

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DARIAN WOLFF, MSc

Unlocking cross-reactivity of antibodies by employing crosslinking mass spectrometry and high-density peptide microarrays

 

PEER REVIEWED PUBLICATIONS

2022

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2020

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Timothy P. Jenkins, Nicolas Lopez Carranza, Amy Bray, Karim Beguir, Andreas H. Laustsen. Can hackathons unlock a new talent pool from the developing world? Nat Biotechnol (2022).

Timothy P. Jenkins, William Michael Laprade, Andrés Sánchez, Tulika Tulika, Carol O’Brien, Christoffer V. Sørensen, Trenton K. Stewart, Thomas Fryer, Andreas H. Laustsen, José María Gutiérrez. ALOHA: AI-guided tool for the quantification of venom-induced haemorrhage in mice. bioRxiv (2022).

Line Ledsgaard, Jack Wade, Kim Boddum, Irina Oganesyan, Julian Harrison, Timothy P. Jenkins, Pedro Villar, Rachael A. Leah, Renato Zenobi, John McCafferty, Bruno Lomonte, José M. Gutiérrez, Andreas H. Laustsen, Aneesh Karatt-Vellatt. Discovery of a broadly-neutralizing human antibody that can rescue mice challenged with neurotoxin-rich snake venoms. bioRxiv (2022).

Andreas H. Laustsen, Bengt H. Gless, Timothy P. Jenkins, Maria Meyhoff-Madsen, Johanna Bjärtun, Andreas S. Munk, Saioa Oscoz, Julián Fernández, José María Gutiérrez, Bruno Lomonte, Brian Lohse. “In vivo neutralization of Myotoxin II, a phospholipase A2 homolog from Bothrops asper venom, using peptides discovered via phage display technology”. ACS Omega (2022).

Wei-qiao Rao, Konstantinos Kalogeropoulos, Morten E. Allentoft, Shyam Gopalakrishnan, Weining Zhao, Christopher T. Workman, Cecilie Knudsen, Belén Jiménez-Mena, Lorenzo Seneci, Mahsa Mousavi-Derazmahalleh, Timothy P. Jenkins, Si-qi Liu, Andreas H. Laustsen “The rise of genomics in snake venom research: recent advances and future perspectives”. GigaScience (2022), 11.

Esperanza Rivera-de-Torre, Charlotte Rimbault, Anna D. Jensen, Christoffer Sorensen, Timothy P. Jenkins, Natalie Saez, Yoan Duhoo, Celeste Menuet, Lars Ellgaard, Andreas H. Laustsen. “Strategies for heterologous expression and purification of animal venom toxins”. Frontiers in Bioengineering and Biotechnology (2022), 9.

Timothy P. Jenkins, Shirin Ahmadi, Matyas Bittenbinder, Trenton Keith Stewart, Dilber E. Akgun, Melissa Hale, Nafiseh N. Nasrabadi, Darian S. Wolff, Freek J. Vonk, Jeroen Kool, and Andreas H. Laustsen. “Terrestrial venomous animals and the envenomings they cause in the Middle East and North Africa”. PLoS NTD (2021), 15 (12).

Nicolai Rügen, Timothy P. Jenkins, Natalie Wielsch, Heiko Vogel, Benjamin-Florian Hempel, Roderich D. Süssmuth, Stuart Ainsworth, Alejandro Cabezas-Cruz, Andreas Vilcinskas, and Miray Tonk. "Hexapod Assassins’ Potion: Venom Composition and Bioactivity from the Eurasian Assassin Bug Rhynocoris iracundus." Biomedicines 9, no. 7 (2021): 819.

Timothy P. Jenkins, David I. Pritchard, Gary Telford, Radu Tanasescu, Cris S. Constantinescu, and Cinzia Cantacessi. “Longitudinal changes in the gut microbiome of human volunteers with remitting-relapsing multiple sclerosis following experimental infection with the hookworm, Necator americanus”. BMC Biology (2021), 19, 74.

Andreas H. Laustsen, Victor Greiff, Aneesh Karatt-Vellatt, Serge Muyldermans, Timothy P. Jenkins. “Animal immunization, in vitro display technologies, and machine learning for antibody discovery”. Trends in Biotechnology (2021).

Timothy P. Jenkins and Andreas H. Laustsen. “Cost of manufacturing for recombinant snakebite antivenoms”. Frontiers in Bioengineering and Biotechnology (2020), 8.

Timothy P. Jenkins, Kamille E. Krause, Carina Skaarup, Mikael Engmark, Nicholas Casewell, Robert Harrison, Stuart Ainsworth, Bruno Lomonte, Julián Fernández, José María Gutiérrez, Andreas H. Laustsen, and Ole Lund. “An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity”. PLoS Neglected Tropical Diseases, (2020), 14, 6.

Radu Tanasescu, Christopher R. Tench, Cris S. Constantinescu, Gary Telford, Sonika Singh, Nanci Frakich, David Onion, Dorothee P. Auer, Bruno Gran, Nikos Evangelou, Yasser Falah, Colin Renshaw, Cinzia Cantacessi, Timothy P. Jenkins and David I. Pritchard. “Hookworm Treatment for Relapsing Multiple Sclerosis: A Randomized Double-Blinded Placebo-Controlled Trial”. JAMA Neurolology, (2020), published online.

 
 

GRANTS & PRIZES

DTU PoC - Immunite

USD 68,520

ERC PoC - CAT

USD 169,000

Alliance PhD

USD 210,000

DTU Discovery grant - Immunite

USD 22,250

Novo Scholarship - Darian Wolff

USD 8,500

H.C. Ørsted Fellowship extension

USD 62,500

InnoExplorer - Sweathut Therapeutics

USD 250,000

Hørslev-Fonden

USD 30,000

Otto Monsted - ‘Bright Idea Award’

USD 40,000

DTU Discovery grant - Sweathut Therapeutics

USD 22,250

Brødrene Hartmanns Fond

USD 13,200

H.C. Ørsted Postdoctoral Fellowship

USD 177,300

 
 

POPULAR SCIENCE

2022

ScienceNordic

Lorenzo Seneci, Timothy P. Jenkins, Shirin Ahmadi, Christoffer V. Sørensen.

“Heading towards mushroom wonderland”

2022

Videnskab

Lorenzo Seneci, Timothy P. Jenkins, Shirin Ahmadi, Christoffer V. Sørensen.

“Hallucinationer og lægemidler: Psykedeliske svampes mange funktioner”

2022

ScienceNordic

Lorenzo Seneci, Timothy P. Jenkins, Shirin Ahmadi, Christoffer V. Sørensen.

“Cell death and vomiting: This happens in your body, if you eat poisonous mushrooms”

2022

Videnskab

Lorenzo Seneci, Timothy P. Jenkins, Shirin Ahmadi, Emilie Henriksen, Christoffer V. Sørensen.

“Celledød og opkast: Det sker i kroppen, hvis du spiser giftige svampe”

2021

Videnskab

Lorenzo Seneci, Timothy P. Jenkins, Christoffer V. Sørensen.

Ekstremt stor forskel på slangernes gift: Ikke to bid er ens”.

2021

ScienceNordic

Lorenzo Seneci, Timothy P. Jenkins, Christoffer V. Sørensen.

Extreme variation in snake venom: no two bites are the same”.

2020

ScienceNordic

Anna D. Jensen, Timothy P. Jenkins, Thomas Fryer, Andreas H. Laustsen.

Nanobodies – a smaller and better version of antibodies?

2020

Videnskab

Anna D. Jensen, Timothy P. Jenkins, Thomas Fryer, Andreas H. Laustsen.

Nanobodies: Gemmer kamelens immunforsvar på en mindre og bedre version af antistoffer?

2020

The Conversation

Andreas H. Laustsen, Line Ledsgard, and Timothy P. Jenkins

Finally, snakebite is getting more attention as a tropical health issue

 
Future of Drug Discovery talkshow

Future of Drug Discovery talkshow

Play Video
 
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JOIN US

At the Digital Biotechnology Lab we are always excited to hear from passionate scientists and students who have an interest in joining our research group. We welcome everyone across ages, nationalities, cultures, genders, and experience levels.


If you would like to join our lab, please follow these guidelines:

FOR ASPIRING INTERNS AND VOLUNTEERS

If you are interested in joining our group as an intern or volunteer and would like to conduct research and learn new techniques, please send the following to tpaje@dtu.dk:

  • Letter of motivation (max 1 page)

  • CV

  • Grade transcripts

Be aware that funding is generally not available to support travel or accommodation expenses for students coming from abroad. Exceptions generally only apply to students/graduates from close collaborators.

FOR BSC AND MSC STUDENTS

If you are interested in joining our group during your bach