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Dr. Andreas Martin Lisewski

Dr. Andreas Martin Lisewski

Senior Lecturer of Science
School of Science
Campus Ring 6 / 28759 Bremen / Germany
Phone number
+49 421 200 3558
Email Address
alisewski@constructor.university
Office
Research II, Room 75
Research Interests

In the broadest sense, our research uses modern computational methods to decode the biological information that is encoded in genomes. The genomic information we are especially interested in is functional information relevant in infectious disease agents, ranging from parasitic eukaryotes, bacteria, to viruses. Following this research, basic elements of molecular biology (such as genomic structure, DNA replication, transcription, translation, structural stability) are analyzed from a modern information engineering perspective that incorporates the transmission of genomic information from a sender, via a coder-channel-encoder device, to a receiver. This biodigital convergence is a far-reaching conjunction of digital communication theory and molecular biology at their most fundamental level.

Our scientific work also focuses on computational approaches to synthetic biology, ranging from understanding basic concepts, such a computational methods to tell synthetic from natural genomes, to developing specific bioengineering applications such as the design and control of thermostability in proteins. Synthetic biology is the disruptive technology of the 2020s. It is historically unprecedented for a single technology to have such an impact on not only medicine, food, livestock, defense sector, but also on the entire human society and the global biosphere.

From it an additional focus of our research are the technological risks and societal impacts that emerge from recent breakthroughs in synthetic biology and from the ongoing process of biodigital convergence.

Selected Publications

A large-scale evaluation of computational protein function prediction

P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ...

Nature methods 10 (3), 221-227

 

Identity and function of a large gene network underlying mutagenic repair of DNA breaks

AAM Al Mamun, MJ Lombardo, C Shee, AM Lisewski, C Gonzalez, D Lin, ...

Science 338 (6112), 1344-1348

 

Automated hypothesis generation based on mining scientific literature

S Spangler, AD Wilkins, BJ Bachman, M Nagarajan, T Dayaram, P Haas, ...

Proceedings of the 20th ACM SIGKDD international conference on Knowledge ...

 

Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate

AM Lisewski, JP Quiros, CL Ng, AK Adikesavan, K Miura, N Putluri, ...

Cell 158 (4), 916-928

 

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

DM Kristensen, RM Ward, AM Lisewski, S Erdin, BY Chen, VY Fofanov, ...

BMC bioinformatics 9, 1-19

 

Graph sharpening plus graph integration: a synergy that improves protein functional classification

H Shin, AM Lisewski, O Lichtarge

Bioinformatics 23 (23), 3217-3224

 

Protein function prediction: towards integration of similarity metrics

S Erdin, AM Lisewski, O Lichtarge

Current opinion in structural biology 21 (2), 180-188

 

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs

BY Chen, VY Fofanov, DH Bryant, BD Dodson, DM Kristensen, ...

Journal of Computational Biology 14 (6), 791-816

 

Rapid detection of similarity in protein structure and function through contact metric distances

AM Lisewski, O Lichtarge

Nucleic Acids Research 34 (22), e152-e152

 

Predicting future scientific discoveries based on a networked analysis of the past literature

M Nagarajan, AD Wilkins, BJ Bachman, IB Novikov, S Bao, PJ Haas, ...

Proceedings of the 21th ACM SIGKDD International Conference on Knowledge …

 

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

DM Kristensen, BY Chen, VY Fofanov, RM Ward, AM Lisewski, M Kimmel, ...

Protein Science 15 (6), 1530-1536

 

Graph sharpening

H Shin, NJ Hill, AM Lisewski, JS Park

Expert Systems with Applications 37 (12), 7870-7879

 

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features

RM Ward, S Erdin, TA Tran, DM Kristensen, AM Lisewski, O Lichtarge

PLoS One 3 (5), e2136

 

Geometric sieving: Automated distributed optimization of 3D motifs for protein function prediction

BY Chen, VY Fofanov, DH Bryant, BD Dodson, DM Kristensen, ...

Research in Computational Molecular Biology: 10th Annual International …

 

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities

E Venner, AM Lisewski, S Erdin, RM Ward, SR Amin, O Lichtarge

PLoS One 5 (12), e14286

 

 

Recent Publications on Scopus
Lisewski, A.M.
The BMJ 2021 373
Lisewski, A.M.
International Journal of Infectious Diseases 2021 106 pp. 169-170
Lisewski, A.M. Quiros, J.P. Mittal, M. Putluri, N. Sreekumar, A. Haeggström, J.Z. Lichtarge, O.
International Journal for Parasitology: Drugs and Drug Resistance 2018 8 (1) pp. 31-35
CV

MSc, University of Hamburg

PhD, Technical University Munich

Andreas Martin Lisewski on Google Scholar

Andreas Martin Lisewski on ResearchGate