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Dr. Andreas Martin Lisewski

Senior Lecturer
School of Science
Campus Ring 6 / 28759 Bremen / Germany
Phone number
+49 421 200 3558
Email Address
Research II, room 75
Research Interests

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. Our research focuses on computational approaches to synthetic biology, from understanding basic concepts through to developing specific medicinal applications such as thermostability of proteins. Following this research, basic elements of molecular biology (such as DNA replication, transcription, translation, structural stability) are analyzed from a modern information engineering perspective that incorporates the transmission of genetic information from a sender to a receiver (see Figure below). This application of (Shannon-Weaver) communication theory at a molecular biology level allows a representation of the basic elements of synthetic biology using a hierarchy of abstraction through parts, modules, devices, and sender-receiver systems. A focus is additionally placed on the technological risks and societal impacts that come from recent breakthroughs in synthetic biology.

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


Constraints on the delayed transition to detonation in Type Ia supernovae

AM Lisewski, W Hillebrandt, SE Woosley

The Astrophysical Journal 538 (2), 831


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


Distributed burning in Type Ia supernovae: A statistical approach

AM Lisewski, W Hillebrandt, SE Woosley, JC Niemeyer, AR Kerstein

The Astrophysical Journal 537 (1), 405


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 …


Association between influenza vaccination rates and SARS-CoV-2 outbreak infection rates in OECD countries

AM Lisewski

SSRN 3558270


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


Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states

AM Lisewski, O Lichtarge

Physica A: Statistical Mechanics and its Applications 389 (16), 3250-3253


The concept of strong and weak virtual reality

AM Lisewski

Minds and machines 16, 201-219