Publications

@techreport{BKL1999a,
title = {BALL: Biochemical Algorithms Library},
author = {Nicolas Pascal Boghossian and Oliver Kohlbacher and Hans-Peter Lenhof},
url = {http://domino.mpi-sb.mpg.de/internet/reports.nsf/NumberView/1999-1-002},
year = {1999},
date = {1999-01-01},
number = {MPI-I-99-1-002},
address = {Saarbrücken, Germany},
institution = {Max-Planck-Institut für Informatik},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}

@inproceedings{procNHL1998,
title = {Investigating the Sugar-Lectin Interaction by Computational Chemistry: Tunneling the Epithelial Barrier},
author = {Dirk Neumann and Elleonore Haltner and Claus-Michael Lehr and Oliver Kohlbacher and Hans-Peter Lenhof},
year = {1998},
date = {1998-01-01},
booktitle = {Abstracts of the 18th Interlec Meeting},
pages = {549},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}

@article{Immel_Comms_Bio_2021,
title = {Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry},
author = {Alexander Immel and Federicia Perini and Christoph Rinne and John Meadows and Rodrigo Barquera and Andras Szolek and Julian SUsat and Lisa Böhme and Janina Dose and Joanna Bonczarowska and Clara Drummer and Katharina Fuchs and David Ellinghaus and Jan-Christian Kässens and Martin Furholt and Oliver Kohlbacher and Sabine Schade-Lindig and Andre Franke and Stefan Schreiber and Johannes Krause and Johannes Müller and Tobias L. Lenz and Almut Nebel and Ben Krause-Kyora},
journal = {Communications Biology},
abstract = {The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of
important demographic and cultural transformations in western Europe. We performed
genome-wide analyses of 42 individuals who were interred in a WBC collective burial in
Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming
population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component
(34–58%). This component was most likely introduced during the cultural transformation
that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct
human leukocyte antigen gene pool, possibly reflecting an immune response that was geared
towards detecting viral infections.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}

@article{EVComplex_NatComm_2020,
title = {Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences},
author = {Anna Green and Hadeer Elhabashy and Kelly Brock and Rohan Maddamsetti and Oliver Kohlbacher and Debora S. Marks},
journal = {Nat. Commun.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}

@article{ProtPrivacyMCP2021,
title = {Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future},
author = {Nuno Bandeira and Eric W Deutsch and Oliver Kohlbacher and Lennart Martens and Juan Antonio Vizcaíno},
doi = {10.1016/j.mcpro.2021.100071},
journal = {Mol. Cell. Prot.},
abstract = {Today it is the norm that all relevant proteomics data that support the conclusions in scientific publications are made available in public proteomics data repositories. However, given the increase in the number of clinical proteomics studies, an important emerging topic is the management and dissemination of clinical, and thus potentially sensitive, human proteomics data. Both in the United States and in the European Union there are legal frameworks protecting the privacy of individuals. Implementing privacy standards for publicly released research data in genomics and transcriptomics has led to processes to control who may access the data, so called "controlled access" data. In parallel with the technological developments in the field it is clear that the privacy risks of sharing proteomics data need to be properly assessed and managed. As the proteome is directly derived from genome data, proteomics data can potentially reveal similarly sensitive data as nucleotide sequencing data. In this manuscript, we summarize the conclusions about this topic that have emerged from two meetings held in 2019 and some follow-up discussions, with a primary focus on data management practices. In our view, the proteomics community must be proactive in addressing these issues. Yet a careful balance must be kept. On the one hand, neglecting to address the potential of identifiability in human proteomics data could lead to reputational damage of the field, while on the other hand, erecting barriers to open access to clinical proteomics data will inevitably reduce re-use of proteomics data and could substantially delay critical discoveries in biomedical research. In order to balance these apparently conflicting requirements for data privacy and efficient use and re-use of research efforts through the sharing of clinical proteomics data, development efforts will be needed at different levels including bioinformatics infrastructure, policy making and mechanisms of oversight.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}