Draft:Knut Reinert

Prof. Dr. Knut Reinert (* 19th January 1968 in Saarlouis) is a German computer scientist and bioinformatician renowned for his contributions to computational biology and algorithm development. He is currently a full professor at the Institute of Computer Science at Freie Universität Berlin, where he leads the Algorithmic Bioinformatics research group.



Early Life and Education
Reinert completed his undergraduate studies in Computer Science at the university of the Saarland in 1994. He then pursued his doctoral studies at the MPI for computer science in Saarbrücken, earning his Ph.D. in Computer Science in 1999 under the supervision of Prof. Dr. Kurt Mehlhorn and Prof. Dr. Hans-Peter Lenhof. His doctoral thesis, titled "A Polyhedral Approach to Sequence Alignment Problems", focused on solving NP-hard sequence alignment problems for Proteins and RNA using methods from combinatorial optimization.

Academic Career
After completing his Ph.D., Reinert worked as a postdoctoral researcher at Celera Genomics (Rockville, USA) from 1999 to 2002. During this time, he worked in the Informatics Research group under the guidance of Prof. Gene Myers on the first whole genome shotgun assemblies of Drosophila melanogaster and Human. Later he also contributed on algorithms for the analysis of mass spectrometry analysis.

In 2002, Reinert joined Freie Universität Berlin as a professor in the institute of computer science. He established the Algorithmic Bioinformatics research group, which has since become a leading center for bioinformatics research in Germany.

Research
Reinert's research lies at the intersection of computer science and biology, focusing on developing efficient algorithms and data structures for analyzing large-scale biological data. His work spans several key areas:

Sequence Analysis Algorithms

 * Development of advanced algorithms for sequence alignment, including multiple sequence alignment and genome-wide alignments
 * Creation of novel indexing structures for large sequence databases

Mass Spectrometry Data Analysis

 * Design of algorithms for protein and peptide identification from mass spectrometry data
 * Development of tools for quantitative proteomics

Next-Generation Sequencing (NGS) Data Processing

 * Creation of efficient algorithms for read mapping
 * Development of methods for variant calling and structural variant detection

Software Development

 * He started the development of SeqAn, an open-source C++ library for biological sequence analysis
 * He co-started the OpenMS project together with Prof. Dr. Oliver Kohlbacher
 * He is a contributor to various bioinformatics software tools and pipelines

SeqAn Library
One of Reinert's most significant contributions is the development of SeqAn, a comprehensive C++ library for biological sequence analysis. SeqAn provides efficient algorithms and data structures that enable researchers to process and analyze large-scale genomic data. The library is widely used in the bioinformatics community and has been incorporated into numerous software tools.

OpenMS Framework
Reinert has been instrumental in the development of OpenMS, an open-source software platform for LC-MS data management and analyses. This framework has become a crucial tool in proteomics research.

Teaching and Mentorship
At Freie Universität Berlin, Reinert teaches a variety of courses in bioinformatics and computational biology, including:
 * Algorithms for Sequence Analysis
 * Advanced Topics in Computational Proteomics

He has supervised over 30 Ph.D. students and several postdoctoral researchers, many of whom have gone on to successful careers in academia and industry.

Publications and Academic Impact
Reinert has authored and co-authored more than 130 peer-reviewed articles in leading journals such as Bioinformatics, Genome Research, and Nature Methods. He also served on the program committees of various international conferences in computational biology. His work has been cited over 40000 times (see Google scholar for up-to-date data), reflecting the significant impact of his research on the field of bioinformatics.

Awards and Honors
Throughout his career, Reinert has received several awards and honors including:
 * He was accepted as a member of the Studienstiftung des Deutschen Volkes
 * He was appointed a Max-Planck fellow in 2014