Lower Bounds for Row Minima Searching (Extended Abstract). - Phillip G. Bradford; Knut Reinert (ICALP, 1996)

A branch-and-cut algorithm for multiple sequence alignment. - Knut Reinert; Hans-Peter Lenhof; Petra Mutzel; Kurt Mehlhorn; John D. Kececioglu (RECOMB, 1997)

A Polyhedral Approach to RNA Sequence Structure Alignment. - Hans-Peter Lenhof; Knut Reinert; Martin Vingron (J. Comput. Biol., 1998)

Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. - Knut Reinert; Jens Stoye; Torsten Will (German Conference on Bioinformatics, 1999)

An exact solution for the segment-to-segment multiple sequence alignment problem. - Hans-Peter Lenhof; Burkhard Morgenstern; Knut Reinert (Bioinform., 1999)

A polyhedral approach to sequence alignment problems. - Knut Reinert (1999)

An iterative method for faster sum-of-pairs multiple sequence alignment. - Knut Reinert; Jens Stoye; Torsten Will (Bioinform., 2000)

A polyhedral approach to sequence alignment problems. - John D. Kececioglu; Hans-Peter Lenhof; Kurt Mehlhorn; Petra Mutzel; Knut Reinert; Martin Vingron (Discret. Appl. Math., 2000)

The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. - Martin Lermen; Knut Reinert (J. Comput. Biol., 2000)

Design of a compartmentalized shotgun assembler for the human genome. - Daniel H. Huson; Knut Reinert; Saul A. Kravitz; Karin A. Remington; Arthur L. Delcher; Ian M. Dew; Michael Flanigan; Aaron L. Halpern; Zhongwu Lai; Clark M. Mobarry; Granger G. Sutton; Eugene W. Myers (ISMB (Supplement of Bioinformatics), 2001)

Visualization challenges for a new cyberpharmaceutical computing paradigm. - Russell J. Turner; Kabir Chaturvedi; Nathan Edwards; Daniel P. Fasulo; Aaron L. Halpern; Daniel H. Huson; Oliver Kohlbacher; Jason R. Miller; Knut Reinert; Karin A. Remington; Russell Schwartz; Brian Walenz; et al. (IEEE Symposium on Parallel and Large-Data Visualization and Graphics, 2001)

The greedy path-merging algorithm for sequence assembly. - Daniel H. Huson; Knut Reinert; Eugene W. Myers (RECOMB, 2001)

Comparing Assemblies Using Fragments and Mate-Pairs. - Daniel H. Huson; Aaron L. Halpern; Zhongwu Lai; Eugene W. Myers; Knut Reinert; Granger G. Sutton (WABI, 2001)

Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. - Ernst Althaus; Alberto Caprara; Hans-Peter Lenhof; Knut Reinert (ECCB, 2002)

Segment Match Refinement and Applications. - Aaron L. Halpern; Daniel H. Huson; Knut Reinert (WABI, 2002)

The greedy path-merging algorithm for contig scaffolding. - Daniel H. Huson; Knut Reinert; Eugene W. Myers (J. ACM, 2002)

Optimal robust non-unique probe selection using Integer Linear Programming. - Gunnar W. Klau; Sven Rahmann; Alexander Schliep; Martin Vingron; Knut Reinert (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). - Oliver Kohlbacher; Knut Reinert (it Inf. Technol., 2004)

Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization. - Markus Bauer 001; Gunnar W. Klau; Knut Reinert (CompLife, 2005)

Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. - Clemens Gröpl; Eva Lange; Knut Reinert; Oliver Kohlbacher; Marc Sturm; Christian G. Huber; Bettina M. Mayr; Christoph L. Klein (CompLife, 2005)

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. - Nathanaël Delmotte; Bettina M. Mayr; Andreas Leinenbach; Knut Reinert; Oliver Kohlbacher; Christoph L. Klein; Christian G. Huber (Computational Proteomics, 2005)

05471 Executive Summary - Computational Proteomics. - Christian G. Huber; Oliver Kohlbacher; Knut Reinert (Computational Proteomics, 2005)

05471 Abstract Collection - Computational Proteomics. - Christian G. Huber; Oliver Kohlbacher; Knut Reinert (Computational Proteomics, 2005)

Multiple Structural RNA Alignment with Lagrangian Relaxation. - Markus Bauer 001; Gunnar W. Klau; Knut Reinert (WABI, 2005)

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. - Witold E. Wolski; Maciej Lalowski; Peter Jungblut; Knut Reinert (BMC Bioinform., 2005)

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. - Witold E. Wolski; Maciej Lalowski; Peter Martus; Ralf Herwig; Patrick Giavalisco; Johan Gobom; Albert Sickmann; Hans Lehrach; Knut Reinert (BMC Bioinform., 2005)

High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. - Eva Lange; Clemens Gröpl; Knut Reinert; Oliver Kohlbacher; Andreas Hildebrandt 001 (Pacific Symposium on Biocomputing, 2006)

A branch-and-cut algorithm for multiple sequence alignment. - Ernst Althaus; Alberto Caprara; Hans-Peter Lenhof; Knut Reinert (Math. Program., 2006)

A General Paradigm for Fast, Adaptive Clustering of Biological Sequences. - Knut Reinert; Markus Bauer 001; Andreas Döring 001; Gunnar W. Klau; Aaron L. Halpern (German Conference on Bioinformatics, 2007)

A geometric approach for the alignment of liquid chromatography - mass spectrometry data. - Eva Lange; Clemens Gröpl; Ole Schulz-Trieglaff; Andreas Leinenbach; Christian G. Huber; Knut Reinert (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. - Ole Schulz-Trieglaff; Rene Hussong; Clemens Gröpl; Andreas Hildebrandt 001; Knut Reinert (RECOMB, 2007)

TOPP - the OpenMS proteomics pipeline. - Oliver Kohlbacher; Knut Reinert; Clemens Gröpl; Eva Lange; Nico Pfeifer; Ole Schulz-Trieglaff; Marc Sturm (Bioinform., 2007)

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. - Markus Bauer 001; Gunnar W. Klau; Knut Reinert (BMC Bioinform., 2007)

Integer linear programming approaches for non-unique probe selection. - Gunnar W. Klau; Sven Rahmann; Alexander Schliep; Martin Vingron; Knut Reinert (Discret. Appl. Math., 2007)

08101 Abstracts Collection - Computational Proteomics. - Knut Reinert; Christian G. Huber; Kathrin Marcus; Michal Linial; Oliver Kohlbacher (Computational Proteomics, 2008)

Segment-based multiple sequence alignment. - Tobias Rausch; Anne-Katrin Emde; David Weese; Andreas Döring 001; Cédric Notredame; Knut Reinert (ECCB, 2008)

Fast and Adaptive Variable Order Markov Chain Construction. - Marcel H. Schulz; David Weese; Tobias Rausch; Andreas Döring 001; Knut Reinert; Martin Vingron (WABI, 2008)

An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. - Markus Bauer 001; Gunnar W. Klau; Knut Reinert (Algorithmic Oper. Res., 2008)

SeqAn An efficient, generic C++ library for sequence analysis. - Andreas Döring 001; David Weese; Tobias Rausch; Knut Reinert (BMC Bioinform., 2008)

Robust consensus computation. - Tobias Rausch; Anne-Katrin Emde; Knut Reinert (BMC Bioinform., 2008)

LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. - Ole Schulz-Trieglaff; Nico Pfeifer; Clemens Gröpl; Oliver Kohlbacher; Knut Reinert (BMC Bioinform., 2008)

OpenMS - An open-source software framework for mass spectrometry. - Marc Sturm; Andreas Bertsch; Clemens Gröpl; Andreas Hildebrandt 001; Rene Hussong; Eva Lange; Nico Pfeifer; Ole Schulz-Trieglaff; Alexandra Zerck; Knut Reinert; Oliver Kohlbacher (BMC Bioinform., 2008)

Computational Quantification of Peptides from LC-MS Data. - Ole Schulz-Trieglaff; Rene Hussong; Clemens Gröpl; Andreas Leinenbach; Andreas Hildebrandt 001; Christian G. Huber; Knut Reinert (J. Comput. Biol., 2008)

Biological Sequence Analysis Using the SeqAn C++ Library. - Andreas Gogol-Döring; Knut Reinert (CRC Press, 2009)

Integer Linear Programming in Computational Biology. - Ernst Althaus; Gunnar W. Klau; Oliver Kohlbacher; Hans-Peter Lenhof; Knut Reinert (Efficient Algorithms, 2009)

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. - Raphael André Bauer; Kristian Rother; Peter Moor; Knut Reinert; Thomas Steinke 001; Janusz M. Bujnicki; Robert Preissner (Algorithms, 2009)

Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. - Ole Schulz-Trieglaff; Egidijus Machtejevas; Knut Reinert; Hartmut Schlüter; Joachim Thiemann; Klaus Unger (BioData Min., 2009)

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. - Tobias Rausch; Sergey Koren; Gennady Denisov; David Weese; Anne-Katrin Emde; Andreas Döring 001; Knut Reinert (Bioinform., 2009)

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. - Knut Reinert; Oliver Kohlbacher (Proteome Bioinformatics, 2010)

MicroRazerS: rapid alignment of small RNA reads. - Anne-Katrin Emde; Marcel Grunert; David Weese; Knut Reinert; Silke R. Sperling (Bioinform., 2010)

Oops I Did it Again... Sustainability in Sequence Analysis via Software Libraries. - Knut Reinert (ERCIM News, 2010)

Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset. - Chris Bauer; Frank Kleinjung; Celia J. Smith; Mark W. Towers; Ali Tiss; Alexandra Chadt; Tanja Dreja; Dieter Beule; Hadi Al-Hasani; Knut Reinert; Johannes Schuchhardt; Rainer Cramer (BMC Bioinform., 2011)

A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. - Manuel Holtgrewe; Anne-Katrin Emde; David Weese; Knut Reinert (BMC Bioinform., 2011)

STELLAR: fast and exact local alignments. - Birte Kehr; David Weese; Knut Reinert (BMC Bioinform., 2011)

Hidden Breakpoints in Genome Alignments. - Birte Kehr; Knut Reinert; Aaron E. Darling (WABI, 2012)

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. - Anne-Katrin Emde; Marcel H. Schulz; David Weese; Ruping Sun; Martin Vingron; Vera M. Kalscheuer; Stefan A. Haas; Knut Reinert (Bioinform., 2012)

RazerS 3: Faster, fully sensitive read mapping. - David Weese; Manuel Holtgrewe; Knut Reinert (Bioinform., 2012)

PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. - Chris Bauer; Frank Kleinjung; Dorothea Rutishauser; Christian Panse; Alexandra Chadt; Tanja Dreja; Hadi Al-Hasani; Knut Reinert; Ralph Schlapbach; Johannes Schuchhardt (BMC Bioinform., 2012)

Fast and sensitive read mapping with approximate seeds and multiple backtracking - Enrico Siragusa; David Weese; Knut Reinert (CoRR, 2012)

Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. - Sandro Andreotti; Gunnar W. Klau; Knut Reinert (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Scalable string similarity search/join with approximate seeds and multiple backtracking. - Enrico Siragusa; David Weese; Knut Reinert (EDBT/ICDT Workshops, 2013)

From the Desktop to the Grid: conversion of KNIME Workflows to gUSE. - Luis de la Garza; Jens Krüger 002; Charlotta Schärfe; Marc Röttig; Stephan Aiche; Knut Reinert; Oliver Kohlbacher (IWSG, 2013)

Optimal precursor ion selection for LC-MALDI MS/MS. - Alexandra Zerck; Eckhard Nordhoff; Hans Lehrach; Knut Reinert (BMC Bioinform., 2013)

The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees. - Sandro Andreotti; Knut Reinert; Stefan Canzar (J. Comput. Biol., 2013)

Lambda: the local aligner for massive biological data. - Hannes Hauswedell; Jochen Singer; Knut Reinert (Bioinform., 2014)

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. - Jialu Hu; Birte Kehr; Knut Reinert (Bioinform., 2014)

Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop. - René Rahn; David Weese; Knut Reinert (Bioinform., 2014)

Fiona: a parallel and automatic strategy for read error correction. - Marcel H. Schulz; David Weese; Manuel Holtgrewe; Viktoria Dimitrova; Sijia Niu; Knut Reinert; Hugues Richard (Bioinform., 2014)

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. - Kathrin Trappe; Anne-Katrin Emde; Hans-Christian Ehrlich; Knut Reinert (Bioinform., 2014)

Genome alignment with graph data structures: a comparison. - Birte Kehr; Kathrin Trappe; Manuel Holtgrewe; Knut Reinert (BMC Bioinform., 2014)

CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. - Stefan Canzar; Sandro Andreotti; David Weese; Knut Reinert; Gunnar W. Klau (RECOMB, 2015)

Methods for the detection and assembly of novel sequence in high-throughput sequencing data. - Manuel Holtgrewe; Léon Kuchenbecker; Knut Reinert (Bioinform., 2015)

LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. - Jialu Hu; Knut Reinert (Bioinform., 2015)

IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. - Léon Kuchenbecker; Mikalai Nienen; Jochen Hecht; Avidan U. Neumann; Nina Babel; Knut Reinert; Peter N. Robinson (Bioinform., 2015)

From the desktop to the grid: scalable bioinformatics via workflow conversion. - Luis de la Garza; Johannes Veit; András Szolek; Marc Röttig; Stephan Aiche; Sandra Gesing; Knut Reinert; Oliver Kohlbacher (BMC Bioinform., 2016)

Constant-time and space-efficient unidirectional and bidirectional FM-indices using EPR-dictionaries. - Christopher Pockrandt; Marcel Ehrhardt; Knut Reinert (CoRR, 2016)

Next Generation Sequencing (Dagstuhl Seminar 16351). - Gene Myers; Mihai Pop; Knut Reinert; Tandy J. Warnow (Dagstuhl Reports, 2016)

EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. - Christopher Pockrandt; Marcel Ehrhardt; Knut Reinert (RECOMB, 2017)

Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence. - Jongkyu Kim; Knut Reinert (WABI, 2017)

Flexbar 3.0 - SIMD and multicore parallelization. - Johannes T. Roehr; Christoph Dieterich; Knut Reinert (Bioinform., 2017)

FAMOUS: Fast Approximate string Matching using OptimUm search Schemes. - Kiavash Kianfar; Christopher Pockrandt; Bahman Torkamandi; Haochen Luo; Knut Reinert (CoRR, 2017)

DREAM-Yara: an exact read mapper for very large databases with short update time. - Temesgen Hailemariam Dadi; Enrico Siragusa; Vitor Piro; Andreas Andrusch; Enrico Seiler; Bernhard Y. Renard; Knut Reinert (Bioinform., 2018)

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. - René Rahn; Stefan Budach; Pascal Costanza; Marcel Ehrhardt; Jonny Hancox; Knut Reinert (Bioinform., 2018)

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. - Vitor Piro; Temesgen Hailemariam Dadi; Enrico Seiler; Knut Reinert; Bernhard Y. Renard (Bioinform., 2020)

GenMap: ultra-fast computation of genome mappability. - Christopher Pockrandt; Mai Alzamel; Costas S. Iliopoulos; Knut Reinert (Bioinform., 2020)

Portability of Scientific Workflows in NGS Data Analysis: A Case Study. - Christopher Schiefer; Marc Bux; Jörgen Brandt; Clemens Messerschmidt; Knut Reinert; Dieter Beule; Ulf Leser (CoRR, 2020)

Ranbow: A fast and accurate method for polyploid haplotype reconstruction. - M-Hossein Moeinzadeh; Jun Yang 043; Evgeny Muzychenko; Giuseppe Gallone; David Heller; Knut Reinert; Stefan A. Haas; Martin Vingron (PLoS Comput. Biol., 2020)

PriSeT: efficient de novo primer discovery. - Marie Hoffmann; Michael T. Monaghan; Knut Reinert (BCB, 2021)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. - Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia N. Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; et al. (Briefings Bioinform., 2021)

RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. - Sara Hetzel; Pay Giesselmann; Knut Reinert; Alexander Meissner; Helene Kretzmer (Bioinform., 2021)

SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria. - Silver A. Wolf; Lennard Epping; Sandro Andreotti; Knut Reinert; Torsten Semmler (Bioinform., 2021)

The Collaborative Research Center FONDA. - Ulf Leser; Marcus Hilbrich; Claudia Draxl; Peter Eisert; Lars Grunske; Patrick Hostert; Dagmar Kainmüller; Odej Kao; Birte Kehr; Timo Kehrer; Christoph Koch 001; Volker Markl; et al. (Datenbank-Spektrum, 2021)

Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. - Marius Knaust; Enrico Seiler; Knut Reinert; Thomas Steinke 001 (FPGA, 2022)

Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. - Mitra Darvish; Enrico Seiler; Svenja Mehringer; René Rahn; Knut Reinert (Bioinform., 2022)

LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. - Jörg Winkler; Gianvito Urgese; Elisa Ficarra; Knut Reinert (BMC Bioinform., 2022)

A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. - Yuwei Wang; Bin Lian; Haohui Zhang; Yuanke Zhong; Jie He; Fashuai Wu; Knut Reinert; Xuequn Shang 001; Hui Yang; Jialu Hu (Bioinform., 2023)

Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models. - Chenxu Pan; René Rahn; David Heller; Knut Reinert (Briefings Bioinform., 2023)

A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. - Somayeh Mohammadi; Latif Pourkarimi; Felix Droop; Ninon De Mecquenem; Ulf Leser; Knut Reinert (J. Supercomput., 2023)

CuttleFlow: Infrastructure-Specific Workflow Adaption for Improved Reusability. - Ninon De Mecquenem; Simon Bosse; Vasilis Bountris; Somayeh Mohammadi; Knut Reinert; Ulf Leser (e-Science, 2024)

Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures. - Somayeh Mohammadi; Latif Pourkarimi; Manuel Zschäbitz; Tristan Aretz; Ninon De Mecquenem; Ulf Leser; Knut Reinert (EDBT/ICDT Workshops, 2024)

Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. - Madalina Giurgiu; Nadine Wittstruck; Elias Rodriguez-Fos; Rocío Chamorro González; Lotte Brückner; Annabell Krienelke-Szymansky; Konstantin Helmsauer; Anne Hartebrodt; Philipp Euskirchen; Richard P. Koche; Kerstin Haase; Knut Reinert; et al. (RECOMB, 2024)

Search Schemes for Approximate Pattern Matching: An Overview. - Lore Depuydt; Jan Fostier; Simon Gottlieb; Gregory Kucherov; Knut Reinert; Luca Renders (The Expanding World of Compressed Data, 2025)