Sequenzalignment auf der Basis von Segmentvergleichen. - Burkhard Morgenstern (1996)

Dialign 1.0: Multiple alignment by Segment rather than by Position comparison. - Burkhard Morgenstern; Thomas Werner (German Conference on Bioinformatics, 1997)

DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment. - Burkhard Morgenstern (German Conference on Bioinformatics, 1998)

Segment-Based Scores for Pairwise and Multiple Sequence Alignments. - Burkhard Morgenstern; William R. Atchley; Klaus Hahn; Andreas W. M. Dress (ISMB, 1998)

DIALIGN: finding local similarities by multiple sequence alignment. - Burkhard Morgenstern; Kornelie Frech; Andreas W. M. Dress; Thomas Werner (Bioinform., 1998)

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

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. - Burkhard Morgenstern (Bioinform., 1999)

Speeding Up the DIALIGN Multiple Alignment Program by Using the 'Greedy Alignment of BIOlogical Sequences LIBrary' (GABIOS-LIB). - Saïd Abdeddaïm; Burkhard Morgenstern (JOBIM, 2000)

A space-efficient algorithm for aligning large genomic sequences. - Burkhard Morgenstern (Bioinform., 2000)

Gene prediction by comparative sequence analysis. - Oliver Rinner; Burkhard Morgenstern (German Conference on Bioinformatics, 2001)

The HIB database of annotated UniGene clusters. - Birgitta Geier; Gabi Kastenmüller; Matthias Fellenberg; Hans-Werner Mewes; Burkhard Morgenstern (Bioinform., 2001)

Fast and Sensitive Alignment of Large Genomic Sequences. - Michael Brudno; Burkhard Morgenstern (CSB, 2002)

A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences. - Burkhard Morgenstern (Appl. Math. Lett., 2002)

Exon discovery by genomic sequence alignment. - Burkhard Morgenstern; Oliver Rinner; Saïd Abdeddaïm; Dirk Haase; Klaus F. X. Mayer; Andreas W. M. Dress; Hans-Werner Mewes (Bioinform., 2002)

AGenDA: Gene prediction by comparative sequence analysis. - Oliver Rinner; Burkhard Morgenstern (Silico Biol., 2002)

MIPS: a database for genomes and protein sequences. - Hans-Werner Mewes; Dmitrij Frishman; Ulrich Güldener; Gertrud Mannhaupt; Klaus F. X. Mayer; Martin Mokrejs; Burkhard Morgenstern; Martin Münsterkötter; Stephen Rudd; B. Weil (Nucleic Acids Res., 2002)

Divide-and-conquer multiple alignment with segment-based constraints. - Michael Sammeth; Burkhard Morgenstern; Jens Stoye (ECCB, 2003)

AltAVisT: Comparing alternative multiple sequence alignments. - Burkhard Morgenstern; Sachin Goel; Alexander Sczyrba; Andreas W. M. Dress (Bioinform., 2003)

AGenDA: homology-based gene prediction. - Leila Taher; Oliver Rinner; Saurabh Garg; Alexander Sczyrba; Michael Brudno; Serafim Batzoglou; Burkhard Morgenstern (Bioinform., 2003)

Fast and sensitive multiple alignment of large genomic sequences. - Michael Brudno; Michael Chapman; Berthold Göttgens; Serafim Batzoglou; Burkhard Morgenstern (BMC Bioinform., 2003)

Multiple sequence alignment with user-defined constraints. - Burkhard Morgenstern; Sonja J. Prohaska; Nadine Werner; Jan Weyer-Menkhoff; Isabelle Schneider; Amarendran Ramaswami Subramanian; Peter F. Stadler (German Conference on Bioinformatics, 2004)

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. - Peter Meinicke; Maike Tech; Burkhard Morgenstern; Rainer Merkl (BMC Bioinform., 2004)

DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. - Martin Schmollinger; Kay Nieselt; Michael Kaufmann 001; Burkhard Morgenstern (BMC Bioinform., 2004)

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. - Michael Brudno; Rasmus Steinkamp; Burkhard Morgenstern (Nucleic Acids Res., 2004)

DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. - Burkhard Morgenstern (Nucleic Acids Res., 2004)

AUGUSTUS: a web server for gene finding in eukaryotes. - Mario Stanke; Rasmus Steinkamp; Stephan Waack; Burkhard Morgenstern (Nucleic Acids Res., 2004)

AGenDA: gene prediction by cross-species sequence comparison. - Leila Taher; Oliver Rinner; Saurabh Garg; Alexander Sczyrba; Burkhard Morgenstern (Nucleic Acids Res., 2004)

Multiple sequence alignment with user-defined constraints at GOBICS. - Burkhard Morgenstern; Nadine Werner; Sonja J. Prohaska; Rasmus Steinkamp; Isabelle Schneider; Amarendran Ramaswami Subramanian; Peter F. Stadler; Jan Weyer-Menkhoff (Bioinform., 2005)

TICO: a tool for improving predictions of prokaryotic translation initiation sites. - Maike Tech; Nico Pfeifer; Burkhard Morgenstern; Peter Meinicke (Bioinform., 2005)

DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. - Amarendran Ramaswami Subramanian; Jan Weyer-Menkhoff; Michael Kaufmann 001; Burkhard Morgenstern (BMC Bioinform., 2005)

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. - Dirk Pöhler; Nadine Werner; Rasmus Steinkamp; Burkhard Morgenstern (Nucleic Acids Res., 2005)

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. - Mario Stanke; Burkhard Morgenstern (Nucleic Acids Res., 2005)

Multiple sequence alignment with user-defined anchor points. - Burkhard Morgenstern; Sonja J. Prohaska; Dirk Pöhler; Peter F. Stadler (Algorithms Mol. Biol., 2006)

New journal: Algorithms for Molecular Biology. - Burkhard Morgenstern; Peter F. Stadler (Algorithms Mol. Biol., 2006)

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. - Anne-Kathrin Schultz; Ming Zhang; Thomas Leitner; Carla Kuiken; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (BMC Bioinform., 2006)

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. - Mario Stanke; Oliver Schöffmann; Burkhard Morgenstern; Stephan Waack (BMC Bioinform., 2006)

AUGUSTUS: ab initio prediction of alternative transcripts. - Mario Stanke; Oliver Keller; Irfan Gunduz; Alec Hayes; Stephan Waack; Burkhard Morgenstern (Nucleic Acids Res., 2006)

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites. - Maike Tech; Burkhard Morgenstern; Peter Meinicke (Nucleic Acids Res., 2006)

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. - Ming Zhang; Anne-Kathrin Schultz; Charles Calef; Carla Kuiken; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Nucleic Acids Res., 2006)

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps. - Peter Meinicke; Thomas Lingner; Alexander Kaever; Kirstin Feussner; Cornelia Göbel; Ivo Feussner; Petr Karlovsky; Burkhard Morgenstern (Algorithms Mol. Biol., 2008)

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. - Amarendran Ramaswami Subramanian; Michael Kaufmann 001; Burkhard Morgenstern (Algorithms Mol. Biol., 2008)

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. - Holger Wagner; Burkhard Morgenstern; Andreas W. M. Dress (Algorithms Mol. Biol., 2008)

Gene prediction in metagenomic fragments: A large scale machine learning approach. - Katharina Jasmin Hoff; Maike Tech; Thomas Lingner; Rolf Daniel; Burkhard Morgenstern; Peter Meinicke (BMC Bioinform., 2008)

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. - Fabian Schreiber; Kerstin Pick; Dirk Erpenbeck; Gert Wörheide; Burkhard Morgenstern (BMC Bioinform., 2009)

AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis. - Dietmar Sommerfeld; Thomas Lingner; Mario Stanke; Burkhard Morgenstern; Harald Richter 001 (Future Gener. Comput. Syst., 2009)

OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences. - Fabian Schreiber; Gert Wörheide; Burkhard Morgenstern (Nucleic Acids Res., 2009)

jpHMM: Improving the reliability of recombination prediction in HIV-1. - Anne-Kathrin Schultz; Ming Zhang; Ingo Bulla; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Nucleic Acids Res., 2009)

HIV classification using the coalescent theory. - Ingo Bulla; Anne-Kathrin Schultz; Fabian Schreiber; Ming Zhang; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Bioinform., 2010)

A min-cut algorithm for the consistency problem in multiple sequence alignment. - Eduardo Corel; Florian Pitschi; Burkhard Morgenstern (Bioinform., 2010)

DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS. - Amarendran Ramaswami Subramanian; Suvrat Hiran; Rasmus Steinkamp; Peter Meinicke; Eduardo Corel; Burkhard Morgenstern (Nucleic Acids Res., 2010)

MolabIS - An Integrated Information System for Storing and Managing Molecular Genetics Data. - Cong V. C. Truong; Linn F. Groeneveld; Burkhard Morgenstern; Eildert Groeneveld (BMC Bioinform., 2011)

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. - Thomas Unterthiner; Anne-Kathrin Schultz; Jan Bulla; Burkhard Morgenstern; Mario Stanke; Ingo Bulla (BMC Bioinform., 2011)

Using protein-domain information for multiple sequence alignment. - Layal Al Ait; Eduardo Corel; Burkhard Morgenstern (BIBE, 2012)

jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. - Anne-Kathrin Schultz; Ingo Bulla; Mariama Abdou-Chekaraou; Emmanuel Gordien; Burkhard Morgenstern; Fabien Zoulim; Paul Dény; Mario Stanke (Nucleic Acids Res., 2012)

Alignment-free sequence comparison with spaced k-mers. - Marcus Boden; Martin Schöneich; Sebastian Horwege; Sebastian Lindner 001; Chris Leimeister; Burkhard Morgenstern (GCB, 2013)

DIALIGN at GOBICS - multiple sequence alignment using various sources of external information. - Layal Al Ait; Zaher Yamak; Burkhard Morgenstern (Nucleic Acids Res., 2013)

Estimating Evolutionary Distances from Spaced-Word Matches. - Burkhard Morgenstern; Binyao Zhu; Sebastian Horwege; Chris-André Leimeister (WABI, 2014)

Fast alignment-free sequence comparison using spaced-word frequencies. - Chris-André Leimeister; Marcus Boden; Sebastian Horwege; Sebastian Lindner 001; Burkhard Morgenstern (Bioinform., 2014)

kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison. - Chris-André Leimeister; Burkhard Morgenstern (Bioinform., 2014)

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches. - Sebastian Horwege; Sebastian Lindner 001; Marcus Boden; Klas Hatje; Martin Kollmar; Chris-André Leimeister; Burkhard Morgenstern (Nucleic Acids Res., 2014)

Estimating evolutionary distances between genomic sequences from spaced-word matches. - Burkhard Morgenstern; Binyao Zhu; Sebastian Horwege; Chris Leimeister (Algorithms Mol. Biol., 2015)

RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison. - Lars Hahn; Chris-André Leimeister; Burkhard Morgenstern (CoRR, 2015)

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. - Lars Hahn; Chris-André Leimeister; Rachid Ounit; Stefano Lonardi; Burkhard Morgenstern (PLoS Comput. Biol., 2016)

Phylogeny reconstruction based on the length distribution of k-mismatch common substrings. - Burkhard Morgenstern; Svenja Schöbel; Chris-André Leimeister (Algorithms Mol. Biol., 2017)

Fast and accurate phylogeny reconstruction using filtered spaced-word matches. - Chris-André Leimeister; Salma Sohrabi-Jahromi; Burkhard Morgenstern (Bioinform., 2017)

Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees. - Thomas Dencker; Chris-André Leimeister; Michael Gerth; Christoph Bleidorn; Sagi Snir; Burkhard Morgenstern (RECOMB-CG, 2018)

Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. - Chris-André Leimeister; Thomas Dencker; Burkhard Morgenstern (Bioinform., 2019)

Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage. - Anna-Katharina Lau; Svenja Dörrer; Chris-André Leimeister; Christoph Bleidorn; Burkhard Morgenstern (BMC Bioinform., 2019)

S-conLSH: alignment-free gapped mapping of noisy long reads. - Angana Chakraborty; Burkhard Morgenstern; Sanghamitra Bandyopadhyay (BMC Bioinform., 2021)

Insertions and deletions as phylogenetic signal in an alignment-free context. - Niklas Birth; Thomas Dencker; Burkhard Morgenstern (PLoS Comput. Biol., 2022)