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

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

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

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

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

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

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

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

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

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

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

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

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

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

Algorithms in Bioinformatics - 14th International Workshop, WABI 2014, Wroclaw, Poland, September 8-10, 2014. Proceedings (Springer, 2014)

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

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

German Conference on Bioinformatics 2013, GCB 2013, September 10-13, 2013, Göttingen, Germany (Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

An exact solution for the Segment-to-Segment multiple sequence alignment problem. - Reinert, Knut; Lenhof, Hans-Peter; Morgenstern, Burkhard (1998)

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

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

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