Steve Hoffmann

According to our database, Steve Hoffmann authored at least 32 papers between 2002 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells.

Aimer Gutierrez-Diaz, Steve Hoffmann, Juan Carlos Gallego-Gómez, Clara Bermudez-Santana

Frontiers Bioinform., 2024

2023

Leveraging quantum computing for dynamic analyses of logical networks in systems biology.

Felix M. Weidner, Julian D. Schwab, Sabine Wölk, Felix Rupprecht, Nensi Ikonomi, Silke D. Werle, Steve Hoffmann, Michael Kühl, Hans A. Kestler

Patterns, March, 2023

2022

Locus-specific expression analysis of transposable elements.

Robert Schwarz, Philipp Koch, Jeanne Wilbrandt, Steve Hoffmann

Briefings Bioinform., 2022

2021

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

Gerhard Mayer, Wolfgang Müller, Karin Schork, Julian Uszkoreit, Andreas Weidemann, Ulrike Wittig, Maja Rey, Christian Quast, Janine Felden, Frank Oliver Glöckner, Matthias Lange, Daniel Arend, Sebastian Beier, Astrid Junker, Uwe Scholz, Danuta Schüler, Hans A. Kestler, Daniel Wibberg, Alfred Pühler, Sven Twardziok, Jürgen Eils, Roland Eils, Steve Hoffmann, Martin Eisenacher, Michael Turewicz

Briefings Bioinform., 2021

2020

Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile.

Manuela M. do Almo, Isabel G. Sousa, Waldeyr Mendes Cordeiro da Silva, Thomas Gatter, Peter F. Stadler, Steve Hoffmann, Andrea Queiroz Maranhão, Marcelo M. Brigido

Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

2018

DIEGO: detection of differential alternative splicing using Aitchison's geometry.

Gero Doose, Stephan H. Bernhart, Rabea Wagener, Steve Hoffmann

Bioinform., 2018

2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen

Nucleic Acids Res., 2017

BAT: Bisulfite Analysis Toolkit.

Helene Kretzmer, Christian Otto, Steve Hoffmann

F1000Research, 2017

Generalized enhanced suffix array construction in external memory.

Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann, Cristina Dutra de Aguiar Ciferri

Algorithms Mol. Biol., 2017

2016

Read mapping.

Steve Hoffmann, Peter F. Stadler

it Inf. Technol., 2016

2015

A simple data-adaptive probabilistic variant calling model.

Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer

Algorithms Mol. Biol., 2015

2014

Genome Informatics for High-Throughput Sequencing Data Analysis: Methods and Applications

Steve Hoffmann

PhD thesis, 2014

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

Christian Otto, Peter F. Stadler, Steve Hoffmann

Bioinform., 2014

Authoring vs. Configuring Affective Agents for Interactive Storytelling.

Stefan Rank, Steve Hoffmann, Hans-Georg Struck, Ulrike Spierling, Simon Mayr, Paolo Petta

Appl. Artif. Intell., 2014

Genominformatische Verfahren zur Analyse von Daten der Hochdurchsatzsequenzierung.

Steve Hoffmann

Proceedings of the Ausgezeichnete Informatikdissertationen 2014, 2014

2012

Fast and sensitive mapping of bisulfite-treated sequencing data.

Christian Otto, Peter F. Stadler, Steve Hoffmann

Bioinform., 2012

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin

Bioinform., 2012

Creativity in Configuring Affective Agents for Interactive Storytelling.

Stefan Rank, Steve Hoffmann, Hans-Georg Struck, Ulrike Spierling, Paolo Petta

Proceedings of the Third International Conference on Computational Creativity, 2012

2011

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann

Nucleic Acids Res., 2011

Fast local fragment chaining using sum-of-pair gap costs.

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler

Algorithms Mol. Biol., 2011

MicroRNA or Not MicroRNA?

David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter F. Stadler

Proceedings of the Advances in Bioinformatics and Computational Biology, 2011

How Authors Benefit from Linear Logic in the Authoring Process of Interactive Storyworlds.

Kim Dung Dang, Steve Hoffmann, Ronan Champagnat, Ulrike Spierling

Proceedings of the Interactive Storytelling, 2011

"Office Brawl": a conversational storytelling game and its creation process.

Florian Glock, Anne Junker, Marina Kraus, Christian Lehrian, Alexander Schäfer, Steve Hoffmann, Ulrike Spierling

Proceedings of the 8th International Conference on Advances in Computer Entertainment Technology, 2011

2010

The primary transcriptome of the major human pathogen <i>Helicobacter pylori</i>.

Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jérémy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler, Jörg Vogel

Nat., 2010

Identification and Classification of Small RNAs in Transcriptome Sequence Data.

David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Tutorial: Introduction to Interactive Story Creation.

Ulrike Spierling, Nicolas Szilas, Steve Hoffmann, Urs Richle

Proceedings of the Interactive Storytelling, 2010

Workshop: Education in Interactive Digital Storytelling.

Ulrike Spierling, Nicolas Szilas, Steve Hoffmann, Urs Richle

Proceedings of the Interactive Storytelling, 2010

Exploring Narrative Interpretation and Adaptation for Interactive Story Creation.

Ulrike Spierling, Steve Hoffmann

Proceedings of the Interactive Storytelling, 2010

2009

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures.

Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller

PLoS Comput. Biol., 2009

Sequence assembly.

K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, Niels Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin

Comput. Biol. Chem., 2009

Evidence for human microRNA-offset RNAs in small RNA sequencing data.

David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovich, Peter F. Stadler

Bioinform., 2009

2002

ORFer - retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

Konrad Büssow, Steve Hoffmann, Volker Sievert

BMC Bioinform., 2002