LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons von Ellinghaus, David, Kurtz, Stefan, Willhoeft, Ute

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GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations von Gremme, Gordon, Steinbiss, Sascha, Kurtz, Stefan

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Fine-grained annotation and classification of de novo predicted LTR retrotransposons von Steinbiss, Sascha, Willhoeft, Ute, Gremme, Gordon, Kurtz, Stefan

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GfaViz: flexible and interactive visualization of GFA sequence graphs von Gonnella, Giorgio, Niehus, Niklas, Kurtz, Stefan

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Readjoiner: a fast and memory efficient string graph-based sequence assembler von Gonnella, Giorgio, Kurtz, Stefan

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A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes von Kurtz, Stefan, Narechania, Apurva, Stein, Joshua C, Ware, Doreen

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DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention von Hausmann, Fabian, Kurtz, Stefan

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Fast mapping of short sequences with mismatches, insertions and deletions using index structures von Hoffmann, Steve, Otto, Christian, Kurtz, Stefan, Sharma, Cynthia M, Khaitovich, Philipp, Vogel, Jörg, Stadler, Peter F, Hackermüller, Jörg

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TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease von Neelagandan, Nagammal, Gonnella, Giorgio, Dang, Stefan, Janiesch, Philipp C, Miller, Katharine K, Küchler, Katrin, Marques, Rita F, Indenbirken, Daniela, Alawi, Malik, Grundhoff, Adam, Kurtz, Stefan, Duncan, Kent E

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Fast index based algorithms and software for matching position specific scoring matrices von Beckstette, Michael, Homann, Robert, Giegerich, Robert, Kurtz, Stefan

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Efficient computation of absent words in genomic sequences von Herold, Julia, Kurtz, Stefan, Giegerich, Robert

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Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8 von Farnbacher, Max, Jahns, Thomas, Willrodt, Dirk, Daniel, Rolf, Haas, Rainer, Goesmann, Alexander, Kurtz, Stefan, Rieder, Gabriele

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Engineering a software tool for gene structure prediction in higher organisms von Gremme, Gordon, Brendel, Volker, Sparks, Michael E., Kurtz, Stefan

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RGFA: powerful and convenient handling of assembly graphs von Gonnella, Giorgio, Kurtz, Stefan

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In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field von Perner, Mirjam, Gonnella, Giorgio, Hourdez, Stephane, Böhnke, Stefanie, Kurtz, Stefan, Girguis, Peter

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Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic... von Böhnke, Stefanie, Sass, Katharina, Gonnella, Giorgio, Diehl, Alexander, Kleint, Charlotte, Bach, Wolfgang, Zitoun, Rebecca, Koschinsky, Andrea, Indenbirken, Daniela, Sander, Sylvia G., Kurtz, Stefan, Perner, Mirjam

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Structator: fast index-based search for RNA sequence-structure patterns von Meyer, Fernando, Kurtz, Stefan, Backofen, Rolf, Will, Sebastian, Beckstette, Michael

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Quantitative high-resolution genomic analysis of single cancer cells von Hannemann, Juliane, Meyer-Staeckling, Sönke, Kemming, Dirk, Alpers, Iris, Joosse, Simon A, Pospisil, Heike, Kurtz, Stefan, Görndt, Jennifer, Püschel, Klaus, Riethdorf, Sabine, Pantel, Klaus, Brandt, Burkhard

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Construction of a Large Signature-Tagged Mini-Tn5 Transposon Library and Its Application to Mutagenesis of Sinorhizobium meliloti von Pobigaylo, Nataliya, Wetter, Danijel, Szymczak, Silke, Schiller, Ulf, Kurtz, Stefan, Meyer, Folker, Nattkemper, Tim W, Becker, Anke

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GfaPy: a flexible and extensible software library for handling sequence graphs in Python von Gonnella, Giorgio, Kurtz, Stefan

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