Works by Kurtz, Stefan

Results: 32

Transcription factor prediction using protein 3D secondary structures.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae762

By:

Liebold, Jeanine;
Neuhaus, Fabian;
Geiser, Janina;
Kurtz, Stefan;
Baumbach, Jan;
Newaz, Khalique

Publication type:

Article

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO<sub>2</sub> Fixation and 16S Tags of the Transcriptome in Incubation Experiments

Published in:

Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.02296

By:

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

Publication type:

Article

Fine-grained annotation and classification of de novo predicted LTR retrotransposons.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 21, p. 7002, doi. 10.1093/nar/gkp759

By:

Steinbiss, Sascha;
Willhoeft, Ute;
Gremme, Gordon;
Kurtz, Stefan

Publication type:

Article

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w301, doi. 10.1093/nar/gkh478

By:

Krüger, Jan;
Sczyrba, Alexander;
Kurtz, Stefan;
Giegerich, Robert

Publication type:

Article

RNA-related tools on the Bielefeld Bioinformatics Server.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3767, doi. 10.1093/nar/gkg576

By:

Sczyrba, Alexander;
Krüger, Jan;
Mersch, Henning;
Kurtz, Stefan;
Giegerich, Robert

Publication type:

Article

REPuter: the manifold applications of repeat analysis on a genomic scale.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 22, p. 4633, doi. 10.1093/nar/29.22.4633

By:

Kurtz, Stefan;
Choudhuri, Jomuna V.;
Ohlebusch, Enno;
Schleiermacher, Chris;
Stoye, Jens;
Giegerich, Robert

Publication type:

Article

Optimized design and assessment of whole genome tiling arrays.

Published in:

Bioinformatics, 2007, v. 23, n. 13, p. i195, doi. 10.1093/bioinformatics/btm200

By:

Stefan Gräf;
Fiona G. G. Nielsen;
Stefan Kurtz;
Martijn A. Huynen;
Ewan Birney;
Henk Stunnenberg;
Paul Flicek

Publication type:

Article

Efficient multiple genome alignment.

Published in:

Bioinformatics, 2002, v. 18, p. S312, doi. 10.1093/bioinformatics/18.suppl_1.S312

By:

Höhl, Michael;
Kurtz, Stefan;
Ohlebusch, Enno

Publication type:

Article

REPuter: fast computation of maximal repeats in complete genomes.

Published in:

Bioinformatics, 1999, v. 15, n. 5, p. 426, doi. 10.1093/bioinformatics/15.5.426

By:

Kurtz, Stefan;
Schleiermacher, Chris

Publication type:

Article

In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field.

Published in:

Environmental Microbiology, 2013, v. 15, n. 5, p. 1551, doi. 10.1111/1462-2920.12038

By:

Perner, Mirjam;
Gonnella, Giorgio;
Hourdez, Stephane;
Böhnke, Stefanie;
Kurtz, Stefan;
Girguis, Peter

Publication type:

Article

An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges.

Published in:

Briefings in Bioinformatics, 2003, v. 4, n. 2, p. 105, doi. 10.1093/bib/4.2.105

By:

Chain, Patrick;
Kurtz, Stefan;
Ohlebusch, Enno;
Slezak, Tom

Publication type:

Article

Microbial Community Compositions and Geochemistry of Sediments with Increasing Distance to the Hydrothermal Vent Outlet in the Kairei Field.

Published in:

Geomicrobiology Journal, 2020, v. 37, n. 3, p. 242, doi. 10.1080/01490451.2019.1694107

By:

Adam, Nicole;
Kriete, Cornelia;
Garbe-Schönberg, Dieter;
Gonnella, Giorgio;
Krause, Stefan;
Schippers, Axel;
Kurtz, Stefan;
Schwarz-Schampera, Ulrich;
Han, Yuchen;
Indenbirken, Daniela;
Perner, Mirjam

Publication type:

Article

GfaViz: flexible and interactive visualization of GFA sequence graphs.

Published in:

Bioinformatics, 2019, v. 35, n. 16, p. 2853, doi. 10.1093/bioinformatics/bty1046

By:

Gonnella, Giorgio;
Niehus, Niklas;
Kurtz, Stefan

Publication type:

Article

GfaPy: a flexible and extensible software library for handling sequence graphs in Python.

Published in:

Bioinformatics, 2017, v. 33, n. 19, p. 3094, doi. 10.1093/bioinformatics/btx398

By:

Gonnella, Giorgio;
Kurtz, Stefan

Publication type:

Article

Significant speedup of database searches with HMMs by search space reduction with PSSM family models.

Published in:

Bioinformatics, 2009, v. 25, n. 24, p. 3251, doi. 10.1093/bioinformatics/btp593

By:

Beckstette, Michael;
Homann, Robert;
Giegerich, Robert;
Kurtz, Stefan

Publication type:

Article

AnnotationSketch: a genome annotation drawing library.

Published in:

Bioinformatics, 2009, v. 25, n. 4, p. 533, doi. 10.1093/bioinformatics/btn657

By:

Sascha Steinbiss;
Gordon Gremme;
Christin Schärfer;
Malte Mader;
Stefan Kurtz

Publication type:

Article

HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 196, doi. 10.1093/nar/29.1.196

By:

Gräf, Stefan;
Strothmann, Dirk;
Kurtz, Stefan;
Steger, Gerhard

Publication type:

Article

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention.

Published in:

Algorithms for Molecular Biology, 2021, v. 16, n. 1, p. 1, doi. 10.1186/s13015-021-00199-0

By:

Hausmann, Fabian;
Kurtz, Stefan

Publication type:

Article

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-226

By:

Meyer, Fernando;
Kurtz, Stefan;
Beckstette, Michael

Publication type:

Article

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Published in:

BMC Bioinformatics, 2012, v. 13, n. 1, p. 82, doi. 10.1186/1471-2105-13-82

By:

Gonnella, Giorgio;
Kurtz, Stefan

Publication type:

Article

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.

Published in:

2008

By:

Ellinghaus, David;
Kurtz, Stefan;
Willhoeft, Ute

Publication type:

Product Review

Efficient computation of absent words in genomic sequences.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-167

By:

Herold, Julia;
Kurtz, Stefan;
Giegerich, Robert

Publication type:

Article

Optimising oligonucleotide array design for ChIP-on-chip.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 1, doi. 10.1186/1471-2105-8-S8-P4

By:

Nielsen, Fiona;
Graef, Stefan;
Xinmin Zhang;
Kurtz, Stefan;
Denissov, Sergei;
Green, Roland;
Birney, Ewan;
Flicek, Paul;
Huynen, Martijn;
Stunnenberg, Henk

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2009, v. 5, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000502

By:

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

Publication type:

Article

TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 341, doi. 10.1093/nar/gky972

By:

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

Publication type:

Article

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.

Published in:

Mobile DNA, 2012, v. 3, n. 1, p. 1, doi. 10.1186/1759-8753-3-18

By:

Steinbiss, Sascha;
Kastens, Sascha;
Kurtz, Stefan

Publication type:

Article

Selective regain of egfr gene copies inCD44+/CD24-/low breast cancer cellularmodel MDA-MB-468.

Published in:

BMC Cancer, 2010, v. 10, p. 78, doi. 10.1186/1471-2407-10-78

By:

Agelopoulos, Konstantin;
Greve, Burkhard;
Schmidt, Hartmut;
Pospisil, Heike;
Kurtz, Stefan;
Bartkowiak, Kai;
Andreas, Antje;
Wieczorek, Marek;
Korsching, Eberhard;
Buerger, Horst;
Brandt, Burkhard

Publication type:

Article

PPFIA1 and CCND1 are frequently coamplified in breast cancer.

Published in:

Genes, Chromosomes & Cancer, 2010, v. 49, n. 1, p. 1, doi. 10.1002/gcc.20713

By:

Dancau, Ana-Maria;
Wuth, Laura;
Waschow, Marcel;
Holst, Frederik;
Krohn, Antje;
Choschzick, Matthias;
Terracciano, Luigi;
Politis, Sotirios;
Kurtz, Stefan;
Lebeau, Annette;
Friedrichs, Kay;
Wencke, Katharina;
Monni, Outi;
Simon, Ronald

Publication type:

Article

Loss of copy numbers of retrotransposons (HERVK) on chromosome 7p11.2 impacts EGFR (Epidermal Growth Factor Receptor)‐induced phenotypes for platinum sensitivity and long‐term survival in ovarian cancer—A study from the OVCAD consortium.

Published in:

International Journal of Cancer, 2024, v. 155, n. 5, p. 934, doi. 10.1002/ijc.34976

By:

Fromhage, Gesa;
Obermayr, Eva;
Bednarz‐Knoll, Natalia;
Van Gorp, Toon;
Welsch, Eva;
Polterauer, Stephan;
Braicu, Elena Ioana;
Mahner, Sven;
Sehouli, Jalid;
Vergote, Ignace;
Concin, Nicole;
Kurtz, Stefan;
Steinbiss, Sascha;
Torge, Antje;
Zeillinger, Robert;
Wölber, Linn;
Brandt, Burkhard

Publication type:

Article

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells.

Published in:

PLoS ONE, 2011, v. 6, n. 11, p. 1, doi. 10.1371/journal.pone.0026362

By:

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

Publication type:

Article

Recurrent deletion of 3p13 targets multiple tumour suppressor genes and defines a distinct subgroup of aggressive ERG fusion-positive prostate cancers.

Published in:

Journal of Pathology, 2013, v. 231, n. 1, p. 130, doi. 10.1002/path.4223

By:

Krohn, Antje;
Seidel, Annemarie;
Burkhardt, Lia;
Bachmann, Frederic;
Mader, Malte;
Grupp, Katharina;
Eichenauer, Till;
Becker, Andreas;
Adam, Meike;
Graefen, Markus;
Huland, Hartwig;
Kurtz, Stefan;
Steurer, Stefan;
Tsourlakis, Maria C;
Minner, Sarah;
Michl, Uwe;
Schlomm, Thorsten;
Sauter, Guido;
Simon, Ronald;
Sirma, Hüseyin

Publication type:

Article

Sequencing, annotation, and comparative genomeanalysis of the gerbil-adapted Helicobacter pyloristrain B8.

Published in:

BMC Genomics, 2010, v. 11, p. 335, doi. 10.1186/1471-2164-11-335

By:

Farnbacher, Max;
Jahns, Thomas;
Willrodt, Dirk;
Daniel, Rolf;
Haas, Rainer;
Goesmann, Alexander;
Kurtz, Stefan;
Rieder, Gabriele

Publication type:

Article