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79 Publikationen

2017 | Zeitschriftenaufsatz | PUB-ID: 2918897
Thijssen, Bram, Dijkstra, Tjeerd M. H., Heskes, Tom, and Wessels, Lodewyk F. A. 2017. “Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates”. Bioinformatics 34 (5): 803-811.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933892
Dirmeier, Simon, Fuchs, Christiane, Mueller, Nikola S, and Theis, Fabian J. 2017. “netReg: network-regularized linear models for biological association studies”. Bioinformatics 34 (5): 896-898.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918707
Beier, Sebastian, Thiel, Thomas, Münch, Thomas, Scholz, Uwe, and Mascher, Martin. 2017. “MISA-web: a web server for microsatellite prediction”. Bioinformatics 33 (16): 2583-2585.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793
Gregor, I., Schönhuth, Alexander, and McHardy, A. C. 2016. “Snowball: strain aware gene assembly of metagenomes”. Bioinformatics 32 (17): i649-i657.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905170 OA
Hilker, Rolf, Stadermann, Kai Bernd, Schwengers, Oliver, Anisiforov, Evgeny, Jaenicke, Sebastian, Weisshaar, Bernd, Zimmermann, Tobias, and Goesmann, Alexander. 2016. “ReadXplorer 2 - detailed read mapping analysis and visualization from one single source”. Bioinformatics 32 (24): 3702-3708.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
Bremges, Andreas, Singer, Esther, Woyke, Tanja, and Sczyrba, Alexander. 2016. “MeCorS: Metagenome-enabled error correction of single cell sequencing reads”. Bioinformatics 32 (14): 2199-2201.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912555
Helfrich, Stefan, Azzouzi, Charaf E., Probst, Christopher, Seiffarth, Johannes, Grünberger, Alexander, Wiechert, Wolfgang, Kohlheyer, Dietrich, and Nöh, Katharina. 2015. “Vizardous: interactive analysis of microbial populations with single cell resolution”. Bioinformatics 31 (23): 3875-3877: btv468.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612 OA
Wittler, Roland, Marschall, Tobias, Schönhuth, Alexander, and Makinen, Veli. 2015. “Repeat- and error-aware comparison of deletions”. Bioinformatics 31 (18): 2947-2954.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. 2014. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30 (16): 2247-2254.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. 2014. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30 (7): 988-995.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2700599
Janssen, Stefan, and Giegerich, Robert. 2014. “The RNA shapes studio”. Bioinformatics 31 (3): 423-425.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836
Marschall, Tobias, Hajirasouliha, Iman, and Schönhuth, Alexander. 2013. “MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels”. Bioinformatics 29 (24): 3143-3150.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2551798
Sauthoff, Georg, Mohl, Mathias, Janssen, Stefan, and Giegerich, Robert. 2013. “Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis”. Bioinformatics 29 (5): 551-560.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2610129
Kessler, Nikolas, Bonte, Anja, Langenkämper, Georg, Niehaus, Karsten, Goesmann, Alexander, and Nattkemper, Tim Wilhelm. 2013. “MeltDB 2.0 - Advances of the metabolomics software system”. Bioinformatics 29 (19): 2452-2459.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839
Marschall, Tobias, Costa, Ivan G., Canzar, Stefan, Bauer, Markus, Klau, Gunnar W., Schliep, Alexander, and Schönhuth, Alexander. 2012. “CLEVER: clique-enumerating variant finder”. Bioinformatics 28 (22): 2875-2882.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840
Hajirasouliha, Iman, Schönhuth, Alexander, de Juan, David, Valencia, Alfonso, and Sahinalp, S. Cenk. 2012. “Mirroring co-evolving trees in the light of their topologies”. Bioinformatics 28 (9): 1202-1208.
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2012 | Zeitschriftenaufsatz | PUB-ID: 2910009
M. Reidys, Christian, W. D. Huang, Fenix, E. Andersen, Jorgen, C. Penner, Robert, F. Stadler, Peter, and Nebel, Markus. 2012. “Addendum: topology and prediction of RNA pseudoknots”. Bioinformatics 28 (2): 300.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, Rolf, Sickinger, Corinna, Pedersen, Christian N. S., and Stoye, Jens. 2012. “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”. Bioinformatics 28 (19): 2509-2511.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2496829
Cox, Anthony J, Bauer, Markus J, Jakobi, Tobias, and Rosone, Giovanna. 2012. “Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform”. Bioinformatics 28 (11): 1415-1419.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2481783 OA
Kölling, Jan, Langenkämper, Daniel, Sylvie, Abouna, Michale, Khan, and Nattkemper, Tim Wilhelm. 2012. “WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages”. Bioinformatics 28 (8): 1143-1150.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842
Hafemeister, Christoph, Costa, Ivan G., Schönhuth, Alexander, and Schliep, Alexander. 2011. “Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions”. Bioinformatics 27 (7): 946-952.
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2011 | Zeitschriftenaufsatz | PUB-ID: 2910018
M. Reidys, Christian, W. D. Huang, Fenix, E. Andersen, Jorgen, C. Penner, Robert, F. Stadler, Peter, and Nebel, Markus. 2011. “Topology and prediction of RNA pseudoknots”. Bioinformatics 27 (8): 1076--1085.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2401665
Hazelhurst, Scott, and Lipták, Zsuzsanna. 2011. “KABOOM! A new suffix-array based algorithm for clustering expression data”. Bioinformatics 27 (24): 3348-3355.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2408590
Huang, Donglin, Huang, Yiling, Bai, Youhuang, Chen, Dijun, Hofestädt, Ralf, Klukas, Cristian, and Chen, Ming. 2011. “MyBioNet: interactively visualize, edit and merge biological networks on the Web”. Bioinformatics 27 (23): 3321-3322.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Blom, Jochen, Jakobi, Tobias, Doppmeier, Daniel, Jaenicke, Sebastian, Kalinowski, Jörn, Stoye, Jens, and Goesmann, Alexander. 2011. “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”. Bioinformatics 27 (10): 1351-1358.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2307115
Dutilh, Bas E., Jurgelenaite, Rasa, Szklarczyk, Radek, van Hijum, Sacha A. F. T., Harhangi, Harry R., Schmid, Markus, de Wild, Bart, et al. 2011. “FACIL: Fast and Accurate Genetic Code Inference and Logo”. Bioinformatics 27 (14): 1929-1933.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2094556
Schleif, Frank-Michael, Riemer, T., Boerner, U., Schnapka-Hille, L., and Cross, M. 2011. “Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications”. Bioinformatics 27 (4): 524-533.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093578
Linke, Burkhard, Giegerich, Robert, and Goesmann, Alexander. 2011. “Conveyor: a workflow engine for bioinformatic analyses”. Bioinformatics 27 (7): 903-911.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893946 OA
Janssen, Stefan, and Giegerich, Robert. 2010. “Faster computation of exact RNA shape probabilities”. Bioinformatics 26 (5): 632-639.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
Husemann, Peter, and Stoye, Jens. 2010. “r2cat: Synteny Plots and Comparative Assembly”. Bioinformatics 26 (4): 570-571.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426487
Böcker, Sebastian, Lipták, Zsuzsanna, Pervukhin, Anton, and Letzel, Matthias C. 2009. “SIRIUS: decomposing isotope patterns for metabolite identification”. Bioinformatics 25 (2): 218-224.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589531
Albaum, Stefan, Neuweger, Heiko, Fraenzel, Benjamin, Lange, Sita, Mertens, Dominik, Troetschel, Christian, Wolters, Dirk, Kalinowski, Jörn, Nattkemper, Tim Wilhelm, and Goesmann, Alexander. 2009. “Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments”. Bioinformatics 25 (23): 3128-3134.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
Brudno, Michael, Medvedev, Paul, Stoye, Jens, and De La Vega, Francisco M. 2009. “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”. BIOINFORMATICS 25 (21): 2863-2864.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589458
Beckstette, Michael, Homann, Robert, Giegerich, Robert, and Kurtz, Stefan. 2009. “Significant speedup of database searches with HMMs by search space reduction with PSSM family models”. Bioinformatics 25 (24): 3251-3258.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590210
Dutilh, Bas E., Huynen, Martijn A., and Strous, Marc. 2009. “Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly”. BIOINFORMATICS 25 (21): 2878-2881.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
Hoffmann, Nils, and Stoye, Jens. 2009. “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”. Bioinformatics 25 (16): 2080-2081.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634374
Homann, Robert, Fleer, David, Giegerich, Robert, and Rehmsmeier, Marc. 2009. “mkESA: enhanced suffix array construction tool”. Bioinformatics 25 (8): 1084-1085.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2603465
Klinger, Roman, Kolarik, Corinna, Fluck, Juliane, Hofmann-Apitius, Martin, and Friedrich, Christoph M. 2008. “Detection of IUPAC and IUPAC-like Chemical Names”. Bioinformatics 24 (13): i268-i276.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
Neuweger, Heiko, Albaum, Stefan, Dondrup, Michael, Persicke, Marcus, Watt, Tony, Niehaus, Karsten, Stoye, Jens, and Goesmann, Alexander. 2008. “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”. Bioinformatics 24 (23): 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587304
Hazelhurst, Scott, Hide, Winston, Lipták, Zsuzsanna, Nogueira, Ramon, and Starfield, Richard. 2008. “An overview of the wcd EST clustering tool”. BIOINFORMATICS 24 (13): 1542-1546.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1592737
Boecker, Sebastian, Lipták, Zsuzsanna, Martin, Marcel, Pervukhin, Anton, and Sudek, Henner. 2008. “DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem”. BIOINFORMATICS 24 (4): 591-593.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587052
Martin, Christian, Diaz, Naryttza N., Ontrup, Jörg, and Nattkemper, Tim Wilhelm. 2008. “Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification”. Bioinformatics 24 (14): 1568-1574.
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2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1594917
Välimäki, Niko, Gerlach, Wolfgang, Dixit, Kashyap, and Mäkinen, Veli. 2007. “Compressed suffix tree - a basis for genome-scale sequence analysis”. BIOINFORMATICS 23 (5): 629-630.
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2007 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1593132
Reeder, Janina, Reeder, Jens, and Giegerich, Robert. 2007. “Locomotif: from graphical motif description to RNA motif search”. In Bioinformatics, 23:I392-I400. Bioinformatics. OXFORD UNIV PRESS.
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2006 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1631967
Schliep, Alexander, and Rahmann, Sven. 2006. “Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree”. In Bioinformatics, 22:e424-e430. Bioinformatics. Oxford Univ. Press.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2499691
Köhler, Jacob, Baumbach, Jan, Taubert, Jan, Specht, Michael, Skusa, Andre, Rüegg, Alexander, Rawlings, Chris, Verrier, Paul, and Philippi, Stephan. 2006. “Graph-based analysis and visualization of experimental results with ONDEX”. Bioinformatics 22 (11): 1383-1390.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659363
Feijão, Pedro, Neiva, L. S., Azeredo-Espin, A. M. L. d., and Lessinger, A. C. 2006. “AMiGA: the arthropodan mitochondrial genomes accessible database”. Bioinformatics 22 (7): 902-903.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1902179
Gerlach, Wolfgang, and Giegerich, Robert. 2006. “GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.”. Bioinformatics 22 (6): 762-764.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599943
Sammeth, Michael, Griebel, Thasso, Tille, Felix, and Stoye, Jens. 2006. “Panta rhei (QAlign2): an open graphical environment for sequence analysis”. BIOINFORMATICS 22 (7): 889-890.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1600421
Steffen, Peter, Voss, Björn, Rehmsmeier, Marc, Reeder, Jens, and Giegerich, Robert. 2006. “RNAshapes: an integrated RNA analysis package based on abstract shapes”. Bioinformatics 22 (4): 500-503.
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