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419 Publikationen

2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2010)
In: Proc. of WABI 2010. LNBI, 6293. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving
Kovac J, Dias Vieira Braga M, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. 13-24.
PUB | DOI
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1794419
Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue
Herold J, Zhou L, Abouna S, Pelengaris S, Epstein D, Khan M, Nattkemper TW (2010)
Computerized Medical Imaging and Graphics 34(6): 446-452.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
The Solution Space of Sorting by DCJ
Dias Vieira Braga M, Stoye J (2010)
Journal of Computational Biology 17(9): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
Genomic Distance with DCJ and Indels
Dias Vieira Braga M, Willing E, Stoye J (2010)
In: Proc. of WABI 2010. LNBI, 6293. 90-101.
PUB | DOI
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1929860
Global gene expression analysis in nonfailing and failing myocardium pre- and postpulsatile and nonpulsatile ventricular assist device support
Schwientek P, Ellinghaus P, Steppan S, D'Urso D, Seewald M, Kassner A, Cebulla R, Schulte-Eistrup S, Morshuis M, Roefe D, El Banayosy A, et al. (2010)
PHYSIOLOGICAL GENOMICS 42(3): 397-405.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1930110
Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence
Joseph B, Schneiker-Bekel S, Schramm-Glueck A, Blom J, Claus H, Linke B, Schwarz RF, Becker A, Goesmann A, Frosch M, Schoen C (2010)
JOURNAL OF BACTERIOLOGY 192(20): 5363-5377.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2009)
Theoretical Computer Science 410(51): 5300-5316.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427059
Simple and fast reoptimizations for the Steiner tree problem
Escoffier B, Milanič M, Paschos VT (2009)
Algorithmic Operations Research 4(2): 86-94.
PUB
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2308924
Competitive evaluation of threshold functions in the priced information model
Cicalese F, Milanic M (2009)
Annals of Operations Research 188(1): 111-132.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426437
MCC/IMS signals in human breath related to sarcoidosis-results of a feasibility study using an automated peak finding procedure
Bunkowski A, Bödeker B, Bader S, Westhoff M, Litterst P, Baumbach JI (2009)
Journal of Breath Research 3(4): 046001.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426487
SIRIUS: decomposing isotope patterns for metabolite identification
Böcker S, Lipták Z, Pervukhin A, Letzel MC (2009)
Bioinformatics 25(2): 218-224.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Preprint | Veröffentlicht | PUB-ID: 2426653
On the Complexity of Searching in Trees: Average-case Minimization
Cicalese F, Jacobs T, Laber ES, Molinaro M (2009) .
PUB | arXiv
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426660
Faster Deterministic Communication in Radio Networks
Cicalese F, Manne F, Xin Q (2009)
Algorithmica 54(2): 226-242.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427118
Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species
Engelmann JA, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, Müller T (2009)
Molecular Ecology Resources 9(1): 83-93.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2305073 OA
Comparing organisms on the level of metabolism
Oehm S (2009)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2301318 OA
MeltDB : a software platform for the analysis and integration of metabolomics experiment data
Neuweger H (2009)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2009 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2659405
SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy
Feijão P, Meidanis J (2009)
In: Algorithms in Bioinformatics. Salzberg SL, Warnow T (Eds); Lecture Notes in Computer Science, 5724. 85-96.
PUB | DOI
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427161
Recent developments on graphs of bounded clique-width
Kamiński M, Lozin VV, Milanič M (2009)
Discrete Appl. Math. 157(12): 2747-2761.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427173
On the plane-width of graphs
Kamiński M, Medvedev P, Milanič M (2009)
Electronic Notes in Discrete Mathematics 34: 633-637.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
Counting All DCJ Sorting Scenarios
Dias Vieira Braga M, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 36-47.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2426605
Searching for Jumbled Patterns in Strings
Cicalese F, Fici G, Lipták Z (2009)
In: Proc. of the Prague Stringology Conference 2009. 105-117.
PUB
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2303240 OA
New algorithms and lower bounds for sequential-access data compression
Gagie T (2009)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2302608 OA PUB | PDF
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2406118
Engineering a compressed suffix tree implementation
Välimäki N, Mäkinen V, Gerlach W, Dixit K (2009)
Journal of Experimental Algorithmics (JEA) 14: 4.2-2:4.23.
PUB | DOI
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2304745 OA
Combinatorial aspects of low-rank matrix factorization and two applications in bioinformatics
Fritzilas E (2009)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
Finding Nested Common Intervals Efficiently
Blin G, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018390
A way towards analyzing high-content bioimage data by means of semantic annotation and visual data mining
Herold J, Abouna S, Zhou L, Pelengaris S, Epstein DBA, Khan M, Nattkemper TW (2009)
In: SPIE Medical Imaging.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018422
BIIGLE - Web 2.0 enabled labelling and exploring of images from the Arctic deep-sea observatory HAUSGARTEN
Ontrup J, Ehnert N, Bergmann M, Nattkemper TW (2009)
In: OCEANS 2009 - Europe. Bremen.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018427
A Robust Adaptive Wavelet-based Method for Classification of Meningioma Histology Images
Qureshi H, Rajpoot N, Nattkemper TW, Hans V (2009)
In: MICCAI«2009 Workshop on Optical Tissue Image Analysis in Microscopy, Histology, and Endoscopy.
PUB
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783187 OA
EDGAR: a software framework for the comparative analysis of prokaryotic genomes
Blom J, Albaum S, Doppmeier D, Pühler A, Vorhölter F-J, Zakrzewski M, Goesmann A (2009)
BMC Bioinformatics 10(1): 154.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636062
Detecting, Assessing, and Monitoring Relevant Topics in Virtual Information Environments
Ontrup J, Ritter H, Scholz S, Wagner R (2009)
IEEE Transactions on Knowledge and Data Engineering 21(3): 415-427.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
Approximative Gencluster und ihre Anwendung in der komparativen Genomik
Jahn K, Stoye J (2009)
Informatik-Spektrum 32(4): 288-300.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2009)
In: Proc. of WABI 2009. LNBI, 5724. 145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635314 OA
TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW (2009)
BMC Bioinformatics 10(1): 56.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635321 OA
EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data
Dondrup M, Albaum S, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Kuester H, Linke B, Mertens D, Mittard-Runte V, et al. (2009)
BMC Bioinformatics 10(1): 50.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
A Unified Approach for Reconstructing Ancient Gene Clusters
Stoye J, Wittler R (2009)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(3): 387-400.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589531
Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
Albaum S, Neuweger H, Fraenzel B, Lange S, Mertens D, Troetschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A (2009)
Bioinformatics 25(23): 3128-3134.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Brudno M, Medvedev P, Stoye J, De La Vega FM (2009)
BIOINFORMATICS 25(21): 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098 OA
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009)
BMC Bioinformatics 10(1): 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588783
Use of machine-learning algorithms for the automated detection of cold-water coral habitats: a pilot study
Purser A, Bergmann M, Ontrup J, Nattkemper TW (2009)
Marine Ecology Progress Series 397: 241-251.
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
Computation of Median Gene Clusters
Böcker S, Jahn K, Mixtacki J, Stoye J (2009)
Journal of Computational Biology 16(8): 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data
Hoffmann N, Stoye J (2009)
Bioinformatics 25(16): 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588760 OA
An asymmetric approach to preserve common intervals while sorting by reversals
Dias Vieira Braga M, Gautier C, Sagot M-F (2009)
Algorithms for Molecular Biology 4(1): 16.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
Rearrangement Models and Single-Cut Operations
Medvedev P, Stoye J (2009)
In: Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Lecture Notes in Computer Science, 5817. Berlin, Heidelberg: Springer: 84-97.
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018440
BIIGLE Tools - A Web 2.0 Approach for Visual Bioimage Database Mining
Schoening T, Ehnert N, Ontrup J, Nattkemper TW (2009)
In: IV 09 - Intl. Conference on Information Visualization.
PUB | DOI
 
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
Computational Short Read Metagenomics
Stoye J (2009)
Presented at the JOBIM 2009, Nantes, France.
PUB
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
Bekel T, Henckel K, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, et al. (2009)
Journal of Biotechnology 140(1-2): 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634615
Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete
Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Horsthemke B (2009)
HUMAN MOLECULAR GENETICS 18(8): 1439-1448.
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2427252
The Maximum Independent Set Problem in Planar Graphs
Alekseev VE, Lozin VV, Malyshev D, Milanič M (2008)
In: Proc. MFCS 2008. 96-107.
PUB | DOI
 

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