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  1. AU="Henkel, Werner"
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  1. Article: The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.

    Teufel, Marc / Henkel, Werner / Sobetzko, Patrick

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1119878

    Abstract: For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins sigma factors and modulation of DNA topology. In this study, we investigate replication- ...

    Abstract For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins sigma factors and modulation of DNA topology. In this study, we investigate replication-induced gene copy numbers - a regulatory concept that is unlike the others not based on modulation of promoter activity but on replication dynamics. We show that a large fraction of genes are predominantly affected by transient copy numbers and identify cellular functions and central pathways governed by this mechanism in
    Language English
    Publishing date 2023-04-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1119878
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Thesis: Postoperative Ergebnisse einzeitiger Kontinuitätsresektionen an der linken Colonhälfte und am Rektum

    Henkel, Werner

    e. Unters. d. Jahre 1975 - 1980

    1984  

    Size 76 S. : Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Marburg, Univ., Diss., 1984
    HBZ-ID HT003089940
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    86 D 845 order for loan Magazin

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  3. Article ; Online: Sequence-based information-theoretic features for gene essentiality prediction.

    Nigatu, Dawit / Sobetzko, Patrick / Yousef, Malik / Henkel, Werner

    BMC bioinformatics

    2017  Volume 18, Issue 1, Page(s) 473

    Abstract: Background: Identification of essential genes is not only useful for our understanding of the minimal gene set required for cellular life but also aids the identification of novel drug targets in pathogens. In this work, we present a simple and ... ...

    Abstract Background: Identification of essential genes is not only useful for our understanding of the minimal gene set required for cellular life but also aids the identification of novel drug targets in pathogens. In this work, we present a simple and effective gene essentiality prediction method using information-theoretic features that are derived exclusively from the gene sequences.
    Results: We developed a Random Forest classifier and performed an extensive model performance evaluation among and within 15 selected bacteria. In intra-organism predictions, where training and testing sets are taken from the same organism, AUC (Area Under the Curve) scores ranging from 0.73 to 0.90, 0.84 on average, were obtained. Cross-organism predictions using 5-fold cross-validation, pairwise, leave-one-species-out, leave-one-taxon-out, and cross-taxon yielded average AUC scores of 0.88, 0.75, 0.80, 0.82, and 0.78, respectively. To further show the applicability of our method in other domains of life, we predicted the essential genes of the yeast Schizosaccharomyces pombe and obtained a similar accuracy (AUC 0.84).
    Conclusions: The proposed method enables a simple and reliable identification of essential genes without searching in databases for orthologs and demanding further experimental data such as network topology and gene-expression.
    Language English
    Publishing date 2017-11-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-017-1884-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Relationship between digital information and thermodynamic stability in bacterial genomes.

    Nigatu, Dawit / Henkel, Werner / Sobetzko, Patrick / Muskhelishvili, Georgi

    EURASIP journal on bioinformatics & systems biology

    2016  Volume 2016, Issue 1, Page(s) 4

    Abstract: Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an "analog" ...

    Abstract Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an "analog" type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA. In this paper, we represented analog information by its thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequences of several bacteria, including
    Language English
    Publishing date 2016-02-02
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2233385-X
    ISSN 1687-4153 ; 1687-4145
    ISSN (online) 1687-4153
    ISSN 1687-4145
    DOI 10.1186/s13637-016-0037-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The empirical codon mutation matrix as a communication channel.

    Nigatu, Dawit / Mahmood, Attiya / Henkel, Werner

    BMC bioinformatics

    2014  Volume 15, Page(s) 80

    Abstract: Background: A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one ... ...

    Abstract Background: A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity.
    Results: The channel capacity of 4.1875 bit, which is needed to preserve the information determined by the amino acid distribution, is obtained with an exponential factor of 0.26 applied to the ECM matrix. Additionally, we have obtained the optimum capacity achieving codon distribution. Compared to the biological distribution, there is an obvious difference, however, the distribution among synonymous codons is preserved. More importantly, the results show that the biological codon distribution allows for a "transmission" at a rate very close to the capacity.
    Conclusion: We computed an exponential factor for the ECM matrix that would still allow for preserving the genetic information given the redundancy that is present in the codon-to-amino acid mapping. This gives an insight how such a mutation matrix relates to the preservation of a species in an information-theoretic sense.
    MeSH term(s) Amino Acids/chemistry ; Amino Acids/genetics ; Animals ; Base Sequence ; Codon ; Humans ; Models, Genetic ; Mutation ; Probability ; Sequence Alignment ; Sequence Analysis, DNA/methods
    Chemical Substances Amino Acids ; Codon
    Language English
    Publishing date 2014-03-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/1471-2105-15-80
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online ; Thesis: The DNA from a Communications and Information Theoretic Perspective

    Nigatu, Dawit Andualem [Verfasser] / Henkel, Werner [Akademischer Betreuer] / Henkel, Werner [Gutachter] / Hütt, Marc-Thorsten [Gutachter] / Muskhelishvili, Georgi [Gutachter] / Ali, Hesham [Gutachter]

    2018  

    Author's details Dawit Andualem Nigatu ; Gutachter: Werner Henkel, Marc-Thorsten Hütt, Georgi Muskhelishvili, Hesham Ali ; Betreuer: Werner Henkel
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher IRC-Library, Information Resource Center der Jacobs University Bremen
    Publishing place Bremen
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

    Full text online

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  7. Article ; Online: Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers

    Yousef, Malik / Nigatu, Dawit / Levy, Dalit / Allmer, Jens / Henkel, Werner

    Eurasip Journal on Advances in Signal Processing

    2017  Volume 2017

    Abstract: Background: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and have been shown to be exploited by ...

    Abstract Background: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and have been shown to be exploited by viruses to modulate their host environment. Since the experimental detection of miRNAs is difficult, computational methods have been developed. Many such tools employ machine learning for pre-miRNA detection, and many features for miRNA parameterization have been proposed. To train machine learning models, negative data is of importance yet hard to come by; therefore, we recently started to employ pre-miRNAs from one species as positive data versus another species’ pre-miRNAs as negative examples based on sequence motifs and k-mers. Here, we introduce the additional usage of information-theoretic (IT) features. Results: Pre-miRNAs from one species were used as positive and another species’ pre-miRNAs as negative training data for machine learning. The categorization capability of IT and k-mer features was investigated. Both feature sets and their combinations yielded a very high accuracy, which is as good as the previously suggested sequence motif and k-mer based method. However, for obtaining a high performance, a sufficiently large phylogenetic distance between the species and sufficiently high number of pre-miRNAs in the training set is required. To examine the contribution of the IT and k-mer features, an information gain-based feature ranking was performed. Although the top 3 are IT features, 80% of the top 100 features are k-mers. The comparison of all three individual approaches (motifs, IT, and k-mers) shows that the distinction of species based on their pre-miRNAs k-mers are sufficient. Conclusions: IT sequence feature extraction enables the distinction among species and is less computationally expensive than motif calculations. However, since IT features need larger amounts of data to have enough statistics for producing highly accurate results, future ...
    Keywords Differentiate miRNAs among species ; Information theory ; Machine learning ; MicroRNA ; Pre-microRNA ; Sequence motifs ; k-mer ; miRNA categorization
    Subject code 006
    Language English
    Publishing country nl
    Document type Article ; Online
    ISSN 1687-6172
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Cyanogen bromide peptides of the fibrillar collagens I, III, and V and their mass spectrometric characterization: detection of linear peptides, peptide glycosylation, and cross-linking peptides involved in formation of homo- and heterotypic fibrils.

    Henkel, Werner / Dreisewerd, Klaus

    Journal of proteome research

    2007  Volume 6, Issue 11, Page(s) 4269–4289

    Abstract: The network of the fibrillar collagens I, III, and V, extracted from fetal calf skin and cleaved with cyanogen bromide, was studied by means of ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI MS). Nearly ...

    Abstract The network of the fibrillar collagens I, III, and V, extracted from fetal calf skin and cleaved with cyanogen bromide, was studied by means of ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI MS). Nearly all of the expected cyanogen bromide peptides of the different alpha chains were detected. Distinct peptides are identified that can serve as a reference signal for the individual alpha-chains. Homo- and heterotypic cross-linking patterns, some of which have not been described before for bovine collagen, are indicated by comparison of the mass spectrometric data with documented amino acid sequences. Potential cross-linking mechanisms are discussed. For example, the mass spectrometric data suggest that the formation of heterotypic I/III and I/V fibrils is substantially determined by the telo-regions of type I collagen, which are covalently connected to the corresponding helical and nonhelical cross-linking domains of adjacent molecules either by 4D or 0D-stagger bonds. The chemical nature of the cross-links can be concluded. The data also indicate a disturbed formation of heterotypic fibrils. Finally, collagen glycosylation can also be identified.
    MeSH term(s) Animals ; Cattle ; Collagen/chemistry ; Collagen Type I/chemistry ; Collagen Type III/chemistry ; Collagen Type V/chemistry ; Cross-Linking Reagents/pharmacology ; Cyanogen Bromide/pharmacology ; Glycosylation ; Mass Spectrometry/methods ; Molecular Weight ; Peptides/chemistry ; Protein Structure, Tertiary ; Proteins/chemistry ; Proteomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Ultraviolet Rays
    Chemical Substances Collagen Type I ; Collagen Type III ; Collagen Type V ; Cross-Linking Reagents ; Peptides ; Proteins ; Collagen (9007-34-5) ; Cyanogen Bromide (OS382OHJ8P)
    Language English
    Publishing date 2007-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2078618-9
    ISSN 1535-3893
    ISSN 1535-3893
    DOI 10.1021/pr070318r
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  9. Book ; Thesis: Zur Decodierung algebraischer Blockcodes über komplexen Aalphabeten

    Henkel, Werner

    (Fortschritt-Berichte VDI : Reihe 10 ; 109)

    1989  

    Author's details Werner Henkel
    Series title Fortschritt-Berichte VDI : Reihe 10 ; 109
    Keywords Decodierung ; Blockcode
    Size III, 127 S, graph. Darst
    Edition Als Ms. gedr
    Publisher VDI-Verl
    Publishing place Düsseldorf
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Techn. Hochsch., Diss.--Zugl.:Darmstadt
    ISBN 3181409103 ; 9783181409107
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  10. Book ; Thesis: Postoperative Ergebnisse einzeitiger Kontinuitätsresektionen an der linken Colonhälfte und am Rektum

    Henkel, Werner

    eine Untersuchung der Jahre 1975-1980

    1984  

    Author's details Werner Henkel
    Language Undetermined
    Size 76 S, Ill., graph. Darst
    Document type Book ; Thesis
    Thesis / German Habilitation thesis @Marburg, Univ., Diss. : 1984
    Database Former special subject collection: coastal and deep sea fishing

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