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  1. Book ; Online: Virus Bioinformatics

    Marz, Manja / Ibrahim, Bashar / Hufsky, Franziska / Robertson, David

    2020  

    Abstract: Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology ... ...

    Abstract Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics
    Keywords Science (General) ; Biology (General)
    Size 1 electronic resource (330 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020480889
    ISBN 9783039218820 ; 9783039218837 ; 3039218824 ; 3039218832
    DOI 10.3390/books978-3-03921-883-7
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article: ESSAY. Engpass Bioinformatik: Warum die Genom-Analyse im Kampf gegen Pandemien essenziell ist

    Hufsky, Franziska

    Laborjournal

    2021  Volume 28, Issue 7/8, Page(s) 62

    Language German
    Document type Article
    ZDB-ID 1237282-1
    ISSN 1612-8354
    Database Current Contents Medicine

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4842: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: The Role of Non-Coding RNAs in the Human Placenta.

    Žarković, Milena / Hufsky, Franziska / Markert, Udo R / Marz, Manja

    Cells

    2022  Volume 11, Issue 9

    Abstract: Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been ... ...

    Abstract Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
    MeSH term(s) Extracellular Vesicles/metabolism ; Female ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Placenta/metabolism ; Pregnancy ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Trophoblasts/metabolism
    Chemical Substances MicroRNAs ; RNA, Untranslated
    Language English
    Publishing date 2022-05-09
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11091588
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online ; Thesis: Novel methods for the analysis of small molecule fragmentation mass spectra

    Hufsky, Franziska

    2014  

    Abstract: The identification of small molecules, such as metabolites, in a high throughput manner plays an important in many research areas. Mass spectrometry (MS) is one of the predominant analysis technologies and is much more sensitive than nuclear magnetic ... ...

    Author's details von Franziska Hufsky
    Abstract The identification of small molecules, such as metabolites, in a high throughput manner plays an important in many research areas. Mass spectrometry (MS) is one of the predominant analysis technologies and is much more sensitive than nuclear magnetic resonance spectroscopy. Fragmentation of the molecules is used to obtain information beyond its mass. Gas chromatography-MS is one of the oldest and most widespread techniques for the analysis of small molecules. Commonly, the molecule is fragmented using electron ionization (EI). Using this technique, the molecular ion peak is often barely visible in the mass spectrum or even absent. We present a method to calculate fragmentation trees from high mass accuracy EI spectra, which annotate the peaks in the mass spectrum with molecular formulas of fragments and explain relevant fragmentation pathways. Fragmentation trees enable the identification of the molecular ion and its molecular formula if the molecular ion is present in the spectrum. The method works even if the molecular ion is of very low abundance. MS experts confirm that the calculated trees correspond very well to known fragmentation mechanisms.Using pairwise local alignments of fragmentation trees, structural and chemical similarities to already-known molecules can be determined. In order to compare a fragmentation tree of an unknown metabolite to a huge database of fragmentation trees, fast algorithms for solving the tree alignment problem are required. Unfortunately the alignment of unordered trees, such as fragmentation trees, is NP-hard. We present three exact algorithms for the problem. Evaluation of our methods showed that thousands of alignments can be computed in a matter of minutes. Both the computation and the comparison of fragmentation trees are rule-free approaches that require no chemical knowledge about the unknown molecule and thus will be very helpful in the automated analysis of metabolites that are not included in common libraries.
    Language English
    Size Online-Ressource (115 S.), graph. Darst
    Publisher Thüringer Universitäts- und Landesbibliothek
    Publishing place Jena
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Jena, 2014
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  5. Book ; Online ; Thesis: Novel methods for the analysis of small molecule fragmentation mass spectra

    Hufsky, Franziska

    2014  

    Abstract: The identification of small molecules, such as metabolites, in a high throughput manner plays an important in many research areas. Mass spectrometry (MS) is one of the predominant analysis technologies and is much more sensitive than nuclear magnetic ... ...

    Author's details von Franziska Hufsky
    Abstract The identification of small molecules, such as metabolites, in a high throughput manner plays an important in many research areas. Mass spectrometry (MS) is one of the predominant analysis technologies and is much more sensitive than nuclear magnetic resonance spectroscopy. Fragmentation of the molecules is used to obtain information beyond its mass. Gas chromatography-MS is one of the oldest and most widespread techniques for the analysis of small molecules. Commonly, the molecule is fragmented using electron ionization (EI). Using this technique, the molecular ion peak is often barely visible in the mass spectrum or even absent. We present a method to calculate fragmentation trees from high mass accuracy EI spectra, which annotate the peaks in the mass spectrum with molecular formulas of fragments and explain relevant fragmentation pathways. Fragmentation trees enable the identification of the molecular ion and its molecular formula if the molecular ion is present in the spectrum. The method works even if the molecular ion is of very low abundance. MS experts confirm that the calculated trees correspond very well to known fragmentation mechanisms.Using pairwise local alignments of fragmentation trees, structural and chemical similarities to already-known molecules can be determined. In order to compare a fragmentation tree of an unknown metabolite to a huge database of fragmentation trees, fast algorithms for solving the tree alignment problem are required. Unfortunately the alignment of unordered trees, such as fragmentation trees, is NP-hard. We present three exact algorithms for the problem. Evaluation of our methods showed that thousands of alignments can be computed in a matter of minutes. Both the computation and the comparison of fragmentation trees are rule-free approaches that require no chemical knowledge about the unknown molecule and thus will be very helpful in the automated analysis of metabolites that are not included in common libraries.
    Language English
    Size Online-Ressource (115 S.), graph. Darst
    Publisher Thüringer Universitäts- und Landesbibliothek
    Publishing place Jena
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Jena, 2014
    Database Former special subject collection: coastal and deep sea fishing

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  6. Article ; Online: Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data.

    Hufsky, Franziska / Böcker, Sebastian

    Mass spectrometry reviews

    2016  Volume 36, Issue 5, Page(s) 624–633

    Abstract: Mass spectrometry (MS) is a key technology for the analysis of small molecules. For the identification and structural elucidation of novel molecules, new approaches beyond straightforward spectral comparison are required. In this review, we will cover ... ...

    Abstract Mass spectrometry (MS) is a key technology for the analysis of small molecules. For the identification and structural elucidation of novel molecules, new approaches beyond straightforward spectral comparison are required. In this review, we will cover computational methods that help with the identification of small molecules by analyzing fragmentation MS data. We focus on the four main approaches to mine a database of metabolite structures, that is rule-based fragmentation spectrum prediction, combinatorial fragmentation, competitive fragmentation modeling, and molecular fingerprint prediction. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:624-633, 2017.
    Language English
    Publishing date 2016-01-13
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1491946-1
    ISSN 1098-2787 ; 0277-7037
    ISSN (online) 1098-2787
    ISSN 0277-7037
    DOI 10.1002/mas.21489
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: New kids on the block: novel informatics methods for natural product discovery

    Hufsky, Franziska / Scheubert, Kerstin / Böcker, Sebastian

    Natural product reports. 2014 May 14, v. 31, no. 6

    2014  

    Abstract: Covering: 2008 to 2014 Mass spectrometry is a key technology for the identification and structural elucidation of natural products. Manual interpretation of the resulting data is tedious and time-consuming, so methods for automated analysis are highly ... ...

    Abstract Covering: 2008 to 2014 Mass spectrometry is a key technology for the identification and structural elucidation of natural products. Manual interpretation of the resulting data is tedious and time-consuming, so methods for automated analysis are highly sought after. In this review, we focus on four recently developed methods for the detection and investigation of small molecules, namely MetFrag/MetFusion, ISIS, FingerID, and FT-BLAST. These methods have the potential to significantly advance the field of computational mass spectrometry for the research of natural products. For example, they may help with the dereplication of compounds at an early stage of the drug discovery process; that is, the detection of molecules that are identical or highly similar to known drugs or drug leads. Furthermore, when a potential drug lead has been determined, these tools may help to identify it and elucidate its structure.
    Keywords automation ; drugs ; mass spectrometry
    Language English
    Dates of publication 2014-0514
    Size p. 807-817.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 2002546-4
    ISSN 1460-4752 ; 0265-0568
    ISSN (online) 1460-4752
    ISSN 0265-0568
    DOI 10.1039/c3np70101h
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Computational mass spectrometry for small-molecule fragmentation

    Hufsky, Franziska / Kerstin Scheubert / Sebastian Böcker

    Trends in analytical chemistry. 2014 Jan., v. 53

    2014  

    Abstract: The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. Computational aspects of identifying small molecules range from searching a reference spectral library to the structural ... ...

    Abstract The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. Computational aspects of identifying small molecules range from searching a reference spectral library to the structural elucidation of an unknown. In this review, we concentrate on five important aspects of the computational analysis. We find that novel computational methods may overcome the boundaries of spectral libraries, by searching in the more comprehensive molecular structure databases, or not requiring any databases at all.
    Keywords chemical structure ; computational methodology ; databases ; mass spectrometry
    Language English
    Dates of publication 2014-01
    Size p. 41-48.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2014041-1
    ISSN 0165-9936
    ISSN 0165-9936
    DOI 10.1016/j.trac.2013.09.008
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: NFDI4Microbiota – national research data infrastructure for microbiota research

    Förstner, Konrad U. / Becker, Anke / Blom, Jochen / Bork, Peer / Clavel, Thomas / Dieckmann, Marius / Goesmann, Alexander / Götz, Barbara / Gübitz, Thomas / Hufsky, Franziska / Jünemann, Sebastian / Körner, Marie-Louise / Marz, Manja / Da Rocha, Ulisses Nunes / Overmann, Jörg / Pühler, A. / Rebholz-Schuhmann, Dietrich / Sczyrba, Alexander / Stoye, Jens /
    Vandendorpe, Justine / Van Rossum, Thea / McHardy, Alice

    Research Ideas and Outcomes. 2023 Aug. 24, v. 9 p.e110501-

    2023  

    Abstract: Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. ... ...

    Abstract Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.
    Keywords Archaea ; antibiotic resistance ; education ; environmental health ; eukaryotic cells ; humans ; infrastructure ; microorganisms ; remediation ; waste management ; water treatment ; Germany ; Research data management ; FAIR principles ; microbiota ; NFDI
    Language English
    Dates of publication 2023-0824
    Publishing place Pensoft Publishers
    Document type Article ; Online
    ZDB-ID 2833254-4
    ISSN 2367-7163
    ISSN 2367-7163
    DOI 10.3897/rio.9.e110501
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.

    Dührkop, Kai / Hufsky, Franziska / Böcker, Sebastian

    Mass spectrometry (Tokyo, Japan)

    2014  Volume 3, Issue Spec Iss 2, Page(s) S0037

    Abstract: We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis ...

    Abstract We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis and fragmentation pattern analysis and is completely independent from any (spectral and structural) database. We correctly identified the molecular formula for ten out of twelve challenges, being the best automated method competing in this category.
    Language English
    Publishing date 2014-07-18
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 2670439-0
    ISSN 2186-5116 ; 2187-137X
    ISSN (online) 2186-5116
    ISSN 2187-137X
    DOI 10.5702/massspectrometry.S0037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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