Publications

@article{Goettsch:21,

title = {ITN—VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics},

author = {Winfried Göttsch and Niko Beerenwinkel and Li Deng and Lars Dölken and Bas E. Dutilh and Florian Erhard and Lars Kaderali and Max Kleist and Roland Marquet and Jelle Matthijnssens and Shawna McCallin and Dino McMahon and Thomas Rattei and Ronald P. Van Rij and David L. Robertson and Martin Schwemmle and Noam Stern-Ginossar and Manja Marz},

doi = {10.3390/v13050766},

year  = {2021},

date = {2021-04-27},

urldate = {2021-04-27},

journal = {Viruses},

volume = {13},

number = {5},

pages = {766},

publisher = {MDPI AG},

abstract = {Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals. },

keywords = {review, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Hufsky:20a,

title = {Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research},

author = {Franziska Hufsky and Kevin Lamkiewicz and Alexandre Almeida and Abdel Aouacheria and Cecilia Arighi and Alex Bateman and Jan Baumbach and Niko Beerenwinkel and Christian Brandt and Marco Cacciabue and Sara Chuguransky and Oliver Drechsel and Robert D Finn and Adrian Fritz and Stephan Fuchs and Georges Hattab and Anne-Christin Hauschild and Dominik Heider and Marie Hoffmann and Martin Hölzer and Stefan Hoops and Lars Kaderali and Ioanna Kalvari and Max Kleist and Renó Kmiecinski and Denise Kühnert and Gorka Lasso and Pieter Libin and Markus List and Hannah F Löchel and Maria J Martin and Roman Martin and Julian Matschinske and Alice C McHardy and Pedro Mendes and Jaina Mistry and Vincent Navratil and Eric P Nawrocki and Áine Niamh O'Toole and Nancy Ontiveros-Palacios and Anton I Petrov and Guillermo Rangel-Pineros and Nicole Redaschi and Susanne Reimering and Knut Reinert and Alejandro Reyes and Lorna Richardson and David L Robertson and Sepideh Sadegh and Joshua B Singer and Kristof Theys and Chris Upton and Marius Welzel and Lowri Williams and Manja Marz},

url = {http://evbc.uni-jena.de/tools/coronavirus-tools/},

doi = {10.1093/bib/bbaa232},

year  = {2020},

date = {2020-11-04},

urldate = {2020-11-04},

journal = {Brief Bioinform},

volume = {22},

number = {2},

pages = {642--663},

publisher = {Oxford University Press (OUP)},

abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories.},

keywords = {coronavirus, evolution, review, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Hoelzer:20,

title = {A decade of de novo transcriptome assembly: Are we there yet?},

author = {Martin Hölzer},

doi = {10.1111/1755-0998.13268},

year  = {2020},

date = {2020-10-08},

urldate = {2020-01-01},

journal = {Mol Ecol Resour},

volume = {21},

number = {1},

pages = {11-13},

publisher = {Wiley},

abstract = {A decade ago, de novo transcriptome assembly evolved as a versatile and powerful approach to make evolutionary assumptions, analyse gene expression, and annotate novel transcripts, in particular, for non-model organisms lacking an appropriate reference genome. Various tools have been developed to generate a transcriptome assembly, and even more computational methods depend on the results of these tools for further downstream analyses. In this issue of Molecular Ecology Resources, Freedman et al. (Mol Ecol Resourc 2020) present a comprehensive analysis of errors in de novo transcriptome assemblies across public data sets and different assembly methods. They focus on two implicit assumptions that are often violated: First, the assembly presents an unbiased view of the transcriptome. Second, the expression estimates derived from the assembly are reasonable, albeit noisy, approximations of the relative frequency of expressed transcripts. They show that appropriate filtering can reduce this bias but can also lead to the loss of a reasonable number of highly expressed transcripts. Thus, to partly alleviate the noise in expression estimates, they propose a new normalization method called length-rescaled CPM. Remarkably, the authors found considerable distortions at the nucleotide level, which leads to an underestimation of diversity in transcriptome assemblies. The study by Freedman et al. (Mol Ecol Resourc 2020) clearly shows that we have not yet reached “high-quality” in the field of transcriptome assembly. Above all, it helps researchers be aware of these problems and filter and interpret their transcriptome assembly data appropriately and with caution.},

keywords = {assembly, review, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Hufsky:20,

title = {Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research},

author = {Franziska Hufsky and Kevin Lamkiewicz and Alexandre Almeida and Abdel Aouacheria and Cecilia Arighi and Alex Bateman and Jan Baumbach and Niko Beerenwinkel and Christian Brandt and Marco Cacciabue and Sara Chuguransky and Oliver Drechsel and Robert D. Finn and Adrian Fritz and Stephan Fuchs and Georges Hattab and Anne-Christin Hauschild and Dominik Heider and Marie Hoffmann and Martin Hölzer and Stefan Hoops and Lars Kaderali and Ioanna Kalvari and Max Kleist and Rene Kmiecinski and Denise Kühnert and Gorka Lasso and Pieter Libin and Markus List and Hannah F. Löchel and Maria J. Martin and Roman Martin and Julian Matschinske and Alice C. McHardy and Pedro Mendes and Jaina Mistry and Vincent Navratil and Eric Nawrocki and Áine Niamh O'Toole and Nancy Palacios-Ontiveros and Anton I. Petrov and Guillermo Rangel-Piñeros and Nicole Redaschi and Susanne Reimering and Knut Reinert and Alejandro Reyes and Lorna Richardson and David L. Robertson and Sepideh Sadegh and Joshua B. Singer and Kristof Theys and Chris Upton and Marius Welzel and Lowri Williams and Manja Marz},

doi = {10.20944/preprints202005.0376.v1},

year  = {2020},

date = {2020-05-23},

urldate = {2020-05-23},

journal = {Preprints},

publisher = {MDPI AG},

abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding, and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are freely available online, either through web applications or public code repositories.

},

note = {Now published in Brief Bioinform: https://dx.doi.org/10.1093/bib/bbaa232},

keywords = {coronavirus, evolution, review, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Barth:20,

title = {Robustness during Aging—Molecular Biological and Physiological Aspects},

author = {Emanuel Barth and Patricia Sieber and Heiko Stark and Stefan Schuster},

doi = {10.3390/cells9081862},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Cells},

volume = {9},

number = {8},

pages = {1862},

publisher = {MDPI AG},

abstract = {Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.},

keywords = {aging, review},

pubstate = {published},

tppubtype = {article}

}

@article{Ibrahim:18a,

title = {A new era of virus bioinformatics},

author = {Bashar Ibrahim and Dino P McMahon and Franziska Hufsky and Martin Beer and Li Deng and Philippe Le Mercier and Massimo Palmarini and Volker Thiel and Manja Marz},

doi = {10.1016/j.virusres.2018.05.009},

year  = {2018},

date = {2018-05-08},

urldate = {2018-01-01},

journal = {Virus Res},

volume = {251},

pages = {86--90},

abstract = {Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of big data. Collaboration between virologists and bioinformaticians is necessary to improve existing analytical tools, cloud-based systems, computational resources, data sharing approaches, new diagnostic tools, and bioinformatic training. Here, we highlight current progress and discuss potential avenues for future developments in this promising era of virus bioinformatics. We end by presenting an overview of current technologies, and by outlining some of the major challenges and advantages that bioinformatics will bring to the field of virology.},

keywords = {review, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Hufsky:18,

title = {Virologists-Heroes need weapons},

author = {Franziska Hufsky and Bashar Ibrahim and Martin Beer and Li Deng and Philippe Le Mercier and Dino P McMahon and Massimo Palmarini and Volker Thiel and Manja Marz},

doi = {10.1371/journal.ppat.1006771},

year  = {2018},

date = {2018-02-08},

urldate = {2018-02-08},

journal = {PLoS Pathog},

volume = {14},

number = {2},

pages = {e1006771},

abstract = {Virologists. You might know a couple of them, but unless you are a virologist yourself, the probability that you have collaborated with one in the past is low. The community is relatively small, but they pack a heavy punch and are expected to play a leading role in the research into pathogens that lies ahead. You may ask why we think virologists are our future. Suffice it to say that it is not just because they have invented technologies that belong to the space age, including use of viruses as vehicles to shuttle genes into cells[1], organic nanoparticles with specific tools attached to their surfaces to get inside target cells[2], and using genetically modified viruses as therapies to fight against cancer[3]. Did you know that virologists currently only know of about 3,200 viral species but that more than 320,000 mammal-associated viruses[4] are thought to await discovery? Just think about the viruses hidden in the Arctic ice[5] or in the insects and other animals from once cut-off regions in the world, which now face ever-increasing human exposure[6]. But a heroic (as well as an apocalyptic) role for virologists may also be on the horizon, as the adoption of phage therapy may, in the future, be used to control harmful bacteria when antibiotics fail[7].},

keywords = {review, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Hoelzer:17,

title = {Software Dedicated to Virus Sequence Analysis },

author = {Martin Hölzer and Manja Marz},

doi = {10.1016/bs.aivir.2017.08.004},

year  = {2017},

date = {2017-09-28},

urldate = {2017-09-28},

journal = {Adv Virus Res},

volume = {99},

pages = {233--257},

abstract = {Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.},

keywords = {DNA / genomics, evolution, phylogenetics, review, RNA / transcriptomics, RNA structure, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Marz:14,

title = {Challenges in RNA virus bioinformatics},

author = {Manja Marz and Niko Beerenwinkel and Christian Drosten and Markus Fricke and Dmitrij Frishman and Ivo L Hofacker and Dieter Hoffmann and Martin Middendorf and Thomas Rattei and Peter F Stadler and Armin Töfer},

doi = {10.1093/bioinformatics/btu105},

year  = {2014},

date = {2014-03-03},

urldate = {2014-03-03},

journal = {Bioinformatics},

volume = {30},

number = {13},

pages = {1793--1799},

abstract = {Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands. The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses.},

keywords = {classification, evolution, review, RNA / transcriptomics, viruses},

pubstate = {published},

tppubtype = {article}

}