Michael T. Wolfinger

Michael T. Wolfinger
University of Vienna | UniWien · Research Group Bioinformatics and Computational Biology (BCB)

Dr. rer. nat.

About

142
Publications
13,196
Reads
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1,521
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Introduction
I am a theoretical chemist in structural and computational biology of ribonucleic acids (RNA). My research agenda comprises algorithmic RNA bioinformatics and computational genomics, with current research projects in RNA structure prediction in 2D and 3D, RNA-protein interactions, co-transcriptional RNA folding dynamics for synthetic biology applications, and microbial genotype-phenotype associations. I am specifically interested in theoretical aspects of virology and structured RNAs in viruses
Additional affiliations
January 2012 - present
University of Vienna
Position
  • Researcher
September 2005 - June 2019
FH Campus Wien
Position
  • Lecturer
Education
October 1995 - October 2004
University of Vienna
Field of study
  • Chemistry

Publications

Publications (142)
Article
Full-text available
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 UTR of tick-borne, insect-specific and no-known-vect...
Article
Full-text available
Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that play...
Chapter
Recent experimental evidence revealed a thorough understanding of the involvement of functional RNA elements in the 3′ untranslated regions (UTRs) of flaviviruses with virus tropism. Comparative genomics and thermodynamic modeling allow for the prediction and functional characterization of homologous structures in phylogenetically related viruses....
Article
Full-text available
The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and...
Article
Full-text available
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne encephalitis, an infectious disease of the central nervous system that is often associated with severe sequelae in humans. While TBEV is typically classified into three subtypes, recent evidence suggests a more varied range of TBEV subtypes and lineages that differ substan...
Presentation
Presentation given at the 7th 'Computational Approaches to RNA Structure and Function' conference, Benasque, Spain on 12 August 2022
Article
Full-text available
The Musashi (MSI) family of RNA-binding proteins, comprising the two homologs Musashi-1 (MSI1) and Musashi-2 (MSI2), typically regulates translation and is involved in cell proliferation and tumorigenesis. MSI proteins contain two ribonucleoprotein-like RNA-binding domains, RBD1 and RBD2, that bind single-stranded RNA motifs with a central UAG trin...
Article
Full-text available
Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well established biophysics based methods exist. The accuracy of these classical methods is limited due to lack of experimental paramete...
Article
Full-text available
In Pseudomonas aeruginosa, the RNA chaperone Hfq and the catabolite repression protein Crc act in concert to regulate numerous genes during carbon catabolite repression (CCR). After alleviation of CCR, the RNA CrcZ sequesters Hfq/Crc, which leads to a rewiring of gene expression to ensure the consumption of less preferred carbon and nitrogen source...
Article
Full-text available
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on th...
Preprint
Full-text available
Many flaviviruses such as Dengue and West Nile virus undergo essential long-range interactions of their 5' and 3' terminal regions (TRs), mediated by a conserved complementary cyclization sequence. However, we lack insights into such long-range interactions for the Japanese Encephalitis virus (JEV). Here, we utilized an extensive, multi-faceted app...
Preprint
Full-text available
Tick-borne encephalitis virus (TBEV) is the etiological agent of tick-borne encephalitis, an infectious disease of the central nervous system that is often associated with severe sequelae in humans. While TBEV is typically classified into three subtypes, recent evidence suggests a more varied range of TBEV subtypes and lineages that differ substant...
Preprint
Full-text available
Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well established biophysics based methods exist. The accuracy of these classical methods is limited due to lack of experimental paramete...
Preprint
Full-text available
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on th...
Presentation
Full-text available
The ability of RNA to fold into intricate structures in 2D and 3D is exploited by viruses to mediate tropism. Therefore, a deep understanding of RNA structure formation is crucial for the emerging field of virus bioinformatics. The ViennaRNA Package comes with a rich portfolio of tools to analyze RNA folding and the traits that are associated with...
Data
Changes in v0.1.2: Add 3'UTR elements found in different subtypes of tick-borne encephalitis virus
Data
We provide a custom Nextstrain build to explore the molecular epidemiology of Tick-borne encephalitis virus, available at https://nextstrain.org/groups/ViennaRNA/TBEVnext/v1.0
Preprint
Full-text available
The Internal Ribosome Entry Site (IRES) RNA of Bovine viral diarrhea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and i...
Article
Full-text available
Pseudomonas aeruginosa ( Pae ) is notorious for its high-level resistance toward clinically used antibiotics. In fact, Pae has rendered most antimicrobials ineffective, leaving polymyxins and aminoglycosides as last resort antibiotics. Although several resistance mechanisms of Pae are known toward these drugs, a profounder knowledge of hitherto uni...
Article
Full-text available
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mp...
Article
Full-text available
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages h...
Preprint
Full-text available
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages h...
Preprint
Full-text available
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages h...
Preprint
Full-text available
Recent experimental evidence revealed a thorough understanding of the involvement of functional RNA elements in the 3’ untranslated regions (UTRs) of flaviviruses with virus tropism. Comparative genomics and thermodynamic modeling allow for the prediction and functional characterization of homologous structures in phylogenetically related viruses....
Chapter
Full-text available
RNA molecules may be subject to independent selection pressures on sequence and structure. This can, in principle, lead to the preservation of structural features without maintaining the exact position on the conserved sequence. Consequently, structurally analogous base pairs are no longer formed by homologous bases, and homologous nucleotides do n...
Preprint
Full-text available
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa is limited. Herein, we report that a novel fla...
Presentation
Full-text available
Chikungunya virus (CHIKV) is an emerging alphavirus, which causes millions of human infections every year. Being the etiological agent of Chikungunya fever, a febrile disease associated with severe arthralgia, CHIKV has probably been circulating in sylvatic transmission cycles for many centuries. Outbreaks have been reported in Africa and Asia sinc...
Article
Full-text available
To monitor the arthropod-borne virus transmission in mosquitoes, we have attempted both to detect and isolate viruses from 3304 wild-caught female mosquitoes in the Livingstone (Southern Province) and Mongu (Western Province) regions in Zambia in 2017. A pan-flavivirus RT-PCR assay was performed to identify flavivirus genomes in total RNA extracted...
Preprint
Full-text available
Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samp...
Article
Full-text available
Carbapenems are often the antibiotics of choice to combat life threatening infections caused by the opportunistic human pathogen Pseudomonas aeruginosa. The outer membrane porins OprD and OpdP serve as entry ports for carbapenems. Here, we report that the RNA chaperone Hfq governs post-transcriptional regulation of the oprD and opdP genes in a dist...
Presentation
Full-text available
RNA viruses cause millions of infections in humans and animals every year, thereby challenging health systems and economies globally. Large-scale outbreaks of emerging and re-emerging agents, such as Dengue, Zika, Chikungunya, and Ebola virus in human and African swine fever virus in animals have been reported over the last years. These outbreaks c...
Data
In silico prediction of evolutionarily conserved RNA secondary structures in the upstream 500 nucleotides of Wuhan seafood market pneumonia virus (Wuhan-nCoV, GenBank MN908947.3, top) and severe acute respiratory syndrome virus (SARS, RefSeq NC_004718.3, bottom). The genomic regions shown here comprise the 5'UTR and the amino-terminal region of the...
Presentation
Full-text available
Arthropod-borne RNA viruses (arboviruses) represent a global health threat, causing millions of human and animal infections every year. Recent outbreaks of emerging and re-emerging viruses have revealed new clinical manifestations, e.g., the accumulation of congenital microcephaly cases during the Zika virus epidemic in the Americas 2015-2016. Whil...
Article
Full-text available
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the curr...
Conference Paper
Full-text available
RNA molecules may experience independent selection pressures on their sequence and (secondary) structure. Structural features then may be preserved without maintaining their exact position along the sequence. In such cases, corresponding base pairs are no longer formed by homologous bases, leading to the incongruent evolutionary conservation of seq...
Preprint
Full-text available
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the curr...
Preprint
Full-text available
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the curr...
Presentation
Full-text available
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the Togaviridae family, has recently emerged in the Americas from two originating continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent re-emergence patterns, and the curre...
Preprint
Full-text available
RNA molecules may experience independent selection pressures on their sequence and (secondary) structure. Structural features then may be preserved without maintaining their exact position along the sequence. In such cases, corresponding base pairs are no longer formed by homologous bases, leading to the incongruent evolutionary conservation of seq...
Article
Full-text available
Zika virus (ZIKV) belongs to a class of neurotropic viruses that have the ability to cause congenital infection, which can result in microcephaly or fetal demise. Recently, the RNA-binding protein Musashi-1 (Msi1), which mediates the maintenance and self-renewal of stem cells and acts as a translational regulator, has been associated with promoting...
Preprint
Full-text available
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vect...
Preprint
Full-text available
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vect...
Article
Full-text available
Translation factor a/eIF5A is highly conserved in Eukarya and Archaea. The eukaryal eIF5A protein is required for transit of ribosomes across consecutive proline codons, whereas the function of the archaeal orthologue remains unknown. Here, we provide a first hint for an involvement of Sulfolobus solfataricus (Sso) aIF5A in translation. CRISPR-medi...
Article
Full-text available
Arboviruses are a group of viruses transmitted by arthropods, mostly ticks, and mosquitoes. Among the members of this group are the families Togaviridae and Flaviviridae, (+)ssRNA viruses, such as Chikungunya, Dengue, and Zika. Multiple of these viruses have demonstrated their ability to cause neuropathology in humans. In Zika, a protein binding mo...
Poster
Full-text available
Purpose: Arboviruses are a group of viruses transmitted by arthropods, mostly ticks, and mosquitoes. Among the members of this group are the families Togaviridae and Flaviviridae, (+)ssRNA viruses, such as Chikungunya, Dengue, and Zika. Multiple of these viruses have demonstrated their ability to cause neuropathology in humans. In Zika, a protein b...
Article
Full-text available
The opportunistic human pathogen Pseudomonas aeruginosa is responsible for ∼ 10% of hospital-acquired infections worldwide. It is notorious for its high level resistance toward many antibiotics, and the number of multi-drug resistant clinical isolates is steadily increasing. A better understanding of the molecular mechanisms underlying drug resista...
Preprint
Full-text available
Zika virus (ZIKV) belongs to a class of neurotropic viruses that have the ability to cause congenital infection, which can result in microcephaly or fetal demise. Recently, the RNA-binding protein Musashi-1 (Msi1), which mediates the maintenance and self-renewal of stem cells and acts as a translational regulator, has been associated with promoting...
Article
Full-text available
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequen...
Presentation
Full-text available
Flaviviruses represent a global health threat and are responsible for millions of infections in humans every year. During the 2015-2017 outbreak of Zika virus (ZIKV) in the Americas accumulation of congenital microcephaly cases was observed, which has been associated with ZIKV infection. However, the underlying biological mechanisms remain elusive....
Poster
Full-text available
Emerging and re-emerging arthropod-borne viruses such as Japanese encephalitis (JEV), Dengue (DENV), Yellow fever (YFV), and Chikungunya (CHIKV) viruses are a growing global health threat. Zika virus (ZIKV) is a neurotropic flavivirus (FV) that can cause congenital infection, which can result in microcephaly and fetal demise. Recently, the translat...
Preprint
Full-text available
The telomerase RNA in yeasts is large, usually > 1, 000 nt, and contains functional elements 1 that have been extensively studied experimentally in several disparate species. Nevertheless, they 2 are very difficult to detect by homology-based methods and so far have escaped annotation in the 3 majority of the genomes of Saccharomycotina. This is a...
Preprint
Full-text available
The telomerase RNA in yeasts is large, usually >1,000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a conseque...
Article
Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge o...
Article
Full-text available
This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.,e., knowing its Kd and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylli...