Kevin Lamkiewicz

E-Mail: kevin.lamkiewicz*
Room: 08S06
Phone: +49-3641-9-46484

*@uni-jena.de

Publications

2021

I. Kalvari, E. P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S. R. Eddy, R. Finn, A. Bateman, and A. I. Petrov, “Rfam 14: expanded coverage of metagenomic, viral and microRNA families,” Nucleic Acids Res, vol. 49, iss. D1, p. D192–D200, 2021.
[Bibtex]

@Article{Kalvari:21,
author = {Ioanna Kalvari and Eric P Nawrocki and Nancy Ontiveros-Palacios and Joanna Argasinska and Kevin Lamkiewicz and Manja Marz and Sam Griffiths-Jones and Claire Toffano-Nioche and Daniel Gautheret and Zasha Weinberg and Elena Rivas and Sean R Eddy and Robert~D Finn and Alex Bateman and Anton I Petrov},
journal = {{Nucleic Acids Res}},
title = {Rfam 14: expanded coverage of metagenomic, viral and {microRNA} families},
year = {2021},
number = {D1},
pages = {D192--D200},
volume = {49},
doi = {10.1093/nar/gkaa1047},
publisher = {Oxford University Press ({OUP})},
}

2020

A. Jordan-Paiz, M. Nevot, K. Lamkiewicz, M. Lataretu, S. Franco, M. Marz, and M. A. Martinez, “HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer,” J Virol, 2020.
[Bibtex]

@Article{Jordan-Paiz:20,
author = {Ana Jordan-Paiz and Maria Nevot and Kevin Lamkiewicz and Marie Lataretu and Sandra Franco and Manja Marz and Miguel Angel Martinez},
title = {{HIV}-1 lethality and loss of {E}nv protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer},
journal = {{J Virol}},
year = {2020},
doi = {10.1128/jvi.01108-20},
publisher = {American Society for Microbiology},
}

F. Hufsky, N. Beerenwinkel, I. M. Meyer, S. Roux, G. M. Cook, C. M. Kinsella, K. Lamkiewicz, M. Marquet, D. F. Nieuwenhuijse, I. Olendraite, S. Paraskevopoulou, F. Young, R. Dijkman, B. Ibrahim, J. Kelly, P. L. Mercier, M. Marz, A. Ramette, and V. Thiel, “The international virus bioinformatics meeting 2020,” Viruses, vol. 12, iss. 12, p. 1398, 2020.
[Bibtex]

@Article{Hufsky:20b,
author = {Franziska Hufsky and Niko Beerenwinkel and Irmtraud M. Meyer and Simon Roux and Georgia May Cook and Cormac M. Kinsella and Kevin Lamkiewicz and Mike Marquet and David F. Nieuwenhuijse and Ingrida Olendraite and Sofia Paraskevopoulou and Francesca Young and Ronald Dijkman and Bashar Ibrahim and Jenna Kelly and Philippe Le Mercier and Manja Marz and Alban Ramette and Volker Thiel},
title = {The International Virus Bioinformatics Meeting 2020},
journal = {Viruses},
year = {2020},
volume = {12},
number = {12},
pages = {1398},
doi = {10.3390/v12121398},
publisher = {{MDPI} {AG}},
}

F. Hufsky, K. Lamkiewicz, A. Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C. Brandt, M. Cacciabue, S. Chuguransky, O. Drechsel, R. D. Finn, A. Fritz, S. Fuchs, G. Hattab, A. Hauschild, D. Heider, M. Hoffmann, M. Hölzer, S. Hoops, L. Kaderali, I. Kalvari, M. von Kleist, R. Kmiecinski, D. Kühnert, G. Lasso, P. Libin, M. List, H. F. Löchel, M. J. Martin, R. Martin, J. Matschinske, A. C. McHardy, P. Mendes, J. Mistry, V. Navratil, E. P. Nawrocki, Á. N. O’Toole, N. Ontiveros-Palacios, A. I. Petrov, G. Rangel-Pineros, N. Redaschi, S. Reimering, K. Reinert, A. Reyes, L. Richardson, D. L. Robertson, S. Sadegh, J. B. Singer, K. Theys, C. Upton, M. Welzel, L. Williams, and M. Marz, “Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research,” Brief Bioinform, 2020.
[Bibtex]

@Article{Hufsky:20a,
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 von Kleist and Ren{\'{o}} 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 {\'{A}}ine 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},
title = {Computational strategies to combat {COVID}-19: useful tools to accelerate {SARS}-{CoV}-2 and coronavirus research},
journal = {{Brief Bioinform}},
year = {2020},
doi = {10.1093/bib/bbaa232},
publisher = {Oxford University Press ({OUP})},
}

M. Hölzer, L. Barf, K. Lamkiewicz, F. Vorimore, M. Lataretu, A. Favaroni, C. Schnee, K. Laroucau, M. Marz, and K. Sachse, “Comparative genome analysis of 33 chlamydia strains reveals characteristic features of chlamydia psittaci and closely related species,” Pathogens, vol. 9, iss. 11, p. 899, 2020.
[Bibtex]

@Article{Hölzer:20,
author = {Martin Hölzer and Lisa-Marie Barf and Kevin Lamkiewicz and Fabien Vorimore and Marie Lataretu and Alison Favaroni and Christiane Schnee and Karine Laroucau and Manja Marz and Konrad Sachse},
title = {Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species},
journal = {Pathogens},
year = {2020},
volume = {9},
number = {11},
pages = {899},
doi = {10.3390/pathogens9110899},
publisher = {{MDPI} {AG}},
}

N. Pappas, S. Roux, M. Hölzer, K. Lamkiewicz, F. Mock, M. Marz, and B. E. Dutilh, “Virus bioinformatics,” in Reference module in life sciences, Elsevier, 2020.
[Bibtex]

@incollection{Pappas:20,
title = {Virus Bioinformatics},
booktitle = {Reference Module in Life Sciences},
publisher = {Elsevier},
year = {2020},
isbn = {978-0-12-809633-8},
doi = {https://doi.org/10.1016/B978-0-12-814515-9.00034-5},
author = {Nikolaos Pappas and Simon Roux and Martin H\"olzer and Kevin Lamkiewicz and Florian Mock and Manja Marz and Bas E. Dutilh},
}

F. Hufsky, K. Lamkiewicz, A. Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C. Brandt, M. Cacciabue, S. Chuguransky, O. Drechsel, R. D. Finn, A. Fritz, S. Fuchs, G. Hattab, A. Hauschild, D. Heider, M. Hoffmann, M. Hölzer, S. Hoops, L. Kaderali, I. Kalvari, M. von Kleist, R. Kmiecinski, D. Kühnert, G. Lasso, P. Libin, M. List, H. F. Löchel, M. J. Martin, R. Martin, J. Matschinske, A. C. McHardy, P. Mendes, J. Mistry, V. Navratil, E. Nawrocki, Á. N. O’Toole, N. Palacios-Ontiveros, A. I. Petrov, G. Rangel-Piñeros, N. Redaschi, S. Reimering, K. Reinert, A. Reyes, L. Richardson, D. L. Robertson, S. Sadegh, J. B. Singer, K. Theys, C. Upton, M. Welzel, L. Williams, and M. Marz, “Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research,” Preprints, 2020.
[Bibtex]

@Article{Hufsky:20,
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 von 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 {\'{A}}ine Niamh O'Toole and Nancy Palacios-Ontiveros and Anton I. Petrov and Guillermo Rangel-Pi{\~{n}}eros 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},
title = {Computational Strategies to Combat {COVID}-19: Useful Tools to Accelerate {SARS}-{CoV}-2 and Coronavirus Research},
journal = {Preprints},
year = {2020},
doi = {10.20944/preprints202005.0376.v1},
publisher = {{MDPI} {AG}},
}

N. F. Mostajo, M. Lataretu, S. Krautwurst, F. Mock, D. Desirò, K. Lamkiewicz, M. Collatz, A. Schoen, F. Weber, M. Marz, and M. Hölzer, “A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes,” NAR Genomics Bioinf, vol. 2, iss. 1, p. lqz006, 2020.
[Bibtex]

@Article{Mostajo:20,
author = {Mostajo, Nelly F and Lataretu, Marie and Krautwurst, Sebastian and Mock, Florian and Desirò, Daniel and Lamkiewicz, Kevin and Collatz, Maximilian and Schoen, Andreas and Weber, Friedemann and Marz, Manja and H\"{o}lzer, Martin},
title = {A comprehensive annotation and differential expression analysis of short and long non-coding {R}{N}{A}s in 16 bat genomes},
journal = {{NAR Genomics Bioinf}},
year = {2020},
volume = {2},
number = {1},
pages = {lqz006},
doi = {10.1093/nargab/lqz006},
eprint = {http://oup.prod.sis.lan/nargab/article-pdf/2/1/lqz006/30076191/lqz006.pdf},
url = {https://doi.org/10.1093/nargab/lqz006},
}

2019

A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, “Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.,” Genome Res, p. 483693, 2019.
[Bibtex]

@Article{Viehweger:19a,
author = {Adrian Viehweger and Sebastian Krautwurst and Kevin Lamkiewicz and Ramakanth Madhugiri and John Ziebuhr and Martin H\"{o}lzer and Manja Marz},
title = {Direct {RNA} nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.},
journal = {{Genome Res}},
year = {2019},
pages = {483693},
doi = {10.1101/gr.247064.118},
publisher = {Cold Spring Harbor Laboratory},
}

F. Hufsky, B. Ibrahim, S. Modha, M. R. J. Clokie, S. Deinhardt-Emmer, B. E. Dutilh, S. Lycett, P. Simmonds, V. Thiel, A. Abroi, E. M. Adriaenssens, M. Escalera-Zamudio, J. N. Kelly, K. Lamkiewicz, L. Lu, J. Susat, T. Sicheritz, D. L. Robertson, and M. Marz, “The third annual meeting of the European Virus Bioinformatics Center,” Viruses, vol. 11, iss. 5, p. 420, 2019.
[Bibtex]

@Article{Hufsky:19,
author = {Franziska Hufsky and Bashar Ibrahim and Sejal Modha and Martha R. J. Clokie and Stefanie Deinhardt-Emmer and Bas E. Dutilh and Samantha Lycett and Peter Simmonds and Volker Thiel and Aare Abroi and Evelien M. Adriaenssens and Marina Escalera-Zamudio and Jenna Nicole Kelly and Kevin Lamkiewicz and Lu Lu and Julian Susat and Thomas Sicheritz and David L. Robertson and Manja Marz},
title = {The Third Annual Meeting of the {E}uropean {V}irus {B}ioinformatics {C}enter},
journal = {Viruses},
year = {2019},
volume = {11},
number = {5},
pages = {420},
doi = {10.3390/v11050420},
publisher = {{MDPI} {AG}},
}

S. Peter, M. Hölzer, K. Lamkiewicz, P. S. di Fenizio, H. A. Hwaeer, M. Marz, S. Schuster, P. Dittrich, and B. Ibrahim, “Structure and hierarchy of influenza virus models revealed by reaction network analysis,” Viruses, vol. 11, iss. 5, p. 449, 2019.
[Bibtex]

@Article{Peter:19,
author = {Stephan Peter and Martin Hölzer and Kevin Lamkiewicz and Pietro Speroni di Fenizio and Hassan Al Hwaeer and Manja Marz and Stefan Schuster and Peter Dittrich and Bashar Ibrahim},
title = {Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis},
journal = {Viruses},
year = {2019},
volume = {11},
number = {5},
pages = {449},
doi = {10.3390/v11050449},
publisher = {{MDPI} {AG}},
}

A. Dukhovny, K. Lamkiewicz, Q. Chen, M. Fricke, N. Jabrane-Ferrat, M. Marz, J. U. Jung, and E. H. Sklan, “A CRISPR activation screen identifies genes protecting from Zika virus infection,” J Virol, 2019.
[Bibtex]

@Article{Dukhovny:19,
author = {Dukhovny, Anna and Lamkiewicz, Kevin and Chen, Qian and Fricke, Markus and Jabrane-Ferrat, Nabila and Marz, Manja and Jung, Jae U. and Sklan, Ella H.},
title = {A {CRISPR} activation screen identifies genes protecting from {Z}ika virus infection},
journal = {{J Virol}},
year = {2019},
abstract = {Zika virus (ZIKV) is an arthropod borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barr{\'e} syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection we used a genome scale CRISPR activation screen. Our highly ranking hits included a short list of interferon stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted IFNL2 and IFI6 as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing sgRNAs for both of these genes displayed lower levels of cell death compared to controls. Furthermore, the identified genes were significantly induced in ZIKV infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiates CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barr{\'e} syndrome, neuropathy and myelitis. Vertical transmission of ZIKV can cause fetus demise, still birth or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.},
doi = {10.1128/JVI.00211-19},
elocation-id = {JVI.00211-19},
eprint = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19.full.pdf},
publisher = {American Society for Microbiology Journals},
url = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19},
}

2018

R. Madhugiri, N. Karl, D. Petersen, K. Lamkiewicz, M. Fricke, U. Wend, R. Scheuer, M. Marz, and J. Ziebuhr, “Structural and functional conservation of cis-acting RNA elements in coronavirus 5′-terminal genome regions,” Virology, vol. 517, p. 44–55, 2018.
[Bibtex]

@Article{Madhugiri:18,
author = {Madhugiri, Ramakanth and Karl, Nadja and Petersen, Daniel and Lamkiewicz, Kevin and Fricke, Markus and Wend, Ulrike and Scheuer, Robina and Marz, Manja and Ziebuhr, John},
title = {Structural and functional conservation of cis-acting {RNA} elements in coronavirus 5'-terminal genome regions},
journal = {{Virology}},
year = {2018},
volume = {517},
pages = {44--55},
abstract = {Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.},
doi = {10.1016/j.virol.2017.11.025},
keywords = {Base Sequence; Cell Line; Coronavirus 229E, Human, genetics; Coronavirus NL63, Human, genetics; Genome, Viral; Humans; Nucleic Acid Conformation; RNA, Viral, chemistry, genetics; Regulatory Sequences, Nucleic Acid, physiology; Virus Replication, physiology; Coronavirus; Coronavirus phylogeny; RNA structure; Replication; Stem-loop; cis-acting RNA element},
pmid = {29223446},
}

K. Lamkiewicz, E. Barth, M. Marz, and B. Ibrahim, “Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis,” bioRxiv, p. 417782, 2018.
[Bibtex]
```
@Article{Lamkiewicz:18,
author = {Kevin Lamkiewicz and Emanuel Barth and Manja Marz and Bashar Ibrahim},
title = {Identification of potential {microRNAs} associated with {H}erpesvirus family based on bioinformatic analysis},
journal = {{bioRxiv}},
year = {2018},
pages = {417782},
doi = {10.1101/417782},
publisher = {Cold Spring Harbor Laboratory},
}
```

Conferences

2020 — 4th International Virus Bioinformatics Meeting in Bern, Switzerland
2020 — 35th TBI Winterseminar in Bled, Slovenia
2019 — 17th Herbstseminar der Bioinformatik in Doubice, Czech Republic
2019 — 3rd Annual Meeting of the European Virus Bioinformatics Center in Glasgow, Scotland
2019 — 28th Annual Meeting of the Society for Virology in Düsseldorf, Germany
2019 — 34th TBI Winterseminar in Bled, Slovenia
2018 — 16th Herbstseminar der Bioinformatik in Doubice, Czech Republic
2018 — German Conference on Bioinformatics 2018 in Vienna, Austria
2018 — Mittelerde-Meeting – 3rd Central German Meeting on Bioinformatics in Mittweida, Germany
2018 — 2nd Annual Meeting of the European Virus Bioinformatics Center in Utrecht, Netherlands
2018 — 28th Annual Meeting of the Society for Virology in Würzburg, Germany
2018 — 33rd TBI Winterseminar in Bled, Slovenia
2017 — 15th Herbstseminar der Bioinformatik in Doubice, Czech
2017 — German Conference on Bioinformatics 2017 in Tübingen, Germany
2017 — Mittelerde-Meeting – 2nd Central German Meeting on Bioinformatics in Leipzig, Germany
2017 — HACKEN – Stay Young or Die Trying!, Hackathon in Jena, Germany
2017 — 1st Annual Meeting of the European Virus Bioinformatics Center in Jena, Germany
2017 — 27th Annual Meeting of the Society for Virology in Marburg, Germany
2017 — 32nd TBI Winterseminar in Bled, Slovenia
2016 — International Symposium on Bioinformatics Research and Applications in Minsk, Belarus
2015 — Recomb-CG in Frankfurt, Germany

Members » Kevin Lamkiewicz

2021

2020

2019

2018