Publications

81 entries « 1 of 2 »

2018

Bashar Ibrahim, Dino P. McMahon, Franziska Hufsky, Martin Beer, Li Deng, Philippe Le Mercier, Massimo Palmarini, Volker Thiel, Manja Marz

A new era of virus bioinformatics (Journal Article)

Virus Research, 251 , pp. 86-90, 2018.

(Abstract | Links | BibTeX)

Ramakanth Madhugiri, Nadja Karl, Daniel Petersen, Kevin Lamkiewicz, Markus Fricke, Ulrike Wend , Robina Scheuer, Manja Marz, John Ziebuhr

Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions (Journal Article)

Virology, 2018.

(Abstract | Links | BibTeX)

Steinbach D, Hölzer M, Marz M, Gajda M, Von Rundstedt FC, Grimm MO

Analysis of molecular mechanism of progression of non-muscle- invasive bladder cancer (NMIBC) by genome-wide exome and UTR mutation analysis (Journal Article)

Eur Urol Suppl., 17 (2), pp. e1523, 2018.

(Links | BibTeX)

Franziska Hufsky, Bashar Ibrahim, Martin Beer, Li Deng, Philippe Le Mercier, Dino P. McMahon, Massimo Palmarini, Volker Thiel, Manja Marz

Virologists—Heroes need weapons (Journal Article)

PLoS Pathog, 14 (2), pp. e1006771, 2018.

(Links | BibTeX)

Falk Hillmann, Gillian Forbes, Silvia Novohradská, Iuliia Ferling, Konstantin Riege, Marco Groth, Martin Westermann, Manja Marz, Thomas Spaller, Thomas Winckler, Pauline Schaap, Gernot Glöckner

Multiple roots of fruiting body formation in Amoebozoa (Journal Article)

Genome Biology and Evolution, pp. evy011, 2018.

(Abstract | Links | BibTeX)

Laura Graf, Alexej Dick, Franziska Sendker, Emanuel Barth, Manja Marz, Oliver Daumke, Georg Kochs

Effects of allelic variations in the human Myxovirus resistance protein A on its antiviral activity (Journal Article)

Journal of Biological Chemistry, 2018.

(Abstract | Links | BibTeX)

Fricke, Markus, Gerst, Ruman, Ibrahim, Bashar, Niepmann, Michael, Marz, Manja

Global importance of RNA secondary structures in protein coding sequences (Journal Article)

Bioinformatics, 2018, (Epub ahead of print).

(BibTeX)

Ibrahim, Bashar, Arkhipova, Ksenia, Andeweg, Arno C, Posada-C'espedes, Susana, Enault, Franccois, Gruber, Arthur, Koonin, Eugene V, Kupczok, Anne, Lemey, Philippe, McHardy, Alice C, others

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. (Journal Article)

Viruses, 10 (5), pp. 256, 2018.

(Abstract | Links | BibTeX)

2017

Martin Hölzer, Manja Marz

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” (Book Chapter)

Academic Press, 2017, ISSN: 0065-3527.

(Abstract | Links | BibTeX)

Mario Baumgart, Emanuel Barth, Aurora Savino, Marco Groth, Philipp Koch, Andreas Petzold, Ivan Arisi, Matthias Platzer, Manja Marz, Alessandro Cellerino

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri (Journal Article)

BMC Genomics, 18 (693), 2017.

(Abstract | Links | BibTeX)

Möbius P, Nordsiek G, Hölzer M, Jarek M, Marz M, Köhler H

Complete Genome sequence of JII-1961, a bovine Mycobacterium avium subsp. paratuberculosis field isolate from Germany (Journal Article)

Genome Announcements, 2017.

(Abstract | Links | BibTeX)

Chaiwangyen W, Gutiérrez-Samudio RN, Markert UR, Marz M, Morales-Prieto DM, Ospina-Prieto S

KL 5 Trophoblast-immune cell communication via microRNA transported in extracellular vesicles (Journal Article)

Pregnancy Hypertension: An International Journal of Women's Cardiovascular Health, 9 (5), 2017.

(Abstract | Links | BibTeX)

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. (Journal Article)

Journal of Biotechnology, 2017.

(Abstract | Links | BibTeX)

Fuchs J, Hölzer M, Schilling M, Patzina C, Schoen A, Hoenen T, Zimmer G, Marz M, Weber F, Müller M, Kochs G

Evolution and antiviral specificity of interferon-induced Mx proteins of bats against Ebola-, Influenza-, and other RNA viruses. (Journal Article)

Journal of Virology, pp. JVI.00361-17, 2017.

(Abstract | Links | BibTeX)

Möbius P, Liebler-Tenorio E, Hölzer M, Köhler H

Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculosis and presence of intestinal lesions characteristic of paratuberculosis (Journal Article)

Veterinary Microbiology, 201 , pp. 188-194, 2017.

(Abstract | Links | BibTeX)

Riege K, Hölzer M, Klassert T E., Barth E, Bräuer J, Collatz M, Hufsky F, Mostajo N, Stock M, Vogel B, Slevogt H, Marz M

Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D (Journal Article)

Scientific Reports (Nature PG), 7 (40598 ), 2017.

(Abstract | Links | BibTeX)

Klassert T E., Bräuer J, Hölzer M, Stock M, Riege K, Zubiria-Barrera C, Müller M M., Rummler S, Skerka C, Marz M, Slevogt H

Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection (Journal Article)

Scientific Reports (Nature PG), 7 (40599), 2017.

(Abstract | Links | BibTeX)

2016

Starke R, Müller M, Gaspar M, Marz M, Küsel K, Totsche K U, von Bergen M, Jehmlich N

Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer (Journal Article)

Journal of Proteomics, 152 , pp. 153–160, 2016.

(Abstract | Links | BibTeX)

Hölzer M, Krähling V, Amman F, Barth E, Bernhart S H, Carmelo V A O, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn L M, Fricke M, Gebauer J, Gruber A J, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun A H, Saunders S J, Seemann S E, Tanzer A, Vogel B, Wehner S, Wolfinger M T, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler P F, Becker S, Marz M

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (Journal Article)

Scientific Reports (Nature PG), 6 (34589 ), 2016.

(Abstract | Links | BibTeX)

Gerresheim G K, Dünnes N, Nieder-Röhrmann A, Shalamova L A, Fricke M, Hofacker I, Höner zu Siederdissen C, Marz M, Niepmann M

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3′ untranslated region: function in replication and influence of RNA secondary structure (Journal Article)

Cellular and Molecular Life Sciences, pp. 1–14, 2016.

(Links | BibTeX)

Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S

Finding approximate gene clusters with Gecko3 (Journal Article)

Nucleic Acids Res, 2016, (Advanced access, doi: 10.1093/nar/gkw843).

(Abstract | Links | BibTeX)

Hölzer M, Laroucau K, Creasy HH, Ott S, Vorimore F, Bavoil PM, Marz M, Sachse K

Whole-genome sequence of Chlamydia gallinacea type strain 08-1274/3 (Journal Article)

Genome Announcements, 2016.

(Abstract | Links | BibTeX)

Fricke M, Marz M

Prediction of conserved long-range RNA-RNA interactions in full viral genomes (Journal Article)

Bioinformatics (Oxford, England), 2016, ISSN: 1367-4811.

(Abstract | Links | BibTeX)

Barth E, Hübler R, Baniahmad A, Marz M

The Evolution of COP9 signalosome in unicellular and multicellular organisms (Journal Article)

Genome Biol Evol, 2016.

(Abstract | Links | BibTeX)

Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh B E, Ghaffaari A, Kersey P, Kloosterman W, Makinen V, Novak A, Paten B, Porubsky D, RIVALS E, Alkan C, Baaijens J, de B P I W, Boeva V, Chiaromonte F, Chikhi R, Ciccarelli F D, Cijvat R, Datema E, Van D C M, Eichler E E, Ernst C, Eskin E, Garrison E, El-Kebir M, Klau G W, Korbel J O, Lameijer E, Langmead B, Martin M, Medvedev P, Mu J C, Neerincx P, Ouwens K, Peterlongo P, Nadia P, Rahmann S, Raphael B, Reinert K, de R D, de R J, Schlesner M, Schulz-Trieglaff O, Sanders A, Sheikhizadeh S, Shneider C, Smit S, Valenzuela D, Wang J, Wessels L, Zhang Y, Guryev V, Vandin F, Ye K, Schoenhuth A

Computational Pan-Genomics: Status, Promises and Challenges (Journal Article)

bioRxiv, 2016.

(Abstract | Links | BibTeX)

Madhugiri R, Fricke M, Marz M, Ziebuhr J

Coronavirus cis-Acting RNA Elements (Book Chapter)

Advances in Virus Research, 95 , pp. 2-227, Elsevier, 2016, ISBN: 978-0-12-804820-7 .

(Abstract | Links | BibTeX)

Starke, R, Müller, M, Gaspar, M, Marz, M, Küsel, K, Totsche, K U, von Bergen, M, Jehmlich, N

Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer (Journal Article)

Journal of Proteomics, 2016.

(Links | BibTeX)

2015

Möbius P, Hölzer M, Felder M, Nordsiek G, Groth M, Köhler H, Reichwald K, Platzer M, Marz M

Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany (Journal Article)

Genome Biol Evol, 2015.

(Abstract | Links | BibTeX)

Sahyoun A H, Hölzer M, Jühling F, Höner zu Siederdissen C, Al-Arab M, Tout K, Marz M, Middendorf M, Stadler P F, Bernt M

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes (Journal Article)

Nucleic Acids Res, 43 (16), pp. 8044-8056, 2015.

(Abstract | Links | BibTeX)

Althoefer I, Kaitschick S, Marz M

Computer-aided Go on high-dan level (Proceeding)

2015.

(BibTeX)

Fricke M, Dünnes N, Zayas M, Bartenschlager R, Niepmann M, Marz M

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses (Journal Article)

RNA, 21 (7), pp. 1219-1232, 2015.

(Abstract | Links | BibTeX)

Marz M, Ferracin M, Klein C

MicroRNAs as biomarker of Parkinson disease? Small but mighty (Journal Article)

Neurology, 84 (7), pp. 636-638, 2015.

(Links | BibTeX)

Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq (Journal Article)

Nucleic Acids Res, 43 (3), pp. 1392-1406, 2015.

(Abstract | Links | BibTeX)

2014

Madhugiri R, Fricke M, Marz M, Ziebuhr J

RNA structure analysis of alphacoronavirus terminal genome regions (Journal Article)

Virus Res, 194 , pp. 76-89, 2014.

(Abstract | Links | BibTeX)

Marz M, Wehner S, Stadler P F

Homology search for small structured non-coding RNAs (Book Chapter)

Hartmann R K, Bindereif A, Schon A, Westhof E (Ed.): Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition, Wiley-VCH Verlag GmbH & Co KGaA Weinheim, 2014.

(BibTeX)

Schwartze V U, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen I D, Marz M, Brakhage A A, Gabald'on T, Böcker S, Voigt K

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina) (Journal Article)

PLoS Genet, 10 (8), 2014.

(Abstract | Links | BibTeX)

Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker I L, Hoffmann D, Middendorf M, Rattei T, Stadler P F, Töpfer A

Challenges in RNA virus bioinformatics (Journal Article)

Bioinformatics, 30 (13), pp. 1793-1799, 2014.

(Abstract | Links | BibTeX)

Sachse K, Laroucau K, Riege K, Wehner S, Dilcher M, Creasy H H, Weidmann M, Myers G, Vorimore F, Vicari N, Magnino S, Liebler-Tenorio E, Ruettger A, Bavoil P M, Hufert F T, Rossell'o-M'ora R, Marz M

Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov (Journal Article)

Syst Appl Microbiol, 37 (2), pp. 79-88, 2014.

(Abstract | Links | BibTeX)

Bauer E, Salem H, Marz M, Vogel H, Kaltenpoth M

Transcriptomic immune response of the cotton stainer Dysdercus fasciatus to experimental elimination of vitamin-supplementing intestinal symbionts (Journal Article)

PLoS One, 9 (12), 2014.

(Abstract | Links | BibTeX)

Qin J, Fricke M, Marz M, Stadler P F, Backofen R

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures (Journal Article)

Algorithms Mol Biol, 9 , pp. 19-19, 2014.

(Abstract | Links | BibTeX)

Beckstein C, Böcker S, Bogdan M, Bruelheide H, Bücker H M, Denzler J, Dittrich P, Grosse I, Hinneburg A, König-Ries B, Löffler F, Marz M, Müller-Hannemann M, Winter M, Zimmermann W

Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data: A Computer Science Perspective on Biodiversity Research (Inproceeding)

M. Helfert, A. Holzinger, O. Belo, C. Francalanci (Ed.): Proceedings of the 3rd International Conference on Data Management Technologies and Applications, DATA 2014, Vienna, Austria, August 29--31, 2014, pp. 251–257, SCITEPRESS, 2014.

(Abstract | BibTeX)

Salem H, Bauer E, Strauss A S, Vogel H, Marz M, Kaltenpoth M

Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host (Journal Article)

Proceedings of the Royal Society of London B: Biological Sciences, 281 (1796), pp. 20141838, 2014.

(BibTeX)

Wehner S, Damm K, Hartmann R K, Marz M

Dissemination of 6S RNA among bacteria (Journal Article)

RNA Biol, 11 (11), pp. 1467-1478, 2014.

(Abstract | Links | BibTeX)

Wehner S, Mannala G K, Qing X, Madhugiri R, Chakraborty T, Mraheil M A, Hain T, Marz M

Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology (Journal Article)

PLoS One, 9 (10), 2014.

(Abstract | Links | BibTeX)

Lechner M, Nickel A I, Wehner S, Riege K, Wieseke N, Beckmann B M, Hartmann R K, Marz M

Genomewide comparison and novel ncRNAs of Aquificales (Journal Article)

BMC Genomics, 15 , pp. 522-522, 2014.

(Abstract | Links | BibTeX)

Wehner S, Dörrich A K, Ciba P, Wilde A, Marz M

pRNA: NoRC-associated RNA of rRNA operons (Journal Article)

RNA Biol, 11 (1), pp. 3-9, 2014.

(Abstract | Links | BibTeX)

2013

Vierna J, Wehner S, Höner zu Siederdissen C, Mart'inez-Lage A, Marz M

Systematic analysis and evolution of 5S ribosomal DNA in metazoans (Journal Article)

Heredity (Edinb), 111 (5), pp. 410-421, 2013.

(Abstract | Links | BibTeX)

Huang Y, Li Y, Burt D W, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor K E, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim K W, Sheng Z, An Y, Searle S, Herrero J, Groenen M A, Crooijmans R P, Faraut T, Cai Q, Webster R G, Aldridge J R, Warren W C, Bartschat S, Kehr S, Marz M, Stadler P F, Smith J, Kraus R H, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin D K, Rao M, Pitel F, Wang J, Li N

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species (Journal Article)

Nat Genet, 45 (7), pp. 776-783, 2013.

(Abstract | Links | BibTeX)

Li Y, Podlevsky J D, Marz M, Qi X, Hoffmann S, Stadler P F, Chen J

Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach (Journal Article)

RNA, 19 (6), pp. 852-860, 2013.

(Abstract | Links | BibTeX)

Lechner M, Marz M, Ihling C, Sinz A, Stadler P F, Krauss V

The correlation of genome size and DNA methylation rate in metazoans (Journal Article)

Theory Biosci, 132 (1), pp. 47-60, 2013.

(Abstract | Links | BibTeX)

81 entries « 1 of 2 »