166 entries « 1 of 4 »

2022

Houwaart, Torsten; Belhaj, Samir; Tawalbeh, Emran; Nagels, Dirk; Fröhlich, Yara; Finzer, Patrick; Ciruela, Pilar; Sabrià, Aurora; Herrero, Mercè; Andrés, Cristina; Antón, Andrés; Benmoumene, Assia; Asskali, Dounia; Haidar, Hussein; von Dahlen, Janina; Nicolai, Jessica; Stiller, Mygg; Blum, Jacqueline; Lange, Christian; Adelmann, Carla; Schroer, Britta; Osmers, Ute; Grice, Christiane; Kirfel, Phillipp P; Jomaa, Hassan; Strelow, Daniel; Hülse, Lisanna; Pigulla, Moritz; Kreuzer, Pascal; Tyshaieva, Alona; Weber, Jonas; Wienemann, Tobias; Vasconcelos, Malte Kohns; Hoffmann, Katrin; Lübke, Nadine; Hauka, Sandra; Andree, Marcel; Scholz, Claus Jürgen; Jazmati, Nathalie; Göbels, Klaus; Zotz, Rainer; Pfeffer, Klaus; Timm, Jörg; Ehlkes, Lutz; Walker, Andreas; Dilthey, Alexander T; (DeCOI), Deutsche COVID-19 OMICS Initiative

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021 Journal Article

In: Euro Surveill, vol. 27, iss. 43, pp. 2101089, 2022.

Abstract | Links | BibTeX | Tags: coronavirus, nanopore, RNA / transcriptomics, viruses

Mock, Florian; Kretschmer, Fleming; Kriese, Anton; Böcker, Sebastian; Marz, Manja

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks Journal Article

In: Proc Natl Acad Sci, vol. 119, iss. 35, pp. e2122636119, 2022.

Abstract | Links | BibTeX | Tags: classification, DNA / genomics, machine learning

Safrastyan, Aram; Wollny, Damian

Network analysis of hepatocellular carcinoma liquid biopsies augmented by single-cell sequencing data Journal Article

In: Front Genet, vol. 13, pp. 921195, 2022.

Abstract | Links | BibTeX | Tags: cancer, single-cell sequencing

Gramzow, Lydia; Klupsch, Katharina; Fernández-Pozo, Noé; Hölzer, Martin; Marz, Manja; Rensing, Stefan A; Theißen, Günter

Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) Journal Article

In: BMC Plant Biol, vol. 22, iss. 1, pp. 340, 2022.

Abstract | Links | BibTeX | Tags: RNA / transcriptomics

Hufsky, Franziska; Abecasis, Ana; Agudelo-Romero, Patricia; Bletsa, Magda; Brown, Katherine; Claus, Claudia; Deinhardt-Emmer, Stefanie; Deng, Li; Friedel, Caroline C.; Gismondi, María Inés; Kostaki, Evangelia Georgia; Kühnert, Denise; Kulkarni-Kale, Urmila; Metzner, Karin J.; Meyer, Irmtraud M.; Miozzi, Laura; Nishimura, Luca; Paraskevopoulou, Sofia; Pérez-Cataluña, Alba; Rahlff, Janina; Thomson, Emma; Tumescheit, Charlotte; van der Hoek, Lia; Espen, Lore Van; Vandamme, Anne-Mieke; Zaheri, Maryam; Zuckerman, Neta; Marz, Manja

Women in the European Virus Bioinformatics Center Journal Article

In: Viruses, vol. 14, iss. 7, pp. 1522, 2022.

Abstract | Links | BibTeX | Tags: viruses

Fuesslin, Valeria; Krautwurst, Sebastian; Srivastava, Akash; Winter, Doris; Liedigk, Britta; Thye, Thorsten; Herrera-León, Silvia; Wohl, Shirlee; May, Jürgen; Fobil, Julius N.; Eibach, Daniel; Marz, Manja; Schuldt, Kathrin

Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon Journal Article

In: Front Microbiol, vol. 13, pp. 909692, 2022.

Abstract | Links | BibTeX | Tags: bacteria, DNA / genomics, nanopore

Wollny, Damian; Vernot, Benjamin; Wang, Jie; Hondele, Maria; Safrastyan, Aram; Aron, Franziska; Micheel, Julia; He, Zhisong; Hyman, Anthony; Weis, Karsten; Camp, J Gray; Tang, T-Y Dora; Treutlein, Barbara

Characterization of RNA content in individual phase-separated coacervate microdroplets Journal Article

In: Nat Commun, vol. 13, iss. 1, pp. 2626, 2022.

Abstract | Links | BibTeX | Tags: RNA / transcriptomics

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

The Role of Non-Coding RNAs in the Human Placenta Journal Article

In: Cells, vol. 11, iss. 9, pp. 1588, 2022.

Abstract | Links | BibTeX | Tags: extracellular vesicles, ncRNAs, pregnancy, RNA / transcriptomics

Hufsky, Franziska; Beslic, Denis; Boeckaerts, Dimitri; Duchene, Sebastian; González-Tortuero, Enrique; Gruber, Andreas J; Guo, Jiarong; Jansen, Daan; Juma, John; Kongkitimanon, Kunaphas; Luque, Antoni; Ritsch, Muriel; Lovate, Gabriel Lencioni; Nishimura, Luca; Pas, Célia; Domingo, Esteban; Hodcroft, Emma; Lemey, Philippe; Sullivan, Matthew B; Weber, Friedemann; González-Candelas, Fernando; Krautwurst, Sarah; Pérez-Cataluña, Alba; Randazzo, Walter; Sánchez, Gloria; Marz, Manja

The International Virus Bioinformatics Meeting 2022 Journal Article

In: Viruses, vol. 14, iss. 5, pp. 973, 2022.

Abstract | Links | BibTeX | Tags: annotation, software, virus host interaction, viruses

Barth, Emanuel; Burggraaff, Johannes; Srivastava, Akash; Winckler, Thomas

Nanopore sequencing for mapping of retrotransposon integration sites in the Dictyostelium discoideum genome Journal Article

In: MicroPubl Biol, 2022.

Abstract | Links | BibTeX | Tags: DNA / genomics, nanopore

Aron, Franziska; Wollny, Damian

Single coacervate sequencing Technical Manual

2022.

Abstract | Links | BibTeX | Tags: RNA / transcriptomics

Sorokina, Maria; Barth, Emanuel; Zulfiqar, Mahnoor; Kwantes, Michiel; Pohnert, Georg; Steinbeck, Christoph

Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75 Journal Article

In: Data Brief, vol. 41, pp. 107931, 2022.

Abstract | Links | BibTeX | Tags: DNA / genomics

Sofer, Summer; Lamkiewicz, Kevin; Eilat, Shir Armoza; Partouche, Shirly; Marz, Manja; Moskovits, Neta; Stemmer, Salomon M; Shlomai, Amir; Sklan, Ella H

A genome-wide CRISPR activation screen reveals Hexokinase 1 as a critical factor in promoting resistance to multi-kinase inhibitors in hepatocellular carcinoma cells Journal Article

In: FASEB J , vol. 36, iss. 3, pp. e22191, 2022.

Abstract | Links | BibTeX | Tags: cancer, DNA / genomics

Morales-Prieto, Diana M; Murrieta-Coxca, José M; Stojiljkovic, Milan; Diezel, Celia; Streicher, Priska E; Henao-Restrepo, Julian A; Röstel, Franziska; Lindner, Julia; Witte, Otto W; Weis, Sebastian; Schmeer, Christian; Marz, Manja

Small Extracellular Vesicles from Peripheral Blood of Aged Mice Pass the Blood-Brain Barrier and Induce Glial Cell Activation. Journal Article

In: Cells, vol. 11, iss. 4, pp. 625, 2022.

Abstract | Links | BibTeX | Tags: aging, extracellular vesicles

Fuchs, Jonas; Lamkiewicz, Kevin; Kolesnikova, Larissa; Hölzer, Martin; Marz, Manja; Kochs, Georg

Comparative study of ten thogotovirus isolates and their distinct in vivo characteristics Journal Article

In: J Virol, 2022.

Abstract | Links | BibTeX | Tags: phylogenetics, viruses

2021

Wendisch, Daniel; Dietrich, Oliver; Mari, Tommaso; von Stillfried, Saskia; Ibarra, Ignacio L.; Mittermaier, Mirja; Mache, Christin; Chua, Robert Lorenz; Knoll, Rainer; Timm, Sara; Brumhard, Sophia; Krammer, Tobias; Zauber, Henrik; Hiller, Anna Luisa; Pascual-Reguant, Anna; Mothes, Ronja; Bülow, Roman David; Schulze, Jessica; Leipold, Alexander M.; Djudjaj, Sonja; Erhard, Florian; Geffers, Robert; Pott, Fabian; Kazmierski, Julia; Radke, Josefine; Pergantis, Panagiotis; Baßler, Kevin; Conrad, Claudia; Aschenbrenner, Anna C.; Sawitzki, Birgit; Landthaler, Markus; Wyler, Emanuel; Horst, David; (DeCOI), Deutsche COVID-19 OMICS Initiative; Hippenstiel, Stefan; Hocke, Andreas; Heppner, Frank L.; Uhrig, Alexander; Garcia, Carmen; Machleidt, Felix; Herold, Susanne; Elezkurtaj, Sefer; Thibeault, Charlotte; Witzenrath, Martin; Cochain, Clément; Suttorp, Norbert; Drosten, Christian; Goffinet, Christine; Kurth, Florian; Schultze, Joachim L.; Radbruch, Helena; Ochs, Matthias; Eils, Roland; Müller-Redetzky, Holger; Hauser, Anja E.; Luecken, Malte D.; Theis, Fabian J.; Conrad, Christian; Wolff, Thorsten; Boor, Peter; Selbach, Matthias; Saliba, Antoine-Emmanuel; Sander, Leif Erik

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis Journal Article

In: Cell, vol. 184, no. 26, pp. 6243-6261, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, virus host interaction, viruses

Barth, Emanuel; Srivastava, Akash; Wengerodt, Diane; Stojiljkovic, Milan; Axer, Hubertus; Witte, Otto W; Kretz, Alexandra; Marz, Manja

Age-dependent expression changes of circadian system-related genes reveal a potentially conserved link to aging Journal Article

In: Aging, vol. 13, no. 24, pp. 25694-25716, 2021.

Abstract | Links | BibTeX | Tags: aging, RNA / transcriptomics

Chaudhari, Narendrakumar M; Overholt, Will A; Figueroa-Gonzalez, Perla Abigail; Taubert, Martin; Bornemann, Till L V; Probst, Alexander J; Hölzer, Martin; Marz, Manja; Küsel, Kirsten

The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers Journal Article

In: Environ Microbiome, vol. 16, no. 1, pp. 24, 2021.

Abstract | Links | BibTeX | Tags: groundwater, metagenomics

Christ, Bruno; Collatz, Maximilian; Dahmen, Uta; Herrmann, Karl-Heinz; Höpfl, Sebastian; König, Matthias; Lambers, Lena; Marz, Manja; Meyer, Daria; Radde, Nicole; Reichenbach, Jürgen R.; Ricken, Tim; Tautenhahn, Hans-Michael

Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function Journal Article

In: Front Physiol, vol. 12, pp. 733868, 2021.

Abstract | Links | BibTeX | Tags: liver, RNA / transcriptomics

Micheel, Julia; Safrastyan, Aram; Wollny, Damian

Advances in Non-Coding RNA Sequencing Journal Article

In: Noncoding RNA, vol. 7, no. 4, pp. 70, 2021.

Abstract | Links | BibTeX | Tags: ncRNAs, RNA / transcriptomics

Martín-Hernández, Giselle C; Müller, Bettina; Chmielarz, Mikołaj; Brandt, Christian; Hölzer, Martin; Viehweger, Adrian; Passoth, Volkmar

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14 Journal Article

In: Genomics, vol. 113, no. 6, pp. 4022-4027, 2021.

Abstract | Links | BibTeX | Tags: annotation, assembly, DNA / genomics, fungi, nanopore

Krämer, Benjamin; Knoll, Rainer; Bonaguro, Lorenzo; ToVinh, Michael; Raabe, Jan; Astaburuaga-García, Rosario; Schulte-Schrepping, Jonas; Kaiser, Kim Melanie; Rieke, Gereon J; Bischoff, Jenny; Monin, Malte B; Hoffmeister, Christoph; Schlabe, Stefan; Domenico, Elena De; Reusch, Nico; Händler, Kristian; Reynolds, Gary; Blüthgen, Nils; Hack, Gudrun; Finnemann, Claudia; Nischalke, Hans D; Strassburg, Christian P; Stephenson, Emily; Su, Yapeng; Gardner, Louis; Yuan, Dan; Chen, Daniel; Goldman, Jason; Rosenstiel, Philipp; Schmidt, Susanne V; Latz, Eicke; Hrusovsky, Kevin; Ball, Andrew J; Johnson, Joe M; Koenig, Paul-Albert; Schmidt, Florian I; Haniffa, Muzlifah; Heath, James R; Kümmerer, Beate M; Keitel, Verena; Jensen, Björn; Stubbemann, Paula; Kurth, Florian; Sander, Leif E; Sawitzki, Birgit; (DeCOI), Deutsche COVID-19 OMICS Initiative; Aschenbrenner, Anna C; Schultze, Joachim L; Nattermann, Jacob

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19 Journal Article

In: Immunity, vol. S1074-7613, no. 21, pp. 00365-4, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, viruses

Collatz, Maximilian

Two Stories about Trying to Trace the Untraceable: B-Cell Epitope Prediction and Deciphering Circadian Clocks PhD Thesis

2021.

Links | BibTeX | Tags: differential expression analysis, machine learning, RNA / transcriptomics

Brandt, Christian; Krautwurst, Sebastian; Spott, Riccardo; Lohde, Mara; Jundzill, Mateusz; Marquet, Mike; Hölzer, Martin

poreCov - An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing Journal Article

In: Front Genet, vol. 12, pp. 711437, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, nanopore, RNA / transcriptomics, software, viruses

Mock, Florian; Kretschmer, Fleming; Kriese, Anton; Böcker, Sebastian; Marz, Manja

BERTax: taxonomic classification of DNA sequences with Deep Neural Networks Journal Article

In: bioRxiv, 2021.

Abstract | Links | BibTeX | Tags: classification, DNA / genomics, machine learning, software

Walker, Andreas; Houwaart, Torsten; Finzer, Patrick; Ehlkes, Lutz; Tyshaieva, Alona; Damagnez, Maximilian; Strelow, Daniel; Duplessis, Ashley; Nicolai, Jessica; Wienemann, Tobias; Tamayo, Teresa; Vasconcelos, Malte Kohns; Hülse, Lisanna; Hoffmann, Katrin; Lübke, Nadine; Hauka, Sandra; Andree, Marcel; Däumer, Martin P; Thielen, Alexander; Kolbe-Busch, Susanne; Göbels, Klaus; Zotz, Rainer; Pfeffer, Klaus; Timm, Jörg; Dilthey, Alexander T; (DeCOI), Deutsche COVID-19 OMICS Initiative

Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting Journal Article

In: Clin Infect Dis, pp. ciab588, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, evolution, nanopore, viruses

Singh, Yogesh; Trautwein, Christoph; Fendel, Rolf; Krickeberg, Naomi; Berezhnoy, Georgy; 6and Stephan Ossowski, Rosi Bissinger; Salker, Madhuri S; Casadei, Nicolas; Riess, Olaf; (DeCOI), Deutsche COVID-19 OMICS Initiative

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells Journal Article

In: Heliyon, vol. 7, no. 6, pp. e07147, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, viruses

Warnat-Herresthal, Stefanie; Schultze, Hartmut; Shastry, Krishnaprasad Lingadahalli; Manamohan, Sathyanarayanan; Mukherjee, Saikat; Garg, Vishesh; Sarveswara, Ravi; Händler, Kristian; Pickkers, Peter; Aziz, N Ahmad; Ktena, Sofia; Tran, Florian; Bitzer, Michael; Ossowski, Stephan; Casadei, Nicolas; Herr, Christian; Petersheim, Daniel; Behrends, Uta; Kern, Fabian; Fehlmann, Tobias; Schommers, Philipp; Lehmann, Clara; Augustin, Max; Rybniker, Jan; Altmüller, Janine; Mishra, Neha; Bernardes, Joana P; Krämer, Benjamin; Bonaguro, Lorenzo; Schulte-Schrepping, Jonas; Domenico, Elena De; Siever, Christian; Kraut, Michael; Desai, Milind; Monnet, Bruno; Saridaki, Maria; Siegel, Charles Martin; Drews, Anna; Nuesch-Germano, Melanie; Theis, Heidi; Heyckendorf, Jan; Schreiber, Stefan; Kim-Hellmuth, Sarah; (COVAS), COVID- Aachen Study; Nattermann, Jacob; Skowasch, Dirk; Kurth, Ingo; Keller, Andreas; Bals, Robert; Nürnberg, Peter; Rieß, Olaf; Rosenstiel, Philip; Netea, Mihai G; Theis, Fabian; Mukherjee, Sach; Backes, Michael; Aschenbrenner, Anna C; Ulas, Thomas; (DeCOI), Deutsche COVID-19 Omics Initiative; Breteler, Monique M B; Giamarellos-Bourboulis, Evangelos J; Kox, Matthijs; Becker, Matthias; Cheran, Sorin; Woodacre, Michael S; Goh, Eng Lim; Schultze, Joachim L

Swarm Learning for decentralized and confidential clinical machine learning Journal Article

In: Nature, vol. 594, no. 7862, pp. 265-270, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, machine learning, viruses

Yates, James A. Fellows; Velsko, Irina M.; Aron, Franziska; Posth, Cosimo; Hofman, Courtney A.; Austin, Rita M.; Parker, Cody E.; Mann, Allison E.; Nägele, Kathrin; Arthur, Kathryn Weedman; Arthur, John W.; Bauer, Catherine C.; Crevecoeur, Isabelle; Cupillard, Christophe; Curtis, Matthew C.; Dalén, Love; Bonilla, Marta Díaz-Zorita; Fernández-Lomana, J. Carlos Díez; Drucker, Dorothée G.; Escrivá, Elena Escribano; Francken, Michael; Gibbon, Victoria E.; Morales, Manuel R. González; Mateu, Ana Grande; Harvati, Katerina; Henry, Amanda G.; Humphrey, Louise; Menéndez, Mario; Mihailović, Dušan; Peresani, Marco; Moroder, Sofía Rodríguez; Roksandic, Mirjana; Rougier, Hélène; Sázelová, Sandra; Stock, Jay T.; Straus, Lawrence Guy; Svoboda, Jiří; Teßmann, Barbara; Walker, Michael J.; Power, Robert C.; Lewis, Cecil M.; Sankaranarayanan, Krithivasan; Guschanski, Katerina; Wrangham, Richard W.; Dewhirst, Floyd E.; Salazar-García, Domingo C.; Krause, Johannes; Herbig, Alexander; Warinner, Christina

The evolution and changing ecology of the African hominid oral microbiome Journal Article

In: Proc Natl Acad Sci, vol. 118, no. 20, pp. e2021655118, 2021.

Abstract | Links | BibTeX | Tags: ancient DNA, bacteria, evolution, phylogenetics

Brandt, Christian; Krautwurst, Sebastian; Spott, Riccardo; Lohde, Mara; Jundzill, Mateusz; Marquet, Mike; Hölzer, Martin

poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing Journal Article

In: bioRxiv, 2021, (Now published in Frontiers in Genetics: https://dx.doi.org/10.3389/fgene.2021.711437).

Abstract | Links | BibTeX | Tags: coronavirus, evolution, nanopore, RNA / transcriptomics, software, viruses

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

ITN—VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics Journal Article

In: Viruses, vol. 13, no. 5, pp. 766, 2021.

Abstract | Links | BibTeX | Tags: review, virus host interaction, viruses

Mostajo, Nelly F.

Reston and Zaire ebolavirus life cycle and host cellular response PhD Thesis

2021.

Abstract | Links | BibTeX | Tags: annotation, differential expression analysis, virus host interaction, viruses

Martín-Hernández, Giselle C.; Müller, Bettina; Chmielarz, Mikołaj; Brandt, Christian; Hölzer, Martin; Viehweger, Adrian; Passoth, Volkmar

Chromosome-level genome assembly and transcriptome- based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14 Journal Article

In: bioRxiv, 2021.

Abstract | Links | BibTeX | Tags: annotation, assembly, DNA / genomics, fungi, nanopore

Wollny, Damian; Vernot, Benjamin; Wang, Jie; Hondele, Maria; Hyman, Anthony; Weis, Karsten; Camp, J. Gray; Tang, T. -Y. Dora; Treutlein, Barbara

Characterization of RNA content in individual phase-separated coacervate microdroplets Journal Article

In: bioRxiv, 2021.

Abstract | Links | BibTeX | Tags: RNA / transcriptomics

Damme, Renaud Van; Hölzer, Martin; Viehweger, Adrian; Müller, Bettina; Bongcam-Rudloff, Erik; Brandt, Christian

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) Journal Article

In: PLOS Comput Biol, vol. 17, no. 2, pp. e1008716, 2021.

Abstract | Links | BibTeX | Tags: annotation, assembly, classification, DNA / genomics, metagenomics, RNA / transcriptomics, software

Heinze, Karolin; Hölzer, Martin; Ungelenk, Martin; Gerth, Melanie; Thomale, Jürgen; Heller, Regine; Morden, Claire R.; McManus, Kirk J.; Mosig, Alexander S.; Dürst, Matthias; Runnebaum, Ingo B.; Häfner, Norman

RUNX3 Transcript Variants Have Distinct Roles in Ovarian Carcinoma and Differently Influence Platinum Sensitivity and Angiogenesis Journal Article

In: Cancers, vol. 13, no. 3, pp. 476, 2021.

Abstract | Links | BibTeX | Tags: cancer, differential expression analysis, proteins, RNA / transcriptomics

Aschenbrenner, Anna C; Mouktaroudi, Maria; Krämer, Benjamin; Oestreich, Marie; Antonakos, Nikolaos; Nuesch-Germano, Melanie; Gkizeli, Konstantina; Bonaguro, Lorenzo; Reusch, Nico; Baßler, Kevin; Saridaki, Maria; Knoll, Rainer; Pecht, Tal; Kapellos, Theodore S; Doulou, Sarandia; Kröger, Charlotte; Herbert, Miriam; Holsten, Lisa; Horne, Arik; Gemünd, Ioanna D; Rovina, Nikoletta; Agrawal, Shobhit; Dahm, Kilian; van Uelft, Martina; Drews, Anna; Lenkeit, Lena; Bruse, Niklas; Gerretsen, Jelle; Gierlich, Jannik; Becker, Matthias; Händler, Kristian; Kraut, Michael; Theis, Heidi; Mengiste, Simachew; Domenico, Elena De; Schulte-Schrepping, Jonas; Seep, Lea; Raabe, Jan; Hoffmeister, Christoph; ToVinh, Michael; Keitel, Verena; Rieke, Gereon; Talevi, Valentina; Skowasch, Dirk; Aziz, N Ahmad; Pickkers, Peter; van de Veerdonk, Frank L; Netea, Mihai G; Schultze, Joachim L; Kox, Matthijs; Breteler, Monique M B; Nattermann, Jacob; Koutsoukou, Antonia; Giamarellos-Bourboulis, Evangelos J; Ulas, Thomas; (DeCOI), Deutsche COVID-19 OMICS Initiative

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients Journal Article

In: Genome Med, vol. 13, no. 1, pp. 7, 2021.

Abstract | Links | BibTeX | Tags: coronavirus, RNA / transcriptomics, viruses

Kotolloshi, Roland; Hölzer, Martin; Gajda, Mieczyslaw; Grimm, Marc-Oliver; Steinbach, Daniel

SLC35F2, a Transporter Sporadically Mutated in the Untranslated Region, Promotes Growth, Migration, and Invasion of Bladder Cancer Cells Journal Article

In: Cells, vol. 10, no. 1, pp. 80, 2021.

Abstract | Links | BibTeX | Tags: cancer, DNA / genomics

Marz, Manja; Frishman, Dmitrij (Ed.)

Virus Bioinformatics Book

CRC Press, Boca Raton, 2021, ISBN: 1000426602.

BibTeX | Tags: viruses

Krautwurst, Sebastian; Dijkman, Ronald; Thiel, Volker; Krumbholz, Andi; Marz, Manja

Direct RNA Sequencing for Complete Viral Genomes Incollection

In: Frishman, Dmitrij; Marz, Manja (Ed.): Virus Bioinformatics, CRC Press, 2021.

Abstract | Links | BibTeX | Tags: assembly, DNA / genomics, nanopore, nucleic acid modifications, RNA / transcriptomics, viruses

Mock, Florian; Marz, Manja

Sequence Classification with Machine Learning at the Example of Viral Host Prediction Incollection

In: Frishman, Dmitrij; Marz, Manja (Ed.): Virus Bioinformatics, CRC Press, 2021.

Abstract | Links | BibTeX | Tags: classification, machine learning, virus host interaction, viruses

Pappas, Nikolaos; Roux, Simon; Hölzer, Martin; Lamkiewicz, Kevin; Mock, Florian; Marz, Manja; Dutilh, Bas E.

Virus Bioinformatics Incollection

In: Reference Module in Life Sciences, vol. 1, pp. 124-132, Elsevier, 2021, ISBN: 978-0-12-809633-8.

Abstract | Links | BibTeX | Tags: evolution, metagenomics, virus host interaction, viruses

2020

Bernardes, Joana P; Mishra, Neha; Tran, Florian; Bahmer, Thomas; Best, Lena; Blase, Johanna I; Bordoni, Dora; Franzenburg, Jeanette; Geisen, Ulf; Josephs-Spaulding, Jonathan; Köhler, Philipp; Künstner, Axel; Rosati, Elisa; Aschenbrenner, Anna C; Bacher, Petra; Baran, Nathan; Boysen, Teide; Brandt, Burkhard; Bruse, Niklas; Dörr, Jonathan; Dräger, Andreas; Elke, Gunnar; Ellinghaus, David; Fischer, Julia; Forster, Michael; Franke, Andre; Franzenburg, Sören; Frey, Norbert; Friedrichs, Anette; Fuß, Janina; Glück, Andreas; Hamm, Jacob; Hinrichsen, Finn; Hoeppner, Marc P; Imm, Simon; Junker, Ralf; Kaiser, Sina; Kan, Ying H; Knoll, Rainer; Lange, Christoph; Laue, Georg; Lier, Clemens; Lindner, Matthias; Marinos, Georgios; Markewitz, Robert; Nattermann, Jacob; Noth, Rainer; Pickkers, Peter; Rabe, Klaus F; Renz, Alina; Röcken, Christoph; Rupp, Jan; Schaffarzyk, Annika; Scheffold, Alexander; Schulte-Schrepping, Jonas; Schunk, Domagoj; Skowasch, Dirk; Ulas, Thomas; Wandinger, Klaus-Peter; Wittig, Michael; Zimmermann, Johannes; Busch, Hauke; Hoyer, Bimba F; Kaleta, Christoph; Heyckendorf, Jan; Kox, Matthijs; Rybniker, Jan; Schreiber, Stefan; Schultze, Joachim L; Rosenstiel, Philip; Network, HCA Lung Biological; (DeCOI), Deutsche COVID-19 Omics Initiative

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19 Journal Article

In: Immunity, vol. 53, no. 6, pp. 1296-1314.e9, 2020.

Abstract | Links | BibTeX | Tags: coronavirus, viruses

Lataretu, Marie; Hölzer, Martin

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow Journal Article

In: Genes, vol. 11, no. 12, pp. 1487, 2020.

Abstract | Links | BibTeX | Tags: differential expression analysis, RNA / transcriptomics, software

Hufsky, Franziska; Beerenwinkel, Niko; Meyer, Irmtraud M.; Roux, Simon; Cook, Georgia May; Kinsella, Cormac M.; Lamkiewicz, Kevin; Marquet, Mike; Nieuwenhuijse, David F.; Olendraite, Ingrida; Paraskevopoulou, Sofia; Young, Francesca; Dijkman, Ronald; Ibrahim, Bashar; Kelly, Jenna; Mercier, Philippe Le; Marz, Manja; Ramette, Alban; Thiel, Volker

The International Virus Bioinformatics Meeting 2020 Journal Article

In: Viruses, vol. 12, no. 12, pp. 1398, 2020.

Abstract | Links | BibTeX | Tags: classification, conference report, evolution, metagenomics, software, viruses

Kalvari, Ioanna; Nawrocki, Eric P; Ontiveros-Palacios, Nancy; Argasinska, Joanna; Lamkiewicz, Kevin; Marz, Manja; Griffiths-Jones, Sam; Toffano-Nioche, Claire; Gautheret, Daniel; Weinberg, Zasha; Rivas, Elena; Eddy, Sean R; Finn, Robert D; Bateman, Alex; Petrov, Anton I

Rfam 14: expanded coverage of metagenomic, viral and microRNA families Journal Article

In: Nucleic Acids Res, vol. 49, no. D1, pp. D192–D200, 2020.

Abstract | Links | BibTeX | Tags: alignment, annotation, bacteria, coronavirus, database, metagenomics, ncRNAs, RNA / transcriptomics, software, viruses

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

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research Journal Article

In: Brief Bioinform, vol. 22, no. 2, pp. 642–663, 2020.

Abstract | Links | BibTeX | Tags: coronavirus, evolution, review, software, viruses

Jordan-Paiz, Ana; Nevot, Maria; Lamkiewicz, Kevin; Lataretu, Marie; Franco, Sandra; Marz, Manja; Martinez, Miguel Angel

HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer Journal Article

In: J Virol, vol. 94, no. 21, 2020.

Abstract | Links | BibTeX | Tags: proteins, RNA structure, splicing, viruses

Flores, David Carrasco; Fricke, Markus; Wesp, Valentin; Desirò, Daniel; Kniewasser, Anja; Hölzer, Martin; Marz, Manja; Mittag, Maria

A marine Chlamydomonas sp. emerging as an algal model Journal Article

In: J Phycol, vol. 57, no. 1, pp. 54–69, 2020.

Abstract | Links | BibTeX | Tags: algae, bacteria, DNA / genomics, phylogenetics

Hölzer, Martin

A decade of de novo transcriptome assembly: Are we there yet? Journal Article

In: Mol Ecol Resour, vol. 21, no. 1, pp. 11-13, 2020.

Abstract | Links | BibTeX | Tags: assembly, review, RNA / transcriptomics

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