Publications

ZORA Publication List

Publications

• 2024

  • Serra Moncadas, Lucas; Hofer, Cyrill; Bulzu, Paul-Adrian; Pernthaler, Jakob; Andrei, Adrian-Stefan (2024). Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis Nature Communications, 15(1):3421.
  • Villena-Alemany, Cristian; Mujakić, Izabela; Fecskeová, Livia K; Woodhouse, Jason; Auladell, Adrià; Dean, Jason; Hanusová, Martina; Socha, Magdalena; Gazulla, Carlota R; Ruscheweyh, Hans-Joachim; Sunagawa, Shinichi; Silva Kavagutti, Vinicius; Andrei, Adrian-Stefan; Grossart, Hans-Peter; Ghai, Rohit; Koblížek, Michal; Piwosz, Kasia (2024). Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters Microbiome, 12(1):65.
  • Zhu, Baoli; Chen, Zengming; Hu, Hangwei; Andrei, Adrian-Stefan; Li, Yong (2024). Greenhouse gas emissions and mitigation: microbes, mechanisms and modeling Frontiers in Microbiology, 15:1363814.
  • Hofer, Cyrill; Wälchli, Denise; Moncadas, Lucas Serra; Rain-Franco, Angel; Andrei, Adrian-Stefan (2024). A high-quality genome of an undescribed Flavobacterium species uncovered using Q20+ Nanopore chemistry Microbiology Resource Announcements, 13(1):online.
  • Serra Moncadas, Lucas; Schnellmann, Vanessa; Hofer, Cyrill; Rain-Franco, Angel; Andrei, Adrian-Stefan (2024). Complete genome of Flavobacterium pectinovorum str. ZE23VCel01 obtained through Nanopore Q20+ chemistry Microbiology Resource Announcements, 13(1):online.
  • Rain-Franco, Angel; Le Moigne, Alizée; Serra Moncadas, Lucas; Silva, Marisa O D; Andrei, Adrian-Stefan; Pernthaler, Jakob (2024). Dispersal shapes compositional and functional diversity in aquatic microbial communities mSystems, 9(12):e0140324.

• 2023

  • Hofer, Cyrill; Lingenhag, Seraina; Serra Moncadas, Lucas; Rain-Franco, Angel; Andrei, Adrian-Stefan (2023). Q20+ Nanopore sequencing data recover a high-quality Asticcacaulis sp. genome Microbiology Resource Announcements, 12(10):online.
  • Serra Moncadas, Lucas; Rogenmoser, Janis; Hofer, Cyrill; Rain-Franco, Angel; Andrei, Adrian-Stefan (2023). Pseudomonas kielensis str. Ze23jcel16 complete genome obtained through R10.4.1 Nanopore Flow cell chemistry Microbiology Resource Announcements:online.
  • Ngugi, David Kamanda; Salcher, Michaela M; Andrei, Adrian-Stefan; Ghai, Rohit; Klotz, Franziska; Chiriac, Maria-Cecilia; Ionescu, Danny; Büsing, Petra; Grossart, Hans-Peter; Xing, Peng; Priscu, John C; Alymkulov, Salmor; Pester, Michael (2023). Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes Science Advances, 9(5):eadc9392.
  • Kavagutti, Vinicius S; Bulzu, Paul-Adrian; Chiriac, Cecilia M; Salcher, Michaela M; Mukherjee, Indranil; Shabarova, Tanja; Grujčić, Vesna; Mehrshad, Maliheh; Kasalický, Vojtěch; Andrei, Adrian-Stefan; Jezberová, Jitka; Seďa, Jaromir; Rychtecký, Pavel; Znachor, Petr; Šimek, Karel; Ghai, Rohit (2023). High-resolution metagenomic reconstruction of the freshwater spring bloom Microbiome, 11:15.

• 2022

  • Bulzu, Paul-Adrian; Kavagutti, Vinicius S; Andrei, Adrian-Stefan; Ghai, Rohit (2022). The Evolutionary Kaleidoscope of Rhodopsins mSystems, 7(5):e0040522.
  • Bernet, Julia; Serra Moncadas, Lucas; Andrei, Adrian-Stefan (2022). Complete Genome Sequence of an Uncultivated Freshwater Flavobacterium sp. Strain Microbiology Resource Announcements, 11(10):e0065922.
  • Mauch, Emanuel; Serra Moncadas, Lucas; Andrei, Adrian-Stefan (2022). Complete Genome Sequence of an Uncultivated Freshwater Bacteroidota Lineage Microbiology Resource Announcements, 11(10):e0076622.
  • Ajvazi, Xhesida; Serra Moncadas, Lucas; Andrei, Adrian-Stefan (2022). Study of Complete Genome Sequence of Uncultivated Hyphomonadaceae sp.
  • Cremer, Franziska; Serra Moncadas, Lucas; Andrei, Adrian-Stefan (2022). Complete Genome Sequence from an Uncultivated Freshwater Elusimicrobiota Lineage Microbiology Resource Announcements, 11(9):e0042622.
  • Zhu, Baoli; Karwautz, Clemens; Andrei, Adrian-Stefan; Klingl, Andreas; Pernthaler, Jakob; Lueders, Tillmann (2022). A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction mLife, 1(3):323-328.
  • Chiriac, Maria-Cecilia; Bulzu, Paul-Adrian; Andrei, Adrian-Stefan; Okazaki, Yusuke; Nakano, Shin-ichi; Haber, Markus; Kavagutti, Vinicius Silva; Layoun, Paul; Ghai, Rohit; Salcher, Michaela M (2022). Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR Microbiome, 10(1):84.
  • Hofer, Cyrill . Long-Read MinION data for microbial community analysis 2022, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2021

  • Bulzu, Paul-Adrian; Kavagutti, Vinicius Silva; Chiriac, Maria-Cecilia; Vavourakis, Charlotte D; Inoue, Keiichi; Kandori, Hideki; Andrei, Adrian-Stefan; Ghai, Rohit (2021). Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms mSphere, 6(6):e00661-21.
  • Durán‐Viseras, Ana; Andrei, Adrian-Stefan; Vera‐Gargallo, Blanca; Ghai, Rohit; Sánchez‐Porro, Cristina; Ventosa, Antonio (2021). Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis Environmental Microbiology, 23(7):3418-3434.
  • Baricz, Andreea; Chiriac, Cecilia Maria; Andrei, Adrian-Stefan; Bulzu, Paul‐Adrian; Levei, Erika Andrea; Cadar, Oana; Battes, Karina Paula; Cîmpean, Mirela; Șenilă, Marin; Cristea, Adorján; Muntean, Vasile; Alexe, Mircea; Coman, Cristian; Szekeres, Edina Kriszta; Sicora, Cosmin Ionel; Ionescu, Artur; Blain, David; O'Neill, William Kenneth; Edwards, Jessica; Hallsworth, John Edward; Banciu, Horia Leonard (2021). Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake Environmental Microbiology, 23(7):3523-3540.
  • Mujakić, Izabela; Andrei, Adrian-Stefan; Shabarova, Tanja; Fecskeová, Lívia Kolesár; Salcher, Michaela M; Piwosz, Kasia; Ghai, Rohit; Koblížek, Michal (2021). Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes mSystems, 6(2):01241-20.

• 2020

  • Andrei, Adrian-Stefan; Bulzu, Paul‐Adrian; Banciu, Horia Leonard (2020). Blossoms of Rot: Microbial Life in Saline Organic-Rich Sediments In: Seckbach, Josef; Stan-Lotter, Helga . Extremophiles as Astrobiological Models. Scrivener Publishing LLC: Wiley-Blackwell Publishing, Inc., 45-82.
  • Mukherjee, Indranil; Salcher, Michaela M; Andrei, Adrian-Stefan; Kavagutti, Vinicius Silva; Shabarova, Tanja; Grujčić, Vesna; Haber, Markus; Layoun, Paul; Hodoki, Yoshikuni; Nakano, Shin-ichi; Šimek, Karel; Ghai, Rohit (2020). A freshwater radiation of diplonemids ArXiv.org 15209, Cornell University.

• 2019

  • Kavagutti, Vinicius S; Andrei, Adrian-Stefan; Mehrshad, Maliheh; Salcher, Michaela M; Ghai, Rohit (2019). Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics Microbiome, 7:135.
  • Bulzu, Paul-Adrian; Andrei, Adrian-Stefan; Salcher, Michaela M; Mehrshad, Maliheh; Inoue, Keiichi; Kandori, Hideki; Beja, Oded; Ghai, Rohit; Banciu, Horia L (2019). Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche Nature Microbiology, 4(7):1129-1137.
  • Andrei, Adrian-Stefan; Salcher, Michaela M; Mehrshad, Maliheh; Rychtecký, Pavel; Znachor, Petr; Ghai, Rohit (2019). Niche-directed evolution modulates genome architecture in freshwater Planctomycetes The ISME journal, 13(4):1056-1071.

• 2018

  • Mehrshad, Maliheh; Salcher, Michaela M; Okazaki, Yusuke; Nakano, Shin-ichi; Šimek, Karel; Andrei, Adrian-Stefan; Ghai, Rohit (2018). Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome, 6(1):176.