Publications according to DDC572: Biochemistry

• Ostash, Bohdan; Anisimova, Maria,

  2020.

  Visualizing codon usage within and across genomes : concepts and tools

  .

  In:

  Srinivasa, K. G.; Siddesh, G. M.; Manisekhar, S. R., eds.,

  Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications.

  pp. 213-288.

  Algorithms for Intelligent Systems.

  Available from: https://doi.org/10.1007/978-981-15-2445-5_13

• Oh, Woo Taek; Jun, Jin Woo; Giri, Sib Sankar; Yun, Saekil; Kim, Hyoun Joong; Kim, Sang Guen; Kim, Sang Wha; Kang, Jeong Woo; Han, Se Jin; Kwon, Jun; Kim, Ji Hyung; Smits, Theo H.M.; Park, Se Chang,

  2019.

  Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney.

  International Journal of Systematic and Evolutionary Microbiology.

  69(12), pp. 3851-3856.

  Available from: https://doi.org/10.1099/ijsem.0.003696

• Tørresen, Ole K; Star, Bastiaan; Mier, Pablo; Andrade-Navarro, Miguel A; Bateman, Alex; Jarnot, Patryk; Gruca, Aleksandra; Grynberg, Marcin; Kajava, Andrey V; Promponas, Vasilis J; Anisimova, Maria; Jakobsen, Kjetill S; Linke, Dirk,

  2019.

  Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

  Nucleic Acids Research.

  47(21), pp. 10994-11006.

  Available from: https://doi.org/10.1093/nar/gkz841

• Smits, Theo H.M.,

  2019.

  The importance of genome sequence quality to microbial comparative genomics.

  BMC Genomics.

  20(662).

  Available from: https://doi.org/10.1186/s12864-019-6014-5

• van Mierlo, Joël; Hagens, Steven; Witte, Sander; Klamert, Silvia; van de Straat, Leoni; Fieseler, Lars,

  2019.

  Complete genome sequences of escherichia coli phages vB_EcoM-EP75 and vB_EcoP-EP335.

  Microbiology Resource Announcements.

  8(16).

  Available from: https://doi.org/10.1128/MRA.00078-19

• Stuby, Johann; Gravestock, Isaac; Wolfram, Evelyn; Pichierri, Giuseppe; Steurer, Johann; Burgstaller, Jakob M.,

  2019.

  Appetite-suppressing and satiety-increasing bioactive phytochemicals : a systematic review.

  Nutrients.

  11(9), pp. 2238.

  Available from: https://doi.org/10.3390/nu11092238

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H.M.,

  2019.

  Comparative genomic analysis of the biotechnological potential of the novel species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T.

  Diversity.

  2019(11), pp. 204.

  Available from: https://doi.org/10.3390/d11110204

• Ruinelli, Michela; Blom, Jochen; Smits, Theo; Pothier, Joël,

  2019.

  Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp.

  BMC Genomics.

  20(172).

  Available from: https://doi.org/10.1186/s12864-019-5555-y

• Faccio, Greta; Cont, Alice; Mailand, Erik; Zare-Eelanjegh, Elaheh; Innocenti Malini, Riccardo; Maniura-Weber, Katharina; Rossi, René M.; Spano, Fabrizio,

  2019.

  Complete inclusion of bioactive molecules and particles in polydimethylsiloxane : a straightforward process under mild conditions.

  Scientific Reports.

  9(1), pp. 17575.

  Available from: https://doi.org/10.1038/s41598-019-54155-5

• Böselt, Lennard; Sidler, Dominik; Kittelmann, Tobias; Stohner, Jürgen; Zindel, Daniel; Wagner, Trixie; Riniker, Sereina,

  2019.

  Determination of absolute stereochemistry of flexible molecules using a vibrational circular dichroism spectra alignment algorithm.

  Journal of Chemical Information and Modeling.

  59(5), pp. 1826-1838.

  Available from: https://doi.org/10.1021/acs.jcim.8b00789

• Weyland, Mathias; Thumser-Henner, Pauline; Rohrer Bley, Carla; Ulzega, Simone; Petri-Fink, Alke; Lattuada, Marco; Scheidegger, Stephan; Füchslin, Rudolf Marcel,

  2019.

  Dynamic DNA damage and repair modelling : bridging the gap between experimental damage readout and model structure [paper].

  In:

  Cagnoni, Stefano; Mordonini, Monica; Pecori, Riccardo; Roli, Andrea; Villani, Marco, eds.,

  Artificial Life and Evolutionary Computation.

  XIII International Workshop on Artificial Life and Evolutionary Computation (WIVACE), Parma, Italy, 10-12 September 2018.

  Cham:

  Springer.

  pp. 127-137.

  Communications in Computer and Information Science ; 900.

  Available from: https://doi.org/10.1007/978-3-030-21733-4_10

• Anisimova, Maria, ed.,

  2019.

  Evolutionary genomics : statistical and computational methods.

  Second Edition.

  New York:

  Humana.

  Methods in Molecular Biology.

  ISBN 978-1-4939-9073-3.

  Available from: https://doi.org/10.1007/978-1-4939-9074-0

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H. M.,

  2019.

  High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T.

  Microbiology Resource Announcements.

  8(3).

  Available from: https://doi.org/10.1128/MRA.01502-18

• Kosiol, Carolin; Anisimova, Maria,

  2019.

  Selection acting on genomes

  .

  In:

  Anisimova, Maria, ed.,

  Evolutionary genomics : statistical and computational methods.

  Springer.

  pp. 373-397.

  Methods in Molecular Biology.

  Available from: https://doi.org/10.1007/978-1-4939-9074-0_12

• Zhao, F. J.; Bonmarin, Mathias; Chen, Z. C.; Larson, M.; Fay, D.; Runnoe, D.; Heikenfeld, J.,

  2019.

  Ultra-simple wearable local sweat volume monitoring patch based on swellable hydrogels.

  Lab on a Chip.

  Available from: https://doi.org/10.1039/C9LC00911F

• Trifan, Adriana; Vasincu, Alexandru; Luca, Simon Vlad; Neophytou, Christiana; Wolfram, Evelyn; Opitz, Sebastian; Sava, Daciana; Bucur, Laura; Cioroiu, Bogdan I.; Miron, Anca; Aprotosoaie, Ana Clara; Cioanca, Oana; Hancianu, Monica; Jitareanu, Alexandra; Constantinou, Andreas I.,

  2019.

  Unravelling the potential of seaweeds from the Black Sea coast of Romania as bioactive compounds sources : part I: Cystoseira barbata (Stackhouse) C. Agardh.

  Food and Chemical Toxicology.

  134(110820).

  Available from: https://doi.org/10.1016/j.fct.2019.110820

• Smits, Theo H.M.; Rezzonico, Fabio; Frasson, David; Vesga, Pilar; Vacheron, Jordan; Blom, Jochen; Pothier, Joël F.; Keel, Christoph; Maurhofer, Monika; Sievers, Martin,

  2019.

  Updated genome sequence and annotation for the full genome of Pseudomonas protegens CHA0.

  Microbiology Resource Announcements.

  8(39).

  Available from: https://doi.org/10.1128/MRA.01002-19

• Fernandes, Camila; Blom, Jochen; Pothier, Joël F.; Tavares, Fernando,

  2018.

  High-quality draft genome sequence of xanthomonas arboricola pv. juglandis CPBF 1521, isolated from leaves of a symptomatic walnut tree in Portugal without a past of phytosanitary treatment.

  Microbiology Resource Announcements.

  7(16).

  Available from: https://doi.org/10.1128/MRA.00887-18

• Fernandes, Camila; Blom, Jochen; Pothier, Joël F.; Tavares, Fernando,

  2018.

  High-Quality draft genome sequence of xanthomonas sp. strain CPBF 424, a walnut-pathogenic strain with atypical features.

  Microbiology Resource Announcements.

  7(15).

  Available from: https://doi.org/10.1128/MRA.00921-18

• Garcia, Victor; Zoller, Stefan; Anisimova, Maria,

  2018.

  Programmed ribosomal frameshifting and codon usage bias [poster].

  In:

  Hirsch, Sven, ed.,

  Life in Numbers 4.0.

  Life in Numbers 4, Wädenswil, 4 October 2018.

  ZHAW Zürcher Hochschule für Angewandte Wissenschaften.

  Available from: https://doi.org/10.21256/zhaw-4023

• Garcia, Victor; Zoller, Stefan; Anisimova, Maria,

  2018.

  Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices.

  G3 - Genes, Genomes, Genetics.

  8(10), pp. 3173-3183.

  Available from: https://doi.org/10.1534/g3.118.200185

• Bliven, Spencer; Anisimova, Maria,

  2018.

  Phylogentics of tandem repeats with circular HMMs : a case study on Armadillo Repeat Proteins [poster].

  In:

  SIB-Days, Biel/Bienne, 26-27 June 2018.

  ZHAW Zürcher Hochschule für Angewandte Wissenschaften.

  Available from: https://doi.org/10.21256/zhaw-3861

• Luginbühl, Vera; Meier, Nicolas; Kovar, Karin; Rohrer, Jack,

  2018.

  Intracellular drug delivery : potential usefulness of engineered Shiga toxin subunit B for targeted cancer therapy.

  Biotechnology Advances.

  36(3), pp. 613-623.

  Available from: https://doi.org/10.1016/j.biotechadv.2018.02.005

• Bergman, Alan J.; Simon, Eszter; Schifferli, Andrea; Vermeirssen, Etienne; Schönborn, Andreas,

  2018.

  Performance of measuring estrogenicity with planar-YES compared to 96-well plate YES [poster].

  In:

  SETAC Europe 28th Annual Meeting, Rome, Italy, 13-17 May 2018.

• Bliven, Spencer E; Lafita, Aleix; Rose, Peter W; Capitani, Guido; Prlic, Andreas; Bourne, Philip,

  2018.

  Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.

  Selbstverlag.

  Available from: https://doi.org/10.1101/297960