© WWU - EvoPAD

Publications

Below you can find publications from work carried out within the EvoPAD framework.

  • 2022

    • Fengjun Zhang, Carsten Alexander Raabe, Margarida Cardoso-Moreira, Jürgen Brosius, Henrik Kaesssmann, Jürgen Schmitz (2022). ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement. Genomics 2022, 114 (4), 110434 10.1016/j.ygeno.2022.110434 [doi]
    • Raphael Steffen, Lynn Ogoniak, Norbert Grundmann, Anna Pawluchin, Oliver Soehnlein and Jürgen Schmitz (2022). paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences. Genes 2022, 13 (6), 1090 10.3390/genes13061090 [doi]
    • Binia Stieger, Rupert Palme, Sylvia Kaiser, Norbert Sachser, S. Helene Richter (2022). When left is right: The effects of paw preference training on behaviour in mice. Behavioural Brain Research, Volume 430, 26 July 2022, 113929 10.1016/j.bbr.2022.113929 [doi]
    • Ana Korša, Lai Ka Lo, Shrey Gandhi, Corinna Bang and Joachim Kurtz (2022). Oral Immune Priming Treatment Alters Microbiome Composition in the Red Flour Beetle Tribolium castaneum. Front. Microbiol., 13 April 2022 10.3389/fmicb.2022.793143 [doi]
    • Marla Keizers, Ulrich Dobrindt and Michael Berger (2022). A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis. ACS Synth. Biol. 2022, 11, 747−759 10.1021/acssynbio.1c00459?ref=PDF [doi]
    • Marisol Herrera-Rivero, Shrey Gandhi, Anika Witten, Amer Ghalawinji, Ulrich Schotten, Monika Stoll (2022). Cardiac chamber-specific genetic alterations suggest candidate genes and pathways implicating the left ventricle in the pathogenesis of atrial fibrillation. Genomics, Volume 114, Issue 2, March 2022, 110320 10.1016/j.ygeno.2022.110320 [doi]

    • Nicolas C H Schröder, Ana Korša, Haleluya Wami, Olena Mantel, Ulrich Dobrindt, Joachim Kurtz (2022). Serial passage in an insect host indicates genetic stability of the human probiotic Escherichia coli Nissle 1917. EMPH, Volume 10 Issue 1 2022. 10.1093/emph/eoac001 [doi]

    • Anna Grandchamp, Katrin Berk, Elias Dohmen, Erich Bornberg-Bauer. New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes 2022, 13(2), 284 10.3390/genes13020284 [doi]

    Preprints

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  • 2021

    • Noble Selasi Gati, Ozan Altan Altinok, Sriram Kumar, Verónica A Ferrando, Joachim Kurtz, Michael Quante, Stephan Ludwig, Alexander Mellmann (2021). Integrating evolutionary aspects into dual-use discussion: the cases of influenza virus and enterohemorrhagic Escherichia coli. EMPH, Volume 9, Issue 1, 2021, Pages 383–392 10.1093/emph/eoab034 [doi]
    • Kumar S, Çalişkan DM, Janowski J, Faist A, Conrad BCG, Lange J, Ludwig S & Brunotte L (2021). Beyond Vaccines: Clinical Status of Prospective COVID-19 Therapeutics. Frontiers in Immunology 10.3389/fimmu.2021.752227 [doi]
    • Valerio Vitali, Rebecca Rothering, Francesco Catania (2021) Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing 10.3390/microorganisms9091979 [doi]
    • Leonie Martens, Frank Rühle, Anika Witten, Benjamin Meder, Hugo A. Katus, Eloisa Arbustini, Gerd Hasenfuß, Moritz F. Sinner, Stefan Kääb, Sabine Pankuweit, Christiane Angermann, Erich Bornberg-Bauer & Monika Stoll (2021) A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy 10.1080/15476286.2021.1952756 [doi]
    • Emily L. Rivard, Andrew G. Ludwig, Prajal H. Patel, Anna Grandchamp, Sarah E. Arnold, Alina Berger, Emilie M. Scott, Brendan J. Kelly, Grace C. Mascha, Erich Bornberg-Bauer, Geoffrey D. Findlay (2021) A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster, PLoS Genetics ‘in press’ 10.1101/2021.06.10.447990 [doi]
    • Shrey Gandhi, Anika Witten, Federica De Majo, Martijn Gilbers, Jos Maessen, Ulrich Schotten, Leon J.de Windt, Monika Stoll (2021) Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology, Genomics 113 (6) 10.1016/j.ygeno.2021.09.002 [doi]
    • Francesco Catania, Beata Ujvari, Benjamin Roche, Jean-Pascal Capp, Frédéric Thomas (2021) Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution, Front. Oncol. 10 September 2021 10.3389/fonc.2021.732081 [doi]
    • Noble Selasi Gati, Imke Johanna Temme, Barbara Middendorf-Bauchart, Alexander Kehl, Ulrich Dobrindt, Alexander Mellmann (2021) Comparative phenotypic characterization of hybrid Shiga toxin-producing / uropathogenic Escherichia coli, canonical uropathogenic and Shiga toxin-producing Escherichia coli, International Journal of Medical Microbiology 311 (7) 10.1016/j.ijmm.2021.151533 [doi]
    • Federica De Majo, Leonie Martens, Jana-Charlotte Hegenbarth, Frank Rühle, Magda R. Hamczyk, Rosa M. Nevado, Vicente Andrés, Erika Hilbold, Christian Bär, Thomas Thum, Martine de Boer, Dirk J. Duncker, Blanche Schroen, Anne-Sophie Armand, Monika Stoll, and Leon J. De Windt (2021) Genomic instability in the naturally and prematurely aged myocardium, PNAS 118 (36) e2022974118 10.1073/pnas.2022974118 [doi]
    • Kalyanaraman D, Gadau J, Lammers M (2021) The generalist parasitoid Nasonia vitripennis shows more behavioural plasticity in host preference than its three specialist sister species, ethologie; International journal of behavioural biology 10.1111/eth.13217 [doi]
    • Catania F, Baedke J, Fábregas‐Tejeda A, Nieves Delgado A, Vitali V, Nguyen Long L. (2021) Global climate change, diet and the complex relationship between human host and microbiome: Towards an integrated picture. BioEssays e2100049. 10.1002/bies.202100049 [doi]
    • Stieger B, Melotti L, Quante SM, Kaiser S, Sachser N, Richter SH (2021) A step in the right direction: the effect of context, strain and sex on paw preference in mice. Animal Behaviour 174:21-30. 10.1016/j.anbehav.2021.01.012 [doi]
    • Schrader L, Winter M, Errbii M, Delabie J, Oettler J, Gadau J (2021) Inhibition of HSP90 causes morphological variation in the invasive ant Cardiocondyla obscurior. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution [online ahead of print] 10.1002/jez.b.23035 [doi]
    • Kranke N (2021) The Trees' Tale: Filigreed Phylogenetic Trees and Integrated Narratives. In: Morgan MS, Hajek KM, Berry DJ (eds.): Narrative Science: Ordering Knowledge from the Nineteenth to Twenty-First Century. Cambridge University Press [in press].
    • Desjardins E, Kurtz J, Kranke N, Lindeza AS, Richter SH (2021) Beyond Standardization: Improving External Validity and Reproducibility in Experimental Evolution. BioScience biab008 10.1093/biosci/biab008 [doi]
    • Patil A, Anhlan D, Ferrando V, Mecate-Zambrano A, Mellmann A, Wixler V, Boergeling Y, Ludwig S (2021) Phosphorylation of influenza A virus NS1 at serine 205 mediates its viral polymerase-enhancing function. Journal of Virology 95(6):e02369-20 10.1128/JVI.02369-20 [doi]
    • Effelsberg N, Stegger M, Peitzmann L, Altinok O, Coombs GW, Pichon B, Kearns A, Randad PR, Heaney CD, Bletz S, Schaumburg F, Mellmann A (2021) Global epidemiology and evolutionary history of Staphylococcus aureus ST45. Journal of Clinical Microbiology 59:e02198-20. 10.1128/JCM.02198-20 [doi]
    • Feige-Diller J, Palme R, Kaiser S, Sachser N, Richter SH (2021) The impact of varying food availability on health and welfare in mice: Testing the Match-Mismatch hypothesis. Physiology & Behavior 228:113193. 10.1016/j.physbeh.2020.113193 [doi]

    Preprints

    • Catania F, Hagen R, Vitali V. Prolonged exposure to constant environmental conditions prompts nonrandom genetic variation. bioRxiv 10.1101/2020.04.07.030270 [doi]
    • Schröder NCH, Korša A, Wami H, Dobrindt U, Kurtz J. Serial passage of the human probiotic E. coli Nissle 1917 in an insect host leads to changed bacterial phenotypes. bioRxiv 10.1101/2021.01.04.425298 [doi]
    • Churakov G, Kuritzin A, Chukharev K, Zhang F, Wünnemann F, Ulyantsev V, Schmitz J. A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees. bioRxiv 10.1101/2020.12.10.419374 [doi]
    • Del Sarto J, Gerlt V, Friedrich ME, Anhlan D, Wixler V, Martins Teixeira M, Boergeling Y, Ludwig S. Phosphorylation of JIP4 at S730 presents anti-viral properties against influenza A virus infection. bioRxiv 10.1101/2021.01.22.427772 [doi]
    • Martens L, Ruehle F, Witten A, Meder B, Katus HA, Arbustini E, Hasenfuss G, Sinner MF, Kaab S, Pankuweit S, Angermann C, Bornberg-Bauer E, Stoll M. A genetic variant aletrs the secondary structure of the lncRNA H19 and is associated with Dilated Cardiomyopathy. bioRxiv 10.1101/2021.01.22.427739 [doi]
    • Gandhi S, Witten A, deMajo F, Gilbers M, Maessen JG, Schotten U, de Windt L, Stoll M. Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology. bioRxiv 10.1101/2021.01.22.427752 [doi]
    • Lindeza AS, Barth K, Kurtz J, Zanchi C. A Gene Knock-Down Approach in Tribolium castaneum to Study Survival and Priming Towards Bacillus thuringiensis var. tenebrionis. Preprints 2021010531 10.20944/preprints202101.0531.v1 [doi]
    • Kranke N. Do concepts of individuality account for individuation practices in studies of host-parasite systems? A modelling account of biological individuality. PhilSci Archive 18610 http://philsci-archive.pitt.edu/id/eprint/18610

     

  • 2020

    • Hagen R, Vitali V, Catania F (2020) Cross-Generational Effects and Non-random Developmental Response to Temperature Variation in Paramecium. Frontiers in Cell and Developmental Biology 8:584219. 10.3389/fcell.2020.584219 [doi]
    • Klees S*, Effelsberg N*, Stührenberg B, Mellmann A, Schwarz S, Köck R (2020) Prevalence and Epidemiology of Multidrug-Resistant Pathogens in the Food Chain and the Urban Environment in Northwestern Germany. Antibiotics 9:708. 10.3390/antibiotics9100708 [doi]
      *equally contributing authors
    • Dowling D, Schmitz JF, Bornberg-Bauer E (2020) Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution 12(11):2183-2195. 10.1093/gbe/evaa194 [doi]
    • Churakov G*, Zhang F*, Grundmann N, Makalowski W, Noll A, Doronina L, Schmitz J (2020) The multi-comparative 2-n-way genome suite. Genome Research 30:1508-1516. 10.1101/gr.262261.120 [doi]
      *equally contributing authors
    • Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, Marcus von Reumont B, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O (2020) Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera. Genome Biol Evol evaa106 [online ahead of print]. 10.1093/gbe/evaa106 [doi]
    • Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa C, Vorburger C, Legeai F, Gadau J (2020) Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 21(1):376. 10.1186/s12864-020-6764-0 [doi]
    • Kranke N (2020) How the Suffering of Nonhuman Animals and Humans in Animal Research is Interconnected. Journal of Animal Ethics 10(1):41-48. 10.5406/janimalethics.10.1.0041 [doi]
    • Zanchi C*, Lindeza AS*, Kurtz J (2020) Comparative Mortality and Adaptation of a Smurf Assay in two Species of Tenebrionid Beetles Exposed to Bacillus thuringiensis. Insects 11:261. 10.3390/insects11040261 [doi]
      *equally contributing authors
    • Thind AS*, Vitali V*, Guarracino MR, Catania F (2020) What's genetic variation got to do with it? Starvation-induced self-fertilizartion enhances survival in Paramecium. Genome Biol Evol 12:626-638. 10.1093/gbe/evaa052 [doi]
      *equally contributing authors
    • Feige-Diller J, Krakenberg V, Bierbaum L, Seifert L, Palme R, Kaiser S, Sachser N, Richter SH (2020) The Effects of Different Feeding Routines on Welfare in Laboratory Mice. Frontiers in Veterinary Science 6:479. 10.3389/fvets.2019.00479 [doi]
    • Effelsberg N, Udarcev S, Müller H, Kobusch I, Linnemann S, Boelhauve M, Köck R, Mellmann A (2020) Genotypic characterization of livestock-associated methicillin-resistant Staphylococcus aureus isolates of clonal complex 398 in pigsty visitors: transient carriage or persistence? Journal of Clinical Microbiology 58:e01276-19. 10.1128/JCM.01276-19 [doi]

     

  • 2019

    • Gati NS, Middendorf-Bauchart B, Bletz S, Dobrindt U & Mellmann A (2019) Origin and evolution of hybrid Shiga toxin-producing and uropathogenic (STEC/UPEC) Escherichia coli of sequencing type 141. Journal of Clinical Microbiology [epub ahead of print] 10.1128/JCM.01309-19 [doi]
    • Vitali V, Hagen R Catania F (2019) Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia. Genome Research 29:1693-1704. 10.1101/gr.245332.118 [doi]
    • Altinok OA (2019) Mao's Marxist Negation of Marxism. Asian Studies 7(1):75-96. 10.4312/as.2019.7.1.75-96 [doi]
    • Gandhi S, Ruehle F & Stoll M (2019) Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology. Noncoding RNA 5(1):15. 10.3390/ncrna5010015 [doi]

     

  • 2018

    • Richter SH & Hintze S (2018) From the individual to the population and back again? Emphasising the role of the individual in animal welfare science. Applied Animal Behaviour Science 212: 1-8. 10.1016/j.applanim.2018.12.012 [doi]
    • Langhanki L, Berger P, Treffon J, Catania F, Kahl BC & Mellmann A (2018) In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans. BMC Microbiology 18: 152. 10.1186/s12866-018-1308-3 [doi]
    • Vitali V, Horn F & Catania F (2018) Insulin-like signalling within and beyond metazoans. Biological Chemistry 399: 851-857. 10.1515/hsz-2018-0135 [doi]
    • Bayersdorf R, Fruscalzo A & Catania F (2018) Linking autoimmunity to the origin of the adaptive immune system. Evolution, Medicine, and Public Health 2018(1): 2-12. 10.1093/emph/eoy001 [doi]
    • Doronina L & Kranke N (2018) Das Verwandtschaftsnetz von Fledermaus, Pferd, Hund und Kuh. Biologie in unserer Zeit 48(5): 287-288. 10.1002/biuz.201870505 [doi]

     

  • 2017

    • Catania F (2017) From intronization to intron loss: How the interplay between mRNA-associated processes can shape the architecture and the expression of eukaryotic genes. The International Journal of Biochemistry & Cell Biology 91: 136-144. 10.1016/j.biocel.2017.06.017 [doi]