Publications of CRC 1076 AquaDiva

Chaudhari N.M., Pérez-Carrascal O.M., Overholt W.A., Totsche K.U. and Küsel K. (2023) Genome streamlining in CPR bacteria transitioning from soil to groundwater. PREPRINT: BioRxiv. DOI: 10.1101/2023.05.10.540099External link.

Pohl F., Schrön M., Rebmann C., Hildebrandt A. (2022) Transforming in-situ measurements allows robust estimation of the spatial average of soil moisture despite sensor failures.  PREPRINT: ESS Open Archive June 24, 2022. DOI: 10.1002/essoar.10511705.1External link.

Spangenberg J., Höner zu Siederdissen C., Zarkovic M., Triebel S., Rose R., Martinez Christophersen C., Paltzow L., Hegab M.M., Wansorra A., Srivastava A., Krumbholz A., Marz M. (2023) Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples. PREPRINT: BioRxiv. DOI: 10.1101/2023.03.17.533105External link.

Algergawy A., Hamed H., Thiel S., König-Ries B. (2024) Towards Semantic Annotation for Scientific Datasets. Poster PaperExternal link at the 21st International Conference - The Semantic Web (ESWC 2024External link). 05/26/2024 - 05/30/2024, Hersonissos, Crete, Greece.

Contreras J., Mostafapour S., Popp J., Bocklitz T. (2024) Siamese networks for clinically relevant bacteria classification based on Raman spectroscopy. Molecules 29(5): 1061. DOI: 10.3390/molecules29051061External link. OPEN ACCESS 

Demir G., Guswa A.J., Filipzik J., Metzger J.C., Römermann C., Hildebrandt A. (2024) Root water uptake patterns are controlled by tree species interactions and soil water variability. Hydrology and Earth System Sciences 28: 1441–1461. DOI: 10.5194/hess-28-1441-2024External link.

Díaz-Yáñez O., Käber Y., Anders T., Bohn F., Braziunas K.H., Brůna J., Fischer R., Fischer S.M., Hetzer J., Hickler T., Hochauer C., Lexer M.J., Lischke H., Mairota P., Merganič J., Merganičová K., Mette T., Mina M., Morin X., Nieberg M., Rammer W., Reyer C.P.O., Scheiter S., Scherrer D., Bugmann H. (2024) Tree regeneration in models of forest dynamics: A key priority for further research. Ecosphere 15(3): e4807. DOI: 10.1002/ecs2.4807External link. OPEN ACCESS 

Frempong S.B., Salbreiter M., Mostafapour S., Pistiki A., Bocklitz T.W., Rösch P., Popp J. (2024) Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 29(5): 1077. DOI: 10.3390/molecules29051077External link. OPEN ACCESS

Khurana S., Heße F., Hildebrandt A., Thullner M. (2024) Microbial mediated carbon and nitrogen cycling in the spatially heterogeneous vadose zone: A modeling study. Vadose Zone Journal 23(2): e20315. DOI: 10.1002/vzj2.20315External link. OPEN ACCESS

Lange M., Azizi-Rad M., Dittmann G., Lange D.F., Orme A.M., Schroeter S.A., Simon C., Gleixner G. (2024) Stability and carbon uptake of the soil microbial community is determined by differences between rhizosphere and bulk soil. Soil Biology and Biochemistry 189: 109280. DOI: 10.1016/j.soilbio.2023.109280External link. OPEN ACCESS

Lehnert A.-S., Cooper R.E., Ignatz R., Rücker A., Gomes-Alves E., Küsel K., Pohnert G., Trumbore S.E. (2024) Dimethyl sulfide emissions from a peatland result more from organic matter degradation than sulfate reduction. JGR Biogeosciences 129(1): e2023JG007449. DOI: 10.1029/2023JG007449External link. OPEN ACCESS

Ryabchykov O., Cialla-May D., Silge A., Mostafapour S., Mokari A., Luo R., Dehbozorgi P., Contreras J., Popp J., Bocklitz T. (2024) 12 - Recent innovations in signal and image processing and data analysis in Raman spectroscopy. In: Armani A., Chalyan T., Sampson D.D. (eds.) Photonic Materials and Applications Series, Biophotonics and Biosensing, pp. 391-416. Elsevier 2024. DOI: 10.1016/B978-0-44-318840-4.00020-6External link.

Sharma A., Taubert M., Pérez-Carasscal O.M., Lehmann R., Ritschel T., Totsche K.U., Lazar C.S., Küsel K. (2024) Iron coatings on carbonate rocks shape the attached bacterial aquifer community. Science of the Total Environment 917: 170384. DOI: 10.1016/j.scitotenv.2024.170384External link. OPEN ACCESS

Zulfiqar M., Singh V., Steinbeck C., Sorokina M. (2024) Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Critical Reviews in Microbiology. DOI: 10.1080/1040841X.2024.2306465External link. OPEN ACCESS

Babalou S., Algergawy A., König-Ries B. (2023) SimBio: Adopting Particle Swarm Optimization for ontology-based biomedical term similarity assessment. Data & Knowledge Engineering 145: 102137. DOI: 10.1016/j.datak.2022.102137External link. OPEN ACCESS

Buivydaitė Z., Aryal L., Borim Corrêa F., Chen T., Langlois V., Lorenzen Elberg C., Netherway T., Wang R., Zhao T., Acharya B., Emerson J.B., Hillary L., Khadka R.B.,  Mason-Jones K., Sapkota R., Sutela S., Trubl G., White R.A., Winding A., Carreira C. (2023) Meeting report: The first soil viral workshop 2022. Virus Research 331: 199121. DOI: 10.1016/j.virusres.2023.199121External link. OPEN ACCESS

Fischer-Bedtke, Metzger J.C., Demir G., Wutzler T., Hildebrandt A. (2023) Throughfall spatial patterns translate into spatial patterns of soil moisture dynamics – empirical evidence. Hydrology and Earth System Sciences 27(15): 2899–2918. DOI: 10.5194/hess-27-2899-2023External link. OPEN ACCESS

Heinze B.M., Küsel K., Jehmlich N., von Bergen M., Taubert M. (2023) Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater. Water Research 244: 120426. DOI: 10.1016/j.watres.2023.120426External link.

Henniger H., Huth A., Bohn F.J. (2023) A new approach to derive productivity of tropical forests using radar remote sensing measurements. Royal Society Open Science 10(11): 231186. DOI: 10.1098/rsos.231186External link. OPEN ACCESS

Henniger H., Huth A., Frank K., Bohn F.J. (2023) Creating virtual forests around the globe and analysing their state space. Ecological Modelling 483: 110404. DOI: 10.1016/j.ecolmodel.2023.110404External link.

Herrmann M., Lehmann K., Totsche K.U., Küsel K. (2023) Seepage-mediated export of bacteria from soil is taxon-specific and driven by seasonal infiltration regimes. Soil Biology and Biochemistry 187: 109192. DOI: 10.1016/j.soilbio.2023.109192External link. OPEN ACCESS

Hohenbrink T.L., Jackisch C., Durner W., Germer K., Iden S.C., Kreiselmeier J., Leuther F., Metzger J.C., Naseri M., Peters A. (2023) Soil water retention and hydraulic conductivity measured in a wide saturation range. Earth System Science Data 15810): 4417–4432.  DOI: 10.5194/essd-15-4417-2023, 2023External link. OPEN ACCESS

Kawa N., Cucchi K., Rubin Y., Attinger S., Heße F. (2023) Defining hydrogeological site similarity with hierarchical agglomerative clustering. Groundwater 61(4): 563-573. DOI: 10.1111/gwat.13261External link. OPEN ACCESS

Krüger M., Chaudhari N., Thamdrup B., Overholt W.A., Bristow L.A., Taubert M., Küsel K., Jehmlich N., von Bergen M., Herrmann M. (2023) Differential contribution of nitrifying prokaryotes to groundwater nitrification. ISME Journal 17: 1601-1611. DOI: 10.1038/s41396-023-01471-4External link. OPEN ACCESS

Lazar C.S., Schwab V.F., Ueberschaar N., Pohnert G., Trumbore S.E., Küsel K. (2023) Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters. Frontiers in Microbiology 14: 1252498. DOI: 10.3389/fmicb.2023.1252498External link. OPEN ACCESS

Mostafapour S., Dörfer T., Heinke R., Rösch P., Popp J., Bocklitz T. (2023) Investigating the effect of different pre-treatment methods on Raman spectra recorded with different excitation wavelengths. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 302: 123100. DOI: 10.1016/j.saa.2023.123100External link. OPEN ACCESS

Otto J.F.M., Kiel C., Nejstgaard J.C., Pohnert G., Berger S.A., Ueberschaar N. (2023) Tracking a broad inventory of cyanotoxins and related secondary metabolites using UHPLC-HRMS. Journal of Hazardous Materials Advances 12: 100370. DOI: 10.1016/j.hazadv.2023.100370External link. OPEN ACCESS

Rangel-Pineros G., Almeida A., Beracochea M., Sakharova E., Marz M., Reyes Muñoz A., Hölzer M., Finn R.D. (2023) VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models. PLOS Computational Biology 19(8): e1011422. DOI: 10.1371/journal.pcbi.1011422External link. OPEN ACCESS

Ritsch M., Cassman N.A., Saghaei S., Marz M. (2023) Navigating the Landscape: A Comprehensive Review of Current Virus Databases. Viruses 15(9): 1834. DOI: 10.3390/v15091834External link. OPEN ACCESS

Samuel S., König-Ries B., Algergawy A. (2023) The role of ontology matching in ontology network development. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E.,  Hassanzadeh O., Trojahn C. (eds.) Proceedings of the 18th International Workshop on Ontology Matching (OM 2023)External link [co-located with the 22nd International Semantic Web Conference ISWC-2023]. 07/11/2023, Athens, Greece. CEUR Workshop Proceedings Vol-3591. OPEN ACCESS

Safrastyan A., Höner zu Siederdissen C., Wollny D. (2023) Decoding cell-type contributions to the cfRNA transcriptomic landscape of liver cancer. Human Genomics 17: 90. DOI: 10.1186/s40246-023-00537-wExternal link. OPEN ACCESS

Santos J.D.N., Vitorino I.R., Kallscheuer N., Srivastava A., Krautwurst S., Marz M., Jogler C., Lobo-da-Cunha A., Catita J., Gonçalves H., González I., Reyes F., Lage O.M. (2023) Streptomyces marispadix sp. nov., isolated from marine beach sediment. International Journal of Systematic and Evolutionary Microbiology 73: 005956. DOI: 10.1099/ijsem.0.005956External link. OPEN ACCESS

Wegner C.E., Stahl R., Velsko I., Hübner A., Fagernäs Z., Warinner C., Lehmann R., Ritschel T., Totsche K.U., Küsel K. (2022) A glimpse of the paleome in endolithic microbial communities. Microbiome 11(1): 210. DOI: 10.1186/s40168-023-01647-2External link. OPEN ACCESS

Abdelmageed N., Löffler F., Feddoul L., Algergawy A., Samuel S., Gaikwad J., Kazem A., König-Ries B. (2022) BiodivNERE: Gold standard corpora for named entity recognition and relation extraction in the biodiversity domain. Biodiversity Data Journal 10: e89481. DOI: 10.3897/BDJ.10.e89481External link. OPEN ACCESS

Akinyede R., Taubert M., Schrumpf M., Trumbore S., Küsel K. (2022a) Dark CO₂ fixation in temperate beech and pine forest soils. Soil Biology and Biochemistry 165: 108526. DOI: 10.1016/j.soilbio.2021.108526External link. 

Akinyede R., Taubert M., Schrumpf M., Trumbore S., Küsel K. (2022b) Temperature sensitivity of dark CO₂ fixation in temperate forest soils. Biogeosciences 19: 4011-4028. DOI: 10.5194/bg-19-4011-2022External link. OPEN ACCESS

Azemtsop Matanfack G., Taubert M., Reilly-Schott V., Küsel K., Rösch P., Popp J. (2022) Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D₂O Labeling. Analytical Chemistry 94(22): 7759–7766. DOI: 10.1021/acs.analchem.1c04097External link.

Blohm A., Kumar S., Knebl A., Herrmann M., Küsel K., Popp J., Frosch T. (2022) Activity and electron donor preference of two denitrifying bacterial strains identified by Raman gas spectroscopy. Analytical and Bioanalytical Chemistry 414: 601-611. DOI:10.1007/s00216-021-03541-yExternal link. OPEN ACCESS

Bruckmann C., Müller S., Höner zu Siederdissen C. (2022) Automatic, fast, hierarchical, and non-overlapping gating of flow cytometric data with flowEMMi v2. Computational and Structural Biotechnology Journal 20: 6473-6489. DOI: 10.1016/j.csbj.2022.11.033External link. OPEN ACCESS

Castro-Morales K., Canning A., Arzberger S., Overholt W.A., Küsel K., Kolle O., Göckede M., Zimov N. and Körtzinger A. (2022) Highest methane concentrations in an Arctic river linked to local terrestrial inputs. Biogeosciences 19(21): 5059-5077. Doi: 10.5194/bg-19-5059-2022External link. OPEN ACCESS

Castro-Morales K., Canning A., Körtzinger A., Göckede M., Küsel K., Overholt W.A., Wichard T., Redlich S., Arzberger S., Kolle O., Zimov N. (2022) Effects of reversal of water flow in an Arctic floodplain river on fluvial emissions of CO₂ and CH₄. Journal of Geophysical Research: Biogeosciences 127(1): e2021JG006485. DOI: 10.1029/2021JG006485External link. OPEN ACCESS

Demir G., Friesen J., Filipzik J., Michalzik B., Hildebrandt A. (2022) A Method Proposal for Throughfall Measurement in Grassland at Plot Scale in Temperate Climate: ‘Interception Tubes’. Frontiers in Earth Sciences 10: 799419. DOI: 10.3389/feart.2022.799419External link. OPEN ACCESS

Demir G., Michalzik B., Filipzik J., Metzger J. and Hildebrandt A. (2022) Spatial variation of grassland canopy affects soil wetting patterns and preferential flow. Hydrological Processes 36(12): e14760. DOI: 10.1002/hyp.14760External link. OPEN ACCESS

Eggers D., Höner zu Siederdissen C., Stadler P.F. (2022) Accuracy of RNA structure prediction depends on the pseudoknot grammar. In: Scherer N.M., de Melo-Minardi R.C. (eds) Advances in Bioinformatics and Computational Biology. BSB 2022. Lecture Notes in Computer Science vol 13523. Springer, Cham. DOI: 10.1007/978-3-031-21175-1_3External link.

Geesink P., Taubert M., Jehmlich N., von Bergen M., Küsel K. (2022) Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome. Microbiology Spectrum 10(4): e00437-22. DOI: 10.1128/spectrum.00437-22External link. OPEN ACCESS

Khurana S., Heße F., Hildebrandt A., Thullner M. (2022) Predicting the impact of spatial heterogeneity on microbially mediated nutrient cycling in the subsurface. Biogeosciences 19(3): 665-688. DOI: 10.5194/bg-19-665-2022External link. OPEN ACCESS

Khurana S., Heße F., Hildebrandt A., & Thullner M. (2022) Should we worry about surficial dynamics when assessing nutrient cycling in the groundwater? Frontiers in Water 4: 780297. DOI: 10.3389/frwa.2022.780297External link. OPEN ACCESS

Mock F., Kretschmer F., Kriese A., Marz M. (2022) Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks. PNAS Biophysics and Computational Biology 119(35): e2122636119. DOI: 10.1073/pnas.2122636119External link. OPEN ACCESS

Orme A.M., Lange M., Schroeter S.A., Wicke M., Kolle O., Pohnert G., Gleixner G. (2022) Drought reduces release of plant matter into dissolved organic matter potentially restraining ecosystem recovery. Frontiers in Soil Science 2: 904259. DOI: 10.3389/fsoil.2022.904259External link. OPEN ACCESS

Overholt W.A., Trumbore S., Xu X., Bornemann T.L.V., Probst A.J., Krüger M., Herrmann M., Thamdrup B., Bristow L.A., Taubert M., Schwab V.F., Hölzer M., Marz M., Küsel K. (2022) Carbon fixation rates in groundwater similar to those in oligotrophic marine systems. Nature Geoscience 15: 561–567. DOI: 10.1038/s41561-022-00968-5External link. OPEN ACCESS

Perez-Molphe-Montoya E., Küsel K., Overholt W. (2022) Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota. Environmental Microbiology 24(11): 5437-5449. DOI: 10.1111/1462-2920.16170External link. OPEN ACCESS

Potthast K., Tischer A., Herrmann M., Weinhold A., Küsel K., van Dam N.M., Michalzik B. (2022) Woolly beech aphid infestation reduces soil organic carbon availability and alters phyllosphere and rhizosphere bacterial microbiomes. Plant and Soil 473: 639–657. DOI: 10.1007/s11104-022-05317-4External link. OPEN ACCESS

Sanchez-Arcos C., Ueberschaar N., Pohnert G. (2022) Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics. Water Research 219: 118566. DOI: 10.1016/j.watres.2022.118566External link. OPEN ACCESS

Savio D., Derx J., Lang R.-P., Kirschner A.K.T., Sommer R., Blaschke A.P., Küsel K., Farnleitner A.H. (2022) From groundwater to drinking water - Microbiology of karstic water resources. In: Tockner K., Mehner T. (eds.) Encyclopedia of Inland Waters 2nd edition. Vol. 3, pp. 560-579. Elsevier, Oxford. DOI: 10.1016/B978-0-12-819166-8.00181-XExternal link. 

Schroeter S.A., Eveillard D., Chaffron S., Zoppi J., Kampe B., Lohmann P., Jehmlich N., von Bergen M., Sanchez-Arcos C., Pohnert G., Taubert M., Küsel K., Gleixner G. (2022). Microbial community functioning during plant litter decomposition. Scientific reports 12(1): 7451. DOI:10.1038/s41598-022-11485-1External link. OPEN ACCESS

Simon C., Dührkop K., Petras D., Roth V.-N., Böcker S., Dorrestein P., Gleixner G. (2022) Mass difference matching unfolds hidden molecular structures of dissolved organic matter. Environmental Science and Technology 56(15): 11027–11040. DOI: 10.1021/acs.est.2c01332External link. OPEN ACCESS

Stolze K., Barnes A.D., Eisenhauer N., Totsche K.U. (2022) Depth-differentiated, multivariate control of biopore number under different land-use practices. Geoderma 418: 115852. DOI:  10.1016/j.geoderma.2022.115852External link. OPEN ACCESS

Tanunchai B., Schroeter S.A., Ji L., Fareed Mohamed Wahdan S., Hossen S., Lehnert A.-S., Grünberg H., Gleixner G., Buscot F., Schulze E.-D., Noll M., Purahong W. (2022) More than you can see: Unraveling the ecology and biodiversity of lichenized fungi associated with leaves and needles of 12 temperate tree species using high-throughput sequencing. Frontiers in Microbiology 13: 907531. DOI: 10.3389/fmicb.2022.907531External link. OPEN ACCESS

Taubert M., Overholt W.A., Heinze B., Azemtsop Matanfak G., Houhou R., Jehmlich N., von Bergen M., Rösch P., Popp J., Küsel K. (2022) Bolstering fitness via CO₂ fixation and organic carbon uptake: mixotrophs in modern groundwater. The ISME Journal 16: 1153–1162. DOI: 10.1038/s41396-021-01163-xExternal link. OPEN ACCESS

Thullner M., Brodie E.L., Meile C., Pagel H. (2022) Editorial: Modeling the link between microbial ecology and biogeochemical process dynamics. Frontiers in Ecology and Evolution 10: 994090. DOI: 10.3389/fevo.2022.994090External link. OPEN ACCESS

Xiong B.J., Kleinsteuber S., Sträuber H., Dusny C., Harms H., Wick L.Y. (2022) Impact of Fungal Hyphae on Growth and Dispersal of Obligate Anaerobic Bacteria in Aerated Habitats. mBio 13(3): e0076922. DOI: 10.1128/mbio.00769-22External link. OPEN ACCESS

Xiong B.J., Stanley C.E., Dusny C., Schlosser D., Harms H., Wick L.Y. (2022) pH Distribution along Growing Fungal Hyphae at Microscale. Journal of Fungi 8(6): 599. DOI: 10.3390/jof8060599External link. OPEN ACCESS

You X., Kallies R., Hild K., Hildebrandt A., Harms H., Chatzinotas A., Wick L.Y. (2022) Transport of marine tracer phage particles in soil. Science of The Total Environment 814: 152704. DOI: 10.1016/j.scitotenv.2021.152704External link. OPEN ACCESS

You X., Kallies R., Kühn I., Schmidt M., Harms H., Chatzinotas A., Wick L. (2022) Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. The ISME Journal 16: 1275-1283. DOI: 10.1038/s41396-021-01155-xExternal link. OPEN ACCESS

You X., Klose N., Kallies R., Harms H., Chatzinotas A., Wick L.Y. (2022) Mycelia-assisted isolation of non-host bacteria able to co-transport phages. Viruses 14(2): 195. DOI: 10.3390/v14020195External link. OPEN ACCESS

Zerfaß C., Lehmann R., Ueberschaar N., Sanchez-Arcos C., Totsche K.U. and Pohnert G. (2022) Groundwater metabolome responds to recharge in fractured sedimentary strata. Water Research 223: 118998. DOI: 10.1016/j.watres.2022.118998External link. OPEN ACCESS

Abdelmageed N., Algergawy A., Samuel S. (2021) BiodivOnto: Towards a core ontology for biodiversity. In: Verborgh R., Dimou A., Hogan A., d'Amato C., Tiddi I., Bröring A., Mayer S., Ongenae F., Tommasini R., Alam M. (eds.) The Semantic Web: ESWC 2021 Satellite EventsExternal link. ESWC 2021, 06/06/2021-06/10/2021, virtual event. Lecture Notes in Computer Science, vol 12739. Springer, Cham. DOI: 10.1007/978-3-030-80418-3_1.External link

Abdelmageed N., Algergawy A., Samuel S., König-Ries B. (2021) A data-driven approach for core biodiversity ontology developmentExternal link. In: Sanfilippo E.M., Kutz O., Troquard N., Hahmann T., Masolo C., Hoehndorf R., Vita R. (eds.) Proceedings of the 3rd International Workshop on Semantics for Biodiversity (S4BioDiv 2021) [held at the Joint Ontology Workshops (JOWO 2021)External link, co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021) and the 12th International Conference on Biomedical Ontologies (ICBO 2021): Episode VII The Bolzano Summer of Knowledge]. 09/11/2021 - 09/18/2021, Bolzano, Italy. CEUR Workshop Proceedings Vol-2969.

Achilles F., Tischer A., Bernhardt-Römermann M., Heinze M., Reinhardt F., Makeschin F., Michalzik B. (2021) European beech leads to more bioactive humus forms but stronger mineral soil acidification as Norway spruce and Scots pine - Results of a repeated site assessment after 63 and 82 years of forest conversion in Central Germany. Forest Ecology and Management 483: 118769. DOI: 10.1016/j.foreco.2020.118769External link.

Algergawy A., Hamed H., König-Ries B. (2021) Towards scientific data synthesis using deep learning and semantic web. In: Verborgh R., Dimou A., Hogan A., d'Amato C., Tiddi I., Bröring A., Mayer S., Ongenae F., Tommasini R., Alam M. (eds.) The Semantic Web: ESWC 2021 Satellite Events.External link ESWC 2021, 06/06/2021-06/10/2021, virtual event. Lecture Notes in Computer Science, vol 12739. Springer, Cham. DOI: 10.1007/978-3-030-80418-3_10External link.

Azemtsop Matanfack G., Pistiki A., Rösch P., Popp J. (2021) Raman ¹⁸O-labeling of bacteria in visible and deep UV-ranges. Journal of Biophotonics 14(6):e202100013. DOI: 10.1002/jbio.202100013.External link

Azemtsop Matanfack G., Pistiki A., Rösch P., Popp J. (2021) Raman stable isotope probing of bacteria in visible and deep UV-ranges. Life 11(10): 1003. DOI: 10.3390/life11101003External link.

Brunzel M., Dirauf M., Sahn M., Czaplewska J.A., Fritz N., Weber C., Nischang I., Schubert U.S. (2021) On the identification and quantification of proton-initiated species in the synthesis of poly(2-alkyl-2-oxazoline)s by high resolution liquid chromatography. Journal of Chromatography A 1653: 462364. DOI: 10.1016/j.chroma.2021.462364External link.

Carrasco Flores D., Fricke M., Vesp V., Desirò D., Kniewasser A., Hölzer M., Marz M., Mittag M. (2021) A marine Chlamydomonas sp. emerging as an algal model. Journal of Phycology 57(1): 54-69. DOI: 10.1111/jpy.13083External link.

Chamanara J., Gaikwad J., Gerlach R., Algergawy A., Ostrowski A., König-Ries B. (2021) BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data. Biodiversity Data Journal 9: e72901. DOI: 10.3897/BDJ.9.e72901External link.

Ehrle A., Kolle O., Tischer A., Trumbore S.E., Michalzik B. (2021) Effects of mound building Lasius flavus on organic carbon and nutrient fluxes in soils of temperate grassland ecosystems. Pedobiologia 84: 150701. DOI: 10.1016/j.pedobi.2020.150701External link.

Herrmann M, Geesink P, Richter R, Küsel K (2021) Canopy position has a stronger effect than tree species identity on phyllosphere bacterial diversity in a floodplain hardwood forest. Microbial Ecology 81: 157-168. DOI: 10.1007/s00248-020-01565-yExternal link.

Houhou R., Rösch P., Popp J., Bocklitz T. (2021) Comparison of functional and discrete data analysis regimes for Raman spectra. Analytical and Bioanalytical Chemistry, 413, 5633–5644. DOI: 10.1007/s00216-021-03360-1External link.

Houhou R., Bocklitz T. (2021) Trends in artificial intelligence, machine learning, and chemometrics applied to chemical data. Analytical Science Advances, 2(3-2), 128–141. DOI: 10.1002/ansa.202000162External link.

Hölzer M., Marz M. (2021) PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. Bioinformatics 37(7): 1018-1020. DOI: 10.1093/bioinformatics/btaa695External link.

Jing M., Kumar R., Attinger S., Li Q., Lu C., Heße F. (2021) Assessing the contribution of groundwater to catchment travel time distributions through integrating conceptual flux tracking with explicit Lagrangian particle tracking. Advances in Water Resources 149: 103849. DOI: 10.1016/j.advwatres.2021.103849External link.

Kraus D., Kleiber A., Ehrhardt E., Leifheit M., Horbert P., Urban M., Gleichmann M., Mayer G., Popp J., Henkel T. (2021) Three step flow focusing enables image-based discrimination and sorting of late stage 1 Haematococcus pluvialis cells. PLoS ONE 16(3): e0249192. DOI: 10.1371/journal.pone.0249192External link.

Krüger M., Potthast K., Michalzik B., Tischer A., Küsel K., Deckner F.F.K., Herrmann M. (2021) Drought and rewetting events enhance nitrate leaching and seepage-mediated translocation of microbes from beech forest soils. Soil Biology and Biochemistry 154: 108153. DOI: 10.1016/j.soilbio.2021.108153External link.

Lehmann K., Lehmann R., Totsche K.U. (2021) Event-driven dynamics of the total mobile inventory in undisturbed soil account for significant fluxes of particulate organic carbon. Sci Total Environ 756: 143774. DOI: 10.1016/j.scitotenv.2020.143774External link.

Löffler F., Wesp V., König-Ries B., Klan F. (2021) Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs? PLoS ONE 16(3): e024609. DOI: 10.1371/journal.pone.0246099External link.

Metzger J.C., Filipzik J., Michalzik B., Hildebrandt A. (2021) Stemflow infiltration hotspots create soil microsites near tree stems in an unmanaged mixed beech forest. Frontiers in Forests and Global Change 4, 701293. DOI: 10.3389/ffgc.2021.701293External link.

Mock F., Viehweger A., Barth E., Marz M. (2021) VIDHOP, viral host prediction with Deep Learning. Bioinformatics 37(3): 318-325. DOI: 10.1093/bioinformatics/btaa705External link.

Potthast K., Meyer S., Tischer A., Gleixner G., Sieburg A., Frosch T., Michalzik B. (2021) Grasshopper herbivory immediately affects element cycling but not export rates in an N-limited grassland system. Ecosphere 12(3): e03449. DOI: 10.1002/ecs2.3449External link

Ritschel T., Lehmann K., Brunzel M., Vitz J., Nischang I., Schubert U.S., Totsche K.U. (2021) Well-defined poly(ethylene glycol) polymers as non-conventional reactive tracers of colloidal transport in porous media. Journal of Colloid and Interface Science 584, 592-601. DOI: 10.1016/j.jcis.2020.09.056External link.

Samuel S., Algergawy A., König-Ries B. (2021) Towards an ontology network for the reproducibility of scientific studiesExternal link. In: Sanfilippo E.M., Kutz O., Troquard N., Hahmann T., Masolo C., Hoehndorf R., Vita R. (eds.) Proceedings of the Joint Ontology Workshops 2021External link [co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021) and the 12th International Conference on Biomedical Ontologies (ICBO 2021): Episode VII The Bolzano Summer of Knowledge]. 09/11/2021 - 09/18/2021, Bolzano, Italy. CEUR Workshop Proceedings Vol-2969.

Simon C., Pimentel T.P., Monteiro M.T.F., Candido L.A., Gastmans D., Geilmann H., da Costa Oliveira R., Rocha J.B., Pires E., Quesada C.A., Forsberg B.R., Ferreira S.J.F., da Cunha H.B., Gleixner G. (2021) Molecular links between whitesand ecosystems and blackwater formation in the Rio Negro watershed. Geochimica et Cosmochimica Acta 311: 274-291. DOI: 10.1016/j.gca.2021.06.036External link.

Starke R., Schäpe S.S., Jehmlich N., von Bergen M. (2021) Protein stable isotope probing with H₂¹⁸O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12. Rapid communications in Mass Spectrometry 35(1): e8941. DOI: 10.1002/rcm.8941External link.

Ueberschaar N., Lehmann K., Meyer S., Zerfaß C., Michalzik B., Totsche K.U., Pohnert G. (2021) Soil solution analysis with untargeted GC-MS - A case study with different lysimeter types. Front Earth Sci 8: 563379. DOI: 10.3389/feart.2020.563379External link.

Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C. (2021) Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Computational Biology 17(2): e1008716. DOI: 10.1371/journal.pcbi.1008716.External link

Voigt E., Rall B.C., Chatzinotas A., Brose U., Rosenbaum B. (2021) Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 9:e12194. Doi: 10.7717/peerj.12194External link

Wegner C.-E., Westermann M., Steiniger F., Gorniak L., Budhraja R., Adrian L., Küsel K. (2021) Extracellular and intracellular lanthanide accumulation in the methylotrophic Beijerinckiaceae bacterium RH AL1. Applied and Environmental Microbiology 87(13): e03144-20. DOI: 10.1128/AEM.03144-20External link.

Xenophontos C., Taubert M., Harpole W.S., Küsel K. (2021) Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities. FEMS Microbiology Ecology 97 (3), fiab017. DOI: 10.1093/femsec/fiab017External link. Selected as Editor´s Choice March 2021.

Yan L., Hermans S.M., Totsche K.U., Lehmann R., Herrmann M., Küsel K. (2021) Groundwater bacterial communities evolve over time in response to recharge. Water Research 201: 117290. DOI: 10.1016/j.watres.2021.117290External link.

Akinyede R., Taubert M. , Schrumpf M., Trumbore S., Küsel K. (2020) Rates of dark CO₂ fixation are driven by microbial biomass in a temperate forest soil. Soil Biology and Biochemistry 150: 107950. DOI: 10.1016/j.soilbio.2020.107950External link.

Algergawy A., Babalou S., Klan F., König-Ries B. (2020) Ontology modularization with OAPT. Journal on Data Semantics 9: 53-83. DOI: 10.1007/s13740-020-00114-7External link

Algergawy A., Stangneth R., Heger T., Jeschke J.M., König-Ries B. (2020) Towards a core ontology for hierarchies of hypotheses in invasion biology. In: Harth A. et al. (eds) The Semantic Web: ESWC 2020 Satellite Events. ESWC 2020. Lecture Notes in Computer Science, vol 12124. Springer, Cham. DOI: 10.1007/978-3-030-62327-2_1External link.

Azemtsop Matanfack G., Rüger J., Stiebing C., Schmitt M., Popp J. (2020) Imaging the invisible - Bioorthogonal Raman probes for imaging of cells and tissues. Journal of Biophotonics 13(9): e202000129. DOI: 10.1002/jbio.202000129External link.

Azemtsop Matanfack G., Taubert M., Guo S., Houhou R., Bocklitz T., Küsel K., Rösch P., PoppJ. (2020) Influence of carbon sources on quantification of deuterium incorporation in heterotrophic bacteria: A Raman-stable isotope labeling approach. Anal. Chem. 92(16): 11429-11437. DOI: 10.1021/acs.analchem.0c02443External link.

Blohm A., Sieburg A., Popp J.,Frosch T. (2020) 6 - Detection of gas molecules by means of spectrometric and spectroscopic methods. In: Baia L., Pap Z., Hernadi K., Baia M. (eds) Micro and Nano Technologies, Advanced Nanostructures for Environmental Health, pp. 251-294. Elsevier, Amsterdam, The Netherlands. DOI: 10.1016/B978-0-12-815882-1.00006-9External link.

Frosch Ta., Knebl A., Frosch T. (2020) Recent advances in nano-photonic techniques for pharmaceutical drug monitoring with emphasis on Raman spectroscopy. Nanophotonics 9(1): 19-37. DOI: 10.1515/nanoph-2019-0401External link.

Geesink P., Wegner C.-E., Probst A.J., Herrmann M., Dam H.T., Kaster A.-K., Küsel K. (2020) Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in oligotrophic groundwater. Environmental Microbiology 22(2): 726-737. DOI: 10.1111.1462-2920.14865External link.

Hawkes J.A., D'Andrilli J., Agar J.N., Barrow M.P., Berg S.M., Catalán N., Chen H., Chu R.K., Cole R.B., Dittmar T., Gavard R., Gleixner G., Hatcher P.G., He C., Hess N.J., Hutchins R.H.S., Ijaz A., Jones H.E., Kew W., Khaksari M., Palacio Lozano D.C., Lv J., Mazzoleni L.R., Noriega‐Ortega B.E., Osterholz H., Radoman N., Remucal C.K., Schmitt N.D., Schum S.K., Shi Q., Simon C., Singer G., Sleighter R.L., Stubbins A., Thomas M.J., Tolic N., Zhang S., Zito P., Podgorski D.C. (2020) An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer? Limnol Oceanogr Methods 18(6): 235-258. DOI: 10.1002/lom3.10364External link.

Herrmann M., Geesink P., Yan L., Lehmann R., Totsche K.U., Küsel K. (2020) Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Research 170: 115306. DOI: 10.1016/j.watres.2019.115306External link.

Hildebrandt A. (2020) Root-water relations and interactions in mixed forest settings. In: Levia D., Carlyle-Moses D., Iida S., Michalzik B., Nanko K., Tischer A. (eds) Forest-Water Interactions. Ecological Studies (Analysis and Synthesis) 240. Pp. 319-348. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-26086-6_14External link.

Houhou R., Barman P., Schmitt M., Meyer T., Popp J., Bocklitz T. (2020) Deep learning as phase retrieval tool for CARS spectra. Optics Express 28(14): 21002-21024. DOI: 10.1364/OE.390413External link.

Jing M., Kumar R., Heße F., Thober S., Rakovec O., Samaniego L., Attinger S. (2020) Assessing the response of groundwater quantity and travel time distribution to 1.5, 2, and 3 °C global warming in a mesoscale central German basin. Hydrol. Earth Syst. Sci. 24(3): 1511-1526. DOI: 10.5194/hess-24-1511-2020External link.

Kampe B., Duan T., Hahn U. (2020) Allgemeine Musikalische Zeitung as a searchable online corpus.External link In: Calzolari N. et al. (eds) Proceedings of the 12th Conference on Language Resources and Evaluation (LREC 2020)External link, pp. 969-976, 05/11/2020-05/16/2020, Marseille, France.

Karam N., Khiat A., Algergawy A., Sattler M., Weiland C., Schmidt M. (2020) Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35: E9. DOI: 10.1017/S0269888920000132External link.

Knebl A., Domes R., Wolf S., Domes C., Popp J., Frosch T. (2020) Fiber-enhanced Raman gas spectroscopy for the study of microbial methanogenesis. Anal. Chem. 92(18): 12564-12571. DOI: 10.1021/acs.analchem.0c02507External link.

Lehmann R. and Totsche K.U. (2020) Multi-directional flow dynamics shape groundwater quality in sloping bedrock strata. Journal of Hydrology 580: 124291. DOI: 10.1016/j.jhydrol.2019.124291External link.

Lehnert A.-S., Behrendt T., Rücker A., Pohnert G., Trumbore S. (2020) SIFT-MS optimization for atmospheric trace gas measurements at varying humidity. Atmos. Meas. Tech. 13: 3507-3520. DOI: 10.5194/amt-13-3507-2020External link.

Lehnert A.-S., Perreca E., Gershenzon J., Pohnert G., Trumbore S.E. (2020) Simultaneous real-time measurement of isoprene and 2-methyl-3-buten-2-ol emissions from trees using SIFT-MS. Frontiers in Plant Science 11: 578204. DOI: 10.3389/fpls.2020.578204External link.

Lohmann P., Benk S., Gleixner G., Potthast K., Michalzik B., Jehmlich N., von Bergen M. (2020) Seasonal patterns of dominant microbes involved in central nutrient cycles in the subsurface. Microorganisms 8(11): 1694. DOI: 10.3390/microorganisms8111694External link.

Lohmann P., Schäpe S.S., Haange S.-B., Oliphant K., Allen-Vercoe E., Jehmlich N., von Bergen M. (2020) Function is what counts: how microbial community complexity affects species, proteome and phathway coverage in metaproteomics. Expert Review of Proteomics 17(2): 163-173. DOI: 10.1080/14789450.2020.1738931External link.

Mostajo N.F., Lataretu M., Krautwurst S., Mock F., Desirò D., Lamkiewicz K., Collatz M., Schoen A., Weber F., Marz M., Hölzer M. (2020) A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes. NAR Genomics and Bioinformatics 2(1): lqz006. DOI: 10.1093/nargab/lqz006External link.

Overholt W.A., Hölzer M., Geesink P., Diezel C., Marz M., Küsel K. (2020) Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system. Environmental Microbiology 22(9): 4000-4013. DOI: 10.1111/1462-2920.15186External link.

Pour M.A.N., Algergawy A., Amini R., Faria D., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Jonquet C., Karam N., Khiat A., Laadhar A., Lambrix P., Li H., Li Y., Hitzler P., Paulheim H., Pesquita C., Saveta T., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Yaman B., Zamazal O., Zhou L. (2020) Results of the Ontology Alignment Evaluation Initiative 2020External link. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Hassanzadeh O., Trojahn C. (eds) Proceedings of the 15th International Workshop on Ontology MatchingExternal link co-located with the 19th International Semantic Web Conference (ISWC 2020), 11/02/2020, virtual conference (originally planned to be in Athens, Greece). CEUR Proceedings Vol-2788.

Reimann, L., Schwäble, A., Fricke, A.L., Mühlhäuser, W.W.D., Leber, Y., Lohanadan, K., Puchinger, M.G., Schäuble, S., Fäßler, E., Wiese, H., Reichenbach, C., Knapp, B., Peikert, C.D., Drepper, F., Hahn, U., Kreutz, C., van der Ven, P.F.M., Radziwill, G., Djinović-Carugo, K., Fürst, D.O., and Warscheid, B. (2020). Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C. Communications Biology 3, 253. DOI: 10.1038/s42003-020-0982-5External link.

Starke R., Oliphant K., Jehmlich N., Schäpe S.S., Sachsenberg T., Kohlbacher O., Allen-Vercoe E., von Bergen M. (2020) Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 222: 103791. DOI: 10.1016/j.jprot.2020.103791External link.

Tischer A., Michalzik B., Lotze R. (2020) Non-uniform but highly preferential stemflow routing along bark surfaces and actual smaller infiltration areas than previously assumed: A case study on European beech (Fagus sylvatica L.) and sycamore maple (Acer pseudoplatanus L.). ECO Letter - Ecohydrology 13(6): e2230. DOI: 10.1002/eco.2230External link.

Van Stan, II J.T., Hildebrandt A., Friesen J., Metzger J.C., Yankine S.A. (2020) Spatial variability and temporal stability of local net precipitation patterns. In: Van Stan, II J.T., Gutmann E., Friesen J. (eds) Precipitation Partitioning by Vegetation. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-29702-2_6External link.

Wick L.Y.  (2020) Bioavailability as a microbial system property: Lessons learned from biodegradation in the mycosphere: In: Ortega-Calvo J.J., Parsons J.R. (eds) The Handbook of Environmental Chemistry. Springer, Berlin, Heidelberg. DOI: 10.1007/698_2020_568External link.

Yan L., Herrmann M., Kampe B., Lehmann R., Totsche K.U., Küsel K. (2020) Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Research 170: 115341. DOI: 10.1016/j.watres.2019.115341External link.

Algergawy A., Faria D., Ferrara A., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Karam N., Khiat A., Lambrix P., Li H., Montanelli S., Paulheim H., Pesquita C., Saveta T., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Zamazal O., Zhou L. (2019) Results of the Ontology Alignment Evaluation Initiative 2019External link. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Hassanzadeh O., Trojahn C. (eds) Proceedings of the 14th International Workshop on Ontology MatchingExternal link co-located with the 18th International Semantic Web Conference (ISWC 2019), 10/26/2019, Auckland, New Zealand. CEUR Proceedings Vol-2536.

Algergawy A., König-Ries B. (2019) Partitioning of BioPortal ontologies: An empirical studyExternal link. In: Cornet R., Waagmester A. (eds.) Proceedings of the 12th International ConferenceExternal link on Semantic Web Applications and Tools for healthcare and Life Sciences (SWATExternal link⁴HCLSExternal link), 12/10/2019-12/11/2019, Edinburgh, UK. CEUR Proceedings Vol-2849.

Baumeister T.U.H., Ueberschaar N., Pohnert G. (2019) Gas-phase chemistry in the GC orbitrap mass spectrometer. Journal of the American Society for Mass Spectrometry 30(4): 573-580. DOI: 10.1007/s13361-018-2117-5External link.

Behrendt T., Agam N., Horn M.A. (2019) Microbial nitric oxide, nitrous oxide, and nitrous acid emissions from drylands. In: D'Odorico P., Porporato A., Wilkinson Runyan C. (eds) Dryland Ecohydrology. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-23269-6_13External link.

Behrendt T., Catao E.C.P., Bunk R., Yi Z., Schweer E., Kolb S., Kesselmeier J., Trumbore S. (2019) Microbial community responses determine how soil-atmosphere exchange of carbonyl sufide, carbon monooxide, and nitric oxide responds to soil moisture. SOIL 5: 121-135. DOI: 10.5194/soil-5-121-2019External link.

Benk S.A., Yan L., Lehmann R., Roth V.-N., Schwab V.F., Totsche K.U., Küsel K., Gleixner G. (2019) Fueling diversity in the subsurface: Composition and age of dissolved organic matter in the Critical Zone. Frontiers in Earth Science 7: 296. DOI: 10.3389/feart.2019.00296External link.

Fischer C., Leimer S., Roscher C., Ravenek J., de Kroon H., Kreutziger Y., Baade J., Beßler H., Eisenhauer N., Weigelt A., Mommer L., Lange M., Gleixner G., Wilcke W., Schröder B., Hildebrandt A. (2019) Plant species richness and functional groups have different effects on soil water content in a decade-long grassland experiment. Journal of Ecology 107(1): 127-141. DOI: 10.1111/1365-2745.13046External link.

Fricke M., Gerst R., Ibrahim B., Niepmann M., Marz M. (2019) Global importance of RNA secondary structures in protein-coding sequences. Bioinformatics 35(4): 579-583, bty678. DOI: 10.1093/bioinformatics/bty678External link.

Frischbier N., Tiebel K, Tischer A., Wagner S. (2019) Small scale rainfall partitioning in a European beech forest ecosystem reveals heterogeneity of Leaf Area Index and its connectivity to hydro- and atmosphere. Geosciences 9(9): 393. DOI: 10.3390/geosciences9090393External link.

Gerst R., Hölzer M. (2019) PCAGO: An interactive tool to analyze RNA-Seq data with principal component analysis. BioRxiv preprint DOI: 10.1101/433078External link.

Ghanem N., Stanley C.E., Harms H., Chatzinotas A., Wick L.Y. (2019) Mycelial effects on phage retention during transport in a microfluidic platform. Environmental Science and Technology 53(20): 11755-11763. DOI: 10.1021/acs.est.9b03502External link.

Hellrich J., Kampe B., Hahn U. (2019) The influence of down-sampling strategies on SVD word embedding stabilityExternal link. In: Proceedings of the 3rd Workshop on Evaluating Vector Space Representations for NLP (RepEval2019), pages 18-26; 06/06/2019; Minneapolis, Minnesota, USA; Association for Computational Linguistics. arXiv:1808.06810v2External link.

Herrmann M., Wegner C.-E., Taubert M., Geesink P., Lehmann K., Yan L., Lehmann R., Totsche K.U., Küsel K. (2019) Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Frontiers in Microbiology 10: article 1407. DOI: 10.3389/fmicb.2019.01407External link.

Hölzer M., Marz M. (2019) De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. GigaScience 8(5): giz039. DOI: 10.1093/gigascience/giz039External link.

Jing M., Heße F., Kumar R., Kolditz O., Attinger S. (2019) Influence of input and parameter uncertainty on the prediction of catchment-scale groundwater travel time distributions. Hydrology & Earth System Sciences 23(1): 171-190. DOI: 10.5194/hess-23-171-2019External link.

Kallies R., Hölzer M., Toscan R.B., da Rocha U.N., Anders J., Marz M., Chatzinotas A. (2019) Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters. Viruses 11(6): 484. DOI: 10.3390/v11060484External link.

Kallies R., Kiesel B., Schmidt M., Ghanem N., Zopfi J., Hackermüller J., Harms H., Wick L.Y., Chatzinotas A. (2019) Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. Marine Genomics 47: 100667. DOI: 10.1016/j.margen.2019.03.002External link.

Knebl A., Domes R., Yan D., Popp J., Trumbore S., Frosch T. (2019) Fiber-enhanced Raman gas spectroscopy for ¹⁸O-¹³C-labelling experiments. Analytical Chemistry 91(12): 7562-7569. DOI: 10.1021/acs.analchem.8b05684External link.

Lazar C.S., Lehmann R., Stoll W., Rosenberger J., Totsche K.U., Küsel K. (2019) The endolithic bacterial diversity of shallow bedrock ecosystems. Science of the Total Environment 679: 35-44. DOI: 10.1016/j.scitotenv.2019.04.281External link.

Metzger J.C., Schumacher J., Lange M., Hildebrandt A. (2019) Neighbourhood and stand structure affect stemflow generation in a heterogeneous deciduous temperate forest. HESS 23: 4433-4452. DOI: 10.5194/hess-23-4433-2019External link.

Moawed S., Algergawy A., Sarhan A., Eldosouky A. (2019) A framework for efficient matching of large-scale metadata models. Arabian Journal for Science and Engineering 44(4): 3117-3135. DOI: 10.1007/s13369-018-3443-4External link.

Nawaz A., Purahong W., Herrmann M., Küsel K., Buscot F., Wubet T. (2019) DNA and RNA derived fungal communities in subsurface aquifers only partly overlap but react similarly to environmental factors. Microorganisms 7(9): 341. DOI: 10.3390/microorganisms7090341External link.

Peter S., Hölzer M., Lamkiewicz K., Peroni di Fenizio P., Al Hwaeer H., Marz M., Schuster S., Dittrich P., Ibrahim B. (2019) Structure and hierarchy of influenza virus models revealed by reaction network analysis. Viruses 11(5): 449. DOI: 10.3390/v11050449External link.

Roth V.-N., Lange M., Simon C., Hertkorn N., Bucher S., Goodall T., Griffiths R.I., Mellado-Vázquez P.G., Mommer L., Oram N.J., Weigelt A., Dittmar T., Gleixner G. (2019) Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nature Geoscience 12: 755-761. DOI: 10.1038/s41561-019-0417-4External link.

Schmidt R., Ulanova D., Wick L.Y., Bode H.B., Garbeva P. (2019) Microbe-driven chemical ecology: past, present and future. The ISME Journal 13: 2656-2663. DOI: 10.1038/s41396-019-0469-xExternal link.

Schwab V., Nowak M.E., Elder C.D., Trumbore S.E., Xu X., Gleixner G., Lehmann R., Pohnert G., Muhr J., Küsel K. (2019) ¹⁴C-free carbon is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary aquifers. Water Resources Research 55(3): 2104-2121. DOI: 10.1029/2017WR022067External link.

Schwab V., Nowak M.E., Trumbore S.E., Xu X., Gleixner G., Muhr J., Küsel K., Totsche K.U. (2019) Isolation of individual saturated fatty acid methyl esters derived from groundwater phospholipids by preparative-high pressure liquid chromatography for compound specific radiocarbon analyses. Water Resources Research 55(3): 2521-2531. DOI: 10.1029/2018WR024076External link.

Sharafeldeen D., Algergawy A., König-Ries B. (2019) Species Association Knowledge Graph Construction - A Demo PaperExternal link. In: Cornet R., Waagmester A. (eds.) Proceedings of the 12th International ConferenceExternal link on Semantic Web Applications and Tools for healthcare and Life Sciences (SWATExternal link⁴HCLSExternal link), 12/10/2019-12/11/2019, Edinburgh, UK. CEUR Proceedings Vol-2849.

Sharafeldeen D., Algergawy A., König-Ries B. (2019) Towards knowledge graph construction using semantic data miningExternal link. In: Indrawan-Santiago M., Pardede E., Salvadori I.L., Steinbauer M., Khalil I., Anderst-Kotsis G. (eds) Proceedings of the 21st International Conference on Information Integration and Web-based Applications & Services (iiWAS2019), pp. 323-329. DOI: 10.1145/3366030.3366035External link.

Sieburg A., Knebl A., Jacob J.M., Frosch T. (2019) Characterization of fuel gases with fiber-enhanced Raman Spectroscopy. Analytical and Bioanalytical Chemistry 411(28): 7399-7408. DOI: 10.1007/s00216-019-02145-xExternal link.

Simon C., Osterholz H., Koschinsky A., Dittmar T. (2019) Riverine mixing at the molecular scale - An ultrahigh-resolution mass spectrometry study on dissolved organic matter and selected metals in the Amazon confluence zone (Manaus, Brazil). Organic Geochemistry 129: 45-62. DOI: 10.1016/j.orggeochem.2019.01.013External link.

Taubert M., Stähly J., Kolb S., Küsel K. (2019) Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLOS ONE 14(3): e0212937. DOI: 10.1371/journal.pone.0212937External link.

Thullner M., Regnier P. (2019) Microbial controls on the biogeochemical dynamics in the subsurface. Reviews in Mineralogy and Geochemistry 85(1): 265-302. DOI: 10.2138/rmg.2019.85.9External link.

Tischer A., Sehl L., Meyer U.-N., Kleinebecker T., Klaus V., Hamer U. (2019) Land-use intensity shapes kinetics of extracellular enzymes in rhizosphere soil of agricultural grassland plant species. Plant and Soil 437(1-2): 215-239. DOI: 10.1007/s11104-019-03970-wExternal link.

Udovenko V., Algergawy A. (2019) Entity extraction in the ecological domain - A practical guide. In: Meyer H., Ritter N., Thor A., Nicklas D., Heuer A., Klettke M. (eds) BTW 2019 - Workshopband, Lecture Notes in Informatics (LNI), Gesellschaft für Informatik, Bonn. Pp. 155-160.  DOI: 10.18420/btw2019-ws-16External link.

Viehweger A., Hölzer M., Brandt C. (2019) Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content. Preprint: bioRxiv 855262. DOI: 10.1101/855262External link.

Viehweger A., Krautwurst S., Lamkiewicz K., Madhugiri R., Ziebuhr J., Hölzer M., Marz M. (2019) Direct RNA nanopore sequencing of full-lenth coronavirus genomes provides novel insights into structural variants and enables modification analysis. Genome Research 29(9): 1545-1554. DOI: 10.1101/gr.247064.118External link.

Wegner C.-E., Gaspar M., Geesink P., Herrmann M., Marz M., Küsel K. (2019) Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon. Applied and Environmental Microbiology 85(5): e02346-18. DOI: 10.1128/AEM.02346-18.External link

Wieczorek A.S., Schmidt O., Chatzinotas A., von Bergen M., Gorissen A., Kolb S. (2019) Ecological functions of agricultural soil bacteria and microeukaryotes in chitin degradation: a case study. Frontiers in Microbiology 10: 1293. DOI: 10.3389/fmicb.2019.01293External link.

Youssef N., Algergawy A., Moawad I.F., EL-Horbaty ES.M. (2019) Combined features for content based image retrieval: A comparative study. In: Hassanien A., Tolba M., Shaalan K., Azar A. (eds) Proceedings of the International Conference on Advanced Intelligent Systems and Informatics 2018. AISI 2018. Advances in Intelligent Systems and Computing, vol 845. Springer, Cham. DOI: 10.1007/978-3-319-99010-1_58External link.

Achich N., Algergawy A., Bouaziz B., König-Ries B. (2018) BioOntoVis: An Ontology Visualization ToolExternal link.  In: Cimiano P., Corby O. (eds) Proceedings of the EKAW 2018 Posters and Demonstrations SessionExternal link co-located with 21st International Conference on Knowledge Engineering and Knowledge Management, 11/12/2018-11/16/2018, Nancy, France. CEUR Proceedings Vol-2262.

Algergawy A., Cheatham M., Faria D., Ferrara A., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Karam N., Khiat A., Lambrix P., Li H., Montanelli S., Paulheim H., Pesquita C., Saveta T., Schmidt D., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Zamazal O., Zhou L. (2019) Results of the Ontology Alignment Evaluation Initiative 2018External link. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Cheatham M., Hassanzadeh O. (eds) Proceedings of the 13th International Workshop on Ontology MatchingExternal link co-located with the 17th International Semantic Web Conference (ISWC 2018), 10/8/2018, Monterey, CA, USA. CEUR Proceedings Vol-2288.

Algergawy A., Klan F., Fäßler E., Hamed H., Kampe B., Koenig-Ries B., Hahn U. (2018) ADOnIS: An ontology-based information system providing seamless integration of structured and unstructured dataExternal link. 11th International Conference on Semantic Web Applications and Tools for Life Sciences (SWATExternal link⁴HCLSExternal link), 12/3/2018-12/6/2018, Antwerp, Bergium. DOI: 10.6084/m9.figshare.7322024.v1External link.

Baumeister T.U.H., Ueberschaar N., Schmidt-Heck W., Mohr F., Deicke M., Wichard T., Guthke R., Pohnert G. (2018) DeltaMS: a tool to track isotopologues in GC- and LC-MS data. Metabolomics 14: 41. DOI: 10.1007/s11306-018-1336-x.External link

Benk S., Li Y., Roth V.-N., Gleixner G. (2018) Lignin dimers as potential markers for ¹⁴C-young terrestrial dissolved organic matter in the Critical Zone. Frontiers in Earth Science 6: article 168. DOI: 10.3389/feart.2018.00168External link.

Bocklitz T., Meyer T., Schmitt M., Rimke I., Hoffmann F., von Eggeling F., Ernst G., Guntinas-Lichius O., Popp J. (2018) Invited Article: Comparison of hyperspectral coherent Raman scattering microscopies for biomedical applications. APL Photonics 3: 092404. DOI: 10.1063/1.5030159External link.

Bourtsoukidis E., Behrendt T., Yanez-Serrano A.M., Hellén H., Diamantopoulos E., Catao E., Ashworth K., Pozzer A., Quesada C.A., Martins D.L., Sá M., Araujo A., Brito J., Artaxo P., Kesselmeier J., Lelieveld J., Williams J. (2018) Strong sesquiterpene emissions from Amazonian soils. Nature Communications 9: article 2226. DOI: 10.1038/s41467-018-04658-y.External link

Brunzel M., Majdanski T.C., Vitz J., Nischang I., Schubert U.S. (2018) Fast screening of diol impurities in methoxy poly(ethylene glycol)s (mPEG)s by liquid chromatography on monolithic silica rods. Polymers 10(12): 1395. DOI: 10.3390/polym10121395External link.

Carlyle-Moses D.E., Iida S., Germer S., Llorens P., Michalzik B., Nanko K., Tischer A., Levia D.F. (2018) Expressing stemflow commensurate with its ecohydrological importance. Advances in Water Resources 121: 472-479. DOI: 10.1016/j.advwatres.2018.08.015. External link

Deveau A., Bonito G., Uehling J., Paoletti M., Becker M., Bindschedler S., Hacquard S., Hervé V., Labbé J., Lastovetsky O.A., Mieszkin S., Millet L.J., Vajna B., Junier P., Bonfante P., Krom B.P., Olsson S., van Elsas J.D., Wick L.Y. (2018) Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews 42(3): 335-352. DOI: 10.1093/femsre/fuy008External link.

Ding S., Kohlhepp B., Trumbore S., Küsel K., Totsche K.U., Pohnert G., Gleixner G., Schwab V.F. (2018) In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater. Organic Geochemistry 126: 1-12. DOI: 10.1016/j.orggeochem.2018.10.005External link.

Fäßler E., Hahn U. (2018) Annotation data management with JeDIS. DocEng '18: Proceedings of the ACM Symposium on Document Engineering 2018, August 28-31, 2018, Halifax, NS, Canada. Article no.: 42, pages 1-4. ACM, New York, NY, USA. DOI: 10.1145/3209280.3229102External link.

Geesink P., Tyc O., Küsel K., Taubert M., van de Velde C., Kumar S., Garbeva P. (2018) Growth promotion and inhibition induced by interactions of groundwater bacteria. FEMS Microbiology Ecology, fiy164. DOI: 10.1093/femsec/fiy164External link.

Gerlach R., Ostrowski A., Gaikwad J., Algergawy A. (2018) Research data management in action - demonstrating the full range of features of the BEXIS 2 platform. In: Jitendra G., König-Ries B., Recknagel F. (eds) Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI2018, p. 288. DOI: 10.22032/dbt.37846External link. (And all other contributions in these proceedings by Algergawy A.)

Ghanem N., Trost M., Sánchez Fontanet L., Harms H., Chatzinotas A., Wick L.Y. (2018) Changes of the specific infectivity of tracer phages during transport in porous media. Environ Sci Technol 52(6): 3486-3492. DOI: 10.1021/acs.est.7b06271.External link

Guderle M., Bachmann D., Milcu A., Gockele A., Bechmann M., Fischer C., Roscher C., Landais D., Ravel O., Devidal S., Roy J., Gessler A., Buchmann N., Weigelt A., Hildebrandt A. (2018) Dynamic niche partitioning in root water uptake facilitates water use in more diverse grassland plant communities. Functional Ecology 32: 214-227. DOI: 10.1111/1365-2435.12948.External link

Huang J., Hartmann H., Hellén H., Wisthaler A., Perreca E., Weinhold A., Rücker A., van Dam N.M., Gershenzon J., Trumbore S., Behrendt T. (2018) New perspectives on CO₂, temperature, and light effects on BVOC emissions using online measurements by PTR-MS and cavity ring-down spectroscopy. Environmental Science & Technology 52(23): 13811-13823. DOI: 10.1021/acs.est.8b01435.External link

Jing M., Heße F., Kumar R., Wang W., Fischer T., Walther M., Zink M., Zech A., Samaniego L., Kolditz O., Attinger S. (2018) Improved regional-scale groundwater representation by the coupling of the mesoscale Hydrologic Model (mHM v5.7) to the groundwater model OpenGeoSys (OGS). Geoscientific Model Development 11(5): 1989-2007. DOI: 10.5194/gmd-11-1989-2018External link.

Knebl A., Yan D., Popp J., Frosch T. (2018) Fiber enhanced Raman gas spectroscopy. Trends in Analytical Chemistry 103: 230-238. DOI: 10.1016/j.trac.2017.12.001.External link

Kumar S., Herrmann M., Blohm A., Hilke I., Frosch T., Trumbore S.E., Küsel K. (2018) Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiology Ecology:DOI: 10.1093/femsec/fiy141External link.

Majdanski T.C., Vitz J., Meier A., Brunzel M., Schubert S., Nischang I., Schubert U.S. (2018) "Green" ethers as solvent alternatives for anionic ring-opening polymerizations of ethylene oxide (EO): In-situ kinetic and advanced characterization studies. Polymer 159: 86-94. DOI: 10.1016/j.polymer.2018.09.049.External link

Nawaz A., Purahong W., Lehmann R., Herrmann M., Totsche K.U., Küsel K., Wubet T., Buscot F. (2018) First insights into the living groundwater mycobiome of the terrestrial biogeosphere. Water Research 145: 50-61. DOI: 10.1016/j.watres.2018.07.067.External link

Oleynik M., Fäßler E., Sasso A.M., Kappattanavar A., Bergner B., Freitas da Cruz H., Sachs J.-P., Datta S., Böttinger E. (2018) HPI-DHC at TREC 2018 Precision Medicine TrackExternal link. In: The 27th Text REtrieval Conference (TREC 2018) ProceedingsExternal link, 11/14/2018-11/16/2018, Gaithersburg, Md, USA.

Simon C., Roth V.-N., Dittmar T., Gleixner G. (2018) Molecular signals of heterogeneous terrestrial environments identified in dissolved organic matter: a comparative analysis of orbitrap and ion cyclotron resonance mass spectrometers. Frontiers in Earth Science 6: article 138. DOI: 10.3389/feart.2018.00138External link.

Taubert M., Stöckel S., Geesink P., Girnus S., Jehmlich N., von Bergen M., Rösch P., Popp J., Küsel K. (2018) Tracking active groundwater microbes with D₂O labelling to understand their ecosystem function. Environmental Microbiology  20: 369-384. DOI: 10.1111/1462-2920.14010External link.

Wutzler T. (2018) Efficient treatment of model discrepancy by Gaussian Processes - Importance for imbalanced multiple constraint inversions.
Preprint arXiv: 1812.07801External link.

Youssef N., Algergawy A., Moawad I.F., EL-Horbaty ES.M. (2018) Combined features for content based image retrieval: A comparative study. In: Hassanien A., Tolba M., Shaalan K., Azar A. (eds) Proceedings of the International Conference on Advanced Intelligent Systems and Informatics 2018 (AISI 2018) Advances in Intelligent Systems and Computing, vol 845, pp. 634-643. Springer, Cham. DOI: 10.1007/978-3-319-99010-1_58External link.

Zhang L., Lehmann K., Totsche K. U., Lueders T. (2018) Selective successional transport of bacterial populations from rooted agricultural topsoil to deeper layers upon extreme precipitation events. Soil Biology and Biochemistry 124: 168-178. DOI: 10.1016/j.soilbio.2018.06.012External link.

Abdelreheim M., Klan F., Soliman T. (2017) Towards personalized support for ontology selectionExternal link. In: Proceedings of the 29th GI-Workshop Grundlagen von Datenbanken, 05/30/2017 - 06/02/2017.  Blankenburg/Harz, Germany.

Algergawy A., Karam N., Klan F., Jonquet C. (2017) Proceedings of the 2nd International Workshop on Semantics for BiodiversitExternal linky (S4BioDiv 2017) co-located with 16th International Semantic Web Conference (ISWC2017), 10/22/2017, Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

Amara J., Bouaziz B., Algergawy A. (2017) A Deep Learning-based approach for banana leaf diseases classificationExternal link. In: BTW 2017 - Workshopband, Lecture Notes in Informatics (LNI), Gesellschaft für Informatik, Bonn 2017, B. Mitschang et al. (ed.). 17th Conference on Database Systems for Business, Technology, and Web; 03/06/2017 - 03/10/2017; Stuttgart, Germany.

Babalou S.,Algergawy A.,König-Ries B. (2017) An ontology-based scientific data integration workflowExternal link. In: Proceedings of the 29th GI-Workshop Grundlagen von Datenbanken, 05/30/2017 - 06/02/2017.  Blankenburg/Harz, Germany.

Babalou S., Algergawy A., König-Ries B. (2017) A particle swarm-based approach for semantic similarity computation. Conference PaperExternal link. In: Panetto H. et al. (eds) On the Move to Meaningful Internet Systems. OTM 2017 Conferences. OTM 2017. Lecture Notes in Computer Science, vol 10574. Springer, Cham. (Proceedings of the 16th International Conference on Ontologies, DataBases, and Applications of Semantics, 10/24/2017 - 10/25/2017. Rhodes, Greece).

Babalou S., Algergawy A., Lantow B., König-Ries B. (2017) Why the mapping process in ontology integration deserves attention. In: Indrawan-Santiago M., Steinbauer M., Salvadori I.L., Khalil I., Anderst-Kotsis G. (eds) Proceedings of the 19st International Conference on Information Integration and Web-based Applications & Services (iiWAS2017), pp. 451-456. DOI: 10.1145/3151759.3151834External link.

Crecelius A.C., Michalzik B., Potthast A., Meyer S., Schubert U.S. (2017) Tracing the fate and transport of secondary plant metabolites in a laboratory mesocosm experiment by employing mass spectrometric imaging. Anal Bioanal Chem 409(15): 3807-3820. DOI: 10.1007/s00216-017-0325-7.External link

Crecelius A.C., Vitz J., Näthe K., Meyer S., Michalzik B., Schubert U.S. (2017) Effect of ecosystem type and fire on chemistry of WEOM as measured by LDI-TOF-MS and NMR. Talanta 162: 589-596. DOI: 10.1016/j.talanta.2016.10.067External link.

Dalla Valle N., Potthast K., Meyer S., Michalzik B., Hildebrandt A., Wutzler T. (2017) Modeling macropore seepage fluxes from soil water content series by inversion of a dual permeability model. Hydrology and Earth System Sciences Discussions (preprint) DOI: 10.5194/hess-2017-336.External link

Fäßler E., Hahn U. (2017) Semedico: A comprehensive semantic search engine for the life sciences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics (ACL 2017)- System Demonstrations, pages 91-96. Vancouver, Canada, July 30 - August 4, 2017. DOI: 10.18653/v1/P17-4016External link.

Fäßler E., Klan F., Algergawy A., König-Ries B., Hahn U. (2017) Selecting and tailoring ontologies with JOYCE. Conference PaperExternal link. In: Ciancarini P. et al. (eds.) Knowledge Engineering and Knowledge Management. EKAW 2016 Lecture Notes in Computer Science, vol 10180: pp. 114-118. Springer, Cham.

Friedmann R.C., Kalkhof S., Doppelt-Azeroual O., Mueller S.A., Chovancová M., von Bergen M., Schwikowski B. (2017) Common and phylogenetically widespread coding for peptides by bacterial small RNAs. BMC Genomics 18: 553. DOI: 10.1186/s12864-017-3932-yExternal link. #

Guo Y., Stärk H. J., Hause G., Schmidt M., Harms H., Wick L.Y. (2017) Heterogenic response of Prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces. Cytometry Part A 91(8): 775-784. DOI: 10.1002/cyto.a.23055External link.

Herrmann M., Opitz S., Harzer R., Totsche K. U., Küsel K. (2017) Attached and suspended denitrifier communities in pristine limestone aquifers harbor high fractions of potential authotrophs oxidizing resduced iron and sulfur compounds. Microb Ecol 74(2): 264-277. DOI: 10.1007/s00248-017-0950-xExternal link

Heße F., Zink M., Kumar R., Samaniego L., Attinger S. (2017) Spatially distributed characterization of soil-moisture dynamics using travel-time distributions. Hydrol Earth Syst Sci 21: 549-570. DOI: 10.5194/hess-21-549-2017External link.

Jochum T., Fastnacht A., Trumbore S.E., Popp J., Frosch T. (2017) Direct Raman spectroscopic measurements of biological nitrogen fixation under natural conditions: An analytical approach for studying nitrogenase activity. Anal Chem 89(2): 1117-1122. DOI: 10.1021/acs.analchem.6b03101External link.

Kallies R., Kiesel B., Schmidt M., Kacza J., Ghanem N., Narr A., Zopfi J., Wick L.Y., Hackermüller J., Harms H., Chatzinotas A. (2017) Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Stand Genomic Sci 12: 20. DOI: 10.1186/s40793-017-0235-5.External link

Kallies R., Kiesel B., Zopfi J., Wick L. Y. (2017) Complete genome sequence of Alteromonas virus vB_AspP-H4/4. Genome Announc. 5(43): e00914-17. DOI: 10.1128/genomeA.00914-17External link

Klan F., Faessler E., Algergawy A., König-Ries B., Hahn U. (2017) Integrated semantic search on structured and unstructured data in the ADOnIS System. Research PaperExternal link. In: Algergawy A., Karam N., Klan F., Jonquet C. (eds.) Proceedings of the 2nd International Workshop on Semantics for BiodiversityExternal link co-located with 16th International Semantic Web Conference (ISWC 2017), 10/22/2017. Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

Kohlhepp B., Lehmann R., Seeber P., Küsel K., Trumbore S., Totsche K.U. (2017) Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany. Hydrology and Earth System Sciences 21(12): 6091-6116. DOI: 10.5194/hess-21-6091-2017External link.

Kuhlisch C., Deicke M., Ueberschaar N., Wichard T., Pohnert G. (2017) A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms. Limnol Oceanogr Methods 15(1): 70-79. DOI: 10.1002/lom3.10143External link.

Kumar S., Herrmann M., Thamdrup B., Schwab V.F., Geesink P., Trumbore S.E., Totsche K.U., Küsel K. (2017) Nitrogen loss from pristine carbonate-rock aquifers of the Hainich Critical Zone Exploratory (Germany) is primarily driven by chemolithoautotrophic anammox processes. Frontiers in Microbiology 8: 1951. DOI: 10.3389/fmicb.2017.01951.External link

Lazar C.S., Baker B.J., Seitz K., Teske A.P. (2017) Genomic reconstruction of multiple lineages of uncultered benthic archaea suggests distinct biogeochemical roles and ecological niches. The ISME Journal 11: 1118-1129. DOI: 10.1038/ismej.2016.189External link.

Lazar C.S., Stoll W., Lehmann R., Herrmann M., Schwab V.F., Akob D.M., Nawaz A., Wubet T., Buscot F., Totsche K.U., Küsel K. (2017) Archaeal diversity and CO₂ fixers in carbonate-/siliciclastic-rock groundwater ecosystems. Archaea 2017: article ID 2136287. DOI: 10.1155/2017/2136287External link.

Löffler F., Pfaff C-T., Karam N., Fichtmüller D., Klan F. (2017) What do biodiversity scholars search for? Identifying high-level entities for biological metadata. Poster PaperExternal link. In: Algergawy A., Karam N., Klan F., Jonquet C. (eds.) Proceedings of the 2nd International Workshop on Semantics for BiodiversityExternal link co-located with 16th International Semantic Web Conference (ISWC 2017), 10/22/2017. Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

Metzger J.C., Wutzler T., Dalla Valle N., Filipzik J., Grauer C, Lehmann R., Roggenbuck M., Schelhorn D., Weckmüller J., Küsel K., Totsche K.U., Trumbore S., Hildebrandt A. (2017) Vegetation impacts soil water content patterns by shaping canopy water fluxes and soil properties. Hydrological Processes 31(22): 3783-3795. DOI: 10.1002/hyp.11274External link.

Mori J.F., Ueberschaar N., Lu S., Cooper R.E., Pohnert G., Küsel K. (2017) Sticking together: Inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling. The ISME Journal 11: 1075-1086. DOI: 10.1038/ismej.2016.186External link.

Narr A., Nawaz A., Wick L. Y., Harms H., Chatzinotas A. (2017) Soil viral communities vary temporally and along a land use transect as revealed by virus-like particle counting and a modified community fingerprinting approach (fRAPD). Front Microbiol 8: article 1975. DOI: 10.3389/fmicb.2017.01975External link

Nowak M., Schwab V.F., Lazar C.S., Behrendt T., Kohlhepp B., Totsche K.U., Küsel K., Trumbore S.E. (2017) Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages. Hydrology and Earth System Sciences 21: 4283-4300. DOI: 10.5194/hess-21-4283-2017.External link

Potthast K., Meyer S., Crecelius A.C., Schubert U.S., Tischer A., Michalzik B. (2017) Land-use and fire drive temporal patterns of soil solution chemistry and nutrient fluxes. Science of The Total Environment 605-606: 514-526. DOI: 10.1016/j.scitotenv.2017.06.182.External link

Samir S., Sarhan A., Algergawy A. (2017) Context-based web service discovery framework with QoS considerations. In: IEEE Xplore Digital Library for the 11th International Conference on Research Challenges in Information Science (RCIS_2017), May 10-12, 2017.  Brighton, UK. DOI: DOI: 10.1109/RCIS.2017.7956531.External link

Schwab V.F., Herrmann M., Roth V.-N., Gleixner G., Lehmann R., Pohnert G., Trumbore S.E., Küsel K., Totsche K.U. (2017) Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches. Biogeosciences 14: 2697-2714. DOI: 10.5194/bg-14-2697-2017.External link

Shehab E., Algergawy A., Sarhan A. (2017) Accelerating relational database operations using both CPU and GPU co-processor. Computers & Electrical Engineering 57: 69-80. DOI: 10.1016/j.compeleceng.2016.12.014External link.

Sieburg A., Jochum T., Trumbore S.E., Popp J., Frosch T. (2017) Onsite cavity enhanced Raman spectrometry for the investigation of gas exchange processes in the Earth's Critical Zone. Analyst 142: 3360-3369. DOI: 10.1039/C7AN01149K.External link

Starke R., Müller M., Gaspar M., Marz M., Küsel K., Totsche K.U., von Bergen M., Jehmlich N. (2017) Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer. Journal of Proteomics 152: 153-160. DOI: 10.1016/j.jprot.2016.11.003.External link

Warnke M., Jacoby C., Jung T., Agne M., Mergelsberg M., Starke R., Jehmlich N., von Bergen M., Richnow H.-H., Brüls T., Boll M. (2017) A patchwork pathway for oxygenase-independent degradation of side chain containing steroids. Environmental Microbiology 19(11): 4684-4699. DOI: 10.1111/1462-2920.13933External link.

Wutzler T., Zaehle S., Schrumpf M., Ahrens B., Reichstein M. (2017) Adaption of microbial resource allocation affects modelled long term soil organic matter and nutrient cycling. Soil Biology and Biochemistry 115: 322-336. DOI: 10.1016/j.soilbio.2017.08.031.External link

Algergawy A., Babalou S., Klan F., König-Ries B. (2016) OAPT: A tool for ontology analysis and partitioning (Demo paperExternal link). In: Proceedings of the 19th International Conference on Extending Database Technology (EDBT 2016). Bordeaux, France, March 15-18, 2016.

Algergawy A., Babalou S., König-Ries B. (2016) A new metric to evaluate ontology modularizationExternal link. In: Proceedings of the 2nd International Workshop on Summarizing and Presenting Entities and Ontologies (SumPre 2016) co-located with the 13th Extended Semantic Web Conference (ESWC 2016), Anissaras, Greece, May 30, 2016; CEUR Workshop Proceedings Vol-1605. Thalhamer A., Cheng G., Gunaratna K. (eds.); available online at http://ceur-ws.org/Vol-1605/External link.

Bastida F., Torres I.F., Moreno J.L., Baldrian P., Ondoño S., Ruiz-Navarro A., Hernández T., Richnow H.H., Starke R., García C., Jehmlich N. (2016) The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils. Mol Ecol 25: 4660-4673. DOI: 10.1111/mec.13783.External link

Berthold T., Centler F., Hübschmann T., Remer R., Thullner M., Harms H., Wick L.Y. (2016) Mycelia as a focal point for horizontal gene transfer among soil bacteria. Scientific reports 6: 36390. DOI: 10.1038/srep36390External link.

Dalle Pezze P., Ruf S., Sonntag A., Langelaar-Makkinje M., Hall P., Heberle A., Razquin Navas P., van Eunen K., Toelle R., Schwarz J., Wiese H., Warscheid B., Deitersen J., Stork B., Fäßler E., Schäuble S., Hahn U., Horvatovich P., Shanley D., Thedieck K. (2016) A system study reveals concurrent activation of AMPK and mTor by amino acids. Nature Communications 7: #13254. DOI: 10.1038/ncomms13254External link.

Ding S., Schwab V.F., Ueberschaar N., Roth V.-N., Lange M., Xu Y., Gleixner G., Pohnert G. (2016) Identification of novel 7-methyl and cyclopentanyl branched glycerol dialkyl glycerol tetraethers in lake sediments. Organic Geochemistry 102: 52-58. DOI: 10.1016/j.orggeochem.2016.09.009.External link

European Commission, Joint Research Centre (2016) Global Soil Biodiversity Atlas - Earth Sciences Research - EU Bookshop: http://bookshop.europa.eu/en/global-soil-biodiversity-atlas-pbLBNA27236/External link. Contributors: Küsel K., Totsche K.U., Trumbore S.E., Buscot F.; Chapter III - Geographical and temporal distribution, p. 73.

Ghanem N., Kiesel B., Kallies R., Harms H., Chatzinotas A., Wick L.Y. (2016) Marine phages as tracers: Effects of size, morphology, and physico-chemical surface properties on transport in a porous medium. Environmental Science & Technology 50(23): 12816-12824. DOI: 10.1021/acs.est.6b04236External link.

Hahn U., Matthies F., Fäßler E., Hellrich J. (2016) UIMA-based JCorRe 2.0 goes GitHub and Maven Central: State-of-the-art software resource engineering and distribution of NLP pipelines. In: Proceedings of the 10th International Conference on Language Resources and Evaluation (LREC 2016). Portorož, Slovenia; pp. 2502-2509External link.

Hildebrandt A., Kleidon A., Bechmann M. (2016) A thermodynamic formulation of root water uptake. Hydrology and Earth System Sciences 20(8): 3441-3454. DOI: 10.5194/hess-20-3441-2016External link.

Jehmlich N., Müller M., Meyer S., Tischer A., Richnow H.H., Potthast K., Michalzik B., von Bergen M. (2016) Proteome data on the microbial microbiome of grasshopper feces. Data in Brief 9: 1147-1154. DOI: 10.1016/j.dib.2016.11.033External link.

Küsel K., Totsche K.U., Trumbore S., Lehmann R., Steinhäuser C., Herrmann M. (2016) How deep can surface signals be traced in the Critical Zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Frontiers in Earth Science 4: 32. DOI: 10.3389/feart.2016.00032.External link

Löffler F., Klan F. (2016) Does term expansion matter for the retrieval of biodiversity data? In: Joint Proceedings of the Posters and Demos Track of the 12th International Conference on Semantic Systems - SEMANTiCS2016, and the 1st International Workshop on Semantic Change & Evolving Semantics (SuCCESS'16). Poster paper. Leipzig, Germany; CEUR Workshop Proceedings Vol-1695; available online at http://ceur-ws.org/Vol-1695/External link.

Lünsmann V., Kappelmeyer U., Benndorf R., Martinez-Lavanchy P.M., Taubert A., Adrian L., Duarte M., Pieper D.H., von Bergen M., Müller J.A., Heipieper H.J., Jehmlich N. (2016) In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model. Environ Microbiol 18(4): 1176-1186. DOI: 10.1111/1462-2920.13133.External link

Lünsmann V., Kappelmeyer U., Taubert A., Nijenhuis I., von Bergen M., Heipieper H.J., Müller J.A., Jehmlich N. (2016) Aerobic toluene degraders in the rhizosphere of a constructed wetland model show diurnal polyhydroxyalkanoate metabolism. Appl Environ Microbiol 82(14): 4126-4132. DOI: 10.1128/AEM.00493-16External link.

Malghani S., Reim A., von Fischer J., Conrad R., Kuebler K., Trumbore S.E. (2016) Soil methanotroph abundance and community composition are not influenced by substrate availability in laboratory incubations. Soil Biology and Biochemistry 101: 184-194. DOI: 10.1016/j.soilbio.2016.07.009External link.

Malik A.A., Roth V.-N., Hébert M., Tremblay L., Dittmar T., Gleixner G. (2016) Linking molecular size, composition and carbon turnover of extractable soil microbial compounds. Soil Biology and Biochemistry 100: 66-73. DOI: 10.1016/j.soilbio.2016.05.019External link.

Nawaz A., Purahong W., Lehmann R., Herrmann M., Küsel K.,Totsche K.U., Buscot F., Wubet T. (2016) Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities. Front Micobiol 7:666. DOI: 10.3389/fmicb.2016.00666External link.

Renner M., Hassler S.K., Blume T., Weiler M., Hildebrandt A., Guderle M., Schymanski S.J., Kleidon A. (2016) Dominant controls of transpiration along a hillslope transect inferred from ecohydrological measurements and thermodynamic limits. Hydrology and Earth System Sciences 20(5): 2063-2083. DOI: 10.5194/hess-20-2063-2016.External link

Rughöft S., Herrmann M., Lazar C.S., Cesarz S., Levick S.R., Trumbore S.E., Küsel K. (2016) Community composition and abundance of bacterial, archaeal and nitrifying populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa. Frontiers Microbiology, Terrestrical Microbiology 7: 1954. DOI: 10.3389/fmicb.2016.01638External link.

Seifert A.-G., Roth V.-N., Dittmar T., Gleixner G., Breuer L., Houska T., Marxsen J. (2016) Comparing molecular composition of dissolved organic matter in soil and stream water: Influence of land use and chemical characteristics. Science of the Total Environment 571: 142-152. DOI: 10.1016/j.scitotenv.2016.07.033External link.

Van Stan J., Lewis E.S., Hildebrandt A., Rebmann C., Friesen J. (2016) Impact of interacting bark structure and rainfall conditions on stemflow variability in a temperate beech-oak forest, central Germany. Hydrological Sciences Journal 61(11): 2071-2083. DOI: 10.1080/02626667.2015.1083104External link.

Zech A., Müller S., Mai J., Heße F., Attinger S. (2016) Extending Theis' solution: Using transient pumping tests to estimate parameters of aquifer heterogeneity. Water Resour Res 52(8): 6156-6170. DOI: 10.1002/2015WR018509External link.

Zimmermann A., Voss S., Metzger J.C., Hildebrandt A., Zimmermann B. (2016) Capturing heterogeneity: The role of a study area's extent for estimating  mean throughfall. Journal of Hydrology 542: 781-789. DOI: 10.1016/j.jhydrol.2016.09.047External link.

Algergawy A., Babalou S., Kargar, M., Davarpanah, S. H. (2015) SeeCOnt: A new seeding-based clustering approach for ontology matching. In: Tadeusz M, Valduriez P, Bellatreche L (eds) Advances in Databases and Information Systems. Springer International PublishingExternal link; Switzerland; pp 245-258.

Algergawy A., Klan F. (2015) A sequence-based tree similarity search. In: 9th IEEE International Conference on Research Challenges in Information Science (RCIS 2015). Athens, Greece; pp. 121-126. DOI: 10.1109/RCIS.2015.7128871External link

Fischer C., Tischer J., Roscher C., Eisenhauer N., Ravenek J., Gleixner G., Attinger S., Jensen B., de Kroon H., Mommer L., Scheu S., Hildebrandt A. (2015) Plant species diversity affects infiltration capacity in an experimental grassland through changes in soil properties. Plant Soil 397: 1-16. DOI: 10.1007/s11104-014-2373-5External link.

Fischer S., Hanf S., Frosch T., Gleixner G., Popp J., Trumbore S., Hartmann H. (2015) Pinus sylvestries switches respiration substrates under shading but not during drought. The New Phytologist 207(3): 542-550. DOI: 10.1111/nph.13452External link.

Guderle M., and Hildebrandt A. (2015). Using measured soil water contents to estimate evapotranspiration and root water uptake profiles - a comparative study. Hydrol Earch Sci 19: 409-425. DOI: 10.5194/hess-19-409-2015External link.

Hanf S., Fischer S., Hartmann H., Trumbore S., Popp J., Frosch T. (2015) Online investigation of respiratory quotients in Pinus sylvestris and Picea abies during drought and shading by means of cavity-enhanced Raman gas spectroscopy. Analyst 140(13): 4473-448. DOI DOI: 10.1039/C5AN00402K.External link

Herrmann M., Rusznyak A., Akob D.M., Schulze I., Opitz S., Totsche K.U., Küsel K. (2015) Large fractions of CO₂-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Applied and Environmental Microbiology 81(7): 2384-2394. DOI: 10.1128/AEM.03269-14External link.

Heße F., Savoy H., Osorio-Murillo C.A., Sege J., Attinger S., Rubin Y. (2015) Characterizing the impact of roughness and connectivity features of aquifer conductivity using Bayesian inversion. Journal of Hydrology 531: 73-87. https://doi.org/10.1016/j.jhydrol.2015.09.067.External link

Jochum T., Michalzik B., Bachmann A., Popp J., Frosch T. (2015) Microbial respiration and natural attenuation of benzene-contaminated soils investigated by cavity-enhanced Raman multi-gas spectroscopy. Analyst 140: 3143-3149. DOI: 10.1039/C5AN00091BExternal link .

Jochum T., von Fischer J.C., Trumbore S., Popp J., Frosch T. (2015) Multigas leakage correction in static environmental chambers using sulfur hexafluoride and Raman spectroscopy. Anal Chem 87(21): 11137-11142. DOI: 10.1021/acs.analchem.5b03312External link.

Keiner R., Gruselle M-C., Michalzik B., Popp J., Frosch T. (2015) Raman spectroscopic investigation of ¹³CO₂ labeling and leaf dark respiration of Fagus sylvatica L. (European beech). Analytical and Bioanalytical Chemistry 407: 1813-1817. DOI: 10.1021/acs.analchem.5b03312.External link

Keiner R., Herrmann M., Küsel K., Popp J., Frosch T. (2015) Rapid monitoring of intermediate states and mass balance of nitrogen during denitrification by means of cavity enhanced Raman multi-gas sensing.  Analytica Chimica Acta 864: 39-47. DOI: 10.1016/j.aca.2015.02.007External link.

Khattab A., Algergawy A., Sarhan A. (2015) MAG: A performance evaluation framework for database systems. Knowledge-Based Systems 85: 245-255. DOI: 10.1016/j.knosys.2015.05.010.External link

König-Ries B., Hahn U. (2015) Semantic technologies for consolidating structured data and unstructured documents in biodiversity research. In: Kolbe T.H., Bill R., Donaubauer A. (eds) Geoinformationssysteme 2015 - Beiträge zur 2. Münchner GI-Runde. Wichmann Verlag; Berlin, Germany.

Palatinszky M., Herbold C., Jehmlich N., Pogoda M., Han P., von Bergen M., Lagkouvardos I., Karst S.M., Galushko A., Koch H., Berry D., Daims H., Wagner M. (2015) Cyanate as an energy source for nitrifiers. Nature 524: 105-108. DOI: 10.1038/nature14856.External link

Roth V.-N., Dittmar T., Gaupp R., Gleixner G. (2015) The molecular composition of dissolved organic matter in forest soils as a function of pH and temperature. PLoS ONE 10(3): e0119188. DOI: 10.1371/journal.pone.0119188External link.

Keiner R., Frosch T., Massad T., Trumbore S., Popp J. (2014) Enhanced Raman multigas sensing - a novel tool for control and analysis of ¹³CO₂ labeling experiments in environmental research. Analyst 139(16): 3879-3884. DOI: 10.1039/C3AN01971C.External link

Opitz S., Küsel K., Spott O., Totsche K.U., Herrmann M. (2014) Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol 90(1): 39-53. DOI: 10.1111/1574-6941.12370External link.

Roth V.N., Dittmar T., Gaupp R., Gleixner G. (2014) Ecosystem-specific composition of dissolved organic matter. Vadose Zone J 13(7). DOI: 10.2136/vzj2013.09.0162External link.

Frosch T., Keiner R., Michalzik B., Fischer B., Popp J. (2013) Investigation of gas exchange processes in peat bog ecosystems by means of innovative Raman gas spectroscopy. Anal Chem 85: 1295-1299. DOI: 10.1021/ac3034163External link.

Keiner R., Frosch T., Hanf S., Rusznyak A., Akob D.M., Küsel K., Popp J. (2013) Raman spectroscopy - an innovative and versatile tool to follow the respirational activity and carbonate biomineralization of important cave bacteria. Anal Chem 85: 8708-8714. DOI: 10.1021/ac401699dExternal link.

Risse-Buhl U., Herrmann M., Lange P., Akob D.M., Pizani N., Schönborn W., Totsche K.U., Küsel K. (2013) Phagotrophic protist diversity in the groundwater of a karstic aquifer - morphological and molecular analysis. J Euk Microbiol 60: 467-479. DOI: 10.1111/jeu.12054External link.

Akob D.M., Küsel K. (2011) Where microorganisms meet rocks in the Earth's Critical Zone. Biogeosciences 8: 3531-3543. DOI: 10.5194/bg-8-3531-2011.External link

Kalbacher T., Delfs J.-O., Shao H., Wang W., Walther M., Samaniego L., Schneider C., Kumar R., Musolff A., Centler F., Sun F., Hildebrandt A., Liedl R., Borchardt D., Krebs P. and Kolditz O. (2011) The IWAS-ToolBox: software coupling for an integrated water resources management. Environ Earth Sci 65: 1367-1380. DOI: 10.1007/s12665-011-1270-y.External link

Kalbacher T., Schneider C.L., Wang W., Hildebrandt A., Attinger S., Kolditz O. (2011) Modeling soil-coupled water uptake of multiple root systems with automatic time stepping. Vadose Zone J 10: 727. DOI: 10.2136/vzj2010.0099External link.

Rusznyák A., Akob D.M., Nietzsche S., Eusterhues K., Totsche K.U., Neu T.R., Frosch T., Popp J., Keiner R., Geletneky J., Katzschmann L., Schulze E.-D., Küsel K. (2012) Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic Herrenberg Cave. Appl Environ Microbiol 78: 1157-1167.
DOI: 10.1128/AEM.06568-11External link.