@article{zvi-kedem_vintila_kleiner_tchernov_rubin-blum_2023, title={Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels}, url={https://doi.org/10.1101/2023.02.09.527947}, DOI={10.1101/2023.02.09.527947}, author={Zvi-Kedem, Tal and Vintila, Simina and Kleiner, Manuel and Tchernov, Dan and Rubin-Blum, Maxim}, year={2023}, month={Feb} }
 @article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2023, title={Re-engineering a lost trait:IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss}, url={https://doi.org/10.1101/2023.03.06.531368}, DOI={10.1101/2023.03.06.531368}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2023}, month={Mar} }
 @article{kleiner_kouris_violette_d'angelo_liu_korenek_tolic_sachsenberg_mccalder_lipton_et al._2023, title={Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes}, volume={11}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01454-1}, number={1}, journal={MICROBIOME}, author={Kleiner, Manuel and Kouris, Angela and Violette, Marlene and D'Angelo, Grace and Liu, Yihua and Korenek, Abigail and Tolic, Nikola and Sachsenberg, Timo and McCalder, Janine and Lipton, Mary S. S. and et al.}, year={2023}, month={Feb} }
 @article{blakeley-ruiz_kleiner_2022, title={Considerations for constructing a protein sequence database for metaproteomics}, volume={20}, ISSN={["2001-0370"]}, url={http://dx.doi.org/10.1016/j.csbj.2022.01.018}, DOI={10.1016/j.csbj.2022.01.018}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, publisher={Elsevier BV}, author={Blakeley-Ruiz, J. Alfredo and Kleiner, Manuel}, year={2022}, pages={937–952} }
 @article{michellod_bien_birgel_jensen_kleiner_fearn_zeidler_gruber-vodicka_dubilier_liebeke_2022, title={De novo phytosterol synthesis in animals}, volume={4}, url={https://doi.org/10.1101/2022.04.22.489198}, DOI={10.1101/2022.04.22.489198}, publisher={Cold Spring Harbor Laboratory}, author={Michellod, Dolma and Bien, Tanja and Birgel, Daniel and Jensen, Marlene and Kleiner, Manuel and Fearn, Sarah and Zeidler, Caroline and Gruber-Vodicka, Harald R and Dubilier, Nicole and Liebeke, Manuel}, year={2022}, month={Apr} }
 @misc{bartlett_kleiner_2022, title={Dietary protein and the intestinal microbiota: An understudied relationship}, volume={25}, ISSN={["2589-0042"]}, DOI={10.1016/j.isci.2022.105313}, number={11}, journal={ISCIENCE}, author={Bartlett, Alexandria and Kleiner, Manuel}, year={2022}, month={Nov} }
 @article{beck_kleiner_garrell_2022, title={Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.910377}, journal={FRONTIERS IN PLANT SCIENCE}, author={Beck, Ashley E. and Kleiner, Manuel and Garrell, Anna-Katharina}, year={2022}, month={Jun} }
 @article{salvato_vintila_finkel_dangl_kleiner_2022, title={Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes}, volume={35}, ISSN={["1943-7706"]}, url={https://doi.org/10.1094/MPMI-05-22-0116-TA}, DOI={10.1094/MPMI-05-22-0116-TA}, number={11}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Salvato, Fernanda and Vintila, Simina and Finkel, Omri M. and Dangl, Jeffery L. and Kleiner, Manuel}, year={2022}, month={Nov}, pages={977–988} }
 @article{sato_wippler_wentrup_ansorge_sadowski_gruber-vodicka_dubilier_kleiner_2022, title={Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium}, volume={10}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01372-2}, number={1}, journal={MICROBIOME}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Ansorge, Rebecca and Sadowski, Miriam and Gruber-Vodicka, Harald and Dubilier, Nicole and Kleiner, Manuel}, year={2022}, month={Oct} }
 @article{smith_salvato_garikipati_kleiner_septer_2021, title={Activation of the Type VI Secretion System in the Squid Symbiont Vibrio fischeri Requires the Transcriptional Regulator TasR and the Structural Proteins TssM and TssA}, volume={203}, ISSN={["1098-5530"]}, DOI={10.1128/JB.00399-21}, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Smith, Stephanie and Salvato, Fernanda and Garikipati, Aditi and Kleiner, Manuel and Septer, Alecia N.}, year={2021}, month={Nov} }
 @article{hinzke_kleiner_meister_schlueter_hentschker_pane-farre_hildebrandt_felbeck_sievert_bonn_et al._2021, title={Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis}, volume={10}, ISSN={["2050-084X"]}, url={https://europepmc.org/articles/PMC7787665}, DOI={10.7554/elife.58371}, journal={ELIFE}, publisher={eLife Sciences Publications, Ltd}, author={Hinzke, Tjorven and Kleiner, Manuel and Meister, Mareike and Schlueter, Rabea and Hentschker, Christian and Pane-Farre, Jan and Hildebrandt, Petra and Felbeck, Horst and Sievert, Stefan M. and Bonn, Florian and et al.}, year={2021}, month={Jan} }
 @article{bossche_kunath_schallert_schaepe_abraham_armengaud_arntzen_bassignani_benndorf_fuchs_et al._2021, title={Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows}, volume={12}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-021-27542-8}, number={1}, journal={NATURE COMMUNICATIONS}, author={Bossche, Tim and Kunath, Benoit J. and Schallert, Kay and Schaepe, Stephanie S. and Abraham, Paul E. and Armengaud, Jean and Arntzen, Magnus O. and Bassignani, Ariane and Benndorf, Dirk and Fuchs, Stephan and et al.}, year={2021}, month={Dec} }
 @article{jensen_wippler_kleiner_2021, title={Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses}, volume={9}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/Spectrum.01429-21}, DOI={10.1128/Spectrum.01429-21}, number={2}, journal={MICROBIOLOGY SPECTRUM}, publisher={American Society for Microbiology}, author={Jensen, Marlene and Wippler, Juliane and Kleiner, Manuel}, editor={Gralnick, Jeffrey A.Editor}, year={2021}, month={Oct} }
 @article{jensen_wippler_kleiner_2021, title={Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses}, volume={6}, url={https://doi.org/10.1101/2021.06.16.448770}, DOI={10.1101/2021.06.16.448770}, publisher={Cold Spring Harbor Laboratory}, author={Jensen, Marlene and Wippler, Juliane and Kleiner, Manuel}, year={2021}, month={Jun} }
 @article{mordant_kleiner_2021, title={Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes}, volume={9}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/Spectrum.01877-21}, DOI={10.1128/Spectrum.01877-21}, number={3}, journal={MICROBIOLOGY SPECTRUM}, publisher={American Society for Microbiology}, author={Mordant, Angie and Kleiner, Manuel}, editor={Khursigara, Cezar M.Editor}, year={2021}, month={Dec} }
 @article{sato_wippler_wentrup_ansorge_sadowski_gruber-vodicka_dubilier_kleiner_2021, title={Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium}, volume={1}, url={https://doi.org/10.1101/2021.01.30.428904}, DOI={10.1101/2021.01.30.428904}, publisher={Cold Spring Harbor Laboratory}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Ansorge, Rebecca and Sadowski, Miriam and Gruber-Vodicka, Harald and Dubilier, Nicole and Kleiner, Manuel}, year={2021}, month={Jan} }
 @misc{salvato_hettich_kleiner_2021, title={Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes}, volume={17}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1009245}, DOI={10.1371/journal.ppat.1009245}, number={2}, journal={PLOS PATHOGENS}, publisher={Public Library of Science (PLoS)}, author={Salvato, Fernanda and Hettich, Robert L. and Kleiner, Manuel}, editor={Hogan, Deborah A.Editor}, year={2021}, month={Feb} }
 @article{mankowski_kleiner_erséus_leisch_sato_volland_hüttel_wentrup_woyke_wippler_et al._2021, title={Highly variable fidelity drives symbiont community composition in an obligate symbiosis}, volume={4}, url={https://doi.org/10.1101/2021.04.28.441735}, DOI={10.1101/2021.04.28.441735}, publisher={Cold Spring Harbor Laboratory}, author={Mankowski, Anna and Kleiner, Manuel and Erséus, Christer and Leisch, Nikolaus and Sato, Yui and Volland, Jean-Marie and Hüttel, Bruno and Wentrup, Cecilia and Woyke, Tanja and Wippler, Juliane and et al.}, year={2021}, month={Apr} }
 @article{maggie sogin_kleiner_borowski_gruber-vodicka_dubilier_2021, title={Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses}, volume={75}, ISSN={["1545-3251"]}, DOI={10.1146/annurev-micro-051021-123130}, journal={ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021}, author={Maggie Sogin, E. and Kleiner, Manuel and Borowski, Christian and Gruber-Vodicka, Harald R. and Dubilier, Nicole}, year={2021}, pages={695–718} }
 @article{wagner_tang_salvato_clouse_bartlett_vintila_phillips_sermons_hoffmann_balint-kurti_et al._2021, title={Microbe-dependent heterosis in maize}, volume={118}, ISSN={["0027-8424"]}, url={https://doi.org/10.1073/pnas.2021965118}, DOI={10.1073/pnas.2021965118}, number={30}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Vintila, Simina and Phillips, Laura and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and et al.}, year={2021}, month={Jul} }
 @article{ataeian_vadlamani_haines_mosier_dong_kleiner_strous_hawley_2021, title={Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology}, volume={24}, ISSN={["2589-0042"]}, url={https://doi.org/10.1016/j.isci.2021.103405}, DOI={10.1016/j.isci.2021.103405}, number={12}, journal={ISCIENCE}, publisher={Elsevier BV}, author={Ataeian, Maryam and Vadlamani, Agasteswar and Haines, Marianne and Mosier, Damon and Dong, Xiaoli and Kleiner, Manuel and Strous, Marc and Hawley, Alyse K.}, year={2021}, month={Dec} }
 @article{kleiner_kouris_jensen_grace_liu_korenek_tolić_sachsenberg_mccalder_lipton_et al._2021, title={Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes}, volume={3}, url={https://doi.org/10.1101/2021.03.29.437612}, DOI={10.1101/2021.03.29.437612}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Kouris, Angela and Jensen, Marlene and Grace, D’Angelo and Liu, Yihua and Korenek, Abigail and Tolić, Nikola and Sachsenberg, Timo and McCalder, Janine and Lipton, Mary S. and et al.}, year={2021}, month={Mar} }
 @article{ponnudurai_heiden_sayavedra_hinzke_kleiner_hentschker_felbeck_sievert_schlüter_becher_et al._2020, title={Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions}, volume={14}, url={https://doi.org/10.1038/s41396-019-0517-6}, DOI={10.1038/s41396-019-0517-6}, number={2}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Ponnudurai, Ruby and Heiden, Stefan E. and Sayavedra, Lizbeth and Hinzke, Tjorven and Kleiner, Manuel and Hentschker, Christian and Felbeck, Horst and Sievert, Stefan M. and Schlüter, Rabea and Becher, Dörte and et al.}, year={2020}, month={Feb}, pages={649–656} }
 @article{speare_smith_salvato_kleiner_septer_2020, title={Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition}, volume={11}, ISSN={["2150-7511"]}, DOI={10.1128/mBio.03060-19}, number={1}, journal={MBIO}, author={Speare, Lauren and Smith, Stephanie and Salvato, Fernanda and Kleiner, Manuel and Septer, Alecia N.}, year={2020} }
 @article{sato_wippler_wentrup_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of Two Deltaproteobacterial Endosymbionts, Delta1a and Delta1b, from the Uncultured Sva0081 Clade, Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00276-20}, number={16}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Dubilier, Nicole and Kleiner, Manuel}, year={2020}, month={Apr} }
 @article{sato_wippler_wentrup_woyke_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISBN={2576-098X}, DOI={10.1128/MRA.00704-20.}, number={31}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Woyke, Tanja and Dubilier, Nicole and Kleiner, Manuel}, year={2020}, month={Jul} }
 @article{sato_wippler_wentrup_woyke_dubilier_kleiner_2020, title={High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00704-20}, DOI={10.1128/MRA.00704-20}, number={31}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, publisher={American Society for Microbiology}, author={Sato, Yui and Wippler, Juliane and Wentrup, Cecilia and Woyke, Tanja and Dubilier, Nicole and Kleiner, Manuel}, editor={Stewart, Frank J.Editor}, year={2020}, month={Jul} }
 @article{assie_leisch_meier_gruber-vodicka_tegetmeyer_meyerdierks_kleiner_hinzke_joye_saxton_et al._2020, title={Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)}, volume={14}, ISSN={["1751-7370"]}, url={https://doi.org/10.1038/s41396-019-0508-7}, DOI={10.1038/s41396-019-0508-7}, number={1}, journal={ISME JOURNAL}, publisher={Springer Science and Business Media LLC}, author={Assie, Adrien and Leisch, Nikolaus and Meier, Dimitri V and Gruber-Vodicka, Harald and Tegetmeyer, Halina E. and Meyerdierks, Anke and Kleiner, Manuel and Hinzke, Tjorven and Joye, Samantha and Saxton, Matthew and et al.}, year={2020}, month={Jan}, pages={104–122} }
 @article{hinzke_kleiner_meister_schlüter_hentschker_pané-farré_hildebrandt_felbeck_sievert_bonn_et al._2020, title={Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila}, volume={4}, url={https://doi.org/10.1101/2020.04.08.032177}, DOI={10.1101/2020.04.08.032177}, publisher={Cold Spring Harbor Laboratory}, author={Hinzke, Tjorven and Kleiner, Manuel and Meister, Mareike and Schlüter, Rabea and Hentschker, Christian and Pané-Farré, Jan and Hildebrandt, Petra and Felbeck, Horst and Sievert, Stefan M. and Bonn, Florian and et al.}, year={2020}, month={Apr} }
 @article{wagner_tang_salvato_clouse_bartlett_sermons_hoffmann_balint-kurti_kleiner_2020, title={Microbe-dependent heterosis in maize}, volume={5}, url={https://doi.org/10.1101/2020.05.05.078766}, DOI={10.1101/2020.05.05.078766}, publisher={Cold Spring Harbor Laboratory}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and Kleiner, Manuel}, year={2020}, month={May} }
 @article{kleiner_bushnell_sanderson_hooper_duerkop_2020, title={Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities}, volume={1}, url={https://doi.org/10.1101/2020.01.15.908442}, DOI={10.1101/2020.01.15.908442}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Bushnell, Brian and Sanderson, Kenneth E. and Hooper, Lora V. and Duerkop, Breck A.}, year={2020}, month={Jan} }
 @article{kleiner_bushnell_sanderson_hooper_duerkop_2020, title={Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities}, volume={8}, ISSN={["2049-2618"]}, url={https://europepmc.org/articles/PMC7667829}, DOI={10.1186/s40168-020-00935-5}, number={1}, journal={MICROBIOME}, publisher={Springer Science and Business Media LLC}, author={Kleiner, Manuel and Bushnell, Brian and Sanderson, Kenneth E. and Hooper, Lora V. and Duerkop, Breck A.}, year={2020}, month={Nov} }
 @article{zorz_sharp_kleiner_gordon_pon_dong_strous_2019, title={A shared core microbiome in soda lakes separated by large distances}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-12195-5}, journal={NATURE COMMUNICATIONS}, author={Zorz, Jackie K. and Sharp, Christine and Kleiner, Manuel and Gordon, Paul M. K. and Pon, Richard T. and Dong, Xiaoli and Strous, Marc}, year={2019}, month={Sep} }
 @article{jaeckle_seah_tietjen_leisch_liebeke_kleiner_berg_gruber-vodicka_2019, title={Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula}, volume={116}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.1818995116}, DOI={10.1073/pnas.1818995116}, number={17}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Jaeckle, Oliver and Seah, Brandon K. B. and Tietjen, Malin and Leisch, Nikolaus and Liebeke, Manuel and Kleiner, Manuel and Berg, Jasmine S. and Gruber-Vodicka, Harald R.}, year={2019}, month={Apr}, pages={8505–8514} }
 @article{rubin-blum_dubilier_kleiner_2019, title={Genetic evidence for two carbon fixation pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in symbiotic and free-living bacteria}, volume={4}, ISSN={["2379-5042"]}, url={https://doi.org/10.1128/mSphere.00394-18}, DOI={10.1128/msphere.00394-18}, number={1}, journal={mSphere}, publisher={American Society for Microbiology}, author={Rubin-Blum, M. and Dubilier, N. and Kleiner, M.}, editor={Hallam, Steven J.Editor}, year={2019}, pages={e00394–18} }
 @article{hinzke_kleiner_breusing_felbeck_häsler_sievert_schlüter_rosenstiel_reusch_schweder_et al._2019, title={Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.}, volume={10}, url={https://europepmc.org/articles/PMC6918071}, DOI={10.1128/mBio.02243-19}, number={6}, journal={mBio}, publisher={American Society for Microbiology}, author={Hinzke, Tjorven and Kleiner, Manuel and Breusing, Corinna and Felbeck, Horst and Häsler, Robert and Sievert, Stefan M. and Schlüter, Rabea and Rosenstiel, Philip and Reusch, Thorsten B. H. and Schweder, Thomas and et al.}, editor={Distel, Daniel and Ruby, Edward G.Editors}, year={2019}, month={Dec} }
 @article{hinzke_kleiner_breusing_felbeck_häsler_sievert_schlüter_rosenstiel_reusch_schweder_et al._2019, title={Host-microbe interactions in the chemosyntheticRiftia pachyptilasymbiosis}, volume={5}, url={https://doi.org/10.1101/651323}, DOI={10.1101/651323}, publisher={Cold Spring Harbor Laboratory}, author={Hinzke, Tjorven and Kleiner, Manuel and Breusing, Corinna and Felbeck, Horst and Häsler, Robert and Sievert, Stefan M. and Schlüter, Rabea and Rosenstiel, Philip and Reusch, Thorsten B. H. and Schweder, Thomas and et al.}, year={2019}, month={May} }
 @article{kleiner_2019, title={Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities}, volume={4}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/mSystems.00115-19}, DOI={10.1128/mSystems.00115-19}, number={3}, journal={MSYSTEMS}, publisher={American Society for Microbiology}, author={Kleiner, Manuel}, year={2019} }
 @article{hinzke_kouris_hughes_strous_kleiner_2019, title={More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics}, volume={10}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2019.00238}, journal={FRONTIERS IN MICROBIOLOGY}, author={Hinzke, Tjorven and Kouris, Angela and Hughes, Rebecca-Ayme and Strous, Marc and Kleiner, Manuel}, year={2019}, month={Feb} }
 @article{seah_antony_huettel_zarzycki_borzyskowski_erb_kouris_kleiner_liebeke_dubilier_et al._2019, title={Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation}, volume={10}, ISSN={["2150-7511"]}, url={https://doi.org/10.1128/mBio.01112-19}, DOI={10.1128/mBio.01112-19}, number={3}, journal={MBIO}, publisher={American Society for Microbiology}, author={Seah, Brandon K. B. and Antony, Chakkiath Paul and Huettel, Bruno and Zarzycki, Jan and Borzyskowski, Lennart Schada and Erb, Tobias J. and Kouris, Angela and Kleiner, Manuel and Liebeke, Manuel and Dubilier, Nicole and et al.}, editor={Giovannoni, Stephen J.Editor}, year={2019} }
 @article{seah_antony_huettel_zarzycki_borzyskowski_erb_kouris_kleiner_liebeke_dubilier_et al._2019, title={Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2fixation}, volume={2}, url={https://doi.org/10.1101/540435}, DOI={10.1101/540435}, publisher={Cold Spring Harbor Laboratory}, author={Seah, Brandon K. B. and Antony, Chakkiath Paul and Huettel, Bruno and Zarzycki, Jan and Borzyskowski, Lennart Schada and Erb, Tobias J. and Kouris, Angela and Kleiner, Manuel and Liebeke, Manuel and Dubilier, Nicole and et al.}, year={2019}, month={Feb} }
 @article{gruber-vodicka_leisch_kleiner_hinzke_liebeke_mcfall-ngai_hadfield_dubilier_2019, title={TheTrichoplaxmicrobiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria}, volume={3}, url={https://doi.org/10.1101/568287}, DOI={10.1101/568287}, publisher={Cold Spring Harbor Laboratory}, author={Gruber-Vodicka, Harald R. and Leisch, Nikolaus and Kleiner, Manuel and Hinzke, Tjorven and Liebeke, Manuel and McFall-Ngai, Margaret and Hadfield, Michael G. and Dubilier, Nicole}, year={2019}, month={Mar} }
 @article{gruber-vodicka_leisch_kleiner_hinzke_liebeke_mcfall-ngai_hadfield_dubilier_2019, title={Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2}, volume={4}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-019-0475-9}, number={9}, journal={NATURE MICROBIOLOGY}, author={Gruber-Vodicka, Harald R. and Leisch, Nikolaus and Kleiner, Manuel and Hinzke, Tjorven and Liebeke, Manuel and McFall-Ngai, Margaret and Hadfield, Michael G. and Dubilier, Nicole}, year={2019}, month={Sep}, pages={1465–1474} }
 @article{kleiner_dong_hinzke_wippler_thorson_mayer_strous_2018, title={A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities}, volume={1}, url={https://doi.org/10.1101/245290}, DOI={10.1101/245290}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Dong, Xiaoli and Hinzke, Tjorven and Wippler, Juliane and Thorson, Erin and Mayer, Bernhard and Strous, Marc}, year={2018}, month={Jan} }
 @article{petersen_kemper_gruber-vodicka_cardini_van der geest_kleiner_bulgheresi_mußmann_herbold_seah_et al._2018, title={Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation}, volume={3}, ISSN={2058-5276}, url={http://dx.doi.org/10.1038/S41564-018-0196-5}, DOI={10.1038/S41564-018-0196-5}, number={8}, journal={Nature Microbiology}, publisher={Springer Science and Business Media LLC}, author={Petersen, Jillian M. and Kemper, Anna and Gruber-Vodicka, Harald and Cardini, Ulisse and van der Geest, Matthijs and Kleiner, Manuel and Bulgheresi, Silvia and Mußmann, Marc and Herbold, Craig and Seah, Brandon K. B. and et al.}, year={2018}, month={Jun}, pages={961–961} }
 @article{hinzke_kleiner_markert_2018, series={Methods in Molecular Biology}, title={Centrifugation-based enrichment of bacterial cell populations for metaproteomic studies on bacteria-invertebrate symbioses}, volume={1841}, DOI={10.1007/978-1-4939-8695-8_22}, journal={Springer}, author={Hinzke, T. and Kleiner, M. and Markert, S.}, editor={Becher, D.Editor}, year={2018}, pages={319–334}, collection={Methods in Molecular Biology} }
 @article{zorz_kozlowski_stein_strous_kleiner_2018, title={Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.}, url={http://europepmc.org/abstract/med/29867847}, DOI={10.3389/fmicb.2018.00938}, journal={Frontiers in microbiology}, author={Zorz, JK and Kozlowski, JA and Stein, LY and Strous, M and Kleiner, M}, year={2018} }
 @article{assié_leisch_meier_gruber-vodicka_tegetmeyer_meyerdirks_kleiner_hinzke_joye_saxton_et al._2018, title={Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)}, volume={10}, url={https://doi.org/10.1101/437616}, DOI={10.1101/437616}, publisher={Cold Spring Harbor Laboratory}, author={Assié, Adrien and Leisch, Nikolaus and Meier, Dimitri V. and Gruber-Vodicka, Harald and Tegetmeyer, Halina E. and Meyerdirks, Anke and Kleiner, Manuel and Hinzke, Tjorven and Joye, Samantha and Saxton, Matthew and et al.}, year={2018}, month={Oct} }
 @article{kleiner_dong_hinzke_wippler_thorson_mayer_strous_2018, title={Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities}, volume={115}, ISSN={["0027-8424"]}, url={http://europepmc.org/abstract/med/29844191}, DOI={10.1073/pnas.1722325115}, number={24}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Kleiner, Manuel and Dong, Xiaoli and Hinzke, Tjorven and Wippler, Juliane and Thorson, Erin and Mayer, Bernhard and Strous, Marc}, year={2018}, month={Jun}, pages={E5576–E5584} }
 @article{duerkop_kleiner_paez-espino_zhu_bushnell_hassell_winter_kyrpides_hooper_2018, title={Murine colitis reveals a disease-associated bacteriophage community}, volume={3}, ISSN={["2058-5276"]}, url={https://doi.org/10.1038/s41564-018-0210-y}, DOI={10.1038/s41564-018-0210-y}, number={9}, journal={NATURE MICROBIOLOGY}, author={Duerkop, Breck A. and Kleiner, Manuel and Paez-Espino, David and Zhu, Wenhan and Bushnell, Brian and Hassell, Brian and Winter, Sebastian E. and Kyrpides, Nikos C. and Hooper, Lora V}, year={2018}, month={Sep}, pages={1023–1031} }
 @article{fida_voordouw_ataeian_kleiner_okpala_mand_voordouw_2018, title={Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors}, volume={9}, ISSN={["1664-302X"]}, url={http://europepmc.org/abstract/med/29867883}, DOI={10.3389/fmicb.2018.00981}, journal={FRONTIERS IN MICROBIOLOGY}, author={Fida, Tekle T. and Voordouw, Johanna and Ataeian, Maryam and Kleiner, Manuel and Okpala, Gloria and Mand, Jaspreet and Voordouw, Gerrit}, year={2018}, month={May} }
 @article{kleiner_thorson_sharp_dong_liu_li_strous_2017, title={Assessing species biomass contributions in microbial communities via metaproteomics}, volume={8}, ISSN={["2041-1723"]}, url={https://www.nature.com/articles/s41467-017-01544-x}, DOI={10.1038/s41467-017-01544-x}, journal={NATURE COMMUNICATIONS}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Thorson, Erin and Sharp, Christine E. and Dong, Xiaoli and Liu, Dan and Li, Carmen and Strous, Marc}, year={2017}, month={Nov} }
 @article{kleiner_thorson_sharp_dong_liu_li_strous_2017, title={Assessing species biomass contributions in microbial communities via metaproteomics}, volume={4}, url={https://doi.org/10.1101/130575}, DOI={10.1101/130575}, publisher={Cold Spring Harbor Laboratory}, author={Kleiner, Manuel and Thorson, Erin and Sharp, Christine E. and Dong, Xiaoli and Liu, Dan and Li, Carmen and Strous, Marc}, year={2017}, month={Apr} }
 @article{dong_kleiner_sharp_thorson_li_liu_strous_2017, title={Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp}, volume={8}, DOI={10.3389/fmicb.2017.01461}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dong, Xiaoli and Kleiner, Manuel and Sharp, Christine E. and Thorson, Erin and Li, Carmen and Liu, Dan and Strous, Marc}, year={2017}, month={Aug} }
 @article{dong_kleiner_sharp_thorson_li_liu_strous_2017, title={Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp}, volume={4}, DOI={10.1101/131631}, publisher={Cold Spring Harbor Laboratory}, author={Dong, Xiaoli and Kleiner, Manuel and Sharp, Christine E. and Thorson, Erin and Li, Carmen and Liu, Dan and Strous, Marc}, year={2017}, month={Apr} }
 @article{genome sequence of the sulfur-oxidizing bathymodiolus thermophilus gill endosymbiont._2017, url={http://europepmc.org/abstract/med/28878861}, DOI={10.1186/s40793-017-0266-y}, journal={Standards in Genomic Sciences}, year={2017} }
 @article{ponnudurai_kleiner_sayavedra_petersen_moche_otto_becher_takeuchi_satoh_dubilier_et al._2017, title={Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis}, volume={11}, url={https://doi.org/10.1038/ismej.2016.124}, DOI={10.1038/ismej.2016.124}, number={2}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Ponnudurai, Ruby and Kleiner, Manuel and Sayavedra, Lizbeth and Petersen, Jillian M and Moche, Martin and Otto, Andreas and Becher, Dörte and Takeuchi, Takeshi and Satoh, Noriyuki and Dubilier, Nicole and et al.}, year={2017}, month={Feb}, pages={463–477} }
 @misc{metaproteomics of phototrophic biomats from two soda lakes in the canadian rocky mountains_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006343}, year={2017} }
 @article{kleiner_2017, title={Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance}, volume={5}, url={https://doi.org/10.7287/peerj.preprints.2846v1}, DOI={10.7287/peerj.preprints.2846v1}, journal={PeerJ Preprints}, publisher={PeerJ}, author={Kleiner, M.}, year={2017}, pages={e2846v1} }
 @article{kleiner_2017, title={Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance}, volume={3}, url={https://doi.org/10.7287/peerj.preprints.2846}, DOI={10.7287/peerj.preprints.2846}, publisher={PeerJ}, author={Kleiner, Manuel}, year={2017}, month={Mar} }
 @misc{quantification of mock microbial communities with metagenomes, 16s rrna gene amplicons and metaproteomics_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006118}, year={2017} }
 @misc{re-analysis of an ultra-deep and quantitative saliva proteome_2017, url={http://www.ebi.ac.uk/pride/archive/projects/PXD006366}, year={2017} }
 @article{rubin-blum_antony_borowski_sayavedra_pape_sahling_bohrmann_kleiner_redmond_valentine_et al._2017, title={Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps}, volume={2}, url={https://doi.org/10.1038/nmicrobiol.2017.93}, DOI={10.1038/nmicrobiol.2017.93}, journal={Nature Microbiology}, publisher={Springer Nature}, author={Rubin-Blum, Maxim and Antony, Chakkiath Paul and Borowski, Christian and Sayavedra, Lizbeth and Pape, Thomas and Sahling, Heiko and Bohrmann, Gerhard and Kleiner, Manuel and Redmond, Molly C. and Valentine, David L. and et al.}, year={2017}, pages={17093} }
 @misc{bathymodiolus azoricus host-symbiont proteomics_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD004061}, year={2016} }
 @article{petersen_kemper_gruber-vodicka_cardini_geest_kleiner_bulgheresi_mußmann_herbold_seah_et al._2016, title={Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation}, volume={2}, url={https://doi.org/10.1038/nmicrobiol.2016.195}, DOI={10.1038/nmicrobiol.2016.195}, journal={Nature Microbiology}, publisher={Springer Nature}, author={Petersen, Jillian M. and Kemper, Anna and Gruber-Vodicka, Harald and Cardini, Ulisse and Geest, Matthijs and Kleiner, Manuel and Bulgheresi, Silvia and Mußmann, Marc and Herbold, Craig and Seah, Brandon K.B. and et al.}, year={2016}, pages={16195} }
 @article{zimmermann_wentrup_sadowski_blazejak_gruber-vodicka_kleiner_ott_cronholm_de_erséus_et al._2016, title={Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla}, volume={25}, url={http://europepmc.org/abstract/med/26826340}, DOI={10.1111/mec.13554}, number={13}, journal={Molecular Ecology}, author={Zimmermann, J and Wentrup, C and Sadowski, M and Blazejak, A and Gruber-Vodicka, H and Kleiner, M and Ott, J and Cronholm, B and De, Wit P and Erséus, C and et al.}, year={2016}, pages={3203–3223} }
 @misc{differential proteomics of lenisia limosa (breviatea) and its epibiotic arcobacter symbiont_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD003275}, year={2016} }
 @article{hamann_gruber-vodicka_kleiner_tegetmeyer_riedel_littmann_chen_milucka_viehweger_becker_et al._2016, title={Environmental Breviatea harbor mutualistic Arcobacter epibionts}, volume={534}, url={http://europepmc.org/abstract/med/27279223}, DOI={10.1038/nature18297}, number={7606}, journal={Nature}, author={Hamann, E. and Gruber-Vodicka, H. and Kleiner, M. and Tegetmeyer, H.E. and Riedel, D. and Littmann, S. and Chen, J. and Milucka, J. and Viehweger, B. and Becker, K.W. and et al.}, year={2016}, pages={254–258} }
 @article{schimak_kleiner_wetzel_liebeke_dubilier_fuchs_2016, title={MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells}, volume={82}, url={http://europepmc.org/abstract/med/26475101}, DOI={10.1128/AEM.02776-15}, number={1}, journal={Applied and Environmental Microbiology}, author={Schimak, M.P. and Kleiner, M. and Wetzel, S. and Liebeke, M. and Dubilier, N. and Fuchs, B.}, year={2016}, pages={62–70} }
 @misc{proteomics of candidatus thiodiazotropha endoloripes, the chemosynthetic symbiont of the lucinid clam loripes lucinalis from the bay of fetovaia_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD004536}, year={2016} }
 @misc{proteomics of cycloclasticus endosymbiont of deep-sea mussel bathymodiolus heckerae from campeche knolls, southern gulf of mexico_2016, url={http://www.ebi.ac.uk/pride/archive/projects/PXD005351}, year={2016} }
 @article{yu_kleiner_velicer_2016, title={Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria}, volume={198}, DOI={10.1128/jb.00389-16}, number={23}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Yu, Yuen-Tsu N. and Kleiner, Manuel and Velicer, Gregory J.}, editor={Mullineaux, C. W.Editor}, year={2016}, month={Sep}, pages={3142–3151} }
 @article{wippler_kleiner_lott_gruhl_abraham_giannone_young_hettich_dubilier_2016, title={Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis}, volume={17}, DOI={10.1186/s12864-016-3293-y}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Wippler, Juliane and Kleiner, Manuel and Lott, Christian and Gruhl, Alexander and Abraham, Paul E. and Giannone, Richard J. and Young, Jacque C. and Hettich, Robert L. and Dubilier, Nicole}, year={2016}, month={Nov} }
 @misc{transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm olavius algarvensis_2016, url={https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=77bbe652de0b4439b9a9e89016f99c93}, year={2016} }
 @article{sayavedra_kleiner_ponnudurai_wetzel_pelletier_barbe_satoh_shoguchi_fink_breusing_et al._2015, title={Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels}, volume={4}, url={http://europepmc.org/abstract/med/26371554}, DOI={10.7554/eLife.07966}, journal={eLife}, author={Sayavedra, L. and Kleiner, M. and Ponnudurai, R. and Wetzel, S. and Pelletier, E. and Barbe, V. and Satoh, N. and Shoguchi, E. and Fink, D. and Breusing, C. and et al.}, year={2015}, pages={e07966} }
 @article{kleiner_hooper_duerkop_2015, title={Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes}, volume={16}, url={http://europepmc.org/abstract/med/25608871}, DOI={10.1186/s12864-014-1207-4}, number={7}, journal={BMC Genomics}, author={Kleiner, M. and Hooper, L.V. and Duerkop, B.A.}, year={2015}, pages={7} }
 @article{kleiner_wentrup_holler_lavik_harder_lott_littmann_kuypers_dubilier_2015, title={Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments}, volume={17}, url={http://europepmc.org/abstract/med/26013766}, DOI={10.1111/1462-2920.12912}, number={12}, journal={Environmental Microbiology}, author={Kleiner, M. and Wentrup, C. and Holler, T. and Lavik, G. and Harder, J. and Lott, C. and Littmann, S. and Kuypers, M.M.M. and Dubilier, N.}, year={2015}, pages={5023–5035} }
 @article{winkel_pjevac_kleiner_littmann_meyerdierks_amann_mußmann_2014, title={Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from deep-sea hydrothermal systems}, volume={90}, url={http://europepmc.org/abstract/med/25244359}, DOI={10.1111/1574-6941.12429}, number={3}, journal={FEMS Microbiology Ecology}, author={Winkel, M. and Pjevac, P. and Kleiner, M. and Littmann, S. and Meyerdierks, A. and Amann, R. and Mußmann, M.}, year={2014}, pages={731–746} }
 @article{kleiner_young_shah_verberkmoes_dubilier_2013, title={Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts}, volume={4}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000321187400018&KeyUID=WOS:000321187400018}, DOI={10.1128/mBio.00223-13}, number={3}, journal={Mbio}, author={Kleiner, Manuel and Young, Jacque C. and Shah, Manesh and VerBerkmoes, Nathan C. and Dubilier, Nicole}, year={2013} }
 @article{kleiner_petersen_dubilier_2012, title={Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer}, volume={15}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311181000012&KeyUID=WOS:000311181000012}, DOI={10.1016/j.mlb.2012.09.003}, number={5}, journal={Current Opinion in Microbiology}, author={Kleiner, Manuel and Petersen, Jillian M. and Dubilier, Nicole}, year={2012}, pages={621–631} }
 @article{kleiner_petersen_dubilier_2012, title={Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer}, volume={15}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2012.09.003}, DOI={10.1016/j.mib.2012.09.003}, number={5}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Kleiner, Manuel and Petersen, Jillian M and Dubilier, Nicole}, year={2012}, month={Oct}, pages={621–631} }
 @article{kleiner_wentrup_lott_teeling_wetzel_young_chang_shah_verberkmoes_zarzycki_et al._2012, title={Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use}, volume={109}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000304090600007&KeyUID=WOS:000304090600007}, DOI={10.1073/pnas.1121198109}, number={19}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Kleiner, Manuel and Wentrup, Cecilia and Lott, Christian and Teeling, Hanno and Wetzel, Silke and Young, Jacque and Chang, Yun-Juan and Shah, Manesh and VerBerkmoes, Nathan C. and Zarzycki, Jan and et al.}, year={2012}, pages={E1173–E1182} }
 @article{markert_gardebrecht_felbeck_sievert_klose_becher_albrecht_thurmer_daniel_kleiner_et al._2011, title={Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont}, volume={11}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000293269100015&KeyUID=WOS:000293269100015}, DOI={10.1002/pmic.201100059}, number={15}, journal={Proteomics}, author={Markert, S. and Gardebrecht, A. and Felbeck, H. and Sievert, S. M. and Klose, J. and Becher, D. and Albrecht, D. and Thurmer, A. and Daniel, R. and Kleiner, M. and et al.}, year={2011}, pages={3106–3117} }
 @article{kleiner_woyke_ruehland_dubilier_2011, title={The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm}, DOI={10.1002/9781118010549.ch32}, journal={Handbook of Molecular Microbial Ecology II}, publisher={Wiley-Blackwell}, author={Kleiner, Manuel and Woyke, Tanja and Ruehland, Caroline and Dubilier, Nicole}, year={2011}, month={Nov}, pages={319–333} }