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Rex R. Malmstrom, Ph.D. - Publications

Affiliations: 
2006 University of Delaware, Newark, DE, United States 
Area:
Ecology, Oceanography, Microbiology
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Ruff SE, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. Biorxiv : the Preprint Server For Biology. PMID 38076927 DOI: 10.1101/2023.11.27.568837  0.338
2023 Vyshenska D, Sampara P, Singh K, Tomatsu A, Kauffman WB, Nuccio EE, Blazewicz SJ, Pett-Ridge J, Louie KB, Varghese N, Kellom M, Clum A, Riley R, Roux S, Eloe-Fadrosh EA, ... ... Malmstrom RR, et al. A standardized quantitative analysis strategy for stable isotope probing metagenomics. Msystems. e0128022. PMID 37377419 DOI: 10.1128/msystems.01280-22  0.317
2022 Needham DM, Poirier C, Bachy C, George EE, Wilken S, Yung CCM, Limardo AJ, Morando M, Sudek L, Malmstrom RR, Keeling PJ, Santoro AE, Worden AZ. The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate. Nature Microbiology. PMID 35970961 DOI: 10.1038/s41564-022-01174-0  0.324
2022 Yu H, Speth DR, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ. Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep. Applied and Environmental Microbiology. e0210921. PMID 35604226 DOI: 10.1128/aem.02109-21  0.371
2021 Bowers RM, Nayfach S, Schulz F, Jungbluth SP, Ruhl IA, Sheremet A, Lee J, Goudeau D, Eloe-Fadrosh EA, Stepanauskas R, Malmstrom RR, Kyrpides NC, Dunfield PF, Woyke T. Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution. The Isme Journal. PMID 34969995 DOI: 10.1038/s41396-021-01178-4  0.306
2021 Boeuf D, Eppley JM, Mende DR, Malmstrom RR, Woyke T, DeLong EF. Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. Microbiome. 9: 172. PMID 34389059 DOI: 10.1186/s40168-021-01119-5  0.33
2020 Sheremet A, Jones GM, Jarett J, Bowers RM, Bedard I, Culham C, Eloe-Fadrosh EA, Ivanova N, Malmstrom RR, Grasby SE, Woyke T, Dunfield PF. Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil. Environmental Microbiology. PMID 32372527 DOI: 10.1111/1462-2920.15054  0.374
2020 Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J. Niche differentiation is spatially and temporally regulated in the rhizosphere. The Isme Journal. PMID 31953507 DOI: 10.1038/S41396-019-0582-X  0.381
2019 Rochman FF, Kwon M, Khadka R, Tamas I, Lopez-Jauregui AA, Sheremet A, V Smirnova A, Malmstrom RR, Yoon S, Woyke T, Dunfield PF, Verbeke TJ. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. The Isme Journal. PMID 31796935 DOI: 10.1038/S41396-019-0561-2  0.353
2019 Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, ... Malmstrom RR, et al. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences of the United States of America. PMID 31548428 DOI: 10.1073/Pnas.1907517116  0.401
2019 Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications. 10: 2770. PMID 31235780 DOI: 10.1038/S41467-019-10542-0  0.329
2019 Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA. Optimizing genome assembly from PCR-amplified metagenomes. Peerj. 7: e6902. PMID 31119088 DOI: 10.7717/Peerj.6902  0.371
2018 Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. Peerj. 6: e6075. PMID 30581671 DOI: 10.7717/Peerj.6075  0.439
2018 Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, ... ... Malmstrom RR, et al. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology. PMID 30556814 DOI: 10.1038/Nbt.4306  0.31
2018 Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T. Hidden diversity of soil giant viruses. Nature Communications. 9: 4881. PMID 30451857 DOI: 10.1038/S41467-018-07335-2  0.303
2018 Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J, Schulz F, Young M, Jay ZJ, Beam JP, Kyrpides NC, Malmstrom RR, Stepanauskas R, Woyke T. Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. Microbiome. 6: 161. PMID 30223889 DOI: 10.1186/S40168-018-0539-8  0.383
2018 Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. The Isme Journal. PMID 29991764 DOI: 10.1038/S41396-018-0223-9  0.446
2018 Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... Malmstrom RR, et al. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 36: 196. PMID 29406516 DOI: 10.1038/Nbt0218-196A  0.326
2018 Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature Microbiology. PMID 29379208 DOI: 10.1038/S41564-017-0098-Y  0.461
2018 Bramucci AR, Labeeuw L, Orata FD, Ryan EM, Malmstrom RR, Case RJ. The bacterial symbiont Phaeobacter inhibens Shapes the life history of its algal host emiliania huxleyi Frontiers in Marine Science. 5: 188. DOI: 10.3389/Fmars.2018.00188  0.365
2017 Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. The Isme Journal. PMID 29222442 DOI: 10.1038/S41396-017-0001-0  0.359
2017 Roux S, Chan LK, Egan R, Malmstrom RR, McMahon KD, Sullivan MB. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications. 8: 858. PMID 29021524 DOI: 10.1038/S41467-017-01086-2  0.394
2017 Cole BJ, Feltcher ME, Waters RJ, Wetmore KM, Mucyn TS, Ryan EM, Wang G, Ul-Hasan S, McDonald M, Yoshikuni Y, Malmstrom RR, Deutschbauer AM, Dangl JL, Visel A. Genome-wide identification of bacterial plant colonization genes. Plos Biology. 15: e2002860. PMID 28938018 DOI: 10.1371/Journal.Pbio.2002860  0.339
2017 Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, Malmstrom RR, Forest KT, McMahon KD. Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. Msystems. 2. PMID 28861526 DOI: 10.1128/mSystems.00091-17  0.309
2017 Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... Malmstrom RR, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35: 725-731. PMID 28787424 DOI: 10.1038/Nbt.3893  0.336
2016 Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. PMID 27487207 DOI: 10.1038/Nature19068  0.437
2016 Hatzenpichler R, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proceedings of the National Academy of Sciences of the United States of America. PMID 27357680 DOI: 10.1073/Pnas.1603757113  0.448
2016 Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environmental Microbiology. PMID 27235779 DOI: 10.1111/1462-2920.13392  0.318
2016 Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, et al. The Epigenomic Landscape of Prokaryotes. Plos Genetics. 12: e1005854. PMID 26870957 DOI: 10.1371/Journal.Pgen.1005854  0.309
2016 Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Communications. 7: 10476. PMID 26814032 DOI: 10.1038/Ncomms10476  0.428
2016 Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, ... ... Malmstrom RR, et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. The Isme Journal. PMID 26744812 DOI: 10.1038/Ismej.2015.241  0.339
2014 O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, ... Malmstrom RR, et al. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proceedings of the National Academy of Sciences of the United States of America. 111: E5096-104. PMID 25385629 DOI: 10.1073/Pnas.1413110111  0.391
2014 Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, ... Malmstrom R, et al. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The Isme Journal. 8: 2503-16. PMID 25093637 DOI: 10.1038/Ismej.2014.135  0.418
2014 Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science (New York, N.Y.). 344: 416-20. PMID 24763590 DOI: 10.1126/Science.1248575  0.387
2014 Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Dmitrieff E, Malmstrom R, Stepanauskas R, Woyke T. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics Nature Protocols. 9: 1038-1048. PMID 24722403 DOI: 10.1038/Nprot.2014.067  0.367
2013 Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. The Isme Journal. 7: 184-98. PMID 22895163 DOI: 10.1038/Ismej.2012.89  0.42
2011 Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng JF. Decontamination of MDA reagents for single cell whole genome amplification. Plos One. 6: e26161. PMID 22028825 DOI: 10.1371/Journal.Pone.0026161  0.319
2010 McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW, DeLong EF. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences of the United States of America. 107: 16420-7. PMID 20807744 DOI: 10.1073/Pnas.1010732107  0.441
2010 Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, Zinser ER, Chisholm SW. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The Isme Journal. 4: 1252-64. PMID 20463762 DOI: 10.1038/Ismej.2010.60  0.314
2009 Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. Plos One. 4: e6864. PMID 19724646 DOI: 10.1371/Journal.Pone.0006864  0.34
2009 Kirchman DL, Hill V, Cottrell MT, Gradinger R, Malmstrom RR, Parker A. Standing stocks, production, and respiration of phytoplankton and heterotrophic bacteria in the western Arctic Ocean Deep-Sea Research Part Ii: Topical Studies in Oceanography. 56: 1237-1248. DOI: 10.1016/J.Dsr2.2008.10.018  0.604
2007 Kirchman DL, Elifantz H, Dittel AI, Malmstrom RR, Cottrell MT. Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean Limnology and Oceanography. 52: 495-507. DOI: 10.4319/Lo.2007.52.2.0495  0.744
2007 Malmstrom RR, Straza TRA, Cottrell MT, Kirchman DL. Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean Aquatic Microbial Ecology. 47: 45-55. DOI: 10.3354/Ame047045  0.639
2006 Cottrell MT, Malmstrom RR, Hill V, Parker AE, Kirchman DL. The metabolic balance between autotrophy and heterotrophy in the western Arctic Ocean Deep-Sea Research Part I: Oceanographic Research Papers. 53: 1831-1844. DOI: 10.1016/j.dsr.2006.08.010  0.533
2005 Elifantz H, Malmstrom RR, Cottrell MT, Kirchman DL. Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary. Applied and Environmental Microbiology. 71: 7799-805. PMID 16332754 DOI: 10.1128/Aem.71.12.7799-7805.2005  0.716
2005 Malmstrom RR, Cottrell MT, Elifantz H, Kirchman DL. Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Applied and Environmental Microbiology. 71: 2979-86. PMID 15932993 DOI: 10.1128/Aem.71.6.2979-2986.2005  0.739
2005 Malmstrom RR, Kiene RP, Vila M, Kirchman DL. Dimethylsulfoniopropionate (DMSP) assimilation by Synechococcus in the Gulf of Mexico and northwest Atlantic Ocean Limnology and Oceanography. 50: 1924-1931. DOI: 10.4319/Lo.2005.50.6.1924  0.631
2005 Kirchman DL, Dittel AI, Malmstrom RR, Cottrell MT. Biogeography of major bacterial groups in the Delaware Estuary Limnology and Oceanography. 50: 1697-1706. DOI: 10.4319/Lo.2005.50.5.1697  0.648
2005 Kirchman DL, Malmstrom RR, Cottrell MT. Control of bacterial growth by temperature and organic matter in the Western Arctic Deep-Sea Research Part Ii: Topical Studies in Oceanography. 52: 3386-3395. DOI: 10.1016/J.Dsr2.2005.09.005  0.579
2004 Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean. Applied and Environmental Microbiology. 70: 4129-35. PMID 15240292 DOI: 10.1128/Aem.70.7.4129-4135.2004  0.661
2004 Malmstrom RR, Kiene RP, Kirchman DL. Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico Limnology and Oceanography. 49: 597-606. DOI: 10.4319/Lo.2004.49.2.0597  0.664
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