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Malmstrom, Rex

TitleBiologist Research Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentJoint Genome Institute
Address1 Cyclotron Road
Berkeley CA 94720
Phone925/927-2821
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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 R, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 Feb 06; 36(2):196. PMID: 29406516.
      View in: PubMed
    2. Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom R, 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. Nat Microbiol. 2018 Mar; 3(3):328-336. PMID: 29379208.
      View in: PubMed
    3. Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom R, McMahon KD. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. ISME J. 2018 Mar; 12(3):742-755. PMID: 29222442.
      View in: PubMed
    4. Roux S, Chan LK, Egan R, Malmstrom R, McMahon KD, Sullivan MB. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat Commun. 2017 10 11; 8(1):858. PMID: 29021524.
      View in: PubMed
    5. He S, Stevens SLR, Chan LK, Bertilsson S, Glavina Del Rio T, Tringe SG, Malmstrom R, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere. 2017 Sep-Oct; 2(5). PMID: 28959738.
      View in: PubMed
    6. Cole BJ, Feltcher ME, Waters RJ, Wetmore KM, Mucyn TS, Ryan EM, Wang G, Ul-Hasan S, McDonald M, Yoshikuni Y, Malmstrom R, Deutschbauer AM, Dangl JL, Visel A. Genome-wide identification of bacterial plant colonization genes. PLoS Biol. 2017 Sep; 15(9):e2002860. PMID: 28938018.
      View in: PubMed
    7. Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, Malmstrom R, Forest KT, McMahon KD. Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems. 2017 Jul-Aug; 2(4). PMID: 28861526.
      View in: PubMed
    8. 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 R, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 08; 35(8):725-731. PMID: 28787424.
      View in: PubMed
    9. Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom R, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 2016 08 11; 536(7615):179-83. PMID: 27487207; PMCID: PMC4990128 [Available on 02/11/17].
    10. Hatzenpichler R, Connon SA, Goudeau D, Malmstrom R, Woyke T, Orphan VJ. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A. 2016 07 12; 113(28):E4069-78. PMID: 27357680; PMCID: PMC4948357.
    11. Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom R, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol. 2016 Nov; 18(11):3949-3961. PMID: 27235779.
      View in: PubMed
    12. Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom R, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ. The Epigenomic Landscape of Prokaryotes. PLoS Genet. 2016 Feb; 12(2):e1005854. PMID: 26870957; PMCID: PMC4752239.
    13. 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, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 2016 Jan 27; 7:10476. PMID: 26814032; PMCID: PMC4737851.
    14. 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, Shade A, Newton RJ, McMahon KD, Malmstrom R. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 2016 07; 10(7):1589-601. PMID: 26744812; PMCID: PMC4918448.
    15. 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 R, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A. 2014 Nov 25; 111(47):E5096-104. PMID: 25385629; PMCID: PMC4250168.
    16. 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, Bertilsson S, McMahon KD. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J. 2014 Dec; 8(12):2503-16. PMID: 25093637; PMCID: PMC4260696.
    17. Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom R, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014 Apr 25; 344(6182):416-20. PMID: 24763590.
      View in: PubMed
    18. 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. Nat Protoc. 2014 May; 9(5):1038-48. PMID: 24722403.
      View in: PubMed
    19. Bendall ML, Luong K, Wetmore KM, Blow M, Korlach J, Deutschbauer A, Malmstrom R. Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol. 2013 Nov; 195(21):4966-74. PMID: 23995632; PMCID: PMC3807482.
    20. Malmstrom R, 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. ISME J. 2013 Jan; 7(1):184-98. PMID: 22895163; PMCID: PMC3526172.
    21. 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. 2011; 6(10):e26161. PMID: 22028825; PMCID: PMC3197606.
    22. McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom R, Chisholm SW, DeLong EF. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A. 2010 Sep 21; 107(38):16420-7. PMID: 20807744; PMCID: PMC2944720.
    23. Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom R, Alm EJ, Chisholm SW. Unlocking short read sequencing for metagenomics. PLoS One. 2010 Jul 28; 5(7):e11840. PMID: 20676378; PMCID: PMC2911387.
    24. Malmstrom R, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, Zinser ER, Chisholm SW. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME J. 2010 Oct; 4(10):1252-64. PMID: 20463762.
      View in: PubMed
    25. Rodrigue S, Malmstrom R, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PLoS One. 2009 Sep 02; 4(9):e6864. PMID: 19724646; PMCID: PMC2731171.
    26. Elifantz H, Malmstrom R, Cottrell MT, Kirchman DL. Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary. Appl Environ Microbiol. 2005 Dec; 71(12):7799-805. PMID: 16332754; PMCID: PMC1317420.
    27. Malmstrom R, Cottrell MT, Elifantz H, Kirchman DL. Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Appl Environ Microbiol. 2005 Jun; 71(6):2979-86. PMID: 15932993; PMCID: PMC1151852.
    28. Malmstrom R, Kiene RP, Cottrell MT, Kirchman DL. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean. Appl Environ Microbiol. 2004 Jul; 70(7):4129-35. PMID: 15240292; PMCID: PMC444831.
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