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Genome-wide identification of bacterial plant colonization genes
Author / Creator:Cole, Benjamin J. ; Feltcher, Meghan E. ; Waters, Robert J. ; Wetmore, Kelly M. ; Mucyn, Tatiana S. ; Ryan, Elizabeth M. ; Wang, Gaoyan ; Ul-Hasan, Sabah ; McDonald, Meredith ; Yoshikuni, Yasuo ; Malmstrom, Rex R. ; Deutschbauer, Adam M. ; Dangl, Jeffery L. ; Visel, Axel
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2017-09, Vol.15 (9), p.e2002860
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Hidden diversity of soil giant viruses
Author / Creator:Schulz, Frederik ; Alteio, Lauren ; Goudeau, Danielle ; Ryan, Elizabeth M. ; Yu, Feiqiao B. ; Malmstrom, Rex R. ; Blanchard, Jeffrey ; Woyke, Tanja
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-11, Vol.9 (1), p.4881-9, Article 4881
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Probing the active fraction of soil microbiomes using BONCAT-FACS
Author / Creator:Couradeau, Estelle ; Sasse, Joelle ; Goudeau, Danielle ; Nath, Nandita ; Hazen, Terry C. ; Bowen, Ben P. ; Chakraborty, Romy ; Malmstrom, Rex R. ; Northen, Trent R.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-06, Vol.10 (1), p.2770-10, Article 2770
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Visualizing in situ translational activity for identifying and sorting slow-growing archaeal–bacterial consortia
Author / Creator:Hatzenpichler, Roland ; Connon, Stephanie A. ; Goudeau, Danielle ; Malmstrom, Rex R. ; Woyke, Tanja ; Orphan, Victoria J.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2016-07, Vol.113 (28), p.E4069-E4078
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Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
Author / Creator:Roux, Simon ; Chan, Leong-Keat ; Egan, Rob ; Malmstrom, Rex R. ; McMahon, Katherine D. ; Sullivan, Matthew B.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2017-10, Vol.8 (1), p.858-12, Article 858
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Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites
Author / Creator:Villalobos-Escobedo, José Manuel ; Mercado-Esquivias, Maria Belen ; Adams, Catharine ; Kauffman, W. Berkeley ; Malmstrom, Rex R. ; Deutschbauer, Adam M. ; Glass, N. Louise
Publisher:San Francisco: Public Library of Science
Journal title:PLoS genetics, 2023-08, Vol.19 (8), p.e1010909-e1010909
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The Epigenomic Landscape of Prokaryotes
Author / Creator:Blow, Matthew J. ; Clark, Tyson A. ; Daum, Chris G. ; Deutschbauer, Adam M. ; Fomenkov, Alexey ; Fries, Roxanne ; Froula, Jeff ; Kang, Dongwan D. ; Malmstrom, Rex R. ; Morgan, Richard D. ; Posfai, Janos ; Singh, Kanwar ; Visel, Axel ; Wetmore, Kelly ; Zhao, Zhiying ; Rubin, Edward M. ; Korlach, Jonas ; Pennacchio, Len A. ; Roberts, Richard J.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2016-02, Vol.12 (2), p.e1005854-e1005854
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Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells
Author / Creator:Schaible, George A. ; Jay, Zackary J. ; Cliff, John ; Schulz, Frederik ; Gauvin, Colin ; Goudeau, Danielle ; Malmstrom, Rex R. ; Ruff, S. Emil ; Edgcomb, Virginia ; Hatzenpichler, Roland
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2024-07, Vol.22 (7), p.e3002638
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
Author / Creator:Bendall, Matthew L ; Stevens, Sarah LR ; Chan, Leong-Keat ; Malfatti, Stephanie ; Schwientek, Patrick ; Tremblay, Julien ; Schackwitz, Wendy ; Martin, Joel ; Pati, Amrita ; Bushnell, Brian ; Froula, Jeff ; Kang, Dongwan ; Tringe, Susannah G ; Bertilsson, Stefan ; Moran, Mary A ; Shade, Ashley ; Newton, Ryan J ; McMahon, Katherine D ; Malmstrom, Rex R
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2016-07, Vol.10 (7), p.1589-1601
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Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
Author / Creator:McCarren, Jay ; Becker, Jamie W. ; Repeta, Daniel J. ; Shi, Yanmei ; Young, Curtis R. ; Malmstrom, Rex R. ; Chisholm, Sallie W. ; DeLong, Edward F.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2010-09, Vol.107 (38), p.16420-16427
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SAR11 bacteria linked to ocean anoxia and nitrogen loss
Author / Creator:Tsementzi, Despina ; Wu, Jieying ; Deutsch, Samuel ; Nath, Sangeeta ; Rodriguez-R, Luis M. ; Burns, Andrew S. ; Ranjan, Piyush ; Sarode, Neha ; Malmstrom, Rex R. ; Padilla, Cory C. ; Stone, Benjamin K. ; Bristow, Laura A. ; Larsen, Morten ; Glass, Jennifer B. ; Thamdrup, Bo ; Woyke, Tanja ; Konstantinidis, Konstantinos T. ; Stewart, Frank J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2016-08, Vol.536 (7615), p.179-183
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Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
Author / Creator:Rodrigue, Sébastien ; Malmstrom, Rex R. ; Berlin, Aaron M. ; Birren, Bruce W. ; Henn, Matthew R. ; Chisholm, Sallie W.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2009-09, Vol.4 (9), p.e6864
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Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
Author / Creator:Probst, Alexander J. ; Ladd, Bethany ; Jarett, Jessica K. ; Geller-McGrath, David E. ; Sieber, Christian M. K. ; Emerson, Joanne B. ; Anantharaman, Karthik ; Thomas, Brian C. ; Malmstrom, Rex R. ; Stieglmeier, Michaela ; Klingl, Andreas ; Woyke, Tanja ; Ryan, M. Cathryn ; Banfield, Jillian F.
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2018-03, Vol.3 (3), p.328-336
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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi
Author / Creator:Nuccio, Erin E. ; Blazewicz, Steven J. ; Lafler, Marissa ; Campbell, Ashley N. ; Kakouridis, Anne ; Kimbrel, Jeffrey A. ; Wollard, Jessica ; Vyshenska, Dariia ; Riley, Robert ; Tomatsu, Andy ; Hestrin, Rachel ; Malmstrom, Rex R. ; Firestone, Mary ; Pett-Ridge, Jennifer
Publisher:England: BioMed Central
Journal title:Microbiome, 2022-11, Vol.10 (1), p.199-20, Article 199
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Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea
Author / Creator:Murali, Ranjani ; Yu, Hang ; Speth, Daan R. ; Wu, Fabai ; Metcalfe, Kyle S. ; Crémière, Antoine ; Laso-Pèrez, Rafael ; Malmstrom, Rex R. ; Goudeau, Danielle ; Woyke, Tanja ; Hatzenpichler, Roland ; Chadwick, Grayson L. ; Connon, Stephanie A. ; Orphan, Victoria J.
Publisher:San Francisco: Public Library of Science
Journal title:PLoS biology, 2023-09, Vol.21 (9), p.e3002292-e3002292
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Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage
Author / Creator:Boeuf, Dominique ; Eppley, John M. ; Mende, Daniel R. ; Malmstrom, Rex R. ; Woyke, Tanja ; DeLong, Edward F.
Publisher:London: BioMed Central
Journal title:Microbiome, 2021-08, Vol.9 (1), p.1-172, Article 172
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Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution
Author / Creator:Bowers, Robert M. ; Nayfach, Stephen ; Schulz, Frederik ; Jungbluth, Sean P. ; Ruhl, Ilona A. ; Sheremet, Andriy ; Lee, Janey ; Goudeau, Danielle ; Eloe-Fadrosh, Emiley A. ; Stepanauskas, Ramunas ; Malmstrom, Rex R. ; Kyrpides, Nikos C. ; Dunfield, Peter F. ; Woyke, Tanja
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2022-05, Vol.16 (5), p.1337-1347
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Unlocking Short Read Sequencing for Metagenomics
Author / Creator:Rodrigue, Sébastien ; Materna, Arne C. ; Timberlake, Sonia C. ; Blackburn, Matthew C. ; Malmstrom, Rex R. ; Alm, Eric J. ; Chisholm, Sallie W.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2010-07, Vol.5 (7), p.e11840-e11840
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Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans
Author / Creator:Malmstrom, Rex R ; Coe, Allison ; Kettler, Gregory C ; Martiny, Adam C ; Frias-Lopez, Jorge ; Zinser, Erik R ; Chisholm, Sallie W
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2010-10, Vol.4 (10), p.1252-1264
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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
Author / Creator:Garcia, Sarahi L. ; Stevens, Sarah L. R. ; Crary, Benjamin ; Martinez-Garcia, Manuel ; Stepanauskas, Ramunas ; Woyke, Tanja ; Tringe, Susannah G. ; Andersson, Siv G. E. ; Bertilsson, Stefan ; Malmstrom, Rex R. ; McMahon, Katherine D.
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2018-03, Vol.12 (3), p.742-755
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Genome-wide identification of bacterial plant colonization genes

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Hidden diversity of soil giant viruses

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Probing the active fraction of soil microbiomes using BONCAT-FACS

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Visualizing in situ translational activity for identifying and sorting slow-growing archaeal–bacterial consortia

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Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

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Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites

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The Epigenomic Landscape of Prokaryotes

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Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

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Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

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SAR11 bacteria linked to ocean anoxia and nitrogen loss

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Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

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Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

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Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea

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Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

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Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

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Unlocking Short Read Sequencing for Metagenomics

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Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

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