Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis von Scholz, Matthew B, Lo, Chien-Chi, Chain, Patrick SG

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A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer von Ishii, Shun’ichi, Suzuki, Shino, Norden-Krichmar, Trina M., Tenney, Aaron, Chain, Patrick S. G., Scholz, Matthew B., Nealson, Kenneth H., Bretschger, Orianna

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High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins von Loh, John T, Beckett, Amber C, Scholz, Matthew B, Cover, Timothy L

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Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage von Dodsworth, Jeremy A., Blainey, Paul C., Murugapiran, Senthil K., Swingley, Wesley D., Ross, Christian A., Tringe, Susannah G., Chain, Patrick S. G., Scholz, Matthew B., Lo, Chien-Chi, Raymond, Jason, Quake, Stephen R., Hedlund, Brian P.

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Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk von O'Connor, Roberta M, Fung, Jennifer M, Sharp, Koty H, Benner, Jack S, McClung, Colleen, Cushing, Shelley, Lamkin, Elizabeth R, Fomenkov, Alexey I, Henrissat, Bernard, Londer, Yuri Y, Scholz, Matthew B, Posfai, Janos, Malfatti, Stephanie, Tringe, Susannah G, Woyke, Tanja, Malmstrom, Rex R, Coleman-Derr, Devin, Altamia, Marvin A, Dedrick, Sandra, Kaluziak, Stefan T, Haygood, Margo G, Distel, Daniel L

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Modification of the Gastric Mucosal Microbiota by a Strain-Specific Helicobacter pylori Oncoprotein and Carcinogenic Histologic Phenotype von Noto, Jennifer M, Zackular, Joseph P, Varga, Matthew G, Delgado, Alberto, Romero-Gallo, Judith, Scholz, Matthew B, Piazuelo, M Blanca, Skaar, Eric P, Peek, Jr, Richard M

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Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern von Godbold, Gene D, Hewitt, F Curtis, Kappell, Anthony D, Scholz, Matthew B, Agar, Stacy L, Treangen, Todd J, Ternus, Krista L, Sandbrink, Jonas B, Koblentz, Gregory D

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Accurate read-based metagenome characterization using a hierarchical suite of unique signatures von Freitas, Tracey Allen K, Li, Po-E, Scholz, Matthew B, Chain, Patrick S G

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SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis von Johnson, Benjamin K, Scholz, Matthew B, Teal, Tracy K, Abramovitch, Robert B

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Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System von Loh, John T., Shum, Miranda, Jossart, Scott D. R., Campbell, Anne M., Sawhney, Neha, McDonald, W. Hayes, Scholz, Matthew B., McClain, Mark S., Forsyth, Mark H., Cover, Timothy L.

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Enhanced Fitness of a Helicobacter pylori babA Mutant in a Murine Model von Harvey, M Lorena, Lin, Aung Soe, Sun, Lili, Koyama, Tatsuki, Shuman, Jennifer H B, Loh, John T, Algood, Holly M Scott, Scholz, Matthew B, McClain, Mark S, Cover, Timothy L

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Endogenous double-stranded Alu RNA elements stimulate IFN-responses in relapsing remitting multiple sclerosis von Heinrich, Maxwell J., Purcell, Caroline A., Pruijssers, Andrea J., Zhao, Yang, Spurlock, Charles F., Sriram, Subramaniam, Ogden, Kristen M., Dermody, Terence S., Scholz, Matthew B., Crooke, Philip S., Karijolich, John, Aune, Thomas M.

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Effect of environmental salt concentration on the Helicobacter pylori exoproteome von Caston, Rhonda R., Loh, John T., Voss, Bradley J., McDonald, W. Hayes, Scholz, Matthew B., McClain, Mark S., Cover, Timothy L.

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Draft Genome Sequence of Bacillus licheniformis Strain YNP1-TSU Isolated from Whiterock Springs in Yellowstone National Park von O'Hair, Joshua A, Li, Hui, Thapa, Santosh, Scholz, Matthew B, Zhou, Suping

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Draft Genome Assembly of Acinetobacter baumannii ATCC 19606 von Davenport, Karen W, Daligault, Hajnalka E, Minogue, Timothy D, Bruce, David C, Chain, Patrick S G, Coyne, Susan R, Jaissle, James G, Koroleva, Galina I, Ladner, Jason T, Li, Po-E, Palacios, Gustavo F, Scholz, Matthew B, Teshima, Hazuki, Johnson, Shannon L

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Genomics for key players in the N cycle from guinea pigs to the next frontier von Chain, Patrick S G, Xie, Gary, Starkenburg, Shawn R, Scholz, Matthew B, Beckloff, Nicholas, Lo, Chien-Chi, Davenport, Karen W, Reitenga, Krista G, Daligault, Hajnalka E, Detter, J Chris, Freitas, Tracey A K, Gleasner, Cheryl D, Green, Lance D, Han, Cliff S, McMurry, Kim K, Meincke, Linda J, Shen, Xiaohong, Zeytun, Ahmet

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High dietary salt–induced DC activation underlies microbial dysbiosis-associated hypertension von Ferguson, Jane F., Aden, Luul A., Barbaro, Natalia R., Van Beusecum, Justin P., Xiao, Liang, Simons, Alan J., Warden, Cassandra, Pasic, Lejla, Himmel, Lauren E., Washington, Mary K., Revetta, Frank L., Zhao, Shilin, Kumaresan, Shivani, Scholz, Matthew B., Tang, Zhengzheng, Chen, Guanhua, Reilly, Muredach P., Kirabo, Annet

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Enhanced Fitness of a Helicobacter pylori babA Mutant n a Murine Model von Harvey, M. Lorena, Lin, Aung Soe, Sun, Lili, Koyama, Tatsuki, Shuman, Jennifer H. B., Loh, John T., Algood, Holly M. Scott, Scholz, Matthew B., McClain, Mark S., Cover, Timothy L.

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Genomics for Key Players in the N Cycle von Chain, Patrick S.G., Xie, Gary, Starkenburg, Shawn R., Scholz, Matthew B., Beckloff, Nicholas, Lo, Chien-Chi, Davenport, Karen W., Reitenga, Krista G., Daligault, Hajnalka E., Detter, J. Chris, Freitas, Tracey A.K., Gleasner, Cheryl D., Green, Lance D., Han, Cliff S., McMurry, Kim K., Meincke, Linda J., Shen, Xiaohong, Zeytun, Ahmet

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Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk von O'Connor, Roberta M., Fung, Jennifer M., Sharp, Koty H., Benner, Jack S., McClung, Colleen, Cushing, Shelley, Lamkin, Elizabeth R., Fomenkov, Alexey I., Henrissat, Bernard, Londer, Yuri Y., Scholz, Matthew B., Posfai, Janos, Malfatti, Stephanie, Tringe, Susannah G., Woyke, Tanja, Malmstrom, Rex R., Coleman-Derr, Devin, Altamia, Marvin A., Dedrick, Sandra, Kaluziak, Stefan T., Haygood, Margo G., Distel, Daniel L.

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