Search Results - "Clum, Alicia"

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data by Chin, Chen-Shan, Alexander, David H, Marks, Patrick, Klammer, Aaron A, Drake, James, Heiner, Cheryl, Clum, Alicia, Copeland, Alex, Huddleston, John, Eichler, Evan E, Turner, Stephen W, Korlach, Jonas

“…Unlike hybrid approaches that use multiple libraries for de novo assembly, the hierarchical genome-assembly process uses data from only a single long-read SMRT…”
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Genetic determinants of endophytism in the Arabidopsis root mycobiome by Mesny, Fantin, Miyauchi, Shingo, Thiergart, Thorsten, Pickel, Brigitte, Atanasova, Lea, Karlsson, Magnus, Hüttel, Bruno, Barry, Kerrie W., Haridas, Sajeet, Chen, Cindy, Bauer, Diane, Andreopoulos, William, Pangilinan, Jasmyn, LaButti, Kurt, Riley, Robert, Lipzen, Anna, Clum, Alicia, Drula, Elodie, Henrissat, Bernard, Kohler, Annegret, Grigoriev, Igor V., Martin, Francis M., Hacquard, Stéphane

“…The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal…”
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Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota by Chang, Ying, Desirò, Alessandro, Na, Hyunsoo, Sandor, Laura, Lipzen, Anna, Clum, Alicia, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis M., Stajich, Jason E., Smith, Matthew E., Bonito, Gregory, Spatafora, Joseph W.

“…• Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form…”
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Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum by Peter, Martina, Kohler, Annegret, Ohm, Robin A., Kuo, Alan, Krützmann, Jennifer, Morin, Emmanuelle, Arend, Matthias, Barry, Kerrie W., Binder, Manfred, Choi, Cindy, Clum, Alicia, Copeland, Alex, Grisel, Nadine, Haridas, Sajeet, Kipfer, Tabea, LaButti, Kurt, Lindquist, Erika, Lipzen, Anna, Maire, Renaud, Meier, Barbara, Mihaltcheva, Sirma, Molinier, Virginie, Murat, Claude, Pöggeler, Stefanie, Quandt, C. Alisha, Sperisen, Christoph, Tritt, Andrew, Tisserant, Emilie, Crous, Pedro W., Henrissat, Bernard, Nehls, Uwe, Egli, Simon, Spatafora, Joseph W., Grigoriev, Igor V., Martin, Francis M.

“…The most frequently encountered symbiont on tree roots is the ascomycete Cenococcum geophilum, the only mycorrhizal species within the largest fungal class…”
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Terabase-scale metagenome coassembly with MetaHipMer by Hofmeyr, Steven, Egan, Rob, Georganas, Evangelos, Copeland, Alex C., Riley, Robert, Clum, Alicia, Eloe-Fadrosh, Emiley, Roux, Simon, Goltsman, Eugene, Buluç, Aydın, Rokhsar, Daniel, Oliker, Leonid, Yelick, Katherine

“…Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have…”
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Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk‐cap (Lactarius) mushrooms by Lebreton, Annie, Tang, Nianwu, Kuo, Alan, LaButti, Kurt, Andreopoulos, William, Drula, Elodie, Miyauchi, Shingo, Barry, Kerrie, Clum, Alicia, Lipzen, Anna, Mousain, Daniel, Ng, Vivian, Wang, Ran, Dai, Yucheng, Henrissat, Bernard, Grigoriev, Igor V., Guerin‐Laguette, Alexis, Yu, Fuqiang, Martin, Francis M.

“…Summary Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved…”
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The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole by Martin, Kara, Schmidt, Katrin, Toseland, Andrew, Boulton, Chris A., Barry, Kerrie, Beszteri, Bánk, Brussaard, Corina P. D., Clum, Alicia, Daum, Chris G., Eloe-Fadrosh, Emiley, Fong, Allison, Foster, Brian, Foster, Bryce, Ginzburg, Michael, Huntemann, Marcel, Ivanova, Natalia N., Kyrpides, Nikos C., Lindquist, Erika, Mukherjee, Supratim, Palaniappan, Krishnaveni, Reddy, T. B. K., Rizkallah, Mariam R., Roux, Simon, Timmermans, Klaas, Tringe, Susannah G., van de Poll, Willem H., Varghese, Neha, Valentin, Klaus U., Lenton, Timothy M., Grigoriev, Igor V., Leggett, Richard M., Moulton, Vincent, Mock, Thomas

“…Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with…”
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One bacterial cell, one complete genome by Woyke, Tanja, Tighe, Damon, Mavromatis, Konstantinos, Clum, Alicia, Copeland, Alex, Schackwitz, Wendy, Lapidus, Alla, Wu, Dongying, McCutcheon, John P, McDonald, Bradon R, Moran, Nancy A, Bristow, James, Cheng, Jan-Fang

“…While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of…”
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The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation by Mavromatis, Konstantinos, Land, Miriam L, Brettin, Thomas S, Quest, Daniel J, Copeland, Alex, Clum, Alicia, Goodwin, Lynne, Woyke, Tanja, Lapidus, Alla, Klenk, Hans Peter, Cottingham, Robert W, Kyrpides, Nikos C

“…The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while…”
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Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato by Beukes, Chrizelle W, Palmer, Marike, Manyaka, Puseletso, Chan, Wai Y, Avontuur, Juanita R, van Zyl, Elritha, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T B K, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, Blom, Jochen, Whitman, William B, Venter, Stephanus N, Steenkamp, Emma T

“…Although the taxonomy of has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and…”
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Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion by Martínez-Hidalgo, Pilar, Humm, Ethan A., Still, David W., Shi, Baochen, Pellegrini, Matteo, de la Roca, Gabriela, Veliz, Esteban, Maymon, Maskit, Bru, Pierrick, Huntemann, Marcel, Clum, Alicia, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Ivanova, Natalia N., Kyrpides, Nikos C., Shapiro, Nicole, Eloe-Fadrosh, Emiley A., Hirsch, Ann M.

“…Purpose Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes…”
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Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics by Van Goethem, Marc W., Osborn, Andrew R., Bowen, Benjamin P., Andeer, Peter F., Swenson, Tami L., Clum, Alicia, Riley, Robert, He, Guifen, Koriabine, Maxim, Sandor, Laura, Yan, Mi, Daum, Chris G., Yoshinaga, Yuko, Makhalanyane, Thulani P., Garcia-Pichel, Ferran, Visel, Axel, Pennacchio, Len A., O’Malley, Ronan C., Northen, Trent R.

“…Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes,…”
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A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production by McKinlay, James B, Laivenieks, Maris, Schindler, Bryan D, McKinlay, Anastasia A, Siddaramappa, Shivakumara, Challacombe, Jean F, Lowry, Stephen R, Clum, Alicia, Lapidus, Alla L, Burkhart, Kirk B, Harkins, Victoria, Vieille, Claire

“…Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a…”
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Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies by Sevim, Volkan, Lee, Juna, Egan, Robert, Clum, Alicia, Hundley, Hope, Lee, Janey, Everroad, R. Craig, Detweiler, Angela M., Bebout, Brad M., Pett-Ridge, Jennifer, Göker, Markus, Murray, Alison E., Lindemann, Stephen R., Klenk, Hans-Peter, O’Malley, Ronan, Zane, Matthew, Cheng, Jan-Fang, Copeland, Alex, Daum, Christopher, Singer, Esther, Woyke, Tanja

“…Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including…”
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DOE JGI Metagenome Workflow by Clum, Alicia, Huntemann, Marcel, Bushnell, Brian, Foster, Brian, Foster, Bryce, Roux, Simon, Hajek, Patrick P, Varghese, Neha, Mukherjee, Supratim, Reddy, T B K, Daum, Chris, Yoshinaga, Yuko, O'Malley, Ronan, Seshadri, Rekha, Kyrpides, Nikos C, Eloe-Fadrosh, Emiley A, Chen, I-Min A, Copeland, Alex, Ivanova, Natalia N

“…The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic…”
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Comparative genomics of xylose-fermenting fungi for enhanced biofuel production by Wohlbach, Dana J, Kuo, Alan, Sato, Trey K, Potts, Katlyn M, Salamov, Asaf A, LaButti, Kurt M, Sun, Hui, Clum, Alicia, Pangilinan, Jasmyn L, Lindquist, Erika A, Lucas, Susan, Lapidus, Alla, Jin, Mingjie, Gunawan, Christa, Balan, Venkatesh, Dale, Bruce E, Jeffries, Thomas W, Zinkel, Robert, Barry, Kerrie W, Grigoriev, Igor V, Gasch, Audrey P

“…Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant…”
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Assessment of Autonomic Nervous System Activity Using Spectral Analysis of Heart Rate Variability After Continuous Positive Airway Pressure (CPAP) Therapy in Patients With Sleep Apnea by Vasilkova, Taisa, Fiore, Valerie F, Clum, Alicia, Wong, Angel, Kabir, Nawshin, Costello, Elizabeth, Crasta, Maxim

“…Heart rate variability (HRV) measurements have emerged as a valuable tool for understanding the functioning of the autonomic nervous system (ANS) and assessing…”
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BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly by Lam, Ka-Kit, Hall, Richard, Clum, Alicia, Rao, Satish

“…The problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the…”
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Next generation sequencing data of a defined microbial mock community by Singer, Esther, Andreopoulos, Bill, Bowers, Robert M., Lee, Janey, Deshpande, Shweta, Chiniquy, Jennifer, Ciobanu, Doina, Klenk, Hans-Peter, Zane, Matthew, Daum, Christopher, Clum, Alicia, Cheng, Jan-Fang, Copeland, Alex, Woyke, Tanja

“…Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome…”
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Leveraging single-cell genomics to expand the fungal tree of life by Ahrendt, Steven R., Quandt, C. Alisha, Ciobanu, Doina, Clum, Alicia, Salamov, Asaf, Andreopoulos, Bill, Cheng, Jan-Fang, Woyke, Tanja, Pelin, Adrian, Henrissat, Bernard, Reynolds, Nicole K., Benny, Gerald L., Smith, Matthew E., James, Timothy Y., Grigoriev, Igor V.

“…Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the…”
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