A Bioinformatician's Guide to Metagenomics

le Kunin, Victor, Copeland, Alex, Lapidus, Alla, Mavromatis, Konstantinos, Hugenholtz, Philip
Foilsithe 2008

Complete Genome Sequence of Lactobacillus buchneri NRRL B-30929, a Novel Strain from a Commercial Ethanol Plant

le Liu, Siqing, Leathers, Timothy D., Copeland, Alex, Chertkov, Olga, Goodwin, Lynne, Mills, David A.
Foilsithe 2011

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

le Olm, Matthew R., Butterfield, Cristina N., Copeland, Alex, Boles, T. Christian, Thomas, Brian C., Banfield, Jillian F.
Foilsithe in mBio (2017)

Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach

le Peng, Ze, Zhao, Zhiying, Nath, Nandita, Froula, Jeff L., Clum, Alicia, Zhang, Tao, Cheng, Jan-fang, Copeland, Alex C., Pennacchio, Len A., Chen, Feng
Foilsithe 2012

Complete genome sequence of Anabaena variabilis ATCC 29413

le Thiel, Teresa, Pratte, Brenda S., Zhong, Jinshun, Goodwin, Lynne, Copeland, Alex, Lucas, Susan, Han, Cliff, Pitluck, Sam, Land, Miriam L., Kyrpides, Nikos C, Woyke, Tanja
Foilsithe 2014

Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX

le Lykidis, Athanasios, Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Land, Miriam, DiBartolo, Genevieve, Martinez, Michele, Lapidus, Alla, Lucas, Susan, Copeland, Alex, Richardson, Paul, Wilson, David B., Kyrpides, Nikos
Foilsithe 2007

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

le Lykidis, Athanasios, Chen, Chia-Lung, Tringe, Susannah G, McHardy, Alice C, Copeland, Alex, Kyrpides, Nikos C, Hugenholtz, Philip, Macarie, Hervé, Olmos, Alejandro, Monroy, Oscar, Liu, Wen-Tso
Foilsithe 2011

Terabase-scale metagenome coassembly with MetaHipMer

le 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
Foilsithe in Sci Rep (2020)

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

le 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.
Foilsithe 2012

High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods

le Aizenberg-Gershtein, Yana, Izhaki, Ido, Lapidus, Alla, Copeland, Alex, Reddy, TBK, Huntemann, Marcel, Pillay, Manoj, Markowitz, Victor, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., Halpern, Malka
Foilsithe in Stand Genomic Sci (2016)

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

le Anderson, Iain J., Sun, Hui, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Tice, Hope, Dalin, Eileen, Lucas, Susan, Barry, Kerrie, Land, Miriam, Richardson, Paul, Huber, Harald, Kyrpides, Nikos C.
Foilsithe 2009

High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass

le Laviad, Sivan, Lapidus, Alla, Copeland, Alex, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Markowitz, Victor M, Pukall, Rüdiger, Klenk, Hans-Peter, Woyke, Tanja, Kyrpides, Nikos C, Halpern, Malka
Foilsithe in Stand Genomic Sci (2015)

High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotale...

le Ntougias, Spyridon, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Klenk, Hans-Peter, Woyke, Tanja, Fasseas, Constantinos, Kyrpides, Nikos C., Zervakis, Georgios I.
Foilsithe in Stand Genomic Sci (2015)

Next generation sequencing data of a defined microbial mock community

le 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
Foilsithe in Sci Data (2016)

One Bacterial Cell, One Complete Genome

le 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
Foilsithe 2010

Assembling the Marine Metagenome, One Cell at a Time

le Woyke, Tanja, Xie, Gary, Copeland, Alex, González, José M., Han, Cliff, Kiss, Hajnalka, Saw, Jimmy H., Senin, Pavel, Yang, Chi, Chatterji, Sourav, Cheng, Jan-Fang, Eisen, Jonathan A., Sieracki, Michael E., Stepanauskas, Ramunas
Foilsithe 2009

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

le Gregory, Ann C., Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, LaButti, Kurt, Copeland, Alex, Sudek, Sebastian, Maitland, Ashley, Chittick, Lauren, dos Santos, Filipa, Weitz, Joshua S., Worden, Alexandra Z., Woyke, Tanja, Sullivan, Matthew B.
Foilsithe in BMC Genomics (2016)

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

le Mackelprang, Rachel, Grube, Alyssa M., Lamendella, Regina, Jesus, Ederson da C., Copeland, Alex, Liang, Chao, Jackson, Randall D., Rice, Charles W., Kapucija, Stefanie, Parsa, Bayan, Tringe, Susannah G., Tiedje, James M., Jansson, Janet K.
Foilsithe in Front Microbiol (2018)

High-resolution phylogenetic microbial community profiling

le Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M, Levy, Asaf, Gies, Esther A, Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J, Hugenholtz, Philip, Tringe, Susannah G, Woyke, Tanja
Foilsithe in ISME J (2016)

Complete genome sequence of Methanocorpusculum labreanum type strain Z

le Anderson, Iain J., Sieprawska-Lupa, Magdalena, Goltsman, Eugene, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Tice, Hope, Dalin, Eileen, Barry, Kerrie, Pitluck, Sam, Hauser, Loren, Land, Miriam, Lucas, Susan, Richardson, Paul, Whitman, William B., Kyrpides, Nikos C.
Foilsithe 2009