BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Por Lam, Ka-Kit, Hall, Richard, Clum, Alicia, Rao, Satish
Publicado no BMC Bioinformatics (2016)

Reconstructing each cell's genome within complex microbial communities—dream or reality?

Por Clingenpeel, Scott, Clum, Alicia, Schwientek, Patrick, Rinke, Christian, Woyke, Tanja
Publicado no Front Microbiol (2015)

Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7

Por Muyzer, Gerard, Sorokin, Dimitry Yu, Mavromatis, Konstantinos, Lapidus, Alla, Clum, Alicia, Ivanova, Natalia, Pati, Amrita, d'Haeseleer, Patrick, Woyke, Tanja, Kyrpides, Nikos C.
Publicado em 2011

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

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

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

Por Bowers, Robert M., Clum, Alicia, Tice, Hope, Lim, Joanne, Singh, Kanwar, Ciobanu, Doina, Ngan, Chew Yee, Cheng, Jan-Fang, Tringe, Susannah G., Woyke, Tanja
Publicado no BMC Genomics (2015)

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

Por Melton, Emily Denise, Sorokin, Dimitry Y., Overmars, Lex, Chertkov, Olga, Clum, Alicia, Pillay, Manoj, Ivanova, Natalia, Shapiro, Nicole, Kyrpides, Nikos C., Woyke, Tanja, Lapidus, Alla L., Muyzer, Gerard
Publicado no Stand Genomic Sci (2016)

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

Por 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.
Publicado em 2012

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T)

Por Nicholson, Wayne L., Davis, Christina L., Shapiro, Nicole, Huntemann, Marcel, Clum, Alicia, Reddy, T. B. K., Pillay, Manoj, Markowitz, Victor, Varghese, Neha, Pati, Amrita, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja
Publicado no Stand Genomic Sci (2016)

Next generation sequencing data of a defined microbial mock community

Por 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
Publicado no Sci Data (2016)

Permanent draft genome of Thiobacillus thioparus DSM 505(T), an obligately chemolithoautotrophic member of the Betaproteobacteria

Por Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, Boden, Rich
Publicado no Stand Genomic Sci (2017)

One Bacterial Cell, One Complete Genome

Por 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
Publicado em 2010

A genomic perspective on the potential of <it>Actinobacillus succinogenes </it>for industrial succinate production

Por Burkhart Kirk B, Lapidus Alla L, Clum Alicia, Lowry Stephen R, Challacombe Jean F, Siddaramappa Shivakumara, McKinlay Anastasia A, Schindler Bryan D, Laivenieks Maris, McKinlay James B, Harkins Victoria, Vieille Claire
Publicado em 2010-11-01

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production

Por 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
Publicado em 2010

Draft genome sequence of Actinotignum schaalii DSM 15541(T): Genetic insights into the lifestyle, cell fitness and virulence

Por Yassin, Atteyet F., Langenberg, Stefan, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos C.
Publicado no PLoS One (2017)

Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate- and Butanol-Producing Thermophile

Por Biswas, Ranjita, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos C., Woyke, Tanja, Guss, Adam M.
Publicado no Genome Announc (2018)

Genomes of Three Methylotrophs from a Single Niche Reveal the Genetic and Metabolic Divergence of the Methylophilaceae

Por Lapidus, Alla, Clum, Alicia, LaButti, Kurt, Kaluzhnaya, Marina G., Lim, Sujung, Beck, David A. C., Glavina del Rio, Tijana, Nolan, Matt, Mavromatis, Konstantinos, Huntemann, Marcel, Lucas, Susan, Lidstrom, Mary E., Ivanova, Natalia, Chistoserdova, Ludmila
Publicado em 2011

Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134(T), a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

Por Boden, Rich, Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos
Publicado no Stand Genomic Sci (2016)

Erratum to: Permanent draft genome of Thermithiobacillus tepidarius DSM 3134(T), a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

Por Boden, Rich, Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos
Publicado no Stand Genomic Sci (2016)

Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales

Por Nouioui, Imen, Gtari, Maher, Göker, Markus, Ghodhbane-Gtari, Faten, Tisa, Louis S., Fernandez, Maria P., Normand, Philippe, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Varghese, Neha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter
Publicado no Genome Announc (2016)

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Por Chang, Ying, Wang, Sishuo, Sekimoto, Satoshi, Aerts, Andrea L., Choi, Cindy, Clum, Alicia, LaButti, Kurt M., Lindquist, Erika A., Yee Ngan, Chew, Ohm, Robin A., Salamov, Asaf A., Grigoriev, Igor V., Spatafora, Joseph W., Berbee, Mary L.
Publicado no Genome Biol Evol (2015)