Array2BIO: from microarray expression data to functional annotation of co-regulated genes

by Rasley Amy, Mabery Shalini, Chain Patrick SG, Loots Gabriela G, Garcia Emilio, Ovcharenko Ivan
Published 2006-06-01

Microbial Finishing at JGI

by Lapidus, Alla, Chain, Patrick, Han, Cliff, Goltsman, Eugene, Martinez, Michele, Malfatty, Stephanie, Chertkov, Olga, Trong, Stephan, Brettin, Tom, Tapia, Roxanne, Copeland, Alex, Richardson, Paul
Published 2005

Genome Improvement with Bubble-PCR and Roche/ 454 Reads

by Tice, Hope N., Lee, Janey, Hamilton, Matt, Foster, Brian, Malfatti, Stephanie, Chain, Patrick, Lapidus, Alla, Lucas, Susan, Cheng, Jan-Fang
Published 2009

Whole-Genome Analysis of Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1

by Kane, Staci R., Chakicherla, Anu Y., Chain, Patrick S.G., Schmidt, Radomir, Shin, Maria W., Legler, Tina C., Scow, Kate M., Larimer, Frank W., Lucas, Susan M., Richardson, Paul M., Hristova, Krassimira R.
Published 2007

The US DOE Joint Genome Institute Microbial Genome Program

by Lapidus, Alla, Chain, Patrick, Han, Cliff, Brettin, Thomas, Copeland, Alex, Detter, Chris, Pitluck, Samuel, Rio, Tijana Glavina del, Lucas, Susan, Barry, Kerrie, Land, Miriam, Larimer, Frank, Kyrpides, Nikos, Ivanova, Natalia, Schmutz, Jeremy, Markowitz, Victor M., Bruce, David, Gilna, Paul, Bristow, Jim, Rubin, Eddy, Richardson, Paul
Published 2006

The US DOE Joint Genome Institute Microbial Genome Program

by Lapidus, Alla, Chain, Patrick, Han, Cliff, Brettin, Thomas, Copeland, Alex, Barry, Kerrie, Detter, J. Chris, Glavina, Tijana, Lucas, Susan, Land, Miriam, Larimer, Frank, Kyrpides, Nikos, Ivanova, Natalia, Schmutz, Jeremy, Markowitz, Victor M., Bruce, David, Gilna, Paul, Bristow, Jim, Rubin, Eddy, Richardson, Paul M.
Published 2005

The National Microbiome Data Collaborative: enabling microbiome science.

by Wood-Charlson, Elisha M, Anubhav, Auberry, Deanna, Blanco, Hannah, Borkum, Mark I, Corilo, Yuri E, Davenport, Karen W, Deshpande, Shweta, Devarakonda, Ranjeet, Drake, Meghan, Duncan, William D, Flynn, Mark C, Hays, David, Hu, Bin, Huntemann, Marcel, Li, Po-E, Lipton, Mary, Lo, Chien-Chi, Millard, David, Miller, Kayd, Piehowski, Paul D, Purvine, Samuel, Reddy, TBK, Shakya, Migun, Sundaramurthi, Jagadish Chandrabose, Vangay, Pajau, Wei, Yaxing, Wilson, Bruce E, Canon, Shane, Chain, Patrick SG, Fagnan, Kjiersten, Martin, Stanton, McCue, Lee Ann, Mungall, Christopher J, Mouncey, Nigel J, Maxon, Mary E, Eloe-Fadrosh, Emiley A
Published 2020

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella...

by Woo, Hannah L, DeAngelis, Kristen M, Teshima, Hazuki, Davenport, Karen, Daligault, Hajnalka, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Lo, Chien-Chi, Munk, Christine, Scholz, Matthew, Xu, Yan, Chain, Patrick, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Simmons, Blake A, Hazen, Terry C
Published 2017

Burkholderia Xenovorans LB400 Harbors a Multi-Replicon, 9.73-Mbp Genome Shaped for Versatility

by Konstantinidis, Konstantinos T., Seeger, Michael, Vergez, Lisa M., Chain, Patrick S. G., Malfatti, Stephanie A., Denef, Vincent J., Zhulin, Igor B., Mahenthiralingam, Eshwar, LiPuma, John J., Lao, Victoria, Larimer, Frank, Cordova, Macarena, Sul, Woo Jun, Tiedje, James M., Spilker, Theodore, Land, Miriam, Tsoi, Tamara V., Ulrich, Luke E., Reyes, Valeria Latorre, Agullo, Loreine, Smith, Daryl, Parnell, J. Jacob, Ramette, Alban, Hauser, Loren, Richardson, Paul, Marx, Christopher, Gonzalez, Myriam, Gomez, Luis
Published 2009

Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".

by Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L, Berrios, Daniel C, Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V, Damerow, Joan, Duncan, William D, Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M, Gibbons, Sean M, Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L, Jaiswal, Pankaj, Joachimiak, Marcin P, Kinkel, Linda, Ladau, Joshua, Martin, Stanton L, McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, TBK, Richardson, Lorna, Roux, Simon, Schriml, Lynn M, Shaffer, Justin P, Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R, Timme, Ruth E, Zheng, Jie, Wood-Charlson, Elisha M, Eloe-Fadrosh, Emiley A
Published 2021

Toward unrestricted use of public genomic data.

by Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, Xenarios, Ioannis
Published 2019

Assessment of 454 Sequencing Errors in Microbial Genomes

by Trong, Stephan, Chain, Patrick, Kirton, Ed, Goltsman, Eugene, Foster, Brian, Richardson, Paul, Lapidus, Alla
Published 2007

Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

by Nolan, Matt, Sikorski, Johannes, Jando, Marlen, Lucas, Susan, Lapidus, Alla, Glavina Del Rio, Tijana, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Sims, David, Meincke, Linda, Brettin, Thomas, Han, Cliff, Detter, John C, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter
Published 2010

Complete genome sequence of Kribbella flavida type strain (IFO 14399).

by Pukall, Rüdiger, Lapidus, Alla, Glavina Del Rio, Tijana, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Labutti, Kurt, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, Brettin, Thomas
Published 2010

Complete genome sequence of Atopobium parvulum type strain (IPP 1246).

by Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Rüdiger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, Detter, John C
Published 2009

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).

by Pati, Amrita, Labutti, Kurt, Pukall, Rüdiger, Nolan, Matt, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Brettin, Thomas, Sikorski, Johannes, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, Lapidus, Alla
Published 2010

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).

by Pukall, Rüdiger, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Glavina Del Rio, Tijana, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Kuske, Cheryl, Brettin, Thomas, Detter, John C, Han, Cliff, Pitluck, Sam, Pati, Amrita, Mavrommatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Schneider, Susanne, Rohde, Manfred, Chain, Patrick, D'haeseleer, Patrik, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Kyrpides, Nikos C, Klenk, Hans-Peter, Hugenholtz, Philip
Published 2009

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).

by Sikorski, Johannes, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Brettin, Thomas, Detter, John C, Han, Cliff, Rohde, Manfred, Lang, Elke, Spring, Stefan, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter
Published 2010

Complete genome sequence of Halorhabdus utahensis type strain (AX-2).

by Anderson, Iain, Tindall, Brian J, Pomrenke, Helga, Göker, Markus, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Glavina Del Rio, Tijana, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chertkov, Olga, Bruce, David, Brettin, Thomas, Detter, John C, Han, Cliff, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Pitluck, Sam, Pati, Amrita, Mavromatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter
Published 2009

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.

by Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L, Berrios, Daniel C, Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V, Damerow, Joan, Duncan, William D, Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M, Gibbons, Sean M, Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L, Jaiswal, Pankaj, Joachimiak, Marcin P, Kinkel, Linda, Ladau, Joshua, Martin, Stanton L, McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, TBK, Richardson, Lorna, Roux, Simon, Schriml, Lynn M, Shaffer, Justin P, Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R, Timme, Ruth E, Zheng, Jie, Wood-Charlson, Elisha M, Eloe-Fadrosh, Emiley A
Published 2021