Kyrpides,: search on Z-Library

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1

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T B K, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susanna

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 67 KB

english, 2018

2

Uncovering Earth’s virome

Paez-Espino, David, Eloe-Fadrosh, Emiley A., Pavlopoulos, Georgios A., Thomas, Alex D., Huntemann, Marcel, Mikhailova, Natalia, Rubin, Edward, Ivanova, Natalia N., Kyrpides, Nikos C.

Journal:

Year:

2016

Language:

english

File:

PDF, 12.67 MB

english, 2016

3

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T B K, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susanna

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.72 MB

english, 2017

4

Universal Protein Families and the Functional Content of the Last Universal Common Ancestor

Kyrpides, Nikos, Overbeek, Ross, Ouzounis, Christos

Journal:

Journal of Molecular Evolution

Year:

1999

Language:

english

File:

PDF, 389 KB

english, 1999

5

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

Ghodhbane-Gtari, Faten, Beauchemin, Nicholas, Louati, Moussa, Nouioui, Imen, Ktari, Amir, Hezbri, Karima, Gueddou, Abdellatif, Chen, Amy, Huntemann, Marcel, Ivanova, Natalia, Kyrpides, Nikos, Markowit

Journal:

Genome Announcements

Year:

2016

Language:

english

File:

PDF, 148 KB

english, 2016

6

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Kyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Göker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chain, Patrick S. G., Chun, Jongsik, Colwell, Rita R., Danch

Journal:

Year:

2014

Language:

english

File:

PDF, 465 KB

english, 2014

7

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T B K, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susanna

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 71 KB

english, 2018

8

COVID-19 pandemic reveals the peril of ignoring metadata standards

Schriml, Lynn M., Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A., Finn, Robert D., Hugenholtz, Philip, Hunter, Christopher I., Hurwitz, Bonnie L., Kyrpides, Nikos C., Meyer, Folker, Mizrachi

Journal:

Scientific Data

Year:

2020

File:

PDF, 1.26 MB

2020

9

Toward a standard in structural genome annotation for prokaryotes

Tripp, H. James, Sutton, Granger, White, Owen, Wortman, Jennifer, Pati, Amrita, Mikhailova, Natalia, Ovchinnikova, Galina, Payne, Samuel H., Kyrpides, Nikos C., Ivanova, Natalia

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

10

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

Luo, Chengwei, Tsementzi, Despina, Kyrpides, Nikos, Read, Timothy, Konstantinidis, Konstantinos T., Rodriguez-Valera, Francisco

Journal:

Year:

2012

Language:

english

File:

PDF, 1.59 MB

english, 2012

11

Arboriscoccus pini gen. nov., sp. nov., an endophyte from a pine tree of the class Alphaproteobacteria , emended description of Geminicoccus roseus , and proposal of Geminicoccaceae fam. nov.

Proença, Diogo N., Whitman, William B., Varghese, Neha, Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Morais, Paula V.

Journal:

Systematic and Applied Microbiology

Year:

2017

Language:

english

File:

PDF, 2.05 MB

english, 2017

12

Complete genome sequence of the plant-associatedSerratia plymuthicastrain AS13

Neupane, Saraswoti, Finlay, Roger D., Kyrpides, Nikos C., Goodwin, Lynne, Alström, Sadhna, Lucas, Susan, Land, Miriam, Han, James, Lapidus, Alla, Cheng, Jan-Fang, Bruce, David, Pitluck, Sam, Peters, L

Journal:

Standards in Genomic Sciences

Year:

2012

Language:

english

File:

PDF, 3.60 MB

english, 2012

13

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

HÃ¶rdt, Anton, LÃ³pez, Marina GarcÃa, Meier-Kolthoff, Jan P., Schleuning, Marcel, Weinhold, Lisa-Maria, Tindall, Brian J., Gronow, Sabine, Kyrpides, Nikos C., Woyke, Tanja, GÃ¶ker, Markus

Journal:

Frontiers in Microbiology

Year:

2020

File:

PDF, 11.14 MB

2020

14

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance

Zhang, Tao, Datta, Supratim, Eichler, Jerry, Ivanova, Natalia, Axen, Seth D., Kerfeld, Cheryl A., Chen, Feng, Kyrpides, Nikos, Hugenholtz, Philip, Cheng, Jan-Fang, Sale, Kenneth L., Simmons, Blake, Ru

Journal:

Green Chemistry

Year:

2011

Language:

english

File:

PDF, 669 KB

english, 2011

15

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

Tschitschko, Bernhard, Williams, Timothy J, Allen, Michelle A, Páez-Espino, David, Kyrpides, Nikos, Zhong, Ling, Raftery, Mark J, Cavicchioli, Ricardo

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 2.58 MB

english, 2015

16

Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T

Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., Lindström, Kristina

Journal:

Standards in Genomic Sciences

Year:

2017

Language:

english

File:

PDF, 1.37 MB

english, 2017

17

Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF

Zhao, B., Mesbah, N. M., Dalin, E., Goodwin, L., Nolan, M., Pitluck, S., Chertkov, O., Brettin, T. S., Han, J., Larimer, F. W., Land, M. L., Hauser, L., Kyrpides, N., Wiegel, J.

Journal:

Journal of Bacteriology

Year:

2011

Language:

english

File:

PDF, 38 KB

english, 2011

18

10.1038/47056

Ouzounis, Christos A., Enright, Anton J., Iliopoulos, Ioannis, Kyrpides, Nikos C.

Journal:

Year:

1999

Language:

english

File:

PDF, 250 KB

english, 1999

19

The genomic basis of trophic strategy in marine bacteria

Lauro, F. M., McDougald, D., Thomas, T., Williams, T. J., Egan, S., Rice, S., DeMaere, M. Z., Ting, L., Ertan, H., Johnson, J., Ferriera, S., Lapidus, A., Anderson, I., Kyrpides, N., Munk, A. C., Dett

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 867 KB

english, 2009

20

IMG ER: a system for microbial genome annotation expert review and curation

Markowitz, V. M., Mavromatis, K., Ivanova, N. N., Chen, I-M. A., Chu, K., Kyrpides, N. C.

Journal:

Year:

2009

Language:

english

File:

PDF, 634 KB

english, 2009

21

Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T

Proença, Diogo N., Whitman, William B., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Morais, Paula V.

Journal:

Standards in Genomic Sciences

Year:

2017

Language:

english

File:

PDF, 1.15 MB

english, 2017

22

A Comparison of Microbial Genome Web Portals

Karp, Peter D., Ivanova, Natalia, Krummenacker, Markus, Kyrpides, Nikos, Latendresse, Mario, Midford, Peter, Ong, Wai Kit, Paley, Suzanne, Seshadri, Rekha

Journal:

Frontiers in Microbiology

Year:

2019

File:

PDF, 700 KB

2019

23

Recombination should not be an afterthought

Neches, Russell Y., McGee, Matthew D., Kyrpides, Nikos C.

Journal:

Nature Reviews Microbiology

Year:

2020

File:

PDF, 432 KB

2020

24

Protein structure determination using metagenome sequence data

Ovchinnikov, Sergey, Park, Hahnbeom, Varghese, Neha, Huang, Po-Ssu, Pavlopoulos, Georgios A., Kim, David E., Kamisetty, Hetunandan, Kyrpides, Nikos C., Baker, David

Journal:

Year:

2017

Language:

english

File:

PDF, 2.20 MB

english, 2017

25

Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants

Sahib, Mohammad Radhi, Yang, Piao, Bokros, Norbert, Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Xia, Ye, DeBolt, Seth, Dunning Hotopp, Julie C.

Journal:

Microbiology Resource Announcements

Year:

2019

File:

PDF, 988 KB

2019

26

Giant virus diversity and host interactions through global metagenomics

Schulz, Frederik, Roux, Simon, Paez-Espino, David, Jungbluth, Sean, Walsh, David A., Denef, Vincent J., McMahon, Katherine D., Konstantinidis, Konstantinos T., Eloe-Fadrosh, Emiley A., Kyrpides, Nikos

Journal:

Year:

2020

File:

PDF, 8.05 MB

2020

27

Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry?

Nikos C Kyrpides, Gary J Olsen

Journal:

Trends in Genetics

Year:

1999

Language:

english

File:

PDF, 98 KB

english, 1999

28

Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium

Young, M., Artsatbanov, V., Beller, H. R., Chandra, G., Chater, K. F., Dover, L. G., Goh, E.-B., Kahan, T., Kaprelyants, A. S., Kyrpides, N., Lapidus, A., Lowry, S. R., Lykidis, A., Mahillon, J., Mark

Journal:

Journal of Bacteriology

Year:

2010

Language:

english

File:

PDF, 3.59 MB

english, 2010

29

Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer

Kouvelis, V. N., Teshima, H., Bruce, D., Detter, C., Tapia, R., Han, C., Tampakopoulou, V.-O., Goodwin, L., Woyke, T., Kyrpides, N. C., Typas, M. A., Pappas, K. M.

Journal:

Genome Announcements

Year:

2014

Language:

english

File:

PDF, 142 KB

english, 2014

30

Genome sequence of the pink–pigmented marine bacterium Loktanella hongkongensis type strain (UST950701–009PT), a representative of the Roseobacter group

Lau, Stanley CK, Riedel, Thomas, Fiebig, Anne, Han, James, Huntemann, Marcel, Petersen, Jörn, Ivanova, Natalia N., Markowitz, Victor, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C., Klenk, Hans-Peter

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 915 KB

english, 2015

31

Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland

Susanti, Dwi, Johnson, Eric F., Lapidus, Alla, Han, James, Reddy, T. B. K., Pilay, Manoj, Ivanova, Natalia N., Markowitz, Victor M., Woyke, Tanja, Kyrpides, Nikos C., Mukhopadhyay, Biswarup

Journal:

Standards in Genomic Sciences

Year:

2016

Language:

english

File:

PDF, 860 KB

english, 2016

32

Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens

Aylward, F. O., Tremmel, D. M., Bruce, D. C., Chain, P., Chen, A., Walston Davenport, K., Detter, C., Han, C. S., Han, J., Huntemann, M., Ivanova, N. N., Kyrpides, N. C., Markowitz, V., Mavrommatis, K

Journal:

Genome Announcements

Year:

2013

Language:

english

File:

PDF, 131 KB

english, 2013

33

Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii

Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat, Kyrpides, Nikos C., Rodrigu

Journal:

Year:

2009

Language:

english

File:

PDF, 393 KB

english, 2009

34

Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes

Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 136 KB

english, 2018

35

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Nouioui, Imen, Carro, Lorena, García-López, Marina, Meier-Kolthoff, Jan P., Woyke, Tanja, Kyrpides, Nikos C., Pukall, Rüdiger, Klenk, Hans-Peter, Goodfellow, Michael, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 5.31 MB

english, 2018

36

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Cooper, Connor J., Zheng, Kaiyuan, Rush, Katherine W., Johs, Alexander, Sanders, Brian C., Pavlopoulos, Georgios A., Kyrpides, Nikos C., Podar, Mircea, Ovchinnikov, Sergey, Ragsdale, Stephen W., Parks

Journal:

Communications Biology

Year:

2020

File:

PDF, 2.39 MB

2020

37

On the evolution of arginases and related enzymes

C. A. Ouzounis, N. C. Kyrpides

Journal:

Journal of Molecular Evolution

Year:

1994

Language:

english

File:

PDF, 352 KB

english, 1994

38

Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka, Russia

Susanti, D., Johnson, E. F., Rodriguez, J. R., Anderson, I., Perevalova, A. A., Kyrpides, N., Lucas, S., Han, J., Lapidus, A., Cheng, J.-F., Goodwin, L., Pitluck, S., Mavrommatis, K., Peters, L., Land

Journal:

Journal of Bacteriology

Year:

2012

Language:

english

File:

PDF, 90 KB

english, 2012

39

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

Walworth, Nathan, Pfreundt, Ulrike, Nelson, William C., Mincer, Tracy, Heidelberg, John F., Fu, Feixue, Waterbury, John B., Glavina del Rio, Tijana, Goodwin, Lynne, Kyrpides, Nikos C., Land, Miriam L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 2.47 MB

english, 2015

40

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balazsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I., Gelfand, M. S., Bhattacharya, A., Kapatral, V., D'Souza, M., Ba

Journal:

Journal of Bacteriology

Year:

2003

Language:

english

File:

PDF, 2.45 MB

english, 2003

41

Draft Genome Sequences of 10 Strains of the Genus Exiguobacterium

Vishnivetskaya, T. A., Chauhan, A., Layton, A. C., Pfiffner, S. M., Huntemann, M., Copeland, A., Chen, A., Kyrpides, N. C., Markowitz, V. M., Palaniappan, K., Ivanova, N., Mikhailova, N., Ovchinnikova

Journal:

Genome Announcements

Year:

2014

Language:

english

File:

PDF, 165 KB

english, 2014

42

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

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.,

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 2.45 MB

english, 2015

43

Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7

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

Journal:

Standards in Genomic Sciences

Year:

2011

Language:

english

File:

PDF, 5.55 MB

english, 2011

44

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

De Meyer, Sofie E, Fabiano, Elena, Tian, Rui, Van Berkum, Peter, Seshadri, Rekha, Reddy, TBK, Markowitz, Victor, Ivanova, Natalia N, Pati, Amrita, Woyke, Tanja, Howieson, John, Kyrpides, Nikos C, Reev

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 1.51 MB

english, 2015

45

Functional Genomics of Novel Secondary Metabolites from Diverse Cyanobacteria Using Untargeted Metabolomics

Baran, Richard, Ivanova, Natalia, Jose, Nick, Garcia-Pichel, Ferran, Kyrpides, Nikos, Gugger, Muriel, Northen, Trent

Journal:

Year:

2013

Language:

english

File:

PDF, 1.40 MB

english, 2013

46

Genome Sequences of Actinobacteria from Extreme Environments in Colombia

Cantillo, Angela, Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Baena, Sandra, Zambrano, María Mercedes, Stewart, Frank J.

Journal:

Microbiology Resource Announcements

Year:

2018

Language:

english

File:

PDF, 165 KB

english, 2018

47

Establishment of computational biology in Greece and Cyprus: Past, present, and future

Chasapi, Anastasia, Aivaliotis, Michalis, Angelis, Lefteris, Chanalaris, Anastasios, Iliopoulos, Ioannis, Kappas, Ilias, Karapiperis, Christos, Kyrpides, Nikos C., Pafilis, Evangelos, Panteris, Elefth

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 841 KB

2019

48

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 291 KB

english, 2007

49

Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki

Sharp, Christine E., Smirnova, Angela V., Kalyuzhnaya, Marina G., Bringel, Françoise, Hirayama, Hisako, Jetten, Mike S. M., Khmelenina, Valentina N., Klotz, Martin G., Knief, Claudia, Kyrpides, Nikos,

Journal:

Genome Announcements

Year:

2015

Language:

english

File:

PDF, 158 KB

english, 2015

50

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil, Klenk, Hans-Peter

Journal:

Standards in Genomic Sciences

Year:

2013

Language:

english

File:

PDF, 398 KB

english, 2013

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