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    Алла Львовна Лапидус
2011
37 Citations (Scopus)

Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20

Hauser, L. J., Land, M. L., Brown, S. D., Larimer, F., Keller, K. L., Rapp-Giles, B. J., Price, M. N., Lin, M., Bruce, D. C., Detter, J. C., Tapia, R., Han, C. S., Goodwin, L. A., Cheng, J. F., Pitluck, S., Copeland, A., Lucas, S., Nolan, M., Lapidus, A. L., Palumbo, A. V. & 1 others, Wall, J. D., 1 Aug 2011, In : Journal of Bacteriology. 193, 16, p. 4268-4269 2 p.

Research output

Desulfovibrio
Poisons
Desulfovibrio desulfuricans
Metals
Genome
18 Citations (Scopus)

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262 T)

Woyke, T., Chertkov, O., Lapidus, A., Nolan, M., Lucas, S., del Rio, T. G., Tice, H., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Huntemann, M., Mavromatis, K., Pati, A., Chen, A., Palaniappan, K., Land, M. & 13 others, Hauser, L., Brambilla, E. M., Rohde, M., Mwirichia, R., Sikorski, J., Tindall, B. J., Göker, M., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Klenk, H. P. & Kyrpides, N. C., 28 Oct 2011, In : Standards in Genomic Sciences. 5, 1, p. 21-29 9 p.

Research output

Open Access
Fresh Water
Genome
Bacteria
Flavobacteriaceae
Encyclopedias
2012
6 Citations (Scopus)

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)

Huntemann, M., Teshima, H., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J. F., Tapia, R., Goodwin, L. A., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M. & 14 others, Hauser, L., Pan, C., Brambilla, E. M., Rohde, M., Spring, S., Göker, M., Detter, J. C., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Woyke, T., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 185-193 9 p.

Research output

Anaerobic Bacteria
Flavobacteriaceae
Genome
Encyclopedias
Bacteroidetes
9 Citations (Scopus)

Erratum: Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis (Proceedings of the National Academy of Sciences (2012) 109 (5458-5463) DOI: 10.1073/pnas. 1119912109)

Fernandez-Fueyo, E., Ruiz-Dueñas, F. J., Ferreira, P., Floudas, D., Hibbett, D. S., Canessa, P., Larrondo, L. F., James, T. Y., Seelenfreund, D., Lobos, S., Polanco, R., Tello, M., Honda, Y., Watanabe, T., Watanabe, T., Ryu, J. S., Kubicek, C. P., Schmoll, M., Gaskell, J., Hammel, K. E. & 46 others, St John, F. J., Vanden Wymelenberg, A., Sabat, G., BonDurant, S. S., Syed, K., Yadav, J. S., Doddapaneni, H., Subramanian, V., Lavín, J. L., Oguiza, J. A., Perez, G., Pisabarro, A. G., Ramirez, L., Santoyo, F., Master, E., Coutinho, P. M., Henrissat, B., Lombard, V., Magnuson, J. K., Kües, U., Hori, C., Igarashi, K., Samejima, M., Held, B. W., Barry, K. W., LaButti, K. M., Lapidus, A., Lindquist, E. A., Lucas, S. M., Riley, R., Salamov, A. A., Hoffmeister, D., Schwenk, D., Hadar, Y., Yarden, O., De Vries, R. P., Wiebenga, A., Stenlid, J., Eastwood, D., Grigoriev, I. V., Berka, R. M., Blanchette, R. A., Kersten, P., Martinez, A. T., Vicuna, R. & Cullen, D., 22 May 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 21, 1 p.

Research output

2011
14 Citations (Scopus)

Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum

Miller, D. A., Suen, G., Bruce, D., Copeland, A., Cheng, J. F., Detter, C., Goodwin, L. A., Han, C. S., Hauser, L. J., Land, M. L., Lapidus, A., Lucas, S., Meincke, L., Pitluck, S., Tapia, R., Teshima, H., Woyke, T., Fox, B. G., Angert, E. R. & Currie, C. R., 1 May 2011, In : Journal of Bacteriology. 193, 9, p. 2357-2358 2 p.

Research output

Clostridium
Genomics
Rivers
Cellulose
Genome
2014

Whole genome sequencing of Mycobacterium tuberculosis strains obtained from patients with pulmonary and extrapulmonary tuberculosis

Chernyaeva, E., Rotkevich, M., Solovieva, N., Zhuravlev, V., Lapidus, A. & O'Brien, S., 2014, The International Journal of Tuberculosis and Lung Disease. p. S156

Research output

2016

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

Aizenberg-Gershtein, Y., Izhaki, I., Lapidus, A., Copeland, A., Reddy, T. B. K., Huntemann, M., Pillay, M., Markowitz, V., Goeker, M., Woyke, T., Klenk, H-P., Kyrpides, N. C. & Halpern, M., 2016, In : Standards in Genomic Sciences. 11, 7 p.

Research output

Phaseolus
Pseudomonas
Microbial Genome
Genome
Encyclopedias
2012
23 Citations (Scopus)

Complete genome sequence of polynucleobacter necessarius subsp. Asymbioticus type strain (QLW-P1DMWA-1 T)

Meincke, L., Copeland, A., Lapidus, A., Lucas, S., Berry, K. W., del Rio, T. G., Hammon, N., Dalin, E., Tice, H., Pitluck, S., Richardson, P., Bruce, D., Goodwin, L., Han, C., Tapia, R., Detter, J. C., Schmutz, J., Brettin, T., Larimer, F., Land, M. & 9 others, Hauser, L., Kyrpides, N. C., Ivanova, N., Göker, M., Woyke, T., Wu, Q. L., Pöckl, M., Hahn, M. W. & Klenk, H. P., 2 Apr 2012, In : Standards in Genomic Sciences. 6, 1, p. 74-83 10 p.

Research output

Fresh Water
Genome
Burkholderiaceae
Euplotes
Betaproteobacteria
2013
9 Citations (Scopus)

Complete genome sequence of Halorhodospira halophila SL1

Challacombe, JF., Majid, S., Deole, R., Brettin, TS., Bruce, D., Delano, SF., Detter, JC., Gleasner, CD., Han, CS., Misra, M., Reitenga, KG., Mikhailova, N., Woyke, T., Pitluck, S., Nolan, M., Land, ML., Saunders, E., Tapia, R., Lapidus, A., Ivanova, N. & 1 others, Hoff, WD., 2013, In : Standards in Genomic Sciences. 8, 2, p. 206-214

Research output

2015
9 Citations (Scopus)

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2<sup>T</sup> (DSM 21788<sup>T</sup>), a valuable source of polysaccharide decomposing enzymes

Hahnke, R. L., Stackebrandt, E., Meier-Kolthoff, J. P., Tindall, B. J., Huang, S., Rohde, M., Lapidus, A., Han, J., Trong, S., Haynes, M., Reddy, T. B. K., Huntemann, M., Pati, A., Ivanova, N. N., Mavromatis, K., Markowitz, V., Woyke, T., Göker, M., Kyrpides, N. C. & Klenk, H-P., 2015, In : Standards in Genomic Sciences. JULY2015, 16 p.

Research output

Bacteroidetes
Polysaccharides
Genome
Enzymes
aprepitant
2012
67 Citations (Scopus)

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Suzuki, H., Macdonald, J., Syed, K., Salamov, A., Hori, C., Aerts, A., Henrissat, B., Wiebenga, A., Vankuyk, PA., Barry, K., Lindquist, E., Labutti, K., Lapidus, A., Lucas, S., Coutinho, P., Gong, Y., Samejima, M., Mahadevan, R., Abou-Zaid, M., de_Vries, RP. & 4 others, Igarashi, K., Yadav, JS., Grigoriev, IV. & Master, ER., 2012, In : BMC Genomics. 13, 444, p. 1-17

Research output

2010
96 Citations (Scopus)

Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium

Ran, L., Larsson, J., Vigil-Stenman, T., Nylander, JA., Ininbergs, K., Zheng, WW., Lapidus, A., Lowry, S., Haselkorn, R. & Bergman, B., 2010, In : PLoS ONE. 5, 7, p. e11486

Research output

2012
15 Citations (Scopus)

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314T)

Göker, M., Saunders, E., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J. F., Han, C., Tapia, R., Goodwin, L. A., Pitluck, S., Liolios, K., Mavromatis, K., Pagani, I., Ivanova, N., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K. & 14 others, Land, M., Chang, Y. J., Jeffries, C. D., Brambilla, E. M., Rohde, M., Spring, S., Detter, J. C., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C. & Klenk, H. P., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 230-239 10 p.

Research output

Sulfur-Reducing Bacteria
Genome
Amino Acids
Encyclopedias
Oil and Gas Fields
2011
15 Citations (Scopus)

Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum spyr1

Kallimanis, A., Karabika, E., Mavromatis, K., Lapidus, A., Labutti, K. M., Liolios, K., Goodwin, L., Woyke, T., Velentzas, A. S. D., Perisynakis, A., Ouzounis, C. C., Kyrpides, N. C., Koukkou, A. I. & Drainas, C., 28 Oct 2011, In : Standards in Genomic Sciences. 5, 1, p. 144-153 10 p.

Research output

Nontuberculous Mycobacteria
Mycobacterium
Creosote
Genome
Greece
2015
4 Citations (Scopus)

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1<sup>T</sup>(DSM 17521<sup>T</sup>) isolated from muddy waters of a drainage system in Chandigarh, India

Mukherjee, S., Lapidus, A., Shapiro, N., Cheng, J-F., Han, J., Reddy, T. B. K., Huntemann, M., Ivanova, N., Mikhailova, N., Chen, A., Palaniappan, K., Spring, S., Göker, M., Markowitz, V., Woyke, T., Tindall, B. J., Klenk, H-P., Kyrpides, N. C. & Pati, A., 2015, In : Standards in Genomic Sciences. FEBRUARY2015, 9 p.

Research output

Cytophagaceae
Sequence Analysis
Drainage
India
Genome
2016
3 Citations (Scopus)

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds

Hwang, C., Copeland, A., Lucas, S., Лапидус, А., Barry, K., Detter, J. C., Glavina Del Rio, T., Hammon, N., Israni, S., Dalin, E., Tice, H., Pitluck, S., Chertkov, O., Brettin, T., Bruce, D., Han, C., Schmutz, J., Larimer, F., Land, M. L., Hauser, L. & 5 others, Kyrpides, N., Ye, Q., Zhou, J., Richardson, P. & Fields, M. W., 2016, In : Genome Announcements. 4, 6

Research output

Metals
Genome
Bacteria
borax
Firmicutes
2013
4 Citations (Scopus)

Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

Stackebrandt, E., Zeytun, A., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, JF., Tapia, R., Goodwin, LA., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K. & 14 others, Chang, YJ., Land, M., Hauser, L., Rohde, M., Pukall, R., Göker, M., Detter, JC., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC. & Klenk, HP., 2013, In : Standards in Genomic Sciences. 8, 1, p. 15-25

Research output

3 Citations (Scopus)

Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T

Elkins, JG., Hamilton-Brehm, SD., Lucas, S., Han, J., Lapidus, A., Cheng, JF., Goodwin, LA., Pitluck, S., Peters, L., Mikhailova, N., Davenport, KW., Detter, JC., Han, CS., Tapia, R., Land, ML., Hauser, L., Kyrpides, NC., Ivanova, NN., Pagani, I., Bruce, D. & 2 others, Woyke, T. & Cottingham, RW., 2013, In : Genome Announcements. 1, 2, p. 1-13

Research output

2012
7 Citations (Scopus)

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)

Copeland, A., Zeytun, A., Yassawong, M., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J. F., Han, C., Tapia, R., Goodwin, L. A., Pitluck, S., Mavromatis, K., Liolios, K., Pagani, I., Ivanova, N., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K. & 17 others, Land, M., Hauser, L., Jeffries, C. D., Brambilla, E. M., Rohde, M., Sikorski, J., Pukall, R., Göker, M., Detter, J. C., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Lapidus, A., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 240-250 11 p.

Research output

Deinococcus
Genome
Encyclopedias
New World Camelids
Archaea
2014
4 Citations (Scopus)

High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway

Ntougias, S., Lapidus, A., Han, J., Mavromatis, K., Pati, A., Chen, A., Klenk, H-P., Woyke, T., Fasseas, C., Kyrpides, N. C. & Zervakis, G. I., 2014, In : Standards in Genomic Sciences. 9, 3, p. 783-93 11 p.

Research output

Genome
Genes
Soil
Xylosidases
Encyclopedias
2015
12 Citations (Scopus)

Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade

Beyersmann, P. G., Chertkov, O., Petersen, J., Fiebig, A., Chen, A., Pati, A., Ivanova, N., Lapidus, A., Goodwin, L. A., Chain, P., Detter, J. C., Rohde, M., Gronow, S., Kyrpides, N. C., Woyke, T., Simon, M., Göker, M., Klenk, H. P. & Brinkhoff, T., 30 Oct 2015, In : Standards in Genomic Sciences. 8, 3, p. 403-419 17 p.

Research output

Roseobacter
Acyl-Butyrolactones
Genome
Alphaproteobacteria
Quorum Sensing
2014
10 Citations (Scopus)

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Visser, M., Parshina, SN., Alves, JI., Sousa, DZ., Pereira, IA., Muyzer, G., Kuever, J., Lebedinsky, AV., Koehorst, JJ., Worm, P., Plugge, CM., Schaap, PJ., Goodwin, LA., Lapidus, A., Kyrpides, NC., Detter, JC., Woyke, T., Chain, P., Davenport, KW., Spring, S. & 3 others, Rohde, M., Klenk, HP. & Stams, AJ., 2014, In : Standards in Genomic Sciences. 9, 3, p. 655-675

Research output

2010
144 Citations (Scopus)

One bacterial cell, one complete genome

Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, JP., McDonald, BR., Moran, NA., Bristow, J. & Cheng, JF., 2010, In : PLoS ONE. 5, 4, p. e10314

Research output

2011
10 Citations (Scopus)

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2 T)

Lapidus, A., Nolan, M., Lucas, S., del Rio, T. G., Tice, H., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Lio-Lios, K., Pagani, I., Huntemann, M., Mavromatis, K., Pati, A., Chen, A., Palaniappan, K., Land, M., Brambilla, E. M., Rohde, M. & 10 others, Abt, B., Verbarg, S., Göker, M., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Woyke, T., 1 Dec 2011, In : Standards in Genomic Sciences. 5, 3, p. 398-406 9 p.

Research output

Open Access
Thiothrix
Thiotrichaceae
aprepitant
Genome
Encyclopedias
8 Citations (Scopus)

Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A T)

Anderson, I., Göker, M., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Pagani, I., Mavromatis, K., Ovchinikova, G., Pati, A., Chen, A., Pala-Niappan, K., Land, M. & 18 others, Hauser, L., Brambilla, E. M., Huber, H., Yasawong, M., Rohde, M., Spring, S., Abt, B., Sikorski, J., Wirth, R., Detter, J. C., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Lapidus, A., 5 Oct 2011, In : Standards in Genomic Sciences. 4, 3, p. 381-392 12 p.

Research output

Pyrodictiaceae
Genome
Hydrothermal Vents
Encyclopedias
Archaea
2015
6 Citations (Scopus)

Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment

Hwang, C., Copeland, A., Lucas, S., Lapidus, A., Barry, K., Glavina Del Rio, T., Dalin, E., Tice, H., Pitluck, S., Sims, D., Brettin, T., Bruce, D. C., Detter, J. C., Han, C. S., Schmutz, J., Larimer, F. W., Land, M. L., Hauser, L. J., Kyrpides, N., Lykidis, A. & 5 others, Richardson, P., Belieav, A., Sanford, R. A., Löeffler, F. E. & Fields, M. W., 2015, In : Genome Announcements. 3, 1

Research output

Uranyl Nitrate
Metals
Genome
Bacteria
Environmental Biodegradation
2011
43 Citations (Scopus)

Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09

Boden, R., Cunliffe, M., Scanlan, J., Moussard, H., Kits, K. D., Klotz, M. G., Jetten, M. S. M., Vuilleumier, S., Han, J., Peters, L., Teshima, H., Tapia, R., Kyrpides, N., Pagani, I., Cheng, J. F., Goodwin, L., Han, C., Hauser, L., Land, M. L., Lapidus, A. & 5 others, Lucas, S., Pitluck, S., Woyke, T., Stein, L. & Murrell, J. C., 1 Dec 2011, In : Journal of Bacteriology. 193, 24, p. 7001-7002 2 p.

Research output

Open Access
Methylomonas
Gammaproteobacteria
Seawater
Genome
2012
37 Citations (Scopus)

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to "Dehalococcoides" strains

Siddaramappa, S., Challacombe, J. F., Delano, S. F., Green, L. D., Daligault, H., Bruce, D., Detter, C., Tapia, R., Han, S., Goodwin, L., Han, J., Woyke, T., Pitluck, S., Pennacchio, L., Nolan, M., Land, M., Chang, Y. J., Kyrpides, N. C., Ovchinnikova, G., Hauser, L. & 6 others, Lapidus, A., Yan, J., Bowman, K. S., da Costa, M. S., Rainey, F. A. & Moe, W. M., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 251-264 14 p.

Research output

Chloroflexi
Negative Staining
Alkanes
Groundwater
Transfer RNA
2011
3 Citations (Scopus)

Complete genome sequence of Staphylothermus hellenicus P8 T

Anderson, I., Wirth, R., Lucas, S., Copeland, A., Lapidus, A., Cheng, J. F., Goodwin, L., Pitluck, S., Davenport, K., Detter, J. C., Han, C., Tapia, R., Land, M., Hauser, L., Pati, A., Woyke, T., Klenk, H. P. & Kyrpides, N., 31 Oct 2011, In : Standards in Genomic Sciences. 5, 1, p. 12-20 9 p.

Research output

Open Access
Desulfurococcaceae
Genome
Desulfurococcales
Crenarchaeota
Hydrothermal Vents
2017
2 Citations (Scopus)

Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Jiao, J. Y., Carro, L., Liu, L., Gao, X. Y., Zhang, X. T., Hozzein, W. N., Lapidus, A., Huntemann, M., Reddy, T. B. K., Varghese, N., Hadjithomas, M., Ivanova, N. N., Göker, M., Pillay, M., Eisen, J. A., Woyke, T., Klenk, H. P., Kyrpides, N. C. & Li, W. J., 3 Feb 2017, In : Standards in Genomic Sciences. 12, 1, 21.

Research output

Open Access
Genome
Multigene Family
Anti-Bacterial Agents
rRNA Genes
Pristinamycin
2013
2 Citations (Scopus)

Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T)

Mavromatis, K., Stackebrandt, E., Munk, C., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, JF., Tapia, R., Goodwin, LA., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K. & 13 others, Land, M., Hauser, L., Rohde, M., Gronow, S., Göker, M., Detter, JC., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP. & Woyke, T., 2013, In : Standards in Genomic Sciences. 8, 1, p. 26-36

Research output

2011

Soil microbe Dechloromonas aromatica Str. RCB metabolic analysis

Salinero, K. K., Keller, K., Feil, W. S., Feil, H., Trong, S., Di Bartolo, G. & Lapidus, A., 15 Dec 2011, Recent Advances in Microbiology. Apple Academic Press, p. 120-147 28 p.

Research output

2019

MGnify: the microbiome analysis resource in 2020

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A. & Finn, R. D., 7 Nov 2019, In : Nucleic Acids Research. 9 p.

Research output

Open Access
Metagenomics
Microbiota
Molecular Sequence Annotation
Protein Databases
Workflow
2015
4 Citations (Scopus)

Draft genome sequence of Halomonas lutea strain YIM 91125<sup>T</sup> (DSM 23508<sup>T</sup>) isolated from the alkaline Lake Ebinur in Northwest China

Gao, X-Y., Zhi, X-Y., Li, H-W., Zhou, Y., Lapidus, A., Han, J., Haynes, M., Lobos, E., Huntemann, M., Pati, A., Ivanova, N. N., Mavromatis, K., Tindall, B. J., Markowitz, V., Woyke, T., Klenk, H-P., Kyrpides, N. C. & Li, W-J., 2015, In : Standards in Genomic Sciences. FEBRUARY2015, 8 p.

Research output

Halomonas
Lakes
China
Genome
Halomonadaceae
2014
29 Citations (Scopus)

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Scheuner, C., Tindall, B. J., Lu, M., Nolan, M., Lapidus, A., Cheng, J. F., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Pagani, I., Mavromatis, K., Ivanova, N., Pati, A., Chen, A., Palaniappan, K., Jeffries, C. D., Hauser, L., Land, M., Mwirichia, R. & 10 others, Rohde, M., Abt, B., Detter, J. C., Woyke, T., Eisen, J. A., Markowitz, V., Hugenholtz, P., Göker, M., Kyrpides, N. C. & Klenk, H. P., 8 Dec 2014, In : Standards in Genomic Sciences. 9, 1, 10.

Research output

aprepitant
Planctomycetales
Genome
Base Composition
Encyclopedias
2012
32 Citations (Scopus)

Complete genome sequence of Thauera aminoaromatica strain MZ1T

Jiang, K., Sanseverino, J., Chauhan, A., Lucas, S., Copeland, A., Lapidus, A., Del Rio, T. G., Dalin, E., Tice, H., Bruce, D., Goodwin, L., Pitluck, S., Sims, D., Brettin, T., Detter, J. C., Han, C., Chang, Y. J., Larimer, F., Land, M., Hauser, L. & 10 others, Kyrpides, N. C., Mikhailova, N., Moser, S., Jegier, P., Close, D., DeBruyn, J. M., Wang, Y., Layton, A. C., Allen, M. S. & Sayler, G. S., 27 Aug 2012, In : Standards in Genomic Sciences. 6, 3, p. 325-335 11 p.

Research output

Thauera
Genome
Rhodocyclaceae
Betaproteobacteria
Methane
2011
27 Citations (Scopus)

Complete genome sequence of odoribacter splanchnicus type strain (1651/6 T)

Göker, M., Gronow, S., Zeytun, A., Nolan, M., Lucas, S., Lapidus, A., Hammon, N., Deshpande, S., Cheng, J. F., Pitluck, S., Liolios, K., Pagani, I., Mavromatis, K., Ovchinikova, G., Pati, A., Tapia, R., Han, C., Goodwin, L., Chen, A., Palaniappan, K. & 13 others, Land, M., Hauser, L., Jeffries, C. D., Brambilla, E. M., Rohde, M., Detter, J. C., Woyke, T., Bristow, J., Markowitz, V., Hugenholtz, P., Eisen, J. A., Kyrpides, N. C. & Klenk, H. P., 11 Oct 2011, In : Standards in Genomic Sciences. 4, 2, p. 200-209 10 p.

Research output

Open Access
Genome
Encyclopedias
Archaea
RNA
Bacteria
1 Citation (Scopus)

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20 t)

Pati, A., Gronow, S., Lu, M., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Mavromatis, K., Huntemann, M., Chen, A., Palaniappan, K., Land, M. & 12 others, Hauser, L., Detter, J. C., Brambilla, E. M., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C. & Klenk, H. P., 28 Oct 2011, In : Standards in Genomic Sciences. 5, 1, p. 41-49 9 p.

Research output

Open Access
Prevotella
Genome
Root Caries
Encyclopedias
Periodontitis
2012
18 Citations (Scopus)

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)

Anderson, I., Held, B., Lapidus, A., Nolan, M., Lucas, S., Tice, H., Del Rio, T. G., Cheng, J. F., Han, C., Tapia, R., Good-win, L. A., Pitluck, S., Liolios, K., Mavromatis, K., Pagani, I., Ivanova, N., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K. & 13 others, Land, M., Brambilla, E. M., Rohde, M., Spring, S., Göker, M., Detter, J. C., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Klenk, H. P. & Kyrpides, N. C., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 174-184 11 p.

Research output

Acidobacteria
Genome
Encyclopedias
Bacteria
Sulfur Compounds
2017

Complete mitochondrial genomes of Baikal oilfishes (Perciformes Cottoidei), earth’s deepest-swimming freshwater fishes

Sandel, M. W., Aguilar, A., Fast, K., O’Brien, S., Lapidus, A., Allison, D. B., Teterina, V. & Kirilchik, S., 20 Dec 2017, In : Mitochondrial DNA. 2, 2, p. 773-775 3 p.

Research output

Open Access
Perciformes
Mitochondrial Genome
Lakes
Electron Transport
Fresh Water
2016
3 Citations (Scopus)

Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T))

Kappler, U., Davenport, K., Beatson, S., Lapidus, A., Pan, C., Han, C., Montero-Calasanz, M. D. C., Land, M., Hauser, L., Rohde, M., Göker, M., Ivanova, N., Woyke, T., Klenk, H-P. & Kyrpides, N. C., 2016, In : Standards in Genomic Sciences. 11, p. 38

Research output

Thiosulfates
Proteobacteria
Sulfides
Lakes
Piscirickettsiaceae
2019
3 Citations (Scopus)

RnaSPAdes: A de novo transcriptome assembler and its application to RNA-Seq data

Bushmanova, E., Antipov, D., Lapidus, A. & Prjibelski, A. D., 18 Sep 2019, In : GigaScience. 8, 9, giz100.

Research output

Open Access
RNA
Transcriptome
Genes
RNA Sequence Analysis
Genome
2016
14 Citations (Scopus)

Complete genome sequence of Methanospirillum hungatei type strain JF1

Gunsalus, R. P., Cook, L. E., Crable, B., Rohlin, L., McDonald, E., Mouttaki, H., Sieber, J. R., Poweleit, N., Zhou, H., Lapidus, A. L., Daligault, H. E., Land, M., Gilna, P., Ivanova, N., Kyrpides, N., Culley, D. E. & McInerney, M. J., 6 Jan 2016, In : Standards in Genomic Sciences. 11, 1, 2.

Research output

Open Access
Methanospirillum
formic acid
Genome
Methanomicrobiales
Hydrogen
2017
105 Citations (Scopus)

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

de Vries, R. P., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Uchima, C. A., Anderluh, G., Asadollahi, M., Askin, M., Barry, K., Battaglia, E., Bayram, O., Benocci, T., Braus-Stromeyer, S. A., Caldana, C., Cánovas, D., Cerqueira, G. C., Chen, F., Chen, W., Choi, C. & 97 others, Clum, A., dos Santos, R. A. C., de Lima Damásio, A. R., Diallinas, G., Emri, T., Fekete, E., Flipphi, M., Freyberg, S., Gallo, A., Gournas, C., Habgood, R., Hainaut, M., Harispe, M. L., Henrissat, B., Hildén, K. S., Hope, R., Hossain, A., Karabika, E., Karaffa, L., Karányi, Z., Kra evec, N., Kuo, A., Kusch, H., LaButti, K., Lagendijk, E. L., Lapidus, A., Levasseur, A., Lindquist, E., Lipzen, A., Logrieco, A. F., MacCabe, A., Mäkelä, M. R., Malavazi, I., Melin, P., Meyer, V., Mielnichuk, N., Miskei, M., Molnár, A. P., Mulé, G., Ngan, C. Y., Orejas, M., Orosz, E., Ouedraogo, J. P., Overkamp, K. M., Park, H-S., Perrone, G., Piumi, F., Punt, P. J., Ram, A. F. J., Ramón, A., Rauscher, S., Record, E., Riaño-Pachón, D. M., Robert, V., Röhrig, J., Ruller, R., Salamov, A., Salih, N. S., Samson, R. A., Sándor, E., Sanguinetti, M., Schütze, T., Sep i, K., Shelest, E., Sherlock, G., Sophianopoulou, V., Squina, F. M., Sun, H., Susca, A., Todd, R. B., Tsang, A., Unkles, S. E., van de Wiele, N., van Rossen-Uffink, D., de Castro Oliveira, J. V., Vesth, T. C., Visser, J., Yu, J-H., Zhou, M., Andersen, M. R., Archer, D. B., Baker, S. E., Benoit, I., Brakhage, A. A., Braus, G. H., Fischer, R., Frisvad, J. C., Goldman, G. H., Houbraken, J., Oakley, B., Pócsi, I., Scazzocchio, C., Seiboth, B., vanKuyk, P. A., Wortman, J., Dyer, P. S. & Grigoriev, I. V., 14 Feb 2017, In : Genome Biology. 18, 1, PMID: 28196534.

Research output

Open Access
Biodiversity
Aspergillus
Genomics
genomics
genome
2015
15 Citations (Scopus)

Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from Geotrichum candidum 3C

Borisova, A. S., Eneyskaya, E. V., Bobrov, K. S., Jana, S., Logachev, A., Polev, D. E., Lapidus, A. L., Ibatullin, F. M., Saleem, U., Sandgren, M., Payne, C. M., Kulminskaya, A. A. & St hlberg, J., 2015, In : FEBS Journal. 282, 23, p. 4515–4537

Research output

13 Citations (Scopus)

IgSimulator: a versatile immunosequencing simulator

Safonova, Y., Lapidus, A. & Lill, J., 2015, In : Bioinformatics. 31, 19, p. 1-2

Research output

2011
4 Citations (Scopus)

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139 T)

Land, M., Held, B., Gronow, S., Abt, B., Lucas, S., del Rio, T. G., Nolan, M., Tice, H., Cheng, J. F., Pitluck, S., Liolios, K., Pagani, I., Mavromatis, K., Pati, A., Tapia, R., Han, C., Goodwin, L., Chen, A., Palaniappan, K., Hauser, L. & 12 others, Brambilla, E. M., Rohde, M., Göker, M., Detter, J. C., Woyke, T., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Lapidus, A., 11 Oct 2011, In : Standards in Genomic Sciences. 4, 2, p. 233-243 11 p.

Research output

Open Access
Bacteroides
Genome
Bacteroidaceae
Encyclopedias
Manure
3 Citations (Scopus)

Complete genome sequence of oceanithermus profundus type strain (506 T)

Pati, A., Zhang, X., Lapidus, A., Nolan, M., Lucas, S., del Rio, T. G., Tice, H., Cheng, J. F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Mavromatis, K., Chen, A., Palaniappan, K., Hauser, L., Jeffries, C. D., Brambilla, E. M. & 16 others, Röhl, A., Mwirichia, R., Rohde, M., Tindall, B. J., Sikorski, J., Wirth, R., Göker, M., Woyke, T., Detter, J. C., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C., Klenk, H. P. & Land, M., 11 Oct 2011, In : Standards in Genomic Sciences. 4, 2, p. 210-220 11 p.

Research output

Open Access
Genome
Encyclopedias
Sulfur Compounds
Charcoal
Archaea
2012
13 Citations (Scopus)

Complete genome sequence of Serratia plymuthica strain AS12

Neupane, S., Finlay, R. D., Alström, S., Goodwin, L., Kyrpides, N. C., Lucas, S., Lapidus, A., Bruce, D., Pitluck, S., Peters, L., Ovchinnikova, G., Chertkov, O., Han, J., Han, C., Tapia, R., Detter, J. C., Land, M., Hauser, L., Cheng, J. F., Ivanova, N. & 4 others, Pagani, I., Klenk, H. P., Woyke, T. & Högberg, N., 12 Jul 2012, In : Standards in Genomic Sciences. 6, 2, p. 165-173 9 p.

Research output

Serratia
Genome
Brassica rapa
rRNA Operon
Enterobacteriaceae
2011
27 Citations (Scopus)

Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium

Kant, R., van Passe, M. W. J., Palva, A., Lucas, S., Lapidus, A., del Rio, T. G., Dalin, E., Tice, H., Bruce, D., Goodwin, L., Pitluck, S., Larimer, F. W., Land, M. L., Hauser, L., Sangwan, P., de Vos, W. M., Janssen, P. H. & Smidt, H., 1 Jun 2011, In : Journal of Bacteriology. 193, 11, p. 2902-2903 2 p.

Research output

Verrucomicrobia
Plant Structures
Pyruvic Acid
Biomass
Soil