Find Research Outputs

Search concepts
Selected filters

Publication Year

  • 2020
  • 2019
  • 2018
  • 2017
  • 2016

Author

  • Алла Львовна Лапидус
2020

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., 8 Jan 2020, In : Nucleic Acids Research. 48, D1, p. D570-D578 9 p.

Research output

Open Access

Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14

Bushman, T. J., Akob, D. M., Bohu, T., Beyer, A., Woyke, T., Shapiro, N., Lapidus, A., Klenk, H-P. & Kuesel, K., 24 Oct 2019, In : Microbiology resource announcements. 8, 43, e01024-19.

Research output

Extending rnaSPAdes functionality for hybrid transcriptome assembly

Prjibelski, A., Bushmanova, E., Giordano, D., Mikheenko, A., Puglia, G., Antipov, D., Viatale, D. & Lapidus, A., 8 Nov 2019, In : BMC Bioinformatics. 20, S17, 2 p., O9.

Research output

Plasmid detection and assembly in genomic and metagenomic datasets

Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A., 1 Jan 2019, In : Genome Research. 29, 6, p. 961-968 8 p.

Research output

2 Citations (Scopus)
Open Access
12 Citations (Scopus)

Sequence Analysis

Пржибельский, А. Д., Коробейников, А. И. & Лапидус, А. Л., 2019, Encyclopedia of Bioinformatics and Computational Biology: Reference Module in Life Sciences. Elsevier, Vol. 3. p. 292-322

Research outputpeer-review

2018

Autoprobiotics as an Approach for Restoration of Personalised Microbiota

Суворов, А. Н., Карасева, А. Б., Котылева, М. П., Кондратенко, Ю. Д., Лавренова, Н., Коробейников, А. И., Козырев, П. А., Крамская, Т. А., Леонтьева, Г., Кудрявцев, И. В., Guo, D., Лапидус, А. Л. & Ермоленко, Е. И., 12 Sep 2018, In : Frontiers in Microbiology. 9, 1869.

Research output

Open Access
3 Citations (Scopus)

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M. & 30 others, Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glöckner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., Mcmahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H. & Eren, A. M., 6 Jul 2018, In : Nature Biotechnology. 36, 7, p. 660-660 1 p.

Research output

3 Citations (Scopus)
2017

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
134 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
2 Citations (Scopus)

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

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Melton, E. D., Sorokin, D. Y., Overmars, L., Lapidus, A. L., Pillay, M., Ivanova, N., del Rio, T. G., Kyrpides, N. C., Woyke, T. & Muyzer, G., 21 Sep 2017, In : Standards in Genomic Sciences. 12, 1, 57.

Research output

Open Access
6 Citations (Scopus)

Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica

Choi, D. H., Jang, G. I. I., Lapidus, A., Copeland, A., Reddy, T. B. K., Mukherjee, S., Huntemann, M., Varghese, N., Ivanova, N., Pillay, M., Tindall, B. J., Göker, M., Woyke, T., Klenk, H. P., Kyrpides, N. C. & Cho, B. C., 30 Oct 2017, In : Standards in Genomic Sciences. 12, 1, 65.

Research output

Open Access

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

The Genome Standards Consortium, 8 Aug 2017, In : Nature Biotechnology. 35, 8, p. 725-731 7 p., PMID: 28787424.

Research output

Open Access
192 Citations (Scopus)

Permanent draft genome sequence of Desulfurococcus amylolyticus strain Z-533T, a peptide and starch degrader isolated from thermal springs in the Kamchatka Peninsula and Kunashir Island, Russia

Susanti, D., Johnson, E. F., Lapidus, A., Han, J., Reddy, T. B. K., Mukherjee, S., Pillay, M., Perevalova, A. A., Ivanova, N. N., Woyke, T., Kyrpides, N. C. & Mukhopadhyay, B., 1 Apr 2017, In : Genome Announcements. 5, 15, e0007817.

Research output

Open Access
2 Citations (Scopus)
2016

Comparative genomics of biotechnologically important yeasts

Riley, R., Haridas, S., Wolfe, K. H., Lopes, M. R., Hittinger, C. T., Göker, M., Salamov, A. A., Wisecaver, J. H., Long, T. M., Calvey, C. H., Aerts, A. L., Barry, K. W., Choi, C., Clum, A., Coughlan, A. Y., Deshpande, S., Douglass, A. P., Hanson, S. J., Klenk, H-P., Labutti, K. M. & 19 others, Lapidus, A., Lindquist, E. A., Lipzen, A. M., Meier-Kolthoff, J. P., Ohm, R. A., Otillar, R. P., Pangilinan, J. L., Peng, Y., Rokas, A., Rosa, C. A., Scheuner, C., Sibirny, A. A., Slot, J. C., Benjamin, S. J., Sun, H., Kurtzman, C. P., Blackwell, M., Grigoriev, I. V. & Jeffries, T. W., 30 Aug 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, p. 9882-9887 6 p.

Research output

120 Citations (Scopus)

Comparing polysaccharide decomposition between the type strains Gramellaechinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicolaNedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriaeLau et al. 2005.

Panschin, I., Huang, S., Meier-Kolthoff, JP., Tindall, BJ., Rohde, M., Verbarg, S., Lapidus, A., Han, J., Trong, S., Haynes, M., Reddy, TB., Huntemann, M., Pati, A., Ivanova, NN., Mavromatis, K., Markowitz, V., Woyke, T., Göker, M., Klenk, HP., Kyrpides, NC. & 1 others, Hahnke, RL., 2016, In : Standards in Genomic Sciences.

Research output

10 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

3 Citations (Scopus)

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

Melton, E. D., Sorokin, D. Y., Overmars, L., Chertkov, O., Clum, A., Pillay, M., Ivanova, N., Shapiro, N., Kyrpides, N. C., Woyke, T., Lapidus, A. L. & Muyzer, G., 2016, In : Standards in Genomic Sciences. 11, 9 p.

Research output

8 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
14 Citations (Scopus)

Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34

Anderson, I. J., DasSarma, P., Lucas, S., Copeland, A., Lapidus, A., Del Rio, T. G., Tice, H., Dalin, E., Bruce, D. C., Goodwin, L., Pitluck, S., Sims, D., Brettin, T. S., Detter, J. C., Han, C. S., Larimer, F., Hauser, L., Land, M., Richardson, P., Cavicchioli, R. & 3 others, DasSarma, S., Woese, C. R. & Kyrpides, N. C., 10 Sep 2016, In : Standards in Genomic Sciences. 11, 1, p. 70

Research output

7 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

3 Citations (Scopus)

Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

Mosier, A. C., Miller, C. S., Frischkorn, K. R., Ohm, R. A., Li, Z., LaButti, K., Lapidus, A., Lipzen, A., Chen, C., Johnson, J., Lindquist, E. A., Pan, C., Hettich, R. L., Grigoriev, I. V., Singer, S. W. & Banfield, J. F., 3 Mar 2016, In : Frontiers in Microbiology. 7, 18 p.

Research output

21 Citations (Scopus)

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Tashkandy, N., Sabban, S., Fakieh, M., Meier-Kolthoff, J. P., Huang, S., Tindall, B. J., Rohde, M., Baeshen, M. N., Baeshen, N. A., Lapidus, A., Copeland, A., Pillay, M., Reddy, T. B. K., Huntemann, M., Pati, A., Ivanova, N., Markowitz, V., Woyke, T., Goeker, M., Klenk, H-P. & 2 others, Kyrpides, N. C. & Hahnke, R. L., 2016, In : Standards in Genomic Sciences. 11, 10 p.

Research output

1 Citation (Scopus)

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

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, D., Johnson, E. F., Lapidus, A., Han, J., Reddy, T. B. K., Pilay, M., Ivanova, N. N., Markowitz, V. M., Woyke, T., Kyrpides, N. C. & Mukhopadhyay, B., 2016, In : Standards in Genomic Sciences. 11, 3, 3.

Research output

Open Access
1 Citation (Scopus)

PlasmidSPAdes: Assembling plasmids from whole genome sequencing data

Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A. & Pevzner, P. A., 15 Nov 2016, In : Bioinformatics. 32, 22, p. 3380-3387 8 p.

Research output

123 Citations (Scopus)

RnaQUAST: A quality assessment tool for de novo transcriptome assemblies

Bushmanova, E., Antipov, D., Lapidus, A., Suvorov, V. & Prjibelski, A. D., 15 Jul 2016, In : Bioinformatics. 32, 14, p. 2210-2212 3 p.

Research output

26 Citations (Scopus)

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

Castanera, R. L., López-Varas, L., Borgognone, A., Labutti, K., Lapidus, A., Schmutz, J., Grimwood, J., Pérez, G. M., Pisabarro, A. G., Grigoriev, I. V., Stajich, J. E. & Ram rez, L. A., 1 Jun 2016, In : PLoS Genetics. 12, 6, e1006108.

Research output

58 Citations (Scopus)