Alla Lapidus

Head of the Laboratory

Alla Lapidus, Ph.D., joined the lab in 2012 from the Fox Chase Cancer Center, PA, USA. Dr. Lapidus received her master’s degree (with honors) from the Department of Theoretical and Experimental Physics, Moscow Physics-Engineering Institute, Moscow, Russia, carried out postdoctoral training at Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia, received her Technical Project Management Certificate from the American management Association.

Academic Appointments:

Head of the Laboratory, Center for Algorithmic Biotechnology, St. Petersburg, Russia
Associate Director, Algorithmic Biology Lab, St. Petersburg, Russia
Principal Investigator, Theodosius Dobzhansky Center For Genome Informatics, St.Petersburg,
Russia
Associate Professor, Institute for Personalized Medicine, Fox chase Cancer Center, PA, USA

Research focus:

Bioinformatics, Genomics, Metagenomics, Genome sequencing, Genome assembly, Comparative genomics

Selected Publications:

Books and Review

Lapidus, A. (2009) Genome Sequence Databases: Sequencing and Assembly. Encyclopedia of Microbiology. (Moselio Schaechter, Editor), pp. 196-210 Oxford: Elsevier.

Kunin V., Copeland A., Lapidus A., Mavromatis K., Hugenholtz P. (2009) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev. 72(4):557-78, Review.

Chistoserdova L., Chen S. W., Lapidus A., Lidstrom M. E. (2003) Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. May;185(10):2980-7. Review.

Other publications:

Abakumov E.V., Loyko S.V., Istigechev G.I., Kulemzina A.I., Lashchinskiy N.N., Andronov E.E., Lapidus A.L.. Soils of Chernevaya taiga of western Siberia — morphology, agrochemical features, microbiome. Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2020, Vol. 55, № 5, p. 1018-1039.
doi: 10.15389/agrobiology.2020.5.1018eng

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., San R.J., Kubicek C. P., Schmoll M., Gaskell J., Hammel K.E., St John F. J., Vanden Wymelenberg A., Sabat G., Splinter Bondurant 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. (2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A. Apr 3;109(14):5458-63. Epub 2012 Mar 20.

Padamsee M., Kumar T. K., Riley R., Binder M., Boyd A., Calvo A. M., Furukawa K., Hesse C., Hohmann S., James T. Y., LaButti K., Lapidus A., Lindquist E., Lucas S., Miller K., Shantappa S., Grigoriev I. V., Hibbett D. S., McLaughlin D. J., Spatafora J. W., Aime M. C. (2012). The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol. Mar; 49(3): 217-26. Epub 2012 Feb 4.

Frese S. A., Benson A. K., Tannock G. W., Loach D. M., Kim J., Zhang M., Oh P. L., Heng N. C., Patil P. B., Juge N., Mackenzie D. A., Pearson B. M., Lapidus A., Dalin E., Tice H., Goltsman E., Land M., Hauser L., Ivanova N., Kyrpides N. C., Walter J. (2011) The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet. Feb;7(2): e1001314. Epub 2011 Feb 17.

Ran L., Larsson J., Vigil-Stenman T., Nylander J. A., Ininbergs K., Zheng W. W., Lapidus A., Lowry S., Haselkorn R., Bergman B. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One. 2010 Jul 8;5(7):e11486. Erratum in: PLoS One. 2010; 5(9)

Sieber J. R., Sims D. R., Han C., Kim E., Lykidis A., Lapidus A., McDonnald E., Rohlin L., Culley D. E., Gunsalus R., McInerney M. J. (2010) The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol. May 12. PMID: 20482737

Janssen P. J., Van Houdt R., Moors H., Monsieurs P., Morin N., Michaux A., Benotmane M. A., Leys N., Vallaeys T., Lapidus A., Monchy S., Médigue C., Taghavi S., McCorkle S., Dunn J., van der Lelie D., Mergeay M. (2010) The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One. May 5;5(5):e10433.PMID: 20463976

Woyke T., Tighe D., Mavromatis K., Clum A., Copeland A., Schackwitz W., Lapidus A., Wu D., McCutcheon J. P., McDonald B. R., Moran N. A., Bristow J., Cheng J. F. (2101) One bacterial cell, one complete genome. PLoS One. Apr 23;5(4):e10314.PMID: 20428247

Strnad H., Lapidus A., Paces J., Ulbrich P., Vlcek C., Paces V., Haselkorn R. (2010) Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol. Apr 23.

Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N. N., Kunin V., Goodwin L., Wu M., Tindall B. J., Hooper S. D., Pati A., Lykidis A., Spring S., Anderson I. J., D’haeseleer P., Zemla A., Singer M., Lapidus A., Nolan M., Copeland A., Han C., Chen F., Cheng J. F., Lucas S., Kerfeld C., Lang E., Gronow S., Chain P., Bruce D., Rubin E. M., Kyrpides N. C., Klenk H. P., Eisen J. A. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. Dec 24;462(7276):1056-60.PMID: 20033048

Chain P. S., Grafham D. V., Fulton R. S., Fitzgerald M. G., Hostetler J., Muzny D., Ali J., Birren B., Bruce D. C., Buhay C., Cole J. R., Ding Y., Dugan S., Field D., Garrity G. M., Gibbs R., Graves T., Han C. S., Harrison S. H., Highlander S., Hugenholtz P., Khouri H. M., Kodira C. D., Kolker E., Kyrpides N. C., Lang D., Lapidus A., Malfatti S. A., Markowitz V., Metha T., Nelson K. E., Parkhill J., Pitluck S., Qin X., Read T. D., Schmutz J., Sozhamannan S., Sterk P., Strausberg R. L., Sutton G., Thomson N. R., Tiedje J. M., Weinstock G., Wollam A., Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter J. C. (2009) Genomics. Genome project standards in a new era of sequencing. Science.Oct 9;326(5950):236-7. No abstract available. PMID: 19815760

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., Detter C., Han C. S., Brown M. V., Robb F. T., Kjelleberg S., Cavicchioli R. (2009) The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15527-33. Epub 2009 Sep 8.PMID: 19805210

Salinero K. K., Keller K., Feil W. S., Feil H., Trong S., Di Bartolo G., Lapidus A. (2009) Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics. Aug 3;10:351.PMID: 19650930

Kislyuk A., Lomsadze A., Lapidus A., Borodovsky M. (2009) Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl. 2009;5(4):458-77.PMID: 19640832

Penn K., Jenkins C., Nett M., Udwary D. W., Gontang E. A., McGlinchey R. P., Foster B., Lapidus A., Podell S., Allen E. E., Moore B. S., Jensen P. R. (2009) Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria, ISME J. May 28.

Herlemann D. P., Geissinger O., Ikeda-Ohtsubo W., Kunin V., Sun H., Lapidus A., Hugenholtz P., Brune A. Genomic analysis of “Elusimicrobium minutum,” the first cultivated representative of the phylum “Elusimicrobia” (formerly termite group 1). (2009) Appl Environ Microbiol. May;75(9):2841-9.

Sela D. A., Chapman J., Adeuya A., Kim J. H., Chen F., Whitehead T. R., Lapidus A., Rokhsar D. S., Lebrilla C. B., German J. B., Price N. P., Richardson P. M., Mills D. A. (2008) The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18964-9. Epub 2008 Nov 24.

Chivian D., Brodie E. L., Alm E. J, Culley D. E., Dehal P. S., Desantis T. Z., Gihring T. M, Lapidus A., Lin L. H., Lowry S. R., Moser D. P., Richardson P. M., Southam G., Wanger G., Pratt L. M., Andersen G. L., Hazen T. C., Brockman F. J., Arkin A. P., Onstott T. C. (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science. Oct 10;322(5899):275-8.

Kalyuzhnaya M. G, Lapidus A., Ivanova N., Copeland A. C., McHardy A. C., Szeto E., Salamov A., Grigoriev I. V., Suciu D., Levine S. R., Markowitz V. M., Rigoutsos I., Tringe S. G., Bruce D. C., Richardson P. M., Lidstrom M. E., Chistoserdova L. (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. Sep;26(9):1029-34.

Mavromatis K., Ivanova N., Shapiro H., Barry K., Goltsman E., McHardy A. C., Rigoutsos I., Salamov A., Korzeniewski F., Land M., Lapidus A., Grigoriev I., Richardson P., Hugenholtz P., Kyrpides N. C. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods. 2007 Jun;4(6):495-500.

Lapidus A.,Goltsman E., Auger S., Galleron N., Segurens B., Dossat C., Land M. L., Broussolle V., Brillard J., Guinebretiere M. H., Sanchis V., Nguen-The C., Lereclus D., Richardson P., Wincker P., Weissenbach J., Ehrlich S. D., Sorokin A. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact. 2008 , Jan30, 171(2):236-49.

Reslewic S., Zhou S., Place M., Zhang Y., Briska A., Goldstein S., Churas C., Runnheim R., Forrest D., Lim A., Lapidus A., Han C. S., Roberts G. P., Schwartz D. C. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl Environ Microbiol. 2005 Sep;71(9):5511-22.

Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V., Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M., Goltsman E., Larsen N., D’Souza M., Walunas T., Grechkin Y., Pusch G., Haselkorn R., Fonstein M., Ehrlich S. D., Overbeek R., Kyrpides N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003 May 1;423(6935):87-91.

Lapidus A., Galleron N., Andersen J. T., Jørgensen P. L., Ehrlich S. D., Sorokin A. Co-linear scaffold of the Bacillus licheniformis and Bacillus subtilis genomes and its use to compare their competence genes. FEMS Microbiol Lett. 2002 Mar 19;209(1):23-30.

Lapidus A., Galleron N., Sorokin A., Ehrlich S.D. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region. Microbiology. 1997 Nov;143 ( Pt 11): 3431-41.

Sorokin A., Lapidus A., Capuano V., Galleron N., Pujic P., Ehrlich S.D. A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing. Genome Res. 1996 May;6(5):448-53.

Lapidus A., Mochul’skii A. V., Podkovyrov S. M., Lebedeva M. I., Antipin A. A., Izotova L. S., Zagnit’ko O. P., Komolova G. S., Klesov A. A., Veiko V. P., et al. Expression of the hAng gene in Escherichia coli; isolation and characterization of human recombinant Ser-(-1) angiogenin. Biomed Sci. 1990;1(6):597-604.

Publications

  1. Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A and Finn RD. MGnify: the microbiome analysis resource in 2020 Nucleic Acids Research, 2020
  2. Andrey D Prjibelski , Alla Mikheenko , Anoushka Joglekar, Dmitry Meleshko , Alla L Lapidus , Hagen Tilgner IsoQuant: isoform analysis and quantification with long error-prone transcriptomic reads (talk), 2020
  4. Antipov D. , Bushmanova E. , Dvorkina T. , Gurevich A. , Kunyavskaya O. , Shlemov A., Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Korobeynikov A. SPAdes Family of Tools for Genome Assembly and Analysis (poster), 2019
  5. Antipov D. , Rayko M. , Lapidus A. L. , Korobeynikov A. metaplasmidSPAdes: Plasmid Detection and Assembly in Genomic and Metagenomic Datasets (talk), 2019
  6. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018
  7. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. L. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , and Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018
  8. Lapidus A. L. Center for Algorithmic Biotechnology of St. Petersburg State University and the smart programs that help with data analysis (talk), 2018
  9. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes: is there anything new we could develop? (talk), 2017
  10. Lapidus A. , Antipov D. , Bankevich A. , Bushmanova E. , Korobeynikov A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
  11. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
  13. Antipov D., Hartwick N., Shen M., Raiko M., Lapidus A., Pevzner P. A. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data. Bioinformatics, 2016
  19. Lapidus A., Antipov D., Bankevich A., Gurevich A., Korobeynikov A., Nurk S., Prjibelski A., Safonova Y., Vasilinetc I., Pevzner P. A. New Frontiers of Genome Assembly with SPAdes 3.0. (poster), 2014
  21. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Clingenpeel S., Woyke T., Tesler G., Alekseyev M. A., Pevzner P. A. Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes in Computer Science, 2013
  22. Lapidus A. Genome assembly and finishing–why high quality references are needed. , 2013
  23. Lapidus A. Bacterial genome assembly. , 2013