Алла Лапидус

Position:
alapidus

Alla Lapidus, Ph.D., joined the lab in 2012 from the Fox Chase Cancer Center, PA, USA. Dr. Lapidus received her master 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:

Principal Investigator, Theodosius Dobzhansky Center For Genome Informatics, St.Petersburg,
Russia (http://dobzhanskycenter.bio.spbu.ru/)
Associate Director, Algorithmic Biology Lab, St. Petersburg, Russia (http://bioinf.spbau.ru/en/)
Associate Professor, Institute for Personalized Medicine, Fox chase Cancer Center, PA, USA (http://www.fccc.edu/research/pid/lapidus/index.html)

Research focus:
Genomics, Genome sequencing, Genome assembly, Clinical sequencing using new sequencing technologies, Comparative sequence analysis, Bioinformatics

Books and Review

  • Lapidus, A. L. (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 SW, Lapidus A, Lidstrom ME. (2003) Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. May;185(10):2980-7. Review.
      Other publications:

      1. Roberts JL, Buckley RH, Luo B, Pei J, Lapidus A, Peri S, Wei Q, Shin J, Parrott RE, Dunbrack RL Jr, Testa JR, Zhong XP, Wiest DL. (2012) CD45-deficient severe combined immunodeficiency caused by uniparental disomy. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10456-61.
      2. Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, San RJ, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter Bondurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, 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.
      3. Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC. (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 SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NC, Patil PB, Juge N, Mackenzie DA, Pearson BM, Lapidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC, 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.

      4. Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, 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)
      5. Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ. (2010) The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol. May 12. PMID: 20482737
      6. Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, 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
      7. 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. (2101) One bacterial cell, one complete genome. PLoS One. Apr 23;5(4):e10314.PMID: 20428247
      8. 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.
      9. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. Dec 24;462(7276):1056-60.PMID: 20033048
      10. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC. (2009) Genomics. Genome project standards in a new era of sequencing. Science. Oct 9;326(5950):236-7. No abstract available. PMID: 19815760
      11. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, 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
      12. Salinero KK, Keller K, Feil WS, 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
      13. Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. (2009) Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl. 2009;5(4):458-77.PMID: 19640832
      14. Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. (2009) Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria, ISME J. May 28.
      15. Herlemann DP, 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.
      16. Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. (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.
      17. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, Desantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC. (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science. Oct 10;322(5899):275-8.
      18. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L. (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. Sep;26(9):1029-34.
      19. Mavromatis K, Ivanova N, Shapiro H, Barry K, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods. 2007 Jun;4(6):495-500.
      20. Lapidus A, Goltsman E, Auger S, Galleron N, Segurens B, Dossat C, Land ML, Broussolle V, Brillard J, Guinebretiere MH, Sanchis V, Nguen-The C, Lereclus D, Richardson P, Wincker P, Weissenbach J, Ehrlich SD, 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.
      21. Reslewic S, Zhou S, Place M, Zhang Y, Briska A, Goldstein S, Churas C, Runnheim R, Forrest D, Lim A, Lapidus A, Han CS, Roberts GP, Schwartz DC. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl Environ Microbiol. 2005 Sep;71(9):5511-22.
      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 SD, Overbeek R, Kyrpides N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003 May 1;423(6935):87-91.
      23. Lapidus A, Galleron N, Andersen JT, Jørgensen PL, Ehrlich SD, 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 SD. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region. Microbiology. 1997 Nov;143 ( Pt 11): 3431-41.

      24. Sorokin A, Lapidus A, Capuano V, Galleron N, Pujic P, Ehrlich SD. 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.
      25. Lapidus AL, Mochul’skii AV, Podkovyrov SM, Lebedeva MI, Antipin AA, Izotova LS, Zagnit’ko OP, Komolova GS, Klesov AA, Veiko VP, 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.