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• Stein LY, Yoon S, Semrau JD, Dispirito AA, Murrell JC, Vuilleumier S, Kalyuzhnaya MG, Op den Camp HJ, Bringel F, Bruce D, Cheng JF, Copeland A, Goodwin L, Han S, Hauser L, Jetten MS, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Klotz MG. Genome sequence of the obligate methanotroph, Methylosinus trichosporium strain OB3b. J Bacteriol. 2010 Oct 15. [Epub ahead of print] PubMed
• Hemme CL, Mouttaki H, Lee YJ, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina Del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Krypides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J. Genome Announcement: Sequencing of Multiple Clostridia Genomes Related to Biomass Conversion and Biofuels Production. J Bacteriol. 2010 Oct 1. [Epub ahead of print] [PubMed - as supplied by publisher] PubMed
• 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. PubMed
• Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ. The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol. 2010 May 12. [Epub ahead of print] [PubMed - as supplied by publisher]. PubMed
• 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. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One. 2010 May 5;5(5):e10433. PubMed
• 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. One bacterial cell, one complete genome. PLoS One. 2010 Apr 23;5(4):e10314. [PubMed - in process] PubMed
• Strnad H, Lapidus A, Paces J, Ulbrich P, Vlcek C, Paces V, Haselkorn R. Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol. 2010 Jul;192(13):3545-6. Epub 2010 Apr 23. PubMed
• Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, González B, Kyrpides NC. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One. 2010 Mar 22;5(3):e9729. [PubMed - in process] PubMed
• 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. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-60. PubMed
• Young M, Artsatbanov V, Beller HR, Chandra G, Chater KF, Dover LG, Goh EB, Kahan T, Kaprelyants AS, Kyrpides N, Lapidus A, Lowry SR, Lykidis A, Mahillon J, Markowitz V, Mavromatis K, Mukamolova GV, Oren A, Rokem JS, Smith MC, Young DI, Greenblatt CL. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. J Bacteriol. 2010 Feb;192(3):841-60. Epub 2009 Nov 30. PubMed
• McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet. 2009 Nov;5(11):e1000714. Epub 2009 Nov 6. PubMed
• 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. Genomics. Genome project standards in a new era of sequencing. Science. 2009 Oct 9;326(5950):236-7. No abstract available. PubMed
• 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. 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. PubMed
• McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. Epub 2009 Aug 28. PubMed
• Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G, Lapidus A. 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. 2009 Aug 3;10:351. PubMed
• Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl. 2009;5(4):458-77. PubMed
• Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N. (2009) Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS ONE, Jun 4;4(6):e5797.
• Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009 Oct;3(10):1193-203. Epub 2009 May 28. PubMed
• Aklujkar M, Krushkal J, Dibartolo G, Lapidus A, Land ML, Lovley DR. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol. 2009 May 27;9:109. PubMed
• 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). Appl Environ Microbiol. 2009 May;75(9):2841-9. Epub 2009 Mar 6.PubMed
• Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D, Chong KW, Pilak O, Chew HH, De Maere MZ, Ting L, Katrib M, Ng C, Sowers KR, Galperin MY, Anderson IJ, Ivanova N, Dalin E, Martinez M, Lapidus A, Hauser L, Land M, Thomas T, Cavicchioli R. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J. 2009 Sep;3(9):1012-35. Epub 2009 Apr 30. PubMed
• Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics. Apr 2;10(1):145. PubMed
• Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM. (2009) Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res. 2009 Jun;19(6):1033-43. Epub 2009 Mar 6. PubMed
• Lapidus, A. L. (2009) Genome Sequence Databases: Sequencing and Assembly. Encyclopedia of Microbiology. (Moselio Schaechter, Editor), pp. 196-210 Oxford: Elsevier. Chapter.
• Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P, Patel B, Kyrpides NC. Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS ONE.; 4(1): e4192. Epub 2009 Jan 15. PubMed
• Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev. 72(4):557-78, Review.
• 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. 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. PubMed
• Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH Jr, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 2008;9(11):R158. PubMed
• 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. Environmental genomics reveals a single-species ecosystem deep within Earth. Science. Oct 10;322(5899):275-8. PubMed
• 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. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. Sep;26(9):1029-34. PubMed
• Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO. “A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8102-7. PubMed
• Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N. “ Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol. 2008 Apr;190(8): 2957-65. PubMed
• Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 2007 Dec;3(12):e231. PubMed
• Auger S, Galleron N, Bidnenko E, Ehrlich SD, Lapidus A, Sorokin A. The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains. Appl Environ Microbiol. 2008 Feb;74(4):1276-80. PubMed
• Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J; USF Genomics Class. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol. 2008 Feb;74(4):1145-56. Epub 2007 Dec 7. PubMed
• Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavrommatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS ONE. 2007 Sep 26;2(9):e955. PubMed
• Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS. - Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. PNAS USA. 2007 Jun 19;104(25):10376-81. LBNL-62942 PubMed
• 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. PubMed
• 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. PubMed
• Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol. 2007 Jun;189 (11):4020-7. PubMed
• Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB, Kyrpides N. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol. 2007 Mar; 189(6):2477-86. PubMed
• Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res. 2007 Jan;17(1):7-15. PubMed
• Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hugler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH Jr, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol. 2006 Nov;4(12):e383. PubMed
• Maeder DL, Anderson I, Brettin TS, Bruce DC, Gilna P, Han CS, Lapidus A, Metcalf WW, Saunders E, Tapia R, Sowers KR. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol. 2006 Nov;188(22):7922-31. PubMed
• Williams LE, Detter C, Barry K, Lapidus A, Summers AO. - Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing. Appl Environ Microbiol. 2006 Jul;72(7):4899-906. PubMed
• Bai X, Zhang J, Ewing A, Miller SA, Jancso Radek A, Shevchenko DV, Tsukerman K, Walunas T, Lapidus A, Campbell JW, Hogenhout SA. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol. 2006 May;188(10):3682-96. PubMed
• Kalyuzhnaya MG, Nercessian O, Lapidus A, Chistoserdova L. Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenome. Environ Microbiol. 2005 Dec;7(12):1909-16. PubMed
• 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. PubMed
• Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, Markd'Souza, Larsen N, Pusch G, Liolios K, Grechkin Y, Lapidus A, Goltsman E, Chu L, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N, Ivanova N. Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis. FEMS Microbiol Lett. 2005 Sep 15;250(2):175-84. PubMed
• Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, Land M, Richardson PM, Kyrpides NC, Ivanova N, Lindow SE. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11064-9. PubMed
• Oren A, Larimer F, Richardson P, Lapidus A, Csonka LN. How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles. 2005 Aug;9(4):275-9. PubMed
• Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 2005 Apr;3(4):e121. PubMed
• Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004 Dec;22(12):1554-8. PubMed
• Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez de Leon A, Xiang H, Gusti V, Clausen IG, Olsen PB, Rasmussen MD, Andersen JT, Jørgensen PL, Larsen TS, Sorokin A, Bolotin A, Lapidus A, Galleron N, Ehrlich SD, Berka RM. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol. 2004;5(10):R77. PubMed
• Chistoserdova L, Jenkins C, Kalyuzhnaya MG, Marx CJ, Lapidus A, Vorholt JA, Staley JT, Lidstrom ME. The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol Biol Evol. 2004 Jul;21(7):1234-41. PubMed
• Kapatral V, Ivanova N, Anderson I, Reznik G, Bhattacharyya A, Gardner WL, Mikhailova N, Lapidus A, Larsen N, D'Souza M, Walunas T, Haselkorn R, Overbeek R, Kyrpides N. Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586. Genome Res. 2003 Jun;13(6A):1180-9. PubMed
• Chistoserdova L, Chen SW, Lapidus A, Lidstrom ME. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. 2003 May;185(10):2980-7. Review. PubMed
• 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. PubMed
• 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. PubMed
• Haselkorn R, Lapidus A, Kogan Y, Vlcek C, Paces J, Paces V, Ulbrich P, Pecenkova T, Rebrekov D, Milgram A, Mazur M, Cox R, Kyrpides N, Ivanova N, Kapatral V, Los T, Lykidis A, Mikhailova N, Reznik G, Vasieva O, Fonstein M. The Rhodobacter capsulatus genome. Photosynth Res. 2001;70(1):43-52. PubMed
• Antelmann H, Engelmann S, Schmid R, Sorokin A, Lapidus A, Hecker M. Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis. J Bacteriol. 1997 Dec; 179(23): 7251-6. PubMed
• 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. PubMed
• 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. PubMed
• Markaryan AN, Mashko SV, Kukel LV, Lapidus AL, Bach AN, Egorov AM. Construction of expression vectors for gene fusions on the model of beta-galactosidase-human fibroblast beta-interferon for the purpose of immunoenzyme assay. Ann N Y Acad Sci. 1991 Dec 27;646:125-35. PubMed
• Mashko SV, Mochulsky AV, Kotenko SV, Lapidus AL, Lebedeva MI, Mochulskaya NA, Izotova LS, Veiko VP, Vinetsky YP, Ketlinsky SA, et al. Use of a dual-origin temperature-controlled amplifiable replicon for optimization of human interleukin-1 beta synthesis in Escherichia coli. Gene. 1991 Jan 15;97(2):259-66. PubMed
• Mashko SV, Lapidus AL, Veiko VP, Lebedeva MI, Mochulsky AV, Shechter II, Trukhan ME, Ratmanova KI, Rebentish BA, Kaluzhsky VE, et al. TGATG vector: a new expression system for cloned foreign genes in Escherichia coli cells. Gene. 1990 Mar 30;88(1):121-6. PubMed
• Mashko SV, Kotenko SV, Veĭko VP, Lebedeva MI, Lapidus AL, Mochul'skiĭ AV, Shekhter II, Izotova LS, Vinetskiĭ IuP, Debabov VG. [The use of the TGATG vector for expression in Escherichia coli cells of cloned cDNA copy of human interleukin-1beta gene] Dokl Akad Nauk SSSR. 1990;312(1):233-6. Russian. No abstract available. PubMed
• 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. PubMed
• Trukhan ME, Gorovits RL, Lebedeva MI, Lapidus AL, Mashko SV. Effectiveness of expression of chloramphenicol acetyltransferase gene controlled by foreign regulatory regions in Escherichia coli. III. Relative effectiveness of cloned promoters of Escherichia coli and coliphages. Mol Biol (Mosk). 1988 Jul-Aug;22(4):1033-44. Russian. PubMed
• Mashko SV, Lapidus AL, Trukhan ME, Stashchuk NA, Debabov VG. Effectiveness of translation coupling in hybrid operons. Mol Biol (Mosk). 1987 Sep-Oct; 21 (5): 1310-21. Russian. PMID: 2960884. PubMed
• Mashko SV, Lapidus AL, Trukhan ME, Lebedeva MI, Podkovyrov SM. Creation of artificial hybrid operons with partially overlapping genes to achieve an expression of heterologous genes in Escherichia coli cells. Mol Biol (Mosk). 1987 Sep-Oct;21(5):1297-309. Russian. PubMed
• Mashko SV, Lebedeva MI, Podkovyrov SM, Lapidus AL, Trukhan ME. Optimization of the gene expression for human alpha F- and beta 1-interferons in Escherichia coli cells Antibiot Med Biotekhnol. 1987 Apr;32(4):248-54. Russian. PubMed
• Mashko SV, Podkovyrov SM, Trukhan ME, Lebedeva MI, Lapidus AL. Effectiveness of expression of the chloramphenicol acetyltransferase gene controlled by foreign regulator regions in Escherichia coli cells. II. Molecular cloning of promoters. Mol Biol (Mosk). 1987 Jan-Feb;21(1):73-86. Russian. PubMed
• Mashko SV, Lapidus AL, Lebedeva MI, Podkovyrov SM, Plotnikova TG. Achievement of highly efficient expression of cloned genes by constructing hybrid operons. Dokl Akad Nauk SSSR. 1984;278(6):1491-6. Russian. No abstract available. PubMed
• Khurges EM, Gening LV, Kozlov IuI, Kochetova LP, Lapidus AL. Isolation and study of hybrid plasmids carrying Escherichia coli threonine operon genes. Genetika. 1982 Oct;18(10):1620-30. Russian. PubMed

Patents

• Berka RM, , Clausen IbG, Bolotine A, Sorokine A, Lapidus A. Bottom of Form Methods for monitoring multiple gene expression. 2006. C12Q1/68M10B; C12Q1/68A6, C40B40/06. Patent application US20100753000 20100401.
• Debabov, V.G., Kozlov, Y.I., Mashko, S.V., Strongin, A.Y., Sterkin, V.E., Yurin,V.L., Lebedeva,M.I., Trukhan, M.E., Podkoviriv, S.M., Lapidus, A.L., Mochulsky, A.V., Izotova, L.S.,Ryzavskaya, A.S., Aleksenko, A.P., Kostrov, S.V., Skvortsova, M.A., Gervinskas, A.V., Nosovskaya, E.A., Evdonina, L.V., Livshitz, V.A., Bumialys, V.V., Boruchov, S.I., Plotnikova, T.G., Bolotin, A.P., Yanulaytis, A.A. Recombinant plasmid DNA pPR-IFN beta1-13, obtaining microbiological synthesis of human fibroblast interferon, the method of plasmid construction, the E.coli strain VNIIGenetica VL903 (pPR-IFN beta1-13) - the producer of the human beta 1 interferon. WO8805819, SU1703692, GB2208866, CH676996, JP1502478T, SE8803567, NL8820103, DE3890050, FI8804556, HU50871, IT1232769. Patent application US 07/279704.
• Debabov VG, Kozlov YI, Khurges EM, Livshits VA, Zhdanova NI, Gusyatiner MM, Sokolov AK, Bachina TA, Chustoserdov AY, Yankovsky NK, Mashko SV, Lapidus AL, Gavrilova OF, Rodionov OA. Novel L-threonine-producing microbacteria and a method for the production of L-threonin. 1994. European Patent EP 0 593 792 A1
• Debabov, V.G., Sverdlov, E.D., Kozlov, Yu.I.Mashko, S.V., Strongin, A.Ya., Stercin, V.E., Stercin,V.E., Yurin,V.L., Lapidus,A.L., Lebedeva,M.I., Izotova,L.S., Alexenco,A.P., Skvortsova.M.A., Ionov,Yu.A., Tzarev,S.A., Monastyrskaya, G.S. "Recombinant plasmid DNA pPR-IFNalphaF-2, deriving the microbiological synthesis of human leukocyte interferon alpha -F, E.coli strain VKPM B4567 - producer of human interferon alpha-F". 1988. RU application 4627942/13.