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Items: 1 to 50 of 399

1.

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data.

Bushmanova E, Antipov D, Lapidus A, Prjibelski AD.

Gigascience. 2019 Sep 1;8(9). pii: giz100. doi: 10.1093/gigascience/giz100.

2.

Plasmid detection and assembly in genomic and metagenomic data sets.

Antipov D, Raiko M, Lapidus A, Pevzner PA.

Genome Res. 2019 Jun;29(6):961-968. doi: 10.1101/gr.241299.118. Epub 2019 May 2.

PMID:
31048319
3.

Safety and efficacy of endoscopist-directed balanced propofol sedation during endoscopic retrograde cholangiopancreatography.

Lapidus A, Gralnek IM, Suissa A, Yassin K, Khamaysi I.

Ann Gastroenterol. 2019 May-Jun;32(3):303-311. doi: 10.20524/aog.2019.0360. Epub 2019 Feb 15.

4.

IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction.

Ershov V, Tarasov A, Lapidus A, Korobeynikov A.

J Comput Biol. 2019 Feb;26(2):124-127. doi: 10.1089/cmb.2018.0152. Epub 2018 Oct 16.

PMID:
30328692
5.

Evaluation of a new pan-enteric video capsule endoscopy system in patients with suspected or established inflammatory bowel disease - feasibility study.

Eliakim R, Spada C, Lapidus A, Eyal I, Pecere S, Fernández-Urién I, Lahat A, Costamagna G, Schwartz A, Ron Y, Yanai H, Adler S.

Endosc Int Open. 2018 Oct;6(10):E1235-E1246. doi: 10.1055/a-0677-170. Epub 2018 Oct 8.

6.

Autoprobiotics as an Approach for Restoration of Personalised Microbiota.

Suvorov A, Karaseva A, Kotyleva M, Kondratenko Y, Lavrenova N, Korobeynikov A, Kozyrev P, Kramskaya T, Leontieva G, Kudryavtsev I, Guo D, Lapidus A, Ermolenko E.

Front Microbiol. 2018 Sep 12;9:1869. doi: 10.3389/fmicb.2018.01869. eCollection 2018.

7.

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

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
8.

Microscopic colitis in patients with ulcerative colitis or Crohn's disease: a retrospective observational study and review of the literature.

Wickbom A, Bohr J, Nyhlin N, Eriksson A, Lapidus A, Münch A, Ung KA, Vigren L, Öst Å, Tysk C; Swedish Organisation for the Study of Inflammatory Bowel Disease (SOIBD).

Scand J Gastroenterol. 2018 Apr;53(4):410-416. doi: 10.1080/00365521.2018.1430252. Epub 2018 Mar 16.

PMID:
29546806
9.

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

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

10.

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

Choi DH, Jang GI, Lapidus A, Copeland A, Reddy TBK, Mukherjee S, Huntemann M, Varghese N, Ivanova N, Pillay M, Tindall BJ, Göker M, Woyke T, Klenk HP, Kyrpides NC, Cho BC.

Stand Genomic Sci. 2017 Oct 30;12:65. doi: 10.1186/s40793-017-0275-x. eCollection 2017.

11.

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

Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G.

Stand Genomic Sci. 2017 Sep 21;12:57. doi: 10.1186/s40793-017-0268-9. eCollection 2017.

12.

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

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Erratum in: Nat Biotechnol. 2018 Feb 6;36(2):196. Nat Biotechnol. 2018 Jul 6;36(7):660.

13.

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 EF, Lapidus A, Han J, Reddy TB, Mukherjee S, Pillay M, Perevalova AA, Ivanova NN, Woyke T, Kyrpides NC, Mukhopadhyay B.

Genome Announc. 2017 Apr 13;5(15). pii: e00078-17. doi: 10.1128/genomeA.00078-17.

14.

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

de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV.

Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0.

15.

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 JY, Carro L, Liu L, Gao XY, Zhang XT, Hozzein WN, Lapidus A, Huntemann M, Reddy TBK, Varghese N, Hadjithomas M, Ivanova NN, Göker M, Pillay M, Eisen JA, Woyke T, Klenk HP, Kyrpides NC, Li WJ.

Stand Genomic Sci. 2017 Feb 3;12:21. doi: 10.1186/s40793-017-0226-6. eCollection 2017.

16.

Complete Mitochondrial Genomes of Baikal Oilfishes (Perciformes: Cottoidei), Earth's Deepest-Swimming Freshwater Fishes.

Sandel MW, Aguilar A, Fast K, O'Brien S, Lapidus A, Allison DB, Teterina V, Kirilchik S.

Mitochondrial DNA B Resour. 2017;2(2):773-775. doi: 10.1080/23802359.2017.1398603. Epub 2017 Nov 7.

17.

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, Lapidus A, Barry K, Detter JC, 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 ML, Hauser L, Kyrpides N, Mikhailova N, Ye Q, Zhou J, Richardson P, Fields MW.

Genome Announc. 2016 Nov 3;4(6). pii: e01226-16. doi: 10.1128/genomeA.01226-16.

18.

Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium.

Velichko N, Rayko M, Chernyaeva E, Lapidus A, Pinevich A.

Stand Genomic Sci. 2016 Oct 18;11:82. eCollection 2016.

19.

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

Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC.

Stand Genomic Sci. 2016 Sep 10;11(1):70. doi: 10.1186/s40793-016-0194-2. eCollection 2016.

20.

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

Melton ED, Sorokin DY, Overmars L, Chertkov O, Clum A, Pillay M, Ivanova N, Shapiro N, Kyrpides NC, Woyke T, Lapidus AL, Muyzer G.

Stand Genomic Sci. 2016 Sep 8;11(1):67. doi: 10.1186/s40793-016-0184-4. eCollection 2016.

21.

Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

22.

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA.

Bioinformatics. 2016 Nov 15;32(22):3380-3387. Epub 2016 Jul 27.

PMID:
27466620
23.

Fischer-Tropsch synthesis over MOF-supported cobalt catalysts (Co@MIL-53(Al)).

Isaeva VI, Eliseev OL, Kazantsev RV, Chernyshev VV, Davydov PE, Saifutdinov BR, Lapidus AL, Kustov LM.

Dalton Trans. 2016 Jul 26;45(30):12006-14. doi: 10.1039/c6dt01394e.

PMID:
27389315
24.

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 JP, Huang S, Tindall BJ, Rohde M, Baeshen MN, Baeshen NA, Lapidus A, Copeland A, Pillay M, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Göker M, Klenk HP, Kyrpides NC, Hahnke RL.

Stand Genomic Sci. 2016 Jun 16;11:42. doi: 10.1186/s40793-016-0159-5. eCollection 2016.

25.

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

Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, Pérez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ramírez L.

PLoS Genet. 2016 Jun 13;12(6):e1006108. doi: 10.1371/journal.pgen.1006108. eCollection 2016 Jun.

26.

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 Mdel C, Land M, Hauser L, Rohde M, Göker M, Ivanova N, Woyke T, Klenk HP, Kyrpides NC.

Stand Genomic Sci. 2016 Jun 3;11:38. doi: 10.1186/s40793-016-0162-x. eCollection 2016.

27.

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

Stand Genomic Sci. 2016 Jun 3;11:37. doi: 10.1186/s40793-016-0163-9. eCollection 2016.

28.

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies.

Bushmanova E, Antipov D, Lapidus A, Suvorov V, Prjibelski AD.

Bioinformatics. 2016 Jul 15;32(14):2210-2. doi: 10.1093/bioinformatics/btw218. Epub 2016 Apr 23.

PMID:
27153654
29.

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.

Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF.

Front Microbiol. 2016 Mar 3;7:238. doi: 10.3389/fmicb.2016.00238. eCollection 2016.

30.

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, Huntemann M, Pillay M, Markowitz V, Göker M, Woyke T, Klenk HP, Kyrpides NC, Halpern M.

Stand Genomic Sci. 2016 Jan 13;11:4. doi: 10.1186/s40793-015-0127-5. eCollection 2016.

31.

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 EF, Lapidus A, Han J, Reddy TB, Pilay M, Ivanova NN, Markowitz VM, Woyke T, Kyrpides NC, Mukhopadhyay B.

Stand Genomic Sci. 2016 Jan 13;11:3. doi: 10.1186/s40793-015-0128-4. eCollection 2016.

32.

Complete genome sequence of Methanospirillum hungatei type strain JF1.

Gunsalus RP, Cook LE, Crable B, Rohlin L, McDonald E, Mouttaki H, Sieber JR, Poweleit N, Zhou H, Lapidus AL, Daligault HE, Land M, Gilna P, Ivanova N, Kyrpides N, Culley DE, McInerney MJ.

Stand Genomic Sci. 2016 Jan 6;11:2. doi: 10.1186/s40793-015-0124-8. eCollection 2016.

33.

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.

de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE.

PLoS Genet. 2015 Dec 22;11(12):e1005775. doi: 10.1371/journal.pgen.1005775. eCollection 2015 Dec. No abstract available.

34.

Genome Sequence of the Atypical Symbiotic Frankia R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium.

Pujic P, Bolotin A, Fournier P, Sorokin A, Lapidus A, Richau KH, Briolay J, Mebarki F, Normand P, Sellstedt A.

Genome Announc. 2015 Nov 25;3(6). pii: e01387-15. doi: 10.1128/genomeA.01387-15.

35.

High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.

Choi DH, Ahn C, Jang GI, Lapidus A, Han J, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Rohde M, Tindall B, Göker M, Woyke T, Klenk HP, Kyrpides NC, Cho BC.

Stand Genomic Sci. 2015 Nov 11;10:98. doi: 10.1186/s40793-015-0088-8. eCollection 2015.

36.

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.

Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, Kyrpides N, Ivanova N, Pagani I, Chain PS, Denef VJ, Woyke T, Hickey WJ.

Stand Genomic Sci. 2015 Aug 15;10:55. doi: 10.1186/s40793-015-0041-x. eCollection 2015.

37.

High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea.

Ntougias S, Lapidus A, Copeland A, Reddy TB, Pati A, Ivanova NN, Markowitz VM, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI.

Stand Genomic Sci. 2015 Aug 13;10:52. doi: 10.1186/s40793-015-0052-7. eCollection 2015.

38.

High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)).

Yassin AF, Lapidus A, Han J, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Klenk HP, Kyrpides NC.

Stand Genomic Sci. 2015 Aug 5;10:50. doi: 10.1186/s40793-015-0036-7. eCollection 2015.

39.

High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.

Sakamoto M, Lapidus AL, Han J, Trong S, Haynes M, Reddy TB, Mikhailova N, Huntemann M, Pati A, Ivanova NN, Pukall R, Markowitz VM, Woyke T, Klenk HP, Kyrpides NC, Ohkuma M.

Stand Genomic Sci. 2015 Aug 2;10:48. doi: 10.1186/s40793-015-0045-6. eCollection 2015.

40.

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

Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2015 Jul 30;10:46. doi: 10.1186/s40793-015-0032-y. eCollection 2015.

41.

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

Borisova AS, Eneyskaya EV, Bobrov KS, Jana S, Logachev A, Polev DE, Lapidus AL, Ibatullin FM, Saleem U, Sandgren M, Payne CM, Kulminskaya AA, Ståhlberg J.

FEBS J. 2015 Dec;282(23):4515-37. doi: 10.1111/febs.13509. Epub 2015 Oct 8.

42.

High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass.

Laviad S, Lapidus A, Han J, Haynes M, Reddy T, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Lang E, Rohde M, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Halpern M.

Stand Genomic Sci. 2015 May 27;10:29. doi: 10.1186/s40793-015-0010-4. eCollection 2015.

43.

High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.

McIlroy SJ, Lapidus A, Thomsen TR, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Markowitz V, Verbarg S, Woyke T, Klenk HP, Kyrpides N, Nielsen PH.

Stand Genomic Sci. 2015 Feb 27;10:23. doi: 10.1186/s40793-015-0013-1. eCollection 2015.

44.

High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass.

Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A, Ivanova NN, Markowitz VM, Pukall R, Klenk HP, Woyke T, Kyrpides NC, Halpern M.

Stand Genomic Sci. 2015 May 8;10:21. doi: 10.1186/s40793-015-0003-3. eCollection 2015.

45.

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

Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy T, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A.

Stand Genomic Sci. 2015 Feb 9;10:8. doi: 10.1186/1944-3277-10-8. eCollection 2015.

46.

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA.

Bioinformatics. 2015 Jun 15;31(12):i53-61. doi: 10.1093/bioinformatics/btv238.

47.

IgSimulator: a versatile immunosequencing simulator.

Safonova Y, Lapidus A, Lill J.

Bioinformatics. 2015 Oct 1;31(19):3213-5. doi: 10.1093/bioinformatics/btv326. Epub 2015 May 25.

PMID:
26007226
48.

Consortium of the 'bichlorophyllous' cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome-based description.

Velichko N, Chernyaeva E, Averina S, Gavrilova O, Lapidus A, Pinevich A.

Environ Microbiol Rep. 2015 Aug;7(4):623-33. doi: 10.1111/1758-2229.12298. Epub 2015 Jun 25.

PMID:
25990300
49.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW.

Genome Announc. 2015 Mar 12;3(2). pii: e00092-15. doi: 10.1128/genomeA.00092-15.

50.

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

Gao XY, Zhi XY, Li HW, Zhou Y, Lapidus A, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Tindall BJ, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Li WJ.

Stand Genomic Sci. 2015 Jan 20;10:1. doi: 10.1186/1944-3277-10-1. eCollection 2015.

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