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Items: 1 to 20 of 372

1.

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

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

Bioinformatics. 2016 Apr 23. pii: btw218. [Epub ahead of print]

PMID:
27153654
2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

PMID:
26367132
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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
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