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Approaches for in silico finishing of microbial genome sequences.

Kremer FS, McBride AJA, Pinto LS.

Genet Mol Biol. 2017 Jul-Sep 01;40(3):553-576. doi: 10.1590/1678-4685-GMB-2016-0230.


First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order.

Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J.

PLoS One. 2017 Sep 8;12(9):e0184464. doi: 10.1371/journal.pone.0184464. eCollection 2017.


Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus.

Song L, Huang W, Kang J, Huang Y, Ren H, Ding K.

Sci Rep. 2017 Aug 14;7(1):8106. doi: 10.1038/s41598-017-08139-y.


Genome-wide signals of positive selection in strongylocentrotid sea urchins.

Kober KM, Pogson GH.

BMC Genomics. 2017 Jul 21;18(1):555. doi: 10.1186/s12864-017-3944-7.


The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome.

Almutairy M, Torng E.

PLoS One. 2017 Jul 7;12(7):e0179046. doi: 10.1371/journal.pone.0179046. eCollection 2017.


Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma.

Fontanilles M, Marguet F, Bohers É, Viailly PJ, Dubois S, Bertrand P, Camus V, Mareschal S, Ruminy P, Maingonnat C, Lepretre S, Veresezan EL, Derrey S, Tilly H, Picquenot JM, Laquerrière A, Jardin F.

Oncotarget. 2017 Jul 18;8(29):48157-48168. doi: 10.18632/oncotarget.18325.


Short Read Mapping: An Algorithmic Tour.

Canzar S, Salzberg SL.

Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):436-458. doi: 10.1109/JPROC.2015.2455551. Epub 2015 Sep 7.


TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element.

Spaller T, Groth M, Glöckner G, Winckler T.

PLoS One. 2017 Apr 13;12(4):e0175729. doi: 10.1371/journal.pone.0175729. eCollection 2017.


Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans.

Navarro-Domínguez B, Ruiz-Ruano FJ, Cabrero J, Corral JM, López-León MD, Sharbel TF, Camacho JP.

Sci Rep. 2017 Apr 3;7:45200. doi: 10.1038/srep45200.


Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.

Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.


Structural Alteration of OmpR as a Source of Ertapenem Resistance in a CTX-M-15-Producing Escherichia coli O25b:H4 Sequence Type 131 Clinical Isolate.

Dupont H, Choinier P, Roche D, Adiba S, Sookdeb M, Branger C, Denamur E, Mammeri H.

Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00014-17. doi: 10.1128/AAC.00014-17. Print 2017 May.


Statistical method to compare massive parallel sequencing pipelines.

Elsensohn MH, Leblay N, Dimassi S, Campan-Fournier A, Labalme A, Roucher-Boulez F, Sanlaville D, Lesca G, Bardel C, Roy P.

BMC Bioinformatics. 2017 Mar 1;18(1):139. doi: 10.1186/s12859-017-1552-9.


Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature.

Kong HK, Law HW, Liu X, Law CO, Pan Q, Gao L, Xiong L, Lau SK, Woo PC, Lau TC.

PLoS One. 2017 Jan 13;12(1):e0169998. doi: 10.1371/journal.pone.0169998. eCollection 2017.


A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data.

Hintzsche JD, Robinson WA, Tan AC.

Int J Genomics. 2016;2016:7983236. doi: 10.1155/2016/7983236. Epub 2016 Dec 14. Review.


Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions.

Haq IU, Dini-Andreote F, van Elsas JD.

Microb Ecol. 2017 Jan;73(1):236-252. doi: 10.1007/s00248-016-0885-7. Epub 2016 Nov 14.


A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut.

Lourenço M, Ramiro RS, Güleresi D, Barroso-Batista J, Xavier KB, Gordo I, Sousa A.

PLoS Genet. 2016 Nov 3;12(11):e1006420. doi: 10.1371/journal.pgen.1006420. eCollection 2016 Nov.


muBLASTP: database-indexed protein sequence search on multicore CPUs.

Zhang J, Misra S, Wang H, Feng WC.

BMC Bioinformatics. 2016 Nov 4;17(1):443.


In vivo continuous evolution of genes and pathways in yeast.

Crook N, Abatemarco J, Sun J, Wagner JM, Schmitz A, Alper HS.

Nat Commun. 2016 Oct 17;7:13051. doi: 10.1038/ncomms13051.


Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species.

Linz B, Ivanov YV, Preston A, Brinkac L, Parkhill J, Kim M, Harris SR, Goodfield LL, Fry NK, Gorringe AR, Nicholson TL, Register KB, Losada L, Harvill ET.

BMC Genomics. 2016 Sep 30;17(1):767.

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