REPuter: the manifold applications of repeat analysis on a genomic scale

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
URN
urn:nbn:de:0070-pub-17733359
Autor*in
Kurtz, Stefan; Choudhuri, Jomuna V.; Ohlebusch, Enno; Schleiermacher, Chris; Stoye, JensUniBi ; Giegerich, RobertUniBi
Einrichtung
Technische Fakultät > AG Praktische Informatik
Abstract / Bemerkung
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
Erscheinungsjahr
2001
Zeitschriftentitel
Nucleic Acids Research
Band
29
Ausgabe
22
Seite(n)
4633-4642
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1773335

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Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research. 2001;29(22):4633-4642.
Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., & Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), 4633-4642. https://doi.org/10.1093/nar/29.22.4633
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. 2001. “REPuter: the manifold applications of repeat analysis on a genomic scale”. Nucleic Acids Research 29 (22): 4633-4642.
Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29, 4633-4642.
Kurtz, S., et al., 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), p 4633-4642.
S. Kurtz, et al., “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, vol. 29, 2001, pp. 4633-4642.
Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R.: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research. 29, 4633-4642 (2001).
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “REPuter: the manifold applications of repeat analysis on a genomic scale”. Nucleic Acids Research 29.22 (2001): 4633-4642.
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He L, Qian J, Li X, Sun Z, Xu X, Chen S., Molecules 22(2), 2017
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Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies.
M Salih RH, Majeský Ľ, Schwarzacher T, Gornall R, Heslop-Harrison P., PLoS One 12(2), 2017
PMID: 28182646
Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response.
Ivanova Z, Sablok G, Daskalova E, Zahmanova G, Apostolova E, Yahubyan G, Baev V., Front Plant Sci 8(), 2017
PMID: 28265281
The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.
Kang JS, Lee BY, Kwak M., PLoS One 12(2), 2017
PMID: 28241056
The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species.
Asaf S, Waqas M, Khan AL, Khan MA, Kang SM, Imran QM, Shahzad R, Bilal S, Yun BW, Lee IJ., Front Plant Sci 8(), 2017
PMID: 28326093
The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L.
Kong WQ, Yang JH., PeerJ 5(), 2017
PMID: 28286710
The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.
Cauz-Santos LA, Munhoz CF, Rodde N, Cauet S, Santos AA, Penha HA, Dornelas MC, Varani AM, Oliveira GC, Bergès H, Vieira ML., Front Plant Sci 8(), 2017
PMID: 28344587
The Complete Chloroplast Genome Sequences of Six Rehmannia Species.
Zeng S, Zhou T, Han K, Yang Y, Zhao J, Liu ZL., Genes (Basel) 8(3), 2017
PMID: 28294981
LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.
Zeng FC, Zhao YJ, Zhang QJ, Gao LZ., Front Plant Sci 8(), 2017
PMID: 28421083
Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium.
Yang J, Yue M, Niu C, Ma XF, Li ZH., Genes (Basel) 8(4), 2017
PMID: 28422071
Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae.
Turmel M, Otis C, Lemieux C., Sci Rep 7(1), 2017
PMID: 28428552
The genome sequence of Agrotis segetum granulovirus, isolate AgseGV-DA, reveals a new Betabaculovirus species of a slow killing granulovirus.
Gueli Alletti G, Eigenbrod M, Carstens EB, Kleespies RG, Jehle JA., J Invertebr Pathol 146(), 2017
PMID: 28442399
The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms.
Li Z, Long H, Zhang L, Liu Z, Cao H, Shi M, Tan X., Sci Rep 7(1), 2017
PMID: 28500291
Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes.
Yang J, Vázquez L, Chen X, Li H, Zhang H, Liu Z, Zhao G., Front Plant Sci 8(), 2017
PMID: 28579999
Chloroplast Genomic Resource of Paris for Species Discrimination.
Song Y, Wang S, Ding Y, Xu J, Li MF, Zhu S, Chen N., Sci Rep 7(1), 2017
PMID: 28611359
Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences.
Dong W, Xu C, Li W, Xie X, Lu Y, Liu Y, Jin X, Suo Z., Front Plant Sci 8(), 2017
PMID: 28713409
Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.
Steinrueck M, Guet CC., Elife 6(), 2017
PMID: 28738969
Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences.
Wang CL, Ding MQ, Zou CY, Zhu XM, Tang Y, Zhou ML, Shao JR., Sci Rep 7(1), 2017
PMID: 28747666
SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis.
Kang X, Hu L, Shen P, Li R, Liu D., Front Microbiol 8(), 2017
PMID: 28798740
The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus.
Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, Aïnouche A., DNA Res 24(4), 2017
PMID: 28338826
Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species.
Asaf S, Khan AL, Aaqil Khan M, Muhammad Imran Q, Kang SM, Al-Hosni K, Jeong EJ, Lee KE, Lee IJ., PLoS One 12(8), 2017
PMID: 28763486
Locus of Adhesion and Autoaggregation (LAA), a pathogenicity island present in emerging Shiga Toxin-producing Escherichia coli strains.
Montero DA, Velasco J, Del Canto F, Puente JL, Padola NL, Rasko DA, Farfán M, Salazar JC, Vidal R., Sci Rep 7(1), 2017
PMID: 28765569
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis.
Asaf S, Khan AL, Khan MA, Waqas M, Kang SM, Yun BW, Lee IJ., Sci Rep 7(1), 2017
PMID: 28790364
Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family.
Sun Y, Moore MJ, Lin N, Adelalu KF, Meng A, Jian S, Yang L, Li J, Wang H., BMC Genomics 18(1), 2017
PMID: 28793854
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua.
Shen X, Wu M, Liao B, Liu Z, Bai R, Xiao S, Li X, Zhang B, Xu J, Chen S., Molecules 22(8), 2017
PMID: 28800082
Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species.
Raman G, Park V, Kwak M, Lee B, Park S., PLoS One 12(8), 2017
PMID: 28809950
Deciphering Single Nucleotide Polymorphisms and Evolutionary Trends in Isolates of the Cydia pomonella granulovirus.
Wennmann JT, Radtke P, Eberle KE, Gueli Alletti G, Jehle JA., Viruses 9(8), 2017
PMID: 28820456
Molecular Structure and Phylogenetic Analyses of Complete Chloroplast Genomes of Two Aristolochia Medicinal Species.
Zhou J, Chen X, Cui Y, Sun W, Li Y, Wang Y, Song J, Yao H., Int J Mol Sci 18(9), 2017
PMID: 28837061
Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis.
Dabbagh N, Bennett MS, Triemer RE, Preisfeld A., PeerJ 5(), 2017
PMID: 28852596
Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis.
Li B, Lin F, Huang P, Guo W, Zheng Y., Sci Rep 7(1), 2017
PMID: 28855603
Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis.
Cai C, Wang L, Zhou L, He P, Jiao B., PLoS One 12(9), 2017
PMID: 28863197
Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships.
Zhang X, Zhou T, Kanwal N, Zhao Y, Bai G, Zhao G., Front Plant Sci 8(), 2017
PMID: 28955369
The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria.
Jiang D, Zhao Z, Zhang T, Zhong W, Liu C, Yuan Q, Huang L., Genes (Basel) 8(9), 2017
PMID: 28902130
The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species.
Chen C, Zheng Y, Liu S, Zhong Y, Wu Y, Li J, Xu LA, Xu M., PeerJ 5(), 2017
PMID: 28948105
Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.
Niu Z, Pan J, Zhu S, Li L, Xue Q, Liu W, Ding X., Front Plant Sci 8(), 2017
PMID: 29046685
The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch.) and comparison with related species of Rosaceae.
Cheng H, Li J, Zhang H, Cai B, Gao Z, Qiao Y, Mi L., PeerJ 5(), 2017
PMID: 29038765
Development of Chloroplast Genomic Resources for Oryza Species Discrimination.
Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M, Chen N., Front Plant Sci 8(), 2017
PMID: 29118779
The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae).
Wang W, Yu H, Wang J, Lei W, Gao J, Qiu X, Wang J., Int J Mol Sci 18(11), 2017
PMID: 29088105
The Complete Amomum kravanh Chloroplast Genome Sequence and Phylogenetic Analysis of the Commelinids.
Wu M, Li Q, Hu Z, Li X, Chen S., Molecules 22(11), 2017
PMID: 29104233
Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species.
Huang J, Chen R, Li X., Genes (Basel) 8(12), 2017
PMID: 29186778
The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer).
Sakulsathaporn A, Wonnapinij P, Vuttipongchaikij S, Apisitwanich S., BMC Res Notes 10(1), 2017
PMID: 29246263
Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.
Vieira Ldo N, Dos Anjos KG, Faoro H, Fraga HP, Greco TM, Pedrosa Fde O, de Souza EM, Rogalski M, de Souza RF, Guerra MP., Curr Genet 62(2), 2016
PMID: 26643654
Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae.
Cusimano N, Wicke S., New Phytol 210(2), 2016
PMID: 26671255
Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny.
Hu Y, Woeste KE, Zhao P., Front Plant Sci 7(), 2016
PMID: 28111577
Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.
Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L, Goulding D, Otto TD, Kay S, Doffinger R, Cooke FJ, Carmichael A, Lever AM, Parkhill J, MacLennan CA, Kumararatne D, Dougan G, Kingsley RA., Nat Microbiol 1(3), 2016
PMID: 27127642
Distinctive Architecture of the Chloroplast Genome in the Chlorodendrophycean Green Algae Scherffelia dubia and Tetraselmis sp. CCMP 881.
Turmel M, de Cambiaire JC, Otis C, Lemieux C., PLoS One 11(2), 2016
PMID: 26849226
Genome of Cnaphalocrocis medinalis Granulovirus, the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced.
Han G, Xu J, Liu Q, Li C, Xu H, Lu Z., PLoS One 11(2), 2016
PMID: 26848752
Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus.
Lei W, Ni D, Wang Y, Shao J, Wang X, Yang D, Wang J, Chen H, Liu C., Sci Rep 6(), 2016
PMID: 26899134
The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae).
Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z., PLoS One 11(3), 2016
PMID: 26950701
The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses.
Zhang Y, Du L, Liu A, Chen J, Wu L, Hu W, Zhang W, Kim K, Lee SC, Yang TJ, Wang Y., Front Plant Sci 7(), 2016
PMID: 27014326
Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays.
Wu TD., Algorithms Mol Biol 11(), 2016
PMID: 27110277
MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.
Shang J, Peng J, Han J., Proc SIAM Int Conf Data Min 2016(), 2016
PMID: 28174677
The Complete Chloroplast Genome of the Hare's Ear Root, Bupleurum falcatum: Its Molecular Features.
Shin DH, Lee JH, Kang SH, Ahn BO, Kim CK., Genes (Basel) 7(5), 2016
PMID: 27187480
Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae.
Lemieux C, Otis C, Turmel M., Front Plant Sci 7(), 2016
PMID: 27252715
RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data.
Catanese HN, Brayton KA, Gebremedhin AH., BMC Genomics 17(), 2016
PMID: 27260942
Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species.
Asaf S, Khan AL, Khan AR, Waqas M, Kang SM, Khan MA, Lee SM, Lee IJ., Front Plant Sci 7(), 2016
PMID: 27379132
The Complete Sequences and Ecological Roles of Two IncP-1β Plasmids, pHB44 and pBS64, Isolated from the Mycosphere of Laccaria proxima.
Zhang M, Brons JK, van Elsas JD., Front Microbiol 7(), 2016
PMID: 27445994
Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species.
Yang Y, Zhou T, Duan D, Yang J, Feng L, Zhao G., Front Plant Sci 7(), 2016
PMID: 27446185
Chloroplast genome structure in Ilex (Aquifoliaceae).
Yao X, Tan YH, Liu YY, Song Y, Yang JB, Corlett RT., Sci Rep 6(), 2016
PMID: 27378489
Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz.
Zheng W, Chen J, Hao Z, Shi J., Int J Mol Sci 17(7), 2016
PMID: 27399686
Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.
Fu J, Liu H, Hu J, Liang Y, Liang J, Wuyun T, Tan X., PLoS One 11(7), 2016
PMID: 27442423
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase.
Ma MY, Lan XR, Niu DK., PeerJ 4(), 2016
PMID: 27547574
The Complete Chloroplast Genome Sequence of the Medicinal Plant Swertia mussotii Using the PacBio RS II Platform.
Xiang B, Li X, Qian J, Wang L, Ma L, Tian X, Wang Y., Molecules 21(8), 2016
PMID: 27517885
The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads.
Shearman JR, Sonthirod C, Naktang C, Pootakham W, Yoocha T, Sangsrakru D, Jomchai N, Tragoonrung S, Tangphatsornruang S., Sci Rep 6(), 2016
PMID: 27530092
The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae.
Hao Z, Cheng T, Zheng R, Xu H, Zhou Y, Li M, Lu F, Dong Y, Liu X, Chen J, Shi J., PLoS One 11(8), 2016
PMID: 27560965
Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice.
Wang WC, Chen SY, Zhang XZ., PLoS One 11(9), 2016
PMID: 27589600
Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns in Gloeotilopsis Green Algae (Ulotrichales, Ulvophyceae).
Turmel M, Otis C, Lemieux C., Genome Biol Evol 8(9), 2016
PMID: 27503298
The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae).
Chaney L, Mangelson R, Ramaraj T, Jellen EN, Maughan PJ., Appl Plant Sci 4(9), 2016
PMID: 27672525
Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome.
Aljohi HA, Liu W, Lin Q, Zhao Y, Zeng J, Alamer A, Alanazi IO, Alawad AO, Al-Sadi AM, Hu S, Yu J., PLoS One 11(10), 2016
PMID: 27736909
Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species.
Zhou T, Chen C, Wei Y, Chang Y, Bai G, Li Z, Kanwal N, Zhao G., Front Plant Sci 7(), 2016
PMID: 27790228
Dynamic Interplay between Nucleoid Segregation and Genome Integrity in Chlamydomonas Chloroplasts.
Odahara M, Kobayashi Y, Shikanai T, Nishimura Y., Plant Physiol 172(4), 2016
PMID: 27756821
The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family.
Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, Michael TP, Varani AM., PLoS One 11(10), 2016
PMID: 27764252
Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae).
Brouard JS, Turmel M, Otis C, Lemieux C., PeerJ 4(), 2016
PMID: 27812423
The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae.
Yao X, Liu YY, Tan YH, Song Y, Corlett RT., PeerJ 4(), 2016
PMID: 27917320
Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae.
Shen L, Guan Q, Amin A, Zhu W, Li M, Li X, Zhang L, Tian J., Springerplus 5(1), 2016
PMID: 27995013
Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform.
Chen X, Li Q, Li Y, Qian J, Han J., Front Plant Sci 6(), 2015
PMID: 25705213
Repetitive genomic sequences as a substrate for homologous integration in the Rhizopus oryzae genome.
Yuzbashev TV, Larina AS, Vybornaya TV, Yuzbasheva EY, Gvilava IT, Sineoky SP., Fungal Biol 119(6), 2015
PMID: 25986546
RECG maintains plastid and mitochondrial genome stability by suppressing extensive recombination between short dispersed repeats.
Odahara M, Masuda Y, Sato M, Wakazaki M, Harada C, Toyooka K, Sekine Y., PLoS Genet 11(3), 2015
PMID: 25769081
Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.
Curci PL, De Paola D, Danzi D, Vendramin GG, Sonnante G., PLoS One 10(3), 2015
PMID: 25774672
Characterization and phylogenetic analysis of the mitochondrial genome of Shiraia bambusicola reveals special features in the order of pleosporales.
Shen XY, Li T, Chen S, Fan L, Gao J, Hou CL., PLoS One 10(3), 2015
PMID: 25790308
Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata].
Yan L, Lai X, Li X, Wei C, Tan X, Zhang Y., PLoS One 10(4), 2015
PMID: 25874767
Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats.
Hu S, Sablok G, Wang B, Qu D, Barbaro E, Viola R, Li M, Varotto C., BMC Genomics 16(), 2015
PMID: 25887666
Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring.
Wang H, Yu Y, Liu T, Pan Y, Yan S, Wang Y., Springerplus 4(), 2015
PMID: 25918685
The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene.
Williams AV, Boykin LM, Howell KA, Nevill PG, Small I., PLoS One 10(5), 2015
PMID: 25955637
Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution.
Yap JY, Rohner T, Greenfield A, Van Der Merwe M, McPherson H, Glenn W, Kornfeld G, Marendy E, Pan AY, Wilton A, Wilkins MR, Rossetto M, Delaney SK., PLoS One 10(6), 2015
PMID: 26061691
Chloroplast Genome Evolution in the Euglenaceae.
Bennett MS, Triemer RE., J Eukaryot Microbiol 62(6), 2015
PMID: 25976746
The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng.
Chen J, Hao Z, Xu H, Yang L, Liu G, Sheng Y, Zheng C, Zheng W, Cheng T, Shi J., Front Plant Sci 6(), 2015
PMID: 26136762
Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae.
Turmel M, Otis C, Lemieux C., Genome Biol Evol 7(7), 2015
PMID: 26139832
Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae.
Redwan RM, Saidin A, Kumar SV., BMC Plant Biol 15(), 2015
PMID: 26264372
Plastome Evolution in Hemiparasitic Mistletoes.
Petersen G, Cuenca A, Seberg O., Genome Biol Evol 7(9), 2015
PMID: 26319577
Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species.
Talat F, Wang K., Iran J Biotechnol 13(3), 2015
PMID: 28959299
A new member of MocR/GabR-type PLP-binding regulator of D-alanyl-D-alanine ligase in Brevibacillus brevis.
Takenaka T, Ito T, Miyahara I, Hemmi H, Yoshimura T., FEBS J 282(21), 2015
PMID: 26279274
Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis.
Li Y, Hu XD, Yang RH, Hsiang T, Wang K, Liang DQ, Liang F, Cao DM, Zhou F, Wen G, Yao YJ., Sci Rep 5(), 2015
PMID: 26370521
Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis.
Panahi B, Mohammadi SA, Ebrahimi Khaksefidi R, Fallah Mehrabadi J, Ebrahimie E., FEBS Lett 589(23), 2015
PMID: 26454178
RECA plays a dual role in the maintenance of chloroplast genome stability in Physcomitrella patens.
Odahara M, Inouye T, Nishimura Y, Sekine Y., Plant J 84(3), 2015
PMID: 26340426
The detection of inherent homologous recombination between repeat sequences in H. pylori 26695 by the PCR-based method.
Fu Y, Zepeda-Gurrola RC, Aguilar-Gutiérrez GR, Lara-Ramírez EE, De Luna-Santillana EJ, Rodríguez-Luna IC, Sánchez-Varela A, Carreño-López R, Moreno-Medina VR, Rodríguez-Pérez MA, López-Vidal Y, Guo X., Curr Microbiol 68(2), 2014
PMID: 24097137
Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae.
Wicke S, Schäferhoff B, dePamphilis CW, Müller KF., Mol Biol Evol 31(3), 2014
PMID: 24344209
Exhaustive computation of exact duplications via super and non-nested local maximal repeats.
Taillefer E, Miller J., J Bioinform Comput Biol 12(1), 2014
PMID: 24467757
A private DNA motif finding algorithm.
Chen R, Peng Y, Choi B, Xu J, Hu H., J Biomed Inform 50(), 2014
PMID: 24412700
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches.
Che D, Hasan MS, Chen B., Pathogens 3(1), 2014
PMID: 25437607
Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.
Azim MK, Khan IA, Zhang Y., Plant Mol Biol 85(1-2), 2014
PMID: 24515595
The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.
Zhang Y, Ma J, Yang B, Li R, Zhu W, Sun L, Tian J, Zhang L., Gene 540(2), 2014
PMID: 24583178
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.
Vieira Ldo N, Faoro H, Rogalski M, Fraga HP, Cardoso RL, de Souza EM, de Oliveira Pedrosa F, Nodari RO, Guerra MP., PLoS One 9(3), 2014
PMID: 24594889
Parallel continuous flow: a parallel suffix tree construction tool for whole genomes.
Comin M, Farreras M., J Comput Biol 21(4), 2014
PMID: 24597675
RepARK--de novo creation of repeat libraries from whole-genome NGS reads.
Koch P, Platzer M, Downie BR., Nucleic Acids Res 42(9), 2014
PMID: 24634442
Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants.
Civaň P, Foster PG, Embley MT, Séneca A, Cox CJ., Genome Biol Evol 6(4), 2014
PMID: 24682153
Investigation of phase shifts for different period lengths in the genomes of C. elegans, D. melanogaster and S. cerevisiae.
Pugacheva V, Frenkel F, Korotkov E., Comput Biol Chem 51(), 2014
PMID: 24840641
A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi.
Moreland RT, Nguyen AD, Ryan JF, Schnitzler CE, Koch BJ, Siewert K, Wolfsberg TG, Baxevanis AD., BMC Genomics 15(), 2014
PMID: 24773765
Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes.
Comin M, Antonello M., IEEE/ACM Trans Comput Biol Bioinform 11(3), 2014
PMID: 26356018
Chloroplast genome evolution in early diverged leptosporangiate ferns.
Kim HT, Chung MG, Kim KJ., Mol Cells 37(5), 2014
PMID: 24823358
A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).
Do HD, Kim JS, Kim JH., Genome Biol Evol 6(7), 2014
PMID: 24951560
Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.
Huang H, Shi C, Liu Y, Mao SY, Gao LZ., BMC Evol Biol 14(), 2014
PMID: 25001059
Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.
Straub SC, Moore MJ, Soltis PS, Soltis DE, Liston A, Livshultz T., Mol Phylogenet Evol 80(), 2014
PMID: 25109653
Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.
Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle J., G3 (Bethesda) 4(10), 2014
PMID: 25155272
Chloroplast genome differences between Asian and American Equisetum arvense (Equisetaceae) and the origin of the hypervariable trnY-trnE intergenic spacer.
Kim HT, Kim KJ., PLoS One 9(8), 2014
PMID: 25157804
Insights into organohalide respiration and the versatile catabolism of Sulfurospirillum multivorans gained from comparative genomics and physiological studies.
Goris T, Schubert T, Gadkari J, Wubet T, Tarkka M, Buscot F, Adrian L, Diekert G., Environ Microbiol 16(11), 2014
PMID: 25186071
Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes.
Luo H, Zhang CT, Gao F., Front Microbiol 5(), 2014
PMID: 25309521
Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species.
Lemieux C, Otis C, Turmel M., BMC Genomics 15(), 2014
PMID: 25281016
Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering.
Yang Y, Dang Y, Li Q, Lu J, Li X, Wang Y., PLoS One 9(11), 2014
PMID: 25365514
HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.
Shariat B, Movahedi NS, Chitsaz H, Boucher C., BMC Genomics 15 Suppl 10(), 2014
PMID: 25558875
Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm.
Glunčić M, Paar V., Nucleic Acids Res 41(1), 2013
PMID: 22977183
MsDetector: toward a standard computational tool for DNA microsatellites detection.
Girgis HZ, Sheetlin SL., Nucleic Acids Res 41(1), 2013
PMID: 23034809
Inverted low-copy repeats and genome instability--a genome-wide analysis.
Dittwald P, Gambin T, Gonzaga-Jauregui C, Carvalho CM, Lupski JR, Stankiewicz P, Gambin A., Hum Mutat 34(1), 2013
PMID: 22965494
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes.
Gao F, Luo H, Zhang CT., Nucleic Acids Res 41(database issue), 2013
PMID: 23093601
Emergence and global spread of epidemic healthcare-associated Clostridium difficile.
He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D'Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD., Nat Genet 45(1), 2013
PMID: 23222960
NucBase, an easy to use read mapper for small RNAs.
Dufourt J, Pouchin P, Peyret P, Brasset E, Vaury C., Mob DNA 4(1), 2013
PMID: 23276284
The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.
Yi X, Gao L, Wang B, Su YJ, Wang T., Genome Biol Evol 5(4), 2013
PMID: 23538991
Tracing the evolution of streptophyte algae and their mitochondrial genome.
Turmel M, Otis C, Lemieux C., Genome Biol Evol 5(10), 2013
PMID: 24022472
The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.
Qian J, Song J, Gao H, Zhu Y, Xu J, Pang X, Yao H, Sun C, Li X, Li C, Liu J, Xu H, Chen S., PLoS One 8(2), 2013
PMID: 23460883
Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses.
Yang JB, Tang M, Li HT, Zhang ZR, Li DZ., BMC Evol Biol 13(), 2013
PMID: 23597078
A genomic distance for assembly comparison based on compressed maximal exact matches.
Garcia SP, Rodrigues JM, Santos S, Pratas D, Afreixo V, Bastos CA, Ferreira PJ, Pinho AJ., IEEE/ACM Trans Comput Biol Bioinform 10(3), 2013
PMID: 25594089
Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.
Stringer SC, Carter AT, Webb MD, Wachnicka E, Crossman LC, Sebaihia M, Peck MW., BMC Genomics 14(), 2013
PMID: 23679073
Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa.
Ahmed I, Matthews PJ, Biggs PJ, Naeem M, McLenachan PA, Lockhart PJ., Mol Ecol Resour 13(5), 2013
PMID: 23718317
Genome sequences of two dehalogenation specialists – Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region.
Pöritz M, Goris T, Wubet T, Tarkka MT, Buscot F, Nijenhuis I, Lechner U, Adrian L., FEMS Microbiol Lett 343(2), 2013
PMID: 23600617
The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.
Ma J, Yang B, Zhu W, Sun L, Tian J, Wang X., Gene 528(2), 2013
PMID: 23900198
Frequent patterns mining in multiple biological sequences.
Chen L, Liu W., Comput Biol Med 43(10), 2013
PMID: 24034736
PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes.
Chen GL, Chang YJ, Hsueh CH., Bioinformatics 29(21), 2013
PMID: 23958725
Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae).
Do HD, Kim JS, Kim JH., Gene 530(2), 2013
PMID: 23973725
Comparative chloroplast genomes of camellia species.
Yang JB, Yang SX, Li HT, Yang J, Li DZ., PLoS One 8(8), 2013
PMID: 24009730
Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum.
Li J, Zhang J, Chen H, Chen X, Lan J, Liu C., PLoS One 8(8), 2013
PMID: 23991034
Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family.
Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM., Plant Cell 25(10), 2013
PMID: 24143802
Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.
Li R, Ma PF, Wen J, Yi TS., PLoS One 8(10), 2013
PMID: 24205264
Insights from the complete chloroplast genome into the evolution of Sesamum indicum L.
Zhang H, Li C, Miao H, Xiong S., PLoS One 8(11), 2013
PMID: 24303020
The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene.
Pombert JF, Otis C, Turmel M, Lemieux C., PLoS One 8(12), 2013
PMID: 24386369
Efficient maximal repeat finding using the burrows-wheeler transform and wavelet tree.
Külekci MO, Vitter JS, Xu B., IEEE/ACM Trans Comput Biol Bioinform 9(2), 2012
PMID: 21968959
A new efficient data structure for storage and retrieval of multiple biosequences.
Steinbiss S, Kurtz S., IEEE/ACM Trans Comput Biol Bioinform 9(2), 2012
PMID: 22084150
Searching microsatellites in DNA sequences: approaches used and tools developed.
Grover A, Aishwarya V, Sharma PC., Physiol Mol Biol Plants 18(1), 2012
PMID: 23573036
The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements.
Kidd MJ, Chen Z, Wang Y, Jackson KJ, Zhang L, Boyd SD, Fire AZ, Tanaka MM, Gaëta BA, Collins AM., J Immunol 188(3), 2012
PMID: 22205028
Mutational dynamics of aroid chloroplast genomes.
Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, Lockhart PJ., Genome Biol Evol 4(12), 2012
PMID: 23204304
The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.
Zhang T, Fang Y, Wang X, Deng X, Zhang X, Hu S, Yu J., PLoS One 7(1), 2012
PMID: 22291979
High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease.
Okoro CK, Kingsley RA, Quail MA, Kankwatira AM, Feasey NA, Parkhill J, Dougan G, Gordon MA., Clin Infect Dis 54(7), 2012
PMID: 22318974
Distribution of the vanG-like gene cluster in Clostridium difficile clinical isolates.
Ammam F, Marvaud JC, Lambert T., Can J Microbiol 58(4), 2012
PMID: 22409319
Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.
Pellegrini M, Renda ME, Vecchio A., BMC Bioinformatics 13 Suppl 4(), 2012
PMID: 22536970
The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants.
Liu Y, Wang B, Cui P, Li L, Xue JY, Yu J, Qiu YL., PLoS One 7(4), 2012
PMID: 22511984
The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.
Yi DK, Lee HL, Sun BY, Chung MY, Kim KJ., Mol Cells 33(5), 2012
PMID: 22555800
Sequencing and analysis of the complete genome of Rana grylio virus (RGV).
Lei XY, Ou T, Zhu RL, Zhang QY., Arch Virol 157(8), 2012
PMID: 22543635
Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora).
Nie X, Lv S, Zhang Y, Du X, Wang L, Biradar SS, Tan X, Wan F, Weining S., PLoS One 7(5), 2012
PMID: 22606302
Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L.
Yi DK, Kim KJ., PLoS One 7(5), 2012
PMID: 22606240
Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae.
Wagner DD, Hug LA, Hatt JK, Spitzmiller MR, Padilla-Crespo E, Ritalahti KM, Edwards EA, Konstantinidis KT, Löffler FE., BMC Genomics 13(), 2012
PMID: 22616984
Extensive variation in surface lipoprotein gene content and genomic changes associated with virulence during evolution of a novel North American house finch epizootic strain of Mycoplasma gallisepticum.
Tulman ER, Liao X, Szczepanek SM, Ley DH, Kutish GF, Geary SJ., Microbiology 158(pt 8), 2012
PMID: 22628486
A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome.
Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, Yu X, Zhang X, Hu S, Al-Mssallem IS, Yu J., PLoS One 7(5), 2012
PMID: 22655034
Detection of dispersed short tandem repeats using reversible jump Markov chain Monte Carlo.
Liang T, Fan X, Li Q, Li SY., Nucleic Acids Res 40(19), 2012
PMID: 22753023
BpMatch: an efficient algorithm for a segmental analysis of genomic sequences.
Felicioli C, Marangoni R., IEEE/ACM Trans Comput Biol Bioinform 9(4), 2012
PMID: 22350206
Four chromosome replication origins in the archaeon Pyrobaculum calidifontis.
Pelve EA, Lindås AC, Knöppel A, Mira A, Bernander R., Mol Microbiol 85(5), 2012
PMID: 22812406
Genotypic homogeneity of multidrug resistant S. Typhimurium infecting distinct adult and childhood susceptibility groups in Blantyre, Malawi.
Msefula CL, Kingsley RA, Gordon MA, Molyneux E, Molyneux ME, MacLennan CA, Dougan G, Heyderman RS., PLoS One 7(7), 2012
PMID: 22848711
The organelle genomes of Hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins.
Zhang T, Hu S, Zhang G, Pan L, Zhang X, Al-Mssallem IS, Yu J., PLoS One 7(7), 2012
PMID: 22870184
Complete genome sequence of Streptococcus mutans GS-5, a serotype c strain.
Biswas S, Biswas I., J Bacteriol 194(17), 2012
PMID: 22887682
Unusual and typical features of a novel restorer-of-fertility gene of sugar beet (Beta vulgaris L.).
Matsuhira H, Kagami H, Kurata M, Kitazaki K, Matsunaga M, Hamaguchi Y, Hagihara E, Ueda M, Harada M, Muramatsu A, Yui-Kurino R, Taguchi K, Tamagake H, Mikami T, Kubo T., Genetics 192(4), 2012
PMID: 22997236
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E, Wain J, Heyderman RS, Obaro S, Alonso PL, Mandomando I, MacLennan CA, Tapia MD, Levine MM, Tennant SM, Parkhill J, Dougan G., Nat Genet 44(11), 2012
PMID: 23023330
The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
Wang W, Wu Y, Messing J., PLoS One 7(10), 2012
PMID: 23056432
Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032.
Jochmann N, Götker S, Tauch A., Microbiology 157(pt 1), 2011
PMID: 20847010
Microbial diversity in saliva of oral squamous cell carcinoma.
Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D., FEMS Immunol Med Microbiol 61(3), 2011
PMID: 21205002
New implications on genomic adaptation derived from the Helicobacter pylori genome comparison.
Lara-Ramírez EE, Segura-Cabrera A, Guo X, Yu G, García-Pérez CA, Rodríguez-Pérez MA., PLoS One 6(2), 2011
PMID: 21387011
Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers.
Gao L, Zhou Y, Wang ZW, Su YJ, Wang T., BMC Plant Biol 11(), 2011
PMID: 21486489
The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.
Brouard JS, Otis C, Lemieux C, Turmel M., Genome Biol Evol 3(), 2011
PMID: 21546564
High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae).
Zhang YJ, Ma PF, Li DZ., PLoS One 6(5), 2011
PMID: 21655229
REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes.
Chung BI, Lee KH, Shin KS, Kim WC, Kwon DN, You RN, Lee YK, Cho K, Cho DH., Genomics 98(5), 2011
PMID: 21803149
Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics.
Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L., Genome 54(8), 2011
PMID: 21793699
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
Janicki M, Rooke R, Yang G., Chromosome Res 19(6), 2011
PMID: 21850457
Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin.
Rodríguez-Moreno L, González VM, Benjak A, Martí MC, Puigdomènech P, Aranda MA, Garcia-Mas J., BMC Genomics 12(), 2011
PMID: 21854637
Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses.
Fleetwood DJ, Khan AK, Johnson RD, Young CA, Mittal S, Wrenn RE, Hesse U, Foster SJ, Schardl CL, Scott B., Genome Biol Evol 3(), 2011
PMID: 21948396
The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution.
Liu Y, Xue JY, Wang B, Li L, Qiu YL., PLoS One 6(10), 2011
PMID: 21998706
The evolution of the tape measure protein: units, duplications and losses.
Belcaid M, Bergeron A, Poisson G., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22151602
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.
Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R., PLoS One 6(10), 2011
PMID: 22003381
The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria.
Georgiades K, Raoult D., Biol Direct 6(), 2011
PMID: 22014084
Complete sequence, analysis and organization of the Orgyia leucostigma nucleopolyhedrovirus genome.
Thumbi DK, Eveleigh RJ, Lucarotti CJ, Lapointe R, Graham RI, Pavlik L, Lauzon HA, Arif BM., Viruses 3(11), 2011
PMID: 22163346
The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts.
Xue JY, Liu Y, Li L, Wang B, Qiu YL., Curr Genet 56(1), 2010
PMID: 19998039
The complete chloroplast genome of tall fescue (Lolium arundinaceum; Poaceae) and comparison of whole plastomes from the family Poaceae.
Cahoon AB, Sharpe RM, Mysayphonh C, Thompson EJ, Ward AD, Lin A., Am J Bot 97(1), 2010
PMID: IND44306593
The mitochondrial genome of the entomoparasitic green alga helicosporidium.
Pombert JF, Keeling PJ., PLoS One 5(1), 2010
PMID: 20126458
Comparative genomic analyses of attenuated strains of Mycoplasma gallisepticum.
Szczepanek SM, Tulman ER, Gorton TS, Liao X, Lu Z, Zinski J, Aziz F, Frasca S, Kutish GF, Geary SJ., Infect Immun 78(4), 2010
PMID: 20123709
A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii.
Turmel M, Otis C, Lemieux C., J Mol Evol 70(2), 2010
PMID: 20135105
The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth.
Ayala-del-Río HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, Murray A, Thomashow M, Tiedje JM., Appl Environ Microbiol 76(7), 2010
PMID: 20154119
Recombination and the maintenance of plant organelle genome stability.
Maréchal A, Brisson N., New Phytol 186(2), 2010
PMID: 20180912
The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum.
Imanian B, Pombert JF, Keeling PJ., PLoS One 5(5), 2010
PMID: 20502706
The Waddlia genome: a window into chlamydial biology.
Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G., PLoS One 5(5), 2010
PMID: 20531937
TRStalker: an efficient heuristic for finding fuzzy tandem repeats.
Pellegrini M, Renda ME, Vecchio A., Bioinformatics 26(12), 2010
PMID: 20529928
The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae.
Brouard JS, Otis C, Lemieux C, Turmel M., Genome Biol Evol 2(), 2010
PMID: 20624729
Microhomology-mediated and nonhomologous repair of a double-strand break in the chloroplast genome of Arabidopsis.
Kwon T, Huq E, Herrin DL., Proc Natl Acad Sci U S A 107(31), 2010
PMID: 20643920
RepMaestro: scalable repeat detection on disk-based genome sequences.
Askitis N, Sinha R., Bioinformatics 26(19), 2010
PMID: 20663848
The comparative analysis of a prophage remnant Lcazh1 in relation to other Lactobacillus prophages, particularly Lp3
ZHANG WY, YU DL, SUN ZH, CHEN W, HU SN, MENG H, ZHANG HP., International journal of dairy technology. 63(3), 2010
PMID: IND44393496
Mosaic graphs and comparative genomics in phage communities.
Belcaid M, Bergeron A, Poisson G., J Comput Biol 17(9), 2010
PMID: 20874413
Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia.
Sloan DB, Alverson AJ, Storchová H, Palmer JD, Taylor DR., BMC Evol Biol 10(), 2010
PMID: 20831793
The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.).
Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, Al-Mssallem IS, Yu J., PLoS One 5(9), 2010
PMID: 20856810
Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison.
Mariotti R, Cultrera NG, Díez CM, Baldoni L, Rubini A., BMC Plant Biol 10(), 2010
PMID: 20868482
The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.
Letek M, González P, Macarthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD, Vázquez-Boland JA., PLoS Genet 6(9), 2010
PMID: 20941392
Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex.
Lynch KH, Stothard P, Dennis JJ., BMC Genomics 11(), 2010
PMID: 20973964
Comparative analysis of iol clusters in Lactobacillus casei strains
Zhang WY, Sun ZH, Yu DL, Airideng C, Chen W, Meng H, Zhang HP., World J Microbiol Biotechnol 26(11), 2010
PMID: IND44437107
PCR screening and sequence analysis of iol clusters in Lactobacillus casei strains isolated from koumiss.
Zhang W, Sun Z, Sun T, Zhang H., Folia Microbiol (Praha) 55(6), 2010
PMID: 21253906
Classification of genomic islands using decision trees and their ensemble algorithms.
Che D, Hockenbury C, Marmelstein R, Rasheed K., BMC Genomics 11 Suppl 2(), 2010
PMID: 21047376
Telomere healing following DNA polymerase arrest-induced breakages is likely the main mechanism generating chromosome 4p terminal deletions.
Hannes F, Van Houdt J, Quarrell OW, Poot M, Hochstenbach R, Fryns JP, Vermeesch JR., Hum Mutat 31(12), 2010
PMID: 20886614
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.
Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR., BMC Bioinformatics 11 Suppl 12(), 2010
PMID: 21210985
Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications.
Balaresque P, Parkin EJ, Roewer L, Carvalho-Silva DR, Mitchell RJ, van Oorschot RA, Henke J, Stoneking M, Nasidze I, Wetton J, de Knijff P, Tyler-Smith C, Jobling MA., Int J Legal Med 123(1), 2009
PMID: 18553096
Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content.
Heuer H, Kopmann C, Binh CT, Top EM, Smalla K., Environ Microbiol 11(4), 2009
PMID: 19055690
Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.
Rosenstein R, Nerz C, Biswas L, Resch A, Raddatz G, Schuster SC, Götz F., Appl Environ Microbiol 75(3), 2009
PMID: 19060169
The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids.
Turmel M, Gagnon MC, O'Kelly CJ, Otis C, Lemieux C., Mol Biol Evol 26(3), 2009
PMID: 19074760
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R., Environ Microbiol 11(5), 2009
PMID: 19187283
Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22.
Volfovsky N, Oleksyk TK, Cruz KC, Truelove AL, Stephens RM, Smith MW., BMC Genomics 10(), 2009
PMID: 19171065
Cloning and sequencing of the breakpoint regions of inversion 5g fixed in Drosophila buzzatii.
Prazeres da Costa O, González J, Ruiz A., Chromosoma 118(3), 2009
PMID: 19198866
MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.
Chen Y, Zhou F, Li G, Xu Y., Gene 436(1-2), 2009
PMID: 19393167
Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications.
Kim YK, Park CW, Kim KJ., Mol Cells 27(3), 2009
PMID: 19326085
A novel heuristic for local multiple alignment of interspersed DNA repeats.
Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP., IEEE/ACM Trans Comput Biol Bioinform 6(2), 2009
PMID: 19407343
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity.
van der Burgt A, Fiers MW, Nap JP, van Ham RC., BMC Genomics 10(), 2009
PMID: 19405940
Genesis, effects and fates of repeats in prokaryotic genomes.
Treangen TJ, Abraham AL, Touchon M, Rocha EP., FEMS Microbiol Rev 33(3), 2009
PMID: 19396957
Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae.
Huang Y, Huang X, Liu H, Gong J, Ouyang Z, Cui H, Cao J, Zhao Y, Wang X, Jiang Y, Qin Q., BMC Genomics 10(), 2009
PMID: 19439104
Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome.
Becher V, Deymonnaz A, Heiber P., Bioinformatics 25(14), 2009
PMID: 19451169
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.
Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR., ISME J 3(10), 2009
PMID: 19474814
The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes.
Li L, Wang B, Liu Y, Qiu YL., J Mol Evol 68(6), 2009
PMID: 19475442
Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.
Gao L, Yi X, Yang YX, Su YJ, Wang T., BMC Evol Biol 9(), 2009
PMID: 19519899
Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist.
Mrázek J., Brief Bioinform 10(5), 2009
PMID: 19553402
The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales.
Turmel M, Otis C, Lemieux C., Mol Biol Evol 26(10), 2009
PMID: 19578159
Characterization of pNC1, a small and mobilizable plasmid for use in genetic manipulation of Desulfovibrio africanus.
Castañeda-Carrión IN, Whiteley M, Krumholz LR., J Microbiol Methods 79(1), 2009
PMID: 19631701
Repeat-associated plasticity in the Helicobacter pylori RD gene family.
Shak JR, Dick JJ, Meinersmann RJ, Perez-Perez GI, Blaser MJ., J Bacteriol 191(22), 2009
PMID: 19749042
The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts.
Wang B, Xue J, Li L, Liu Y, Qiu YL., Curr Genet 55(6), 2009
PMID: 19756627
Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity.
Arrieta-Montiel MP, Shedge V, Davila J, Christensen AC, Mackenzie SA., Genetics 183(4), 2009
PMID: 19822729
Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome.
Odom OW, Baek KH, Dani RN, Herrin DL., Plant J 53(5), 2008
PMID: 18036204
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.
Defrance M, Janky R, Sand O, van Helden J., Nat Protoc 3(10), 2008
PMID: 18802440
Multiple organism algorithm for finding ultraconserved elements.
Christley S, Lobo NF, Madey G., BMC Bioinformatics 9(), 2008
PMID: 18186941
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
Ellinghaus D, Kurtz S, Willhoeft U., BMC Bioinformatics 9(), 2008
PMID: 18194517
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution.
Janky R, van Helden J., BMC Bioinformatics 9(), 2008
PMID: 18215291
RAP: a computer program for exploring similarities in behavior sequences using random projections.
Quera V., Behav Res Methods 40(1), 2008
PMID: 18411523
Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus species.
Hu X, Fan W, Han B, Liu H, Zheng D, Li Q, Dong W, Yan J, Gao M, Berry C, Yuan Z., J Bacteriol 190(8), 2008
PMID: 18296527
Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes.
Haberle RC, Fourcade HM, Boore JL, Jansen RK., J Mol Evol 66(4), 2008
PMID: 18330485
The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences.
Brinkrolf K, Plöger S, Solle S, Brune I, Nentwich SS, Hüser AT, Kalinowski J, Pühler A, Tauch A., Microbiology 154(pt 4), 2008
PMID: 18375800
The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.
Formighieri EF, Tiburcio RA, Armas ED, Medrano FJ, Shimo H, Carels N, Góes-Neto A, Cotomacci C, Carazzolle MF, Sardinha-Pinto N, Thomazella DP, Rincones J, Digiampietri L, Carraro DM, Azeredo-Espin AM, Reis SF, Deckmann AC, Gramacho K, Gonçalves MS, Moura Neto JP, Barbosa LV, Meinhardt LW, Cascardo JC, Pereira GA., Mycol Res 112(pt 10), 2008
PMID: 18786820
Origins of replication in Sorangium cellulosum and Microcystis aeruginosa.
Gao F, Zhang CT., DNA Res 15(3), 2008
PMID: 18477575
RSAT: regulatory sequence analysis tools.
Thomas-Chollier M, Sand O, Turatsinze JV, Janky R, Defrance M, Vervisch E, Brohée S, van Helden J., Nucleic Acids Res 36(web server issue), 2008
PMID: 18495751
Genome evolution of Wolbachia strain wPip from the Culex pipiens group.
Klasson L, Walker T, Sebaihia M, Sanders MJ, Quail MA, Lord A, Sanders S, Earl J, O'Neill SL, Thomson N, Sinkins SP, Parkhill J., Mol Biol Evol 25(9), 2008
PMID: 18550617
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer.
Brouard JS, Otis C, Lemieux C, Turmel M., BMC Genomics 9(), 2008
PMID: 18558012
Detecting short tandem repeats from genome data: opening the software black box.
Merkel A, Gemmell N., Brief Bioinform 9(5), 2008
PMID: 18621747
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.
Luo Y, Xu X, Ding Z, Liu Z, Zhang B, Yan Z, Sun J, Hu S, Hu X., BMC Genomics 9(), 2008
PMID: 18700039
The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation.
Alix K, Joets J, Ryder CD, Moore J, Barker GC, Bailey JP, King GJ, Pat Heslop-Harrison JS., Plant J 56(6), 2008
PMID: 18764926
ReRep: computational detection of repetitive sequences in genome survey sequences (GSS).
Otto TD, Gomes LH, Alves-Ferreira M, de Miranda AB, Degrave WM., BMC Bioinformatics 9(), 2008
PMID: 18782453
Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.
Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND., Plant Physiol 148(4), 2008
PMID: 18842825
Refinement of macaque synteny arrangement with respect to the official rheMac2 macaque sequence assembly.
Roberto R, Misceo D, D'Addabbo P, Archidiacono N, Rocchi M., Chromosome Res 16(7), 2008
PMID: 18841486
Aggressive assembly of pyrosequencing reads with mates.
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G., Bioinformatics 24(24), 2008
PMID: 18952627
Replication of nonautonomous retroelements in soybean appears to be both recent and common.
Wawrzynski A, Ashfield T, Chen NW, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND, Innes RW., Plant Physiol 148(4), 2008
PMID: 18952860
A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
Kurtz S, Narechania A, Stein JC, Ware D., BMC Genomics 9(), 2008
PMID: 18976482
Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y.
Jobling MA, Lo IC, Turner DJ, Bowden GR, Lee AC, Xue Y, Carvalho-Silva D, Hurles ME, Adams SM, Chang YM, Kraaijenbrink T, Henke J, Guanti G, McKeown B, van Oorschot RA, Mitchell RJ, de Knijff P, Tyler-Smith C, Parkin EJ., Hum Mol Genet 16(3), 2007
PMID: 17189292
A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences.
Gupta R, Sarthi D, Mittal A, Singh K., EURASIP J Bioinform Syst Biol (), 2007
PMID: 17713591
A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies.
Lemieux C, Otis C, Turmel M., BMC Biol 5(), 2007
PMID: 17222354
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction.
Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y., Mol Biol Evol 24(4), 2007
PMID: 17251180
The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms.
Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H., Plant Biotechnol J 5(2), 2007
PMID: 17309688
A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats
Timme RE, Kuehl JV, Boore JL, Jansen RK., Am J Bot 94(3), 2007
PMID: IND43890995
Recurrent DNA inversion rearrangements in the human genome.
Flores M, Morales L, Gonzaga-Jauregui C, Domínguez-Vidaña R, Zepeda C, Yañez O, Gutiérrez M, Lemus T, Valle D, Avila MC, Blanco D, Medina-Ruiz S, Meza K, Ayala E, García D, Bustos P, González V, Girard L, Tusie-Luna T, Dávila G, Palacios R., Proc Natl Acad Sci U S A 104(15), 2007
PMID: 17389356
Consensus higher order repeats and frequency of string distributions in human genome.
Paar V, Basar I, Rosandić M, Gluncić M., Curr Genomics 8(2), 2007
PMID: 18660848
RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits.
Schijlen EG, de Vos CH, Martens S, Jonker HH, Rosin FM, Molthoff JW, Tikunov YM, Angenent GC, van Tunen AJ, Bovy AG., Plant Physiol 144(3), 2007
PMID: 17478633
Evolutionary history of chromosome 11 featuring four distinct centromere repositioning events in Catarrhini.
Cardone MF, Lomiento M, Teti MG, Misceo D, Roberto R, Capozzi O, D'Addabbo P, Ventura M, Rocchi M, Archidiacono N., Genomics 90(1), 2007
PMID: 17490852
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.
Grissa I, Vergnaud G, Pourcel C., BMC Bioinformatics 8(), 2007
PMID: 17521438
Simultaneous identification of long similar substrings in large sets of sequences.
Kleffe J, Möller F, Wittig B., BMC Bioinformatics 8 Suppl 5(), 2007
PMID: 17570866
Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes.
Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Daniell H, Clarke JL., Theor Appl Genet 115(4), 2007
PMID: 17534593
An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus.
Turmel M, Otis C, Lemieux C., BMC Genomics 8(), 2007
PMID: 17537252
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
Grissa I, Vergnaud G, Pourcel C., Nucleic Acids Res 35(web server issue), 2007
PMID: 17537822
Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.
Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK., BMC Genomics 8(), 2007
PMID: 17573971
Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae).
Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK., Mol Phylogenet Evol 45(2), 2007
PMID: 17644003
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P., BMC Bioinformatics 8(), 2007
PMID: 17577412
The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae.
de Cambiaire JC, Otis C, Turmel M, Lemieux C., BMC Genomics 8(), 2007
PMID: 17610731
Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts.
Guo X, Castillo-Ramírez S, González V, Bustos P, Fernández-Vázquez JL, Santamaría RI, Arellano J, Cevallos MA, Dávila G., BMC Genomics 8(), 2007
PMID: 17623083
Analysis of invariant sequences in 266 complete genomes.
Goto N, Kurokawa K, Yasunaga T., Gene 401(1-2), 2007
PMID: 17728079
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level.
Iannelli F, Griggio F, Pesole G, Gissi C., BMC Evol Biol 7(), 2007
PMID: 17764550
Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome.
Smith DR, Snyder M., J Mol Evol 65(4), 2007
PMID: 17922075
Mining microsatellites in eukaryotic genomes.
Sharma PC, Grover A, Kahl G., Trends Biotechnol 25(11), 2007
PMID: 17945369
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.
Aerts S, van Helden J, Sand O, Hassan BA., PLoS One 2(11), 2007
PMID: 17973026
High-throughput sequence alignment using Graphics Processing Units.
Schatz MC, Trapnell C, Delcher AL, Varshney A., BMC Bioinformatics 8(), 2007
PMID: 18070356
WindowMasker: window-based masker for sequenced genomes.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R., Bioinformatics 22(2), 2006
PMID: 16287941
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
Sobreira TJ, Durham AM, Gruber A., Bioinformatics 22(3), 2006
PMID: 16332714
DNAVis: interactive visualization of comparative genome annotations.
Fiers MW, van de Wetering H, Peeters TH, van Wijk JJ, Nap JP., Bioinformatics 22(3), 2006
PMID: 16332715
Application of a superword array in genome assembly.
Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK., Nucleic Acids Res 34(1), 2006
PMID: 16397298
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
Gerlach W, Giegerich R., Bioinformatics 22(6), 2006
PMID: 16403789
Translocation-excision-deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1.
Van Roy N, Vandesompele J, Menten B, Nilsson H, De Smet E, Rocchi M, De Paepe A, Påhlman S, Speleman F., Genes Chromosomes Cancer 45(2), 2006
PMID: 16235245
The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes.
Pombert JF, Lemieux C, Turmel M., BMC Biol 4(), 2006
PMID: 16472375
New softwares for automated microsatellite marker development.
Martins W, de Sousa D, Proite K, Guimarães P, Moretzsohn M, Bertioli D., Nucleic Acids Res 34(4), 2006
PMID: 16493138
Zygote arrest 1 gene in pig, cattle and human: evidence of different transcript variants in male and female germ cells.
Uzbekova S, Roy-Sabau M, Dalbiès-Tran R, Perreau C, Papillier P, Mompart F, Thelie A, Pennetier S, Cognie J, Cadoret V, Royere D, Monget P, Mermillod P., Reprod Biol Endocrinol 4(), 2006
PMID: 16551357
The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms.
Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H., BMC Genomics 7(), 2006
PMID: 16553962
Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes.
Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK., Theor Appl Genet 112(8), 2006
PMID: 16575560
Autonomous cytoplasmic linear plasmid pPac1-1 of Pichia acaciae: molecular structure and expression studies.
Jeske S, Meinhardt F., Yeast 23(6), 2006
PMID: 16652393
Efficient algorithms and software for detection of full-length LTR retrotransposons.
Kalyanaraman A, Aluru S., J Bioinform Comput Biol 4(2), 2006
PMID: 16819780
Decomposition of overlapping patterns by cumulative local cross-correlation.
Kogan SB., J Bioinform Comput Biol 4(2), 2006
PMID: 16819803
Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.
Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H., BMC Evol Biol 6(), 2006
PMID: 16603088
The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands.
de Cambiaire JC, Otis C, Lemieux C, Turmel M., BMC Evol Biol 6(), 2006
PMID: 16638149
Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment.
Stiens M, Schneiker S, Keller M, Kuhn S, Pühler A, Schlüter A., Appl Environ Microbiol 72(5), 2006
PMID: 16672515
Identification of consensus RNA secondary structures using suffix arrays.
Anwar M, Nguyen T, Turcotte M., BMC Bioinformatics 7(), 2006
PMID: 16677380
Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.
Arguello JR, Chen Y, Yang S, Wang W, Long M., PLoS Genet 2(5), 2006
PMID: 16715176
The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae.
Pombert JF, Beauchamp P, Otis C, Lemieux C, Turmel M., Curr Genet 50(2), 2006
PMID: 16721603
Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome.
Duffy SP, Young AM, Morin B, Lucarotti CJ, Koop BF, Levin DB., J Virol 80(14), 2006
PMID: 16809301
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs.
Dezulian T, Schaefer M, Wiese R, Weigel D, Huson DH., Nucleic Acids Res 34(web server issue), 2006
PMID: 16845036
The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.
Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK., Mol Biol Evol 23(11), 2006
PMID: 16916942
Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae.
Lindroos H, Vinnere O, Mira A, Repsilber D, Näslund K, Andersson SG., J Bacteriol 188(21), 2006
PMID: 16936024
Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum.
Bélanger AS, Brouard JS, Charlebois P, Otis C, Lemieux C, Turmel M., Mol Genet Genomics 276(5), 2006
PMID: 16944205
Mobilizable IncQ-related plasmid carrying a new quinolone resistance gene, qnrS2, isolated from the bacterial community of a wastewater treatment plant.
Bönemann G, Stiens M, Pühler A, Schlüter A., Antimicrob Agents Chemother 50(9), 2006
PMID: 16940104
The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms.
Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H., BMC Plant Biol 6(), 2006
PMID: 17010212
Browsing repeats in genomes: Pygram and an application to non-coding region analysis.
Durand P, Mahé F, Valin AS, Nicolas J., BMC Bioinformatics 7(), 2006
PMID: 17067389
Global variation in copy number in the human genome.
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME., Nature 444(7118), 2006
PMID: 17122850
XML schemas for common bioinformatic data types and their application in workflow systems.
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R., BMC Bioinformatics 7(), 2006
PMID: 17087823
RAP: a new computer program for de novo identification of repeated sequences in whole genomes.
Campagna D, Romualdi C, Vitulo N, Del Favero M, Lexa M, Cannata N, Valle G., Bioinformatics 21(5), 2005
PMID: 15374857
The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants.
Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M., Mol Genet Genomics 272(6), 2005
PMID: 15583938
Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements.
Tennstedt T, Szczepanowski R, Krahn I, Pühler A, Schlüter A., Plasmid 53(3), 2005
PMID: 15848226
Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins.
Brayton KA, Kappmeyer LS, Herndon DR, Dark MJ, Tibbals DL, Palmer GH, McGuire TC, Knowles DP., Proc Natl Acad Sci U S A 102(3), 2005
PMID: 15618402
An Eulerian path approach to local multiple alignment for DNA sequences.
Zhang Y, Waterman MS., Proc Natl Acad Sci U S A 102(5), 2005
PMID: 15668398
Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains.
Ogasawara M, Imanishi T, Moriwaki K, Gaudieri S, Tsuda H, Hashimoto H, Shiroishi T, Gojobori T, Koide T., Gene 349(), 2005
PMID: 15777662
Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein.
Schlüter A, Heuer H, Szczepanowski R, Poler SM, Schneiker S, Pühler A, Top EM., Plasmid 54(2), 2005
PMID: 16122561
Space-efficient whole genome comparisons with Burrows-Wheeler transforms.
Lippert RA., J Comput Biol 12(4), 2005
PMID: 15882139
Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae).
Kim KJ, Choi KS, Jansen RK., Mol Biol Evol 22(9), 2005
PMID: 15917497
The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages.
Pombert JF, Otis C, Lemieux C, Turmel M., Mol Biol Evol 22(9), 2005
PMID: 15930151
Finding approximate tandem repeats in genomic sequences.
Wexler Y, Yakhini Z, Kashi Y, Geiger D., J Comput Biol 12(7), 2005
PMID: 16201913
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK, Wang J., PLoS Comput Biol 1(4), 2005
PMID: 16184192
The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales.
Turmel M, Otis C, Lemieux C., BMC Biol 3(), 2005
PMID: 16236178
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.
Haft DH, Selengut J, Mongodin EF, Nelson KE., PLoS Comput Biol 1(6), 2005
PMID: 16292354
Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.
Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA., PLoS Genet 1(5), 2005
PMID: 16311624
GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.
Ben Zakour N, Gautier M, Andonov R, Lavenier D, Cochet MF, Veber P, Sorokin A, Le Loir Y., Nucleic Acids Res 32(1), 2004
PMID: 14704339
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol 5(2), 2004
PMID: 14759262
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.
Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF., Genome Res 14(3), 2004
PMID: 14962987
Transcriptional regulation of protein complexes in yeast.
Simonis N, van Helden J, Cohen GN, Wodak SJ., Genome Biol 5(5), 2004
PMID: 15128447
Chromosomal anomalies on 6p25 in iris hypoplasia and Axenfeld-Rieger syndrome patients defined on a purpose-built genomic microarray.
Ekong R, Jeremiah S, Judah D, Lehmann O, Mirzayans F, Hung YC, Walter MA, Bhattacharya S, Gant TW, Povey S, Wolfe J., Hum Mutat 24(1), 2004
PMID: 15221791
A novel algorithm for finding interspersed repeat regions.
Li D, Wang Z, Ni Q., Genomics Proteomics Bioinformatics 2(3), 2004
PMID: 15862119
Insertions generating the 5'RUNX1/3'CBFA2T1 gene in acute myeloid leukemia cases show variable breakpoints.
Specchia G, Albano F, Anelli L, Zagaria A, Liso A, La Starza R, Mancini M, Sebastio L, Giugliano E, Saglio G, Liso V, Rocchi M., Genes Chromosomes Cancer 41(1), 2004
PMID: 15236320
The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
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Bioinformatics: harvesting information for plant and crop science.
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