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
 
Download
OA
Autor*in
Kurtz, Stefan; Choudhuri, Jomuna V.; Ohlebusch, Enno; Schleiermacher, Chris; Stoye, JensUniBi ; Giegerich, RobertUniBi
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

Zitieren

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. doi:10.1093/nar/29.22.4633
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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T08:48:07Z
MD5 Prüfsumme
c972349ea27e185101a4a40d6ace2101

451 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae).
Mustafina FU, Yi DK, Choi K, Shin CH, Tojibaev KS, Downie SR., Ecol Evol 9(1), 2019
PMID: 30680120
Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains.
Montero DA, Canto FD, Velasco J, Colello R, Padola NL, Salazar JC, Martin CS, Oñate A, Blanco J, Rasko DA, Contreras C, Puente JL, Scheutz F, Franz E, Vidal RM., Emerg Microbes Infect 8(1), 2019
PMID: 30924410
The Plastid Genome of Deschampsia cespitosa (Poaceae).
Chiapella JO, Barfuss MHJ, Xue ZQ, Greimler J., Molecules 24(2), 2019
PMID: 30634385
First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees.
Khan A, Asaf S, Khan AL, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Khan A, Shehzad T, Alsaady N, Al-Lawati A, Al-Rawahi A, Shinwari ZK., PLoS One 14(1), 2019
PMID: 30629590
The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species.
Li Y, Sylvester SP, Li M, Zhang C, Li X, Duan Y, Wang X., Molecules 24(2), 2019
PMID: 30641990
Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen.
Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P., Front Plant Sci 10(), 2019
PMID: 30873197
Dot2dot: accurate whole-genome tandem repeats discovery.
Genovese LM, Mosca MM, Pellegrini M, Geraci F., Bioinformatics 35(6), 2019
PMID: 30165507
Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine.
Chen X, Cui Y, Nie L, Hu H, Xu Z, Sun W, Gao T, Song J, Yao H., Biomed Res Int 2019(), 2019
PMID: 30941367
A systematic comparison of eight new plastome sequences from Ipomoea L.
Sun J, Dong X, Cao Q, Xu T, Zhu M, Sun J, Dong T, Ma D, Han Y, Li Z., PeerJ 7(), 2019
PMID: 30881765
Interspecific delimitation and relationships among four Ostrya species based on plastomes.
Jiang Y, Yang Y, Lu Z, Wan D, Ren G., BMC Genet 20(1), 2019
PMID: 30866795
Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill.
Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L., Plants (Basel) 8(4), 2019
PMID: 30987216
Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome.
Huang Y, Yang Z, Huang S, An W, Li J, Zheng X., Plants (Basel) 8(4), 2019
PMID: 30987338
ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.
Shamanskiy VA, Timonina VN, Popadin KY, Gunbin KV., BMC Genomics 20(suppl 3), 2019
PMID: 31284879
The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae.
Zhou T, Ruhsam M, Wang J, Zhu H, Li W, Zhang X, Xu Y, Xu F, Wang X., Front Genet 10(), 2019
PMID: 31156705
Genome plasticity in Candida albicans is driven by long repeat sequences.
Todd RT, Wikoff TD, Forche A, Selmecki A., Elife 8(), 2019
PMID: 31172944
CPGAVAS2, an integrated plastome sequence annotator and analyzer.
Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C., Nucleic Acids Res 47(w1), 2019
PMID: 31066451
Coding palindromes in mitochondrial genes of Nematomorpha.
Mikhailov KV, Efeykin BD, Panchin AY, Knorre DA, Logacheva MD, Penin AA, Muntyan MS, Nikitin MA, Popova OV, Zanegina ON, Vyssokikh MY, Spiridonov SE, Aleoshin VV, Panchin YV., Nucleic Acids Res 47(13), 2019
PMID: 31194871
Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae.
Khan A, Asaf S, Khan AL, Khan A, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Al-Saady N, Al-Rawahi A., PeerJ 7(), 2019
PMID: 31328036
Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales.
Lu L, Li X, Hao Z, Yang L, Zhang J, Peng Y, Xu H, Lu Y, Zhang J, Shi J, Chen J, Cheng T., Mitochondrial DNA A DNA Mapp Seq Anal 29(5), 2018
PMID: 28712318
The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales.
de Santana Lopes A, Pacheco TG, Santos KGD, Vieira LDN, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F, Rogalski M., Plant Cell Rep 37(2), 2018
PMID: 29086003
Finding Statistically Significant Repeats in Nucleic Acids and Proteins.
Jelovic AM, Mitic NS, Eshafah S, Beljanski MV., J Comput Biol 25(4), 2018
PMID: 29272145
The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses.
Chen H, Zhang W, Li X, Pan Y, Yan S, Wang Y., BMC Genomics 19(1), 2018
PMID: 29334892
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.
Guo S, Guo L, Zhao W, Xu J, Li Y, Zhang X, Shen X, Wu M, Hou X., Molecules 23(2), 2018
PMID: 29373520
Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences.
Menezes APA, Resende-Moreira LC, Buzatti RSO, Nazareno AG, Carlsen M, Lobo FP, Kalapothakis E, Lovato MB., Sci Rep 8(1), 2018
PMID: 29396532
The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis.
Chi X, Wang J, Gao Q, Zhang F, Chen S., Molecules 23(3), 2018
PMID: 29518967
Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm.
Chen H, Shao J, Zhang H, Jiang M, Huang L, Zhang Z, Yang D, He M, Ronaghi M, Luo X, Sun B, Wu W, Liu C., Front Plant Sci 9(), 2018
PMID: 29593773
Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny.
Wu Y, Liu F, Yang DG, Li W, Zhou XJ, Pei XY, Liu YG, He KL, Zhang WS, Ren ZY, Zhou KH, Ma XF, Li ZH., Front Plant Sci 9(), 2018
PMID: 29619041
Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species.
Asaf S, Khan AL, Khan MA, Shahzad R, Lubna, Kang SM, Al-Harrasi A, Al-Rawahi A, Lee IJ., PLoS One 13(3), 2018
PMID: 29596414
The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales.
Gu C, Dong B, Xu L, Tembrock LR, Zheng S, Wu Z., Molecules 23(4), 2018
PMID: 29642470
Plastome characteristics of Cannabaceae.
Zhang H, Jin J, Moore MJ, Yi T, Li D., Plant Divers 40(3), 2018
PMID: 30175293
Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species.
Meng J, Li X, Li H, Yang J, Wang H, He J., Molecules 23(5), 2018
PMID: 29701675
Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales.
Lin N, Moore MJ, Deng T, Sun H, Yang LS, Sun YX, Wang HC., Appl Plant Sci 6(4), 2018
PMID: 30131882
Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea.
Jiang M, Chen H, He S, Wang L, Chen AJ, Liu C., Int J Mol Sci 19(5), 2018
PMID: 29747436
Genome skimming provides new insight into the relationships in Ludwigia section Macrocarpon, a polyploid complex.
Liu SH, Edwards CE, Hoch PC, Raven PH, Barber JC., Am J Bot 105(5), 2018
PMID: 29791715
The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species.
Androsiuk P, Jastrzębski JP, Paukszto Ł, Okorski A, Pszczółkowska A, Chwedorzewska KJ, Koc J, Górecki R, Giełwanowska I., PeerJ 6(), 2018
PMID: 29844954
Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species.
Li Q, Chen C, Xiong C, Jin X, Chen Z, Huang W., Appl Microbiol Biotechnol 102(14), 2018
PMID: 29799088
Characterization of the Complete Mitochondrial Genome Sequences of Three Croakers (Perciformes, Sciaenidae) and Novel Insights into the Phylogenetics.
Yang H, Xia J, Zhang JE, Yang J, Zhao H, Wang Q, Sun J, Xue H, Wu Y, Chen J, Huang J, Liu L., Int J Mol Sci 19(6), 2018
PMID: 29895774
Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode.
Chen X, Zhou J, Cui Y, Wang Y, Duan B, Yao H., Front Pharmacol 9(), 2018
PMID: 30034337
Assembly of the Mitochondrial Genome in the Campanulaceae Family Using Illumina Low-Coverage Sequencing.
Lee HO, Choi JW, Baek JH, Oh JH, Lee SC, Kim CK., Genes (Basel) 9(8), 2018
PMID: 30061537
First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis.
Khan AL, Asaf S, Lee IJ, Al-Harrasi A, Al-Rawahi A., PLoS One 13(7), 2018
PMID: 30063732
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima.
Li X, Li Y, Zang M, Li M, Fang Y., Int J Mol Sci 19(8), 2018
PMID: 30126202
Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants.
Liao X, Zhao Y, Kong X, Khan A, Zhou B, Liu D, Kashif MH, Chen P, Wang H, Zhou R., Sci Rep 8(1), 2018
PMID: 30143661
Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species.
Meng XX, Xian YF, Xiang L, Zhang D, Shi YH, Wu ML, Dong GQ, Ip SP, Lin ZX, Wu L, Sun W., Molecules 23(9), 2018
PMID: 30149578
Comparative study on mitogenomes of green tide algae.
Cai C, Liu F, Jiang T, Wang L, Jia R, Zhou L, Gu K, Ren J, He P., Genetica 146(6), 2018
PMID: 30377874
Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment.
Gao R, Wang W, Huang Q, Fan R, Wang X, Feng P, Zhao G, Bian S, Ren H, Chang Y., Sci Rep 8(1), 2018
PMID: 30413776
Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq.
Osuna-Mascaró C, Rubio de Casas R, Perfectti F., Sci Rep 8(1), 2018
PMID: 30479362
Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics.
He D, Gichira AW, Li Z, Nzei JM, Guo Y, Wang Q, Chen J., Int J Mol Sci 19(12), 2018
PMID: 30486510
Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses.
Zhao Z, Wang X, Yu Y, Yuan S, Jiang D, Zhang Y, Zhang T, Zhong W, Yuan Q, Huang L., PeerJ 6(), 2018
PMID: 30533315
Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications.
Gao X, Zhang X, Meng H, Li J, Zhang D, Liu C., BMC Genomics 19(suppl 10), 2018
PMID: 30598104
Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae).
Ma Q, Li S, Bi C, Hao Z, Sun C, Ye N., Curr Genet 63(1), 2017
PMID: 27206980
The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman.
Khan AL, Al-Harrasi A, Asaf S, Park CE, Park GS, Khan AR, Lee IJ, Al-Rawahi A, Shin JH., PLoS One 12(1), 2017
PMID: 28085925
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 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 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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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 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
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
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
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
Plastome Evolution in Hemiparasitic Mistletoes.
Petersen G, Cuenca A, Seberg O., Genome Biol Evol 7(9), 2015
PMID: 26319577
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
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
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
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 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
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
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
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
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
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
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
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
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
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
Frequent patterns mining in multiple biological sequences.
Chen L, Liu W., Comput Biol Med 43(10), 2013
PMID: 24034736
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
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
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
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
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
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
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
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
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
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
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
Janicki M, Rooke R, Yang G., Chromosome Res 19(6), 2011
PMID: 21850457
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 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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Efficient algorithms and software for detection of full-length LTR retrotransposons.
Kalyanaraman A, Aluru S., J Bioinform Comput Biol 4(2), 2006
PMID: 16819780
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
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
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
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
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
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
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.
Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glöckner FO, Lupas AN, Amann R, Klenk HP., Environ Microbiol 6(9), 2004
PMID: 15305914
De novo repeat classification and fragment assembly.
Pevzner PA, Tang H, Tesler G., Genome Res 14(9), 2004
PMID: 15342561
Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements.
Doulatov S, Hodes A, Dai L, Mandhana N, Liu M, Deora R, Simons RW, Zimmerly S, Miller JF., Nature 431(7007), 2004
PMID: 15386016
The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis.
Minion FC, Lefkowitz EJ, Madsen ML, Cleary BJ, Swartzell SM, Mahairas GG., J Bacteriol 186(21), 2004
PMID: 15489423
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD., J Bacteriol 186(22), 2004
PMID: 15516593
Bioinformatics: harvesting information for plant and crop science.
King GJ., Semin Cell Dev Biol 15(6), 2004
PMID: 15561592
ZmDB, an integrated database for maize genome research.
Dong Q, Roy L, Freeling M, Walbot V, Brendel V., Nucleic Acids Res 31(1), 2003
PMID: 12519992
Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.
Glöckner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R., Proc Natl Acad Sci U S A 100(14), 2003
PMID: 12835416
Annotating large genomes with exact word matches.
Healy J, Thomas EE, Schwartz JT, Wigler M., Genome Res 13(10), 2003
PMID: 12975312
DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.
Cannon SB, Kozik A, Chan B, Michelmore R, Young ND., Genome Biol 4(10), 2003
PMID: 14519203
Frequency and coverage of trinucleotide repeats in eukaryotes.
Astolfi P, Bellizzi D, Sgaramella V., Gene 317(1-2), 2003
PMID: 14604799
Comparative genomics of Arabidopsis and maize: prospects and limitations.
Brendel V, Kurtz S, Walbot V., Genome Biol 3(3), 2002
PMID: 11897028
A complete sequence of the T. tengcongensis genome.
Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H., Genome Res 12(5), 2002
PMID: 11997336

25 References

Daten bereitgestellt von Europe PubMed Central.

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium., Nature 409(6822), 2001
PMID: 11237011
Short-sequence DNA repeats in prokaryotic genomes.
van Belkum A, Scherer S, van Alphen L, Verbrugh H., Microbiol. Mol. Biol. Rev. 62(2), 1998
PMID: 9618442

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
The REPRO server: finding protein internal sequence repeats through the Web.
George RA, Heringa J., Trends Biochem. Sci. 25(10), 2000
PMID: 11203383

AUTHOR UNKNOWN, 0
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982

AUTHOR UNKNOWN, 0
The complete genome sequence of Escherichia coli K-12.
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y., Science 277(5331), 1997
PMID: 9278503
Alignment of whole genomes.
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL., Nucleic Acids Res. 27(11), 1999
PMID: 10325427
REPuter: fast computation of maximal repeats in complete genomes.
Kurtz S, Schleiermacher C., Bioinformatics 15(5), 1999
PMID: 10366664

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
A chromosomal deletion map of human malformations.
Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D., Am. J. Hum. Genet. 63(4), 1998
PMID: 9758599
Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome.
Edelmann L, Pandita RK, Morrow BE., Am. J. Hum. Genet. 64(4), 1999
PMID: 10090893
Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis.
Shaikh TH, Kurahashi H, Saitta SC, O'Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS., Hum. Mol. Genet. 9(4), 2000
PMID: 10699172
Prediction of complete gene structures in human genomic DNA.
Burge C, Karlin S., J. Mol. Biol. 268(1), 1997
PMID: 9149143
Complementary DNA sequencing: expressed sequence tags and human genome project.
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF., Science 252(5013), 1991
PMID: 2047873

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 11713313
PubMed | Europe PMC

Suchen in

Google Scholar