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Items: 1 to 50 of 352

1.

Erratum for Navia et al., "Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi".

Navia D, Novelli VM, Rombauts S, Freitas-Astúa J, Santos de Mendonça R, Nunes MA, Machado MA, Lin YC, Le P, Zhang Z, Grbić M, Wybouw N, Breeuwer JAJ, Van Leeuwen T, Van de Peer Y.

Microbiol Resour Announc. 2019 Jul 3;8(27). pii: e00710-19. doi: 10.1128/MRA.00710-19. No abstract available.

2.

Multiple Independent Recruitment of Sodefrin Precursor-like Factors in Anuran Sexually Dimorphic Glands.

Bossuyt F, Schulte LM, Maex M, Janssenswillen S, Yu Novikova P, Biju SD, Van de Peer Y, Matthijs S, Roelants K, Martel A, Van Bocxlaer I.

Mol Biol Evol. 2019 Jun 25. pii: msz115. doi: 10.1093/molbev/msz115. [Epub ahead of print]

PMID:
31238339
3.

Loss of wood formation genes in monocot genomes.

Roodt D, Li Z, Van de Peer Y, Mizrachi E.

Genome Biol Evol. 2019 Jun 7. pii: evz115. doi: 10.1093/gbe/evz115. [Epub ahead of print]

PMID:
31173081
4.

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly.

Heydari M, Miclotte G, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2019 Jun 3;20(1):298. doi: 10.1186/s12859-019-2906-2.

5.

Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates.

Zwaenepoel A, Van de Peer Y.

Mol Biol Evol. 2019 Jul 1;36(7):1384-1404. doi: 10.1093/molbev/msz088.

PMID:
31004147
6.

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude.

Zhang T, Qiao Q, Novikova PY, Wang Q, Yue J, Guan Y, Ming S, Liu T, De J, Liu Y, Al-Shehbaz IA, Sun H, Van Montagu M, Huang J, Van de Peer Y, Qiong.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):7137-7146. doi: 10.1073/pnas.1817580116. Epub 2019 Mar 20.

7.

Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi.

Navia D, Novelli VM, Rombauts S, Freitas-Astúa J, Santos de Mendonça R, Nunes MA, Machado MA, Lin YC, Le P, Zhang Z, Grbić M, Wybouw N, Breeuwer JAJ, Van Leeuwen T, Van de Peer Y.

Microbiol Resour Announc. 2019 Feb 7;8(6). pii: e01563-18. doi: 10.1128/MRA.01563-18. eCollection 2019 Feb. Erratum in: Microbiol Resour Announc. 2019 Jul 3;8(27):.

8.

Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.

Xu CQ, Liu H, Zhou SS, Zhang DX, Zhao W, Wang S, Chen F, Sun YQ, Nie S, Jia KH, Jiao SQ, Zhang RG, Yun QZ, Guan W, Wang X, Gao Q, Bennetzen JL, Maghuly F, Porth I, Van de Peer Y, Wang XR, Ma Y, Mao JF.

Gigascience. 2019 Feb 1;8(2). pii: giy164. doi: 10.1093/gigascience/giy164.

9.

Optimising orbit counting of arbitrary order by equation selection.

Melckenbeeck I, Audenaert P, Van Parys T, Van De Peer Y, Colle D, Pickavet M.

BMC Bioinformatics. 2019 Jan 15;20(1):27. doi: 10.1186/s12859-018-2483-9.

10.

Finding Evidence for Whole Genome Duplications: A Reappraisal.

Zwaenepoel A, Li Z, Lohaus R, Van de Peer Y.

Mol Plant. 2019 Feb 4;12(2):133-136. doi: 10.1016/j.molp.2018.12.019. Epub 2018 Dec 29. No abstract available.

PMID:
30599206
11.

The draft genomes of five agriculturally important African orphan crops.

Chang Y, Liu H, Liu M, Liao X, Sahu SK, Fu Y, Song B, Cheng S, Kariba R, Muthemba S, Hendre PS, Mayes S, Ho WK, Yssel AEJ, Kendabie P, Wang S, Li L, Muchugi A, Jamnadass R, Lu H, Peng S, Van Deynze A, Simons A, Yana-Shapiro H, Van de Peer Y, Xu X, Yang H, Wang J, Liu X.

Gigascience. 2019 Mar 1;8(3). pii: giy152. doi: 10.1093/gigascience/giy152.

12.

Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae.

Burgess STG, Bartley K, Nunn F, Wright HW, Hughes M, Gemmell M, Haldenby S, Paterson S, Rombauts S, Tomley FM, Blake DP, Pritchard J, Schicht S, Strube C, Øines Ø, Van Leeuwen T, Van de Peer Y, Nisbet AJ.

Microbiol Resour Announc. 2018 Nov 8;7(18). pii: e01221-18. doi: 10.1128/MRA.01221-18. eCollection 2018 Nov.

13.

wgd-simple command line tools for the analysis of ancient whole-genome duplications.

Zwaenepoel A, Van de Peer Y.

Bioinformatics. 2019 Jun 1;35(12):2153-2155. doi: 10.1093/bioinformatics/bty915.

14.

Size does matter.

Van de Peer Y.

Nat Plants. 2018 Nov;4(11):859-860. doi: 10.1038/s41477-018-0293-8. No abstract available.

PMID:
30390078
15.

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.

Lin YC, Wang J, Delhomme N, Schiffthaler B, Sundström G, Zuccolo A, Nystedt B, Hvidsten TR, de la Torre A, Cossu RM, Hoeppner MP, Lantz H, Scofield DG, Zamani N, Johansson A, Mannapperuma C, Robinson KM, Mähler N, Leitch IJ, Pellicer J, Park EJ, Van Montagu M, Van de Peer Y, Grabherr M, Jansson S, Ingvarsson PK, Street NR.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10970-E10978. doi: 10.1073/pnas.1801437115. Epub 2018 Oct 29.

16.

Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.

De Clerck O, Kao SM, Bogaert KA, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano G, Charrier B, Clewes R, Del Cortona A, D'Hondt S, Fernandez-Pozo N, Gachon CM, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs CA, Popper ZA, Raven JA, Van Bel M, Wilhelmsson PKI, Bhattacharya D, Coates JC, Rensing SA, Van Der Straeten D, Vardi A, Sterck L, Vandepoele K, Van de Peer Y, Wichard T, Bothwell JH.

Curr Biol. 2018 Sep 24;28(18):2921-2933.e5. doi: 10.1016/j.cub.2018.08.015. Epub 2018 Sep 13.

PMID:
30220504
17.

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs.

Heydari M, Miclotte G, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2018 Sep 4;19(1):311. doi: 10.1186/s12859-018-2319-7.

18.

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.

Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, Ullrich KK, Haas FB, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson PKI, Janitza P, Kern R, Heyl A, Rümpler F, Villalobos LIAC, Clay JM, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington AJ, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan GV, Van Nieuwerburgh F, Deforce D, Chang C, Karol KG, Hedrich R, Ulvskov P, Glöckner G, Delwiche CF, Petrášek J, Van de Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theißen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing SA.

Cell. 2018 Jul 12;174(2):448-464.e24. doi: 10.1016/j.cell.2018.06.033.

PMID:
30007417
19.

Agulhas Current properties shape microbial community diversity and potential functionality.

Phoma S, Vikram S, Jansson JK, Ansorge IJ, Cowan DA, Van de Peer Y, Makhalanyane TP.

Sci Rep. 2018 Jul 12;8(1):10542. doi: 10.1038/s41598-018-28939-0.

20.

The 'TranSeq' 3'-end sequencing method for high-throughput transcriptomics and gene space refinement in plant genomes.

Tzfadia O, Bocobza S, Defoort J, Almekias-Siegl E, Panda S, Levy M, Storme V, Rombauts S, Jaitin DA, Keren-Shaul H, Van de Peer Y, Aharoni A.

Plant J. 2018 Oct;96(1):223-232. doi: 10.1111/tpj.14015. Epub 2018 Jul 29.

PMID:
29979480
21.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GK, Pryer KM.

Nat Plants. 2018 Jul;4(7):460-472. doi: 10.1038/s41477-018-0188-8. Epub 2018 Jul 2.

PMID:
29967517
22.

Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato.

Ramšak Ž, Coll A, Stare T, Tzfadia O, Baebler Š, Van de Peer Y, Gruden K.

Plant Physiol. 2018 Sep;178(1):488-499. doi: 10.1104/pp.18.00450. Epub 2018 Jun 22.

23.

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.

Defoort J, Van de Peer Y, Vermeirssen V.

Nucleic Acids Res. 2018 Jul 27;46(13):6480-6503. doi: 10.1093/nar/gky468.

24.

Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum.

de Jonge R, Ebert MK, Huitt-Roehl CR, Pal P, Suttle JC, Spanner RE, Neubauer JD, Jurick WM 2nd, Stott KA, Secor GA, Thomma BPHJ, Van de Peer Y, Townsend CA, Bolton MD.

Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5459-E5466. doi: 10.1073/pnas.1712798115. Epub 2018 May 29. Erratum in: Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8324.

25.

Editorial overview: Genome studies and molecular genetics: Treasure troves of evolution.

Van de Peer Y, Pires JC.

Curr Opin Plant Biol. 2018 Apr;42:iii-v. doi: 10.1016/j.pbi.2018.04.015. Epub 2018 May 8. No abstract available.

PMID:
29748036
26.

Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis.

Burgess STG, Bartley K, Marr EJ, Wright HW, Weaver RJ, Prickett JC, Hughes M, Haldenby S, Thi Le P, Rombauts S, Van Leeuwen T, Van de Peer Y, Nisbet AJ.

Genome Announc. 2018 Apr 19;6(16). pii: e00265-18. doi: 10.1128/genomeA.00265-18.

27.

MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants.

Zwaenepoel A, Diels T, Amar D, Van Parys T, Shamir R, Van de Peer Y, Tzfadia O.

Front Plant Sci. 2018 Mar 19;9:352. doi: 10.3389/fpls.2018.00352. eCollection 2018.

28.

A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils.

Van Goethem MW, Pierneef R, Bezuidt OKI, Van De Peer Y, Cowan DA, Makhalanyane TP.

Microbiome. 2018 Feb 23;6(1):40. doi: 10.1186/s40168-018-0424-5.

29.

Polyploid Arabidopsis species originated around recent glaciation maxima.

Novikova PY, Hohmann N, Van de Peer Y.

Curr Opin Plant Biol. 2018 Apr;42:8-15. doi: 10.1016/j.pbi.2018.01.005. Epub 2018 Feb 12. Review.

30.

A genome for gnetophytes and early evolution of seed plants.

Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H, Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM.

Nat Plants. 2018 Feb;4(2):82-89. doi: 10.1038/s41477-017-0097-2. Epub 2018 Jan 29.

PMID:
29379155
31.

IMA Genome-F 8: Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips.

Wingfield BD, Berger DK, Steenkamp ET, Lim HJ, Duong TA, Bluhm BH, de Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier N, Lin YC, Van de Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, van der Nest MA, van der Merwe NA, van Wyk S, Wilken PM, Wingfield MJ.

IMA Fungus. 2017 Dec;8(2):385-396. doi: 10.5598/imafungus.2017.08.02.10. Epub 2017 Nov 21.

32.

Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution.

Causier B, Li Z, De Smet R, Lloyd JPB, Van de Peer Y, Davies B.

Sci Rep. 2017 Nov 30;7(1):16692. doi: 10.1038/s41598-017-16942-w.

33.

The sociobiology of genes: the gene's eye view as a unifying behavioural-ecological framework for biological evolution.

De Tiège A, Van de Peer Y, Braeckman J, Tanghe KB.

Hist Philos Life Sci. 2017 Nov 22;40(1):6. doi: 10.1007/s40656-017-0174-x.

PMID:
29168053
34.

Genome of wild olive and the evolution of oil biosynthesis.

Unver T, Wu Z, Sterck L, Turktas M, Lohaus R, Li Z, Yang M, He L, Deng T, Escalante FJ, Llorens C, Roig FJ, Parmaksiz I, Dundar E, Xie F, Zhang B, Ipek A, Uranbey S, Erayman M, Ilhan E, Badad O, Ghazal H, Lightfoot DA, Kasarla P, Colantonio V, Tombuloglu H, Hernandez P, Mete N, Cetin O, Van Montagu M, Yang H, Gao Q, Dorado G, Van de Peer Y.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9413-E9422. doi: 10.1073/pnas.1708621114. Epub 2017 Oct 9.

35.

Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana.

De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y.

Plant Cell. 2017 Nov;29(11):2786-2800. doi: 10.1105/tpc.17.00531. Epub 2017 Oct 25.

36.

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.

Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1190-D1196. doi: 10.1093/nar/gkx1002.

37.

Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity.

Tasdighian S, Van Bel M, Li Z, Van de Peer Y, Carretero-Paulet L, Maere S.

Plant Cell. 2017 Nov;29(11):2766-2785. doi: 10.1105/tpc.17.00313. Epub 2017 Oct 23.

38.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 12;5(41). pii: e01175-17. doi: 10.1128/genomeA.01175-17. No abstract available.

39.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 12;5(41). pii: e01152-17. doi: 10.1128/genomeA.01152-17. No abstract available.

40.

Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples".

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Oct 5;5(40). pii: e01176-17. doi: 10.1128/genomeA.01176-17. No abstract available.

41.

The Apostasia genome and the evolution of orchids.

Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ.

Nature. 2017 Sep 21;549(7672):379-383. doi: 10.1038/nature23897. Epub 2017 Sep 13.

PMID:
28902843
42.

Evidence for an ancient whole genome duplication in the cycad lineage.

Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E.

PLoS One. 2017 Sep 8;12(9):e0184454. doi: 10.1371/journal.pone.0184454. eCollection 2017.

43.

Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 24;5(34). pii: e00894-17. doi: 10.1128/genomeA.00894-17. Erratum in: Genome Announc. 2017 Oct 12;5(41):.

44.

Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 24;5(34). pii: e00884-17. doi: 10.1128/genomeA.00884-17. Erratum in: Genome Announc. 2017 Oct 5;5(40):.

45.

Evaluation of the impact of Illumina error correction tools on de novo genome assembly.

Heydari M, Miclotte G, Demeester P, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2017 Aug 18;18(1):374. doi: 10.1186/s12859-017-1784-8.

46.

Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples.

Orr RJS, Rombauts S, Van de Peer Y, Shalchian-Tabrizi K.

Genome Announc. 2017 Aug 17;5(33). pii: e00787-17. doi: 10.1128/genomeA.00787-17. Erratum in: Genome Announc. 2017 Oct 12;5(41):.

47.

Revisiting ancestral polyploidy in plants.

Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S.

Sci Adv. 2017 Jul 5;3(7):e1603195. doi: 10.1126/sciadv.1603195. eCollection 2017 Jul.

48.

The gene expression landscape of pine seedling tissues.

Cañas RA, Li Z, Pascual MB, Castro-Rodríguez V, Ávila C, Sterck L, Van de Peer Y, Cánovas FM.

Plant J. 2017 Sep;91(6):1064-1087. doi: 10.1111/tpj.13617. Epub 2017 Aug 4.

49.

The evolutionary significance of polyploidy.

Van de Peer Y, Mizrachi E, Marchal K.

Nat Rev Genet. 2017 Jul;18(7):411-424. doi: 10.1038/nrg.2017.26. Epub 2017 May 15. Review.

PMID:
28502977
50.

OMSim: a simulator for optical map data.

Miclotte G, Plaisance S, Rombauts S, Van de Peer Y, Audenaert P, Fostier J.

Bioinformatics. 2017 Sep 1;33(17):2740-2742. doi: 10.1093/bioinformatics/btx293.

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