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Items: 1 to 50 of 335

1.

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
2.

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.

3.

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 Jul 6. doi: 10.1111/tpj.14015. [Epub ahead of print]

PMID:
29979480
4.

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
5.

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato.

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

Plant Physiol. 2018 Jun 22. pii: pp.00450.2018. doi: 10.1104/pp.18.00450. [Epub ahead of print]

6.

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.

7.

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.

8.

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
9.

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.

10.

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.

11.

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.

12.

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.

13.

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
14.

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.

15.

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.

16.

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
17.

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.

18.

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.

19.

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.

20.

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.

PMID:
29061868
21.

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.

22.

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.

23.

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.

24.

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
25.

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.

26.

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):.

27.

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):.

28.

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.

29.

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):.

30.

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.

31.

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.

PMID:
28635135
32.

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
33.

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.

34.

Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.

Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, Cabezas JA, Cervera MT, Ingvarsson PK, Van de Peer Y.

Genome Biol Evol. 2017 May 1;9(5):1130-1147. doi: 10.1093/gbe/evx070.

35.

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants.

De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK.

Mol Biol Evol. 2017 Jun 1;34(6):1363-1377. doi: 10.1093/molbev/msx069.

36.

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes.

Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD.

Gigascience. 2017 Feb 1;6(2):1-11. doi: 10.1093/gigascience/giw015.

37.

A Cytoscape app for motif enumeration with ISMAGS.

Van Parys T, Melckenbeeck I, Houbraken M, Audenaert P, Colle D, Pickavet M, Demeester P, Van de Peer Y.

Bioinformatics. 2017 Feb 1;33(3):461-463. doi: 10.1093/bioinformatics/btw626.

PMID:
28158465
38.

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing.

Mizrachi E, Verbeke L, Christie N, Fierro AC, Mansfield SD, Davis MF, Gjersing E, Tuskan GA, Van Montagu M, Van de Peer Y, Marchal K, Myburg AA.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1195-1200. doi: 10.1073/pnas.1620119114. Epub 2017 Jan 17.

39.

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment.

Yao Y, Storme V, Marchal K, Van de Peer Y.

PeerJ. 2016 Dec 21;4:e2812. doi: 10.7717/peerj.2812. eCollection 2016.

40.

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus.

Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, Monsoor M, Godfroy O, Lipinska A, Perrineau MM, Van De Peer Y, Hitte C, Corre E, Coelho SM, Cock JM.

New Phytol. 2017 Apr;214(1):219-232. doi: 10.1111/nph.14321. Epub 2016 Nov 21.

41.

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.

Christie N, Myburg AA, Joubert F, Murray SL, Carstens M, Lin YC, Meyer J, Crampton BG, Christensen SA, Ntuli JF, Wighard SS, Van de Peer Y, Berger DK.

Plant J. 2017 Feb;89(4):746-763. doi: 10.1111/tpj.13419. Epub 2017 Feb 13.

42.

Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore.

Ngoc PC, Greenhalgh R, Dermauw W, Rombauts S, Bajda S, Zhurov V, Grbić M, Van de Peer Y, Van Leeuwen T, Rouzé P, Clark RM.

Genome Biol Evol. 2016 Dec 14;8(11):3323-3339.

43.

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

Perazzolli M, Herrero N, Sterck L, Lenzi L, Pellegrini A, Puopolo G, Van de Peer Y, Pertot I.

BMC Genomics. 2016 Oct 27;17(1):838.

44.

Erratum to: An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens.

Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R.

BMC Evol Biol. 2016 Sep 8;16(1):184. No abstract available.

45.

Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.

Le PT, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, Cowan DA.

Genome Biol Evol. 2016 Sep 11;8(9):2737-47. doi: 10.1093/gbe/evw189.

46.

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph.

Meysman P, Saeys Y, Sabaghian E, Bittremieux W, van de Peer Y, Goethals B, Laukens K.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jun 7. [Epub ahead of print]

PMID:
27295680
47.

Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis.

Kerchev P, Waszczak C, Lewandowska A, Willems P, Shapiguzov A, Li Z, Alseekh S, Mühlenbock P, Hoeberichts FA, Huang J, Van Der Kelen K, Kangasjärvi J, Fernie AR, De Smet R, Van de Peer Y, Messens J, Van Breusegem F.

Plant Physiol. 2016 Jul;171(3):1704-19. doi: 10.1104/pp.16.00359. Epub 2016 May 25.

48.

Jabba: hybrid error correction for long sequencing reads.

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

Algorithms Mol Biol. 2016 May 3;11:10. doi: 10.1186/s13015-016-0075-7. eCollection 2016.

49.

RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction.

Bolton MD, Ebert MK, Faino L, Rivera-Varas V, de Jonge R, Van de Peer Y, Thomma BP, Secor GA.

Fungal Genet Biol. 2016 Jul;92:1-13. doi: 10.1016/j.fgb.2016.04.003. Epub 2016 Apr 23.

PMID:
27112724
50.

hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms.

Xie Q, Tzfadia O, Levy M, Weithorn E, Peled-Zehavi H, Van Parys T, Van de Peer Y, Galili G.

Autophagy. 2016 May 3;12(5):876-87. doi: 10.1080/15548627.2016.1147668. Epub 2016 Apr 12.

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