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Items: 1 to 50 of 368

1.

The hornwort genome and early land plant evolution.

Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD.

Nat Plants. 2020 Feb;6(2):107-118. doi: 10.1038/s41477-019-0588-4. Epub 2020 Feb 10.

PMID:
32042158
2.

"Winter Is Coming": How did Polyploid Plants Survive?

Li Z, Van de Peer Y.

Mol Plant. 2020 Jan 6;13(1):4-5. doi: 10.1016/j.molp.2019.12.003. Epub 2019 Dec 6. No abstract available.

PMID:
31951572
3.

The water lily genome and the early evolution of flowering plants.

Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, Wang H, Chen X, Hu J, Liu Y, Qin Y, Wang K, Dong S, Liu Y, Zhang S, Yu X, Wu Q, Wang L, Yan X, Jiao Y, Kong H, Zhou X, Yu C, Chen Y, Li F, Wang J, Chen W, Chen X, Jia Q, Zhang C, Jiang Y, Zhang W, Liu G, Fu J, Chen F, Ma H, Van de Peer Y, Tang H.

Nature. 2020 Jan;577(7788):79-84. doi: 10.1038/s41586-019-1852-5. Epub 2019 Dec 18.

4.

Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants.

Wong GK, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M.

Annu Rev Plant Biol. 2019 Dec 18. doi: 10.1146/annurev-arplant-042916-041040. [Epub ahead of print]

PMID:
31851546
5.

Genomes of early-diverging streptophyte algae shed light on plant terrestrialization.

Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GK, Melkonian M, Liu H, Liu X.

Nat Plants. 2020 Feb;6(2):95-106. doi: 10.1038/s41477-019-0560-3. Epub 2019 Dec 16.

PMID:
31844283
6.

Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review.

Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SA, Sung YY, Van de Peer Y, Sorgeloos P, Danish-Daniel M.

Evol Bioinform Online. 2019 Dec 5;15:1176934319892284. doi: 10.1177/1176934319892284. eCollection 2019. Review.

7.

Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host-Pathogen Interactions.

Gonçalves MFM, Nunes RB, Tilleman L, Van de Peer Y, Deforce D, Van Nieuwerburgh F, Esteves AC, Alves A.

Int J Mol Sci. 2019 Dec 3;20(23). pii: E6083. doi: 10.3390/ijms20236083.

8.

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L.

Gigascience. 2019 Dec 1;8(12). pii: giz138. doi: 10.1093/gigascience/giz138.

9.

ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.

Yssel AEJ, Kao SM, Van de Peer Y, Sterck L.

Genes (Basel). 2019 Nov 20;10(12). pii: E950. doi: 10.3390/genes10120950.

10.

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression.

Burgess STG, Marr EJ, Bartley K, Nunn FG, Down RE, Weaver RJ, Prickett JC, Dunn J, Rombauts S, Van Leeuwen T, Van de Peer Y, Nisbet AJ.

BMC Genomics. 2019 Oct 23;20(1):756. doi: 10.1186/s12864-019-6082-6.

11.

A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes.

Félix C, Meneses R, Gonçalves MFM, Tilleman L, Duarte AS, Jorrín-Novo JV, Van de Peer Y, Deforce D, Van Nieuwerburgh F, Esteves AC, Alves A.

Sci Rep. 2019 Sep 11;9(1):13144. doi: 10.1038/s41598-019-49551-w.

12.

Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos.

Rodrigues AS, Chaves I, Costa BV, Lin YC, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM.

Sci Rep. 2019 Aug 5;9(1):11327. doi: 10.1038/s41598-019-47789-y.

13.

Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.

Yao Y, Carretero-Paulet L, Van de Peer Y.

PLoS One. 2019 Jul 31;14(7):e0220257. doi: 10.1371/journal.pone.0220257. eCollection 2019.

14.

The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication.

Defoort J, Van de Peer Y, Carretero-Paulet L.

Genome Biol Evol. 2019 Aug 1;11(8):2292-2305. doi: 10.1093/gbe/evz156.

15.

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.

16.

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

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

Mol Biol Evol. 2019 Sep 1;36(9):1921-1930. doi: 10.1093/molbev/msz115.

PMID:
31238339
17.

Loss of Wood Formation Genes in Monocot Genomes.

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

Genome Biol Evol. 2019 Jul 1;11(7):1986-1996. doi: 10.1093/gbe/evz115.

18.

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.

19.

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
20.

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.

21.

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):.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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
40.

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.

41.

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.

42.

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.

43.

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.

44.

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
45.

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.

46.

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.

47.

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
48.

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.

49.

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.

50.

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.

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