Comparative (pan)genomics

We believe pangenomics is the future of comparative genomics, which aims to understand the content, organization and evolution of genomes, and explain genotype-phenotype relationships. Motivated by large sequencing projects and a desire to link genomic variation to phenotypic variation, my team works on the transition from reference-based approaches to pangenomic approaches for comparative genomics.

We develop novel methods for pangenomics and apply them across the tree of life, with a focus on plants and plant pathogens. Our software:

PanTools
PanUtils
PanVA

Publications

Operophtera brumata RefSeq Genome

Derks, M.F.L. , Smit, S. , Salis, L. , Schijlen, E.G.W.M. , Bossers, A. , Mateman, C. , Pijl, A.S. , de Ridder, D. , Groenen, M.A.M. , Visser, M.E. , Megens, H.J.W.C. (2015)
Making the difference: integrating structural variation detection tools

Lin, K. , Smit, S. , Bonnema, A.B. , Sanchez Perez, G.F. , de Ridder, D. (2015) Briefings in Bioinformatics (2015), Volume: 16, Issue: 5 - ISSN 1467-5463 - p. 852-864.
The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology

Derks, M.F.L. , Smit, S. , Salis, L. , Schijlen, E.G.W.M. , Bossers, A. , Mateman, C. , Pijl, A.S. , de Ridder, D. , Groenen, M.A.M. , Visser, M.E. , Megens, H.J.W.C. (2015) Genome Biology and Evolution (2015), Volume: 7, Issue: 8 - ISSN 1759-6653 - p. 2321-2332.
Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

Shearer, L.A. , Anderson, L.K. , de Jong, H. , Smit, S. , Goicoechea, J.L. , Roe, B.A. , Hua, A. , Giovannoni, J.J. , Stack, S.M. (2014) G3 : Genes Genomes Genetics (2014), Volume: 4, Issue: 8 - ISSN 2160-1836 - p. 1395-1405.
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Aflitos, S.A. , Schijlen, E.G.W.M. , de Jong, J.H.S.G.M. , de Ridder, D. , Smit, S. , Finkers, H.J. , Bakker, F.T. , van de Geest, H.C. , te Lintel Hekkert, B. , van Haarst, J.C. , Smits, L.W.M. , Koops, A.J. , Sanchez-Perez, M.J. , van Heusden, A.W. , Visser, R.G.F. , Schranz, M.E. , Peters, S.A. (2014) The Plant Journal (2014), Volume: 80, Issue: 1 - ISSN 0960-7412 - p. 136-148.
Using fluorescence in situ hybridization (FISH) to improve the assembly of the tomato genome

Shearer, L.A. , Anderson, L.K. , de Jong, J.H.S.G.M. , Smit, S. , Goicoechea, J.L. , Roe, B.A. , Hua, A. , Giovannoni, J.J. , Stack, S.M. (2013) Tomato Genetics Cooperative Report (2013), Volume: 63 - ISSN 0495-8306 - p. 5-14.
Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines

Schalkwyk, A. , Wenzl, P. , Smit, S. , Lopez-Cobollo, R. , Kilian, A. , Bishop, G. , Hefer, C. , Berger, D.K. (2012) Theoretical and Applied Genetics (2012), Volume: 124, Issue: 5 - ISSN 0040-5752 - p. 947-956.
The tomato genome sequence provides insights into fleshy fruit evolution

Sato, S. , Tabata, S. , Hirakawa, H. , Klein Lankhorst, R.M. , de Jong, H. , van Ham, R.C.H.J. , Datema, E. , Smit, S. , Schijlen, E.G.W.M. , van Haarst, J.C. , Peters, S.A. , Henkens, M.H.C. , van Staveren, M.J. , Mooijman, P.J.W. , Hesselink, T. , van de Belt, J. , Szinay, D. , Bai, Y. , Visser, R.G.F. (2012) Nature (2012), Volume: 485 - ISSN 0028-0836 - p. 635-641.
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

Widmann, J. , Stombaugh, J. , Mcdonald, D. , Chocholousova, J. , Gardner, P. , Iyer, M.K. , Liu, Z.Z. , Lozupone, C.A. , Quinn, J. , Smit, S. , Wikman, S. , Zaneveld, J.R.R. , Knight, R. (2012) RNA-A Publication of the RNA Society (2012), Volume: 18, Issue: 7 - ISSN 1355-8382 - p. 1319-1327.

Publications

Operophtera brumata RefSeq Genome

Making the difference: integrating structural variation detection tools

The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology

Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Using fluorescence in situ hybridization (FISH) to improve the assembly of the tomato genome

Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines

The tomato genome sequence provides insights into fleshy fruit evolution

RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs