Functional Genomics

Using a systems biology approach, we are modeling biochemical pathways and regulatory processes that affect plant function and development. Among the central biochemical pathways in plants, isoprenoid synthesis produces key molecules for cellular function and metabolites of pharmacological interest. Genetic or biochemical disruption of pathway flux triggers changes in gene expression and metabolite end products. We are linking databases to explore the interdependence of biochemical pathway information and regulatory networks. A similar approach is applied to cell cycle regulation, which is the basis for developmental and differentiation processes.

The complete analysis of the chloroplast proteome is at the frontiers of understanding the organelle as a functional system. Exploiting advanced technologies and computing algorithms, we are discovering many novel proteins. Their genetic characterization will provide important new information on chloroplast pathways. The combined knowledge from systems approaches will allow us to model and predict plant functions.

• Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome
  Uhrig, R. Glen; Echevarria-Zomeno, Sira; Schlapfer, Pascal; Grossmann, Jonas; Roschitzki, Bernd; et al.
  Plant Cell And Environment,  10.1111/pce.13969, MAR 2021
• Multiplying the efficiency and impact of biofortification through metabolic engineering
  Van Der Straeten, Dominique; Bhullar, Navreet K.; De Steur, Hans; Gruissem, Wilhelm; MacKenzie, Donald; et al.
  Nature Communications  DOI: 10.1038/s41467-020-19020-4  OCT 15 2020
• Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains
  Wu, Ting-Ying; Mueller, Marlen; Gruissem, Wilhelm; Bhullar, Navreet K.
  Rice  DOI: 10.1186/s12284-020-00421-4  SEP 7 2020
• Morpho-physiological and molecular evaluation of drought tolerance in cassava (Manihot esculenta Crantz)
  Orek, Charles; Gruissem, Wilhelm; Ferguson, Morag; Vanderschuren, Herve
  Field Crops Research  DOI: 10.1016/j.fcr.2020.107861  SEP 15 2020
• Screening for Resistance in Farmer-Preferred Cassava Cultivars from Ghana to a Mixed Infection of CBSV and UCBSV
  Elegba, Wilfred; Gruissem, Wilhelm; Vanderschuren, Herve
  Plants-Basel  DOI: 10.3390/plants9081026  AUG 2020 
• The Cassava Source-Sink project: opportunities and challenges for crop improvement by metabolic engineering
  Sonnewald, Uwe; Fernie, Alisdair R.; Gruissem, Wilhelm; Schlaepfer, Pascal; Anjanappa, Ravi B.; et al.
  Plant Journal   DOI: 10.1111/tpj.14865  AUG 2020
• Symplasmic phloem unloading and radial post-phloem transport via vascular rays in tuberous roots of Manihot esculenta
  Mehdi, Rabih; Lamm, Christian E.; Bodampalli Anjanappa, Ravi; Muedsam, Christina; Saeed, Muhammad; et al.
  Journal Of Experimental Botany,  https://doi.org/10.1093/jxb/erz297, OCT 15 2019
• Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
  Kuon, JE; Qi, WH; Schlapfer, P; Hirsch-Hoffmann, M; von Bieberstein, PR; Patrignani, A; Poveda, L; Grob, S; Keller, M; Shimizu-Inatsugi, R; Grossniklaus, U; Vanderschuren, H; Gruissem, W
  BMC BIOLOGY, 17 (1):10.1186/s12915-019-0697-6 SEP 18 2019
• Enhancement of vitamin B-6 levels in rice expressing Arabidopsis vitamin B-6 biosynthesis de novo genes
  Mangel, N; Fudge, JB; Li, KT; Wu, TY; Tohge, T; Fernie, AR; Szurek, B; Fitzpatrick, TB; Gruissem, W; Vanderschuren, H
  PLANT JOURNAL, 10.1111/tpj.14379 
• Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings
  Uhrig, RG; Schlapfer, P; Roschitzki, B; Hirsch-Hoffmann, M; Gruissem, W
  PLANT JOURNAL, 99 (1):176-194; 10.1111/tpj.14315 JUL 2019
• A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field
  Mehta, D; Hirsch-Hoffmann, M; Were, M; Patrignani, A; Zaidi, SSEA; Were, H; Gruissem, W; Vanderschuren, H
  NUCLEIC ACIDS RESEARCH, 47 (2):10.1093/nar/gky914 JAN 25 2019
• Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses
  Mehta, D; Sturchler, A; Anjanappa, RB; Zaidi, SSEA; Hirsch-Hoffmann, M; Gruissem, W; Vanderschuren, H
  GENOME BIOLOGY, 20 10.1186/s13059-019-1678-3 APR 25 2019
• Targeting intracellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice
  Wu, Ting-Ying; Gruissem, Wilhelm; Bhullar, Navreet K.
  PLANT BIOTECHNOLOGY JOURNAL, 17 (1):9-20; 10.1111/pbi.12943 JAN 2019
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• Pathway functional genomics
• Cell cycle and chromatin
• Biotechnology of crop improvement

• Functional genomics technologies
• Reverse engineering