The “green lineage” is a large group of green algae and higher plants that have adapted to a wide variety of niches and vary tremendously with respect to morphology and ecology. I am interested in using computational approaches to study the role of systems-level interactions of the cellular components, genome, and gene family evolution in the processes of plant diversification and adaptation.
 
Systems Biology approach towards the study of photosynthesis in Chlamydomonas
It has become clear that the functioning and evolution of cells cannot be fully understood by understanding their individual components. Instead, an integration of experimentation, data processing, and modeling is required and allows us to study the systems-level interactions of cellular components. In the context of the GoFORSYS program, a collaboration between four research centers, and with the aim to enforce the quantitative comprehension of biological networks and regulation, I am working on a systems biology approach to study photosynthesis in the green alga Chlamydomonas reinhardtii. One of the goals of a systems analysis of the expression and regulation of the photosynthetic molecular apparatus to selected environmental stimuli will be to identify important constraints on photosynthesis efficiency and productivity. Ultimately, this will alllow transfer of knowledge from the model algal system to crop plants.
 
 
Phylogenomics: Development of analysis methods and tools for large scale analysis of gene families
  1. Before the wealth of new genome data can be applied to questions of organismal function and evolution, it has to be
    captured, centralized, and made accessible to the research community. I have participated in the development of Phytome, an online comparative genomics resource for functional plant genomics, molecular breeding, and evolutionary studies.  Phytome contains predicted protein sequences, protein family assignments, multiple sequence alignments, phylogenies, and functional annotations for proteins from a large, phylogenetically diverse set of plant taxa.
  2. •Hartmann S, D Lu, J Phillips, TJ Vision. (2006) Phytome: a plant comparative genomics resource. Nucleic Acids Research. Volume 34, Database Issue

  3. A challenge in phylogenomics, the large scale analysis of gene families, is that much of the available data is incomplete: Expressed Sequence Tags (ESTs) represent only partial sequences of expressed genes, but they are the primary source of sequence data for plant genes. I have used simulated data to show that incomplete, EST-based alignments pose serious
    problems for inferring protein family phylogenies, even in the absence of alignment error. I explored how to most accurately compute phylogenies from such gappy alignments.
  4. •Hartmann S, T Vision. Can one accurately infer a phylogenetic tree from a gappy alignment? In preparation for BMC Evolutionary Biology.
  5. •Cheng F, S Hartmann, C Falls, M Gupta, J Snoeyink, J Ibrahim, and TJ Vision. Hierarchical models for incomplete alignments in phylogenetic inference. In preparation for Bioinformatics.
 
 
Phylogenomics: large-scale phylogenetic studies of gene families, used to study the evolution and function of the genes and proteins
  1. From organisms to cellular components and genes and gene families — coevolution is an important process at all levels of life. Previous work has suggested that the co-evolution of gene family trees is a common phenomenon that may have  
    facilitated the evolution of complex morphologies or pathways. I am interested in determining whether the criterion of coevolving gene trees can be used as a predictor of gene families that act in the same pathway. This strategy is aimed to predict functions for many of the protein families for which we currently don’t know their cellular function.
 
 
Phylogenomics: large-scale phylogenetic studies of gene families, applied to questions in organismal systematics
  1. Phytome stores a large number of gene family phylogenies that were collected from a broad taxonomic range of angiosperms. I am interested in taking advantage of this data to resolve critical nodes in the phylogeny of the green lineage. The approach of “gene tree reconciliation” is well suited to this problem: it identifies evolutionary events that lead to incongruence between gene trees and species trees. It then combines information from multiple gene trees by searching for the species tree that minimizes duplications and losses when reconciling it with each source tree. Thus, it aims to find the species tree that best represents the evolution of the source trees (gene trees) in a biologically meaningful way.
 
 
other interests and past work: Molecular biology and evolution of …
 
… genes and gene families
  1. •ARABIDOPSIS meeting, Berlin, Germany. SYSTERS Protein Family Web Server: Shortcut from large-scale sequence information to phylogenetic information (poster); T Meinel, A Krause, E Staub, H Luz, S Hartmann, U Krämer, J Selbig, and M Vingron (external)
  2. •Zhou J, S Hartmann, BK Shepherd, JE Poulton. (2002) Investigation of the microheterogeneity and aglycone specificity-conferring residues of black cherry prunasin hydrolases. Plant Physiology 129: 1252-1264.
  3. •Hartmann S, J Nason, D Bhattacharya (2001). Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. Journal of Molecular Evolution 53: 124-134.
  4. •Bhattacharya D, J Aubry, EC Twait, S Jurk. (2000) Actin gene duplication and the evolution of morphological complexity in land plants. Journal of Phycology 36:813-820.
 
… higher plant organelles
  1. •Stegemann S, S Hartmann, S Ruf, R Bock. (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A. 100(15):8828-8833.
 
… plant species and populations
  1. •Poslusny N, S. Hartmann, TJ Vision. Molecular phylogeography of Platystemon californicus. In preparation for Molecular Ecology.
  2. •Hartmann S, J Nason, D Bhattacharya.(2002) Phylogenetic origins of Lophocereus and the senita cactus – senita moth pollination mutualism. American Journal of Botany 89(7): 1085–1092.