Gabor Szabo

Bio: Gabor Szabo is an academic researcher from ETH Zurich. The author has contributed to research in topics: Greedy algorithm & Generalized assignment problem. The author has an hindex of 5, co-authored 6 publications receiving 1768 citations.

Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.

Abstract: The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.

An Algorithmic View on OVSF Code Assignment

Abstract: Orthogonal Variable Spreading Factor (OVSF) codes are used in UMTS to share the radio spectrum among several connections of possibly different bandwidth requirements. The combinatorial core of the OVSF code assignment problem is to assign some nodes of a complete binary tree of height h (the code tree) to n simultaneous connections, such that no two assigned nodes (codes) are on the same root-to-leaf path. A connection that uses a 2-d fraction of the total bandwidth requires some code at depth d in the tree, but this code assignment is allowed to change over time. Requests for connections that would exceed the total available bandwidth are rejected. We consider the one-step code assignment problem: Given an assignment, move the minimum number of codes to serve a new request. Minn and Siu propose the so-called DCA algorithm to solve the problem optimally. In contrast, we show that DCA does not always return an optimal solution, and that the problem is NP-hard. We give an exact nO(h)-time algorithm, and a polynomial-time greedy algorithm that achieves approximation ratio Θ(h). A more practically relevant version is the online code assignment problem, where future requests are not known in advance. Our objective is to minimize the overall number of code reassignments. We present a Θ(h)-competitive online algorithm, and show that no deterministic online algorithm can achieve a competitive ratio better than 1.5. We show that the greedy strategy (minimizing the number of reassignments in every step) is not better than Ω(h) competitive. We give a 2-resource augmented online algorithm that achieves an amortized constant number of (re-)assignments. Finally, we show that the problem is fixed-parameter tractable.

An algorithmic view on OVSF code assignment

Abstract: The combinatorial core of the OVSF code assignment problem that arises in UMTS is to assign some nodes of a complete binary tree of height h (the code tree) to n simultaneous connections, such that no two assigned nodes (codes) are on the same root-to-leaf path. Each connection requires a code on a specified level. The code can change over time as long as it is still on the same level. We consider the one-step code assignment problem: Given an assignment, move the minimum number of codes to serve a new request. Minn and Siu proposed the so-called DCA-algorithm to solve the problem optimally. We show that DCA does not always return an optimal solution, and that the problem is NP-hard. We give an exact n O(h) -time algorithm, and a polynomial time greedy algorithm that achieves approximation ratio Θ(h). Finally, we consider the online code assignment problem for which we derive several results.

An Algorithmic View on OVSF Code Assignment

Abstract: The combinatorial core of the OVSF code assignment problem that arises in UMTS is to assign some nodes of a complete binary tree of height h (the code tree) to n simultaneous connections, such that no two assigned nodes (codes) are on the same root-to-leaf path. Each connection requires a code on a specified level. The code can change over time as long as it is still on the same level. We consider the one-step code assignment problem: Given an assignment, move the minimum number of codes to serve a new request. Minn and Siu proposed the so-called DCA-algorithm to solve the problem optimally. We show that DCA does not always return an optimal solution, and that the problem is NP-hard. We give an exact n O( h)-time algorithm, and a polynomial time greedy algorithm that achieves approximation ratio Θ(h). Finally, we consider the online code assignment problem for which we derive several results.

An Algorithmic View on OVSF Code Assignment

Abstract: The combinatorial core of the OVSF code assignment problem that arises in UMTS is to assign some nodes of a complete binary tree of height h (the code tree) to n simultaneous connections, such that no two assigned nodes (codes) are on the same root-to-leaf path. Each connection requires a code on a specified level. The code can change over time as long as it is still on the same level. We consider the one-step code assignment problem: Given an assignment, move the minimum number of codes to serve a new request. Minn and Siu proposed the so-called DCA-algorithm to solve the problem optimally. We show that DCA does not always return an optimal solution, and that the problem is NP-hard. We give an exact n O( h)-time algorithm, and a polynomial time greedy algorithm that achieves approximation ratio Θ(h). Finally, we consider the online code assignment problem for which we derive several results.

Sugar transporters for intercellular exchange and nutrition of pathogens

Abstract: Sugar efflux transporters are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. Despite broad biological importance, the identity of sugar efflux transporters has remained elusive. Using optical glucose sensors, we identified a new class of sugar transporters, named SWEETs, and show that at least six out of seventeen Arabidopsis, two out of over twenty rice and two out of seven homologues in Caenorhabditis elegans, and the single copy human protein, mediate glucose transport. Arabidopsis SWEET8 is essential for pollen viability, and the rice homologues SWEET11 and SWEET14 are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter. Bacterial symbionts and fungal and bacterial pathogens induce the expression of different SWEET genes, indicating that the sugar efflux function of SWEET transporters is probably targeted by pathogens and symbionts for nutritional gain. The metazoan homologues may be involved in sugar efflux from intestinal, liver, epididymis and mammary cells.

The role of gibberellin signalling in plant responses to abiotic stress

Abstract: Plant hormones are small molecules that regulate plant growth and development, as well as responses to changing environmental conditions. By modifying the production, distribution or signal transduction of these hormones, plants are able to regulate and coordinate both growth and/or stress tolerance to promote survival or escape from environmental stress. A central role for the gibberellin (GA) class of growth hormones in the response to abiotic stress is becoming increasingly evident. Reduction of GA levels and signalling has been shown to contribute to plant growth restriction on exposure to several stresses, including cold, salt and osmotic stress. Conversely, increased GA biosynthesis and signalling promote growth in plant escape responses to shading and submergence. In several cases, GA signalling has also been linked to stress tolerance. The transcriptional regulation of GA metabolism appears to be a major point of regulation of the GA pathway, while emerging evidence for interaction of the GA-signalling molecule DELLA with components of the signalling pathway for the stress hormone jasmonic acid suggests additional mechanisms by which GA signalling may integrate multiple hormone signalling pathways in the response to stress. Here, we review the evidence for the role of GA in these processes, and the regulation of the GA signalling pathway on exposure to abiotic stress. The potential mechanisms by which GA signalling modulates stress tolerance are also discussed.

Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models

Abstract: Hydrogen peroxide (H(2)O(2)) is an important signal molecule involved in plant development and environmental responses. Changes in H(2)O(2) availability can result from increased production or decreased metabolism. While plants contain several types of H(2)O(2)-metabolizing proteins, catalases are highly active enzymes that do not require cellular reductants as they primarily catalyse a dismutase reaction. This review provides an update on plant catalase genes, function, and subcellular localization, with a focus on recent information generated from studies on Arabidopsis. Original data are presented on Arabidopsis catalase single and double mutants, and the use of some of these lines as model systems to investigate the outcome of increases in intracellular H(2)O(2) are discussed. Particular attention is paid to interactions with cell thiol-disulphide status; the use of catalase-deficient plants to probe the apparent redundancy of reductive H(2)O(2)-metabolizing pathways; the importance of irradiance and growth daylength in determining the outcomes of catalase deficiency; and the induction of pathogenesis-related responses in catalase-deficient lines. Within the context of strategies aimed at understanding and engineering plant stress responses, the review also considers whether changes in catalase activities in wild-type plants are likely to be a significant part of plant responses to changes in environmental conditions or biotic challenge.

A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion

Abstract: Plant cells are immobile; thus, plant growth and development depend on cell expansion rather than cell migration. The molecular mechanism by which the plasma membrane initiates changes in the cell expansion rate remains elusive. We found that a secreted peptide, RALF (rapid alkalinization factor), suppresses cell elongation of the primary root by activating the cell surface receptor FERONIA in Arabidopsis thaliana. A direct peptide-receptor interaction is supported by specific binding of RALF to FERONIA and reduced binding and insensitivity to RALF-induced growth inhibition in feronia mutants. Phosphoproteome measurements demonstrate that the RALF-FERONIA interaction causes phosphorylation of plasma membrane H+–adenosine triphosphatase 2 at Ser899, mediating the inhibition of proton transport. The results reveal a molecular mechanism for RALF-induced extracellular alkalinization and a signaling pathway that regulates cell expansion.