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Michael Kaufmann

Bio: Michael Kaufmann is an academic researcher from University of Tübingen. The author has contributed to research in topics: Planar graph & ASDEX Upgrade. The author has an hindex of 54, co-authored 430 publications receiving 10475 citations. Previous affiliations of Michael Kaufmann include Saarland University & Princeton University.


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01 May 2001
TL;DR: This paper presents a meta-modelling procedure for graph drawing that automates the very labor-intensive and therefore time-heavy and expensive process of drawing graphs.
Abstract: Graph Drawing and Its Applications.- Drawing Planar Graphs.- Drawing Trees, Series-Parallel Digraphs, and Lattices.- Drawing on Physical Analogies.- Layered Drawings of Digraphs.- Orthogonal Graph Drawing.- 3D Graph Drawing.- Drawing Clusters and Hierarchies.- Dynamic Graph Drawing.- Map Labeling with Application to Graph Drawing.- Software Packages.

432 citations

Journal ArticleDOI
TL;DR: DIALIGN-TX is presented, a substantial improvement of DIAL IGN-T that combines the previous greedy algorithm with a progressive alignment approach and produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly.
Abstract: DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach. Our new heuristic produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly. The new method is based on a guide tree; to detect possible spurious sequence similarities, it employs a vertex-cover approximation on a conflict graph. We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively. For alignment of nucleic acid sequences, we used BRAliBase II for global alignment and a newly developed database of locally related sequences called DIRM-BASE 1. IRMBASE 2 and DIRMBASE 1 are constructed by implanting highly conserved motives at random positions in long unalignable sequences. On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX.

261 citations

Journal ArticleDOI
TL;DR: A complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment.
Abstract: Background We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level.

226 citations

Journal ArticleDOI
TL;DR: In this article, the authors used deuterium pellets to accelerate type-I edge localized modes (ELMs) in high-constraint mode (H-mode) discharges.
Abstract: In ASDEX Upgrade, experimental efforts aim to establish pace making and mitigation of type-I edge localized modes (ELMs) in high confinement mode (H-mode) discharges. Injection of small size cryogenic deuterium pellets (~(1.4?mm)2 ? 0.2?mm ? 2.5 ? 1019?D) at rates up to 83?Hz imposed persisting ELM control without significant fuelling, enabling for investigations well inside the type-I ELM regime. The approach turned out to meet all required operational features. ELM pace making was realized with the driving frequency ranging from 1 to 2.8 times the intrinsic ELM frequency, the upper boundary set by hardware limits. ELM frequency enhancement by pellet pace making causes much less confinement reduction than by engineering means like heating, gas bleeding or plasma shaping. Confinement reduction is observed in contrast to the typical for engineering parameters. Matched discharges showed triggered ELMs ameliorated with respect to intrinsic counterparts while their frequency was increased. No significant differences were found in the ELM dynamics with the available spatial and temporal resolution. By breaking the close correlation of ELM frequency and plasma parameters, pace making allows the establishment of fELM as a free parameter giving enhanced operational headroom for tailoring H-mode scenarios with acceptable ELMs. Use was made of the pellet pace making tool in several successful applications in different scenarios. It seems that further reduction of the pellet mass could be possible, eventually resulting in less confinement reduction as well.

205 citations

Journal ArticleDOI
TL;DR: In this paper, local edge parameters on the ASDEX upgrade tokamak are investigated at the L-mode to H-mode transition, during phases with various types of edge-localized modes (ELMs), and at the density limit.
Abstract: Local edge parameters on the ASDEX Upgrade tokamak are investigated at the L-mode to H-mode transition, during phases with various types of edge-localized modes (ELMs), and at the density limit. A scaling law for the boundary electron temperature, , is found which describes the H-mode threshold for deuterium-puffed discharges with favourable ion -drift direction. The region of stable operation is bounded by type I ELMs near the ideal ballooning limit and by a minimum temperature necessary to avoid thermal instability of the plasma edge. Stationary operation with type III ELMs imposes an upper limit on the edge temperature. Within the entire range of boundary densities investigated , both L-mode and H-mode are found to be accessible. During type I ELMy H-mode, a relation of global confinement with the edge pressure gradient is found which is connected with a loss of the favourable density dependence predicted by the ITER-92P and ITER-93H ELMy H-mode scalings. At high density, better confinement is achieved in H-modes with an edge pressure gradient below the ideal ballooning limit, e.g. during type III ELMy H-mode with impurity-seeded radiation.

201 citations


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08 Dec 2001-BMJ
TL;DR: There is, I think, something ethereal about i —the square root of minus one, which seems an odd beast at that time—an intruder hovering on the edge of reality.
Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

33,785 citations

Journal ArticleDOI
TL;DR: A biologist-oriented portal that provides a gene list annotation, enrichment and interactome resource and enables integrated analysis of multi-OMICs datasets, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
Abstract: A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era

6,282 citations

Journal ArticleDOI
TL;DR: The initial version of the MAFFT program was developed in 2002 and was updated in 2007 with two new techniques: the PartTree algorithm and the Four-way consistency objective function, which improved the scalability of progressive alignment and the accuracy of ncRNA alignment.
Abstract: The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional noncoding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these problems, in 2007, we updated MAFFT to Version 6 with two new techniques: the PartTree algorithm and the Four-way consistency objective function. The former improved the scalability of progressive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques that MAFFTuses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/.

3,278 citations

Journal ArticleDOI
TL;DR: The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.
Abstract: Most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. In the KEGG database resource (http://www.genome.jp/kegg/), diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. Disease information is computerized in two forms: pathway maps and gene/ molecule lists. The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. This database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

2,181 citations