Stefan Burkhardt

Vatican Secret Archives

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Juha Kärkkäinen

University of Helsinki

Achim Schweikard

University of Lübeck

Rainer Burgkart

Klinikum rechts der Isar

Michael Roth

Deutsches Zentrum für Luft- und Raumfahrt e. V. (DLR)

Margit Mersch

Ruhr University Bochum

ÉR

Éric Rivals

Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier

Esko Ukkonen

University of Helsinki

Kimmo Fredriksson

University of Eastern Finland

Janne Ravantti

University of Helsinki

T. Ojamies

University of Helsinki

Cooperative Institutions

Deutsche Nationalbibliothek

Vatican Secret Archives

University of Helsinki

Max Planck Society

Heidelberg University

University of Freiburg

Freie Universität Berlin

Saarland University

Leipzig University

Max Planck Institute for Informatics

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Segmentation des Knochens aus MR Tomogrammen

Stefan Burkhardt

Source

Cite

Citations (0)

q-gram Based Database Searching Using a Suffix Array (QUASAR)

Untitled Event (1999)

Stefan Burkhardt Andreas Crauser Paolo Ferragina Hans‐Peter Lenhof Éric Rivals

Suffix array

Gram

Source

Cite

Citations (17)

Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences

Journal of Virology (2005)

Aline Flockerzi Stefan Burkhardt W. Schempp Eckart Meese Jens Mayer

ABSTRACT The human genome harbors many distinct families of human endogenous retroviruses (HERVs) that stem from exogenous retroviruses that infected the germ line millions of years ago. Many HERV families remain to be investigated. We report in the present study the detailed characterization of the HERV-K14I and HERV-K14CI families as they are represented in the human genome. Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line ∼39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock. Proviruses of both families were formed during a brief period. A majority of HERV-K14CI proviruses on the Y chromosome mimic a higher evolutionary age, showing that LTR-LTR divergence data can indicate false ages. Fully translatable consensus sequences encoding major retroviral proteins were generated. Most HERV-K14I loci lack an env gene and are structurally reminiscent of LTR retrotransposons. A minority of HERV-K14I variants display an env gene. HERV-K14I proviruses are associated with three distinct LTR families, while HERV-K14CI is associated with a single LTR family. Hybrid proviruses consisting of HERV-K14I and HERV-W sequences that appear to have produced provirus progeny in the genome were detected. Several HERV-K14I proviruses harbor TRPC6 mRNA portions, exemplifying mobilization of cellular transcripts by HERVs. Our analysis contributes essential information on two more HERV families and on the biology of HERV sequences in general.

Provirus

Retrotransposon

Endogenous retrovirus

10.1128/jvi.79.5.2941-2949.2005

Cite

Citations (37)

Fast Lightweight Suffix Array Construction and Checking

Lecture notes in computer science (2003)

Stefan Burkhardt Juha Kärkkäinen

Suffix array

Compressed suffix array

Sublinear function

10.1007/3-540-44888-8_5

Cite

Citations (52)

Idoneität im Spannungsfeld von Verwandtschaft und päpstlicher Begutachtung. Zwei Fälle mediterranen Kaisertums

Böhlau Verlag eBooks (2013)

Stefan Burkhardt

Download

10.7788/9783412211868-010

Cite

Citations (0)

Genetic and ultrastructural characterization of a European isolate of the fatal endotheliotropic elephant herpesvirus

Journal of General Virology (2001)

Bernhard Ehlers Stefan Burkhardt Michael Goltz V. Bergmann A. Ochs

A male Asian elephant ( Elephas maximus ) died at the Berlin zoological gardens in August 1998 of systemic infection with the novel endotheliotropic elephant herpesvirus (ElHV-1). This virus causes a fatal haemorrhagic disease in Asian elephants, the so-called endothelial inclusion body disease, as reported from North American zoological gardens. In the present work, ElHV-1 was visualized ultrastructurally in affected organ material. Furthermore, a gene block comprising the complete glycoprotein B (gB) and DNA polymerase (DPOL) genes as well as two partial genes was amplified by PCR-based genome walking and sequenced. The gene content and arrangement were similar to those of members of the Betaherpesvirinae . However, phylogenetic analysis with gB and DPOL consistently revealed a very distant relationship to the betaherpesviruses. Therefore, ElHV-1 may be a member of a new genus or even a new herpesvirus subfamily. The sequence information generated was used to set up a nested-PCR assay for diagnosis of suspected cases of endothelial inclusion body disease. Furthermore, it will aid in the development of antibody-based detection methods and of vaccination strategies against this fatal herpesvirus infection in the endangered Asian elephant.

Asian elephant

Subfamily

10.1099/0022-1317-82-3-475

Cite

Citations (43)

Bestimmung der Gradientenstärken von MR-Sequenzen mit Hilfe von Kalibrierkörpern

Informatik aktuell (2003)

Stefan Burkhardt Achim Schweikard Rainer Burgkart

10.1007/978-3-642-18993-7_26

Cite

Citations (0)

Staufisches Kaisertum im 12. Jahrhundert : Konzepte - Netzwerke - politische Praxis

Schnell & Steiner eBooks (2010)

Stefan Burkhardt

Source

Cite

Citations (22)

BDD-BASED ANALYSIS OF GAPPED q-GRAM FILTERS

International Journal of Foundations of Computer Science (2005)

Marc Fontaine Stefan Burkhardt Juha Kärkkäinen

Recently, there has been a surge of interest in gapped q-gram filters for approximate string matching. Important design parameters for filters are for example the value of q, the filter-threshold and in particular the shape (aka seed) of the filter. A good choice of parameters can improve the performance of a q-gram filter by orders of magnitude and optimizing these parameters is a nontrivial combinatorial problem. We describe a new method for analyzing gapped q-gram filters. This method is simple and generic. It applies to a variety of filters, overcomes many restrictions that are present in existing algorithms and can easily be extended to new filter variants. To implement our approach, we use an extended version of BDDs (Binary Decision Diagrams), a data structure that efficiently represents sets of bit-strings. In a second step, we define a new class of multi-shape filters and analyze these filters with the BDD-based approach. Experiments show that multi-shape filters can outperform the best single-shape filters, which are currently in use, in many aspects. The BDD-based algorithm is crucial for the design and analysis of these new and better multi-shape filters. Our results apply to the k-mismatches problem, i.e. approximate string matching with Hamming distance.

Hamming distance

10.1142/s0129054105003698

Cite

Citations (3)

Korrektur von geometrischen Verzeichnungen bei MR-Aufnahmen vom Femur

Informatik aktuell (2002)

Stefan Burkhardt Michael Roth Achim Schweikard Rainer Burgkart

10.1007/978-3-642-55983-9_25

Cite

Citations (3)