Arndt von Haeseler

Last updated
Arndt von Haeseler
Born (1959-02-28) 28 February 1959 (age 63)
Bremen [1]
Alma mater
Scientific career
Fields
Institutions
Thesis Rekonstruktion phylogenetischer Bäume mit Hilfe von Varianten der Vier-Punkt-Bedingung [2]  (1988)
Doctoral advisor
Doctoral students
Website www.cibiv.at/~haeseler/

Arndt von Haeseler (born 28 February 1959) is a German bioinformatician and evolutionary biologist. He is the scientific director of the Max F. Perutz Laboratories at the Vienna Biocenter and a professor of bioinformatics at the University of Vienna and the Medical University of Vienna.

Contents

Education

Arndt von Haeseler obtained a doctorate in mathematics from the University of Bielefeld in 1988 under the supervision of Andreas Dress and Hans-Georg Carstens. [1] [2] He habilitated in 1994 at the Department of Zoology of the University of Munich, [1] where he remained as a lecturer until 1998. [3]

Research and career

From 1998 until 2001, von Haeseler was a group leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig. [3] From 2001 until 2005, he was professor of bioinformatics at the University of Düsseldorf. [1] He was a group leader in bioinformatics at Forschungszentrum Jülich. [3] In 2005, he joined the Max F. Perutz Laboratories (MFPL) in Vienna, where he leads the Center for Integrative Bioinformatics Vienna (CIBIV). [1] In 2017, he became the scientific director of the MFPL. [4] [5] He is a professor of bioinformatics at the University of Vienna and the Medical University of Vienna. [4] At the University Vienna, he is the dean of the Center for Molecular Biology. [6] At the Medical University of Vienna, he is the head of the Department for Medical Biochemistry. [7]

His research focuses on developing computational methods for the reconstruction of phylogenetic trees. [3] He co-authored the phylogenetics software packages TREEFINDER, [8] TREE-PUZZLE, [9] and its successor, IQ-TREE. [10] [11]

He sits on the editorial boards of Molecular Biology and Evolution and BMC Evolutionary Biology . [12] [13] [14]

Awards and honours

In 2015, von Haeseler was elected as a corresponding member of the mathematics and science class of the Austrian Academy of Sciences. [12] [15]

Since 1999, he holds an honorary professorship in theoretical biology at the University of Leipzig. [12] [16]

Related Research Articles

<span class="mw-page-title-main">Max Perutz</span> Austrian-born British molecular biologist (1914–2002)

Max Ferdinand Perutz was an Austrian-born British molecular biologist, who shared the 1962 Nobel Prize for Chemistry with John Kendrew, for their studies of the structures of haemoglobin and myoglobin. He went on to win the Royal Medal of the Royal Society in 1971 and the Copley Medal in 1979. At Cambridge he founded and chaired (1962–79) The Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), fourteen of whose scientists have won Nobel Prizes. Perutz's contributions to molecular biology in Cambridge are documented in The History of the University of Cambridge: Volume 4 published by the Cambridge University Press in 1992.

Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics:

Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms.

PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 65 portable programs, i.e., the source code is written in the programming language C. As of version 3.696, it is licensed as open-source software; versions 3.695 and older were proprietary software freeware. Releases occur as source code, and as precompiled executables for many operating systems including Windows, Mac OS 8, Mac OS 9, OS X, Linux ; and FreeBSD from FreeBSD.org. Full documentation is written for all the programs in the package and is included therein. The programs in the phylip package were written by Professor Joseph Felsenstein, of the Department of Genome Sciences and the Department of Biology, University of Washington, Seattle.

Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics.

<span class="mw-page-title-main">Roderic D. M. Page</span> New Zealand-born evolutionary biologist

Roderic Dugald Morton Page is a New Zealand-born evolutionary biologist at the University of Glasgow, Scotland, and the author of several books. As of 2015 he is professor at the University of Glasgow and was editor of the journal Systematic Biology until the end of 2007. His main interests are in phylogenetics, evolutionary biology and bioinformatics.

TREE-PUZZLE is a computer program used to construct phylogenetic trees from sequence data by maximum likelihood analysis. Branch lengths can be calculated with and without the molecular clock hypothesis.

Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences. It was written by Gangolf Jobb, a former researcher at the University of Munich, Germany, and was originally released in 2004. Treefinder is free of charge, though the most recent license prohibits its use in the USA and eight European countries.

<span class="mw-page-title-main">Gregor Mendel Institute</span> Research institute in Vienna, Austria

The Gregor Mendel Institute of Molecular Plant Biology (GMI) is a basic research institute in Vienna, Austria. It was founded in 2000 by the Austrian Academy of Sciences (ÖAW) to promote cutting-edge research in the field of molecular plant biology. The GMI employs about 130 people. Its founding director was Dieter Schweizer, and the current scientific director is Magnus Nordborg. The institute is named after Gregor Mendel, who is also known as the "Father of genetics," due to his scientific work and the fact that he studied at the University of Vienna in the mid-19th century.

<span class="mw-page-title-main">Institute of Molecular Biotechnology</span>

The Institute of Molecular Biotechnology (IMBA) is an independent biomedical research organisation founded by the Austrian Academy of Sciences in cooperation with the pharmaceutical company Boehringer Ingelheim. The institute employs around 250 people from over 40 countries, who perform basic research. IMBA is located at the Vienna BioCenter (VBC) and shares facilities and scientific training programs with the Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences and the Research Institute of Molecular Pathology (IMP), the basic research center of Boehringer Ingelheim.

A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets or a different selection of taxa. Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities. The input trees of a supertree should behave as samples from the larger tree.

Horizontal or lateral gene transfer is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages.

<span class="mw-page-title-main">Max Perutz Labs</span>

The Max Perutz Labs Vienna are a molecular biology research centre operated jointly by the University of Vienna and the Medical University of Vienna located at the Vienna Biocenter. The institute is named after the Viennese-born biochemist and Nobel laureate Max Ferdinand Perutz. On average, the institute hosts 50 independent research groups. Max Perutz Labs scientists participate in the undergraduate curricula for students of the University of Vienna and the Medical University of Vienna.

Bacterial phylodynamics is the study of immunology, epidemiology, and phylogenetics of bacterial pathogens to better understand the evolutionary role of these pathogens. Phylodynamic analysis includes analyzing genetic diversity, natural selection, and population dynamics of infectious disease pathogen phylogenies during pandemics and studying intra-host evolution of viruses. Phylodynamics combines the study of phylogenetic analysis, ecological, and evolutionary processes to better understand of the mechanisms that drive spatiotemportal incidence and phylogenetic patterns of bacterial pathogens. Bacterial phylodynamics uses genome-wide single-nucleotide polymorphisms (SNP) in order to better understand the evolutionary mechanism of bacterial pathogens. Many phylodynamic studies have been performed on viruses, specifically RNA viruses which have high mutation rates. The field of bacterial phylodynamics has increased substantially due to the advancement of next-generation sequencing and the amount of data available.

<span class="mw-page-title-main">Vienna Biocenter</span> Group of life science research institutes in Vienna, Austria

The Vienna BioCenter is a cluster of life science research institutes and biotechnology companies located in the 3rd municipal District of Vienna, Austria. It grew around the Research Institute of Molecular Pathology (IMP), which opened in 1988. The entities at the Vienna BioCenter employ more than 2,000 people, including 600 students.

Korbinian Strimmer is a German statistician specialising in biomedical data science. He is a professor in statistics at the University of Manchester.

Minimum evolution is a distance method employed in phylogenetics modeling. It shares with maximum parsimony the aspect of searching for the phylogeny that has the shortest total sum of branch lengths.

<span class="mw-page-title-main">Phylogenetic reconciliation</span>

In phylogenetics, reconciliation is an approach to connect the history of two or more coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree representing the evolution of an entity can be drawn within another phylogenetic tree representing an encompassing entity to reveal their interdependence and the evolutionary events that have marked their shared history. The development of reconciliation approaches started in the 1980s, mainly to depict the coevolution of a gene and a genome, and of a host and a symbiont, which can be mutualist, commensalist or parasitic. It has also been used for example to detect horizontal gene transfer, or understand the dynamics of genome evolution.

References

  1. 1 2 3 4 5 "Prof. von Haeseler hält seine Antrittsvorlesung an der VUW" (PDF). Veterinärmedizinische Universität Wien (in German).
  2. 1 2 Arndt von Haeseler at the Mathematics Genealogy Project
  3. 1 2 3 4 "Arndt von Haeseler – Austrian Computer Science Day 2016". Austrian Computer Science Day 2016. Retrieved 2018-02-17.
  4. 1 2 "Organisation". Max F. Perutz Laboratories. Retrieved 2018-02-11.
  5. "MFPL History". Home. Retrieved 2018-02-16.
  6. "Center for molecular biology". Zentrum für molekulare Biologie (ZMB). Retrieved 2018-02-11.
  7. Vienna, Medical University of. "Zentrum für Medizinische Biochemie". Medical University of Vienna. Retrieved 2018-02-17.
  8. Jobb, Gangolf; von Haeseler, Arndt; Strimmer, Korbinian (2004). "TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics". BMC Evolutionary Biology. Springer Nature. 4 (1): 18. doi:10.1186/1471-2148-4-18. ISSN   1471-2148. PMC   459214 . PMID   15222900. (Retracted, see doi:10.1186/s12862-015-0513-z)
  9. Schmidt, Heiko A.; Strimmer, Korbinian; Vingron, Martin; Haeseler, von (2002-03-01). "TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing". Bioinformatics. 18 (3): 502–504. doi: 10.1093/bioinformatics/18.3.502 . ISSN   1367-4803. PMID   11934758 . Retrieved 2018-02-17.
  10. Nguyen, Lam-Tung; Schmidt, Heiko A.; Haeseler, von; Minh, Bui Quang (2014-11-03). "IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies". Molecular Biology and Evolution. 32 (1): 268–274. doi:10.1093/molbev/msu300. ISSN   0737-4038. PMC   4271533 . PMID   25371430.
  11. Trifinopoulos, Jana; Nguyen, Lam-Tung; von Haeseler, Arndt; Minh, Bui Quang (2016-04-15). "W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis". Nucleic Acids Research. 44 (W1): W232–W235. doi:10.1093/nar/gkw256. ISSN   0305-1048. PMC   4987875 . PMID   27084950.
  12. 1 2 3 "ÖAW Mitglieder Detail". Österreichische Akademie der Wissenschaften (in German). Retrieved 2018-02-16.
  13. "BMC Evolutionary Biology". BMC Evolutionary Biology. Retrieved 2018-02-16.
  14. "Editorial Board - Molecular Biology and Evolution". Oxford Academic. Retrieved 2018-02-16.
  15. "Three MFPL group leaders elected as members of the Austrian Academy of Sciences ÖAW". Home. 2015-10-15. Retrieved 2018-02-16.
  16. "Bericht des Rektoratskollegiums 1999/2000" (PDF). University of Leipzig (in German).[ permanent dead link ]