Publications by authors named "Arndt von Haeseler"

100Publications

A human tissue screen identifies a regulator of ER secretion as a brain-size determinant.

Science 2020 Nov 29;370(6519):935-941. Epub 2020 Oct 29.

Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1126/science.abb5390DOI Listing
November 2020

Structure of the space of taboo-free sequences.

J Math Biol 2020 Nov 17;81(4-5):1029-1057. Epub 2020 Sep 17.

Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030, Vienna, Austria.

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http://dx.doi.org/10.1007/s00285-020-01535-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560954PMC
November 2020

Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function.

Mol Biol Evol 2020 Sep 15. Epub 2020 Sep 15.

Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.

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http://dx.doi.org/10.1093/molbev/msaa234DOI Listing
September 2020

Distinguishing Felsenstein zone from Farris zone using neural networks.

Mol Biol Evol 2020 Jul 8. Epub 2020 Jul 8.

Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/msaa164DOI Listing
July 2020

A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.

Genome Biol Evol 2020 04;12(4):345-357

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/gbe/evaa046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186786PMC
April 2020

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.

Mol Biol Evol 2020 05;37(5):1530-1534

Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.1093/molbev/msaa015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182206PMC
May 2020

Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host-Microbe Interactions.

Curr Protoc Plant Biol 2019 09;4(3):e20097

Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1002/cppb.20097DOI Listing
September 2019

GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments.

Syst Biol 2020 03;69(2):249-264

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/sysbio/syz051DOI Listing
March 2020

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.

BMC Bioinformatics 2019 May 20;20(1):258. Epub 2019 May 20.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, VBC, 1030, Vienna, Austria.

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http://dx.doi.org/10.1186/s12859-019-2849-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528199PMC
May 2019

Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.

Mol Biol Evol 2019 06;36(6):1294-1301

Centre for Biological Diversity, University of St Andrews, St Andrews, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msz043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526911PMC
June 2019

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.

J Pers Med 2019 Feb 1;9(1). Epub 2019 Feb 1.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria.

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http://dx.doi.org/10.3390/jpm9010010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463100PMC
February 2019

The Evolutionary Traceability of a Protein.

Genome Biol Evol 2019 02;11(2):531-545

Applied Bioinformatics Group, Institute of Cell Biology & Neuroscience, Goethe University, Frankfurt, Germany.

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http://dx.doi.org/10.1093/gbe/evz008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394115PMC
February 2019

Accurate detection of complex structural variations using single-molecule sequencing.

Nat Methods 2018 06 30;15(6):461-468. Epub 2018 Apr 30.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1038/s41592-018-0001-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990442PMC
June 2018

In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction.

PLoS Biol 2018 04 23;16(4):e2005129. Epub 2018 Apr 23.

Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1371/journal.pbio.2005129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5912717PMC
April 2018

TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers.

Bioinformatics 2018 09;34(18):3137-3144

Center for Integrative Bioinformatics Vienna (CIBIV), Joint Institute of the University of Vienna and Medicial University of Vienna, Max F. Perutz Laboratories (MFPL), Vienna, Austria.

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https://academic.oup.com/bioinformatics/article/34/18/3137/4
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http://dx.doi.org/10.1093/bioinformatics/bty283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157883PMC
September 2018

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.

Nat Commun 2018 04 17;9(1):1517. Epub 2018 Apr 17.

Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.

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http://dx.doi.org/10.1038/s41467-018-03861-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904100PMC
April 2018

Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria.

G3 (Bethesda) 2018 05 4;8(5):1475-1480. Epub 2018 May 4.

Department of Dermatology, Medical University of Vienna, Austria

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http://dx.doi.org/10.1534/g3.117.300394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940141PMC
May 2018

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

BMC Evol Biol 2018 02 2;18(1):11. Epub 2018 Feb 2.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria.

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http://dx.doi.org/10.1186/s12862-018-1131-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5796505PMC
February 2018

Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model.

Syst Biol 2018 May;67(3):552-558

Center for Integrative Bioinformatics Vienna, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria.

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http://dx.doi.org/10.1093/sysbio/syx092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204645PMC
May 2018

UFBoot2: Improving the Ultrafast Bootstrap Approximation.

Mol Biol Evol 2018 02;35(2):518-522

Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.

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http://dx.doi.org/10.1093/molbev/msx281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850222PMC
February 2018

Thiol-linked alkylation of RNA to assess expression dynamics.

Nat Methods 2017 Dec 25;14(12):1198-1204. Epub 2017 Sep 25.

Institute of Molecular Biotechnology, Vienna Biocenter Campus, Vienna, Austria.

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http://dx.doi.org/10.1038/nmeth.4435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712218PMC
December 2017

ModelFinder: fast model selection for accurate phylogenetic estimates.

Nat Methods 2017 Jun 8;14(6):587-589. Epub 2017 May 8.

Land &Water, CSIRO, Canberra, Australian Capital Territory, Australia.

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http://www.nature.com/doifinder/10.1038/nmeth.4285
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http://dx.doi.org/10.1038/nmeth.4285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453245PMC
June 2017

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile.

J Comput Biol 2017 Mar 23;24(3):200-212. Epub 2016 Sep 23.

1 Max F. Perutz Laboratories (MFPL), Center for Integrative Bioinformatics Vienna (CIBIV), University of Vienna, Medical University of Vienna , Vienna, Austria .

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http://dx.doi.org/10.1089/cmb.2016.0096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346924PMC
March 2017

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

J Theor Biol 2016 10 29;407:362-370. Epub 2016 Jul 29.

Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.07.042DOI Listing
October 2016

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices.

Syst Biol 2016 Nov 26;65(6):997-1008. Epub 2016 Apr 26.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Vienna, Austria and

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http://dx.doi.org/10.1093/sysbio/syw037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066062PMC
November 2016

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.

Nucleic Acids Res 2016 07 15;44(W1):W232-5. Epub 2016 Apr 15.

Center for Integrative Bioinformatics, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, 1030 Vienna, Austria

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http://dx.doi.org/10.1093/nar/gkw256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987875PMC
July 2016

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha.

Genome Res 2016 Apr 21;26(4):462-73. Epub 2016 Jan 21.

Department of Medical Biochemistry, Medical University of Vienna, A-1030 Vienna, Austria;

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http://dx.doi.org/10.1101/gr.196220.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817770PMC
April 2016

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

Genome Biol 2015 Oct 22;16:235. Epub 2015 Oct 22.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1186/s13059-015-0803-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618857PMC
October 2015

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

J Comput Biol 2015 Dec 8;22(12):1129-42. Epub 2015 Oct 8.

1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .

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http://dx.doi.org/10.1089/cmb.2015.0146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663649PMC
December 2015

Split diversity in constrained conservation prioritization using integer linear programming.

Methods Ecol Evol 2015 Jan 6;6(1):83-91. Epub 2014 Dec 6.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna Vienna, Austria ; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna Vienna, Austria.

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http://dx.doi.org/10.1111/2041-210X.12299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392707PMC
January 2015

Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.

BMC Vet Res 2015 Apr 10;11:90. Epub 2015 Apr 10.

VetCore Facility for Research, University of Veterinary Medicine Vienna, A-1210, Vienna, Austria.

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http://dx.doi.org/10.1186/s12917-015-0378-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424575PMC
April 2015

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Authors:
Ariel D Chipman David E K Ferrier Carlo Brena Jiaxin Qu Daniel S T Hughes Reinhard Schröder Montserrat Torres-Oliva Nadia Znassi Huaiyang Jiang Francisca C Almeida Claudio R Alonso Zivkos Apostolou Peshtewani Aqrawi Wallace Arthur Jennifer C J Barna Kerstin P Blankenburg Daniela Brites Salvador Capella-Gutiérrez Marcus Coyle Peter K Dearden Louis Du Pasquier Elizabeth J Duncan Dieter Ebert Cornelius Eibner Galina Erikson Peter D Evans Cassandra G Extavour Liezl Francisco Toni Gabaldón William J Gillis Elizabeth A Goodwin-Horn Jack E Green Sam Griffiths-Jones Cornelis J P Grimmelikhuijzen Sai Gubbala Roderic Guigó Yi Han Frank Hauser Paul Havlak Luke Hayden Sophie Helbing Michael Holder Jerome H L Hui Julia P Hunn Vera S Hunnekuhl LaRonda Jackson Mehwish Javaid Shalini N Jhangiani Francis M Jiggins Tamsin E Jones Tobias S Kaiser Divya Kalra Nathan J Kenny Viktoriya Korchina Christie L Kovar F Bernhard Kraus François Lapraz Sandra L Lee Jie Lv Christigale Mandapat Gerard Manning Marco Mariotti Robert Mata Tittu Mathew Tobias Neumann Irene Newsham Dinh N Ngo Maria Ninova Geoffrey Okwuonu Fiona Ongeri William J Palmer Shobha Patil Pedro Patraquim Christopher Pham Ling-Ling Pu Nicholas H Putman Catherine Rabouille Olivia Mendivil Ramos Adelaide C Rhodes Helen E Robertson Hugh M Robertson Matthew Ronshaugen Julio Rozas Nehad Saada Alejandro Sánchez-Gracia Steven E Scherer Andrew M Schurko Kenneth W Siggens DeNard Simmons Anna Stief Eckart Stolle Maximilian J Telford Kristin Tessmar-Raible Rebecca Thornton Maurijn van der Zee Arndt von Haeseler James M Williams Judith H Willis Yuanqing Wu Xiaoyan Zou Daniel Lawson Donna M Muzny Kim C Worley Richard A Gibbs Michael Akam Stephen Richards

PLoS Biol 2014 Nov 25;12(11):e1002005. Epub 2014 Nov 25.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043PMC
November 2014

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.

Mol Biol Evol 2015 Jan 3;32(1):268-74. Epub 2014 Nov 3.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria

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http://dx.doi.org/10.1093/molbev/msu300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271533PMC
January 2015

ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.

Nucleic Acids Res 2014 Oct 26;42(19):12155-68. Epub 2014 Sep 26.

Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, A-1030 Vienna, Austria

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http://dx.doi.org/10.1093/nar/gku844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231736PMC
October 2014

A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity.

BMC Genomics 2014 Aug 27;15:725. Epub 2014 Aug 27.

Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Waehringer Guertel 18 - 20, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2164-15-725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156628PMC
August 2014

Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria.

Mol Microbiol 2014 Sep 5;93(5):1066-78. Epub 2014 Aug 5.

Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen Straße, D-52428, Jülich, Germany.

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http://dx.doi.org/10.1111/mmi.12719DOI Listing
September 2014

SNP2GO: functional analysis of genome-wide association studies.

Genetics 2014 May 21;197(1):285-9. Epub 2014 Feb 21.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1534/genetics.113.160341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012486PMC
May 2014

The evolution of the ribosome biogenesis pathway from a yeast perspective.

Nucleic Acids Res 2014 Feb 14;42(3):1509-23. Epub 2013 Nov 14.

Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt 60438, Germany, Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna 1030, Austria, Institute for Molecular Biosciences, Goethe University, Frankfurt 60438, Germany, Faculty of Computer Science, University of Vienna, Vienna 1030, Austria, Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt 60438, Germany, Department of Biochemistry I, Universitätsmedizin Göttingen, Göttingen 37073, Germany and Center of Membrane Proteomics, Goethe University, Frankfurt 60438, Germany.

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http://dx.doi.org/10.1093/nar/gkt1137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919561PMC
February 2014

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Bioinformatics 2013 Nov 23;29(21):2790-1. Epub 2013 Aug 23.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria and Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btt468DOI Listing
November 2013

Exploring the sampling universe of RNA-seq.

Stat Appl Genet Mol Biol 2013 Apr 16;12(2):175-88. Epub 2013 Apr 16.

Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1515/sagmb-2012-0049DOI Listing
April 2013

Ultrafast approximation for phylogenetic bootstrap.

Mol Biol Evol 2013 May 15;30(5):1188-95. Epub 2013 Feb 15.

Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/mst024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670741PMC
May 2013

Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets.

Genomics 2013 Mar 12;101(3):204-9. Epub 2012 Dec 12.

Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.ygeno.2012.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580289PMC
March 2013

On the group theoretical background of assigning stepwise mutations onto phylogenies.

Algorithms Mol Biol 2012 Dec 15;7(1):36. Epub 2012 Dec 15.

Department of Statistics and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.

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http://dx.doi.org/10.1186/1748-7188-7-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558369PMC
December 2012

NGC: lossless and lossy compression of aligned high-throughput sequencing data.

Nucleic Acids Res 2013 Jan 12;41(1):e27. Epub 2012 Oct 12.

Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr Bohr Gasse 9, Vienna A-1030, Austria.

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http://dx.doi.org/10.1093/nar/gks939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592443PMC
January 2013

Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

PLoS One 2012 20;7(7):e41528. Epub 2012 Jul 20.

Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna, Vienna, Austria.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041528PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401099PMC
February 2013

TreeSnatcher plus: capturing phylogenetic trees from images.

BMC Bioinformatics 2012 May 24;13:110. Epub 2012 May 24.

Department of Bioinformatics, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, Duesseldorf 40225, Germany.

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http://dx.doi.org/10.1186/1471-2105-13-110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411374PMC
May 2012

Identification of an ancient haemophilia A splice site mutation.

Thromb Res 2012 Sep 6;130(3):445-50. Epub 2012 Mar 6.

Division of Haematology and Haemostaseology, Department of Medicine I, Medical University of Vienna, Austria.

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http://dx.doi.org/10.1016/j.thromres.2012.02.008DOI Listing
September 2012

REvolver: modeling sequence evolution under domain constraints.

Mol Biol Evol 2012 Sep 1;29(9):2133-45. Epub 2012 Mar 1.

University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/mss078DOI Listing
September 2012

Do we still need supertrees?

BMC Biol 2012 Feb 27;10:13. Epub 2012 Feb 27.

Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna and Medical University Vienna, Dr,-Bohr-Gasse 9, 1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1741-7007-10-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287151PMC
February 2012

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs.

Genome Res 2012 Aug 6;22(8):1468-76. Epub 2012 Feb 6.

Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1101/gr.133025.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409260PMC
August 2012

A consistent phylogenetic backbone for the fungi.

Mol Biol Evol 2012 May 22;29(5):1319-34. Epub 2011 Nov 22.

Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/msr285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339314PMC
May 2012

ImOSM: intermittent evolution and robustness of phylogenetic methods.

Mol Biol Evol 2012 Feb 22;29(2):663-73. Epub 2011 Sep 22.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msr220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258038PMC
February 2012

The performance of phylogenetic algorithms in estimating haplotype genealogies with migration.

Mol Ecol 2011 May 4;20(9):1952-63. Epub 2011 Apr 4.

Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.

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http://dx.doi.org/10.1111/j.1365-294X.2011.05066.xDOI Listing
May 2011

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets.

Algorithms Mol Biol 2010 Dec 6;5:37. Epub 2010 Dec 6.

Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Dr, Bohr-Gasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-5-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022592PMC
December 2010

Random Tree-Puzzle leads to the Yule-Harding distribution.

Mol Biol Evol 2011 Feb 12;28(2):873-7. Epub 2010 Aug 12.

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http://dx.doi.org/10.1093/molbev/msq212DOI Listing
February 2011

FACT: functional annotation transfer between proteins with similar feature architectures.

BMC Bioinformatics 2010 Aug 9;11:417. Epub 2010 Aug 9.

Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohrgasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2105-11-417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931517PMC
August 2010

MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.

Mol Biol Evol 2011 Jan 19;28(1):143-52. Epub 2010 Jul 19.

Max F Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/msq180DOI Listing
January 2011

Taxon Selection under Split Diversity.

Syst Biol 2009 Dec 21;58(6):586-94. Epub 2009 Sep 21.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr.-Bohr-Gasse 9/6, 1030 Vienna, Austria.

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http://dx.doi.org/10.1093/sysbio/syp058DOI Listing
December 2009

Quantitative detection and typing of hepatitis D virus in human serum by real-time polymerase chain reaction and melting curve analysis.

Diagn Microbiol Infect Dis 2010 Jun;67(2):172-9

Institute of Medical Virology, Helmut-Ruska-Haus, Charité Universitätsmedizin, D-10117 Berlin, Germany.

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http://dx.doi.org/10.1016/j.diagmicrobio.2010.02.003DOI Listing
June 2010

Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis.

Plant Cell 2010 Jan 22;22(1):34-47. Epub 2010 Jan 22.

Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Viena, Austria.

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http://dx.doi.org/10.1105/tpc.109.072819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828703PMC
January 2010

TonB-dependent transporters and their occurrence in cyanobacteria.

BMC Biol 2009 Oct 12;7:68. Epub 2009 Oct 12.

JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.

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http://dx.doi.org/10.1186/1741-7007-7-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771747PMC
October 2009

Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life.

J Bacteriol 2009 Dec 25;191(23):7234-42. Epub 2009 Sep 25.

Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.

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http://dx.doi.org/10.1128/JB.00923-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786558PMC
December 2009

A phylogenomic approach to resolve the basal pterygote divergence.

Mol Biol Evol 2009 Dec 27;26(12):2719-30. Epub 2009 Aug 27.

Institute of Ecology & Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany.

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http://dx.doi.org/10.1093/molbev/msp191DOI Listing
December 2009

Loss of matK RNA editing in seed plant chloroplasts.

BMC Evol Biol 2009 Aug 13;9:201. Epub 2009 Aug 13.

Institut für Biologie, Humboldt Universität zu Berlin, Molekulare Genetik, Berlin D-10115, Germany.

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http://dx.doi.org/10.1186/1471-2148-9-201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744683PMC
August 2009

HaMStR: profile hidden markov model based search for orthologs in ESTs.

BMC Evol Biol 2009 Jul 8;9:157. Epub 2009 Jul 8.

Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2148-9-157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723089PMC
July 2009

Evolutionarily evolved discriminators in the 3-TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria.

J Mol Model 2009 Aug 6;15(8):971-82. Epub 2009 Feb 6.

Cluster of Excellence and Center of Membrane Proteomics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, N200, 60438, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1007/s00894-008-0449-yDOI Listing
August 2009

Budgeted phylogenetic diversity on circular split systems.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):22-9

Center for Integrative Bioinformatics Vienna (CIBIV), Vienna.

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http://dx.doi.org/10.1109/TCBB.2008.54DOI Listing
August 2009

Comment on 'A congruence index for testing topological similarity between trees'.

Bioinformatics 2009 Jan 14;25(1):147-9; author reply 150-1. Epub 2008 Oct 14.

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http://dx.doi.org/10.1093/bioinformatics/btn539DOI Listing
January 2009

The impact of single substitutions on multiple sequence alignments.

Philos Trans R Soc Lond B Biol Sci 2008 Dec;363(1512):4041-7

Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University Vienna, Veterinary University Vienna, Max F. Perutz Laboratories, Dr Bohrgasse 9, 1030 Wien, Austria.

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http://dx.doi.org/10.1098/rstb.2008.0140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607407PMC
December 2008

An exact algorithm for the geodesic distance between phylogenetic trees.

J Comput Biol 2008 Jul-Aug;15(6):577-91

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna, Austria.

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http://dx.doi.org/10.1089/cmb.2008.0068DOI Listing
October 2008

Rooted triple consensus and anomalous gene trees.

BMC Evol Biol 2008 Apr 25;8:118. Epub 2008 Apr 25.

Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Dr, Bohr Gasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2148-8-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409437PMC
April 2008

Maximum-likelihood analysis using TREE-PUZZLE.

Curr Protoc Bioinformatics 2007 Mar;Chapter 6:Unit 6.6

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Vienna, Austria.

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http://dx.doi.org/10.1002/0471250953.bi0606s17DOI Listing
March 2007

EST sequencing of Onychophora and phylogenomic analysis of Metazoa.

Mol Phylogenet Evol 2007 Dec 12;45(3):942-51. Epub 2007 Sep 12.

Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S105579030700315
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http://dx.doi.org/10.1016/j.ympev.2007.09.002DOI Listing
December 2007

The tetratricopeptide repeats of receptors involved in protein translocation across membranes.

Mol Biol Evol 2007 Dec 28;24(12):2763-74. Epub 2007 Sep 28.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/msm211DOI Listing
December 2007

TreeSnatcher: coding trees from images.

Bioinformatics 2007 Dec 24;23(24):3384-5. Epub 2007 Sep 24.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr-Bohr-Gasse 9/6, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btm438DOI Listing
December 2007

pIPHULA--parallel inference of population parameters using a likelihood approach.

Bioinformatics 2007 Oct 12;23(19):2636-7. Epub 2007 Aug 12.

Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btm391DOI Listing
October 2007

Mapping human genetic ancestry.

Mol Biol Evol 2007 Oct 28;24(10):2266-76. Epub 2007 Jul 28.

Center for Integrative Bioinformatics of Vienna, Max F. Perutz Laboratories, Vienna, Austria.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msm156DOI Listing
October 2007

A likelihood framework to measure horizontal gene transfer.

Mol Biol Evol 2007 Jun 20;24(6):1312-9. Epub 2007 Mar 20.

Department of Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany.

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http://dx.doi.org/10.1093/molbev/msm052DOI Listing
June 2007

Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family.

J Biol Chem 2007 Jan 6;282(3):1882-90. Epub 2006 Nov 6.

Ludwig Maximilians University (LMU), Department of Biology I, Menzinger Strasse 67, 80638 München, Germany.

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http://dx.doi.org/10.1074/jbc.M609598200DOI Listing
January 2007