Dr. Patrick Kück

Head of Section

Algorithmic Development

Tel: +49 228 9122-404

Fax: +49 228 9122-212

Mail: P.Kueck [at] leibniz-lib.de

Tabs

Profile

Field of work

''Divide and Conquer'' Algorithms in Molecular Phylogenetics

Development of ''divide and conquer'' algorithms and their implementation in new software scripts, usable for quality evaluation-- and/or phylogenetic reconstruction of molecular sequence data.

Systematic Biases in Molecular Phylogenetics

Identification of systematic biases in probabilistic based tree reconstruction approaches

Availability of developed software scripts

Source

Developed software scripts (see projects), manuals, and example input files are updated regulary and downloadable on GitHub:

https://github.com/PatrickKueck

Developed Software Scripts

PENGUIN (PhyQuart Environment)
AliGROOVE
BaCoCa
FASconCAT-G
FASconCAT
AMARE
AliCUT

Research interests

Phylogenetic Reconstruction

Supertrees and supermatrix based molecular phylogenetic analyses
''Divide and Conquer'' approaches based on triplets, quartets, and quintets
Split decomposition analyses
Systematic biases and their impact on molecular phylogenetic reconstructions
Inconsistency of tree model assumptions due to branch length heterogeneities
Statistical evaluation of phylogenetic trees and phylogenetic signal
Probabilistic based tree reconstruction methods
Phylogenetic networks

Multiple Sequence Alignments

Alignment algorithms
Masking techniques
Evaluation of alignment quality
String similarities and their role for homology assessments
Consideration of secondary rRNA structure information

Programming / Software Development

Pipeline development for data simulation and molecular phylogenetic analyses
Script development for molecular phylogenetic purposes
Perl, Julia, C++

Awards

Dissertation Award of the Alexander Koenig Society (AKG) 2012

External websites and profiles

https://github.com/PatrickKueck

https://www.researchgate.net/profile/Patrick_Kueck

Projects

2019

APPETITE

APPETITE is a new automated process-pipeline for molecular phylogenetic purposes with nearly endless analytical possibilities. APPETITE

Unit:

Algorithmic Development, Chair Systematic Zoology, Centre for Biodiversity Monitoring and Conservation Science (zbm)

Project lead:

Dr. Patrick Kück

2018

Sherlock

Sherlock is an automated process pipeline for statistical evaluation of patristic tree-distance variation given partitioned or non-partitioned molecular sequence data.

Unit:

Algorithmic Development, Chair Systematic Zoology, Directorate, Administration, ZFMK International Graduate School

Project lead:

Dr. Patrick Kück

2014

Countering Systematic Bias in Phylogenetics

PhyQuart, a new algorithm combining Hennigian logic and Maximum Likelihood estimation, represents a completely new strategy for the evaluation of molecular data based on a site pattern classification for quartets of aligned sequences.

Unit:

Algorithmic Development, Chair Systematic Zoology, Centre for Biodiversity Monitoring and Conservation Science (zbm), Directorate, Centre for Molecular Biodiversity Research (zmb), Chair Molecular Biodiversity Research

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig, European Union

2013

FASconCAT-G: extensive alignment preparations

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences and the generation of partitioned files for MrBayes and RAxML analyses.

Unit:

Algorithmic Development

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

AliGROOVE – visualization of heterogeneous sequence divergence

AliGROOVE determines and visualizes the content of potentially randomized sequence similarities and alignment ambiguities in multiple sequence alignments.The AliGROOVE algorithm is an adaptation of the recently published ALISCORE masking algorithm (Misof & Misof, 2009, Kück et al., 2010). AliGROOVE summarizes site scores of profiles of sequence similarity normalized over the whole alignment length from each pairwise comparison and translates the obtained scoring distances between sequences into a similarity Matrix

Unit:

Algorithmic Development, Biodiversity Informatics, Chair Systematic Zoology, Centre for Biodiversity Monitoring and Conservation Science (zbm), Directorate, Centre for Molecular Biodiversity Research (zmb), Chair Molecular Biodiversity Research

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

BaCoCa – assessment of sequence biases

BaCoCa is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions.The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in Perl and works on WindowsPCs, Macs and Linux running systems.

Unit:

Algorithmic Development

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2012

Identification of sources of error in molecular phylogenetic analyses

The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees.

Unit:

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2011

Automated masking of AFLP markers

AMARE is designed to optimize the signal-to-noise ratio in AFLP data sets (single or multiple primer combinations). It identifies potentially erroneous AFLP genotyping errors as the number of non-reproducible scored markers between replicated AFLP profiles of single individuals. As a measure of overall data quality, it simultaneously estimates general replicate error rates.

Unit:

Algorithmic Development, Biobank, Phylogenetics and Evolutionary Biology, Directorate, Centre for Molecular Biodiversity Research (zmb), Chair Molecular Biodiversity Research

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2010

FASconCAT - convenient handling of data matrices

FASconCAT is a user-friendly software that concatenates rapidly different kinds of sequence data into one supermatrix file.

Unit:

Algorithmic Development, Chair Molecular Biodiversity Research

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2009

ALISCORE - Masking of Multiple Sequence Alignments

Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies.

Unit:

Directorate, Chair Systematic Zoology, Algorithmic Development, Directorate Staff, Biodiversity Informatics

Project lead:

Prof. Dr. Bernhard Misof

Funding:

Zoological Research Museum Alexander Koenig

Publications

Published in

2010

Letsch HO, Kück P, Stocsits RR, Misof B: The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Mol. Biol. Evol. 27(11):2507-2521

[more]

Links:

https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msq140

Meusemann K, von Reumont BM, Simon S, Roeding F, Kueck P, Ebersberger I, Strauss S, Walzl M, Pass G, Breuers S, Achter V, Wägele J-W, Hadrys H, Burmester T, von Haeseler A, Misof B (2010): A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol. 27(11):2451-2464. doi: 10.1093/molbev/msq130

[more]

Links:

https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msq130

2009

Letsch HO, Greve C, Kück P, Fleck G, Stocsits RR, Misof B (2009). Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation. Mol. Phylogen. Evol., 53(3):758-771

[more]

Links:

http://www.sciencedirect.com/science/article/pii/S1055790309003091?via%3Dihub

Pages

Presentations

Talks

2018

TU Delft, Netherlands, Faculty of Electrical Engineering, Mathematics and Computer Science, invited guest speaker. Kück P: PhyQuart - quartet mapping to highlight molecular phylogenetic incongruence

2017

BioSyst.EU 2017, Gothenburg, Sweden. Kück P: PhyQuart – a new quartet mapping method to evaluate phylogenetic signal and the robustness of given hypotheses a priori or a posteriori tree reconstruction

2016

Bioinformatics 2016, The 7th International Conference on Bioinformatics Models, Methods and Algorithms, Rome, Italy. Kück P: PhyQuart: a new algorithm to avoid systematic bias & phylogenetic incongruence – Are directed quartets the key for more reliable supertrees?

2015

Systematics 2015, Oxford, United Kingdom. Kück P, Groß C: 4BaSAl - First insights on a new supertree method based on single quartet analyses and its performance with respect to different starting triplets

Marie Curie IEF Project Meeting & Symposium, Bonn, Germany. Kück P, Groß C: Quartet based phylogenetic inference: New algorithms for tree reconstruction and evaluation

2013

BioSyst.EU 2013 (GfBS), Vienna, Austria. Kück P, Wägele JW: Biases in phylogenetic reconstruction – Long branches & short branch attraction (SBA)

2012

Meeting of the Alexander Koenig Society (AKG) 2012, Bonn, Germany. Kück P: Homology assessment in molecular phylogenetics

2011

Deep Metazoan Phylogeny 2011, Munich, Germany (keynote speacker). Kück P: Long branch artefacts – Discovery of Maximum Likelihood assassins

Systematics 2011, Berlin, Germany. Kück P: Detection of long branch artefacts in simulated and real data

Deep Metazoan Priority Programme Meeting, Hannover, Germany. Kück P: Maximum likelihood (ML) inconsistency in terms of long branch attraction

2009

“Celebrating Darwin: From The Origin of Species to Deep Metazoan Phylogeny”: 1st International Congress on Deep Metazoan Phylogeny (SPP 1174), Berlin, Germany. Kück P: Aliscore – A new method for masking of random sequence similarity (RSS)

2008

Systematics 2008, Göttingen, Germany. Kück P, Misof B, Misof K: Aliscore – Identifying random similarity within sequence alignments

Teaching

Courses

2018

Natural History Museum, University of Oslo, Norway. Co-organizing and lecture of the ForBio (research school in biosystematics) course: ''Phylogenomics Part I & II''

Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany. Organizing and course lecture within the Alexander-Koenig-Society (AKG) science club. Title: "Molecular-phylogenetic sequence-analyses"

2017

Natural History Museum, University of Oslo, Norway. Co-organizing and lecture of the ForBio (research school in biosystematics) course: ''Phylogenomics Part II''

2016

Natural History Museum, University of Oslo, Norway. Co-organizing and lecture of the ForBio (research school in biosystematics) course: ''Phylogenomics Part I''

2012–2008

Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany. Organizing and course lecture of a regular course (MOMENTO) within the molecular biology department of the ZFMK, specified on ''Phylogenetic methods, algorithms and analyses''

2009

Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany. Organizing and course lecture: ''Introduction into LATEX for students''

2008

Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany. Organizing and course lecture: ''Perl programming for students''

Alumni

2021

Seidel N, M.Sc., Thesis: Development and testing of a phylogenetic root Informative supertree algorithm
based on PhyQuart quartet evaluation

2015

Groß C, M.Sc., Thesis: The impact of the selection of start triplets on the success of maximum likelihood validated tree puzzling algorithms

2013

Groß C, B.Sc., Thesis: Testing new phylogenetic algorithms using a new developed process pipeline for comparative tree reconstruction analyses

Supervision of Student-Projects

2018

Seidel N, B.Sc., Development of an automated process pipeline for statistical evaluation of patristic tree-distance variation (6-week project)

Seidel N, B.Sc., Development of an "Divide & Conquer" tree mapping algorithm based on polarised quartets for molecular phylogenetic purposes (6-week project)

2014

Groß C, Programming of an automized process pipeline (LoBraTe) for testing long branch
attraction behaviour in molecular phylogenetics based on simulations (6-week project)

Supervision of Pupil-Practica

2018

Duda L, Introduction into molecular phylogenetics and bioinformatics, incl. courses of programming and theory of molecular phylogenetics (2-week project)

Academic Degree

2011

Dr. rer. nat. (= Ph.D. equivalent) at the Zoological Research Museum Alexander Koenig, Rheinische Friedrich-Wilhelms-University of Bonn, Germany, thesis title: Homology assessment in molecular phylogenetics – evaluation, improvement, and influence of data quality on tree reconstruction, supervisors: Prof. Dr. J. W. Wägele and Prof. Dr. B. Misof

2006

Dipl. Biol. (= M.Sc. equivalent) at the Zoological Research Museum Alexander Koenig, Rheinische Friedrich-Wilhelms-University of Bonn, Germany. Main courses: zoology, cell biology, organic chemistry, thesis title: Phylogenetic reconstruction of relationships in the superfamily Aeshnoidea (Odonata, Anisoptera) using 28S rRNA and its secondary structure, supervisors: Prof. Dr. B. Misof and Prof. Dr. J. W. Wägele

2003

Pre-Diploma (= B.Sc. equivalent) in Biology at the Rheinische Friedrich- Wilhelms-University of Bonn, Germany. Main courses: zoology, cell biology, genetics, botany

University Education

as of 2017

Zoological Research Museum Alexander Koenig, Bonn, Germany, Postdoctoral Researcher

2015 - 2016

Natural History Museum, London, United Kingdom, Postdoctoral Marie Curie intra-european research fellow

2011 - 2014

Rheinische Friedrich-Wilhelms-University of Bonn, Germany, Postdoctoral researcher at the Zoological Research Museum Alexander Koenig

2007 - 2011

Rheinische Friedrich-Wilhelms-University of Bonn, Germany, PhD student at the Zoological Research Museum Alexander Koenig

2007

Max-Planck Institute for Evolutionary Biology, Pön, Germany, Research fellow, supervised by Prof. Dr. D. Tautz. Thesis topic: Population-genetic studies of african cichlid populations using microsatellite data

2006

Institute for Genetics at the University of Cologne, Germany, Research assistant in the workgroup of Prof. Dr. D. Tautz

2001 - 2006

Rheinische Friedrich-Wilhelms-University of Bonn, Germany, Study of Biology

Research Fellowships

2014

Marie Curie Intra-European research fellowship for career development (IEF)

2011

PROMOS fellowship of the German Academic Exchange Servise (DAAD)

2007

Fellowship of the Max-Planck-Society (MPI)

Awards

2012

Dissertation award of the A. Koenig Society for outstanding academic achievments in the field of molecular systematics

Organisation of Converences and Seminars

2017

BioSyst.EU 2017, Gothenburg, Sweden. Co-organizing of the Gesellschaft für Biologische Systematik (GfBS) symposium: Identification and avoidance of sources of error in phylogeny inference

2015

Marie Curie IEF Project Meeting & Symposium, Bonn, Germany. Organizing of the project meeting

Reviewer Activities

Journal of Statistical Theory and Practice
Evolutionary Bioinformatics
PLOS Currents
Molecular Phylogenetics and Evolution
BMC Bioinformatics

Further Education

1996 - 1998

Technical college of Ostfriesland, Emden, Germany, Study of Biotechnology

1996

Central Military Immunology Department, Koblenz, Germany, work as Technical-Laboratory-Assistant

1992 - 1995

''Rheinische Akademie'' of Cologne, Germany, apprenticeship as Biological-Technical-Assistant

Computer Skills

UNIX, Mac OSX and MS operating systems
Application of various phylogenetic software
Advanced skills in command line based software
LATEX
Perl programming
C++ programming
Julia programming

Languages

German
English

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Dr. Patrick Kück

Tabs

Field of work

''Divide and Conquer'' Algorithms in Molecular Phylogenetics

Systematic Biases in Molecular Phylogenetics

Availability of developed software scripts

Source

Developed Software Scripts

Research interests

Phylogenetic Reconstruction

Multiple Sequence Alignments

Programming / Software Development

Awards

External websites and profiles

2019

2018

2014

2013

2012

2011

2010

2009

Pages

2010

2009

Pages

Talks

2018

2017

2016

2015

2013

2012

2011

2009

2008

Courses

2018

2017

2016

2012–2008

2009

2008

Alumni

2021

2015

2013

Supervision of Student-Projects

2018

2014

Supervision of Pupil-Practica

2018

Academic Degree

2011

2006

2003

University Education

as of 2017

2015 - 2016

2011 - 2014

2007 - 2011

2007

2006

2001 - 2006

Research Fellowships

2014

2011

2007

Awards

2012

Organisation of Converences and Seminars

2017

2015

Reviewer Activities

Further Education

1996 - 1998

1996

1992 - 1995

Computer Skills