MPI-CBG Scientific Computing Facility

Bioinformatics Team

The bioinformatics team assists MPI-CBG scientists with a wide range of bioinformatics data analysis tasks. Services range from small scale single gene or protein characterization up to global studies involving deep sequencing technologies.

	Name	Job Title	Interests
	Ian Henry	Facility Leader	Info here
	Holger Brandl	Senior Data Engineer	Info here
	Lena Hersemann	Bioinformatician	Info here

Classical Bioinformatics

Sequence Analysis

• Protein sequence analysis & functional prediction
• DNA/RNA sequence analysis

Evolutionary Analysis

• Phylogenetic tree construction
• Orthologue / Paralogue searching

Structural Analysis

• Protein/RNA structure prediction

NGS applications

NGS data analysis workflows are designed to run in an HPC environment and include automated report generation using R/markdown, linking to underlying source data and/or QC reports. We are currently also developing a RNA-seq analysis workflow single cell data.

Bioinformatics Software Development

• Scripting and small tools (R/Python)
• Plugin development for Geneious Pro
• Large workflow design & implementation
• Large data handling, visualization & exploration
• Interactive data presentation (R/Shiny)

Useful links

Bioinformatics gitlab repo

Scientific Computing gitlab repo

Publications

2018

Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex.
Elife, 7 Art. No. e32332 (2018)

Markus Grohme, Siegfried Schloissnig, Andrei Rozanski, Martin Pippel, George Robert Young, Sylke Winkler, Holger Brandl, Ian Henry, Andreas Dahl, Sean Powell, Michael Hiller, Eugene Myers, Jochen Rink
The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms.
Nature, 554(7690) 56-61 (2018)

Ioannis Mitroulis, Klara Ruppova, Baomei Wang, Lan-Sun Chen, Michal Grzybek, Tatyana Grinenko, Anne Eugster, Maria Troullinaki, Alessandra Palladini, Ioannis Kourtzelis, Antonios Chatzigeorgiou, Andreas Schlitzer, Marc Beyer, Leo A B Joosten, Berend Isermann, Mathias Lesche, Andreas Petzold, Kai Simons, Ian Henry, Andreas Dahl, Joachim L Schultze, Ben Wielockx, Nicola Zamboni, Peter Mirtschink, Ünal Coskun, George Hajishengallis, Mihai G Netea, Trian Chavakis
Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity.
Cell, 172(1-2) 147-161 (2018)

2017

Ivana Viktorinová, Ian Henry, Pavel Tomancak
Epithelial rotation is preceded by planar symmetry breaking of actomyosin and protects epithelial tissue from cell deformations.
PLoS Genet, 13(11) Art. No. 1007107 (2017)

Barbara Tavares, Raquel Jacinto, Pedro Sampaio, Sara Pestana, Andreia Pinto, Andreia Vaz, Mónica Roxo-Rosa, Rui Gardner, Telma Lopes, Britta Schilling, Ian Henry, Leonor Saúde, Susana Lopes
Notch/Her12 signalling modulates, motile/immotile cilia ratio downstream of Foxj1a in zebrafish left-right organizer.
Elife, 6 Art. No. e25165 (2017)

Mareike Albert, Nereo Kalebic, Marta Florio, Naharajan Lakshmanaperumal, Christiane Haffner, Holger Brandl, Ian Henry, Wieland B. Huttner
Epigenome profiling and editing of neocortical progenitor cells during development.
EMBO J, 36(17) 2642-2658 (2017)

2016

Raphael Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie Dye, Benoit Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
TissueMiner: a multiscale analysis toolkit to quantify how cellular processes create tissue dynamics.
Elife, 5 Art. No. e14334 (2016)

Michaela Müller-McNicoll, Valentina Botti, Antonio Domingues, Holger Brandl, Oliver D Schwich, Michaela Steiner, Tomaz Curk, Ina Poser, Kathi Zarnack, Karla M. Neugebauer
SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export.
Genes Dev, 30(5) 553-566 (2016)

Holger Brandl, HongKee Moon, Miquel Vila-Farré, Shang-Yun Liu, Ian Henry, Jochen Rink
PlanMine - a mineable resource of planarian biology and biodiversity.
Nucleic Acids Res, 44 Art. No. D764–D773 (2016)

2015

Anja Zeigerer, Roman L Bogorad, Kirti Sharma, Jerome Gilleron, Sarah Seifert, Susanne Sales, Nikolaus Berndt, Sascha Bulik, Giovanni Marsico, Rochelle C J D'Souza, Naharajan Lakshmanaperumal, Kesavan Meganathan, Karthick Natarajan, Agapios Sachinidis, Andreas Dahl, Hermann-Georg Holzhütter, Andrej Shevchenko, Matthias Mann, Victor Koteliansky, Marino Zerial
Regulation of Liver Metabolism by the Endosomal GTPase Rab5.
Cell Rep, 11(6) 884-892 (2015)

Marta Florio, Mareike Albert, Elena Taverna, Takashi Namba, Holger Brandl, Eric Lewitus, Christiane Haffner, Alex Sykes, Fong Kuan Wong, Jula Peters, E. Guhr, Sylvia Klemroth, Kay Prüfer, Janet Kelso, Ronald Naumann, Ina Nüsslein, Andreas Dahl, Robert Lachmann, Svante Pääbo, Wieland B. Huttner
Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.
Science, 347(6229) 1465-1470 (2015)

Raphael Etournay, Marko Popović, Matthias Merkel, Amitabha Nandi, Corinna Blasse, Benoit Aigouy, Holger Brandl, Gene Myers, Guillaume Salbreux, Frank Jülicher, Suzanne Eaton
Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing.
Elife, 4 Art. No. e07090 (2015)

Hanh Thi-Kim Vu, Jochen Rink, Sean A McKinney, Melainia McClain, Naharajan Lakshmanaperumal, Richard Alexander, Alejandro Sánchez Alvarado
Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ.
Elife, 4 Art. No. e07405 (2015)

2014

Tatyana Grinenko, Kathrin Arndt, Melanie Portz, Nicole Mende, Marko Günther, Kadriye Nehir Cosgun, Dimitra Alexopoulou, Naharajan Lakshmanaperumal, Ian Henry, Andreas Dahl, Claudia Waskow
Clonal expansion capacity defines two consecutive developmental stages of long-term hematopoietic stem cells.
J Exp Med, 211(2) 209-215 (2014)

2013

Shang-Yun Liu, Claudia Selck, Benjamin Friedrich, Richard Lutz, Miquel Vila-Farré, Andreas Dahl, Holger Brandl, Naharajan Lakshmanaperumal, Ian Henry, Jochen Rink
Reactivating head regrowth in a regeneration-deficient planarian species.
Nature, 500(7460) 81-84 (2013)

2012

Simone Fietz, Robert Lachmann, Holger Brandl, Martin Kircher, Nikolay Samusik, Roland Schröder, Naharajan Lakshmanaperumal, Ian Henry, Johannes Vogt, Axel Riehn, Wolfgang Distler, Robert Nitsch, Wolfgang Enard, Svante Pääbo, Wieland B. Huttner
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal.
Proc Natl Acad Sci U.S.A., 109(29) 11836-11841 (2012)

Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M. Neugebauer
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.
Genome Biol, 13(3) Art. No. R17 (2012)

2011

Ivana Viktorinova, Lucie Kucerova, Marta Bohmova, Ian Henry, Marek Jindra, Petr Dolezal, Martina Zurovcova, Michal Zurovec
Characterization of two closely related α-amylase paralogs in the bark beetle, Ips typographus (L.).
Arch Insect Biochem Physiol, 77(4) 179-198 (2011)

2010

Minna-Liisa Änkö, Lucia Morales, Ian Henry, Andreas Beyer, Karla M. Neugebauer
Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells.
Nat Struct Mol Biol, 17(8) 962-970 (2010)