JULIUS MÜLLER

Bioinformatician

I'm a Heidelberg Germany based senior bioinformatics analyst with more than ten years of experience. My main expertises are biomarker discovery, scientific software and pipeline development, multi omics data analysis and integration as well as statistical data analysis including machine learning.

I have acquired deep understanding of immunology, vaccine research, cancer and epigenetics and my main research interests are cancer immunotherapy including prioritization of cancer neoantigens and patient stratification based on multi omics profiles including transcriptomics, peptidomics and genetics data sets.

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I would appreciate any comments, contributions, critics or suggestions.

Work Experience
2018-now	Senior Bioinformatician, Molecular Health GmbH, Heidelberg, Germany
2014-2018	Bioinformatician, The Jenner Institute, University of Oxford, UK
2012-2014	Bioinformatics Consultant, Zurich, Switzerland
2009-2012	Research Fellow in Bioinformatics, IMCB, Singapore
Education
2005-2009	PhD, ETH, Zurich, Institute of Cell Biology. Thesis: Transcriptional dynamics in immune cells under hypoxic conditions.
1999-2005	Diploma in Biology, Karls-Ruprecht University, Heidelberg, Major Biochemistry/Biophysics. Thesis: mRNA stability and degradation.
Computer Skills
OS	Linux, Cluster handling (PBS server), Windows
Programming	Daily use during work: R, Python, MySQL
	Frequent use: Linux Tools (awk, sed …) , C
	Past projects: Matlab, Java, Perl, C++, VBA-Excel
	Web Development: HTML+CSS, JavaScript
Publications (up to date list)
Salvany L, Muller J, Guccione E, and Rorth P. The core and conserved role of MAL is homeostatic regulation of actin levels. Genes & Development, May 15, 2014; 28 (10)
Loh SL, Teh C, Muller J, Guccione E, Hong W and Korzh V. Zebrafish yap1 plays a role in differentiation of hair cells in posterior lateral line. Science Reports, Mar 6, 2014; 4:4289
Jachowicz J, Santenard A, Bender A, Muller J and Torres-Padilla ME. Heterochromatin establishment at pericentromeres depends on nuclear position. Genes & Development, Nov 15, 2013; 27(22):2427-32
Wang X, Zhao Z, Muller J, Iyu A, Khng AJ, Guccione E, Ruan Y, and Ingham PW. * Equally contributing Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish. Biology Open, Nov 15, 2013; 2(11):1203-13
Burton A, Muller J, Padilla-Longoria P, Guccione E and Torres-Padilla ME. * Equally contributing Single-Cell Profiling of Epigenetic Modifiers Identifies PRDM14 as an Inducer of Cell Fate in the Mammalian Embryo. Cell Reports, Nov 14, 2013; 5(3):687-701 (Video Featured Article)
Filipponi D, Muller J, Emelyanov A and Bulavin DV. Wip1 Controls Global Heterochromatin Silencing via ATM/BRCA1-Dependent DNA Methylation. Cancer Cell, Oct 14, 2013; 24(4):528-41 (Featured Article)
Windak R, Muller J, Felley A, Akhmedov A, Wagner EF, Pedrazzini T, Sumara G, and Ricci R. The AP-1 Transcription Factor c-Jun Prevents Stress-Imposed Maladaptive Remodeling of the Heart. PLoS One, Sep 10, 2013; 8(9)
Bezzi M, Teo SX, Muller J, Mok WC, Sahu SK, Vardy LA, Bonday ZQ and Guccione E. Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery. Genes & Development, Sep 1, 2013; 27(17):1903-16
Bard-Chapeau EA, Gunaratne J, Kumar P, Chua B, Muller J, Bard FA, Blackstock W, Copeland NG, and Jenkins NA. EVI1 oncoprotein interacts with a large and complex network of proteins and integrates signals through protein phosphorylation. PNAS, Jul 30, 2013; 110(31):2885-94
Kumpf S, Mihlan M, Goginashvili A, Grandl G, Gehart H, Godel A, Schmidt J, Muller J, Bezzi M, Ittner A, Guccione E, Wolfrum C, Ricci R. Hairless promotes PPARγ expression and is required for white adipogenesis EMBO Reports, Nov 6, 2012; 13(11):1012-20
Bard-Chapeau EA, Jeyakani J, Kok CH, Muller J, Chua B, Gunaratne J, Batagov A, Jenjaroenpun P, Kuznetsov VA, Wei CL, D'Andrea R, Bourque G, Jenkins NA and Copeland NG. Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors PNAS, Feb 7, 2012; 109(6):2168-73
Migliori V, Muller J, Low D, Phalke S, Bezzi M, Gunaratne J, Mok WC, Capasso P, Bassi C, Cecatiello V, Kuznetsov V, Blackstock W, Amati B, Mapelli M and Guccione E. Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance Nature Structural & Molecular Biology, Jan 8, 2012; 19(2):136-44 (Cover Article)
Järve A, Muller J, Kim IH, Rohr K, MacLean C, Fricker G, Massing U, Eberle F, Dalpke A, Fischer R, Trendelenburg MF and Helm M. Surveillance of siRNA integrity by FRET imaging Nucleic Acids Research, Sep 22, 2007; 35(18)
Kurschat WC, Muller J, Wombacher R and Helm M. Optimizing splinted ligation of highly structured small RNAs RNA, Oct 26, 2005; 11(12):1909-14

Experience

Task	Experience	Estimated Duration
Experimental planning; Sample size and power analysis	good	Hours
Sequencing; Mapping, standard QA and basic analysis	extensive	Hours
Microarray and QPCR; Standard QA and basic analysis	extensive	Hours
Biological interpretation and thorough data mining	extensive	Days-Weeks
Bioinformatics Software development	extensive	Days-Weeks
Annotation	extensive	Hours
Proteomics; SILAC	good
Genomics: SNP finding, de novo assembly, GWAS	good

Tools

This section contains Bioinformatics related tools and code snippets which are freely available. This section will be expanded over time and tools will be made available on public repositories such as GitHub. Comments, contributions and critics or collaborations are very welcome.

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+BED to ELAND converter
- Description: A lightweight tool to convert a bed file to the widely used eland format as output from the CASAVA pipeline
- Requirements: Python 2.7
- Source: bed2eland.py (GitHub)

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+Calculation of Shapiro scores
- Description: Two functions to calculate the divergence of Donors and Acceptors from a reference. Based on the method published by Shapiro et al in 1987.
- Requirements: R 2.10+
- Source: calculate_shapiro.R (GitHub)
+TransView, bioconductor package
- Description: TransView provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.
- Requirements: R 2.15+; Bioconductor 2.11+
- Source: TransView (Bioconductor)
+PANTHER.db, bioconductor package
- Description: A set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.
- Requirements: R 2.7+; Bioconductor 2.13+
- Source: PANTHER.db (Bioconductor)

Code Snippets

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+Malformed phred scores in SAM and SAM to BED conversion
- Description: A typical scenario making the conversion from the richer SAM format to the slim BED format necessary, are malicious phred scores in the SAM file body which make a SAM to BAM conversion by samtools impossible. bedtools applied to the output of the following awk snippet can circumvent this problem. The command is embedded in an optional bash script which works on all sam files found in a directory and returns a sorted and indexed bam file. Do note that all original quality scores are lost using this pipeline.
- Requirements: awk/bash;samtools;bedtools
- Source:
```
#!/bin/bash
for i in $(find . -name '*.sam' -type f)
do
	echo "Processing $i"
	awk '{OFS="\t";print($3,$4+1,$4+length($5),0,0,$2)}' $i | bedtools sort | bedtools bedtobam -g genome_file.fai > $i.bam ; samtools index $i.bam
done
```