Services

The topics I work on are diverse (biology, ecology, finance privately) but they share one common goal: interpret data to understand processes. I often contribute to specific tasks within a project and sometimes I manage the entire process from data to insights (i.e., scientific publication). In all cases, I focus on providing a concise solution specifically tailored to the project and your needs. This may include experimental design, data analytics, scientific software development, scientific writing, and preparing a data management plan for SNSF grants. In addition, I also offer customized training and teaching.

Experimental Design

The success of a scientific project critically depends on the design of the experiments. Often, this requires a good understanding of the technology employed and experience with the analysis of the data produced by it. I can directly design experiments involving omics (e.g., RNA-Seq, BS-Seq, and ChIP-Seq) and I maintain active contacts with academic experts for more general experimental designs (e.g., ecological field experiments).

Data Analytics

Data analytics are the core of my work as a scientist. I employ techniques from classical statistics, mathematical modelling, and machine learning to turn data into insights. I use widely adopted open-source software packages for the implementation of my analytics (mostly R and sometimes Python). Whenever needed, I develop new packages (R), implement novel algorithms (R, Python, C++), or write workflows for distributed computing on cloud infrastructures. To ensure reproducibility, I keep track of my analytics by documenting each and every step. My core expertise are omics data (e.g., RNA-Seq, BS-Seq, ChIP-Seq, 16SRNA-Seq, 4C, HiC, reduced representation sequencing) and ecological data from field experiments. However, I am genuinely interested in any type of data.

Scientific Software Development

Research projects are often at the forefront of science employing the most recent methods for data collection. Solutions for such new types of data my be scarce or yet to be developed. Thus, it can be necessary to design and implement a brand new software or software package. I have experience in developing packages in R and small to medium scale scientific software in Python or C++ (i.e., focused on data processing and analysis). Examples can be found on my GitHub account.

Scientific Writing

Data analytics are tightly connected to scientific communication: manuscript and project proposal writing, internal reporting, and content for conference presentation. I have so far managed several entire projects from data to the final publication (Research). This included data analysis, interpretation, visualization, and writing the manuscript. Based on this experience, I offer support in scientific writing and I deliver publication ready content derived from my data analytics.

Data Management Plan for SNSF Grants

From October 2017 on, the Swiss National Science Foundation (SNSF) requires researchers to include a data management plan (DMP) in their funding application (Open Research Data). The SNSF also expects that data generated by funded projects will be publicly accessible in digital databases. Working together with different research groups, I know which kind of documentation and metadata are required to understand and effectively share data. However, I am also aware that certain data management policies can inhibit creativity and innovation. Aside discussing or writing your DMP, I also offer to implement it during the course of your SNSF funded project.

Training and Teaching

Many fields in life-sciences experienced a rapid digitalization. This requires a realistic, flexible, and swift adaptation of analytical skills. For example, molecular biologists should not aim to become experts in biostatistics and bioinformatics within a short 1-2 years time-line, in parallel to their daily research and experimental workload. Instead, with a carefully focused and tailored training and education, experts in biology can acquire thorough basic skills that allow them to independently and correctly perform analytics at their level. Furthermore, such skills promote efficient communication with bioinformaticians, converging in an overall better analytics that benefits from collaborative work of mixed expertise. I offer one-on-one or small group teaching and hands-on training in specific aspects of programming and data analytics. In addition, I maintain good contacts with academic and non-academic experts for programming, data analytics, and statistics to whom I can forward requests I cannot cover myself.

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Research

Below you can find my projects as a main contributor and my collaborations.

Projects as a main contributor

van Moorsel, S.J.#, Schmid, M.W.#, Hahl, T.#, Wagg, C., de Deyn, G.B., Niklaus, P.A., Schmid, B. (in preparation): Effects of plant-community and soil history on the relationship between plant and soil microbial diversity. # equal contribution.

van Moorsel, S.J.#, Schmid, M.W.#, Wagemaker, N.C.A.M., van Gurp, T., Schmid, B., Vergeer, P. (in preparation): Evidence for rapid evolution into monoculture and mixture types in a grassland biodiversity experiment. # equal contribution.

Schmid, M.W.#, Hahl, T.#, van Moorsel, S.J.#, Wagg, C., de Deyn, G.B., Schmid, B. (in preparation): Effects of plant diversity on rhizophere microbiomes of eight plant species. # equal contribution.

Schmid, M.W., Schmidt, A., Herrmann, A., Guthörl, D., Grob, S., Schmid, P.D., Klostermeier, U.C., Rosenstiel, P., Grossniklaus, U. (in preparation): Polarized distribution of mRNA in the syncytial female gametophyte of Arabidopsis thaliana preceedes cellularization and cell specification.

Schmid, M.W.#, Heichinger, C.#, Coman, D., Guthörl, D., Bruggmann, R., Aluri, S., Aquino, C., Schmid, B., Turnbull, L.A., Grossniklaus, U. (in preparation): Selection of epigenetic variation in Arabidopsis. # equal contribution.

Schmid, M.W.#, Giraldo Fonseca, A.#, Smetanin, D., Grossniklaus, U.: Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha. Genome Biology, in press # equal contribution.

Schmid, M.W. (2017): RNA-Seq data analysis protocol: Combining in-house and publicly available data. Methods in Molecular Biology. DOI: 10.1007/978-1-4939-7286-9_24; RNAseq protocols and packages on GitHub

Schmid, M.W.#, Schmidt, A.#, Grossniklaus, U. (2015): The female gametophyte: An emerging model for cell type-specific systems biology in plant development. Frontiers in Plant Science, 6:907. # equal contribution. DOI: 10.3389/fpls.2015.00907

Schmid, M.W., Grob, S., Grossniklaus, U. (2015): HiCdat: a fast and easy-to-use Hi-C data analysis tool. BMC Bioinformatics, 16: 277. DOI: 10.1186/s12859-015-0678-x; HiCdat on GitHub

Schmid, M.W., Grossniklaus, U. (2015): Rcount: simple and flexible RNA-Seq read counting. Bioinformatics, 31(3): 436-437. DOI: 10.1093/bioinformatics/btu680; Rcount on GitHub

Schmid, M.W., Schmidt, A., Klostermeier, U.C., Barann, M., Rosenstiel, P., and Grossniklaus, U. (2012): A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLOS ONE, 7(1): e29685. DOI: 10.1371/journal.pone.0029685

Collaborations

van Moorsel, S.J., Schmid, M.W., Hahl, T., Zuppinger-Dingley, D., Schmid, B. (2017): Selection in response to community diversity alters plant performance in newly assembled test communities. BioRxiv. DOI: 10.1101/158709

Hahl, T., van Moorsel, S.J., Schmid, M.W., Zuppinger-Dingley, D., Schmid, B., Wagg, C. (in preparation): Diversity loss selects for altered plant phenotypic responses to local arbuscular mycorrhizal communities.

Kartal, Ö., Schmid, M.W., Grossniklaus, U. (in preparation): Information-theoretic analysis of Arabidopsis methylomes uncovers epigenetic population structure.

Krattinger, S.G., Kang, J., Chauhan, H., Selter, L.L., Robinson, M.D., Schmid, M.W., Jordan, T., Wiederhold, E., Boni, R., Sucher, J., Martinoia, E., Keller, B. (in preparation): A cereal ABC transporter conferring durable disease resistance modulates abscisic acid fluxes.

Lippuner, C., Ramakrishnan, C., Basso, W., Schmid, M.W., Okoniewski, M., Smith, N., Hässig, M., Deplazes, P., Hehl, A.B.: RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites. International Journal for Parasitology, in press

Bowman, J.L., Kohchi, T., Yamato, K.T., Jenkins, J., Shu, S., et. al. (2017): Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell, 171(2): 287-304. DOI: 10.1016/j.cell.2017.09.030

Graf, U., Casanova, E.A., Wyck, S., Dalcher, D., Gatti, M., Vollenweider, E., Okoniewski, M.J., Weber, F.B., Patel, S.S., Schmid, M.W., Li, J., Sharif, J., Wanner, G.A., Koseki, H., Wong, J., Pelczar, P., Penengo, L., Santoro, R., Cinelli, P. (2017): Pramel7 mediates ground state pluripotency through proteasomal-epigenetic combined pathways. Nature Cell Biology, 19: 763–773. DOI: 10.1038/ncb3554

Hedhly, A., Vogler, H., Schmid, M.W., Pazmino, D., Gagliardini, V., Santelia, D., Grossniklaus, U. (2016): Starch turnover and metabolism during flower and early embryo development in Arabidopsis thaliana. Plant Physiology, 172(4): 2388-2402. DOI: 10.1104/pp.16.00916

Gossmann, T.I., Saleh, D., Schmid, M.W., Spence, M.A., Schmid, K.J. (2016): Plant reproductive development is characterised by a transcriptomic evolutionary bulge. Molecular Biology and Evolution, 33(7): 1669-1678. DOI: 10.1093/molbev/msw044

Schmidt, A., Schmid, M.W., Grossniklaus, U. (2015): Plant germline formation: molecular insights define common concepts and illustrate developmental flexibility in apomictic and sexual reproduction. Development, 142: 229-241. DOI: 10.1242/dev.102103

Grob, S., Schmid, M.W., Grossniklaus, U. (2014): HiC Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Molecular Cell, 55(5): 678-693. DOI: 10.1016/j.molcel.2014.07.009

Schmidt, A., Schmid, M.W., Klostermeier, U.C., Qi, W., Guthörl, D., Sailer, C., Waller, M., Rosenstiel, P., and Grossniklaus, U. (2014): Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. PLOS Genetics, 10(7): e1004476. DOI: 10.1371/journal.pgen.1004476

Gossmann, T.I., Schmid, M.W., Grossniklaus, U., and Schmid, K.J. (2014): Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana. Molecular Biology and Evolution, 31(3): 574-583. DOI: 10.1093/molbev/mst226

Grob, S., Schmid, M.W., Luedtke, N.W., Wicker, T., and Grossniklaus, U. (2013): Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biology, 14:R129. DOI: 10.1186/gb-2013-14-11-r129

Wuest, S.E., Schmid, M.W., and Grossniklaus, U. (2013): Cell-specific expression profiling of rare cell types as exemplified by its impact on our understanding of female gametophyte development. Current Opinion in Plant Biology, 16: 1-9. DOI: 10.1016/j.pbi.2012.12.001

You, W., Tyczewska, A., Spencer, M., Daxinger, L., Schmid, M.W., Grossniklaus, U., Simon, S., Meyers, B.C., Matzke, A.J.M., and Matzke, M. (2012): Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biology, 12: 51. DOI: 10.1186/1471-2229-12-51

Schmidt, A., Schmid, M.W., and Grossniklaus, U. (2012): Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. The Plant Journal, 70(1): 18-29. DOI: 10.1111/j.1365-313X.2012.04897.x

McKeown, P.C., Laouielle-Duprat, S., Prins, P., Wolff, P., Schmid, M.W., Donoghue, M.T.A., Fort, A., Duszynska, D., Comte, A., Lao, N.T., Wennblom, T.J., Smant, G., Köhler, C., Grossniklaus, U., and Spillane, C. (2011): Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. BMC Plant Biology, 11: 113. DOI: 10.1186/1471-2229-11-113

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About

Details about my education, research and work experience, and work-related skills are given below.

Skills

Programming and Software

Development and implementation of novel algorithms for data processing and integration of different data sets. Advanced in C++, Python and R programming with a focus on fast and efficient data processing. Basic knowledge in MySQL, SQLite, Ansible and Bash. Proficient with Linux, Windows, Mac, QtCreator, RStudio, MS-Office, LibreOffice, LaTex and Inkscape. Several months experience with Cloud Computing (OpenStack, GC3pie). Publicly available software which I developed are available on my GitHub account.

Data and Statistics

Seven years experience with the analysis and visualization of small and large data sets from different research projects and research groups within biology ("omics" and "traditional" statistics). Emphasis on the integration of diverse data sets to understand complex biological processes. Basic knowledge and few months experience in mathematical modeling of environmental systems and cellular processes with multi-variable differential equation models. Some experience with machine learning and financial data.

Experiments and Approaches

Eight years research in plant developmental biology at the Department of Plant and Microbial Biology (UZH) and intensive collaborations with other scientists. Active exchange of methods, approaches and ideas within and outside of the institute.

Communication and Interaction

Presentation of research results at national and international meetings. Publication of scientific articles in peer-reviewed journals. Internal and independent external collaborations with other scientists. Consulting and training of PhD students and PostDocs at the UZH (experimental design, data analysis and interpretation). Native German speaking, fluent in English and basic knowledge in French.

Research Experience

2015-2017: Bioinformatician/Scientist (S3IT, UZH)

Statistical analysis and visualization of diverse data sets from life sciences. Writing scientific articles. Consulting and training of PhD students and PostDocs at the UZH (experimental design, data analysis and interpretation).

2010-2015: PhD Student (Department of Plant and Microbial Biology, UZH)

In addition to my own research, I also contributed with programming, data analysis, and interpretation to various collaborative projects addressing many aspects of plant biology from the evolution of sex-specific genes to the architecture of the nucleus. Consequently, my work comprised many research topics, experimental procedures, and data analysis approaches. The unifying theme was the attempt to understand plant life with the help of quantitative data.

2008-2010: MSc Student (Department of Plant and Microbial Biology, UZH)

Reproductive plant biology using microgenomics, systems biology, and molecular approaches.

Education

2010-2015: Doctorate at the Faculty of Science (UZH)

Title: Genome-Scale Quantitative Biology of Arabidopsis thaliana.

2008-2010: Master of Science UZH (Biology)

Title: A microgenomics approach to analyse the polarity of the four-nucleate embryo sac of Arabidopsis thaliana. Overall final grade: 5.9 out of 6.

2005-2008: Bachelor of Science ETHZ (Environmental Sciences)

Interdisciplinary studies covering the basics of mathematics, physics, chemistry, biology, economy, law and psychology. Emphasis on the integration of different fields to understand and transform complex environmental systems. Bachelor theses in molecular plant biology and consumer behaviour. Overall final grade: 5.6 out of 6.

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