Sebastian J. Schultheiß

Bernstein Center for Computational Neuroscience Tübingen

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Jörg Hagmann

Bernstein Center for Computational Neuroscience Tübingen

Claude Becker

Ludwig-Maximilians-Universität München

Adam Nunn

Institute of Bioinformatics

Detlef Weigel

Max Planck Institute for Biology

Ioanna Kakoulidou

Technical University of Munich

Rahul Pisupati

Gregor Mendel Institute of Molecular Plant Biology

Frank Johannes

Technical University of Munich

David Langenberger

Leipzig University

Patrick Hüther

Institute of Molecular Biology

Gunnar Rätsch

ETH Zurich

Cooperative Institutions

Max Planck Society

Max Planck Institute for Developmental Biology

Agricultural Research Service

United States Department of Agriculture

University of Toronto

Heidelberg University

Memorial Sloan Kettering Cancer Center

University of Tübingen

University of New Orleans

University of Maryland, College Park

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Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data

BMC Bioinformatics (2011)

Sebastian J. Schultheiß Géraldine Jean Jonas Behr Regina Bohnert Philipp Drewe

First published by BioMed Central: Schultheiss, Sebastian J.; Jean, Geraldine; Behr, Jonas; Bohnert, Regina; Drewe, Philipp; Gornitz, Nico; Kahles, Andre; Mudrakarta, Pramod; Sreedharan, Vipin T.; Zeller, Georg; Ratsch, Gunnar: Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data - In: BMC Bioinformatics. - ISSN 1471-2105 (online). - 12 (2011), suppl. 11, art. A7. - doi:10.1186/1471-2105-12-S11-A7.

10.1186/1471-2105-12-s11-a7

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Citations (3)

Transcriptional Control of a Plant Stem Cell Niche

Developmental Cell (2010)

Wolfgang Busch Andrej Miotk Federico Ariel Zhong Zhao Joachim Forner

Cell fate determination

Multicellular organism

Polycomb-group proteins

10.1016/j.devcel.2010.03.012

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Citations (211)

Editorial: Nar Awards 2011

Nucleic Acids Research (2011)

Claudine Baraquet Caroline S. Harwood Amit G. Deshwar Gerald Quon Quaid Morris

A major biofilm-related effect of the secondary messenger c-di-GMP in Pseudomonas aeruginosa is to stimulate Pel and Psl exopolysaccharide production.In this work, the authors showed that the transcriptional regulator FleQ is a dual function protein, able to both repress pel expression in the absence of c-di-GMP and activate the expression of pel in the presence of c-di-GMP.

10.1093/nar/gkr1206

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Citations (0)

Learn from the Best

PLoS Computational Biology (2014)

Virginie Bernard Sebastian J. Schultheiß Magali Michaut

What is more inspiring than a discussion with the leading scientists in your field? As a student or a young researcher, you have likely been influenced by mentors guiding you in your career and leading you to your current position. Any discussion with or advice from an expert is certainly very helpful for young people. But how often do we have the opportunity to meet experts? Do we make the most out of these situations? Meetings organized for young scientists are a great opportunity not only for the attendees: they are an opportunity for experts to meet bright students and learn from them in return. In this article, we introduce several successful events organized by Regional Student Groups all around the world, bridging the gap between experts and young scientists. We highlight how rewarding it is for all participants: young researchers, experts, and organizers. We then discuss the various benefits and emphasize the importance of organizing and attending such meetings. As a young researcher, seeking mentorship and additional skills training is a crucial step in career development. Keep in mind that one day, you may be an inspiring mentor, too.

Mentorship

10.1371/journal.pcbi.1003645

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Citations (1)

Crowd-Sourcing Design: Sketch Minimization using Crowds for Feedback

National Conference on Artificial Intelligence (2012)

David Engel Verena A. Kottler Christoph Malisi Marc Roettig Eva‐Maria Willing

Design tasks are notoriously difficult, because success is defined by the perception of the target audience, whose feedback is usually not available during design stages. Commonly, design is performed by professionals who have specific domain knowledge (i.e., an intuitive understanding of the implicit requirements of the task) and do not need the feedback of the perception of the viewers during the process. In this paper, we present a novel design methodology for creating minimal sketches of objects that uses an iterative optimization scheme. We define minimality for a sketch via the minimal number of straight line segments required for correct

Sketch

Design process

Source

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Decision: MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data — R2/PR13

Patrick Hüther Jörg Hagmann Adam Nunn Ioanna Kakoulidou Rahul Pisupati

Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype–epigenotype associations .

Differentially methylated regions

Bisulfite sequencing

Bisulfite

10.1017/qpb.2022.14.pr13

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Crossing Borders for Science

PLoS Computational Biology (2014)

Sebastian J. Schultheiß Joshua SungWoo Yang Wataru Iwasaki Shu-Hsi Lin Angela Jean

Exchanging ideas with like-minded, enthusiastic people interested in the same topic is crucial for the advancement of a scientist's career. Several Regional Student Groups (RSGs) of the International Society for Computational Biology (ISCB) Student Council have cooperated in the last six years to organize scientific workshops and conferences. With motivated students, it is possible to create a memorable event for fellow scientists; in doing so, the organizers gain valuable experiences. While collaborating across borders and time zones can be difficult, feedback from event organizers was always positive. When limited resources are juxtaposed with great ideas and a network of contacts, the outcome is always an amazing experience, despite organizers being separated geographically across different countries.

10.1371/journal.pcbi.1003519

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Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Nature (2011)

Xiangchao Gan Oliver Stegle Jonas Behr Joshua G. Steffen Philipp Drewe

Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions.

10.1038/nature10414

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Citations (660)

Ten Simple Rules for Providing a Scientific Web Resource

PLoS Computational Biology (2011)

Sebastian J. Schultheiß

Many projects in computational biology lead to the creation of a small application program or collection of scripts that can be of use to other scientists. A natural progression is to make this tool available via a Web site or by creating a service for it, from now on collectively called “Web resource.” We conducted a survey among providers and users of scientific Web resources, as well as a study on availability. The following rules reflect the experiences and opinions of over 250 scientists who have answered our questions and who use Web resources regularly, as well as our own experience. The study of availability allows us to draw objective conclusions about the characteristics of those Web resources that are still available and correlate the features that distinguish them from disappeared or nonfunctional ones. These ten simple rules aid you in designing and maintaining a scientific Web resource that is available to anyone interested in using it.

Web resource

Web engineering

10.1371/journal.pcbi.1001126

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Citations (15)

Recommendation: MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data — R1/PR9

Patrick Hüther Jörg Hagmann Adam Nunn Ioanna Kakoulidou Rahul Pisupati

Differentially methylated regions

Bisulfite sequencing

Bisulfite

10.1017/qpb.2022.14.pr9

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Citations (0)