„I had the privilege to work with Kristian: a brilliant mind and a humorous person. We both were part of the Manegement Team at Spiced Academy, a coding bootcamp based out of Berlin offering courses in multiple locations in Germany. Apart from his highly rewarded skills as a Data Science Teacher, I got to know a person who is a master of open communication and questioning, who was empathetic both with colleagues and his team and paid attention on being precise and contributing to high-quality work: may it be a strategic proposal, a teacher's training or a team event. He continuously sought new ways to support his team and represent their interest, while the company was growing rapidly and there were constant changes both in the team structure and the areas of responsibilities. Even though I was responsible for the business and customer operations, I enjoyed participating on his thoughtful lessons and engaging in eye-opening conversations with him about problem solving, analysing, teaching or Berlin's history. I highly recommend working with Kristian. I also encourage anyone who encounters him to take the opportunity and enjoy his good sense of humor!“
Kristian Rother
Metropolregion Berlin/Brandenburg
2328 Follower:innen
500+ Kontakte
Info
I am running a 3-month Data Science boot camp in Berlin. The curriculum covers Python…
Aktivitäten
-
Probably Fun: using games to teach #statistics. How about a game of memory in the classroom and then calculate probabilities for how many turns it…
Probably Fun: using games to teach #statistics. How about a game of memory in the classroom and then calculate probabilities for how many turns it…
Geteilt von Kristian Rother
-
The 🌯 Burrito Optimization Game 🌯 (https://lnkd.in/eA5W3BEN) is a great exercise to introduce optimizers in a class on algorithms or ML-related…
The 🌯 Burrito Optimization Game 🌯 (https://lnkd.in/eA5W3BEN) is a great exercise to introduce optimizers in a class on algorithms or ML-related…
Geteilt von Kristian Rother
-
The first of three interesting days of PyConDE & PyData Berlin is in the books. These are my takeaways: Like most of the time there were to many…
The first of three interesting days of PyConDE & PyData Berlin is in the books. These are my takeaways: Like most of the time there were to many…
Beliebt bei Kristian Rother
Berufserfahrung
Ausbildung
-
magna cum laude
-
-
-
-
Ehrenamt
-
President
Spreeredner Toastmasters
-
Club Treasurer
Verbal Victory Toastmasters
-
Vice President Membership
Spreeredner Toastmasters
-
Club Treasurer
Spreeredner Toastmasters
-
Organizer
RuPy Conference
-
Coach
Open Tech School
-
Speaker
AKAI Poznan
-
Speaker
JUG - Java User Group Poznan
-
Vice President Education
Vice President Education
Toastmasters International
Bescheinigungen und Zertifikate
Veröffentlichungen
-
Pro Python Best Practices: Debugging, Testing and Maintenance
Apress
Learn software engineering and coding best practices to write Python code right and error free. In this book you’ll see how to properly debug, organize, test, and maintain your code, all of which leads to better, more efficient coding.
-
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.
Nucleic Acids Research
We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative…
We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.
Andere Autor:innenVeröffentlichung anzeigen -
MODOMICS: a database of RNA modification pathways--2012 update
Nucleic Acids Research
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue…
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue of 'building blocks' for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.
Andere Autor:innenVeröffentlichung anzeigen -
RNA tertiary structure prediction with ModeRNA
Briefings in Bioinformatics
Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a detailed study on using the ModeRNA software. The tool uses the comparative modeling approach and can be applied when a structural template is available and an alignment of reasonable quality can be performed. We guide the reader through the entire…
Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a detailed study on using the ModeRNA software. The tool uses the comparative modeling approach and can be applied when a structural template is available and an alignment of reasonable quality can be performed. We guide the reader through the entire process of modeling Escherichia coli tRNA(Thr) in a conformation corresponding to the complex with an aminoacyl-tRNA synthetase (aaRS). We describe the choice of a template structure, preparation of input files, and explore three possible modeling strategies. In the end, we evaluate the resulting models using six alternative benchmarks. The ModeRNA software can be freely downloaded from http://iimcb.genesilico.pl/moderna/ under the conditions of the General Public License. It runs under LINUX, Windows and Mac OS. It is also available as a server at http://iimcb.genesilico.pl/modernaserver/. The models and the script to reproduce the study from this article are available at http://www.genesilico.pl/moderna/examples/.
Andere Autor:innenVeröffentlichung anzeigen -
Computational methods for prediction of protein-RNA interactions
Journal of Structural Biology
Understanding the molecular mechanism of protein–RNA recognition and complex formation is a major challenge in structural biology. Unfortunately, the experimental determination of protein–RNA complexes by X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) is tedious and difficult. Alternatively, protein–RNA interactions can be predicted by computational methods. Although less accurate than experimental observations, computational predictions can be sufficiently accurate to…
Understanding the molecular mechanism of protein–RNA recognition and complex formation is a major challenge in structural biology. Unfortunately, the experimental determination of protein–RNA complexes by X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) is tedious and difficult. Alternatively, protein–RNA interactions can be predicted by computational methods. Although less accurate than experimental observations, computational predictions can be sufficiently accurate to prompt functional hypotheses and guide experiments, e.g. to identify individual amino acid or nucleotide residues. In this article we review 10 methods for predicting protein–RNA interactions, seven of which predict RNA-binding sites from protein sequences and three from structures. We also developed a meta-predictor that uses the output of top three sequence-based primary predictors to calculate a consensus prediction, which outperforms all the primary predictors. In order to fully cover the software for predicting protein–RNA interactions, we also describe five methods for protein–RNA docking. The article highlights the strengths and shortcomings of existing methods for the prediction of protein–RNA interactions and provides suggestions for their further development.
Andere Autor:innenVeröffentlichung anzeigen -
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinformatics
Abstract
SUMMARY:
The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates…Abstract
SUMMARY:
The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. AVAILABILITY AND
IMPLEMENTATION:
ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver.
CONTACT:
iamb@genesilico.pl.Andere Autor:innenVeröffentlichung anzeigen -
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinformatics
Abstract
SUMMARY:
The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates…Abstract
SUMMARY:
The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. AVAILABILITY AND
IMPLEMENTATION:
ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver.
CONTACT:
iamb@genesilico.pl.Andere Autor:innenVeröffentlichung anzeigen -
A toolbox for developing bioinformatics software
Briefings in Bioinformatics
Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and…
Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers.
Andere Autor:innenVeröffentlichung anzeigen -
ModeRNA: a tool for comparative modeling of RNA 3D structure
Nucleic Acids Research
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative…
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.
Andere Autor:innenVeröffentlichung anzeigen
Kurse
-
Seminargruppen leiten und führen - Bettina Ritter-Mamczek
-
Projekte
-
ModeRNA - computer software for modeling of RNA 3D structures
–Heute
ModeRNA is a computer programs for modeling of RNA 3D structures. It relies on the "comparative modeling" approach. It requires a sequence alignment between the target RNA molecule to be modeled and a "template" RNA molecule with known structure. The modeling can be either fully automated or can be based on the use of a series of scripts. ModeRNA is capable of handling various chemically modified resisdues. Apart from that, ModeRNA offers a multitude of functions to examine and modify RNA…
ModeRNA is a computer programs for modeling of RNA 3D structures. It relies on the "comparative modeling" approach. It requires a sequence alignment between the target RNA molecule to be modeled and a "template" RNA molecule with known structure. The modeling can be either fully automated or can be based on the use of a series of scripts. ModeRNA is capable of handling various chemically modified resisdues. Apart from that, ModeRNA offers a multitude of functions to examine and modify RNA structure files. ModeRNA can be integrated into other programs via Python scripting. We are currently working on extending ModeRNA to use multiple templates.
Andere Mitarbeiter:innenProjekt anzeigen -
Book Translation: Data Science from Scratch by Joel Grus (O'Reilly / dpunkt)
–
I translated an introductory book into Data Science from English to German. The book explains both Python and basics statistical / machine learning concepts in an easily understandable way.
-
Python for Data Analysis
–
Translation of Wes McKinney's famous book to German, and porting of everything to Python 3
Andere Mitarbeiter:innenProjekt anzeigen -
RNApathwaysDB - a database of RNA maturation and decay
Many RNA molecules undergo complex maturation, involving e.g. excision from primary transcripts, removal of introns, post-transcriptional modification and polyadenylation. The level of mature, functional RNAs in the cell is controlled not only by the synthesis and maturation but also by degradation, which proceeds via many different routes. The systematization of data about RNA metabolic pathways and enzymes taking part in RNA maturation and degradation is essential for the full understanding…
Many RNA molecules undergo complex maturation, involving e.g. excision from primary transcripts, removal of introns, post-transcriptional modification and polyadenylation. The level of mature, functional RNAs in the cell is controlled not only by the synthesis and maturation but also by degradation, which proceeds via many different routes. The systematization of data about RNA metabolic pathways and enzymes taking part in RNA maturation and degradation is essential for the full understanding of these processes. RNApathwaysDB, available online at http://iimcb.genesilico.pl/rnapathwaysdb, is an online resource about maturation and decay pathways involving RNA as the substrate. The current release presents information about reactions and enzymes that take part in the maturation and degradation of tRNA, rRNA and mRNA, and describes pathways in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. RNApathwaysDB can be queried with keywords, and sequences of protein enzymes involved in RNA processing can be searched with BLAST. Options for data presentation include pathway graphs and tables with enzymes and literature data. Structures of macromolecular complexes involving RNA and proteins that act on it are presented as 'potato models' using DrawBioPath-a new javascript tool.
Andere Mitarbeiter:innenProjekt anzeigen -
RNAmetaserver - A gateway to bioinformatics methods predicting RNA secondary structure
The RNAmetaserver provides access to single-sequence (20 programs) and comparative methods (10 programs) predicting RNA secondary structure.
Andere Mitarbeiter:innenProjekt anzeigen -
Modomics - a database of RNA modification pathways
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue…
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue of 'building blocks' for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.
Andere Mitarbeiter:innenProjekt anzeigen
Sprachen
-
Finnish
Muttersprache oder zweisprachig
-
Polish
Fließend
-
Latin
Fließend
-
German
Muttersprache oder zweisprachig
-
English
Verhandlungssicher
Organisationen
-
Django Software Foundation
Vice Chair of Grants Committee
-
EuroPython Society
Member
-
Spreeredner Toastmasters
Vice President Membership
-
GOBLET - Global Organization on Bioinformatics Education and Training
individual member
-
Data Science Retreat
Presentation Coach
-
Urlist
Technical Editor
Erhaltene Empfehlungen
6 Personen haben Kristian Rother empfohlen Jetzt anmelden und ansehen
Weitere Aktivitäten von Kristian Rother
Yesterday I visited my favourite conference where my friend Inessa Pawson gave a wonderful keynote about building strong open source communities. 🪴…
Beliebt bei Kristian Rother
That's it for my first PyConDE & PyData Berlin! Loved it SO much. Here are my highlights ✨ 🦈🎲 The most entertaining lightning talks I have ever…
Beliebt bei Kristian Rother
❓ ‘How was the transition into (tech) leadership been affected by your gender?’ I got this question during my talk today at PyConDE & PyData…
Beliebt bei Kristian Rother
Wrote front-end code for my upcoming tutorial at PyConDE (https://lnkd.in/ePcGfrQ3). It went super fast with Pico CSS (https://picocss.com/). Thanks…
Geteilt von Kristian Rother
Weitere Mitglieder, die Kristian Rother heißen
Es gibt auf LinkedIn 2 weitere Personen, die Kristian Rother heißen.
Weitere Mitglieder anzeigen, die Kristian Rother heißen