HELLO, WORLD!
I'M OLGA! :)

Mathematician / Bioinformatician
Computational Scientist
ABOUT ME \\ Olga Chernomor, PhD
O.Chernomor, PhD
O.Chernomor, PhD

I blame (read thank) my elder sister Yuliia;) She "played" Maths with me before I learned to read. I also blame her to motivate me to learn English. Eventually, I also blame my parents, who got me a book "Encyclopedia of Professor Fortran", when I was around 4 years old. My first "computer" was printed on page 70 of that book and I would fiercely "type" my first code on the keyboard printed on page 71. I'm serious, by the way!

Well, after some considerations, now it all makes sense!

I'm a trained mathematician with two Master degrees, one in theoretical and another in applied Maths. After mathematical Masters' I obtained a PhD degree in Bioinformatics.

I love working with complex abstract concepts, coming up with algorithms and developing methods, pipelines and software to tackle biologically inspired problems. I appreciate clear though informative visualisation in science and tech communication and also enjoy technical writing. In summary, working on challenging projects, that require knowledge from different disciplines and sophisticated approaches, is what I consider an exciting task.
CV

EDUCATION


PhD in Bioinformatics, 2015
Vienna Graduate School in Computational Science
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna, Austria

M.Sc. in Mathematical Engineering, 2011
MathMods Joint Master Degree programme
University of L'Aquila, Italy
University of Nice - Sophia Antipolis, France

Magister in Mathematics, 2009
Oles Honchar Dnipro National University, Ukraine

Bachelor in Mathematics, 2008
Oles Honchar Dnipro National University, Ukraine

POSITIONs


since 12/2021 Principal Scientist
Boehringer Ingelheim

01/2016 - 11/2021 Research Associate
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna, Austria

08/2017 - 06/2018 Maternity leave

10/2011 - 12/2015 Research Assistant
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna, Austria

TEACHING


SS2019, SS2020, SS2021 - Bioinformatik für Biologen
WS2013, WS2014 - Grundlagen der Bioinformatik
University of Vienna, Austria
Research \\ Selected projects
TreeSpaceGraph

Phylogenetic terraces

TreeSpaceGraph

Phylogenetic terraces


In phylogenomics one infers an evolutionary tree for a group of species using genetic information from multiple genes. In the presence of missing data the tree space (solution space) is split into groups of equally optimal solutions, called Phylogenetic Terraces.
LPOR-tree

Evolution of LPOR protein

AAPB-LPOR-subtree

Evolution of LPOR protein


Light-dependent protochlorophyllide oxidoreductase (LPOR) is one of the proteins used in synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. Here, we uncover complex evolution of the protein in bacteria.
multifurcating-primate-tree

Evolution of cognitive traits

nine-ILS-trees

Evolution of cognitive traits


The evolution of closely related species is often accompanied by Incomplete Lineage Sorting (ILS), which leads to differences in evolutionary species tree and separate gene trees. The figure is the visualisation of different expected scenarious of gene evolution among Gorilla, Chimp, Human, and its ancient relatives, Denisovan and Neanderthal.
Experienced in
  • Development of algorithms and methods to solve computational problems arisen in biology
  • Algorithms implementation, data structure design and software development
  • Software testing and benchmarking (using simulated and biological datasets)
  • Development of custom pipelines and scripts tuned for specific project needs
  • Bioinformatics data analysis: data retrieval, preprocessing, analysis, reporting and visualization
  • Scientific writing, grant writing, reporting to collaborators and funding agencies
  • Communicating scientific and technical projects at conferences as well as to non-experts
Tech & Dev Skills
C++, bash, R, Python, Nextflow
\\ production-level software, custom pipelines, generation of simulated datasets, summary of results, visualisation
Contributor to IQ-TREE (git, website; C++)
\\ development of data structures, algorithms to solve computationally demanding problems
git, linux, MacOS, HPC/grid clusters, SGE, AWS
\\ experienced with version control and large scale analysis, benchmarking and testing
HTML, CSS, Bootstrap, Jekyll
\\ intermediate knowledge of web development; designed and coded: current website, parts of CIBIV website and LOGO, MASAMB2017 webpage and LOGO
pipeline development: bash, Nextflow
\\ developed custom pipelines for numerous projects, primarily using bash; basic knowledge of Nextflow is covered and ready to be employed
moodle learning platform
\\ managed exercises as part of the tutoring for bioinformatics courses at UniVie
Communication and Writing
Transform complex scientific ideas into simple and easy to follow concepts
Scientific writing, grant writing
\\ published articles in peer-reviewed journals, book chapter, co-author on grant proposal for FWF international project "Lost in Tree Space"
Experienced in science communication and tutoring
\\ gave talks at international scientific conferences/meetings as well as numerous internal talks; tutor for bioinformatics courses at UniVie
Visualisation skills
\\ skilled in communicating data and technical details by means of clear and understandable visualisation
¡MI CASA ES TU CASA!
  • Ukrainian \\ mother tongue
  • English \\ advanced
  • Deutsch \\ intermediate
  • Italiano, Español, Français \\ basic
Soft Skills

Quick learner, strong problem solving skills

Responsible and disciplined

Prefer working in small teams/independently

Experience of working in international teams

Creative and open-minded

 Conference organizer

\\ I was part of the local organising committee for MASAMB2017, responsible for scientific organization: management of abstracts submission via easychair, scheduling sessions, communication with programme committee and conference attendees

Reviewer for scientific journals

\\ reviewed articles for Systematic Biology, Bioinformatics, Methods in Ecology and Evolution, Genome Biology and Evolution, Journal of Theoretical Biology

Scripting, Programming and Software

I'm experienced in development of custom pipelines as well as implementation of algorithms either in standalone packages or as a part of the existing large software projects.

The "regulars" are C++, bash, R, python.


Regular Contribution

\\ IQ-TREE: Efficient software for phylogenomic inference >>>

Latest project

\\ implementation of the algorithm to generate equally optimal solutions in phylogenetic inference >>>

GitHub profile >>>

Designed and coded by O. Chernomor

© 2023