People

I received a Ph.D. in Biochemistry in 2006 (Åbo Akademi University, Finland). Since 2008, I have served as group leader in the CDR where he leads the Computational Drug Discovery Group. My main interests are computational drug discovery, molecular modeling, sequence-structure-function relationships in proteins, and membrane proteins (especially G protein-coupled receptors and transporters).

I am leading the Pharmaceutical Design and Discovery Unit.

I obtained my PhD at the University of Nancy in 2010 in the field of Chemoinformatics. I have worked in both academic and industrial projects. Since then I work as a expert Chemoinformatician for the Drug Discovery and Chemical Biology Consortium (DDCB, under the HILIFE/EU-openscreen).

My research interest computer artificial intelligence, in particular databases and machine learning. I am also routinely using molecular modeling and virtual screen tools.

The focus of my work is :

  • Expert service in Chemical Biology as part of DDCB: library preparation, virtual screens, follow-up screens, data analysis..
  • Connecting compound to target to disease data. This involves both machine learning application and database construction. See IDAAPM database http://idaapm.helsinki.fi/, from Legehar et al. 2016.

I am now postoctoral researcher working for the SUDDEN project.

During my PhD, with a background in biology, I have first worked in the classification of GPCRs. I have them moved to structural analysis and docking studies, then to partly work in the lab to study early receptor orexin evolution (collaboration with Prof. Kukkonen). Thus in addition to being acquainted with computational applications, I am experienced in pharmacology and molecular biology. I have also conducted virtual screen and experimental hit validation and pathway analysis on the Toll-like receptor ligands. I have conducted a research visit in Monash University (Melbourne, AUS) as part of my PhD studies.

My research interests G protein-coupled receptors, orexin receptors, protein sequence mining, molecular evolution, phylogenetic reconstruction, molecular pharmacology, and computational drug discovery.

In my free time, I play roller derby in Helsinki Roller Derby All-Stars, and I have also played for Team Finland in two previous World Cups. Additionally I do gym, horseback riding and hanging out with my two dogs Rölli and Piku.

I have a B.Sc. in software engineering followed by a M.Sc. in bioinformatics from the University of Turku (FI). I have been working in start-up companies as a developer before starting my PhD studies. I have experience in data mining, data analysis and machine learning as well as web development (including as team leader).

My research interests are in the developement of chemogenomics and chemoinformatic tools. I am particularly interested into recent developments of machine learning to conduct predictive modeling and data analysis.

My project is about the development and integration of chemical databases, for example the IDAAPM data (Legehar et al., 2016), see http://idaapm.helsinki.fi

I am also involved in the discovery of novel quorum sensing inhibitors and antibacterial compounds using virtual screens, structural modeling (docking studies) and QSAR modeling (in collaboration with the groups of Prof. Jari Yli-Kauhaluoma (medicinal chemistry) and Docent Adyary Fallerero (in vitro studies).

I am a chemoinformatician with a BSc in computer science, MSc in pharmacy (University of Helsinki), and work experience as a data scientist from a major company. I have advanced programming skills with particular insights in homology modeling and membrane proteins (see Grazhdankin et al., J. Struct. Biol., 2019).

My research interests are tied to artificial intelligence and machine learning, and to Bayesian and graph-based theories. I seek to solve challenging problems in multi-objective optimization of molecular complexes. In addition, I work on a hit-to-lead optimization (confidential, funded by Business-Finland TUTL).

I graduated in from the University of Paris-Diderot (Paris 7) with a master in cheminformatics (in-silico drug design (external link)). From August 2018 I have been working in the Xhaard group.

My research interest are the methods to convert chemical knowledge into numbers. I am experienced and sometimes enjoy coding in Python and R.

My project aims to devise efficient scoring based functions. I am working with refernece states, atom types, and the ability to introduce and score water molecules. Simultaneously, I am working on the design of inhibitor for the membrane-bound pyrophosphatase. I conduct  follow-up similarity screens and virtual screens, and conduct through computational simulation a fragment-based optimization in connection with medicinal chemists from the Yli-Kauhaluoma group.

In free time, I go bouldering and also play volley ball. I eat a lot of goodies too.

 

I am from the French city of Nantes where I followed a training the Ecole Centrale, a competitive engineer school in the French system. Following a final year internship in the group, I followed up as a PhD student. I enjoy learning on anything that is even remotely related to physics, biology or a bunch of other research fields, thus making me an easy target for nerd-sniping. That's also how I ended up here starting from my computer-science-focused background.

My research interests are connected to digital science, in particular machine learning and the use of graphs in chemoinformatics applications. As part of the SUDDEN project, I am building computational data analysis tools to mine and analyze pharmaceutically active ingredients in the environment (circulating water and waste water, activated sludge) with aim to drive policy making. I believe that the field would benefit from data integration and standardization.

 

 

 

There is generally 1-3 M.Sc. rotating students in the lab, especially in spring time. We are welcoming regularly summer workers, interns and erasmus students (typically at M2 internship). We have had students form Greece (Thessalonica), France (Nantes, Paris, Toulouse), Italy (Urbino, Padova), as well as summer workers from Finland (University of Helsinki/University of Eastern Finland).

Currently: Lauri Urvas (UH Faculty of Pharmacy, researcher line; see picture); for the spring 2020 two more students are expected (erasmus exchange to University Paris-Sorbonne, Master ISDD, and University of Nantes).

[Updated November 2019]

Postdoctoral researchers

  • 2012-2013 Pavel Kydryavtsev (PhD from Moscow state University)
  • 2010 Joonas Jämsen (PhD from University of Turku). Corresponded to a Civil Service.
  • 2009-2010 Leslie Regad (PhD from University Paris VII).
  • Many graduated PhD students have been also employed a few months during transitioning.

PhD theses

  • 27.09.2019 Maiju Rinne. e-thesis (external link). Molecular evolution of G protein-coupled receptors – insights into the orexin system. The experimental part was conducted in the laboratory of Prof. Kukkonen. Maiju conducted a two months research visit to Monash University (AU).
  • 26.10.2018 Lasse Karhu. e-thesis (external link). Computational analysis of orexin receptors and their interactions with natural and synthetic ligands. Lasse is now Lecturer at our Faculty.
  • 17.08.2018 Ainoleena Turku. e-thesis (external link). Discovery of OX1 and OX2 Orexin Receptor Ligands. The experimental part was conducted in the laboratory of Prof. Kukkonen. The thesis included a three months visit to the University of Leeds. Ainoleena is now postdoctoral researcher at the Karolinska Institute, Stockholm, SE.
  • 21.08.2016 Michal Stepniewski. e-thesis (external link). Computational studies on membrane proteins and membrane-drug interactions. The thesis included a three months visit to the University of Krakow (PL).
  • 21.12.2016 Vigneshwari Subramanian. e-thesis (external link). Field-based Proteochemometric Models Derived from 3D Protein Structures: A Novel Approach to Visualize Affinity and Selectivity Features. The thesis work was conducted jointly at Orion Pharma Ldt. Vignesh is now postdoctoral researcher at AstraZeneca (Moldaln, SE).
  • 26.05.2016 Alexandre Borrel. e-thesis (external link). Development of Computational Methods to Predict Protein Pocket Druggability and Profile Ligands using Structural Data. The thesis was conducted under a cotutelle agreement with Prof. Anne Claude Camproux (UP7, FR) with a shared presence in both countries. Alexandre is now working for the NIH (US) following a postdoc in the group of D. Fourches (North Carolina State Univ).
  • 29.05.2015 Gloria Wissel. e-thesis (external link). ABCC2 transporter and α2 adrenoceptors: Identification of novel compounds and their mode of action. The experimental work was conducted in the laboratory of Dr Heidi Kidron. The thesis included a four months research visit to the University of Rome.
  • 19.12.2014 Zhang Yuezhou. e-thesis (external link). Investigating phosphate structural replacements through computational and experimental approaches. The experimental work (medicinal chemistry) was conducted in the laboratory of Professor Jari Yli-Kauhaluoma. Yuezhou is now Principal Investigator at the Northwestern Polytechnical University, X'ian, China.

PhD theses (second supervisor)

  • 24.08.2014 Aniket Magarkar. e-thesis (external link). Aniket is now in the industry.
  • 11.09.2015 Eva Del Amo (UEF). e-thesis (external link).

Visiting PhD students

  • 2016 Jelica Vucicevic, University of Belgrade (SB).
  • 2011-2014 Heikki Käsnänen, University of Eastern Finland.
  • 2012 Tanoli-Ur-Rehman, Pakistan PIEAS (PK).
  • 2011 Maria Matveeva, Kazhan state University (RU), 

M.Sc. theses

  • 2019 Lauri Urvas. Pharmacy, UH. In progress (the thesis includes an erasmus visit to the University Paris VII)
  • 2019 Céline Pierrot, Ecole Centrale de Nantes (FR, visitor).
  • 2019 Cyril Bigot, University Paris VII, Master ISDD (FR, erasmus)
  • 2018 Evgeni Grazhdankin. Pharmacy, UH. e-thesis (external link) [*]
  • 2018 Mael Briand, Ecole Centrale de Nantes (FR, visitor). [*]
  • 2018 Loic Dreano, University Paris VII, Master ISDD (FR, erasmus). [*].
  • 2016 Ashenafi Legehar, University of Turku, Bioinformatics. [*].
  • 2016 Fabio Vedovi, University of Urbino (IT, erasmus).
  • 2016 Matti Tamminen. In collaboration with the Medicinal Chemistry Unit. Pharmacy, UH. e-thesis (external link)
  • 2016 Cedric Gageat, University Paris VII, Master ISDD (FR, erasmus)
  • 2015 Karen Culotta, University of Nantes, Bioinformatics (FR, visitor)
  • 2014 Ali Bakiri, University Paris VII, Master ISDD (FR, erasmus)
  • 2012 Kim Ng. Bioinformatics UH.
  • 2012. Melaine Kuenemann, University Paris VII, Master ISDD (FR, erasmus)
  • 2012 Vigneshwari Subramanian. Bioinformatics, UH. [*]
  • 2011 Lasse Karhu. Pharmacy, UH. e-thesis (external link) [*]
  • 2010 Ainoleena Turku. Pharmacy, UH. e-thesis (external link) [*]
  • 2010 Gloria Wissel. Pharmacy, Padova/Åbo Akademi (IT, erasmus) [*]
  • 2010 Anna Gerhardo. Pharmacy, Padova/Åbo Akademi (IT, erasmus)
  • 2009 Rossato GianLuca. Pharmacy, University of Padova (IT, erasmus).

[*] continuation in the group as PhD student.