Martti Tolvanen profile picture
Martti
Tolvanen
University Lecturer, Health Technology
PhD
I collaborate with a group at Tampere University led by prof. Seppo Parkkila, on carbonic anhydrases.

Contact

Vesilinnantie 5
20500
Turku

Areas of expertise

Bioinformatics
Genomics
Molecular evolution
Biochemistry
Protein structures
Glycobiology

Biography

I am a biochemist who turned into a bioinformatician during 1990's. I got an MSc in 1986 and Ph.Lic in 1989, both in biochemistry at the University of Helsinki. I did my PhD at the U of Tampere based on my research there from 2004 to 2012. I became a PhD student in 2012 and defended my thesis in 2013. I have worked at the U of Helsinki from 1985 to 1997; North Karelia Polytechnic from 1998 to 2001; U of Tampere 2001 to 2013, and U of Turku 2013 to present.

Teaching

I have developed and taught at least six different bioinformatics courses and taught several courses developed by others. My main specialities and greatest interest areas in teaching are research tools in molecular bioinformatics, in particular sequence analyses and comparisons, use of bioinformatics databases, and structural bioinformatics for work with protein 3D structures. My main teaching method is learning by doing, which means that all theoretical concepts are understood better when applied in the context of actual problem-solving and pursuit of understanding biomolecules and biological processes with the help of bioinformatics tools.

I have a been teaching at Finnish Universities for more than 30 years, and since 2001 I have developed on-line teaching in bioinformatics. Since 2006 I have been teaching in international master's degree programmes of bioinformatics, and more recently in wider MSc programmes which include bioinformatics as one specialization line.

On-line teaching is also a special interest of mine, from long before the pandemic times. At the U of Tampere I was part of a three-person team (Lehtiniemi-Tolvanen-Vihinen) who won the national award of on-line teaching of the Finnish Ministry of Education, in 2002.

The courses which I have been teaching in the current curriculum cycle include Bioinformatics Methods, Structural  Bioinformatics, Algorithms in Bioinformatics, and Bioinformatics Project, in addition to thesis supervising and co-supervising, and being a member is various PhD thesis committees.


Research

My research topic is bioinformatics of carbonic anhydrases, focusing on genomics, molecular evolution and structural aspects, such as protein and glycoprotein modelling.

Publications

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Neural Network and Random Forest Models in Protein Function Prediction (2020)

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Hakala Kai, Kaewphan Suwisa, Björne Jari, Mehryary Farrokh, Moen Hans, Tolvanen Martti, Salakoski Tapio, Ginter Filip
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019)

Genome Biology
Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )