Meet the teachers – Bioinformatics Centre - University of Copenhagen

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Bioinformatics Centre > Education > Master's degree in Bioinformatics > Meet the teachers

 Meet the teachers 

The main teachers on the programs are leaders of internationally respected research groups that cover a large part of the bioinformatics field. They are responsible for most of the courses but you will also be involved in their research in hands-on projects and in your master thesis. 

 

Anders Krogh, Professor
Anders Krogh is a pioneer in the use of hidden Markov models (HMMs) in biological sequence analysis. As a postdoc with David Haussler at UCSC he developed the so-called profile Hidden Mrkov Models, now one of the corner stones of bioinformatics.  Now, he works on non-coding RNAs and ancient genomes. Anders has written one of the most used textbooks in bioinformatics(Biological Sequence Analysis). This book is used for our courses in biological sequence analysis.

Selected publications:

Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010 Feb 11;463(7282):757-62. 

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA. 2011 May;17(5):820-34.  

What are artificial neural networks?  Nat Biotechnol. 2008 Feb;26(2):195-7. 


 

Thomas Hamelryck, Associate Professor
We are engaged with predicting, designing and determining the 3D structure of RNA and proteins, by developing sophisticated probabilistic models that describe aspects of protein structure. These models are mainly based on machine learning methods (including dynamic Bayesian networks), and directional statistics, the statistics of angles, directions and orientations.

Selected publications:.  

A probabilistic model of RNA conformational space. PLoS Comput Biol. 2009 Jun;5(6):e1000406.

A generative, probabilistic model of local protein structure. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8932-7. 

Sampling realistic protein conformations using local structural bias. PLoS Comput Biol. 2006 Sep 22;2(9):e131.   

Albin Sandelin, Associate Professor
The Sandelin lab is a computation/experimental group with scientists from many fields. We focus on gene regulation, transcriptomics, epigenetics and technological and informatics aspects. With the help of computers, we probe large biological datasets that are generated using novel genomics techniques. One of our strengths is our many collaborations with high-profile experimental laboratories, which supply data to be analyzed.

Selected publications:  

 
 

Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006 Jun;38(6):626-35  

Hans Siegismund, Associate Professor
We focus on the inference of demographic changes of populations, and inference of evolutionary processes involved in the speciation process among large African mammals. My group contribute to the Great Ape Genome Consortium, which aims at sequencing 100 genomes from the six great ape species. Other research includes work on the evolutionary genetics of foot-and-mouse-disease virus in East Africa

Selected publications:  

Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants.Proc Biol Sci. 2009 Oct 7;276(1672):3513-21

Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants. Mol Ecol. 2008 Sep;17(17):3788-99.

Jeppe Vinther, Associate Professor
In our group we aim to determine how RNA structure and RNA-protein interactions affect basal cellular processes. This knowledge is important to understand ways of improving the effeciency and specificity of RNA based drugs

Selected publications: 

Mutation of miRNA target sequences during human evolution. Trends Genet. 2008 Jun;24(6):262-5.

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes.BMC Genomics. 2007 Jul 23;8:244.

Origin of introns by 'intronization' of exonic sequences.Trends Genet. 2008 Aug;24(8):378-81  

Ole Winther, Associate Professor
My group is engaged with Machine Learning and novel methods for solving difficult inference problems. We are interested in probabilistic modelling of genomic data such as gene expression micro-array type and sequence tags, chip-on-chip and CAGE in close collaboration with experimental groups at BRIC, the University hospital and Riken, Japan.

Selected publications:

BayesMD: flexible biological modeling for motif discovery.J Comput Biol. 2008 Dec;15(10):1347-63.

Teaching computers to fold proteins.Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Sep;70(3 Pt 1):030903. 

Morten Lindow, Affiliated Associate Professor
Since doing my PhD on the computational biology of microRNAs, I have been engaged with microRNA research and the development of oligonucleotide drugs. I am currently Associate Director for Informatics at Santaris Pharma A/S and involved in supervising students and teaching at the Section for Bioinformatics, and also in collaborating with the section through the Centre for Applied and Computational Transcriptomics (COAT).

LNA-mediated microRNA silencing in non-human primates.Nature. 2008 Apr 17;452(7189):896-9. 

Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection.Science. 2010 Jan 8;327(5962):198-201.

Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants PLoS Comput Biol. 2007 Nov;3(11):e238.