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Last update: November 2009 |
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Research topics
Systems biology (*): Structure
and function of modules in biological networks
In a great paper,
Hartwell & co explain the principle that cellular
functions are carried out by modules. Modules are composed of
many types of molecules and have discrete functions that arise from
the interactions among their components. Modules can be
- Insulated from each other: to carry out diverse
reactions without cross-talk.
- Connected to each other: one function can
influence another.
- Overlapping: a component may belong to different
modules at different times.
The main
questions in the study of biological modules are:
- What are the parts of modules and what are the
general principles that govern their structure?
- How do the interactions between the components
produce a given function?
- How are modules constructed during
evolution?
- How do connections between modules change under
evolution to alter the behavior of cells and organisms?
My current research focuses on the first question, more precisely on
developing computational methods for the automatic identification of
modules from various kinds of biological
networks. In our
group, we have developed a software
package for learning module networks from gene expression data [paper 1, paper 2, paper
3]. Recently, I have started working on matrix and tensor methods
for identifying modules in integrated networks [poster]. An
initial matrix
algorithm is already available. For more information, have a look
at this
recent presentation.
(*) What is systems biology?
"Systems biology is the study of dynamic networks of interacting biological elements."
R. Aebersold, Molecular Systems Biology: a new journal for a new
biology?, Molecular
Systems Biology 1:2005.0005 (2005).
"We expect to encounter fascinating and, I believe, very
fundamental questions at each stage in fitting together less
complicated pieces into the more complicated system and understanding
the basically new types of behavior which can result."
P.W. Anderson, More is
Different, Science
177:393 (1972).
"Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better."
J.E. Cohen, PLoS Biol 2:e439 (2004).
The computation of the thermal stability and statistical physics of
nucleic acids is a classical problem going back to the 1960's, with
recent results relating the physics of denaturation (DNA strand
separation) to the biology of genomes. Other experimental
developments, which can also be modeled accurately by statistical
physics, have made it possible to manipulate single polymeric
molecules directly and offer access to a whole new range of DNA
properties. Coming from physics, this topic was a nice introduction
into the world of biology. I developed a Matlab
toolbox for analyzing the melting properties of a non-linear
helicoidal DNA model [paper].
This is the area where I worked for my PhD
(at the ITF in Leuven) and
first postdoc (at UCDavis).
I still have a pleasant collaboration with Bruno Nachtergaele and
Wolfgang Spitzer
on this topic, nowadays mostly limited to writing
code for numerical analysis, leaving the difficult mathematics to
them. In our latest project we studied the transport of domain walls
in quantum spin systems by moving external fields [paper]. For this
study we developed a Matlab
toolbox for performing ground state and time-dependent Density
Matrix Renormalization Group computations for one-dimensional quantum
spin systems which need not be translation invariant.
The links below lead to an abstract of the paper and a choice of
download formats. [arXiv] points to the arXiv Preprint server
and [journal] to the publisher of the
paper; you can also download a [PDF] file directly.
-
Enrichment and aggregation of topological motifs are independent
organizational principles of integrated interaction networks
(2009) (submitted).
(T. Michoel, B. Nachtergaele,
Y. Van de Peer)
-
Characterizing regulatory path motifs in integrated networks using perturbational
data (2009) (submitted).
(A. Joshi,
T. Van Parys,
Y. Van de Peer,
T. Michoel).
-
Network inference from a cancer gene expression data set identifies microRNA
regulatory modules (2009) (submitted).
(E. Bonnet,
M. Tatari,
A. Joshi,
T. Michoel, K. Marchal, G. Berx,
Y. Van de Peer)
-
Transcription regulatory networks in Caenorhabditis elegans inferred
through reverse-engineering of gene expression profiles constitute biological
hypotheses for metazoan development, Mol. BioSyst. 5, 1817 - 1830 (2009).
(V. Vermeirssen,
A. Joshi,
T. Michoel,
E. Bonnet,
T. Casneuf,
Y. Van de Peer)
[journal]
-
Comparative analysis of module-based versus direct methods for reverse-engineering
transcriptional regulatory networks, BMC Systems Biology 3, 49 (2009).

(T. Michoel,
R. De Smet,
A. Joshi,
Y. Van de Peer,
K. Marchal)
[arXiv]
[journal]
[PDF]
[Supplementary
information]
-
Implementing quantum gates using the ferromagnetic spin-J XXZ chain with kink boundary conditions,
New. J. Phys. (accepted) (2009).
(T. Michoel, J. Mulherkar, B. Nachtergaele)
[arXiv]
[PDF]
-
Module networks revisited: computational assessment and prioritization
of model predictions, Bioinformatics 25, 490 - 496 (2009).

(A. Joshi,
R. De Smet,
K. Marchal,
Y. Van de Peer,
T. Michoel)
[arXiv]
[journal]
[PDF]
[Supplementary
information]
-
Reverse-engineering transcriptional modules from gene expression data,
Ann. N. Y. Acad. of Sci. 1158, 36 - 43 (2009).
(T. Michoel,
R. De Smet,
A. Joshi,
K. Marchal,
Y. Van de Peer).
[arXiv]
[journal]
[PDF]
-
Analysis of a Gibbs sampler method for model based clustering of gene expression data,
Bioinformatics 24, 176 - 183 (2008).
(A. Joshi,
Y. Van de Peer,
T. Michoel).
[arXiv]
[journal]
[PDF]
[Supplementary
information]
-
Transport of interface states in the Heisenberg chain,
J. Phys. A: Math. Theor. 41, 492001 (2008). FastTrack
(T. Michoel,
B. Nachtergaele,
W. Spitzer).
[arXiv]
[journal]
[PDF]
-
Validating module networks learning algorithms using simulated data,
BMC Bioinformatics 8, S5 (2007).
(T. Michoel,
S. Maere,
E. Bonnet,
A. Joshi,
Y. Saeys,
T. Van den Bulcke, K. van Leemput, P. van Remortel, M. Kuiper, K. Marchal,
Y. Van de Peer).
[arXiv]
[journal]
[PDF]
[Supplementary Information]
-
A helicoidal transfer matrix model for inhomogeneous DNA melting,
Phys. Rev. E 73, 011908 (2006).
(T. Michoel,
Y. Van de Peer).
[arXiv]
[journal]
[PDF]
-
The large-spin asymptotics of the ferromagnetic XXZ chain,
Markov Proc. Rel. Fields 11, 237 - 266 (2005).
(T. Michoel, B. Nachtergaele).
[arXiv]
[PDF]
-
Central limit theorems for the large-spin asymptotics of quantum spins,
Prob. Th. Rel. Fields 130, 493 - 517 (2004).
(T. Michoel, B. Nachtergaele).
[arXiv]
[journal]
[PDF]
-
The Goldstone Boson, PhD Thesis, Katholieke Universiteit Leuven, April 2001.
[PDF]
[PS]
-
Goldstone boson normal coordinates,
Comm. Math. Phys. 216, 461 - 490 (2001).
(T. Michoel, A. Verbeure).
[arXiv]
[mp_arc]
[journal]
[PDF]
-
Interferencing in coupled Bose-Einstein condensates,
J. Stat. Phys. 102, 1383 - 1405 (2001).
(T. Michoel, A. Verbeure).
[arXiv]
[mp_arc]
[journal]
[PDF]
-
Mathematical structure of magnons in quantum ferromagnets,
J. Phys. A: Math. Gen. 32, 5875 - 5883 (1999).
(T. Michoel, A. Verbeure).
[arXiv]
[mp_arc]
[journal]
[PDF]
-
Goldstone boson normal coordinates in interacting Bose gases,
J. Stat. Phys. 96, 1125 - 1162 (1999).
(T. Michoel, A. Verbeure).
[arXiv]
[mp_arc]
[journal]
[PDF]
-
Nonextensive Bose-Einstein condensation model,
J. Math. Phys. 40, 1268 - 1279 (1999).
(T. Michoel, A. Verbeure).
[arXiv]
[journal]
[PDF]
-
CCR-algebra structure of normal k-mode fluctuations,
Rep. Math. Phys. 41, 361 - 395 (1998).
(T. Michoel, B. Momont, A. Verbeure).
[mp_arc]
[journal]
[PDF]
The links below lead to a [download] location of the
software package and a list of [paper]'s which have
used it.
-
MINT - a Cytoscape plugin for Module Identification in
Integrated NeTworks. MINT is a graphical user interface for the
Network Motif Clustering Toolbox.
-
Network Motif Clustering Toolbox - a Matlab toolbox for
clustering topological motifs in integrated networks.
[download]
-
Pathicular - a Cytoscape plugin for identifying regulatory path
motifs in integrated networks.
[download]
-
MatrixClust - a Matlab toolbox for fuzzy clustering of a
symmetric matrix, typically the weighted adjacency matrix of an
undirected network.
[download]
[paper]
[paper]
-
LeMoNe - a Java package for learning module networks from gene
expression data.
[download]
[paper]
[paper]
[paper]
[paper]
[paper]
-
GaneSh - a Java package for 2-way clustering of gene expression
data using a Gibbs sampling method. Ganesh is also part of the LeMoNe package.
[download]
[paper]
-
D-MiRaGe - a Matlab toolbox for performing ground state and
time-dependent Density Matrix Renormalization Group computations for
one-dimensional quantum spin systems which need not be translation
invariant.
[download]
[paper]
[paper]
-
DNAmelt - a Matlab toolbox to compute DNA melting properties
using a helicoidal transfer matrix model.
[download]
[paper]
-
Enrichment and aggregation of topological motifs in integrated
interaction networks, CWI-NISB Life Sciences Seminar (25
September 2009).
[PDF]
-
Identification of functional modules in integrated biological networks,
VIB Seminar (12 March 2009).
[PDF]
-
Motif based module identification in integrated networks,
RECOMB Regulatory Genomics / RECOMB Systems Biology / DREAM3
(29 October - 2 November 2008) (poster).
[PDF]
-
Module identification in biological networks,
Mathematical biology seminar, Department of Mathematics,
University of California, Davis (23 October 2008).
[PDF]
-
Module networks revisited: assessment and prioritization of model predictions,
BioMAGNet workshop (28 May 2008).
[PDF]
-
Ensemble method for reverse-engineering transcriptional modules,
BioFrame User Meeting (25 January 2008).
[PDF]
-
Introduction to systems biology and reverse engineering biological networks,
Institute for Theoretical Physics, KULeuven
(9 January 2008).
[PDF]
-
Reverse-engineering transcriptional modules from gene expression data,
DREAM2
(3-4 December 2007) (poster).
[PDF]
-
Module networks ensembles for reverse engineering transcription regulatory networks,
ISMB/ECCB 2007
(21-25 July 2007) (poster).
[PDF]
-
Bioframe kick-off: algorithms and modeling,
[PDF]
-
Validating module networks learning algorithms using simulated data,
The 3rd
EMBL Biennial Symposium: From Functional Genomics to Systems Biology
(14 October 2006) (poster).
[PDF]
- Inferring regulatory networks from transcriptome data,
PSB Lab Meeting (14 September 2006).
[PDF]
- Transport of one-dimensional interfaces in the Heisenberg model,
Mathematical Physics Seminar,
Department of Mathematics,
University of California, Davis
(25 May 2006).
[PDF]
Service as reviewer
Genome Biology,
PLoS Computational Biology,
Bioinformatics,
BMC Systems Biology,
BMC Bioinformatics,
Journal of Mathematical Physics,
EURASIP Journal on Bioinformatics and Systems Biology,
Current Proteomics
-
Senior Researcher,
Bioinformatics and Evolutionary Genomics,
Plant Systems Biology,
VIB and UGent,
since 1 October 2007.
-
Postdoctoral Fellow of the Research Foundation -
Flanders (F.W.O.-Vlaanderen),
Bioinformatics and Evolutionary Genomics,
Plant Systems Biology,
VIB, UGent,
1 October 2004 - 30 September 2007.
-
Postdoctoral Fellow of the Research Foundation -
Flanders (F.W.O.-Vlaanderen),
Institute for Theoretical Physics,
KULeuven,
1 October 2002 - 30 September 2004.
-
Postdoctoral Fellow of the Research
Foundation - Flanders (F.W.O.-Vlaanderen) and Visiting Scholar, Department of Mathematics, University of California, Davis, 1
October 2001 - 30 September 2002.
-
Doctor in Science: Physics (PhD),
KULeuven, 20 April 2001.
Thesis: The Goldstone Boson (Advisor: A. Verbeure)
-
Research Assistant of the Research Foundation -
Flanders (F.W.O.-Vlaanderen),
Institute for Theoretical Physics,
KULeuven,
1 October 1997 - 30 September 2001.
- Licentiate in Science: Physics (Master),
KULeuven, July 1997.
Thesis: Repulsive interactions and Bose-Einstein condensation
(Advisor: A. Verbeure)
-
Date of birth: 27 February 1975