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CBBP seminars 2002-2009

2009

Dec 14: José Teles
Lineage commitment and differentiation in hematopoiesis
Dec 7: Ingemar André, Dept of Chemistry
Structure prediction and design of protein assembly
Nov 30: Pawel Krupinski
Modeling the dynamics of the cells - plants and animals
Nov 23: Jérémy Gruel, Univ of Rennes
 
Nov 16: Iskra Staneva
More peptide binding
Nov 9: Henrik Jönsson
Models of genes, hormones, and physical forces in the plant shoot
Oct 26: Tobias Ambjörnsson
What is he doing there?
Oct 19: Erica Manesso, Univ of Padova
Dynamics of pancreatic beta cells
Oct 12: Christopher Sturk
An analysis of a synthetic transcriptional oscillator
Oct 5: Lloyd Sanders, Univ of Auckland
Periastron advance effects in extrasolar planetary systems
Sep 28: Bo Söderberg
Clustering in random graphs
Sep 24: Victor Olariu, Univ of Sheffield
Nonlinear modelling of stem cell dynamics
Jun 15: Carl Troein, University of Edinburgh
The origins of complexity in circadian clocks
Jun 8: Karoline Wiesner, University of Bristol
Landauer's principle lurking behind measures of complexity
Jun 1: Ralf Eichhorn, Nordita
Transport phenomena in non-equilibrium systems: Paradoxes and benefits of noise
May 25: Kajsa Paulsson, Dept of Experimental Medical Science
Antigen presentation in the context of MHC class I - focus on quality control
May 18: Anders Irbäck
The initial stages of protein aggregation
May 11: Peter Apell, Chalmers
Biological physics in Göteborg
May 4: Patrik Sahlin
Reintroducing stem cells to plant development modeling
Apr 27: Mattias Larsson, Swedish University of Agricultural Sciences
Information transfer in chemical signalling: Emitters, signals and receivers
Apr 6: Carsten Peterson
Serum proteome profiling of breast cancer
Mar 30: Federico Collechia
Novel glioma stem cell surface markers - prediction via cross-database searches
Mar 16: Stefan Wallin
Aggregation of two short peptide sequences with a knowledge-based potential
Mar 2: Jonas Tegenfeldt, Solid State Physics
Melting mapping of DNA in small channels
Feb 23: Patrik Éden
A simple population model for neurosphere formation
Feb 16: José Teles
Genetic regulation of hematopoiesis
Feb 9: Pawel Krupinski
The logic of mammalian embryogenisis
Feb 2: Mattias Olsson
Some active/going todo projects
Jan 26: Morten Krogh
Mass spectrometry with an orbitrap mass analyzer
Jan 19: Johan Nilsson, Thoracic Surgery
Heart and lung transplantation: Prediction of long-term survival
Jan 12: Iskra Staneva
Binding to a PDZ domain

2008

Dec 15: Erik Börjesson
Adsorption at surfaces, what forces interact?
Dec 8: Bo Söderberg
Fitting a factorized model to rectangular data
Dec 1: Mikael Borg, Copenhagen University
Instrinsically disordered proteins in regulatory processes
Nov 17: Helena Stjernberg, Lund University Libraries / Henrik Jönsson
Parallel publication in LUP
Nov 10: Simon Mitternacht
A revision of our protein model... and a few words about Alzheimers
Oct 27: Giorgio Favrin, Univ of Cambridge
Structural reorganization and potential toxicity of oligomeric species
Oct 20: Anders Irbäck
Formation and growth of oligomers: an MC study of a protein tau fragment
Oct 13: Pontus Melke
Benefits of having a shape
Oct 6: Alberto Imparato, Univ of Aarhus
Work and heat probability distribution of driven Brownian particles: Theory and experiments.
Sep 29: Patrik Sahlin
Cell division in Drosophila wing primordium and plant tissue.
Sep 22: Carsten Peterson
Hematopoiesis by the numbers and by design.
Sep 15: Federico Collechia
Dimensionality and dynamics in the behavior of C. Elegans
Sep 8: Stefan Wallin
Thermodynamics and kinetics of protein knot formation.
Jun 11: Michael Green (dissertation lecture)
Improving diagnosis of acute coronary syndromes in an emergency setting: A machine learning approach
May 26: José Teles
In silico gene expression microdissection in heterogeneous cell population samples
May 19: Björn Samuelsson
Aspects of nonhuman intuition: testing how horses learn
May 12: Anders Svensson (Diploma work presentation)
Periodiska fixpunkter till en modell av auxintransport
May 5: Pawel Krupinski
Patterns of growth - simulations of biomechanical deformation in plant tissue
Apr 28: Patrik Edén
Simultaneous regulation of proliferation and self-renewal
Apr 21: Ben Smith, Physical Geography and Ecosystems Analysis
Transcending time, space and scientific tradition in a global model of vegetation and ecosystem response to climate change
Apr 14: Mattias Ohlsson
Exini Diagnostics
Apr 7: Eric Warrant, Cell and Organism Biology
A tale of two fishes: the visual ecology of two deep-sea predatory fishes
Mar 31: Michael Green
Machine learning and the art of covering too many topics in 45 minutes
Mar 17: Bo Söderberg
Chemical reaction dynamics with finite molecule numbers
Mar 10: Lars Gislén
Ancient mathematical astronomy
Mar 3: Henrik Jönsson
Mechanisms for spontaneous pattern formation in biology
Feb 25: Simon Mitternacht
Report from Biophysical Society 52nd Annual Meeting
Feb 20: Stefan Wallin, Harvard
Redesign of PDZ-PDZ domain interfaces
Feb 11: Sven Nelander, Gothenburg
Using drug combinations to construct regulatory models of cancer cells
Feb 4: Pontus Melke
Planar polarity and root hair positioning
Jan 28: Anders Irbäck
Force-induced unfolding of a fibronectin module
Jan 21: Katarina Sjögreen Gleisner, Radiation Physics
Modeling and prediction of the biodistribution and absorbed doses in radionuclide therapy
Jan 14: Federico Colecchia
In-silico investigation of tissue-specific transcriptional regulatory networks

2007

Dec 17: Christian Balkenius, Cognitive Science
Attention and anticipation
Dec 10: Stanley Brown, Copenhagen Univ.
Genetics and carbon nanotubes
Dec 3: Carsten Peterson
Embryonic stem cells revisited - lineage determination and epigenetics
Nov 27: Paul Higgs, McMaster Univ.
Evolution of the genetic code
Nov 19: Liwen You
Computational prediction models for proteolytic cleavage and epitope identification
Nov 12: Jörgen Ripa, Theoretical Ecology
Gradual evolution in stochastic environments - on the feedback between environmental fluctuations, population dynamics and long term evolutionary change
Nov 5: Thore Husfeldt, Computer Science
A new algorithm for Steiner trees with applications to signaling pathways and phylogenetic trees
Oct 29: Thoas Fioretos, Clinical Genetics
Molecular changes in leukemia
Oct 22: Patrik Sahlin
A pattern generating model inspired by plant phyllotaxis
Oct 15: Pawel Krupinski
Mechanics of plant cells or what finite elements can do
Oct 8: Morten Krogh
Sequencing technologies
Oct 1: Patrik Edén
False Discovery Rate: the rate of false discoveries or a false rate of discoveries?
Sep 24: Michael Green
On the dark side of artificial neural network ensembles
Sep 17: Mattias Ohlsson
Survival after heart tranplantation - an analysis using ANN
Sep 10: Stefano Luccioli, Florence
Reconstructing the free energy landscape of a protein model from mechanical unfolding manipulations
Sep 3: Alex Gremiaux, Toulouse/Chalmers
Relation between protein and water dynamics: Low frequency dielectric study of relaxation processes in hydrated protein
Aug 13: Karsten Goede, Leipzig
AFM experiments on specfic adhesion of peptides on semiconductors
Aug 7: Jose Teles, Lisbon
RheugulationDB: an integrative tool for the study of rheumatoid arthritis
Jun 11: Liwen You
Using uncertainty and Gaussian process to detect targets in pathogens' genomes
Jun 4: Pramod Wangikar, IIT, Mumbai
Prediction of Protein Structure Using Backbone Fragment Library and a Multilayered Learning Algorithm
May 28: Vijay Chickarmane, Caltech
Robust network dynamics of DNA damage control
May 21: Sigismund Kobe, Dresden
Exact energy landscapes of proteins using a coarse grained model
May 14: Rikard Alm, Biochemistry
Proteome profiling of strawberry and characterization of a Bet v 1-homologous allergen
May 7: Mikael Akke, Biophysical Chemistry
Protein unfolding studied by nuclear spin relaxation
Apr 23: Cecilia Ritz
Classification and computational methods in gene expression data analysis
Apr 16: Ronald Kröger, Cell and Organism Biology
Physical aspects of vertebrate color vision
Apr 2: Carl Troein
Gene regulatory networks: dynamics and stability
Mar 26: Lund Systems Biology Group
Mathematical aspects of systems biology
Mar 19: Bo Söderberg
Mode locking, binary sequences, and the Farey tree
Mar 12: Hans-Uno Bengtsson
Undergraduate education, Theoretical Physics
Mar 5: Henrik Jönsson
Plants solve the da Vinci code
Feb 26: Igor N. Berezovsky, Harvard
Thermophilic adaptation through the looking glass of physics
Feb 19: Simon Mitternacht
Differences in solution behavior between four semiconductor-binding peptides
Feb 12: Anders Irbäck
Self-assembly into a beta-barrel
Feb 5: Wolfhard Janke, Leipzig
Geometrical picture of criticality
Jan 29: Sayan Mukherjee, Duke Univ.
Integrating multiple genomic sources and modelling tumor progression -- borrowing strength
Jan 22: Yingchun Liu
Statistical and functional analysis of genomic and proteomic data
Jan 15: Federico Colecchia
Database/software for tissue-specific investigation of gene regulation
Jan 8: Pontus Melke
Modeling bacterial growth

Fall 2006

Dec 18: Patrik Edén
A physicist's stem cell definition
Dec 11: Carsten Peterson
Stem cell switch dynamics
Dec 4: Carl Troein
The why of regulation
Nov 27: Morten Krogh
Local recurrence of breast cancer
Nov 20: Ulf Olsson, Physical Chemistry
Surfactant self-assembly in micelles and microemulsions
Nov 13: Markus Ringnér
Challenges in the use of microarray data for classification
Nov 06: Christer Wingren, Immunology
High-throughput cancer proteomics using recombinant antibody microarrays
Oct 30: Michael Bachmann
Folding and aggregation of protein-like heteropolymers at mesoscopic scales
Oct 23: Mattias Ohlsson
Mortality Prediction in Cardiac Surgery
Oct 16: Michael Green
Selection of ECG leads using ANN ensembles for pre-clinical assessment of chest pain patients
Oct 9: Bo Söderberg
Can you see the index profile of a lens?
Sep 25: Yingchun Liu
Unravel deregulated cellular signaling pathways by integrating gene expression and regulatory motifs analyses
Sep 18: Cecilia Ritz
Reducing overestimation in microarray missing value imputation
Sep 11: Anders Dellson, Mitrionics AB
Open source blasting with field programmable gate arrays
Sep 4: Anders Irbäck
Beta-hairpin folding
Jun 12: Thomas Breslin, Malmö University Hospital
Venous thromboembolism: from good old clinical markers to proteomic treasure hunting
May 29: Karoline Wiesner, University of California Davis
Complexity in quantum processes
May 22: Christer Löfstedt, Chemical Ecology and Ecotoxicology
Evolution of pheromone communication in moths
May 15: Henrik Jönsson
Computational Biology & Biological Physics in Arabidopsis
May 8: Dan-E. Nilsson, Cell and Organism Biology
The eye machine
Apr 24: Pontus Melke
A rate equation approach to elucidate the kinetics and robustness of the TGF-β pathway
Apr 10: Simon Mitternacht
Thermal unfolding of Ubiquitin and charges in water
Apr 3: Hans-Uno Bengtsson
On the universality of capillary properties
Mar 27: Peter Johansson
Building a classifier - a comparison of six strategies
Mar 20: Patrik Edén
Mathematical modelling of cancer stem cells
Mar 13: Mai Suan Li, Warsaw
Scaling properties of protein folding and misfolding
Mar 6: Liwen You
Detect rare cases vs. decrease false positive rate
Feb 27: Carl Troein
A toy genome
Feb 20: Morten Krogh
Missing values in 2D gel data sets
Feb 13: Carsten Peterson
Transcriptional dynamics of the embryonic stem cell switch
Feb 6: Stefan Schnabel Thomas Vogel, Leipzig
Multicanonical and chain-growth simulations of polymer chains
Jan 30: Markus Ringnér
Taxonomy of breast cancer
Jan 23: Anders Castor, Hematopoietic Stem Cell Lab.
Normal and malignant stem cells in leukemia
Jan 16: Michael Green
Automatic relevance determination and model comparison in neural networks
Jan 9: Dennis Hasselquist, Animal Ecology
Genomics of birdsong behaviour

2005

Dec 12: Jari Häkkinen
Automatic de novo detection of protein modifications
Dec 5: Jure Piškur, Cell and Organism Biology
Comparative genomics: a tool to understand yeast evolution
Nov 28: Mattias Ohlsson
Scored area under curve (AUC)
Nov 21: Bo Söderberg
Fish-eye lenses and the Abel transform
Nov 14: Marcus Heisler, Caltech
Plant development
Nov 7: Yingchun Liu
Pathway activity analysis by using motifs
Oct 31: Cecilia Ritz
Missing values in microarray data - useful or not?
Oct 24: Henrik Jönsson
Microfluidic chemostat experiments and computational models
Oct 17: Anders Irbäck
PROFASI: a Monte Carlo simulation package for protein folding and aggregation
Oct 10: Sune Lehmann, DTU, Denmark
Segmentation and tracking in biological systems
Oct 3: Ulrike Nuber, Cancer Stem Cell Biology
Adult neural stem cells: from genes to systems
Sep 26: Dag Ahren, Microbial Ecology
Measuring genome conservation across taxa: divided strains and united kingdoms
Sep 19: Michael Bachmann, Leipzig
Polymers astray: folding and binding near attractive substrates
Sep 12: Henrik Semb, Stem Cell and Pancreas Developmental Biology
Human embryonic stem cells
Sep 5: Björn Canbäck, Microbial Ecology
The global distribution of marine bacterioplankton
Jun 13: Peter Johansson
WeNNI: a weighted approach for preprocessing of microarray data
May 30: Hans-Uno Bengtsson
On the universality of capillary constants, or capillaries as biological atoms
May 23: Lars Gislén
Advanced optics in a jellyfish eye.
May 16: Garry Gippert
Information beast and protein beauty : distance-based statistical potentials used to evaluate 3D models
May 9: Cecilia Ritz
Leukemia diagnosis - classification using kNN
May 2: Rikard Alm
A proteomic study of strawberry allergen
Apr 25: Carl Troein
Scaling of gene categories in genomes
Apr 18: Morten Krogh
Microarray analysis of brain cancer
Apr 11: Björn Samuelsson
Attractors in synchronous random boolean networks
Apr 4: Liwen You
Apoptosis and caspases
Mar 21: Michael Green
Performance estimation using cross testing
Mar 14: Markus Ringnér
Untranslated regions of mRNA
Mar 7: Jari Häkkinen
Cluster analysis of mass spectra
Feb 28: Bo Söderberg
Why I like the expression eN2/2 so much more than 2N(N-1)/2
Feb 21: Mattias Ohlsson
Decision support for acute coronary syndromes
Feb 14: Yingchun Liu
Proteomics strategies for biology and medicine
Feb 7: Kasper Astrup Eriksen
An experimental screen for non-neutrally evolving genes in a clade of symbiotic fungi
Jan 31: Sandipan Mohanty
Protein folding, unfolding, and misfolding
Jan 24: Andreas Wacker, Math. Physics
Superlattices - a model system for non-linear transport
Jan 17: Henrik Jönsson
An explicit spatial model of yeast microcolony growth
Jan 10: Peter Johansson
Key players in melanoma

2004

Dec 13: Kiran Raosaheb Patil (Guest)
Understanding transcriptional regulation of metabolism
Dec 6: Anders Irbäck
Mechanical unfolding of ubiquitin
Nov 29: Patrik Edén
Gene expression analysis of 5q- myelodysplastic syndroms
Nov 22: Garry Gippert
Proline pucker, pair potentials and positional disorder in protein structure modeling. (Thursday surprise menu)
Nov 15: Thomas Breslin
Chipping B cell differentiation
Nov 8: Kim Sneppen (Guest)
Transcription/translation dynamics modeling
Oct 25: Thomas Hamelryck (Guest)
A measure of amino solvent exposure & Biopython and Mocapy (a dynamic bayesian networks toolkit)
Oct 18: Ala Trusina (Guest)
Information horizons in complex networks
Oct 11: Carl Troein
Pathway profiling of breast cancer tumors
Oct 4: Cecilia Ritz
Predicting distant recurrences in CMF-treated breast cancer
Sep 27: Morten Krogh
Proteomics analysis of cancer tissues
Sep 20: Björn Samuelsson
Nested canalyzing rules in random Boolean networks
Sep 13: Liwen You
ISMB2004 paper: predicting genetic regulatory response using classification
Sep 6: Markus Ringnér
ISMB/ECCB 2004 overview
Jun 14: Ylva Aspenberg
Modelling the stem cells of the adult mammalian brain
Jun 7: Michael Green
Recognising a pattern featured object in a RoboCup environment
May 24: Jacob Bock Axelsen (Guest)
On the efficiency of translation regulation: the unfolded protein response
May 17: Uli Hansmann (Guest)
Computer simulations of small proteins
May 10: No group meeting
Källén symposium in the afternoon
May 3: Udo Haecker, Dept. of Cell & Mol. Biology
The role of polysaccharides in the shaping of morphogen gradients
Apr 26: Jari Häkkinen
Proteios and HUPO PSI standards
Apr 19: Mattias Ohlsson
Cross-validation
Apr 5: Kasper Eriksen
Localization of DNA damage by charge exchanging repair enzymes: effects of cooperativity on detection time
Mar 29: Bo Söderberg
Generating function techniques in branching processes
Mar 22: Sandipan Mohanty
Simulating peptide aggregation
Mar 15: Jan Forsman, Theor. Chemistry
Theoretical models of surface forces in polymer solutions: the importance of explicit solvent representation
Mar 8: Hemang Parikh (Guest)
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
Mar 1: Carsten Peterson
Random Boolean genetic networks revisited
Feb 23: Peter Johansson
An ML-estimation of discrimination when using measurements with varying quality
Feb 9: Henrik Jönsson
Phyllotaxis in plants
Feb 2: Giorgio Favrin
Non-native structures and amyloid formations
Jan 26: Jesper Borg(Guest)
Fold-x: a force field to predict protein folding and stability
Jan 19: Anders Irbäck
Peptide folding and aggregation
Jan 12: Selpi (Guest)
An FDM prototype for pathway and protein interaction data

2003

Dec 15: Thomas Breslin
Rank based meta analysis of genomic data
Dec 8: Garry Gippert, Dept. of Mol. Biophysics
Sidechain packing models and statistical potentials used to evalute the quality of protein sequence-to-structure alignments
Dec 1: Patrik Edén
Effects of different BrdU staining protocols
Nov 24: Carl Troein
Random boolean network models and the yeast transcriptional network
Nov 17: Yingchun Liu
Murine embryonic fibroblast (MEF) project
Nov 10: Cecilia Ritz
Gene expression profiles and clinical observables in breast cancer prognosis
Nov 3: Morten Krogh
A rat model of ischemic stroke
Oct 27: Stefan Karlsson, Dept. of Mol. Med.
The role of TGF-beta in the regulation of hematopoiesis
Oct 20: Björn Samuelsson
Diffusion in a periodic potential - with applications from fluidics for DNA analysis
Oct 13: Liwen You
Why neural networks should not be used for HIV-1 protease cleavage site prediction
Oct 6: Andreas Arvidsson, Restorative Neurology Section
Neurogenesis from stem- and progenitor cells in the adult brain
Sep 29: Markus Ringnér
RNA interference
Sep 22: Jari Häkkinen
The Lund Swegene Bioinformatics Facility
Sep 15: Mattias Ohlsson
Regional cerebral blood flow in Alzheimers disease: classification and analysis of heterogeneity
Sep 8: Kasper Eriksen
A connection between gene expression and the strength of transcription factor binding
Sep 1: Fredrik Sjunnesson
A model study of folding thermodynamics of three beta-sheet peptides
Aug 25: Hans-Uno Bengtsson
Are capillary properties really universal?
Aug 18: Peter Johansson
Support vector machines
Aug 11: Jonas Tegenfeldt, Div. of Solid State Physics
Micro- and nanofluidics for DNA analysis
Jun 16: Henrik Jönsson
Plant stem cells - from in vivo to in silico, and back?
Jun 10: Samuel Andersson
Bioinformatic exploration of antisense transcripts
Jun 2: Cecilia Clementi, Rice University
Topology and energetics in protein systems: from folding to function
May 26: Bo Söderberg
Random Feynman graphs
May 19: Carl Troein
Bioarray software environment (BASE)
May 12: Stefan Wallin
Two-state folding over a weak free-energy barrier
May 5: Fredrik Sjunnesson
Context dependent hydrogen bonds and the green mamba
Apr 28: Giorgio Favrin
A Transition State Analysis with a Derived Potential for SH3
Apr 22: György Marko-Varga, AstraZeneca
Protein expression analysis in disease - the new challenge
Apr 14: Sten Eirik Jakobsen, Stem Cell Center
Identification, characterization and molecular regulation of hematopoietic stem cells
Apr 7: Anders Irbäck
Study of a protein that is unstructured in isolation
Mar 31: Thomas Breslin
Review of selected talks at AAAS/MGED (Denver, Febr. 2003)
Mar 17: Patrik Edén
Simplistic systems biology?
Mar 10: Carsten Peterson
Computational aspects of biology development
Mar 3: Morten Krogh
Regulation at a distance in Yeast?
Feb 24: Yingchun Liu
Class discovery in expression data
Feb 17: Björn Samuelsson
To simulate protein folding with monte carlo dynamics
Feb 10: Markus Ringnér
The impact of DNA copy number on gene expression
Feb 3: Carl Troein
A new approach to random boolean networks
Jan 27: Patrik Medstrand, Dept. of Cell & Mol. Biology
Transposable elements in humans: genome distribution and impact on gene regulation
Jan 20: Kasper Eriksen
The Young data
Jan 13: Henrik Haraldsson
Hermite decomposition of ECGs for training Neural Networks

2002

Dec 10: Peter Johansson
Analysis of gene expression profiles of melanoma
Dec 3: Jari Häkkinen
Protein identification
Nov 22: Pär-Ola Bendahl, Dept. of Oncology
Linkage-disequilibrium analysis
Nov 19: Mattias Ohlsson
Protein structure alignment
Nov 12: Hans-Uno Bengtsson
A simple model for the arterial system
Nov 5: Bo Söderberg
Random graphs
Oct 21: Stefan Wallin
Similarity measures for proteins
Oct 21: Fredrik Sjunnesson
Why water makes protein folding messy
Oct 14: Giorgio Favrin
Protein structure prediction
Oct 7: Anders Irbäck
Protein folding
Sep 30: Thomas Breslin
Probabilistic estimation of microarray data reliability and underlying gene expression
Sep 23: Patrik Edén
Monkey Index, now with P-values

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