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 e^N2/2 so much more than 2^N(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