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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