CBBP seminar series

Preliminary schedule

Nov 16

Björn Linse

Multiple Imputation by Chained Equations (zoom link: https://lu-se.zoom.us/j/63094598155 )

Previous seminars

Spring 2020

Mar 9	Emil Andersson	Constructing energy landscapes of logical gene networks
Mar 2	Anders Irbäck	Simulating protein droplet formation
Feb 24	Jens Krog	Photophysical image segmentation
Feb 10	Victor Olariu	3D model of the neural tube patterning

Fall 2019

Dec 16	Carl Troein	OCTAVVS: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data
Dec 9	Daniel Nilsson	Finite-size scaling analysis of protein droplet formation
Dec 2	Albertas Dvirnas	Similarity analysis for time series using a matrix profile
Nov 28	Ludvig Lizana, Dept. of Physics, Umeå University	Modelling protein search on human DNA
Nov 25	Syahril Siregar	Non-negative matrix factorization (NNMF) in hyperspectral imaging
Nov 18	Björn Linse	Neural network design for survival analysis
Nov 11	Behruz Bozorg	Towards studying liquid-liquid phase separation in a simple HP protein model, using field theoretic simulations
Nov 4	Anders Björkelund	Predicting heart disease in the emergency room
Oct 21	Bo Söderberg	Transforming interacting polymers into a field theory, simulated using complex Langevin dynamics
Oct 14	Tobias Ambjörnsson	Random pairing clustering
Oct 7	Carsten Peterson	Artificial neural networks as generic function approximators
Sep 30	Najmeh Abiri	Statistical inference with deep latent variable models
Sep 23	Patrik Edén	How to win the FDA omics mislabeling challenge

Spring 2019

Jun 14	Adriaan Merlevede	Direct reprogramming of fibroblasts to neurons
May 27	Yuan Li	A foreign gene in competition with its native counterpart in protein dimer formation
May 20	Albertas Dvirnas	High-resolution dots in nanochannels
May 6	Tobias Ambjörnsson	Bacterial species identification using DNA barcodes
Apr 29	Jens Krog	Shallow learning: Bayesian image segmentation
Apr 15	Mattias Ohlsson	Two 'new' collaborations
Apr 8	Daniel Nilsson	Simulating protein droplet formation
Apr 1	Victor Olariu	Naive and Primed Pluripotent Stem Cells
Mar 25	Anders Irbäck	Dissecting protein stability changes in crowded environments by NMR and Monte Carlo
Mar 11	Björn Linse	Survival analysis of heart transplants using machine learning
Feb 11	Carl Troein	Correction and analysis of large FTIR image datasets
Jan 28	Vinay S Swaminathan, Div. of Oncology and Pathology	Encoding mechanical information through multi molecular structure: Lessons from Directed Cell Migration

2018

Oct 29	Patrik Edén	Growing ANN topologies
Oct 8	Albertas Dvirnas	Structural variations in densely labelled DNA maps
Sep 10	Tomas Martin-Bertelsen	Analysis of short time-series RNA-Seq expression data to elucidate the soil organic matter decomposition mechanisms in ectomychorrizal fungi
Mar 5	Peter Jönsson, Physical Chemistry	Interactions between membrane-associated molecules – from aggregating proteins to immune-cell contacts
Feb 26	Yuan Li & Anders Irbäck	What will happen if a foreign gene meets its native counterpart?
Jan 15	Joakim Stenhammar, Physical Chemistry	Correlations and collective behaviours in suspensions of swimming microorganisms

Spring 2017

Jun 28	Jens Krog, University of Southern Denmark	Bayesian analysis of unfolding DNA
Jun 12	André Larsson	Thesis presentation
May 22	Daniel Nilsson	Markov state models for studying protein crowding dynamics
Feb 8	Henrik Jönsson	How do you develop a computable flower and who needs it?

Fall 2016

Dec 19	Adriaan Merlevede	The chemistry of artificial life
Dec 12	Carl Troein	A dynamical model of the regulation of Fenton chemistry in the litter decomposer Paxillus involutus
Dec 5	Najmeh Abiri	Improving Imputtation using Stacked Denoising Autoencoders
Nov 28	Mattias Ohlsson	Image segmentation using deep convolutional neural networks
Nov 21	Pawel Krupinski	TBA
Nov 15	Lucy Colwell, Cambridge	Using evolutionary sequence variation to build predictive models of protein structure and function
Nov 7	George Napolitano, Mathematical Statistics	Ising model on Random Triangulations
Oct 24	André Larsson	Models of auxin signalling in the shoot apical meristem and initiation of root hairs
Oct 17	Tobias Ambjörnsson	Gene and plasmid ID using DNA barcodes and cell phone based microscopy
Oct 3	Tatyana Turova, Mathematical Statistics	Phase transitions in the one-dimensional Coulomb gas ensembles

Spring 2016

Jun 16	Alexander Schug, KIT, Karlsruhe	Protein and RNA structure prediction via co-evolutionary analysis
Jun 9	Björn Linse	Classification for heart transplant decisions with heterogeneous and missing data
May 25	Behruz Bozorg	Models of mechanics and growth in developmental biology: A Computational Morphodynamics approach
May 31	Anna Bille	Peptide folding and local unfolding of SOD1 in the presence of interacting macromolecular crowders - a Monte Carlo approach
May 16	Carl Troein	Activation and repression in circadian clock networks
May 9	Anders Irbäck	Local unfolding of the protein SOD1 in the presence of protein crowders
May 2	Karl Fogelmark	On gene regulatory networks and data fitting
Apr 18	Adriaan Merlevede	Crossover algorithms for variable-length genomes
Mar 21	Bo Söderberg	Apollonian Tiling and the Lorentz Group
Apr 4	Denni Rögnvaldsson	Self-organising approaches for deviation detection
Mar 1	Charles Kurland	Modular protein domains track genome evolution
Feb 15	Martin Trulsson, Theoretical Chemistry	Shear flows of non-Brownian and Brownian hard sphere suspensions (from jammed to glassy states)
Feb 1	Najmeh Abiri	Unbiased Optimization of Microarray Pre-processing
Jan 25	Victor Olariu	Nanog, Oct4 and Tet1 interplay in establishing pluripotency
Jan 18	Pawel Krupinski	Regulation of T-cell commitment

Autumn 2015

Dec 7	Björn Linse	Efficient simulations of proteins in crowded environments
Nov 23	Anna Bille	Crowding continuation
Nov 16	Henrik Jönsson	When is it time to divide?
Oct 26	Tobias Ambjörnsson	Plasmid analysis using DNA barcodes
Oct 19	Ingemar André (Biochemistry & Structural Biology)	Computational Design of Protein and Peptide Self-assembly
Oct 12	-	COMPUTE seminar (Grand Hotel, 14:15)
Oct 5	Behruz Bozorg	Mechanical signals and morphogenesis
Sep 28	André Larsson	A Boolean approach to inferring biological interactions
Sep 14	David Ansari	The impact of Human Leukocyte Antigen on outcome in heart transplantation
Sep 21	Carl Troein	Separation of activation and repression in transcriptional networks

Spring 2015

Jun 1	Patrik Edén	Estimating concordance for machine learning
May 25	Anders Irbäck	Effects of macromolecular crowding on a miniprotein
Thu May 21	Jonas Kalderstam	PhD thesis presentation: Neural network approaches to survival analysis
May 11	Michaela Reiter-Schad	PhD thesis presentation: Statistical physics of DNA: Melting and confinement effects
May 4	Jonas Kalderstam	Identifying risk groups by optimizing on the area under the survival curve
Apr 27	Joakim Stenhammar, Physical Chemistry	Thermodynamics and phase equilibria of self-propelled colloids
Apr 20	Bo Söderberg	(Non-)conservation in 2D discrete dynamics
Apr 13	Mattias Ohlsson	Deep neural networks
Mar 23	COMPUTE seminar
Mar 20	Jes Frellsen, Department of Engineering, University of Cambridge	Bayesian generalized ensemble Markov chain Monte Carlo
Mar 2	Dimitrios Floudas, Microbial Ecology	Evolution of wood decay in Agaricomycetes: Clues from comparative genomics.
Feb 23	Carsten Peterson	T-cell specification is an irreversible process - insights from computational modelling of a minimal network architecture
Feb 9	Håkan Wallander	Soil - reflections on the basis of our existence
Feb 2	Tomas Martin-Bertelsen	Molecular interactions controlling soil carbon sequestration (MICCS) — Mapping transcriptome data to spectral changes
Jan 26	Henrik Persson Immunology	From fakhir cells to silicone blood vessels

Autumn 2014

Dec 15	Compute Seminar	Compute Seminar at 14:15 - 15:30 in Lundmark, Astronomy building.
Dec 8	Stefan Wallin	Lipoproteins: a new challenge for molecular modeling
Nov 24	Najmeh Abiri	A set of Python/Cython wrappers for extrapolation based solvers for differential algebraic systems
Nov 17	Compute Seminar	Compute Seminar at 14:15 - 15:30 in Lundmark, Astronomy building.
Nov 10	Henrik Jönsson	Revisiting the stem cell regulatory network in plants
Nov 3	Pawel Krupinski
Oct 27	Anna Bille	Crowding
Sep 29	Tobias Ambjörnsson	Nano-channel based DNA barcoding: an overview of some recent progress
Sep 22	Karl Fogelmark	The digital organism
Sep 15	Christian Holzgräfe	Protein fold switching in coarse-grained models

Spring 2014

May 26	André Larsson	Radial patterning in the shoot meristem
May 19	Charleston Noble	A Pair Hidden Markov Model for Detecting Structural Variation in DNA Melting Maps
May 12	Christian Holzgräfe	Hybrid Monte-Carlo
Apr 28	Siddhaling Urolagin Dept. of Experimental Medical Science
Apr 14	Carl Troein	Optimizing ODE models in C++
Apr 7	Heiner Linke Solid state physics	Parallel computation using self-propelled biological agents in designed networks
Mar 31	Jonas Kalderstam	Survival Likelihood
Mar 3	Patrik Edén	Preprocessing protein array data
Feb 20	Ingve Simonsen Norwegian University of Science and Technology, Trondheim	Cascading failures in complex networks: Generic modeling and examples of power blackouts and the domino effect
Feb 24	Anders Irbäck	Aggregation of apolipoprotein A-I
Feb 13	Flavio Seno Padua University	Exploring the universe of protein folds
Feb 3	Mauno Vihinen Dept of Experimental Medical Science	Systematic description and prediction of DNA, RNA and protein variations and their effects
Jan 27	Joop Vermeer University of Lausanne	Talking with the neighbors: Understanding spatial accommodation during plant development
Jan 20	Mattias Ohlsson
Jan 13	Bo Söderberg	Energy conservation (or not) in discrete time Newtonian dynamics

Autumn 2013

Dec 16	Stefan Wallin	How do new protein folds arise?
Dec 9	Bettina Greese	Towards new insights from an extended model for polarity of root hair cells
Dec 2	Michaela Reiter-Schad	A simplified model for DNA melting
Nov 25	Ramune Kuktaite, SLU	Understanding bio-based materials structure and function: a closer step towards sustainable uses
Oct 21	Lloyd Sanders	Canonical epidemics on networks: another look
Oct 7	Behruz Bozorg	Stress and strain as developmental cues in plants
Sep 30	Henrik Jönsson	ERC interview rehearsal
Sep 23	Pawel Krupinski	Why do we need mechanical models of tissues and why we still do not have what we want?
Sep 16	Victor Olariu	Gene Network Landscapes by Numbers

Spring 2013

Jun 10	Karl Fogelmark	Keeping the error in check
Jun 3	Christian Holzgräfe
May 20	André Larsson	Increased stability through KANADI autocatalysis
May 13	Carl Troein	Phytophthora and potatoes
May 6	Juan MR Parrondo Universidad Complutense de Madrid	Diffusive proofreading in transcription
Apr 29	Jonas Kalderstam	Python - My scientific hammer
Apr 15	Sigurður Jónsson	Mechanical resistance in unstructured proteins
Apr 22	Tobias Ambjörnsson	Hitchhiker's guide
Apr 8	Lars Holmgren Department of Oncology-Pathology, Karolinska Institute	Formation and dissociation of multicellular structures in development and cancer
Mar 25	Patrik Edén	High throughput pre-processing - a project worth weighting for?
Mar 18	Charleston Noble	The role of caretakers in disease dynamics
Mar 12	Philip Gerlee Sahlgrenska Cancer Center & Mathematical Sciences, Gothenburg	The impact of phenotypic switching on brain tumour growth and invasion
Mar 4	Anders Irbäck	Aggregate geometry in amyloid fibril nucleation
Feb 25	Stefan Wallin	Antibody-peptide interactions.
Feb 18	Arnab Bhattacherjee	How advantagerous is it to be disordered?
Feb 11	Bo Söderberg	Leapfrog and conservation
Feb 4	Erica Manesso	Computational modeling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence at early stages
Jan 28	Henrik Jönsson	Incoherent feedforward loops in a spatial context
Jan 14	Bettina Greese	Modelling planar cell polarity in the Arabidopsis root epidermis

Autumn 2012

Dec 17	Simon Pigeon	Diffusion of particle in crowded system
Dec 3	Charles Kurland (Dept. of Biology, LU)	Cataclysmic rooting of the current phylogenetic tree
Nov 26	Lloyd Sanders	Stochastic SIRS epidemics in city networks
Nov 19	Mattias Ohlsson	Extreme learning machines
Oct 22	Pawel Krupinski	Finite element method modeling of plant tissue
Oct 15	Carsten Peterson	The Nobel Prize in Physiology or Medicine 2012
Oct 8	Victor Olariu	Molecular dynamics of stem cells differentiation and reprogramming
Sep 17	José Teles	Computational modeling in the hematopoietic system (thesis presentation)
Sep 10	Carl Troein	A digital organism for exploring clock evolution

Spring 2012

Jun 18	Anders Tunlid Microbial Ecology	Soil molecular biology – towards a new understanding of carbon and nutrient cycling in forest soils
Jun 11	Karl Fogelmark	The circadian clock in Arabidopsis and Ostreococcus
Jun 4	Leif Bülow Department of Pure and Applied Biochemistry	Hemoglobins – a radical view
May 28	Behruz Bozorg	Modeling mechanics in plant cells by using triangular biquadratic springs
May 21	Erik Werner (University of Gothenburg)	DNA extension in rather thin channels
May 14	Christian Holzgräfe	Mutation and binding-induced fold switching
May 7	Iskra Staneva	Monte Carlo approach to binding and aggregation of disordered peptides
Apr 25	Stefan Wallin	Mechanisms of protein-DNA interactions
Apr 2	Michaela Reiter-Schad	Extended Azbel approach for DNA melting profiles
Mar 19	Jonas Kalderstam	Training neural networks on incomplete datausing genetic algorithms
Mar 12	Tobias Ambjörnsson	Transfer matrices with applications to protein–DNA binding
Feb 27	Sigurður Jónsson	Accelerating atomic-level protein simulations by flat-histogram techniques
Feb 20	Arnab Bhattacherjee	Intrinsically disordered proteins at work: Coupled folding-binding in a simple model
Feb 13	Anders Irbäck	Exploring the conformational ensembles sampled by Aβ and α-synuclein
Feb 6	Stefan Wallin	Characterizing the peptide binding properties of proteins: a Monte Carlo approach
Jan 30	Patrik Edén	Still a simple population model for neurosphere formation: the quest for b
Jan 23	Erica Manesso	Computational modelling of thymocytopoiesis reveals the importance of proliferation at early stages
Jan 16	Anna Bille	Misfolding of SOD1 and TDP-43, role in ALS

Autumn 2011

Dec 19	Lloyd Sanders	Two-strain mutant SIS modelling: Stochasticity vs. Mean Field
Dec 12	Henrik Jönsson	The 10000 kronor question, or Can auxin flux dynamics be described in a single model?
Dec 5	Bo Söderberg	Area preserving maps: the mystery with the missing parameter
Nov 28	Mattias Ohlsson	Random forest classification and modeling survival for heart transplantation patients
Nov 22	Erika Kuchen (John Innes Center, Norwich)	Feedback between polarity, growth and geometry in leaf shape generation
Nov 17	Bettina Greese (Albert Ludwigs University, Freiburg)	Trichome pattern formation: New insights from mathematical modelling and quantitative analysis
Nov 14	Michael Green (Data Intelligence, Copenhagen)	Sales modeling and the art of quantifying media’s effect on consumer behavior
Nov 7	José Teles	Stem cell fate decisions - on the nature of landscapes
Oct 24	Victor Olariu	Minimal architecture with computational means for stem cell commitment and reprogramming
Oct 17	Pawel Krupinski	Modeling interplay of mechanical and biochemical signals in morphogenesis
Oct 10	Erik Alexandersson (Swedish University of Agricultural Sciences)	Late Blight Resistance in Potato - an overview of related research at SLU Alnarp and Lund University
Oct 3	Iskra Staneva	Grabbing the master watchman with an EF-hand protein
Sep 26	Nikolay Oskolnikov (DTU Nanotech)	Cold denaturation of Lennard-Jones helices with applications to alpha-helical polypeptides
Sep 19	Carl Troein	Worming the EARLY BIRD into the Arabidopsis clock
Sep 12	Wouter Boomsma	Increasing the efficiency of protein structure calculations

Spring 2011

June 13	Charles Kurland (Dept. of Biology, LU)	Evolution differently: the origin of prokaryotes
May 30	Heiner Linke (Nano Center, LTH)	Constructing molecular motors
May 16	Christian Holzgräfe	HP model
May 9	Tobias Ambjörnsson	Forced dynamics in crowded systems
May 2	Susanne Widell (Dept. of Biology)	Cancer and plants
Apr 18	Michaela Schad	DNA melting
Apr 11	Björn Samuelsson	Evolutionary modeling and the complexity of natural selection
Apr 4	Arnab Bhattacherjee	Designing Misfolded Proteins: A Statistical Theory Based Approach
Mar 28	Jeremy Gruel	Modeling the spatial gene expression in the shoot apical meristem
Mar 14	Sigurdur Aegir Jónsson	Wang-Landau simulation of alpha-synuclein
Mar 7	Carsten Peterson	Molecular serum portraits in patients with primary breast cancer predict the development of distant metastases
Feb 21	Anders Irbäck	Monomers and dimers of Aβ42 variants
Feb 14	Stefan Wallin	A simple model for coupled folding and binding
Feb 7	Ajith Harish (Dept. of Biology, LU)	Tracing the evolution of RNA and protein structure in the ribosome
Jan  31	Per Petersson (Med. fak., LU)	Brain control of motor programs in health and disease
Jan 24	Dag Arhén (Dept. of Biology, LU)	Introduction to next generation sequencing with preliminary results for fungal pathogenicity
Jan 17	Patrik Edén	Pre-clinical drug prioritization via prognosis-guided genetic interaction networks

Fall 2010

Dec 20	Erica Manesso	Dynamics Inside the Hematopoietic Hierarchy in Adult Mice
Dec 6	Lloyd Sanders	Single File Diffusion and First Passage Times in Biological Systems
Nov 29	Bo Söderberg	Quasiperiodicity and Pattern Formation
Nov 22	Mattias Ohlsson	Decoding and simulations of neurons
Nov 8	José Teles	To be or not to be.. - fate decision in hematopoietic stem cells
Nov 1	Victor Olariu	1. Erythroid Lineage Dynamics, 2. Ground State Differentiation and Reprogramming in ES cells system.
Oct 25	Johan Nilsson	Virtual Cross-matching in Heart Transplantation
Oct 18	Pawel Krupinski	Why do we need better mechanical models of living cells?
Oct 4	Namiko Mitarai (Niels Bohr Institute)	Choice of Synonymous Codons and Ribosome Traffic
Sept 27	Karoline Wiesner (LU & Univ. of Bristol)	Information and all that -- A summary of four months exploration into information acquisition and sharing of bio-systems
Sep 20	Bernhard Mehlig (Univ of Gothenburg)	Statistics of genetic variation in a changing environment
Sep 13	Iskra Staneva	Can we do helices?
Sep 6	Martin Linden (Caltech)	Understanding the cell shape and locomotion of Spiroplasma
Aug 30	Philippe Robert (LU/ENS-Lyon)	Comparison of Evolutionary Algorithms to optimise biological network parameters.

Spring 2010

Jun 22	Mile Gu (Univ of Singapore)	Can the laws of biology be derived?
Jun 7	Daniel Otzen (Univ of Aarhus)	Protein-lipid interactions and the biophysics of cytotoxicity
May 31	David Kelly (Univ of Bristol)	Causal state models of Flourescence Resonance Energy Transfer (FRET)
May 24	David Gisselsson Nord (Dept of Clinical Genetics)	Chromosome segregation errors in cancer
May 17	Jérémy Gruel	Stabilizing the SAM
May 10	Philip Gerlee (Niels Bohr Institute)	Structural correlations in bacterial metabolic networks
May 3	Patrik Brundin (Experimental Medical Science)	Cell therapy in Parkinson's disease: will it fly?
Apr 29	Nick Monk (Univ of Nottingham)	Models for spaced cell fate assignment in plants and animals
Apr 26	Patrik Sahlin	Modelling the development of phyllotactic patterns at the shoot apical meristem of Arabidopsis thaliana
Apr 12	Martin Nilsson Jacobi (Chalmers)	Targeted self-organization
Apr 9	Carl Troein (Univ of Edinburgh)	The life and timekeeping of Ostreococcus tauri
Mar 29	Erica Manessa	Modeling pancreatic beta cell lifetime
Mar 22	Sigurdur Aegir Jónsson	A minimal sequence code for switching protein structure and function
Mar 15	Petros Koumoutsakos (ETH, Zürich)	Multiscale simulations using particles
Mar 8	Pontus Melke	Cell signaling: a systems approach
Mar 1	Anders Irbäck	Conformational switching in the HP model
Feb 22	Christopher Sturk	A study of the shoot apical meristem by means of computational modeling and microarray analysis
Feb 15	Dag Ahrén (Dept of Biology)	Fungal host interactions - Are you a friend or a foe?
Feb 8	Thomas Laurell (Dept of Electrical Measurements)	Acoustic separation of cells
Feb 1	Mattias Olsson	Some active/going todo projects
Jan 25	Stefan Wallin	PDZ domain-peptide interactions: some new results
Jan 18	Henrik Jönsson	Beräkningsbiologi och biologisk fysik
Jan 11	Patrik Éden	ANN and Cox regression

Fall 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 (Mon 14.15)	Lloyd Sanders (Univ of Auckland)	Periastron advance effects in extrasolar planetary systems
Sep 28	Bo Söderberg	Clustering in random graphs
Sep 24 (Thu 15.15)	Victor Olariu (Univ of Sheffield)	Nonlinear modelling of stem cell dynamics

Spring 2009

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

Fall 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 (Head office, 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.

Spring 2008

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 (Wed. 15.15)	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

Fall 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 Tuesd. 15.15	Paul Higgs (McMaster Univ.)	Evolution of the genetic code
Nov 19	Liwen You 13.15, Sem. room F	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

Spring 2007

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

Spring 2006

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

Fall 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

Spring 2005

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

Fall 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
Nov 1
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

Spring 2004

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 Selpi (Guest)	An FDM prototype for pathway and protein interaction data

Fall 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

Spring 2003

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

Fall 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