Computational Biology & Biological Physics
Dept. of Astronomy and Theoretical Physics | Faculty of Science | Lund University

CBBP seminar series

Seminars take place Mondays at 11.15 in the Theoretical Physics coffee room.

The schedule is also available on Google Calendar:
or iCal format

Preliminary schedule

Postponed until further notice

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


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
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
Understanding the cell shape and locomotion of Spiroplasma
Aug 30
Philippe Robert
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
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
Redesign of PDZ-PDZ domain interfaces
Feb 11 Sven Nelander
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

(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
Reconstructing the free energy landscape of a protein model from mechanical unfolding manipulations
Sep 3 Alex Gremiaux
Relation between protein and water dynamics: Low frequency dielectric study of relaxation processes in hydrated protein
Aug 13 Karsten Goede
AFM experiments on specfic adhesion of peptides on semiconductors
Aug 7 Jose Teles
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
Robust network dynamics of DNA damage control
May 21 Sigismund Kobe
Exact energy landscapes of proteins using a coarse grained model
May 14 Rikard Alm
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
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
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
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
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

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
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
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
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
Transcription/translation dynamics modeling
Nov 1
Oct 25 Thomas Hamelryck
A measure of amino solvent exposure & Biopython and Mocapy (a dynamic bayesian networks toolkit)
Oct 18 Ala Trusina
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
On the efficiency of translation regulation: the unfolded protein response
May 17 Uli Hansmann
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
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
Fold-x: a force field to predict protein folding and stability
Jan 19 Anders Irbäck Peptide folding and aggregation
Jan 12 Selpi Selpi
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
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