Past CBBP seminars
This page lists pasts talks at the CBBP seminars (2002 to 2023). The Computation Biology and Biological Physics group is now part of COSHE. See the calendar for future and recent COSHE seminars.
2023
- Nov 08: Andreas Nilsson and Jesper Sjolte, Geology
Synchronising and synthesising paleo data with chronologic uncertainties - Oct 30: Dmytro Perepolkin, CEC
Introduction to Bayesian Parametric Quantile Regression - Oct 03: Silas Boye Nissen, Stanford University
The molecular mechanism of the core planar cell polarity complex elucidated with single-molecule imaging techniques in live Drosophila wing cells - Jun 14: Kristoffer Carlsson
Julia for Scientific Computing - May 16: Ullrika Sahlin, CEC
An introduction to communicating uncertainty when producing scientific advice - May 09: Najmeh Abiri
Developing an AI model to classify tick species in a citizen science project: Challenges and solutions - May 03: Christoffer Åberg, University of Groningen
Exploring glass-like characteristics of intracellular motion in mammalian cells - Mar 13: Emil Andersson
Spectroscopically guided tumour delineation by machine learning: Towards personalised tumour diagnostics - Feb 27: Nikolay Oskolkov
Dimension reduction techniques for Life Science applications - Jan 13: Daqu Zhang
Deep learning models for patient selection based on nodal status
2022
- Dec 05: Jonas Tegenfeldt
Order-disorder transition in DNA solutions in microfluidic arrays - May 23: Stefan Wallin, Memorial University of Newfoundland, Canada
Folding, fold switching and energy landscape of regulatory protein RfaH - May 18: Suze Julia Roostee
Spatial and quantitative analysis of IHC stains in breast cancer - May 02: Anders Björkelund
(Rapid) triage of chest pain patients with respect to acute myocardial infarction - Apr 28: Victor Olariu Ahnell
Cell reprogramming: from a systems perspective. - Apr 04: Malin Hjärtström
Prediction model for breast cancer treatment. - Mar 30: Carl Troein
From biochemical reactions to the fate of stem cells - Mar 21: Patrik Eden
Basic nuisance: size, learning rate, epochs - Mar 03: Fredrik Bertilsson
Modelling of gene regulatory and spatial mechanisms which pattern the early human neural tube - Feb 21: Daesung Cho
Evolutionary properties of neural networks: Exploration of robustness and evolvability in the genotype-phenotype map - Feb 07: Carl Troein
Challenges in MCR-ALS analysis of spectroscopic imaging data
2021
- Dec 13: Nils Ryde
Spectroscopy challenges in astrophysics - Dec 6: Anders Irbäck
Putting lattice proteins on a quantum annealer - Nov 22: Axel Nyström
Serial ECG analysis using machine learnin - May 24: Emil Andersson
A multi-scale dynamical model for T cell development - May 17: Victor Olariu
Models of direct cell reprogramming - May 3: Tobias Ambjörnson
Pandemics modelling 101 - April 12: Anders Irbäck
Simulating protein droplet phase diagrams
2020
- Nov 30: Carl Troein
Infrared spectroscopy methods and data processing challenges - Nov 16: Björn Linse
Multiple imputation by chained equations - 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
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 - 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 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? 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 - 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 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 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 - Jun 1: Patrik Edén
Estimating concordance for machine learning - May 25: Anders Irbäck
Effects of macromolecular crowding on a miniprotein - 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 2014
- 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 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 - 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 LinkeSolid 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 SenoPadua 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 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 - Jun 10: Karl Fogelmark
Keeping the error in check - Jun 3: Christian Holzgräfe
Exploring protein fold switching in an off-lattice hydrophobic-polar model - 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 2012
- Dec 17: Simon Pigeon
Diffusion of particle in crowded system - Dec 3: Charles Kurland, Dept. of Biology
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 - 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 data using 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 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 - June 13: Charles Kurland, Dept. of Biology
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
Tracing the evolution of RNA and protein structure in the ribosome - Jan 31: Per Petersson, Med. fak.
Brain control of motor programs in health and disease - Jan 24: Dag Arhén, Dept. of Biology
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 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. - 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 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 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