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CBBP seminars 2010-2019


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


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


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?


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
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


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


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
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


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
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


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


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


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


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