CBBP seminars 2010-2019
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
- 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
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