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