neural connectivity

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Three PhD projects in modelling brain diseases and brain development

author Posted by: admin on date Jan 5th, 2016 | filed Filed under: Uncategorized

We are currently advertising the following three 4-year PhD positions for our lab. 

The funding covers living expenses and UK/EU fees over four years and, using overseas research studentships, potentially also the higher fees for non-EU applicants.

Students are chosen in competition with students who choose projects in other fields, which means that we would particularly encourage strong applicants with very good academic marks and previous research experience to apply. 

Please follow the links below for more information. 

Newcastle-DTA PhD studentships

(1) Building brains: Which developmental pathways lead to better performance in information processing? (School: Computing Science Ref: DTA122)

Within this project, a student will help to develop detailed simulations of brain network development. In addition, the student will test the performance of the grown networks on visual tasks. Through this, we will investigate (a) how developmental mechanisms are linked to the resulting topology and (b) how the resulting network is linked to processing performance. As a result, we will get a better understanding how changes during development are linked to brain architecture and how they can lead to cognitive deficits.

Supervisors: Prof. Marcus Kaiser, Dr Gavin Clowry, and Dr Roman Bauer

(2) Predicting patient outcomes following traumatic brain injury (School: Computing Science Ref: DTA123)

In this study we will investigate the impact of simulated brain lesions using human brain connectivity data and computer simulations. We shall aim to produce biomarkers for patient outcomes. These techniques may hive wider applications in stroke, multiple sclerosis and ageing.

Supervisors: Prof. Marcus Kaiser and Dr Peter Taylor

Please apply by 22 January at

Newcastle-Singapore PhD studentships

(3) Improving surgery in focal epilepsy using computational modelling (School: Computing Science Ref: NSS12)

In this project we shall attempt to predict which patients will be seizure free after surgery. For those patients predicted to be not seizure free we shall suggest alternative strategies for surgery. See also our recent article in PLOS CB:

Supervisors: Dr. Peter Taylor, Prof. Marcus Kaiser, and Asst. Prof. Justin Dauwels (NTU, Singapore). The student will be based at Newcastle but also visit Singapore

Please apply by 26 February at

Research Environment

There are currently 12 faculty members with a link to neuroinformatics and computational neuroscience. Using computational models for clinical applications is a strong interest of our group (see for an overview). Students will be based in the School of Computing Science, which was ranked #9 for research and #1 for impact in the recent UK Research Excellence Framework evaluation, as part of the ICOS Group ( ). They will also be affiliated with the Institute of Neuroscience which integrates more than 100 principal investigators across medicine, psychology, computer science, and engineering and which was ranked #9 overall and #5 for impact in the UK ( 

Newcastle University, with 20,000 students, lies in the city of Newcastle-upon-Tyne — an area in the North-East of England with around one million inhabitants. The university is at the centre of Newcastle which itself is on the main train-line between London and Edinburgh, 20 minutes away from both the airport and the sand beach by public transport ( ). 

Using connectome-based simulations to inform personalised epilepsy treatment

author Posted by: admin on date Jan 4th, 2016 | filed Filed under: Uncategorized

A computer model that identifies the parts of a person’s brain responsible for epileptic seizures could be used to design personalised surgical procedures, researchers say.

Scientists at Newcastle University have used brain scans from patients with the most common type of epilepsy – temporal lobe epilepsy – and computer modelling techniques to look at the brain as an example of a computer network.

By simulating brain activity within each patient-specific network, they successfullyidentified regions that were more prone to seizures.

The research is published today in PLOS Computational Biology, and is believed to be the first study to combine computational modelling of brain dynamics with patient-specific MRI data from individuals with temporal lobe epilepsy.

Around 1% of the UK population suffers from epilepsy and, in many cases, it is an extremely debilitating illness. Currently, anti-convulsant drugs are the main treatment but these are not always effective. In these cases, surgical removal of the parts of the brain indicated by EEG readings to be the source of the seizure is carried out. However, in about 30% of cases, surgery does not result in preventing seizures.

The research team, based in the School of Computing Science at Newcastle University, simulated surgery by disconnecting sections of the network that corresponded to the parts of the brain most commonly removed. They also ran individual patient simulations, removing the most seizure-prone parts of the model for each person. By mimicking seizures before and after ‘surgery’, they found that patient-specific surgery showed, in every case, a significant improvement compared to removal of the regions most commonly taken out.

Dr Peter Taylor, who co-led the study, explained: “This research may help to explain why surgery is so often unsuccessful, as this work predicts that the areas most commonly removed in surgery are not always involved in starting and spreading seizures.

“It also takes us a step further towards rectifying the problem, as identifying the most seizure prone areas on an individual basis has the potential to show when the usual surgery procedures may not work for a patient.”

Research lead Frances Hutchings added: “Removal of brain tissue is often the final option for treatment of temporal lobe epilepsy but we know that it is not always effective. It’s early days and there is more work to be done, but this model could assist surgeons in targeting surgical procedures more effectively and help people with epilepsy lead a more normal life.”

In future, the team intend to check the model’s predictions against patient-specific surgical outcomes. Professor Marcus Kaiser, Professor of Neuroinformatics at Newcastle University, said: “The next steps are to compare the computationally predicted outcomes with the actual surgery outcomes in individual patients and to investigate how alternative surgery targets can be included in the future treatment.”

Reference: Hutchings F, Han CE, Keller S, Weber B, Taylor PN, Kaiser M. Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations. 

PLOS Computational Biology, December 2015

Find out more about the research from the University press release, and at ChronicleLive and also YouTube.

From Caenorhabditis elegans to the human connectome: a specific modular organization increases metabolic, functional and developmental efficiency

author Posted by: admin on date Sep 5th, 2014 | filed Filed under: blog, Uncategorized

Brain networks, ranging from C. elegans to the human connectome, are modular – but in a specific way

Special Issue: Complex Network Theory in the Neurosciences

author Posted by: admin on date Sep 5th, 2014 | filed Filed under: blog, Uncategorized

What has complex network theory ever done for neuroscience? Find out in this Phil Trans R Soc special issue:

Reproducing local brain dynamics in a computer simulation

author Posted by: admin on date Aug 24th, 2014 | filed Filed under: blog, Uncategorized

#Simulator of mammalian brain activity reproduces multi-electrode #LFP recordings in resected cortical tissue:

Human and C. elegans connectome animations

author Posted by: admin on date Aug 6th, 2014 | filed Filed under: blog, Uncategorized

Human and C. elegans brain network animations are now visible on our YouTube channel. Subscribe for future videos.

Developing implantable devices for epilepsy patients

author Posted by: admin on date Mar 28th, 2014 | filed Filed under: blog, Uncategorized

Our £10m grant on optogenetic stimulation is now officially announced

Big Data PhD programme at Newcastle University

author Posted by: admin on date Mar 28th, 2014 | filed Filed under: blog, Uncategorized

EPSRC just announced a cloud doctoral training centre including applications in healthcare for Newcastle.

Girls brains mature earlier

author Posted by: admin on date Dec 20th, 2013 | filed Filed under: blog, Uncategorized

and long-distance connections are preserved during human brain development (see press release)

Our research according to grant proposals

author Posted by: admin on date Nov 12th, 2013 | filed Filed under: blog, Uncategorized

Words we used for funding proposals from the Computing Science Word-Cloud puzzle