Author: Michael

Postdoctoral, Programming and Graduate Student opportunities in Computational Systems Biology@Sheffield

The Hide Lab https://hidelab.wordpress.com is recruiting programmers, postdoctoral fellows and graduate students to a set of new and well established projects that are part of our new Centre for Genome Translation.

Please go the positions available at the website to learn more.

The lab has relocated from Harvard School of Public Health to the Centre for Genome Translation at the Sheffield Institute for Translational Neuroscience (SITraN); a purpose built research facility which was opened in November 2010 by Her Majesty the Queen. The Institute houses computational, clinical and basic scientists with a focus on neurodegenerative disorders such as Motor Neurone Disease (MND), Alzheimer’s Disease and Parkinson’s disease.

Successful candidates will be joining a global team working on best practice computational systems genetics approaches and discovery in genome translation – literally working with the best clinicians, machine learning experts, genome scientists, wet lab scientists and a global bioinformatics team to deliver new interventions against lethal neurodegenerative diseases in an environment where there is access to thousands of whole human genome sequences and associated phenotypes. We use systems approaches to integrate across genome-wide analyses of variation found within human genomes in meaningful new ways with quantitative functional and clinical phenotypes

Postdocs: A PhD in an appropriate field. Strong programming skills; strong oral and written communication skills in English; Strong knowledge of biology. Track record of excellence in publications. Ability to develop creative powerful methods that solve complex integrative problems in computational systems biology. Strength in mathematics and biology. Ability to co-ordinate and take part in collaborations. Motivation to make meaningful translatable discoveries that will yield actionable results. You can build molecular networks from high-content genome-wide data, you are familiar with genome variant data and can assess the value of gene – disease prioritisation approaches, you are comfortable with developing prediction of intervention approaches by application of therapeutics.

Graduate students: You have a high calibre Masters degree (or equivalent qualification) in computational biology, biomedical research, genomics, computer science, mathematics, biostatistics, systems biology or combination of these. You have a strong biological background, and are skilled in scripting with demonstrated understanding of working together with biomedical researchers and quantitative biologists. You are confident in aspects of data integration and are enthusiastic about construction and analysis of biological networks and/or data integration. Highly motivated, you wish to work in a stimulating, international, scientific environment. You have excellent interpersonal, written and oral communication skills and seek exposure to a diversity of scientific projects.

Programmers: You have a combination of skills, with a strong emphasis upon programming, but with an understanding of biology, some statistics, and potentially machine learning. We welcome candidates with a desire and demonstrated ability to learn new areas and a desire to develop code in a global environment. Please include links to some of your previous code in GitHub or another repository hosting service, as well as a cover letter describing why this position interests you and how it fits your experience and interests.

Sheffield is an awesome place to live – the people are kind, professional and team oriented. The Peak district is within ten minutes and is a wonderful place to relax. An online presentation (minute 47:00) at the end of my inaugural lists why this place is a great environment.

Programming applicants and Post doctoral candidates should send a C.V. and statement of interest as one PDF document to winhide [at] sheffield.ac.uk. Screening of applications begins immediately and will continue until the positions are filled. The positions are expected to start on or after April-May 2015.

Enquiries:
Interested candidates should in the first instance contact Prof. Winston Hide on +44 114 222 22233 or by email winhide – at – sheffield.ac.uk

Graduate student applicants:
Please complete a University Postgraduate Research Application form available from www.shef.ac.uk/postgraduate/research/apply
Please clearly state the prospective main supervisor in the respective box and select (neuroscience) as the department.

Your Late-Night Emails Are Hurting Your Team

Around 11 p.m. one night, you realize there’s a key step your team needs to take on a current project. So, you dash off an email to the team members while you’re thinking about it.

No time like the present, right?

Wrong. As a productivity trainer specializing in attention management, I’ve seen over the past decade how after-hours emails speed up corporate cultures — and that, in turn, chips away at creativity, innovation, and true productivity.

If this is a common behavior for you, you’re missing the opportunity to get some distance from work — distance that’s critical to the fresh perspective you need as the leader. And, when the boss is working, the team feels like they should be working.

via Your Late-Night Emails Are Hurting Your Team – HBR.

Internship opportunities at Point Mugu

College Juniors & Seniors apply on this ad:

Point Mugu – Permanent Interns
EE, ME, Physicists, mathematicians & computer science apply on this ad — Student Trainee (Engineering)(Computer Science) – https://www.usajobs.gov/GetJob/ViewDetails/396433300

College freshman & sophomores apply on this ad:

Lowest grade level applicant will accept – “1” – Human Resources will evaluate application and assess if qualifications meet a higher grade level.

Point Mugu – Temporary Interns (One year appointment/NTE)
EE, ME, Physicists, mathematicians & computer science apply on this ad  — Student Trainee (Engineering)(Computer Science) – https://www.usajobs.gov/GetJob/ViewDetails/396450000

A new paper: Non-repetitive strings, with Neerja Mhaskar

Title: Non-repetitive strings over alphabet lists

Authors: Neerja Mhaskar and Michael Soltys

Abstract: A word is non-repetitive if it does not contain a subword of the form vv. Given a list of alphabets L = L1, L2, . . . , Ln, we investigate the question of generating non-repetitive words w = w1w2 . . . wn, such that the symbol wi is a letter in the alphabet Li. This problem has been studied by several authors (e.g., [GKM10], [Sha09]), and it is a natural extension of the original problem posed and solved by A. Thue. While we do not solve the problem in its full generality, we show that such strings exist over many classes of lists. We also suggest techniques for tackling the problem, ranging from online algorithms, to combinatorics over 0-1 matrices, and to proof complexity. Finally, we show some properties of the extension of the problem to abelian squares.

Source:

A new paper: String Shuffle, with Neerja Mhaskar

Title: String Shuffle: Circuits and Graphs

Authors: Neerja Mhaskar and Michael Soltys

Abstract: We show that shuffle, the problem of determining whether a string w can be composed from an order preserving shuffle of strings x and y, is not in AC0, but it is in AC1. The fact that shuffle is not in AC0 is shown by a reduction of parity to shuffle and invoking the seminal result of Furst et al., while the fact that it is in AC1 is implicit in the results of Mansfield. Together, the two results provide a lower and upper bound on the complexity of this combinatorial problem. We also explore an interesting relationship between graphs and the shuffle problem, namely what types of graphs can be represented with strings exhibiting the anti-Monge condition.

Source:

Computing PhD Scholarships – Research Degrees – Faculty of Engineering

The School of Computing, ranked in the top 10 for research impact in REF2014, is making a substantial investment in 6 new PhD Scholarships. This is an exciting opportunity for prospective UK/EU PhD students to engage in world class research from theoretical foundations of computer science and artificial intelligence through to highly applied computational modelling and systems engineering, carried out in collaboration with leading companies.

The six available fully funded UK/EU PhD scholarships are each worth over £65k covering fees, stipend and RTSG. The scholarships are fully supported by School and EPSRC funding; however, requests for part-funding will also be considered where the balance is covered from elsewhere.

via Computing PhD Scholarships – Research Degrees – Faculty of Engineering.