Category Archives: appliedtopology

Two postdoc positions in Aberdeen

Dear Topologists,

The Institute of Mathematics in Aberdeen is now advertising two postdoctoral positions funded by an EPSRC grant obtained by myself. The project is entitled “Topological Analysis of Neural Systems”. It is a collaborative and interdisciplinary project by its very nature, and aims to apply the powerful tools of algebraic topology to questions in neuroscience. A summary of the project can be found on the EPSRC website.  A large part of the project will be carried out in collaboration with the Blue Brain Project at EPFL, led by neuroscientist Henry Markram, and the Laboratory for Topology and Neuroscience led by Kathryn Hess. The post in Aberdeen is funded for 3 years, and will include a generous travel and equipment budget. Work on this project will involve both theoretical and applied topology. Start date is 1st September 2017, but a later start date may be negotiated. 

The first position is intended for a person holding a PhD in algebraic topology with a strong interest in studying and applying theoretical and computational tools of algebraic topology to neuroscience, and other relevant subjects. Experience in computations and/or applied algebraic topology would be an advantage but is not a requirement. Basic training in neuroscience and in computational topology will be available if necessary.

This post is currently advertised at with closing date 4th May 2017. 

The second post is intended for either a computer scientist or a mathematician with a strong background in high level coding, who is interested in applying their skill to computational and applied algebraic topology in the context of the project. While this post is not formally advertised yet (it will be in two weeks), all applications for the post already advertised will be considered for both positions.

Informal inquiries are very welcome. Please email

Best wishes, Ran

3D-printing Research Assistantship at the University of Sheffield

The department of Automatic Control and Systems Engineering and the School of Mathematics at the University of Sheffield anticipate to hire jointly a research assistant to work various computational aspects of 3-D printing including the identification of printability issues, fragility and optimization. A formal description of the position will be available in due course, and this is an informal announcement encouraging potential candidates with a strong background in

  • geometrical applications, e.g., applied topology
  •  software development
  • development and implementation of computational algorithms

to contact Dr. Moty Katzman ( for obtaining further details as they become available.

Postdoctoral Research Scientist in viral evolution, genomics, and mathematical modeling. Columbia University Medical Center

The Rabadan Lab is a multi-disciplinary team at the Columbia University Medical Center consisting of computational and evolutionary biologists, applied mathematicians, physicists, and physicians. As part of the Departments of Systems Biology and Biomedical Informatics, we collaborate with clinicians and public health researchers from around the world to explore the genetic underpinnings and epidemiology of infectious diseases and cancer. As part of the Center for Topology of Cancer Evolution and Heterogeneity, we are building a vibrant community of researchers who use insights and techniques from computational topology to solve pressing biomedical problems.

We are seeking a postdoctoral researcher who wants to work in a creative and collaborative environment on new mathematical approaches for understanding viral evolution.

Candidate qualifications include:

  •  PhD in any quantitative science (preferably mathematics, computer science, physics, astrophysics, computational biology, statistics, or engineering) or in life sciences with strong focus on mathematical modeling, evolution, and/or computation.
  • Expertise in high-throughput sequencing technologies is highly valued.
  • Excellent organizational and communication skills are a must.

Application Process:

Please send the following to

  1. Cover letter, highlighting experience with quantitative methods for understanding biological data and evolutionary processes
  2. CV
  3. Names and contact information for three references

Columbia University is an affirmative action/equal opportunity employer and encourages applications from women and underrepresented minorities.

PhD Studentships in Italy

The Italian Institute of High Mathematics offers the opportunity to students from all over the world to enter a PhD School in Italy with a fellowship. All domains of research in Mathematics and/or its applications are eligible for funding. The project proposals are presented by applicants who meet the eligibility criteria. The candidate must choose the University and the Doctorate program where the fellowship will be spent. The applicant can freely choose one of the over 20 PhD Schools participating to the program. The fellowships have a duration of 36 months. Fellowships include social security coverage and social benefits.
The average funding will be € 3.000 per month, including a living allowance, a mobility allowance, a travel allowance, a research cost contribution, and expenses for secondment periods.

In Italy at least three Universities have people working in Applied Topology: the University of Modena and Reggio Emilia (UniMORE), the Politecnico di Torino (PoliTO), and the University of Bologna (UniBO).

The deadline for applications is: 31 March 2017.

The application procedure is described at

For further information please contact Prof. Claudia Landi (, Prof. Fancesco Vaccarino (, Prof. Massimo Ferri (

Machine Learning Fellowship position for PhD students at SAS

The following link is from Ilknur Kabul, who is a manager for the Machine Learning group at SAS Institute in Cary, NC. Recently they became interested in topological data analysis for exploring large data sets. They're opening a Machine Learning fellowship for next summer for graduate students to work in this area:

The position is funded. The program provides a salary and housing support for a twelve-week internship at SAS headquarters in Cary, North Carolina, during the summer of 2017.

Funding opportunities for interdisciplinary research from the Center for Topology of Cancer Evolution and Heterogeneity

The Columbia University Center for Topology of Cancer Evolution and Heterogeneity is an interdisciplinary center formed to develop an integrated experimental and computational approach for characterizing tumor evolution within solid tumors.

Clonal evolution and tumor heterogeneity are believed to play key roles in generating patient-specific variations in cancer phenotype and in the emergence of resistance to treatment during disease progression. Due to difficulties in performing longitudinal assessments and limitations in identifying the cell(s) of origin, the process of clonal evolution in solid tumors (such as prostate and brain cancers) is not well understood.  The Center, as part of the National Cancer Institute’s Physical Sciences in Oncology Network, will employ novel experimental techniques such as multi-color organoid systems for tracing cellular lineages, as well as innovative single-cell sequencing technologies. We are combining these methods with emerging approaches from topological data analysis that are well suited to analyzing the high-dimensional data that single-cell approaches generate.

The Center has announced its opening call for proposals for pilot grants. These grants are intended to facilitate collaborations between mathematicians/physicists and cancer researchers that will lead to innovative new applications for the analysis of large biological data sets. This year’s round of funding will support five projects, including:

  • one pilot grant of $40,000 to support technology development and/or research involving wet lab experimentation
  • four collaborative grants of $10,000 each to support mathematical/computational research in collaboration with the Center. Collaborations are required to involve at least one researcher within the Center.

The goal of the program is to foster the development of new technologies and quantitative methods for the analysis of cancer genomic data. All applications must demonstrate close interdisciplinary collaboration between quantitative scientists and cancer biologists. Pilot projects and collaborative grants will enable the development and testing of new mathematical approaches within the context of cancer research, give mathematicians and physicists experience working in biological settings, and provide cancer biologists opportunities to explore how mathematical methods can be used to guide research agendas.

More information about the center and proposal requirements and deadlines can be found in the following link.

Releasing SimPers software for computing persistence under simplicial maps

We are happy to announce the release of the software SimPers that  can compute topological persistence of a sequence of simplicial complexes connected with SIMPLICIAL MAPS. We hope that this will fill the need for computing persistence under maps more general than inclusions. The software has been developed by the computational geometry/topology research group at CSE, OSU based on the  paper:

Computing topological persistence for simplicial maps
T. K. Dey,  F. Fan, and Y. Wang., (SoCG 2014), Proc. 30th Annu. Sympos. Comput. Geom. (2013).

Please visit to get the details.


Tamal Dey and Yusu Wang

ATMCS7 Torino July 25-29

ATMCS7: 25-29 July 2016 -- Torino, Italy

We are excited to announce the 7th edition of Algebraic Topology: Computation, Methods, and Science (ATMCS), scheduled from 25-29 July 2016 in Torino, Italy! This conference is a joint effort of the Polytechnic University of Turin (Politecnico di Torino) and the ISI Foundation, to be hosted at the Politecnico.

We are now welcoming submissions for our Contributed sessions. For more information, please visit:

The website is continually being updated with more logistical information, so be sure to check back often for updates. Don't hesitate to contact us if you have any questions, we are available at

Looking forward to seeing you in Torino in July!
- The ATMCS Team

Main Organizers for ATMCS7:
Vin de Silva, Pomona College, USA
Anthea Monod, Duke University, USA

Local Organizers:
Giovanni Petri, ISI Foundation, Italy
Francesco Vaccarino, ISI Foundation & Politecnico di Torino, Italy