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 has opened in May 2015 as 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 three projects, including:

  • one grant of $40,000 to support technology development and/or research involving wet lab experimentation
  • two grants of $20,000 each to support mathematical/computational research

The goal of this pilot grant 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.

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

PhD position in Computational Topology and Geometry at TU Graz

The Institute of Geometry at Graz University of Technology offers a PhD position in the newly established research area “Computational Topology and Geometry”. The focus lies on the emerging field of persistent homology, a theory that turns homological algebra robust to noise and has paved the way to the topological analysis of real-world data. Besides theoretical aspects, the group works on algorithmic tools in the context of this data analysis techniques, on the connections to low- and high-dimensional computational geometry, and on applications of topological data analysis.

We offer a 4-year university assistant position (30 h/week) with a net salary of approximately 20,000 EUR per year. The position is available starting October 1 2015, and should be filled as soon as possible. The position is integrated into the field of expertise “Information, Communication, and Computing” at TU Graz, providing a stimulating interdisciplinary research environment. The graduate school “Discrete Mathematics” additionally contributes to the quality of TU Graz as a research center.

We are looking for outstanding students with a master’s degree in Mathematics/Computer Science or a closely related field. Knowledge in at least one of the fields computational geometry, computational topology, or algebraic topology, and programming skills, in particular in C++, are desirable.

Applications should include:
* a letter of application and motivation
* a detailed curriculum vitae
* a reference letter (for instance, by the Master thesis supervisor)
* email addresses of additional references (if applicable)
* a preferred starting date

and should be sent until August 23, 2015 using the reference number 5070/15/007 to (email is enough):

Technische Universität Graz
Dekan der Fakultät für Mathematik, Physik und Geodäsie
Univ.-Prof. Dipl.-Phys. Dr.rer.nat. Wolfgang Ernst
Petersgasse 16
A-8010 Graz

For further questions, please contact Michael Kerber (

Women in Computational Topology

Brittany Fasy writes:

Recently, a listserv for women in Computational Topology was initiated. The idea is that we can use this mailing list to remind each other about upcoming deadlines, find out who is going to SoCG or CCCG next year, etc. Feel free to encourage others (men or women) to join our network too! If you are interested in joining, send a blank email to <>. If you have any trouble joining or posting to the listserv, please email Brittany <>.

Exercises in Materials Geometry and Topology

Shape Up 2015
Exercises in Materials Geometry and Topology

Berlin (Germany), 14-18 September 2015

Dear Scientists and Mathematicians,

We wish to announce our upcoming conference:

Shape Up 2015

Exercises in Materials Geometry and Topology

The conference will be an interdisciplinary discussion meeting on
patterns and geometry, and their role in biological and synthetic
microstructured materials and tissue.. We invite contributions
from biology, chemistry, materials science, mathematics, physics
and related fields addressing the genesis, properties and function
of complex nano-scale geometries, as well as underlying geometric
and topological concepts for the study of complex structure and shape..

The key areas of interest include:

* Geometric and topological concepts in soft condensed matter
* Characterization of structure and function
* Topological data analysis and image reconstruction
* Self-assembly of bi- and polycontinuous phases
* Negatively curved surfaces and hyperbolic geometry
* Structure enumeration & network-like phases
* Function of complex nanostructures in biology
* Bio-inspired design of materials
* Knots and entanglements in physics
* Emergence of chirality, order and the role of disorder
* Symmetry, graphs and discrete geometry
* Tessellations, area-minimising foams and packings
* Three-dimensional topology of cellular microstructures
* Pattern formation and complex structures in soft materials

The conference will run from Monday morning 14 September 2015 to the
late afternoon of Friday 18 September and will feature an extended
poster session, 15-20 contributed talks as well as invited lectures

* Simon Copar (U Ljubljana)
* Herbert Edelsbrunner (IST Austria)
* Karsten Grosse-Brauckmann (TU Darmstadt)
* Jemal Guven (U Nacional Autonoma de Mexico)
* Stephen Hyde (Australian National University)
* Motoko Kotani (Tohoku U)
* Rob Kusner (UMass Amherst)
* Jeremy Mason (Bogazici U)
* Elisabetta Matsumoto (Harvard U)
* Konstantin Mischaikow (Rutgers U)
* Piotr Pieranski (U Poznan)
* James Sethian (UC Berkeley)
* Ullrich Steiner (U Fribourg)
* John M. Sullivan (TU Berlin)
* Adam Squires (U Reading)
* Salvatore Torquato (U Princeton)
* Silvia Vignolini (U Cambridge)

The conference is hosted at the Technical University of Berlin on
Strasse des 17. Juni that leads right up to the famous Brandenburg Gate,
next to Reichstag, the parliament of Germany. Museum Island, Berliner
Philharmonie, Opera Houses, Checkpoint Charlie, Berlin Television Tower
and other famous sites are within a few kilometers walking distance and
are easily accessible via public transport that connects all of inner
Berlin – from vibrant Prenzlauer Berg to Gendarmenmarkt at the heart
of Berlin. All lectures and the poster session will take place at the
Institute of Mathematics, Strasse des 17. Juni 136.

We are inviting abstracts for contributed oral presentations and for
posters. We encourage you to use the latex-template on the website
( and to include both attractive images
and references in your abstract. The deadline for abstract submission

***  31 May 2015  ***

Registration will open 15 June 2015.

We are hopeful of encouraging people from a wide variety of scientific
and mathematical backgrounds to attend. Any queries can be addressed
to the organising committee at

Best regards, and we hope to see you in Berlin,

The Organising Committee

Myfanwy Evans (TU Berlin), Andrew Kraynik (Sandia, (Ret.)), Frank Lutz
(TU Berlin), Gerd Schroeder-Turk (Murdoch) and Bodo Wilts (Fribourg)

Special issue on "Algorithms and Software for Computational Topology"

…in the Journal of Symbolic Computation

Aim and Scope:

The interest in algorithms on topological problems and their implementation has rapidly grown during the last decade. One driving force is the emergence of “topological data analysis” which connects topological concepts like Morse theory and homology to the investigation of real-world data. Another recent track of research substantially expands the realm of possibility for computational approaches in 3-manifold and knot theory. Common to these and other developments is the ability to handle large data collections through an efficient algorithmic framework as well as mature software implementations of those. A workshop session at the International Congress of Mathematical Software (ICMS) in August 2014 was dedicated to this topic (

The Journal of Symbolic Computation (JSC) invites high-quality contributions from researchers in the area of Computational Topology reporting on original research achievements towards algorithms, software, and applications. The list of topics includes, but is not limited to

  • (Persistent) homology
  • Topological data analysis
  • 3-manifold topology and knot theory
  • (Discrete) Morse theory

Researchers which are unsure whether their contribution is suitable are encouraged to contact the guest editor.

Submission instructions:

It is recommended to prepare submission in the same format as regular submission to JSC (see the “Guide for Authors” at

The paper must start with a introduction that

  • clearly states the considered problem
  • discusses its relevance and related work
  • explains the main contribution of the paper
  • explains why the contribution is original and non-trivial

There is no page limit on submitted manuscripts. It is required, however, that

  • all related work is completely and carefully discussed
  • all theorems are rigorously proved
  • important definitions/theorems/algorithms are illustrated by well-chosen examples.

All submitted papers will be refereed according to the high standards of JSC.

Guest editor:

Michael Kerber (Max Planck Institute for Informatics) –


The submission deadline is January 31 2015. The special issue is planned to appear in Fall 2015

AATRN Seminar: Robert Ghrist

Today, the promised AATRN seminar series got started with Robert Ghrist as the inaugural speaker. His lecture, through WebEx, builds up the cellular sheaf perspective on networks with capacity, Max Flow / Min Cut, and the work done by Ghrist, Yasu Hiraoka, and Sanjeevi Krishnan on categorifying and sheafifying MF/MC.

Among the novel insights coming from this talk even if one has been following the UPenn developments for a while was the connection to Poincare Duality: “Flow duality is a form of Poincare duality” — S. Krishnan

The approach detailed by Krishnan in his preprint (on ) encodes a flow network as a sheaf of semi-modules of capacities over a semi-ring over the directed graph of the network. Flows correspond to homology, cuts to cohomology.

MF/MC translates to:

Theorem (S. Krishnan)

Given a network X, a distinguished (virtual) edge e and a capacity sheaf F, (all) flowvalues at e of flows on F correspond to the homotopy limit over all cuts of cutvalues of cuts on F.

This approach, and connecting flows and cuts to a lattice structure on the constraints produces a setting where multi-kind flows can easily be analyzed with the same tools as ordinary flows, and where the algebra fixes the duality gaps that show up when naively searching for minima and maxima.

The talk culminated in a primer on the homology and cohomology of directed sheaves, to set us up to read Krishnan’s paper, constructing compact support cohomology and Borel-Moore homology for sheaves over directed spaces.

The added abstraction levels seem to enable MF/MC theorems for, for instance, probability distributions. It also carries a promise for insights into duality gaps in MF/MC type problems.

Applied Algebraic Topology Research Network

Peter Bubenik writes:

[…] Robert Ghrist, Konstantin
Mischaikow, Fadil Santosa and I are starting a Research Network in Applied Algebraic Topology. To start, the main activity of the network will be a weekly interactive online seminar. We have plans to expand our activities in the future.

Rob Ghrist will give the first talk on Tue Sept 23.

Please check out our web site at and become a member.