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

Postdoctoral Research Scientist, Columbia University Medical Center

We are searching for a postdoctoral researcher commencing spring / summer 2016.

The Rabadan Lab ( is a multi-disciplinary team at the Columbia University Medical Center consisting of applied mathematicians, computational and evolutionary biologists, physicists, and physicians. 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. Research topics include:

  • How does HIV evolve and adapt within the host environment? Evolutionary trees may not be the best way to understand and visualize a viral population that recombines, draws upon a reservoir of archival virus, and starts and stops replicating in response to changes in treatment. Major decisions about the direction of HIV cure research are being made on the basis of evolutionary studies, and building accurate analytical tools for these studies is a priority. What topological structures, other than trees, can help us understand and communicate viral evolution?
  • How do tumors diversify as they develop? Single-cell and deep sequencing of tumors have revealed considerable heterogeneity in both solid and blood tumors. Therapies targeted to single genes that are mutated in only one part of the tumor – even the largest part of it – may fail to eradicate the entire disease. We are using methods of computational topology to visualize and analyze the genetic and transcriptomic relationships between different parts of tumors.

We are searching for a postdoctoral researcher who wants to work in a creative and collaborative environment on these and other questions related to human health and evolution, carcinogenesis, and microbial pathogens. Candidate qualifications include:

  • PhD in Mathematics, Applied Mathematics, or a computational science;
  • Experience building tools for computational topology and visualization of complex data;
  • Experience and/or demonstrated interest in biological and/or clinical questions;
  • Strong programming background and interest in building tools for the broader research community.

Candidates with only some of the above qualifications are also highly encouraged to apply – we are always looking for talented and dedicated pre- and post-doctoral scientists!

Application Process

Option 1: Please send CV and one or two relevant publications/pre-prints to me at In your email, please highlight any important aspects of your experience. Recommendations/references are not necessary in your initial email, but may be requested for follow-up. I look forward to hearing from you!

Option 2: Follow instructions at

Best wishes,

Daniel Scholes Rosenbloom

Equal Opportunity Employment

Columbia University is an Equal Opportunity and Affirmative Action employer – Race/Gender/Disability/Veterans. It is committed to a workforce of faculty and staff that reflects the diversity and talent of New York City, the larger metropolitan area, and the nation. It is also committed to a working and learning environment supportive of its faculty and staff in their pursuit of productive and fulfilling professional and personal lives. See for more information.

Local Hiring

Columbia University is committed to the hiring of qualified local residents.

Disability Accommodations

Columbia University provides reasonable accommodations to qualified individuals with disabilities who can perform the essential functions of the position. If you need a reasonable accommodation for any part of the application and hiring process, please notify: Manager of Return to Work Program, Office of Human Resources, at Decisions on granting reasonable accommodation will be made on a case-by-case basis.

PhD position at Queen Mary, University of London

PhD Studentship in Mathematics

We invite applications for a fully funded 3 years’ PhD studentship commencing in January 2016. The research project will deal with developing new topological and geometric algorithms for video data compression and with other problems of analysis of large data. The project will be sponsored by the Queen Mary, University of London and by the Penteract 28 and will be supervised by representatives of both institutions. The candidates must have basic knowledge of pure and applied mathematics; it is desirable that the candidates are familiar with geometry, topology, statistics, elements of computer science and data analysis.

The deadline for applications is: November 16, 2015.

The application procedure is described at

For further enquiries please contact Prof. Michael Farber ( or Dr Danijela Horak (