Thursday, October 30, 2014

[DMANET] Research grant (BI-D) - BacHBerry project

Dear colleague,
Please distribute widely and sorry for crossposting. Thank you.
Best regards,
Susana Vinga


1 Research Grant – Post-doc (BI-D)

We are seeking one postdoc candidate in the context of a FP7 KBBE
European Project, BacHBerry - "BACterial Hosts for production of
Bioactive phenolics from bERRY fruits, (European
Union FP7- 613793).

Scientific Area: Optimization and Operations Research.

Required education Level and research experience: PhD in one of the
following areas: optimization, operations research, machine learning,
computer science, mathematics, statistics or related, with a taste for
inter-disciplinary research, and with very good interpersonal skills.
Ideally, the person will have a long experience with optimization
techniques, machine learning and graphical models. Unusual CVs are

Workplan: With the development of genetic and metabolic engineering is
it now possible to increase the cells' production of given substances
by manipulating the corresponding metabolic networks, which can be
defined as hypergraphs (nodes are compounds, edges are chemical
reactions). BachBerry is interested in the generation of bacterial
platforms for sustainable bio-based production of phenolic compounds
found in berry fruits. This is accomplished by maximizing the fluxes
in the network, a problem similar to those occurring in transportation
and logistics optimization. The candidate will work on the development
and application of optimization methods and algorithms, in particular
expanding techniques based on linear programming (FBA), bi-level
mixed-integer (OptKnock) and multi-level optimization (OptCom). Also
sparse optimization might provide relevant solutions and will be
explored during the project.

Workplace and scientific supervision: The candidate will work in the
Center of Intelligent Systems at the IDMEC
(, Instituto Superior Técnico, Lisboa,
Portugal, under the supervision of Susana Vinga and in interaction
with the partners of BacHBerry, in particular the BAMBOO team at the
Inria-UCBL in Lyon, France ( and
Marie-France Sagot. Both CSI and BAMBOO are methodological teams with
an expertise in computational and systems biology.

Duration: 12 months, from December 2014, and renewable for up to the
duration of the project.

Evaluation Criteria: The criteria for selection consists on the
academic record of the candidate (30%), publications in areas of the
grant (30%) and evidence of specialized knowledge in the area of the
grant, in particular in optimization (40%). The Jury may decide to
interview the candidates in order to perform a more objective
evaluation of some of the criteria.

Application Dates: From 10th November to 1st December 2014.

Documents to be submitted: Detailed curriculum vitae; motivation
letter; copy of academic study certificates; name of two personal
references. The applications should be submitted via email to

For more details:

Susana Vinga, PhD
Av. Rovisco Pais, 1049-001 Lisboa, Portugal
Tel. (+351) 218 419 504 Fax: (+351) 218 498 097

* Contributions to be spread via DMANET are submitted to
* Replies to a message carried on DMANET should NOT be
* addressed to DMANET but to the original sender. The
* original sender, however, is invited to prepare an
* update of the replies received and to communicate it
* via DMANET.