Motif representation and discovery
Alexandra M. Carvalho,
R – INESC-ID Lisboa –
An important part of gene regulation is mediated by specific proteins, called transcription factors (TF), which influence the transcription of a particular gene by binding to specific sites on DNA sequences, called transcription factor binding sites (TFBS). Such binding sites are relatively short stretches of DNA, normally 5 to 25 nucleotides long. A commonly used representation of TFBS is a position specific scoring matrices (PSSM) which assumes independence of nucleotides in
the binding sites. Recently, some works argued in the direction of non-additivity in protein-DNA interactions making a way for more complex models to appear which account for nucleotide interactions. We propose to model TFBS representing nucleotide interactions with consistent k-graph Bayesian networks (where k represents the maximum number of interactions between nucleotides) jointly with a set of features, directly scored from each base sequence, which appear to be relevant for TFBS characterization. The model is flexible to incorporate any set of features scored from base sequences. We consider discriminative learning of such models since it
outperforms generative learning in the context of classification with a large set of features.
Date: 2010-Jan-08 Time: 14:30:00 Room: 04
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Research data repositories and tools for human genomics data sharing
Inform the human research community of the status and availability of BioData.pt Local EGA and discuss its need and usability challenges.
The European Genome-phenome Archive (EGA) is a repository for all sequence and genotype experiment types, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data, including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters.
Responding to national regulations over human data sharing and other constraints, BioData.pt deploys and operates a Local EGA instance and tools that allow data discovery of genomic and phenoclinic data, following the GA4GH standard and international best practices.
This workshop aims at informing the human research community of the status and availability of BioData.pt Local EGA and discuss from several perspectives its need and usability challenges.
Further details and registration are available here.
OLISSIPO Summer School in Lisbon | Computational phylogenetics to analyse the evolution of cells and communities
We are happy to announce the OLISSIPO Summer School on Computational phylogenetics to analyse the evolution of cells and communities, which will be held in Lisbon, Portugal, at INESC-ID, between July 2-7, 2023.
David Posada, University of Vigo (class)
João Alves, University of Vigo (hands-on)
Nadia El-Mabrouk, Université de Montréal (class)
Mattéo Delabre, Université de Montréal (hands-on)
Ran Libeskind-Hadas, Claremont McKenna College (class and hands-on)
Russell Schwartz, Carnegie Mellon University (class and hands-on)
See the preliminary agenda at: https://olissipo.inesc-id.pt/tree-tango-school
Registration is mandatory. You can register at: https://forms.gle/VsASFHW5E7MJvaCc9
The registration fee is 250€ for students and OLISSIPO members and 350€ for postdocs or other researchers (meals indicated at the schedule of the school are included, accommodation and flights are not). All details will be made available upon registration.
We will have slots for flash talks (3-10 min depending on the number of submissions) to present yourself and the work you have been developing in your research.
The 13th Lisbon Machine Learning School | LxMLS 2023
The Lisbon Machine Learning Summer School (LxMLS) takes place yearly at Instituto Superior Técnico (IST). LxMLS 2023 will be a 6-day event (14-20 July, 2023), scheduled to take place as an in-person event.
The school covers a range of machine learning topics, from theory to practice, that are important in solving natural language processing problems arising in different application areas. It is organized jointly by Instituto Superior Técnico (IST), a leading Engineering and Science school in Portugal, the Instituto de Telecomunicações, the Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa (INESC-ID), the Lisbon ELLIS Unit for Learning and Intelligent Systems (LUMLIS), Unbabel, Zendesk, and IBM Research.
Check online for information about past editions: LxMLS 2011, LxMLS 2012, LxMLS 2013, LxMLS 2014, LxMLS 2015, LxMLS 2016, LxMLS 2017, LxMLS 2018, LxMLS 2019, LxMLS 2020, LxMLS 2021, LxMLS 2022 (you can also watch the videos of the lectures for 2016, 2017, 2018, and 2020).
31st International Conference on Information Systems Development (ISD 2023)
The 31st International Conference on Information Systems Development (ISD 2023) conference provides a forum for research and developments in the field of information systems. The theme of ISD 2023 is “Information systems development, organizational aspects and societal trends”. New trends in developing information systems emphasize the continuous collaboration between developers and operators in order to optimize the software delivery time. The conference promotes research on methodological and technological issues and how IS developers and operators are transforming organizations and society through information systems.
The ISD 2023 conference held this year also provides an opportunity for researchers and practitioners to promote their research, practical experience, and to discuss issues related to Information Systems through papers, posters, and journal-first paper presentations.
ISD 2023 will be hosted by Instituto Superior Técnico, in Lisbon, Portugal, on August 30–September 1, 2023.