6th Severo Ochoa Research Seminar Lectures at BSC, Barcelona, 2019-20: book of abstracts
The SO Research Seminars Series is a multidisciplinary focal point for exchange of ideas as well as giving a forum to the Severo Ochoa Mobility Grant holders to make a presentation related to the research focus of their collaborations funded by the awarded grants.
Summary
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Error-free and error-prone DNA repair shape mutation landscapes in human tumors
(2020)
Conference report
Open AccessMany processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint ... -
Combining transcriptional and post-transcriptional regulation to predict somatic mutations altering the gene regulatory program in cancer cells
(2020)
Conference report
Open AccessWhile most cancer studies focused on patient variations lying in protein-coding regions, the noncoding ~98% of the genome, containing cis-regulatory regions that control when and where genes are expressed, is largely ... -
A flux balance approach to integrate cell metabolism into multicelluar agent-based simulations
(2020)
Conference report
Open AccessThe study of multicellular systems such as tumors, tissues, or organoids is critical to improve our understanding of the complex dynamics exhibited by these systems. For instance, the emergence of resistant cancer cells ... -
Big Data analytics using flash storage with near-storage hardware accelerator
(2020)
Conference report
Open AccessAs capacity for data collection and storage continues to grow, data analytics requirements regularly exceed the DRAM capacity of a single machine. In order to avoid the cost and communication overhead of distributed ... -
MI6: secure enclaves in a speculative out-of-order processor
(2020)
Conference report
Open AccessMI6 is an aggressive, speculative out-of-order processor to support Secure Enclaves, which restore the process isolation guarantees broken by recent attacks exploiting microarchitectural sidechannels.Our threat model ... -
The development of the application software for PEZY SC2 many core processors
(2020)
Conference report
Open AccessWe have developed application software for PEZY SC2 many core processors.PEZY SC2 are the brand-new many-core processors (2048 cores). Shoubu system B with 672 SC2 processors was awarded world number 1 in Green top 100 ... -
Mesh: automatically compacting memory for C/C++ applications
(2020)
Conference report
Open AccessPrograms written in C and C++ — and languages implemented in C, like Python and Ruby — can suffer from serious memory fragmentation, leading to low utilization of memory, degraded performance, and application failure due ... -
Tropical cyclones and climate change: recent results and uncertainties
(2020)
Conference report
Open AccessIn the first part of the talk I’ll give an overview of the current understanding and recent progress on the influence of climate changes on tropical cyclones. I’ll discuss both attribution of current trends, as well as ... -
Found in translation: a machine learning model for mouse-to-human inference
(2020)
Conference report
Open AccessCross-species differences form barriers to translational research that ultimately hinder the success of clinical trials, yet knowledge of species differences has yet to be systematically incorporated in the interpretation ... -
A lightweight tool for detecting inter-thread communication
(2020)
Conference report
Open AccessIn a multicore environment, inter-thread communication can provide valuable insights about application performance. Literature detecting inter-thread communication either employs hardware simulators or binary instrumentation. ... -
Low-dimensional representations of Niño 3.4 evolution in observations and models.
(2020)
Conference report
Open AccessOver the last decade, there have been El Niño forecasts that looked promising in the spring but faltered later. Historically, there is a significant positive correlation between observed springtime tendencies in Niño-3.4 ... -
High-throughput characterization of lncRNA regulation, evolution, and function
(2020)
Conference report
Open AccessIn this talk, I will present an overview of my PhD work, which has focused on understanding three fundamental aspects of long non-coding RNA (lncRNA) biology—regulation, evolution, and function — using both computational ... -
Data-driven approach to cardiovascular disease: deep phenotyping, omics and machine learning
(2020)
Conference report
Open AccessMost cardiovascular (CV) risk scores used in clinical practice predict the probability of CV events using information on the seven traditional cardiovascular risk factors: age, gender, hypertension, dyslipidemia, obesity, ... -
Characterization of regulatory variants in promoters with enhancer activity and their relation with human diseases
(2020)
Conference report
Open AccessGene regulation is driven by the interaction of regulatory sequences, commonly categorized as either enhancers or promoters. Recently, using a modification of the STARR- seq assay, we identified sets of promoters with ... -
Development of the 4D program for simulation of human intrauterine frontal cortex development
(2020)
Conference report
Open AccessThe brain as a complex energy-informational system is dynamic structure, which during intrauterine development in humans changes within each gestational week. The dramatic introduction of endocrine disruptors in living ... -
Technological and evolutionary challenges for reconstructing our ancestor’s genome from 500 million years ago
(2020)
Conference report
Open AccessIt was long known that our genome harbors redundant components, which was introduced by the so-called two-round whole genome duplications (2R-WGD). In 2009, the speaker of this seminar proposed for the first time that ... -
Simulation methods and molecular interactions: challenges and opportunities
(2020)
Conference report
Open AccessNowadays, the computer simulation methods are powerful tools to understand and to predict the macroscopic properties of matter from molecular interactions. The trajectory of molecules in a molecular dynamics are generated ... -
From heterogeneous co-execution to DSAs: an overview of past, present and future research lines
(2020)
Conference report
Open AccessHeterogeneous architectures are prevalent, ranging from supercomputing to handheld devices. However, the collaboration of devices with different capabilities poses challenges of its own. This talk will introduce different ... -
Transforming the health system into an open ended prospective clinical study by using artificial intelligence on clinical big data/ real word data
(2020)
Conference report
Open AccessBecause of the continuous decrease of sequencing prices the GA4GH has estimated that by 2023 over 80% of sequencing will be done in a clinical environment. In addition, more than two decades of generalized digitalization ... -
Several stories about tripeptides: basic components for modeling flexible protein structures
(2020)
Conference report
Open AccessFrom a mechanical point of view, fragments of three consecutive amino acid residues (called tripeptides hereafter) are very interesting elements of polypeptide chains. Indeed, if we consider the bond torsion angles as ... -
Team strategy for hardware development
(2020)
Conference report
Open AccessFive founding members of the former Samsung Austin Research Center (SARC) will share their thoughts on how to build a high performance team, how industry is different from the academic experience, how things are different ... -
Actionable models of control in complex systems for the biomedical domain
(2020)
Conference report
Open AccessModern artificial intelligence (AI) and machine learning (ML) techniques predict system behavior from previous observations. However, in biology, and in true complex systems in general, profound transformation in system ... -
Advances in machine learning for modelling and understanding in earth sciences
(2020)
Conference report
Open AccessThe Earth is a complex dynamic network system. Modelling and understanding the system is at the core of scientific endeavour. We approach these problems with machine learning algorithms. I will review several ML approaches ... -
Template for reproducible scientific datasets/papers
(2020)
Conference report
Open AccessThe increasing volume, diversity, and role of data in modern research has been very fruitful. However, these same factors, have also made it harder to describe (in sufficient detail) the processing behind a scientific ... -
Towards predictable, secure, and verified cyber-physical systems- on-chip
(2020)
Conference report
Open AccessThe unleashed Cyber-Physical Systems (CPS) and Internet of Things (IoT) revolution creates exceptional opportunities in many domains such as healthcare, smart power grid, automotive, industrial robots, and transportation ... -
A short introduction to the aims and status of modern C++
(2020)
Conference report
Open AccessC++20 is here. How does it reflect the aims and ideals of C++? What are the major features of C++20? What is in the works for future standards? I will - necessarily briefly - touch upon type-safety, resource-safety, type ... -
Systematic discovery of germline cancer predisposition genes through large-scale cancer genomics
(2020)
Conference report
Open AccessThe genetic causes of cancer include both somatic mutations and inherited germline variants. Large-scale tumor sequencing has revolutionized the identification of somatic driver alterations but has had limited impact on ... -
Annotating clinical text produced in Chile
(2020)
Conference report
Open AccessPublic hospitals in Chile have waiting lists for specialty consultations that are both numerous and with long waiting times. The reason for referral is in the form of unstructured text and therefore it is hard for ... -
Bias on the web
(2020)
Conference report
Open AccessThe Web is the most powerful communication medium and the largest public data repository that humankind has created. Its content ranges from great reference sources such as Wikipedia to ugly fake news. Indeed, social ... -
Towards secure cyber-physical systems for autonomous vehicles
(2020)
Conference report
Open AccessCyber-Physical systems have become ubiquitous. These systems integrate different functionalities to satisfy the performance requirements and take advantage of the available processing power of multi-core systems. Safety ... -
Gender bias and natural language processing
(2020)
Conference report
Open AccessDemographic biases are widely affecting artificial intelligence. In particular, gender bias is clearly spread in natural language processing applications, e.g. from stereotyped translations to poorer speech recognition ...
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