Back to Table of contents

Primeur weekly 2019-02-25

Special

Astronomers publish new sky map detecting hundreds of thousands of previously unknown galaxies ...

LOFAR and APERTIF telescope systems tooled with machine learning and FPGA/GPU technology make cosmic explosions more visible to astronomers ...

Focus

Over 700 million euro of budget allocated to e-Infrastructure related projects in H2020 - close to 600 million euro to HPC related projects ...

German Government reconfirms its support for supercomputing development on a national and European scale ...

Quantum computing

Dutch King opens Microsoft Quantum Lab on TU Delft campus ...

ISARA Corp. unveils tools to simplify and accelerate quantum-safe cryptography roll-out ...

Exploring the global landscape of quantum technology research ...

Focus on Europe

International research collaboration computes climate past, present, and future ...

Supercomputing Frontiers Europe again in Poland ...

Middleware

Open Compute Project announces updated market forecast ...

Excelero appoints HPC industry visionary Sven Breuner as Field CTO ...

Hardware

vScaler to perform ResNet benchmarks on the NVIDIA DGX-2 server ...

Cray elects Stephen Gold to Board of Directors ...

Atos helps CALMIP achieve leading calculation results with BullSequana supercomputer ...

Indian Prime Minister Shri Narendra Modi launches PARAM Shivay at the Indian Institute of Technology ...

HDR 200G InfiniBand sets new performance records, accelerating multiple high-performance computing and Artificial Intelligence platforms around the world ...

Supermicro expands Intelligent Edge product portfolio to address emerging AI and 5G technologies ...

Applications

HLRS Visualization supports Stuttgart 21 Construction ...

Lorentz-eScience competition 2020 to issue Call for Applications ...

Supercomputers target bovine tuberculosis ...

NESAP hosts first NERSC-9 GPU hackathon for application developers ...

Artificial Intelligence allows for identification of new cancer genes ...

Novel material properties of hybrid perovskite nanostructures for next-generation non-linear electronic devices ...

Clarkson University awarded National Science Foundation Research Experience for Undergraduate Site on High Performance Computing ...

The Cloud

Hyperion Research releases Cloud Application Assessment Tool ...

Artificial Intelligence allows for identification of new cancer genes


The method, published in the journal Nature Communications, has been biologically tested in breast, prostate, lung and colon cancer cell lines, as well as retrospective analysis of survival of thousands of patients. It pointed 63 genes and experimentation confirmed that 36 of them contribute to the irregular cell growth. The method computationally recreates the biological interactions that take place in our cells.
19 Feb 2019 Barcelona - Barcelona Supercomputing Center's (BSC) researcher Natasa Przulj has led the creation of a new artificial intelligence-based computational method that accelerates the identification of new genes related to cancer. The method and its results, which have been biologically tested, have been published inNature Communications.

Prof. Przulj uses Machine Learning techniques to relate large amounts of omic data and recreate them in a computational prototype, Integrated Cell or iCell. Specifically, it fuses three tissue-specific molecular interaction networks: protein-protein interaction, gene co-expression, and genetic interaction networks. The technique by which this fusion is performed is Non-negative Matrix Tri-Factorization, a machine learning technique originally proposed for co-clustering and dimensionality reduction that was recently used for data-integration.

The authors of theNature Communicationsarticle titled " Towards a data-integrated cell ", have applied this method to reconstruct cells from four of the most common types of cancer - breast, prostate, lung and colon - and in all of them, it has proven useful in locating new genes related to these diseases. The method has indicated 63 genes, and a biological validation process has confirmed that at least 36 of them contribute to the irregular growth of the cells. The validation has been carried out through gene deactivation experiments followed by cell viability tests and analysis of patient survival data.

The experimentation revealed, for instance, that breast cancer patients with high expression of MRPL3, a mitochondrial ribosomal protein which was not related to cancer previously, have reduced survival. This is an example of how the new method may be used to uncover new biomarker genes, which may be relevant in the stratification and prediction of survival in cancer patients.

Natasa Przulj is ICREA Professor and has just joined the BSC as the leader of the Computational Integrative Network Biology group.

Alfonso Valencia, ICREA Professor and Director of BSC's Life Sciences Department stated that "Natasa's iCells perfectly complement our BSC cancer genome analysis portfolio, and it is only the first one of the many strong computational methods that we are expecting to see developed by her new group in the coming years".

Prof. Przulj highlighted that this new method to analyze cells "enables the identification of perturbed genes in cancer that do not appear as perturbed in any data type alone. This discovery emphasizes the importance of integrative approaches to analyze biological data and paves the way towards comparative integrative analyzes of all cells".

Possible applications range from various other diseases to aging, with the ultimate goal being uncovering intrinsic principles of inner organization of life on Earth.
Source: Barcelona Supercomputing Center - BSC

Back to Table of contents

Primeur weekly 2019-02-25

Special

Astronomers publish new sky map detecting hundreds of thousands of previously unknown galaxies ...

LOFAR and APERTIF telescope systems tooled with machine learning and FPGA/GPU technology make cosmic explosions more visible to astronomers ...

Focus

Over 700 million euro of budget allocated to e-Infrastructure related projects in H2020 - close to 600 million euro to HPC related projects ...

German Government reconfirms its support for supercomputing development on a national and European scale ...

Quantum computing

Dutch King opens Microsoft Quantum Lab on TU Delft campus ...

ISARA Corp. unveils tools to simplify and accelerate quantum-safe cryptography roll-out ...

Exploring the global landscape of quantum technology research ...

Focus on Europe

International research collaboration computes climate past, present, and future ...

Supercomputing Frontiers Europe again in Poland ...

Middleware

Open Compute Project announces updated market forecast ...

Excelero appoints HPC industry visionary Sven Breuner as Field CTO ...

Hardware

vScaler to perform ResNet benchmarks on the NVIDIA DGX-2 server ...

Cray elects Stephen Gold to Board of Directors ...

Atos helps CALMIP achieve leading calculation results with BullSequana supercomputer ...

Indian Prime Minister Shri Narendra Modi launches PARAM Shivay at the Indian Institute of Technology ...

HDR 200G InfiniBand sets new performance records, accelerating multiple high-performance computing and Artificial Intelligence platforms around the world ...

Supermicro expands Intelligent Edge product portfolio to address emerging AI and 5G technologies ...

Applications

HLRS Visualization supports Stuttgart 21 Construction ...

Lorentz-eScience competition 2020 to issue Call for Applications ...

Supercomputers target bovine tuberculosis ...

NESAP hosts first NERSC-9 GPU hackathon for application developers ...

Artificial Intelligence allows for identification of new cancer genes ...

Novel material properties of hybrid perovskite nanostructures for next-generation non-linear electronic devices ...

Clarkson University awarded National Science Foundation Research Experience for Undergraduate Site on High Performance Computing ...

The Cloud

Hyperion Research releases Cloud Application Assessment Tool ...