en News - BIOINFORMATICS BARCELONA News Thu, 16 Feb 2017 14:08:04 +0000 Thu, 16 Feb 2017 14:08:04 +0000 Houdini 2 (http://houdini.antaviana.cat/) http://www.bioinformaticsbarcelona.eu/news A new study reveals the level of physical activity and sport per European country

Sweden, Finland and Denmark are the European countries that do more sport on a regular basis, according to a study published in the Open Access Library Journal, by the experts Antonio Monleón-Getino, Marta Cubedo, Martín Ríos, from the Faculty of Biology of the University of Barcelona, and Daniel Ríos, professor at the Sales Upper Secondary School in Viladecans (Barcelona). According to the conclusions, people in Portugal, Italy, Spain and especially Greece, are listed below the European average regarding the indicators on population and sport.

Sedentarism and lack of physical activity is having more and more incidences in the public health of western countries. According to the World Health Organization (WHO) , which has been reminding about the value of physical activity to promote health and prevent some pathologies, the lack of physical activity is the fourth risk factor in global mortality, and the main cause of more than 21% breast and colon cancers, the 27% of diabetes cases and around the 30% of the coronary heart diseases.

The new study published in Open Access Library covers general aspects of the physical activity and does not focus on any sport in particular. It is based on the multivariate analysis of data from around 27.000 people from 27 European countries according to the information published by the Eurobarometer of the European Commission on the practice of sport stated by people over 15. For each analysed country, the experts analyse the practice of physical exercise and sport of their inhabitants, who are listed in four categories: the ones who never play sport, barely play, occasionally play, and regularly play sport.



Physical activity in Europe: a new inequality map?

"Once we analysed the regularity with which people do sport in 27 countries of the European Union, we saw that Nordic countries, Sweden, Finland and Denmark, play sport more regularly" says Daniel Ríos, lecturer of secondary education at the Sales High School.

After Sweden, Finland and Denmark, the countries with best indicators of physical activity are Slovenia, the Netherlands, Belgium, Luxembourg, Germany, the United Kingdom and France. The lower levels in physical activity were recorded in Bulgaria and Greece.

"As a conclusion -says Daniel Ríos- we think educational and economical levels of these countries are highly related to the practice of physical activity and sport of the people". This scientific study describes how the regular practice of sport and exercise is related to adults involved in educational activities, and with a high level of satisfaction with their economic status and career profile.

In the case of Spain, "the level of sport practice is co-related with the socioeconomic status, as it was seen in the Survey of Sporting Habits in Spain 2015. The survey, carried out in the National Statistics Plan 2013-2016 by the Ministry of Education, Culture and Sport; the Senior Council for Sports and the National Institute of Statistics, aimed to bring the main indicators of sporting habits and practices of people from all the country" says Antonio Monleón-Getino, from the Department of Genetics, Microbiology and Statistics of the University of Barcelona, and member of the Research Group on Biostatistics and Bioinformatics (GRBIO), team integrated in the platform Bioinformatics Barcelona (BIB).

A multivariate statistical technique with great analytical power

The study uses a multidimensional scaling method (MDS) to represent the series of variables or the 27 European studied countries and a country with an average value (which would be the average of the countries that make the European Union up).

According to professor Daniel Ríos, "the MDS method tries to show in a Euclidean space, with few dimensions, the proximities or distances between a set of objects, countries in this case. This technique combines a great capacity to reduce data with high a high graphic potential and represent them in a space with few dimensions (two or three)".

"The MDS is very interesting because it complements other multivariate techniques (factor analysis, cluster, etc.) and allows resolving complex multivariate data collections where the relation between variables is defined with statistical proximity or distance. In this article, as a methodological novelty, the Bhattacharyya distance is applied to calculate the distance between countries" said the authors.

According to the experts, the new study wants to promote future researches based on the application of multivariate methods on the management and interpretation of statistical information.


Original article

D. Ríos, T. Monleón-Getino, M. Cubedo, M. Ríos. «A Graphical Classification of European Countries According to Physical Activity Level of Its Citizens». Open Access Library Journal, December, 2016.

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Thu, 16 Feb 2017 14:08:04 +0000 http://www.bioinformaticsbarcelona.eu/news//news/49/a-new-study-reveals-the-level-of-physical-activity-and-sport-per-european-country http://www.bioinformaticsbarcelona.eu/news/49 0
CompBioMed, a centre of excellence in computational biomedicine, is born

Predictive models of diseases are gaining importance in medicine thanks to their usefulness when customizing treatments. Hence, computational methods based on human biology have become a key factor for the development of customized medicine. This scenario has led to the birth of CompBioMed project, a centre of excellence in biomedical computing that promotes the uptake and exploitation of high performance computing (HPC) in the field of biomedicine. Basic, clinical and industrial researchers will be able to participate as users in the new project, which, for the moment, will work in three different areas: cardiovascular, molecular and neuromusculoskeletal. University College of London is leading the initiative, which promotes interdisciplinary business opportunities by getting its industrial partners to participate, as well as support and facilitate modelling and simulation activities and provide education to a diverse set of communities.

Among the 14 centres participating in the project is the Computational Biophysics research group, led by the ICREA researcher Gianni de Fabritiis, at the Research Programme on Biomedical Informatics (GRIB), a joint programme between Universitat Pompeu Fabra (UPF) and Hospital del Mar Medical Research Institute (IMIM). This group will play a substantial role in work package 2 of CompBioMed: Molecularly-based Medicine Exemplar Research, and also in work package 6: Empowering Biomedical Applications

The Barcelona Supercomputing Center, (BSC-CNS) is another CompBioMed partner. The researcher Mariano Vázquez, team leader of the CASE Department, is the CompBioMed application manager, responsible for coordinating the research work of the Centre of Excellence. CompBioMed will develop parallel software (including Alya, the BSC's multiphysics simulation code) that will be installed in European supercomputing centres (BSC-CNS, SurfSARA in the Netherlands and EPCC in Scotland) for use by biomedical researchers.

CompBioMed is part of one of the new centres of excellence funded by the Horizon 2020 programme and has funding of more than 4.9 million euros. In addition to University College of London and Pompeu Fabra University, the universities of Amsterdam, Edinburgh, Oxford, Geneva and Sheffield, as well as the Barcelona Supercomputing Centre (Spain); the SURFsara organization (Netherlands); consultant CBK Sci Con (United Kingdom); companies LIFETEC Group (Holland), Bull Sas (France), Janssen Pharmaceutica (Belgium), and Acellera (Spain) and Evotec Ag (Germany), will be the project partners.

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Wed, 15 Feb 2017 12:39:34 +0000 http://www.bioinformaticsbarcelona.eu/news//news/47/compbiomed-a-centre-of-excellence-in-computational-biomedicine-is-born http://www.bioinformaticsbarcelona.eu/news/47 0
Connecting Computational Biomechanics and Systems Biology in Frontiers Journal

Frontiers Journal has introduced a new research topic: Advanced HPC-based Computational Modeling in Biomechanics and Systems Biology. This research topic should contribute to bridging the gap between Computational Biomechanics and Systems Biology, with HPC-based Computational Modeling as the link. 

The topic  is co-edited by Mariano Vázquez, Peter V Coveney, Alfons Hoekstra, and Bastien Chopard from CompBioMed. These concepts are in the core of the European Center of Excellence in Computational Biomedicine (CompBioMed).  

BSC encourages researchers to submit their papers. Submission Deadlines: 31 March 2017 for abstracts and 30 September 2017 for manuscripts.

Further information here.

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Wed, 15 Feb 2017 12:28:09 +0000 http://www.bioinformaticsbarcelona.eu/news//news/45/connecting-computational-biomechanics-and-systems-biology-in-frontiers-journal http://www.bioinformaticsbarcelona.eu/news/45 0
How did some plants become carnivorous?

For the English naturalist Charles Darwin, carnivorous plants were one of the most fascinating species due their extraordinary physiological and ecological properties. These plants live in habitats poor in nutrients -mostly on nitrogen and phosphorous- and have compensated this lack with the ability to digest animals such as insects and other arthropods.

After more than 140 years of Darwin's publication of Insectivorous Plants, an international team identified the key genomic changes that allowed some plants to adopt a carnivorous diet, as seen in a study in which Julio Rozas, Pablo Librado and Alejandro Sánchez-Garcia, from the Faculty of Biology and the Biodiversity Research Institute of the University of Barcelona (IRBio) take part.

Adapting and surviving with a carnivorous diet in nutrient-poor soils is an evolutionary process that some evolutionary unrelated species have been going through, repeatedly and independently, from a same set of genes and proteins, according to the study published in the journal Nature Ecology & Evolution, and coordinated by Mitsuyasu Hasebe and Kenji Fukushima (National Institute for Basic Biology, Japan), Shuaicheng Li (City University of Hong Kong, China), and Victor A. Albert (University at Buffalo, United States).



Discovering the genetic mechanisms that make carnivorous diets possible

All plants are photosynthetic organisms, that is, they turn transform the inorganic matter of the environment into organic molecules (glucose). To complete the lack of nutrients of some soils, carnivorous plants can catch and absorb nutrients from a prey, thanks to an exclusively biological mechanism.

The experts have sequenced the genome of the pitcher plant (Cephalotus follicularis), an Australian species that can be identified for its insectivorous leaves -pit-fall traps that catch insects-, very different from the other leaves. The genome of this species -the second carnivorous plant with the complete genome sequenced after Utricularia gibba- is relatively large, and consists of 1,6 Gb, which is almost half of the human genome. The researchers have identified more than 36.000 genes.

According to Professor Julio Rozas, from the Department of Genetics, Microbiology and Statistics, "these plants' ability to feed from animals in poor soils is the result of the action of natural selection, which independently favoured several genetic changes on the same set of genes. With the comparative analysis of differentially expressed genes in these two kinds of leaves, the genetic changes related to plants' carnivorous diet have been identified".

"According to the results, leaves that catch insects have gained new enzymatic functions: basic chitinase, which breaks down chitin (main component of insects' exoskeleton), and purple acid phosphatase which releases phosphate groups from molecules, and it contributes to  the mobilization of the prey's phosphate", says professor Julio Rozas, who leads the Evolutionary Genomics and Bioinformatics research group at the University of Barcelona and the association Bioinformatics Barcelona (BIB).



Carnivorous plants: parallel evolution

Natural selection has acted on specific evolutionary routes so that plants can feed from animals. According to Dr Alejandro Sánchez-Gracia, "In addition to developing a a different strategy to catch animals, natural selection has also often acted recurrently on the same parts of particular pitcher plant genes in order to gain the ability to digest the prey, a phenomenon known as 'parallel evolution'".

The case of these carnivorous plants is a clear example of convergent evolution, probably due the heavy biological restrictions imposed by extreme nutrient-poor ecosystems. Moreover, the fact that this convergence was accompanied by a parallel molecular evolution in digestive enzymes makes this system an interesting example from the perspective of the study of the evolutionary process. "The examples of parallel evolution at a molecular scale are not very common. Therefore they are very interesting to understand the genetic causes of molecular adaptation and their study can help us to determine the relative role of the different evolutionary forces in biological diversification" says Sánchez-Gracia.


The evolutionary journey of plants towards a carnivorous diet

Which molecular strategies have carnivorous plants used as an adaptive evolutionary response? In their adaptation to the carnivorous diet, the generation of new genes is not always necessary: already existing genes in the plant genome have acquired new biological functions, a process known as co-option.

According to the expert Pablo Librado, "in the study, we have stated that genes originally involved in the defence against certain diseases -or the response to biotic and abiotic stress- have acquired new functions (co-option) related to the ability of feeding from animals. This is the case, for instance, of a specific set of proteins that evolved to act as digestive enzymes".

"The results of co-option, regarding both the digestive enzymes and the amino acid changes seen in these enzymes, show that evolution has acted on a limited number of evolutionary routes in the adaptive transition to the carnivorous diet" explains Librado, who is currently working at Center for Geogenetics, from the University of Copenhagen and the Natural History Museum of Denmark. 



BadiRate, a bioinformatics software created at the University of Barcelona

As part of the research, the experts of the UB and IRBio have remarkably contributed to the genomic analysis, integrating the uncertainty that exists on the species' phylogenetic relations to infer which type of genes have preferentially duplicated or lost in the different plant species. This genomic analysis was carried out mainly with BadiRate, a bioinformatics software created by Pablo Librado and Julio Rozas (University of Barcelona) that proved to be essential to discover which kinds of genes, including digestive enzymes, recurrently accompanied the emergence of carnivorous diets in unrelated plant lineages.


Original Article

K. Fukushima, X. Fang, D. Alvarez-Ponce, H. Cai, L. Carretero-Paulet, C. Chen, T. Chang, K. M. Farr, T. Fujita, Y. Hiwatashi, Y. Hoshi,  T. Imai, M. Kasahara, P. Librado, L. Mao, H. Mori, T. Nishiyama, M. Nozawa, G. Pálfalvi, S. T. Pollard, J. Rozas, A. Sánchez-Gracia, D. Sankoff, T. F. Shibata, S. Shigenobu, N. Sumikawa, T. Uzawa, M. Xie, C. Zheng, D. D. Pollock, V. A. Albert, S. Li, M. Hasebe. «The pitcher plant Cephalotus genome reveals genetic changes associated with carnivory». Nature Ecology & Evolution,  February 2017

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Tue, 07 Feb 2017 11:52:25 +0000 http://www.bioinformaticsbarcelona.eu/news//news/43/how-did-some-plants-become-carnivorous http://www.bioinformaticsbarcelona.eu/news/43 0
The fundamental causes of human ageing explained

Natural selection favours fragile and unhealthy old age if it is due to mutations that are beneficial during childhood. As of 40-50 years of age, natural selection is blind because we have already passed on our genes, whether beneficial or not, to our descendants. Knowing the genes and mutations involved in ageing may help to develop new strategies for the treatment of age-related diseases.

A team led by scientists at the Department of Experimental and Health Sciences at Pompeu Fabra University (UPF) and the Institute of Evolutionary Biology (IBE), a joint UPF-CSIC centre, have shown which are the latest genetic causes of human ageing. The results are published this week in the journal Nature Ecology & Evolution.

Ageing has for a long time been a challenge for the public health system and poses evolutionary biologists with a fascinating scientific puzzle. There is no universal theory about the causes, nor is it clear what its overall impact will be on human health. Now, this study has used all the data accumulated over a decade of research on the genetic bases of complex diseases (from Parkinson's to cancer through diabetes) to test different evolutionary theories of senescence.

To date, efforts to understand the evolutionary causes of ageing had been limited to experimental models like the fruit fly, and the findings were often contradictory. But today, the amount of data available concerning the relationship between genotype and phenotype represents an unprecedented opportunity to conduct these tests in humans. This information is available to the scientific community from large international databases such as the European Genome Phenome Archive (EGA): a joint project between the European Bioinformatics Institute (EBI, Cambridge) and the Centre for Genomic Regulation (CRG, Barcelona).

Arcadi Navarro, former ICREA research professor at UPF, has co-led the study that has examined the results of more than 3,000 studies with over 2,500 markers out of a total of 120 diseases. According to Navarro, "the power to determine whether an individual is healthy or any disease will develop during their life has increased greatly as more and more data have been collected".

To start with, scientists have considered whether the markers for each disease have an effect on youth or old age. The distinction is important because if a mutation has harmful effects in old age, our genes will already have passed on to our offspring and natural selection cannot act.  The results of this study show that the frequency and the effect of the mutations that cause diseases in old age are greater than those that cause disease in early age. "We have found an evolutionary threshold at 40-50 years, a biologically significant age because it limits the reproductive period", says Navarro.

The bioinformatic studies carried out by Juan Antonio Rodríguez, first author of the study, have also shown that there are mutations that are beneficial to youth but are harmful later in old age. However, "as they are positive in the reproductive period they will be favoured by natural selection and passed on to the offspring, and so it will be difficult to remove them", explains Rodríguez.

"The physical decline in old age could be the evolutionary price we have to pay to reach the age of having children healthily", says Elena Bosch, co-leader of the study and group leader at the IBE. For example, a drug that we give to a child can have negative effects when it is old. Conversely, it can also happen that a person that is very sickly as a child, if s/he survives, will enjoy excellent health as a senior citizen.

To start with, scientists have considered whether the markers for each disease have an effect on youth or old age. The distinction is important because if a mutation has harmful effects in old age, our genes will already have passed on to our offspring and natural selection cannot act.  The results of this study show that the frequency and the effect of the mutations that cause diseases in old age are greater than those that cause disease in early age. "We have found an evolutionary threshold at 40-50 years, a biologically significant age because it limits the reproductive period", says Navarro.

The bioinformatic studies carried out by Juan Antonio Rodríguez, first author of the study, have also shown that there are mutations that are beneficial to youth but are harmful later in old age. However, "as they are positive in the reproductive period they will be favoured by natural selection and passed on to the offspring, and so it will be difficult to remove them", explains Rodríguez.

"The physical decline in old age could be the evolutionary price we have to pay to reach the age of having children healthily", says Elena Bosch, co-leader of the study and group leader at the IBE. For example, a drug that we give to a child can have negative effects when it is old. Conversely, it can also happen that a person that is very sickly as a child, if s/he survives, will enjoy excellent health as a senior citizen.

 

Reference: Juan Antonio Rodríguez, Urko M. Marigorta, David A. Hughes, Nino Spataro, Elena Bosch,  Arcadi Navarro. Antagonistic pleiotropy and mutation accumulation influence human senescence and disease. Nature Ecology & Evolution, 2017

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Fri, 03 Feb 2017 11:31:06 +0000 http://www.bioinformaticsbarcelona.eu/news//news/41/the-fundamental-causes-of-human-ageing-explained http://www.bioinformaticsbarcelona.eu/news/41 0
Key genes for disease

What makes a gene cause disease? Do all the genes linked to pathologies have something in common? Is there any relationship between disease and evolutionary adaptation? These are some of the questions raised by researchers at the Institute of Evolutionary Biology (IBE), a joint centre of Pompeu Fabra University (UPF) and the CSIC, in their latest study published in the journal Human Molecular Genetics. To answer them, the team has compared genes that can cause diseases with genes that have never been linked to any, concluding that the genes linked to diseases share evolutionary characteristics and have different protein networks from the rest of the genome.

The surge in information technology that has recently transformed the field of biology provides an opportunity for large-scale analysis and comparisons of genomes through computational methods. Thus, taking advantage of projects like the 1000 Genomes Project, Elena Bosch (IBE, CSIC-UPF) and her team of scientists have been able to study a total of 3,275 genes linked to diseases. It appears that these genes are more conserved in evolution, more relevant in the protein-protein interaction network, and are expressed in a greater quantity and in more tissues than genes not associated with disease.

"The features observed suggest that these genes play such a significant role that many of the variants they harbour may lead to an out-of-equilibrium organism resulting in disease", says Bosch, leader of the Evolutionary Population Genetics Laboratory (IBE, CSIC- UPF).

The researchers have also explored the differences that exist between genes linked only to Mendelian diseases, genes linked only to complex diseases and genes related to both types of pathologies. Mendelian diseases are those whose inheritance depends on a mutation in a single gene, such as cystic fibrosis or haemophilia; while complex diseases depend on the combination of several genetic and environmental factors and are more frequent in the population, such as obesity or cancer. "An increasing amount of evidence, including the present study, proves a role for genes linked to Mendelian diseases in the aetiology of complex diseases", says Nino Spataro, first author of the study. "After compiling 887 Mendelian-related genes, we observed that more than 23% of genes are linked to a Mendelian disorder are also associated with at least one complex disease".

The results of the comparison also demonstrate that genes linked to both types of diseases have a greater weight in susceptibility to them. In fact, scientists have seen a degree of biological relevance within the genome: genes that are essential for life and are not linked to any disease represent an extremely important subgroup of genes, disease-linked genes play an intermediate functional role, while non-essential genes that do not appear altered in any disease seem to play a relatively minor role in the organism.

"Improving our understanding of genetic mutations and risk factors that lead to disease provides us with new tools to understand the evolutionary and molecular basis of the disease," concludes Bosch.

 

Reference work: Nino Spataro, Juan Antonio Rodríguez, Arcadi Navarro, Elena Bosch. Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. Human Molecular Genetics. doi: 10.1093/hmg/ddw405

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Fri, 03 Feb 2017 11:13:23 +0000 http://www.bioinformaticsbarcelona.eu/news//news/39/key-genes-for-disease http://www.bioinformaticsbarcelona.eu/news/39 0
Researchers from UdL and IRBLleida build a web tool for the assisted diagnosis of rare diseases

Researchers from Universitat de Lleida (UdL) and Institut de Recerca Biomèdica de Lleida Fundació Dr. Pifarré (IRBLleida) developed the prototype for a free web tool that assists the diagnosis of more than 4.000 rare diseases, such as Beta thalassemia; Turner syndrome, or Canavan's disease, among others.

Rare Disease Discovery was built using publicly available datasets that associate rare diseases to their known symptoms. The tool uses the list of symptoms from the patient to provide the medical professionals with a list of rare diseases that can be associated to that patient, ranked from the most to the least likely disease.

The tool was benchmarked retrospectively in a group of 187 patients that had a confirmed rare disease diagnostic, showing a precision of around 80%, as described in the paper that was recently published in Peer J. Further benchmarking with larger and more diverse sets of patients is the logical next step to confirm the utility of the tool.

Most known rare diseases have genetic origins. They are hard to diagnose by family doctors due to their low frequency and a final diagnosis almost always requires genetic testing. Because of this it is important to provide family doctors with tools that assist in the initial diagnosis of those rare diseases. Developing such a tool was the goal of researchers from the Departments of Ciències Mèdiques Bàsiques i Informàtica i Enginyeria Industrial from UdL and IRBLleida. This free web prototype can be accessed at http://disease-discovery.udl.cat/

The tool was developed by Rui Alves, Joaquim Cruz, Ester Vilaprinyó i Albert Sorribas (Department of Ciències Mèdiques Bàsiques, UdL and IRBLleida), Jorge Comas (UdL-Institut de Tecnologia Química i Biològica António Xavier, Portugal), Marc Piñol (Department of Informàtica i Enginyeria Industrial, UdL), Francesc Solsona, Jordi Vilaplana i Ivan Teixidó (Department of Informàtica i Enginyeria Industrial, UdL and INSPIRES).

 

Reference article: Alves et al. (2016), Computer-assisted initial diagnosis of rare diseases. Peer J 4:e2211; DOI10.7717/peerj.2211

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Thu, 26 Jan 2017 14:02:38 +0000 http://www.bioinformaticsbarcelona.eu/news//news/37/researchers-from-udl-and-irblleida-build-a-web-tool-for-the-assisted-diagnosis-of-rare-diseases http://www.bioinformaticsbarcelona.eu/news/37 0
Enrolment opened for the Graduate Diploma in Big Data Processing for Life Sciences

Enrolment is open for the Graduate Diploma in Big Data Processing for Life Sciences offered by the Universitat Autònoma de Barcelona. This new programme will begin on 17 February and is offered in collaboration with several institutions, such as Fundació i2cat, Hospital Sant Joan de Déu, IDIAP Jordi Gol, Consorci Hospitalari Parc Taulí and the Centre for Genomic Regulation (CRG).

The diploma is promoted and coordinated by the Bioinformatics Barcelona (BIB) association. It offers training in the processing and management of great volumes of data in the health and agro-food fields, and the possibility of going on to a professional career as data scientist, data analyst, designer of data exploitation systems and big-data architect within the life sciences.

The programme, which lasts 6 months and has 25 available places, is addressed to graduates in the areas of Technology (computer engineering and similar fields), Health Sciences (medicine, nursing, or physiotherapy), and Science and Bioscience (biology, bioinformatics and other similar fields).

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Tue, 24 Jan 2017 09:31:42 +0000 http://www.bioinformaticsbarcelona.eu/news//news/35/enrolment-opened-for-the-graduate-diploma-in-big-data-processing-for-life-sciences http://www.bioinformaticsbarcelona.eu/news/35 0
Sequentia Biotech launches AIR, a cloud platform revolutionizing transcriptomics

Sequentia Biotech launches a cloud computing platform called A.I.R. (Artificial Intelligence RNAseq), the first predictive bioinformatics tool that automatically analyzes mass transcriptomic data (ie data linked to the RNA) from the genome of any species, generated by new generation sequencing technologies (Next Generation Sequencing, NGS), providing a complete report in less than 24 hours.

Transcriptomics studies the transcriptome, the set of ribonucleic acid molecules (RNA) that exist in a cell, tissue or organ, which play a key role in the regulation of gene expression and other important processes in cell biology. Transcriptomes are highly variable because they provide information on the whole set of genes that are being expressed under certain conditions at a given time and differ considerably from one cell to another.

The development of new transcriptome sequencing technologies, such as RNA-Seq, has allowed us to advance the knowledge of the dynamics of gene expression and its influence on the development of many biological processes. Transcriptomes of cancer cells, for example, can help to understand carcinogenesis and stem cell processes, as well as cell development and differentiation.

A.I.R.'s innovation lies in the fact that it is the first RNA-Seq data analysis platform in the world capable of solving three important obstacles in the field of genomics: computing issues (specifically data storage, automation of results and duration of analysis); scientific issues generated by new Generation Sequencing technologies (interpretation and integration of data, in addition to offering new bioinformatics and statistical functions); and social issues (the lack of simple, easy-to use tools available to researchers, who are not highly proficient with bioinformatics).

The new era of transcriptomics

By launching A.I.R., Sequentia Biotech is enabling the scientific community with the possibility of analyzing and comparing RNA samples automatically, as well as interpreting the resulting data, all within the same package and more diligently than other existing methods. In addition, A.I.R. is not limited to model organisms; it works with any sequenced species, currently using a database of 45.000 genomes. The platform uses the latest algorithms and bioinformatics methods published, and they are updated accordingly. It is also scalable, that is, an unlimited number of users can connect without compromising the quality and speed of the service, and users can upload data from their own G-drive without having to connect to the cloud.

"A.I.R. is the first disruptive SaaS (Software as a Service) solution because, in addition to using robust scientific methods, it is a fast and user-friendly software. It only requires three steps and results can be obtained in just 2 hours, in fact, depending on the type and number of samples, the time of analysis can be reduced to only 30 minutes. The cost of analysis with A.I.R. is also 50 times lower than other comparable methods (in terms of the quality offered). Furthermore, the system is automated and only requires users to upload their data and define their species reference genome, no specialized training is required. Any researcher who is not a bioinformatics expert can use the system", further explains Walter Sanseverino, co-founder and CEO of Sequentia Biotech.

Sequentia has procured funding from SME Instrument Phase,1 -as part of the Horizon 2020 program- under the category 'Open Disruptive Innovation Scheme' for the A.I.R project. This 50,000 € grant is intended for small and medium-sized European companies that invest in innovative projects with great economic and social impact.

Sequentia is formally introducing this revolutionary platform to the scientific community at PAG (Plant and Animal Genome Conference) held from 14 to 18 January in San Diego, California (USA), the world's largest and most important agrigenomics meeting, bringing together more than 3,000 outstanding scientists and researchers from different areas of plant molecular biology and animal genetics every year. 

More info about AIR: http://www.transcriptomics.cloud

 

About Sequentia

Sequentia Biotech (www.sequentiabiotech.com) was founded in 2013 by Walter Sanseverino (CEO) and Riccardo Aiese Cigliano (CSO), two young researchers with a real passion for genetics and omics sciences, as a spin-off of the Centre for Research in Agricultural Genomics (CRAG), a consortium composed by CSIC, IRTA, UAB and the UB. The objective of Sequentia Biotech is to create proprietary know-how to increase the access of the scientific community to the information produced by new generation sequencing technologies (Next Generation Sequencing, NGS) efficiently and affordably.

The company based in the Parc Cientific de Barcelona from UB and in the Parc de Recerca from UAB, focuses its work on the design and development of new bioinformatic tools for the analysis and integration of genomic and post-genomic data that expedite basic and applied research. Currently, and just three years since its inception, Sequentia has achieved a large highly diversified portfolio of clients and partners, consisting of over 30 public and private research centers, companies and hospitals. The company is taking part in more than 160 R & D public and private projects; and it has two open source biodata banks.

Cofounders Walter Sanseverino and Riccardo Aiese have published more than 40 scientific articles in high impact journals such as Nature Genetics, Scientific Report or DNA Research. 

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Mon, 16 Jan 2017 11:18:18 +0000 http://www.bioinformaticsbarcelona.eu/news//news/33/sequentia-biotech-launches-air-a-cloud-platform-revolutionizing-transcriptomics http://www.bioinformaticsbarcelona.eu/news/33 0
ViCOROB (Girona) wins a competition for automatically detecting lesions of multiple sclerosis

Researchers of the Computer Vision and Robotics Institute (ViCOROB) of the University of Girona (UdG) obtained the best results in the international competition entitled "MS segmentation challenge using a data management and processing infrastructure". The competition consisted in the development of automated tools to aid in the detection and segmentation of multiple sclerosis lesions on magnetic resonance imaging. The event took place in Athens, Greece, in the framework of the 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016).

The purpose of the two proposals submitted in the challenge was to obtain software tools applicable to clinical practice in both specialised units in multiple sclerosis and generic radiological centres. The tools automatically analyse the images taken with MRI to identify the lesions which are characteristic of the disease, to determine the degree of cerebral atrophy of the patients, and also to facilitate the measurement and the assessment of changes over time. In the future, this technology will be used in an objective and automatic monitoring of the effects of the different treatments in multiple sclerosis patients.

The database of images that was used in the competition contained data from 38 patients from four different centres and scanners. Each patient's injuries were manually annotated by a group of seven experts. During the competition the objective was to assess both the detection of lesions (the overall number of detected lesions per patient) and the segmentation of lesions (the degree of precision that each lesion is delimited). The tools presented, which provided the best results in both detection and segmentation of lesions, are the result of research carried out in the projects BiomarkEM.cat and NICOLE, funded by Fundació La Marató de TV3 and the Spanish Ministry of Economy and Competitiveness, respectively.

The ViCOROB team was formed by researchers Sergi Valverde, Eloy Roura, Mariano Cabezas, Sandra González-Villà, Xavier Lladó, Arnau Oliver, Joaquim Salvi and Jordi Freixenet, in collaboration with radiologists and neurologists from the University Hospital of Girona Dr. Josep Trueta, the Hospital Parc Martí and Julià (Salt), the Multiple Sclerosis Center of Catalonia (CEMCAT), the Vall d'Hebron University Hospital, the Institute of Biomedical Research of Girona (IdIBGi) and the Vall d'Hebron Research Institute (VHIR).

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Mon, 09 Jan 2017 11:13:46 +0000 http://www.bioinformaticsbarcelona.eu/news//news/31/vicorob-girona-wins-a-competition-for-automatically-detecting-lesions-of-multiple-sclerosis http://www.bioinformaticsbarcelona.eu/news/31 0