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DTSTART;TZID=Europe/Madrid:20150706T150000
DTEND;TZID=Europe/Madrid:20150706T160000
DTSTAMP:20260509T110922
CREATED:20150701T122222Z
LAST-MODIFIED:20150701T122253Z
UID:17897-1436194800-1436198400@ibecbarcelona.eu
SUMMARY:IBEC Seminar: Prof. Saman K. Halgamuge
DESCRIPTION:Big Data Analytics in Metagenomics\nSaman K. Halgamuge\, Melbourne School of Engineering\, University of Melbourne\, Australia\nIn collaboration with researchers in Academia Sinica and Metabolomics Australia/Department of Botany at Melbourne\, we have been working in two areas of Bioinformatics: Metabolomics focusing on microbes and Metagenomics focusing on plants. Profiling large sets of data resulted from technological advances in whole genome sequencing and MALDI Imaging type technologies that can reveal vital information about the environment and plants\, which is our major or primary source of food on Earth. Recently we have demonstrated considerable success in using unsupervised clustering techniques to analyse genetic and metabolomic data. This includes analysis of viral quasi species\, metabolomics and microbial metagenomes.  \nSome microbes in the environment appear to look very similar and found “living together” in communities in non-separable ways\, making them harder to culture in a lab. To make matters worst\, considering our belief\, if it is correct at all\, that we know only about up to 2% of the microbes around us. When we know only so little about the data labels\, in this case\, about the identity of the species. It is even more challenging to recognise patterns associated with the genomes of the quasispecies (a set of genetically related but non-identical viral mutant types\, which can also be referred to as strains\,) that are able to co-exist within the host. Uncovering information about quasi-species populations of microbes significantly benefits the study of disease progression\, antiviral drug design\, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes.
URL:https://ibecbarcelona.eu/ca/event/ibec-seminar-prof-saman-k-halgamuge/
CATEGORIES:IBEC Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150706T150000
DTEND;TZID=Europe/Madrid:20150706T160000
DTSTAMP:20260509T110922
CREATED:20150701T122222Z
LAST-MODIFIED:20150701T122222Z
UID:95860-1436194800-1436198400@ibecbarcelona.eu
SUMMARY:IBEC Seminar: Prof. Saman K. Halgamuge
DESCRIPTION:Big Data Analytics in Metagenomics\nSaman K. Halgamuge\, Melbourne School of Engineering\, University of Melbourne\, Australia\nIn collaboration with researchers in Academia Sinica and Metabolomics Australia/Department of Botany at Melbourne\, we have been working in two areas of Bioinformatics: Metabolomics focusing on microbes and Metagenomics focusing on plants. Profiling large sets of data resulted from technological advances in whole genome sequencing and MALDI Imaging type technologies that can reveal vital information about the environment and plants\, which is our major or primary source of food on Earth. Recently we have demonstrated considerable success in using unsupervised clustering techniques to analyse genetic and metabolomic data. This includes analysis of viral quasi species\, metabolomics and microbial metagenomes.  \nSome microbes in the environment appear to look very similar and found “living together” in communities in non-separable ways\, making them harder to culture in a lab. To make matters worst\, considering our belief\, if it is correct at all\, that we know only about up to 2% of the microbes around us. When we know only so little about the data labels\, in this case\, about the identity of the species. It is even more challenging to recognise patterns associated with the genomes of the quasispecies (a set of genetically related but non-identical viral mutant types\, which can also be referred to as strains\,) that are able to co-exist within the host. Uncovering information about quasi-species populations of microbes significantly benefits the study of disease progression\, antiviral drug design\, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes.
URL:https://ibecbarcelona.eu/ca/event/ibec-seminar-prof-saman-k-halgamuge-2/
CATEGORIES:IBEC Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150710T100000
DTEND;TZID=Europe/Madrid:20150710T110000
DTSTAMP:20260509T110922
CREATED:20150527T073448Z
LAST-MODIFIED:20150527T073448Z
UID:16868-1436522400-1436526000@ibecbarcelona.eu
SUMMARY:PhD Discussions Session: Verónica Hortigüela & Anna Crespo
DESCRIPTION:Developing a platform for receptor clustering studies\nVerónica Hortigüela\, Biomimetic systems for cell engineering group\nReceptors are signaling units that usually require interactions and associations with other molecules in complexes to trigger a signaling pathway. This process is known as receptor clustering and comes typically along with a simultaneous ligand clustering underneath the cell membrane. We have developed a strategy to precisely control the ligand distribution on a substrate at the nanoscale to study in detail receptor clustering processes. Herein we present a tunable platform based on self-assembled di-block copolymers that tend to segregate into nanostructures. Di-block copolymers are confined to a thin film providing a template for ligand patterning.  \n  \nRibonucleotide Reductase anaerobic enzymes are essential for biofilm formation of Pseudomonas aeruginosa\nAnna Crespo\, Bacterial infections: antimicrobial therapies group\nMost chronic infections in humans are caused by communities of microorganisms living in organized structures\, known as biofilms. Biofilm-related infections\, such as pneumonia (in patients suffering for cystic fibrosis or chronic obstructive pulmonary disease –COPD-) and catheter-associated infections\, affect millions of people in the developed world. \nCell clusters in biofilms are characterized by presenting\, in its extracellular polymeric matrix\, gradients of oxygen\, nutrients and metabolic waste products. The so-formed chemical heterogeneity (e.g.\, the presence of anoxic areas) leads to the appearance of different metabolic activities. \nPseudomonas aeruginosa has been used as a model bacterium for biofilm research; it causes biofilm-related chronic infections and presents high metabolic versatility\, together with an extreme antibiotic resistance. \nIn this work we have studied P. aeruginosa\, focusing in an essential enzyme for its growth\, Ribonucleotide Reductase (RNR). Ribonucleotide Reductases catalyse the reduction of ribonucleotides (NTPs) to deoxyribonucleotides (dNTPs)\, thereby providing the building blocks for DNA synthesis. There are three different RNR classes\, named class I\, class II and class III\, which are\, respectively\, oxygen-dependent\, oxygen-independent and oxygen-sensitive. The last two ones\, essential for anaerobic growth in Pseudomonas aeruginosa\, have been proved to be necessary for biofilm formation\, and therefore putative targets for new therapies against P. aeruginosa chronic infections.
URL:https://ibecbarcelona.eu/ca/event/phd-discussions-session-veronica-hortiguela-anna-crespo/
CATEGORIES:PhD Discussions Session
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150710T100000
DTEND;TZID=Europe/Madrid:20150710T110000
DTSTAMP:20260509T110922
CREATED:20150527T073448Z
LAST-MODIFIED:20150527T073448Z
UID:95855-1436522400-1436526000@ibecbarcelona.eu
SUMMARY:PhD Discussions Session: Verónica Hortigüela & Anna Crespo
DESCRIPTION:Developing a platform for receptor clustering studies\nVerónica Hortigüela\, Biomimetic systems for cell engineering group\nReceptors are signaling units that usually require interactions and associations with other molecules in complexes to trigger a signaling pathway. This process is known as receptor clustering and comes typically along with a simultaneous ligand clustering underneath the cell membrane. We have developed a strategy to precisely control the ligand distribution on a substrate at the nanoscale to study in detail receptor clustering processes. Herein we present a tunable platform based on self-assembled di-block copolymers that tend to segregate into nanostructures. Di-block copolymers are confined to a thin film providing a template for ligand patterning.  \n  \nRibonucleotide Reductase anaerobic enzymes are essential for biofilm formation of Pseudomonas aeruginosa\nAnna Crespo\, Bacterial infections: antimicrobial therapies group\nMost chronic infections in humans are caused by communities of microorganisms living in organized structures\, known as biofilms. Biofilm-related infections\, such as pneumonia (in patients suffering for cystic fibrosis or chronic obstructive pulmonary disease –COPD-) and catheter-associated infections\, affect millions of people in the developed world. \nCell clusters in biofilms are characterized by presenting\, in its extracellular polymeric matrix\, gradients of oxygen\, nutrients and metabolic waste products. The so-formed chemical heterogeneity (e.g.\, the presence of anoxic areas) leads to the appearance of different metabolic activities. \nPseudomonas aeruginosa has been used as a model bacterium for biofilm research; it causes biofilm-related chronic infections and presents high metabolic versatility\, together with an extreme antibiotic resistance. \nIn this work we have studied P. aeruginosa\, focusing in an essential enzyme for its growth\, Ribonucleotide Reductase (RNR). Ribonucleotide Reductases catalyse the reduction of ribonucleotides (NTPs) to deoxyribonucleotides (dNTPs)\, thereby providing the building blocks for DNA synthesis. There are three different RNR classes\, named class I\, class II and class III\, which are\, respectively\, oxygen-dependent\, oxygen-independent and oxygen-sensitive. The last two ones\, essential for anaerobic growth in Pseudomonas aeruginosa\, have been proved to be necessary for biofilm formation\, and therefore putative targets for new therapies against P. aeruginosa chronic infections.
URL:https://ibecbarcelona.eu/ca/event/phd-discussions-session-veronica-hortiguela-anna-crespo-2/
CATEGORIES:PhD Discussions Session
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150717T150000
DTEND;TZID=Europe/Madrid:20150717T170000
DTSTAMP:20260509T110922
CREATED:20150713T053848Z
LAST-MODIFIED:20150714T085909Z
UID:18094-1437145200-1437152400@ibecbarcelona.eu
SUMMARY:PhD Thesis Defense: Carlos Ruiz
DESCRIPTION:“A computational study of intervertebral disc degeneration in relation to changes in regional tissue composition and disc nutrition”\n \nCarlos Ruiz Wills\, Biomechanics & Mechanobiology group\nCarles will be defending his PhD thesis on Friday 17th July at 15:00 in the Aula Capella\, Facultad de Ingeniería Industrial (ETSEIB)\, Av. Diagonal 647. \nEverybody is welcome to attend. \n—\nIf you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar\, please contact vleigh@ibecbarcelona.eu
URL:https://ibecbarcelona.eu/ca/event/phd-thesis-defense-carlos-ruiz/
LOCATION:Aula Capella\, Facultad de Ingeniería Industrial (ETSEIB)\, Av. Diagonal 647\, Barcelona\, Spain
CATEGORIES:PhD Thesis Defence
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150717T150000
DTEND;TZID=Europe/Madrid:20150717T170000
DTSTAMP:20260509T110922
CREATED:20150713T053848Z
LAST-MODIFIED:20150713T053848Z
UID:95861-1437145200-1437152400@ibecbarcelona.eu
SUMMARY:PhD Thesis Defense: Carlos Ruiz
DESCRIPTION:“A computational study of intervertebral disc degeneration in relation to changes in regional tissue composition and disc nutrition”\n \nCarlos Ruiz Wills\, Biomechanics & Mechanobiology group\nCarles will be defending his PhD thesis on Friday 17th July at 15:00 in the Aula Capella\, Facultad de Ingeniería Industrial (ETSEIB)\, Av. Diagonal 647. \nEverybody is welcome to attend. \n—\nIf you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar\, please contact vleigh@ibecbarcelona.eu
URL:https://ibecbarcelona.eu/ca/event/phd-thesis-defense-carlos-ruiz-2/
LOCATION:Aula Capella\, Facultad de Ingeniería Industrial (ETSEIB)\, Av. Diagonal 647\, Barcelona\, Spain
CATEGORIES:PhD Thesis Defence
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150721T110000
DTEND;TZID=Europe/Madrid:20150721T130000
DTSTAMP:20260509T110922
CREATED:20150714T085454Z
LAST-MODIFIED:20150714T085454Z
UID:95863-1437476400-1437483600@ibecbarcelona.eu
SUMMARY:PhD Thesis Defense: Erola Pairo
DESCRIPTION:“Detection of transcription factor binding sites by multivariate signal processing”\n \nErola Pairo\, Signal and information processing for sensing systems  group\nErola will be defending her PhD thesis on Tuesday 21st July at 11:00 in the Eduard Fontsere room at the Faculty of Physics. \nEverybody is welcome to attend. \n—\nIf you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar\, please contact vleigh@ibecbarcelona.eu
URL:https://ibecbarcelona.eu/ca/event/phd-thesis-defense-erola-pairo-2/
LOCATION:Sala de Graus Eduard Fontseré\, Martí i Franquès\, 1-11\, Barcelona\, 08028
CATEGORIES:PhD Thesis Defence
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150721T110000
DTEND;TZID=Europe/Madrid:20150721T130000
DTSTAMP:20260509T110922
CREATED:20150714T085454Z
LAST-MODIFIED:20150714T085823Z
UID:18116-1437476400-1437483600@ibecbarcelona.eu
SUMMARY:PhD Thesis Defense: Erola Pairo
DESCRIPTION:“Detection of transcription factor binding sites by multivariate signal processing”\n \nErola Pairo\, Signal and information processing for sensing systems  group\nErola will be defending her PhD thesis on Tuesday 21st July at 11:00 in the Eduard Fontsere room at the Faculty of Physics. \nEverybody is welcome to attend. \n—\nIf you’re an IBEC PhD student and would like to advertise your PhD defense on the IBEC calendar\, please contact vleigh@ibecbarcelona.eu
URL:https://ibecbarcelona.eu/ca/event/phd-thesis-defense-erola-pairo/
LOCATION:Sala de Graus Eduard Fontseré\, Martí i Franquès\, 1-11\, Barcelona\, 08028
CATEGORIES:PhD Thesis Defence
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150724T100000
DTEND;TZID=Europe/Madrid:20150724T110000
DTSTAMP:20260509T110922
CREATED:20150720T092247Z
LAST-MODIFIED:20150720T102616Z
UID:18148-1437732000-1437735600@ibecbarcelona.eu
SUMMARY:IBEC Seminar: Dr. François St. Pierre
DESCRIPTION:Imaging electrical activity in vivo with ultrafast protein sensors  \nDr. François St. Pierre\, Department of Neuroscience\, Baylor College of Medicine / \nDepartment of Electrical and Computer Engineering\, Rice University\nImaging of rapid brain electrical activity has been on the wish list of neurobiologists for many years and has received renewed attention with the launch of the BRAIN initiative by the White House in the U.S.A. In particular\, neuroscientists have long sought voltage sensors based on proteins to reveal brain activity in genetically defined neuronal circuits. I will present novel protein voltage sensors that leverage optimized parts and creative new designs to report neural activity with unprecedented temporal resolution in vitro\, in brain slices and in vivo. Importantly\, these synthetic sensors report neural activity at the millisecond timescale over which key information processing functions are thought to take place. I will show how these new optical tools enable us to follow neural information processing in the fly visual system with subcellular resolution. I will also present our recent success at monitoring spontaneous electrical activity in stem cell-derived cardiomyocytes.
URL:https://ibecbarcelona.eu/ca/event/ibec-seminar-dr-francois-st-pierre/
CATEGORIES:IBEC Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Madrid:20150724T100000
DTEND;TZID=Europe/Madrid:20150724T110000
DTSTAMP:20260509T110922
CREATED:20150720T092247Z
LAST-MODIFIED:20150720T092247Z
UID:95864-1437732000-1437735600@ibecbarcelona.eu
SUMMARY:IBEC Seminar: Dr. François St. Pierre
DESCRIPTION:Imaging electrical activity in vivo with ultrafast protein sensors  \nDr. François St. Pierre\, Department of Neuroscience\, Baylor College of Medicine / \nDepartment of Electrical and Computer Engineering\, Rice University\nImaging of rapid brain electrical activity has been on the wish list of neurobiologists for many years and has received renewed attention with the launch of the BRAIN initiative by the White House in the U.S.A. In particular\, neuroscientists have long sought voltage sensors based on proteins to reveal brain activity in genetically defined neuronal circuits. I will present novel protein voltage sensors that leverage optimized parts and creative new designs to report neural activity with unprecedented temporal resolution in vitro\, in brain slices and in vivo. Importantly\, these synthetic sensors report neural activity at the millisecond timescale over which key information processing functions are thought to take place. I will show how these new optical tools enable us to follow neural information processing in the fly visual system with subcellular resolution. I will also present our recent success at monitoring spontaneous electrical activity in stem cell-derived cardiomyocytes.
URL:https://ibecbarcelona.eu/ca/event/ibec-seminar-dr-francois-st-pierre-2/
CATEGORIES:IBEC Seminar
END:VEVENT
END:VCALENDAR