Co-Investigators – Portabolomics https://portabolomics.ico2s.org Synthetic biology Wed, 08 Feb 2023 13:09:41 +0000 en-GB hourly 1 https://wordpress.org/?v=4.4.2 https://portabolomics.ico2s.org/wp-content/uploads/2016/11/cropped-favicon-32x32.png Co-Investigators – Portabolomics https://portabolomics.ico2s.org 32 32 Dr Paolo Zuliani https://portabolomics.ico2s.org/dr-paolo-zuliani/ Fri, 28 Oct 2016 09:38:20 +0000 http://portabolomics.ico2s.org/?p=510 Dr. Paolo Zuliani is a Lecturer in the School of Computing Science at Newcastle University, UK. He received his Laurea degree in computer science from Universita’ degli Studi di Milano, Italy, and his DPhil in computer science from the University of Oxford, UK.

Dr. Zuliani’s expertise lies largely in formal methods for reasoning about computing systems with an emphasis on probabilistic and quantum systems.


Dr Paolo ZulianiRead more]]>
Dr. Paolo Zuliani is a Lecturer in the School of Computing Science at Newcastle University, UK. He received his Laurea degree in computer science from Universita’ degli Studi di Milano, Italy, and his DPhil in computer science from the University of Oxford, UK.

Dr. Zuliani’s expertise lies largely in formal methods for reasoning about computing systems with an emphasis on probabilistic and quantum systems. He is in particular interested in the verification of biological systems, cyber-physical systems and quantum programs.

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Professor Anil Wipat https://portabolomics.ico2s.org/professor-anil-wipat/ Fri, 28 Oct 2016 09:37:12 +0000 http://portabolomics.ico2s.org/?p=505 Anil Wipat is Professor of Bioinformatics in the School of Computing Science, co-directs the Interdisciplinary Computing and Complex Biology Systems Group (ICOS – http://ico2s.org/), director of the Centre for Health and Bioinformatics (CHaBi) and co-founder, and associate-director, of the Newcastle Centre for Synthetic Biology and Bioeconomy (CSBB).


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Anil Wipat is Professor of Bioinformatics in the School of Computing Science, co-directs the Interdisciplinary Computing and Complex Biology Systems Group (ICOS – http://ico2s.org/), director of the Centre for Health and Bioinformatics (CHaBi) and co-founder, and associate-director, of the Newcastle Centre for Synthetic Biology and Bioeconomy (CSBB).

Anil trained first as a molecular microbiologist (with a special interest in Gram positive bacteria) and subsequently as a computer scientist. Recent work has focused on both bioinformatics and design in Synthetic Biology. He now carries out research at the interface of all of these subjects including an significant number of laboratory-based projects.

Anil is also very active in the development of standards for data exchange in Synthetic Biology and is the Chair of the International SBOL steering committee. He has over 100 refereed publications many of which are interdisciplinary in nature.

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Dr Phillip Lord https://portabolomics.ico2s.org/dr-phillip-lord/ Fri, 28 Oct 2016 09:33:24 +0000 http://portabolomics.ico2s.org/?p=496 Dr. Phillip Lord is a computing scientist with 20 years of world-leading expertise in bio-medical data handling. Originally a geneticist, he moved to informatics after this PhD and has worked on data integration for patient dysmorphology, comparative genomics and neurosciences.

He has contributed to many data and reporting standards.


Dr Phillip LordRead more]]>
Dr. Phillip Lord is a computing scientist with 20 years of world-leading expertise in bio-medical data handling. Originally a geneticist, he moved to informatics after this PhD and has worked on data integration for patient dysmorphology, comparative genomics and neurosciences.

He has contributed to many data and reporting standards. He is a world-expert on the use of ontologies, pioneered the use of semantic similarity metrics in biology, and is now exploring novel methodologies for knowledge formalisation. He will use this expertise, as part of the Portabolomics project to help describe and formalise the data generating by the project and pre-existing, to support the analysis, use and downstream dissemination. In short, he will help the project move from data and toward knowledge.

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Dr Yulia Yuzenkova https://portabolomics.ico2s.org/dr-yulia-yuzenkova/ Fri, 28 Oct 2016 09:26:06 +0000 http://portabolomics.ico2s.org/?p=481 Yulia is a Royal Society University Research Fellow; before moving to Britain she did her PhD in Academy of Science (Russia), and postdoctoral research at Rutgers University (USA).

Her group’s main research topic is the regulation of gene expression in various bacteria, including major human pathogens and cyanobacteria.


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Yulia is a Royal Society University Research Fellow; before moving to Britain she did her PhD in Academy of Science (Russia), and postdoctoral research at Rutgers University (USA).

Her group’s main research topic is the regulation of gene expression in various bacteria, including major human pathogens and cyanobacteria. Yulia’s group is working on basic mechanisms of transcription, the first stage of gene expression, and modes of action of antibiotics targeting this stage.

Photosynthetic cyanobacteria developed unique mechanisms to control gene expression in adaptation to day/night changes. The central control mechanism, which synchronizes gene expression with daily light cycles, is circadian clock. The clock sends the signals to the gene expression machinery to activate or repress target genes using network of regulators.

In the Portabolomics project, Yulia’s group is investigating circadian regulators, which switch genes on/off at the level of transcription. Ultimately, they aim to design elements of circadian control to use as tools for Synthetic Biology applications in industrially important microorganisms.

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Professor Nikolay Zenkin https://portabolomics.ico2s.org/professor-nikolay-zenkin/ Fri, 28 Oct 2016 09:25:44 +0000 http://portabolomics.ico2s.org/?p=483 Prof Nikolay Zenkin graduated from Moscow State University, Department of Molecular Biology of the Biological Faculty in 2001, and obtained his PhD from the Institute of Molecular Genetics of Russian Academy of Sciences in 2004. Part of his PhD was done in the laboratory of Konstantin Severinov in Waksman Institute of Rutgers University in New Jersey,


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Prof Nikolay Zenkin graduated from Moscow State University, Department of Molecular Biology of the Biological Faculty in 2001, and obtained his PhD from the Institute of Molecular Genetics of Russian Academy of Sciences in 2004. Part of his PhD was done in the laboratory of Konstantin Severinov in Waksman Institute of Rutgers University in New Jersey, where he returned to as a post-doc. In 2007 Prof Zenkin started a Lectureship in the Institute for Cell and Molecular Biosciences in Newcastle University and was promoted to a full Professorship in 2013.

His laboratory investigates molecular mechanisms underlining transcription and translation, as well as processes mechanistically connected to them. They have uncovered plenty of mechanistic details for both steps of gene expression and developed unique in vitro experimental systems. Recently, the lab also discovered new types of RNA polymerases that may represent minimal requirements for RNA synthesis by cellular enzymes and will be used for construction of minimal RNA polymerases.

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Dr Richard Daniel https://portabolomics.ico2s.org/dr-richard-daniel/ Fri, 28 Oct 2016 09:23:18 +0000 http://portabolomics.ico2s.org/?p=476 The Daniel group focuses primarily on basic aspects of bacterial cell biology. The group has investigated cell division and growth, using a combination of genetic analysis combined with sub-cellular localisation techniques, with the objective of defining the essential components of both the cell division and cell elongation complexes and shed light on how they are positioned in the cell to fulfill their function.


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The Daniel group focuses primarily on basic aspects of bacterial cell biology. The group has investigated cell division and growth, using a combination of genetic analysis combined with sub-cellular localisation techniques, with the objective of defining the essential components of both the cell division and cell elongation complexes and shed light on how they are positioned in the cell to fulfill their function. Other areas of research look at the properties of the cell wall and membrane to determine how they can act both structurally to maintain the cells shape and yet permit the selective passage of a large range of molecules.

The objective of the Daniel group is, thought a combination of understanding both the mechanics of cellular processes and the physical properties of the cell envelope, to develop novel ways to redirect the biochemical capability of a bacterial cell toward specific biotechnological applications.

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Dr Heath Murray https://portabolomics.ico2s.org/dr-heath-murray/ Fri, 28 Oct 2016 09:22:28 +0000 http://portabolomics.ico2s.org/?p=475 The Murray Lab studies bacterial DNA replication initiation in the model organism Bacillus subtilis. Using a combination of genetics, cell biology, molecular biology, and biochemistry, they are investigating the structure of the bacterial chromosome origin (oriC) and the activity of the master DNA replication initiation protein DnaA.


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The Murray Lab studies bacterial DNA replication initiation in the model organism Bacillus subtilis. Using a combination of genetics, cell biology, molecular biology, and biochemistry, they are investigating the structure of the bacterial chromosome origin (oriC) and the activity of the master DNA replication initiation protein DnaA. One of the tools the group has developed is an artificial chromosome origin that allows them to bypass the normally essential endogenous factors. They are keen to explore the utility of more sophisticated synthetic replication systems, both for fundamental understanding of DNA replication and for exploitation in biotechnology.

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Dr Simon Woods https://portabolomics.ico2s.org/dr-simon-woods/ Fri, 28 Oct 2016 09:20:08 +0000 http://portabolomics.ico2s.org/?p=471 Simon Woods is Senior Lecturer and Deputy Director of the Policy Ethics and Life Sciences Research Institute (PEALS www.ncl.ac.uk ) at Newcastle University (an interdisciplinary bioethics research centre). Simon has a longstanding interest in developments within the life sciences, medical ethics and bioethics more broadly. His research explores the social and ethical aspects of new and emerging biotechnologies.


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Simon Woods is Senior Lecturer and Deputy Director of the Policy Ethics and Life Sciences Research Institute (PEALS www.ncl.ac.uk ) at Newcastle University (an interdisciplinary bioethics research centre). Simon has a longstanding interest in developments within the life sciences, medical ethics and bioethics more broadly. His research explores the social and ethical aspects of new and emerging biotechnologies.

Simon has been work-package leader, or ethics advisor to ten EU projects and several with a focus on rare disease genomics in which issues related to the care and treatment of children have been central. Simon holds bachelor and doctoral degrees in philosophy and over the past 13 years he has pursued a career of teaching and research within bioethics.

Simon has considerable expertise in the ethics and regulation of bioscience research; he has been a member and vice-chair of NHS research ethics committees and is a member of the NHS Health Research Authority’s National Ethics Advisors’ Panel.

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Dr Jaume Bacardit https://portabolomics.ico2s.org/dr-jaume-bacardit/ Tue, 25 Oct 2016 14:39:33 +0000 http://portabolomics.ico2s.org/?p=445 Jaume’s research interests include the development of machine learning methods for large-scale problems and their application to challenging problems, mostly involving biological data. He has published papers on algorithmic advances to improve the scalability of machine learning methods, tackling challenges such as large dimensionality spaces, large sets of records, or the use of data-intensive computing technologies such as GPUs and MapReduce.


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Jaume’s research interests include the development of machine learning methods for large-scale problems and their application to challenging problems, mostly involving biological data. He has published papers on algorithmic advances to improve the scalability of machine learning methods, tackling challenges such as large dimensionality spaces, large sets of records, or the use of data-intensive computing technologies such as GPUs and MapReduce. The main focus of his applied research on biological data is knowledge discovery: analysing the structure of the machine learning models to discover useful knowledge, such as (panels of) biomarkers or functional networks and in this way bring the data mining process closer to the domain experts. Jaume applied his methods to a variety of biological/biomedical domains: the process of germination in plants, cancer in humans or osteoarthritis both in humans and model organisms and multiple data-generating biotechnologies: transcriptomics, proteomics, lipidomics, etc.

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