3,085 search results for “genome scale metabolic reconstruction” in the Public website
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Neandertal genome from Les Cottés site sequenced
On March 21 2018, a study was published in Nature, co-authored by Professor M. Soressi from the Faculty of Archaeology of Leiden University, announcing the sequencing of five new Neandertals, raising the number of high-coverage sequenced Neandertals from two to seven. A tooth lost by a Neandertal woman…
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Management of small-scale -African fisheries: The Case of Elephant Marsh in Malawi
How does the management of Elephant Marsh Fishery in Malawi relate to wider contexts of policies, theories and regions? And how can the current management system be adapted to achieve long-term sustainability of the fishery?
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Freedom of additional signals on genes: on the combination of DNA mechanics, genetics and translation speed
DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information.
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Snake genomes revealed for King Cobra and Burmese Python
Freek Vonk and Mike Richardson, with many collaborators, have published two snake genomes in two parallel articles in the prestigious journal PNAS. Their new findings provide insight into the co-evolutionary arms race between predator and prey.
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Management of Small-Scale Fisheries at the Elephant Marsh in Malawi
Wetlands provide many ecosystem goods and services which include fish production. The sustainability of small-scale fisheries (SSF) has received considerable attention in recent years because fish is one of the major sources of animal protein to a considerable fraction of the global population which…
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Hans Aerts
Science
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Gerring & Wouter Veenendaal, Population and Politics: The Impact of Scale
Political scientists John Gerring (University of Texas, Austin) and Wouter Veenendaal (Universiteit Leiden) evaluate the political implications stemming from the size of a political unit – on social cohesion, the number of representatives, overall representativeness, particularism ('pork'), citizen…
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Barbara Gravendeel
Science
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Solvent tolerance mechanisms in Pseudomonas putida
Bacterial biocatalysis constitutes a sustainable alternative for high-value chemicals production by enabling the utilization of renewable feedstocks.
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Responding to environmental cues: the adaptive qualities of chromatin compaction proteins
Promotor: M. Ubbink, Co-Promotor: R. T. Dame
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Computational optimisation of optical projection tomography for 3D image analysis
Optical projection tomography (OPT) is a tomographic 3D imaging technique used for specimens in the millimetre scale.
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Mapping of bacterial genomes to combat infectious diseases
Mapping of bacterial genomes to combat infectious diseases
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Topology of polymer chains under nanoscale confinement: insights into genome folding
This month, a paper was published in Nanoscale by scientists from Dr. Alireza Mashaghi group at the Systems Biomedicine and Pharmacology Division in collaboration with the group of Dr. Sander Tans from TU Delft/AMOLF. In this paper, the authors studied how nanoscale spatial confinement affects the fold…
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Reconstructing a Medieval house in Vlaardingen
Nine Archaeology students have built a reconstruction of an early medieval house in Vlaardingen. The house, built according to a houseplan discovered during excavations at Rotta, has already played an important role as the backdrop of the re-enactment of the battle of Vlaardingen of 1018.
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Nanofluidic tools for bioanalysis: the large advantages of the nano-scale
Promotor: Prof.dr. T. Hankemeier, Prof.dr. J.C.T. Eijkel (Twente University)
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Signalling pathways that control development and antibiotic production in streptomyces
Bacteria are highly complex and diverse organisms that have adapted to survive in ecological niches ranging from the most extreme to the most heterogeneous environments.
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1st Leiden Centre for Interdisciplinary Genome Research meeting
The 1st CIGR meeting was held on March 30, 2021, with talks by representatives of all participating groups.
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Network flow algorithms for discrete tomography
Promotor: R. Tijdeman, Co-promotor: H.J.J. te Riele
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Leiden researchers visualise the 'guardian of our genome’
The guardian of our genome, the protein MutS, scans the DNA for spelling errors and makes sure they are corrected. An essential process for our health. Researchers at Leiden University Medical Centre (LUMC) have discovered precisely how this protein works by making MutS visible with cryo-electron microscopy.…
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Ilse Kamerling
Faculteit Archeologie
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Ecology and genomics of Actinobacteria and their specialised metabolism
PhD defence
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What makes us ill?
Genes predict whether you have a propensity for an illness but environmental factors often have the last word: nutrition, air pollution, lifestyle, stress. The exposome as both culprit and chance. Large-scale research is being carried out into this at Leiden. Thomas Hankemeier, Professor of Analytical…
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CAM-PaC
The overall aim of CAM-PaC is to contribute to solving the socioeconomic and health challenges of PDAC by an integrative and systematic functional analysis of pancreatic cancer candidate genes. CAM-PaC will develop novel cellular and animal models, as well as novel strategies to analyse and integrate…
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Statistical Science
The research programme Statistical Science is concerned with the analysis and interpretation of masses of data, the quantification of uncertainty using probability models, and the development and benchmarking of algorithms and methods with these aims.
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management of chemicals and products in a circular economy at a global scale
How can we, together international experts, define future needs of R+D contributions for innovations in the field of risk-based management of chemicals and products in a global perspective using alternative testing strategies to minimize animal tests?
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Startup brings new genetic knowledge to companies
On 29 June the startup company Future Genomics Technologies will be launched. Its aim is to make DNA technology and research available for businesses faster. Future Genomics Technologies is a collaboration between DNA research laboratory BaseClear and Leiden University.
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Archaeologists reconstruct ancient Greek urge to build
An enormous number of monumental buildings, such as burial tombs, appeared in Mycenaean Greece after 1600 BC. Why did this urge to build come to an abrupt end 400 years later? Archaeologist Ann Brysbaert investigates the possible causes thanks to her ERC Consolidator Grant.
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Animal Sciences
We perform multidisciplinary research at molecular, cellular, and organismal levels of animal biology to increase fundamental understanding of health and disease.
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Terpenoids and terpenoid indole alkaloids in Catharanthus roseus cell suspension cultures
Promotor: Prof.dr. R. Verpoorte, Co-Promotores: N.R. Mustafa, A.E. Schulte
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Constraints on large-scale implementation of BioSolarCells, Early stage assessment of environmental value propositions
What performance criteria does a new technology have to fulfill in order to be added to the list of future energy options and what constraints exist in terms of broad market penetration?
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Miranda van Eck
Science
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Willem Meilink
Science
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Expertise
The CIGR brings together a diverse range of unique expertise in genome research rooted in biology, chemistry and physics. Members of the CIGR investigate genome folding and genome transactions. An important aspect is direct as well as long term relevance for medicine. The available expertise extends…
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Evolutionary traps – Balanced lethal systems
How do balanced lethal systems originate and persist in nature?
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Metabolomics and Analytics Centre
The ambition of the Metabolomics and Analytics Centre led by Thomas Hankemeier is to develop innovative analytical strategies for metabolomics-driven health monitoring and systems biology studies. Understanding the intricate balance between health, disease and adaptation to challenges relies on the…
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Shape Analysis for Phenotype Characterisation from High-throughput Imaging
We have studied shape with a particular focus on the zebrafish model system. The shape is an essential appearance of the phenotype of a biological specimen and it can be used to read out a current state or response or to study gene expression.
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From methanol to medicine – Sustainable microbial production of polyketide antibiotics
Can the pink-pigmented microbe Methylobacterium extorquens be genetically engineered to convert the sustainable raw material methanol into antibiotics?
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New tenure track: understanding and engineering microbial metabolism for health and sustainability
On 1 March, Lennart Schada von Borzyskowski will start on a tenure track position at the Institute of Biology Leiden (IBL). With a focus on the natural and synthetic biochemistry of environmental bacteria, he wants to apply their features to health and sustainability issues.
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Multi-omics studies of the control of growth and antibiotic production of Streptomyces
Actinobacteria are Gram-positive bacteria that have a complex multicellular life cycle and are well known for their ability to produce a wide range of bioactive natural products (NPs).
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Cryptic species discovery
Do understudied animals contain hidden species?
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Triceratops Bonebed Excavation
Since 2013, the National Natural History Museum of the Netherlands, Naturalis Biodiversity Center, is unearthing the largest bonebed of the horned dinosaur Triceratops discovered so far. In order to answer questions about sedimentology, taphonomy and palaeobiology, palaeontologists and geologists collaborated…
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Discrete tomography with two directions
Promotores: R. Tijdeman, K.J. Batenburg
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Final Report 'Assessing Legislation for Libya's Reconstruction'
The Van Vollenhoven Institute for Law, Governance and Development and Benghazi Centre for Law and Society Studies, Benghazi University have released their final report, in English and Arabic, on Assessing Legislation for Libya’s Reconstruction.
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Animal Sciences
We perform multidisciplinary research at molecular, cellular, and organismal levels of animal biology to increase fundamental understanding of health and disease.
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Understanding the uptake and internal distribution of metallic nanoparticles in Danio rerio larvae
The aim is to discover where differently shaped metal nanoparticles distributes in Danio rerio, linking the distribution with genomic responses and so come up with a Mode of Action.
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Focus Raqqa: reconstruction of a Syrian museum collection
In the civil war in Syria, the country's cultural heritage is also under threat. There have been further acts of vandalism in Palmyra and many of the city's museums have been looted. Leiden archaeologist Olivier Nieuwenhuijse's Focus Raqqa project aims to make a digital inventory of the plundered archaeology…
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Cultural evolutionary modeling of patterns in language change. Exercises in evolutionary linguistics
This thesis describes the use of the evolutionary approach in the study of language change, aiming to provide a better insight in the mechanisms that play a role in language change and to validate this approach in the field of language change.
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Plant Sciences
The mission of the Plant Science research programme is to contribute to the sustainable production of high quality crops, flowers and high-value bio-based products. This is realised by generating fundamental knowledge of basic biological processes related to development of plants and their interaction…
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Functions of autophagy in the filamentous fungus Aspergillus niger
What are the functions of autophagy in the filamentous fungus Aspergillus niger?
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PROTEOMINING: a novel proteomics-based pipeline for drug and enzyme discovery in filamentous actinomycetes
Can a new proteomics workflow be developed to link genes and gene clusters to bioactive molecules, identify novel compounds and enhance the production in the Streptomyces lividans enzyme?