Publications by Professor Natalio Krasnogor - ePrints

Browsing publications by Professor Natalio Krasnogor.

Newcastle Authors	Title	Year
Professor Thomas Curtis Professor Natalio Krasnogor	Scaling-up Engineering Biology for Enhanced Environmental Solutions	2024
Dr Yuchun Ding Dr Gaurav Dhawan Claire Jones Esme Nichols Professor Natalio Krasnogor et al.	An open source pipeline for quantitative immunohistochemistry image analysis of inflammatory skin disease using artificial intelligence	2023
Dr Emanuela Torelli Dr Benjamin Shirt-Ediss Dr Silvia Navarro Professor Natalio Krasnogor	Co-transcriptionally folded RNA origami and DNA stack memory as potential interfaces able to operate in vivo	2023
Daniel Todd Professor Natalio Krasnogor	Homebrew Photolithography for the Rapid and Low-Cost, "Do It Yourself" Prototyping of Microfluidic Devices	2023
Dr Emanuela Torelli Dr Benjamin Shirt-Ediss Dr Silvia Navarro Professor Natalio Krasnogor	Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing	2023
Dr Jichun Li Professor Natalio Krasnogor	Modified Noise-Immune Fuzzy Neural Network for Solving the Quadratic Programming With Equality Constraint Problem	2023
Dr Benjamin Shirt-Ediss Dr Jordan Connolly Dr Emanuela Torelli Dr Silvia Navarro Professor Jaume Bacardit et al.	Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence list	2023
Professor Natalio Krasnogor	Verifiable biology	2023
Dr Silvia Navarro Dr Emanuela Torelli Professor Natalio Krasnogor	INTEGRONS: natural DNA-based data structures	2022
Dr Benjamin Shirt-Ediss Dr Jordan Connolly Dr Emanuela Torelli Dr Silvia Navarro Professor Jaume Bacardit et al.	Multi-Objective Sequence Selection for Scaffolded Origami Nanostructures	2022
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production	2022
Dr Emanuela Torelli Dr Benjamin Shirt-Ediss Dr Silvia Navarro Professor Natalio Krasnogor	Towards in vivo RNA origami self-assembly	2022
Jonathan Tellechea Luzardo Leanne Hobbs Dr Lenka Pelechova Emeritus Professor Simon Woods Professor Natalio Krasnogor et al.	Versioning biological cells for trustworthy cell engineering	2022
Dr Annunziata Lopiccolo Dr Benjamin Shirt-Ediss Dr Emanuela Torelli Dr Harold Fellermann Professor Natalio Krasnogor et al.	A last-in first-out stack data structure implemented in DNA	2021
Dr Birgit Koch Professor Natalio Krasnogor	Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System	2021
Professor Natalio Krasnogor	For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!	2021
Dr Jordan Connolly Dr Benjamin Shirt-Ediss Dr Emanuela Torelli Leanne Hobbs Professor Jaume Bacardit et al.	NAOMEE: Nucleic Acid Origami Minimal Exchange Format.	2021
Jonathan Tellechea Luzardo Professor Natalio Krasnogor	Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection	2021
Dr Harold Fellermann Dr Bradley Brown Professor Anil Wipat Professor Natalio Krasnogor	Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation	2021
Dr Nadia Rostami Dr Halah Ahmed Professor Natalio Krasnogor Professor Nicholas Jakubovics	Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis	2021
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization	2020
Professor Marcus Kaiser Professor Natalio Krasnogor	AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation	2020
Dr Maria Franco Gaviria Professor Natalio Krasnogor Professor Jaume Bacardit	Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification	2020
Dr Emanuela Torelli Dr Benjamin Shirt-Ediss Professor Natalio Krasnogor	Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami	2020
Dr Darin Zerti Dr Birthe Hilgen Majed Felemban Dr Ali Ghareeb Dr Min Yu et al.	Developing a simple method to enhance the generation of cone and rod photoreceptors in pluripotent stem cell‐derived retinal organoids	2020
Dr Michael White Dr Rashmi Maheshwari Dr Scott Anderson Dr Rolando Berlinguer Palmini Claire Jones et al.	In situ analysis reveals that CFTR is expressed in only a small minority of β-cells in normal adult human pancreas	2020
Jonathan Tellechea Luzardo Dr Charles Winterhalter Dr Paweł Widera Dr Jurek Kozyra Professor Natalio Krasnogor et al.	Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering	2020
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	NIHBA: a network interdiction approach for metabolic engineering design	2020
Dr Birgit Koch Jonathan Tellechea Luzardo Professor Natalio Krasnogor	Protein interactions within and between two F-type type IV secretion systems	2020
Sarah Armour Dr Scott Anderson Dr Yuchun Ding Dr Christopher Carey Dr Rashmi Maheshwari et al.	Reduced expression of the co-regulator TLE1 in type 2 diabetes is associated with increased islet α-cell number	2020
Dr Benjamin Shirt-Ediss Dr Jordan Connolly Dr Emanuela Torelli Professor Natalio Krasnogor	REVNANO: An Algorithm to Reverse Engineer Scaffolded DNA/RNA Origami Designs from Sequence Information Only	2020
Dr Emanuela Torelli Dr Jurek Kozyra Dr Benjamin Shirt-Ediss Professor Natalio Krasnogor	Towards in vivo origami: bio-orthogonal scaffolded RNA nanoribbons self-assembled via co-transcriptional folding	2020
Dr Emanuela Torelli Dr Jurek Kozyra Dr Benjamin Shirt-Ediss Professor Natalio Krasnogor	Towards in vivo origami: co-transcriptional folding of a bio-orthogonal scaffolded RNA nanoribbon	2020
Majed Felemban Dr Birthe Hilgen Dr Darin Zerti Dr Nicola Hunt Dr Dean Hallam et al.	Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids	2019
Jonny Naylor Dr Harold Fellermann Professor Natalio Krasnogor	Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations	2019
Dr David Swan Professor Chris Lamb Dr Karin Engelhardt Dr Rui Chen Dr Yuchun Ding et al.	Immunodeficiency, autoimmune thrombocytopenia and enterocolitis caused by autosomal recessive deficiency of PIK3CD-encoded phosphoinositide 3-kinase δ	2019
Dr Emanuela Torelli Dr Jurek Kozyra Professor Ulrich Stimming Professor Natalio Krasnogor	Switchable 2D/3D DNA origami nanodevices and light-up bio-orthogonal RNA nanoribbon	2019
Professor Natalio Krasnogor Geok Yuan Annie Tan Professor Nicholas Jakubovics	Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq	2019
Dr Emanuela Torelli Dr Jurek Kozyra Professor Ulrich Stimming Professor Natalio Krasnogor	Walk on the Origami Side: From Switchable DNA Nanodevices to Light-up Bio-orthogonal RNA Nanoribbon	2019
Waleed Mohammed Professor Natalio Krasnogor Professor Nicholas Jakubovics	Streptococcus gordonii Challisin protease is required for sensing cell-cell contact with Actinomyces oris	2018
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	An Empirical Study of Dynamic Triobjective Optimisation Problems	2018
Professor Natalio Krasnogor	Automatic Selection of Verification Tools for Efficient Analysis of Biochemical Models	2018
Dr Adriana Buskin Dr Lili Zhu Dr Valeria Chichagova Dr David Dolan Dr Joseph Collin et al.	Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa	2018
Majed Felemban Dr Birthe Hilgen Dr Nicola Hunt Dr Dean Hallam Dr Darin Zerti et al.	Extracellular matrix components expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis in vivo and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix	2018
Dr Emanuela Torelli Dr Jurek Kozyra Dr Jingying Gu Professor Ulrich Stimming Professor Natalio Krasnogor et al.	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon	2018
Dr Emanuela Torelli Dr Jurek Kozyra Dr Jingying Gu Professor Ulrich Stimming Professor Natalio Krasnogor et al.	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon	2018
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	Less detectable environmental changes in dynamic multiobjective optimisation	2018
Jonny Naylor Professor Natalio Krasnogor Dr Harold Fellermann	Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World	2018
Omer Markovitch Professor Natalio Krasnogor	Predicting species emergence in simulated complex pre-biotic networks	2018
Dr Shouyong Jiang Professor Marcus Kaiser Professor Natalio Krasnogor	Strain design as multiobjective network interdiction problem: A preliminary approach	2018
Dr Benjamin Shirt-Ediss Professor Natalio Krasnogor Dr Harold Fellermann	The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators	2018
Professor Natalio Krasnogor Geok Yuan Annie Tan Professor Nicholas Jakubovics	Transcriptional Responses of Streptococcus gordonii and Fusobacterium nucleatum to Coaggregation	2018
Dr Harold Fellermann Daven Sanassy Professor Natalio Krasnogor	An integrated in silico simulation and biomatter compilation approach to cellular computation	2017
Dr Angel Goni-Moreno Professor Anil Wipat Professor Natalio Krasnogor	CSBB: Synthetic biology research at Newcastle University	2017
Dr Jurek Kozyra Alessandro Ceccarelli Dr Emanuela Torelli Dr Annunziata Lopiccolo Dr Jingying Gu et al.	Designing uniquely addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami	2017
Dr Emanuela Torelli Professor Natalio Krasnogor	DNA origami as device at the nanoscale	2017
Dr Jurek Kozyra Dr Harold Fellermann Dr Benjamin Shirt-Ediss Dr Annunziata Lopiccolo Professor Natalio Krasnogor et al.	Optimizing nucleic acid sequences for a molecular data recorder	2017
Jonny Naylor Dr Harold Fellermann Dr Yuchun Ding Professor Nicholas Jakubovics Professor Catherine Biggs et al.	Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations	2017
Alessandro Ceccarelli Dr Emanuela Torelli Dr Annunziata Lopiccolo Dr Harold Fellermann Dr Benjamin Shirt-Ediss et al.	Toward in vivo nanostructures: hybrid origami scaffolds on De Bruijn sequence	2017
Dr Harold Fellermann Nunzia Lopiccolo Jurek Kozyra Professor Natalio Krasnogor	In vitro implementation of a stack data structure based on DNA strand displacement	2016
Nicola Lazzarini Dr Paweł Widera Dr Stuart Williamson Professor Rakesh Heer Professor Natalio Krasnogor et al.	Functional networks inference from machine learning models	2016
Dr Birgit Koch Professor Natalio Krasnogor	Synthesis and cell-free cloning of DNA libraries using programmable microfluidics	2016
Professor Natalio Krasnogor	Algorithms and models for complex natural systems	2015
Professor Natalio Krasnogor	Complexity Measurement Based on Information Theory and Kolmogorov Complexity	2015
Daven Sanassy Dr Paweł Widera Professor Natalio Krasnogor	Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology	2015
Professor Natalio Krasnogor	Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems	2015
Professor Natalio Krasnogor	Blind optimisation problem instance classification via enhanced universal similarity metric	2014
Dr Harold Fellermann Professor Natalio Krasnogor	Chemical Production and Molecular Computing in Addressable Reaction Compartments	2014
Professor Natalio Krasnogor	Conventional Verification for Unconventional Computing: a Genetic XOR Gate Example	2014
Professor Natalio Krasnogor	Executable biology for rapid model prototyping in synthetic biology: implications for regenerative medicine and tissue engineering	2014
Dr Harold Fellermann Professor Natalio Krasnogor	Formalizing Modularization and Data Hiding in Synthetic Biology	2014
Professor Jaume Bacardit Dr Paweł Widera Dr Nicola Lazzarini Professor Natalio Krasnogor	Hard Data Analytics Problems Make for Better Data Analysis Algorithms: Bioinformatics as an Example	2014
Professor Jaume Bacardit Dr Paweł Widera Professor Natalio Krasnogor	Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly	2014
Dr Charles Winterhalter Dr Paweł Widera Professor Natalio Krasnogor	JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks	2014
Dr Harold Fellermann Daven Sanassy Professor Natalio Krasnogor	Modeling and Analysis of Genetic Boolean Gates using Infobiotics Workbench	2014
Daven Sanassy Dr Harold Fellermann Professor Natalio Krasnogor	Modelling and stochastic simulation of synthetic biological Boolean gates	2014
Professor Natalio Krasnogor	Photochromic molecular implementations of universal computation	2014
Professor Natalio Krasnogor	Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes	2013
Professor Natalio Krasnogor	Exploring programmable self-assembly in non-DNA based molecular computing	2013
Professor Natalio Krasnogor Professor Jaume Bacardit	GAssist vs. BioHEL: critical assessment of two paradigms of genetics-based machine learning	2013
Professor Jaume Bacardit Professor Natalio Krasnogor	Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features	2012
Professor Jaume Bacardit Professor Natalio Krasnogor	Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization;Sample Classification of Cancer Gene Expression Data	2012
Professor Natalio Krasnogor	Automated probe microscopy via evolutionary optimization at the atomic scale	2011
Professor Natalio Krasnogor	Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions	2011
Professor Natalio Krasnogor	Evolving cell models for systems and synthetic biology	2010
Professor Jaume Bacardit Professor Natalio Krasnogor	Automated Alphabet Reduction for Protein Datasets	2009