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SBOL Visual: A Graphical Language for Genetic Designs.
Published in:
PLoS Biology, 2015, v. 13, n. 12, p. 1, doi. 10.1371/journal.pbio.1002310
By:
- Quinn, Jacqueline Y.;
- IIICox, Robert Sidney;
- Adler, Aaron;
- Beal, Jacob;
- Bhatia, Swapnil;
- Cai, Yizhi;
- Chen, Joanna;
- Clancy, Kevin;
- Galdzicki, Michal;
- Hillson, Nathan J.;
- Le Novère, Nicolas;
- Maheshwari, Akshay J.;
- McLaughlin, James Alastair;
- Myers, Chris J.;
- P, Umesh;
- Pocock, Matthew;
- Rodriguez, Cesar;
- Soldatova, Larisa;
- Stan, Guy-Bart V.;
- Swainston, Neil
Publication type:
Article
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32661-x
By:
- Hérisson, Joan;
- Duigou, Thomas;
- du Lac, Melchior;
- Bazi-Kabbaj, Kenza;
- Sabeti Azad, Mahnaz;
- Buldum, Gizem;
- Telle, Olivier;
- El Moubayed, Yorgo;
- Carbonell, Pablo;
- Swainston, Neil;
- Zulkower, Valentin;
- Kushwaha, Manish;
- Baldwin, Geoff S.;
- Faulon, Jean-Loup
Publication type:
Article
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Published in:
BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-116
By:
- Büchel, Finja;
- Rodriguez, Nicolas;
- Swainston, Neil;
- Wrzodek, Clemens;
- Czauderna, Tobias;
- Keller, Roland;
- Mittag, Florian;
- Schubert, Michael;
- Glont, Mihai;
- Golebiewski, Martin;
- van Iersel, Martijn;
- Keating, Sarah;
- Rall, Matthias;
- Wybrow, Michael;
- Hermjakob, Henning;
- Hucka, Michael;
- Kell, Douglas B.;
- Müller, Wolfgang;
- Mendes, Pedro;
- Zell, Andreas
Publication type:
Article
Further developments towards a genome-scale metabolic model of yeast.
Published in:
BMC Systems Biology, 2010, v. 4, p. 145, doi. 10.1186/1752-0509-4-145
By:
- Dobson, Paul D.;
- Smallbone, Kieran;
- Jameson, Daniel;
- Simeonidis, Evangelos;
- Lanthaler, Karin;
- Pir, Pinar;
- Chuan Lu;
- Swainston, Neil;
- Dunn, Warwick B.;
- Fisher, Paul;
- Hull, Duncan;
- Brown, Marie;
- Oshota, Olusegun;
- Stanford, Natalie J.;
- Kell, Douglas B.;
- King, Ross D.;
- Oliver, Stephen G.;
- Stevens, Robert D.;
- Mendes, Pedro
Publication type:
Article
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks.
Published in:
BMC Systems Biology, 2010, v. 4, p. 114, doi. 10.1186/1752-0509-4-114
By:
- Radrich, Karin;
- Tsuruoka, Yoshimasa;
- Dobson, Paul;
- Gevorgyan, Albert;
- Swainston, Neil;
- Baart, Gino;
- Schwartz, Jean-Marc
Publication type:
Article
Towards a genome-scale kinetic model of cellular metabolism.
Published in:
BMC Systems Biology, 2010, v. 4, p. 6, doi. 10.1186/1752-0509-4-6
By:
- Smallbone, Kieran;
- Simeonidis, Evangelos;
- Swainston, Neil;
- Mendes, Pedro
Publication type:
Article
Pride Wizard: generation of standards compliant quantitative proteomics data.
Published in:
2007
By:
- Swainston, Neil;
- Siepen, Jennifer A.;
- Jones, Andrew R.;
- Hart, Sarah R.;
- Hermjakob, Henning;
- Jones, Phil;
- Hubbard, Simon J.
Publication type:
Abstract
Deep learning and generative methods in cheminformatics and chemical biology: navigating small molecule space intelligently.
Published in:
Biochemical Journal, 2020, v. 477, n. 23, p. 4559, doi. 10.1042/BCJ20200781
By:
- Kell, Douglas B.;
- Samanta, Soumitra;
- Swainston, Neil
Publication type:
Article
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 1, p. D1214, doi. 10.1093/nar/gkv1031
By:
- Hastings, Janna;
- Owen, Gareth;
- Dekker, Adriano;
- Ennis, Marcus;
- Kale, Namrata;
- Muthukrishnan, Venkatesh;
- Turner, Steve;
- Swainston, Neil;
- Mendes, Pedro;
- Steinbeck, Christoph
Publication type:
Article
GeneGenie: optimized oligomer design for directed evolution.
Published in:
Nucleic Acids Research, 2014, v. 42, n. W1, p. W395, doi. 10.1093/nar/gku336
By:
- Swainston, Neil;
- Currin, Andrew;
- Day, Philip J.;
- Kell, Douglas B.
Publication type:
Article
A community-driven global reconstruction of human metabolism.
Published in:
Nature Biotechnology, 2013, v. 31, n. 5, p. 419, doi. 10.1038/nbt.2488
By:
- Thiele, Ines;
- Swainston, Neil;
- Fleming, Ronan M T;
- Hoppe, Andreas;
- Sahoo, Swagatika;
- Aurich, Maike K;
- Haraldsdottir, Hulda;
- Mo, Monica L;
- Rolfsson, Ottar;
- Stobbe, Miranda D;
- Thorleifsson, Stefan G;
- Agren, Rasmus;
- Bölling, Christian;
- Bordel, Sergio;
- Chavali, Arvind K;
- Dobson, Paul;
- Dunn, Warwick B;
- Endler, Lukas;
- Hala, David;
- Hucka, Michael
Publication type:
Article
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Published in:
Nature Biotechnology, 2008, v. 26, n. 10, p. 1155, doi. 10.1038/nbt1492
By:
- Herrgård, Markus J;
- Swainston, Neil;
- Dobson, Paul;
- Dunn, Warwick B;
- Arga, K Yalçin;
- Arvas, Mikko;
- Büthgen, Nils;
- Borger, Simon;
- Costenoble, Roeland;
- Heinemann, Matthias;
- Hucka, Michael;
- Le Novère, Nicolas;
- Li, Peter;
- Liebermeister, Wolfram;
- Mo, Monica L;
- Oliveira, Ana Paula;
- Petranovic, Dina;
- Pettifer, Stephen;
- Simeonidis, Evangelos;
- Smallbone, Kieran
Publication type:
Article
SynBiopython: an open-source software library for Synthetic Biology.
Published in:
Synthetic Biology (23977000), 2021, v. 6, n. 1, p. 1, doi. 10.1093/synbio/ysab001
By:
- Yeoh, Jing Wui;
- Swainston, Neil;
- Vegh, Peter;
- Zulkower, Valentin;
- Carbonell, Pablo;
- Holowko, Maciej B;
- Peddinti, Gopal;
- Poh, Chueh Loo
Publication type:
Article
Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol.
Published in:
Synthetic Biology (23977000), 2020, v. 5, n. 1, p. 1, doi. 10.1093/synbio/ysaa012
By:
- Dunstan, Mark S;
- Robinson, Christopher J;
- Jervis, Adrian J;
- Yan, Cunyu;
- Carbonell, Pablo;
- Hollywood, Katherine A;
- Currin, Andrew;
- Swainston, Neil;
- Feuvre, Rosalind Le;
- Micklefield, Jason;
- Faulon, Jean-Loup;
- Breitling, Rainer;
- Turner, Nicholas;
- Takano, Eriko;
- Scrutton, Nigel S
Publication type:
Article
DNA Scanner: a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors.
Published in:
Synthetic Biology (23977000), 2020, v. 5, n. 1, p. 1, doi. 10.1093/synbio/ysaa011
By:
- Doçi, Gledon;
- Fuchs, Lukas;
- Kharbanda, Yash;
- Schickling, Paul;
- Zulkower, Valentin;
- Hillson, Nathan;
- Oberortner, Ernst;
- Swainston, Neil;
- Kabisch, Johannes
Publication type:
Article
Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries.
Published in:
Synthetic Biology (23977000), 2019, v. 4, n. 1, p. N.PAG, doi. 10.1093/synbio/ysz025
By:
- Currin, Andrew;
- Swainston, Neil;
- Dunstan, Mark S;
- Jervis, Adrian J;
- Mulherin, Paul;
- Robinson, Christopher J;
- Taylor, Sandra;
- Carbonell, Pablo;
- Hollywood, Katherine A;
- Yan, Cunyu;
- Takano, Eriko;
- Scrutton, Nigel S;
- Breitling, Rainer
Publication type:
Article
A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data.
Published in:
Proteomics, 2011, v. 11, n. 2, p. 329, doi. 10.1002/pmic.201000454
By:
- Swainston, Neil;
- Jameson, Daniel;
- Carroll, Kathleen
Publication type:
Article
Capture and analysis of quantitative proteomic data.
Published in:
Proteomics, 2007, v. 7, n. 16, p. 2787, doi. 10.1002/pmic.200700127
By:
- Lau, King Wai;
- Jones, Andrew R.;
- Swainston, Neil;
- Siepen, Jennifer A.;
- Hubbard, Simon J.
Publication type:
Article
MassGenie: A Transformer-Based Deep Learning Method for Identifying Small Molecules from Their Mass Spectra.
Published in:
Biomolecules (2218-273X), 2021, v. 11, n. 12, p. 1793, doi. 10.3390/biom11121793
By:
- Shrivastava, Aditya Divyakant;
- Swainston, Neil;
- Samanta, Soumitra;
- Roberts, Ivayla;
- Wright Muelas, Marina;
- Kell, Douglas B.
Publication type:
Article
Recon 2.2: from reconstruction to model of human metabolism.
Published in:
Metabolomics, 2016, v. 12, n. 7, p. 1, doi. 10.1007/s11306-016-1051-4
By:
- Swainston, Neil;
- Smallbone, Kieran;
- Hefzi, Hooman;
- Dobson, Paul;
- Brewer, Judy;
- Hanscho, Michael;
- Zielinski, Daniel;
- Ang, Kok;
- Gardiner, Natalie;
- Gutierrez, Jahir;
- Kyriakopoulos, Sarantos;
- Lakshmanan, Meiyappan;
- Li, Shangzhong;
- Liu, Joanne;
- Martínez, Veronica;
- Orellana, Camila;
- Quek, Lake-Ee;
- Thomas, Alex;
- Zanghellini, Juergen;
- Borth, Nicole
Publication type:
Article
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs.
Published in:
Metabolomics, 2015, v. 11, n. 2, p. 323, doi. 10.1007/s11306-014-0733-z
By:
- O′Hagan, Steve;
- Swainston, Neil;
- Handl, Julia;
- Kell, Douglas
Publication type:
Article
Erratum to: A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs.
Published in:
2015
By:
- O'Hagan, Steve;
- Swainston, Neil;
- Handl, Julia;
- Kell, Douglas
Publication type:
Erratum
An analysis of a 'community-driven' reconstruction of the human metabolic network.
Published in:
Metabolomics, 2013, v. 9, n. 4, p. 757, doi. 10.1007/s11306-013-0564-3
By:
- Swainston, Neil;
- Mendes, Pedro;
- Kell, Douglas
Publication type:
Article
Systematic integration of experimental data and models in systems biology.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 582, doi. 10.1186/1471-2105-11-582
By:
- Li, Peter;
- Dada, Joseph O.;
- Jameson, Daniel;
- Spasic, Irena;
- Swainston, Neil;
- Carroll, Kathleen;
- Dunn, Warwick;
- Khan, Farid;
- Malys, Naglis;
- Messiha, Hanan L.;
- Simeonidis, Evangelos;
- Weichart, Dieter;
- Winder, Catherine;
- Wishart, Jill;
- Broomhead, David S.;
- Goble, Carole A.;
- Gaskell, Simon J.;
- Kell, Douglas B.;
- Westerhoff, Hans V.;
- Mendes, Pedro
Publication type:
Article
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it.
Published in:
BMC Bioinformatics, 2006, v. 7, p. 532, doi. 10.1186/1471-2105-7-532
By:
- Garwood, Kevin;
- Garwood, Christopher;
- Hedeler, Cornelia;
- Griffiths, Tony;
- Swainston, Neil;
- Oliver, Stephen G;
- Paton, Norman W
Publication type:
Article
EnzymeML—a data exchange format for biocatalysis and enzymology.
Published in:
FEBS Journal, 2022, v. 289, n. 19, p. 5864, doi. 10.1111/febs.16318
By:
- Range, Jan;
- Halupczok, Colin;
- Lohmann, Jens;
- Swainston, Neil;
- Kettner, Carsten;
- Bergmann, Frank T.;
- Weidemann, Andreas;
- Wittig, Ulrike;
- Schnell, Santiago;
- Pleiss, Jürgen
Publication type:
Article
An automated pipeline for the screening of diverse monoterpene synthase libraries.
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-48452-2
By:
- Leferink, Nicole G. H.;
- Dunstan, Mark S.;
- Hollywood, Katherine A.;
- Swainston, Neil;
- Currin, Andrew;
- Jervis, Adrian J.;
- Takano, Eriko;
- Scrutton, Nigel S.
Publication type:
Article
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach.
Published in:
Journal of Cheminformatics, 2020, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13321-020-00454-3
By:
- Khemchandani, Yash;
- O'Hagan, Stephen;
- Samanta, Soumitra;
- Swainston, Neil;
- Roberts, Timothy J.;
- Bollegala, Danushka;
- Kell, Douglas B.
Publication type:
Article
libChEBI: an API for accessing the ChEBI database.
Published in:
Journal of Cheminformatics, 2016, v. 8, n. 1, p. 1, doi. 10.1186/s13321-016-0123-9
By:
- Swainston, Neil;
- Hastings, Janna;
- Dekker, Adriano;
- Muthukrishnan, Venkatesh;
- May, John;
- Steinbeck, Christoph;
- Mendes, Pedro
Publication type:
Article
STRENDA DB: enabling the validation and sharing of enzyme kinetics data.
Published in:
FEBS Journal, 2018, v. 285, n. 12, p. 2193, doi. 10.1111/febs.14427
By:
- Swainston, Neil;
- Baici, Antonio;
- Bakker, Barbara M.;
- Cornish‐Bowden, Athel;
- Fitzpatrick, Paul F.;
- Halling, Peter;
- Leyh, Thomas S.;
- O'Donovan, Claire;
- Raushel, Frank M.;
- Reschel, Udo;
- Rohwer, Johann M.;
- Schnell, Santiago;
- Schomburg, Dietmar;
- Tipton, Keith F.;
- Tsai, Ming‐Daw;
- Westerhoff, Hans V.;
- Wittig, Ulrike;
- Wohlgemuth, Roland;
- Kettner, Carsten
Publication type:
Article
Enzyme kinetics informatics: from instrument to browser.
Published in:
FEBS Journal, 2010, v. 277, n. 18, p. 3769, doi. 10.1111/j.1742-4658.2010.07778.x
By:
- Swainston, Neil;
- Golebiewski, Martin;
- Messiha, Hanan L.;
- Malys, Naglis;
- Kania, Renate;
- Kengne, Sylvestre;
- Krebs, Olga;
- Mir, Saqib;
- Sauer-Danzwith, Heidrun;
- Smallbone, Kieran;
- Weidemann, Andreas;
- Wittig, Ulrike;
- Kell, Douglas B.;
- Mendes, Pedro;
- Müller, Wolfgang;
- Paton, Norman W.;
- Rojas, Isabel
Publication type:
Article
SYNBIOCHEM - a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.
Published in:
Biochemical Society Transactions, 2016, v. 44, n. 3, p. 675, doi. 10.1042/BST20160009
By:
- Carbonell, Pablo;
- Currin, Andrew;
- Dunstan, Mark;
- Fellows, Donal;
- Jervis, Adrian;
- Rattray, Nicholas J. W.;
- Robinson, Christopher J.;
- Swainston, Neil;
- Vinaixa, Maria;
- Williams, Alan;
- Cunyu Yan;
- Barran, Perdita;
- Breitling, Rainer;
- George Guo-Qiang Chen;
- Jean-Loup Faulon;
- Goble, Carole;
- Goodacre, Royston;
- Kell, Douglas B.;
- Le Feuvre, Rosalind;
- Micklefield, Jason
Publication type:
Article
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.
Published in:
Communications Biology, 2018, v. 1, n. 1, p. N.PAG, doi. 10.1038/s42003-018-0076-9
By:
- Carbonell, Pablo;
- Jervis, Adrian J.;
- Robinson, Christopher J.;
- Yan, Cunyu;
- Dunstan, Mark;
- Swainston, Neil;
- Vinaixa, Maria;
- Hollywood, Katherine A.;
- Currin, Andrew;
- Rattray, Nicholas J. W.;
- Taylor, Sandra;
- Spiess, Reynard;
- Sung, Rehana;
- Williams, Alan R.;
- Fellows, Donal;
- Stanford, Natalie J.;
- Mulherin, Paul;
- Le Feuvre, Rosalind;
- Barran, Perdita;
- Goodacre, Royston
Publication type:
Article
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.
Published in:
FEBS Letters, 2013, v. 587, n. 17, p. 2832, doi. 10.1016/j.febslet.2013.06.043
By:
- Smallbone, Kieran;
- Messiha, Hanan L.;
- Carroll, Kathleen M.;
- Winder, Catherine L.;
- Malys, Naglis;
- Dunn, Warwick B.;
- Murabito, Ettore;
- Swainston, Neil;
- Dada, Joseph O.;
- Khan, Farid;
- Pir, Pınar;
- Simeonidis, Evangelos;
- Spasić, Irena;
- Wishart, Jill;
- Weichart, Dieter;
- Hayes, Neil W.;
- Jameson, Daniel;
- Broomhead, David S.;
- Oliver, Stephen G.;
- Gaskell, Simon J.
Publication type:
Article
VAE-Sim: A Novel Molecular Similarity Measure Based on a Variational Autoencoder.
Published in:
Molecules, 2020, v. 25, n. 15, p. 3446, doi. 10.3390/molecules25153446
By:
- Samanta, Soumitra;
- O'Hagan, Steve;
- Swainston, Neil;
- Roberts, Timothy J.;
- Kell, Douglas B.;
- McPhee, Derek J.
Publication type:
Article
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts.
Published in:
Bioinformatics, 2018, v. 34, n. 13, p. 2327, doi. 10.1093/bioinformatics/bty105
By:
- Swainston, Neil;
- Dunstan, Mark;
- Jervis, Adrian J;
- Robinson, Christopher J;
- Carbonell, Pablo;
- Williams, Alan R;
- Faulon, Jean-Loup;
- Scrutton, Nigel S;
- Kell, Douglas B
Publication type:
Article
Selenzyme: enzyme selection tool for pathway design.
Published in:
Bioinformatics, 2018, v. 34, n. 12, p. 2153, doi. 10.1093/bioinformatics/bty065
By:
- Carbonell, Pablo;
- Wong, Jerry;
- Swainston, Neil;
- Takano, Eriko;
- Turner, Nicholas J;
- Scrutton, Nigel S;
- Kell, Douglas B;
- Breitling, Rainer;
- Faulon, Jean-Loup
Publication type:
Article
libAnnotationSBML: a library for exploiting SBML annotations.
Published in:
Bioinformatics, 2009, v. 25, n. 17, p. 2292, doi. 10.1093/bioinformatics/btp392
By:
- Swainston, Neil;
- Mendes, Pedro
Publication type:
Article
biochem4j: Integrated and extensible biochemical knowledge through graph databases.
Published in:
PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0179130
By:
- Swainston, Neil;
- Batista-Navarro, Riza;
- Carbonell, Pablo;
- Dobson, Paul D.;
- Dunstan, Mark;
- Jervis, Adrian J.;
- Vinaixa, Maria;
- Williams, Alan R.;
- Ananiadou, Sophia;
- Faulon, Jean-Loup;
- Mendes, Pedro;
- Kell, Douglas B.;
- Scrutton, Nigel S.;
- Breitling, Rainer
Publication type:
Article
SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution.
Published in:
PEDS: Protein Engineering, Design & Selection, 2014, v. 27, n. 9, p. 273, doi. 10.1093/protein/gzu029
By:
- Currin, Andrew;
- Swainston, Neil;
- Day, Philip J.;
- Kell, Douglas B.
Publication type:
Article
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Published in:
Proteome Science, 2007, v. 5, p. 1, doi. 10.1186/1477-5956-5-4
By:
- Siepen, Jennifer A.;
- Swainston, Neil;
- Jones, Andrew R.;
- Hart, Sarah R.;
- Hermjakob, Henning;
- Jones, Philip;
- Hubbard, Simon J.
Publication type:
Article
Growth control of the eukaryote cell: a systems biology study in yeast.
Published in:
Journal of Biology, 2007, v. 6, p. 4.1, doi. 10.1186/jbiol54
By:
- Castrillo, Juan I.;
- Zeef, Leo A.;
- Hoyle, David C.;
- Zhang, Nianshu;
- Hayes, Andrew;
- Gardner, David C. J.;
- Cornell, Michael J.;
- Petty, June;
- Hakes, Luke;
- Wardleworth, Leanne;
- Rash, Bharat;
- Brown, Marie;
- Dunn, Warwick B.;
- Broadhurst, David;
- O'Donoghue, Kerry;
- Hester, Svenja S.;
- Dunkley, Tom P. J.;
- Hart, Sarah R.;
- Swainston, Neil;
- Li, Peter
Publication type:
Article

Found: 42