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Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011-2013.
Published in:
2016
By:
- Toleman, Michelle S.;
- Reuter, Sandra;
- Coll, Francesc;
- Harrison, Ewan M.;
- Peacock, Sharon J.
Publication type:
historical material
Prospective genomic surveillance of meticillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.
Published in:
Eurosurveillance (15607917), 2019, v. 24, n. 4, p. 42, doi. 10.2807/1560-7917.ES.2019.24.4.1800215
By:
- Toleman, Michelle S.;
- Reuter, Sandra;
- Jamrozy, Dorota;
- Wilson, Hayley J.;
- Blane, Beth;
- Harrison, Ewan M.;
- Coll, Francesc;
- Hope, Russell J.;
- Kearns, Angela;
- Parkhill, Julian;
- Peacock, Sharon J.;
- Török, M. Estée
Publication type:
Article
PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.
Published in:
Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03194-2
By:
- Coll, Francesc;
- Gouliouris, Theodore;
- Bruchmann, Sebastian;
- Phelan, Jody;
- Raven, Kathy E.;
- Clark, Taane G.;
- Parkhill, Julian;
- Peacock, Sharon J.
Publication type:
Article
Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya.
Published in:
Antibiotics (2079-6382), 2022, v. 11, n. 12, p. 1726, doi. 10.3390/antibiotics11121726
By:
- Obanda, Benear Apollo;
- Gibbons, Cheryl L.;
- Fèvre, Eric M.;
- Bebora, Lilly;
- Gitao, George;
- Ogara, William;
- Wang, Shu-Hua;
- Gebreyes, Wondwossen;
- Ngetich, Ronald;
- Blane, Beth;
- Coll, Francesc;
- Harrison, Ewan M.;
- Kariuki, Samuel;
- Peacock, Sharon J.;
- Cook, Elizabeth A. J.
Publication type:
Article
Correction to: The impacts of agricultural and urban land-use changes on plant and bird biodiversity in Costa Rica (1986–2014)
Published in:
2021
By:
- Montero, Andrea;
- Marull, Joan;
- Tello, Enric;
- Cattaneo, Claudio;
- Coll, Francesc;
- Pons, Manel;
- Infante-Amate, Juan;
- Urrego-Mesa, Alexander;
- Fernández-Landa, Alfredo;
- Vargas, Manuel
Publication type:
Correction Notice
The impacts of agricultural and urban land-use changes on plant and bird biodiversity in Costa Rica (1986–2014).
Published in:
Regional Environmental Change, 2021, v. 21, n. 2, p. 1, doi. 10.1007/s10113-021-01767-1
By:
- Montero, Andrea;
- Marull, Joan;
- Tello, Enric;
- Cattaneo, Claudio;
- Coll, Francesc;
- Pons, Manel;
- Infante-Amate, Juan;
- Urrego-Mesa, Alexander;
- Fernández-Landa, Alfredo;
- Vargas, Manuel
Publication type:
Article
The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.
Published in:
International Journal of Mycobacteriology, 2015, v. 4, n. 3, p. 207, doi. 10.1016/j.ijmyco.2015.05.001
By:
- Phelan, Jody;
- Maitra, Arundhati;
- McNerney, Ruth;
- Nair, Mridul;
- Gupta, Antima;
- Coll, Francesc;
- Pain, Arnab;
- Bhakta, Sanjib;
- Clark, Taane G.
Publication type:
Article
Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan.
Published in:
International Journal of Mycobacteriology, 2015, v. 4, p. 116, doi. 10.1016/j.ijmyco.2014.10.051
By:
- Kanji, Akbar;
- Hasan, Zahra;
- Ali, Asho;
- McNerney, Ruth;
- Mallard, Kim;
- Coll, Francesc;
- Hill-Cawthorne, Grant;
- Pain, Arnab;
- Nair, Mridul;
- Clark, Taane G.;
- Zaver, Ambreen;
- Jafri, Sana;
- Hasan, Rumina
Publication type:
Article
Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan.
Published in:
International Journal of Mycobacteriology, 2015, v. 4, p. 11, doi. 10.1016/j.ijmyco.2014.10.050
By:
- Hasan, Zahra;
- Ali, Asho;
- McNerney, Ruth;
- Mallard, Kim;
- Hill-Cawthorne, Grant;
- Coll, Francesc;
- Nair, Mridul;
- Pain, Arnab;
- Clark, Taane G.;
- Hasan, Rumina
Publication type:
Article
Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology.
Published in:
International Journal of Mycobacteriology, 2015, v. 4, p. 27, doi. 10.1016/j.ijmyco.2015.01.001
By:
- Perdigão, João;
- Silva, Hugo;
- Machado, Diana;
- Macedo, Rita;
- Maltez, Fernando;
- Silva, Carla;
- Jordao, Luisa;
- Couto, Isabel;
- Mallard, Kim;
- Coll, Francesc;
- Hill-Cawthorne, Grant A.;
- McNerney, Ruth;
- Pain, Arnab;
- Clark, Taane G.;
- Viveiros, Miguel;
- Portugal, Isabel
Publication type:
Article
Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan.
Published in:
International Journal of Mycobacteriology, 2015, v. 4, n. 1, p. 73, doi. 10.1016/j.ijmyco.2014.11.049
By:
- Kanji, Akbar;
- Hasan, Zahra;
- Ali, Asho;
- McNerney, Ruth;
- Mallard, Kim;
- Coll, Francesc;
- Hill-Cawthorne, Grant;
- Nair, Mridul;
- Clark, Taane G.;
- Zaver, Ambreen;
- Jafri, Sana;
- Hasan, Rumina
Publication type:
Article
Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan.
Published in:
PLoS ONE, 2015, v. 10, n. 2, p. 1, doi. 10.1371/journal.pone.0117771
By:
- Ali, Asho;
- Hasan, Zahra;
- McNerney, Ruth;
- Mallard, Kim;
- Hill-Cawthorne, Grant;
- Coll, Francesc;
- Nair, Mridul;
- Pain, Arnab;
- Clark, Taane G.;
- Hasan, Rumina
Publication type:
Article
Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing.
Published in:
PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0083012
By:
- Clark, Taane G.;
- Mallard, Kim;
- Coll, Francesc;
- Preston, Mark;
- Assefa, Samuel;
- Harris, David;
- Ogwang, Sam;
- Mumbowa, Francis;
- Kirenga, Bruce;
- O’Sullivan, Denise M.;
- Okwera, Alphonse;
- Eisenach, Kathleen D.;
- Joloba, Moses;
- Bentley, Stephen D.;
- Ellner, Jerrold J.;
- Parkhill, Julian;
- Jones-López, Edward C.;
- McNerney, Ruth
Publication type:
Article
Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England.
Published in:
2016
By:
- Toleman, Michelle S.;
- Reuter, Sandra;
- Coll, Francesc;
- Harrison, Ewan M.;
- Blane, Beth;
- Brown, Nicholas M.;
- Török, M. Estée;
- Parkhill, Julian;
- Peacock, Sharon J.
Publication type:
journal article
Recurrence due to Relapse or Reinfection With Mycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up.
Published in:
Journal of Infectious Diseases, 2015, v. 211, n. 7, p. 1154, doi. 10.1093/infdis/jiu574
By:
- Guerra-Assunção, José Afonso;
- Houben, Rein M. G. J.;
- Crampin, Amelia C.;
- Mzembe, Themba;
- Mallard, Kim;
- Coll, Francesc;
- Khan, Palwasha;
- Banda, Louis;
- Chiwaya, Arthur;
- Pereira, Rui P. A.;
- McNerney, Ruth;
- Harris, David;
- Parkhill, Julian;
- Clark, Taane G.;
- Glynn, Judith R.
Publication type:
Article
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2467-y
By:
- Phelan, Jody E.;
- Coll, Francesc;
- Bergval, Indra;
- Anthony, Richard M.;
- Warren, Rob;
- Sampson, Samantha L.;
- Gey van Pittius, Nicolaas C.;
- Glynn, Judith R.;
- Crampin, Amelia C.;
- Alves, Adriana;
- Bessa, Theolis Barbosa;
- Campino, Susana;
- Dheda, Keertan;
- Grandjean, Louis;
- Hasan, Rumina;
- Hasan, Zahra;
- Miranda, Anabela;
- Moore, David;
- Panaiotov, Stefan;
- Perdigao, Joao
Publication type:
Article
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.65828
By:
- Stirrup, Oliver;
- Hughes, Joseph;
- Parker, Matthew;
- Partridge, David G.;
- Shepherd, James G.;
- Blackstone, James;
- Coll, Francesc;
- Keeley, Alexander;
- Lindsey, Benjamin B.;
- Marek, Aleksandra;
- Peters, Christine;
- Singer, Joshua B.;
- Tamuri, Asif;
- de Silva, Thushan I.;
- Thomson, Emma C.;
- Breuer, Judith
Publication type:
Article
Flavour index and aroma profiles of fresh and processed honeys.
Published in:
Journal of the Science of Food & Agriculture, 2003, v. 83, n. 4, p. 275, doi. 10.1002/jsfa.1308
By:
- Serra Bonvehí, Josep;
- Ventura Coll, Francesc
Publication type:
Article
Mathematical modelling for antibiotic resistance control policy: do we know enough?
Published in:
2019
By:
- Knight, Gwenan M.;
- Davies, Nicholas G.;
- Colijn, Caroline;
- Coll, Francesc;
- Donker, Tjibbe;
- Gifford, Danna R.;
- Glover, Rebecca E.;
- Jit, Mark;
- Klemm, Elizabeth;
- Lehtinen, Sonja;
- Lindsay, Jodi A.;
- Lipsitch, Marc;
- Llewelyn, Martin J.;
- Mateus, Ana L. P.;
- Robotham, Julie V.;
- Sharland, Mike;
- Stekel, Dov;
- Yakob, Laith;
- Atkins, Katherine E.
Publication type:
journal article
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Published in:
BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0603-3
By:
- Benavente, Ernest D.;
- Coll, Francesc;
- Furnham, Nick;
- McNerney, Ruth;
- Glynn, Judith R.;
- Campino, Susana;
- Pain, Arnab;
- Mohareb, Fady R.;
- Clark, Taane G.
Publication type:
Article
Exploring the links between forest transition and landscape changes in the Mediterranean. Does forest recovery really lead to better landscape quality?
Published in:
Agroforestry Systems, 2015, v. 89, n. 4, p. 705, doi. 10.1007/s10457-015-9808-8
By:
- Marull, Joan;
- Otero, Iago;
- Stefanescu, Constantí;
- Tello, Enric;
- Miralles, Marta;
- Coll, Francesc;
- Pons, Manel;
- Diana, Giovanna
Publication type:
Article
Detecting vegetable oil adulteration in hazelnut paste ( Corylus avellana L.).
Published in:
International Journal of Food Science & Technology, 2009, v. 44, n. 3, p. 456, doi. 10.1111/j.1365-2621.2008.01742.x
By:
- Bonvehi, Josep Serra;
- Coll, Francesc Ventura
Publication type:
Article
Land abandonment, landscape, and biodiversity: questioning the restorative character of the forest transition in the Mediterranean.
Published in:
2015
By:
- Otero, Iago;
- Marull, Joan;
- Tello, Enric;
- Diana, Giovanna L.;
- Pons, Manel;
- Coll, Francesc;
- Boada, Martí
Publication type:
Case Study
Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya.
Published in:
Pathogens, 2022, v. 11, n. 12, p. 1504, doi. 10.3390/pathogens11121504
By:
- Obanda, Benear Apollo;
- Cook, Elizabeth A. J.;
- Fèvre, Eric M.;
- Bebora, Lilly;
- Ogara, William;
- Wang, Shu-Hua;
- Gebreyes, Wondwossen;
- Ngetich, Ronald;
- Wandede, Dolphine;
- Muyodi, Johnstone;
- Blane, Beth;
- Coll, Francesc;
- Harrison, Ewan M.;
- Peacock, Sharon J.;
- Gitao, George C.
Publication type:
Article
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.
Published in:
Nature Communications, 2014, v. 5, n. 9, p. 4812, doi. 10.1038/ncomms5812
By:
- Coll, Francesc;
- McNerney, Ruth;
- Guerra-Assunção, José Afonso;
- Glynn, Judith R.;
- Perdigão, João;
- Viveiros, Miguel;
- Portugal, Isabel;
- Pain, Arnab;
- Martin, Nigel;
- Clark, Taane G.
Publication type:
Article
Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.
Published in:
Science Translational Medicine, 2017, v. 9, n. 413, p. 1, doi. 10.1126/scitranslmed.aak9745
By:
- Coll, Francesc;
- Harrison, Ewan M.;
- Toleman, Michelle S.;
- Reuter, Sandra;
- Raven, Kathy E.;
- Blane, Beth;
- Palmer, Beverley;
- Kappeler, A. Ruth M.;
- Brown, Nicholas M.;
- Török, M. Estée;
- Parkhill, Julian;
- Peacock, Sharon J.
Publication type:
Article
Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: A Mathematical Early Modeling Study of Cost-effectiveness.
Published in:
Clinical Infectious Diseases, 2020, v. 70, n. 8, p. 1613, doi. 10.1093/cid/ciz480
By:
- Dymond, Amy;
- Davies, Heather;
- Mealing, Stuart;
- Pollit, Vicki;
- Coll, Francesc;
- Brown, Nicholas M;
- Peacock, Sharon J
Publication type:
Article
Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting.
Published in:
Clinical Infectious Diseases, 2017, v. 65, n. 12, p. 2069, doi. 10.1093/cid/cix539
By:
- Toleman, Michelle S.;
- Watkins, Emmeline R.;
- Williams, Tom;
- Blane, Beth;
- Sadler, Belinda;
- Harrison, Ewan M.;
- Coll, Francesc;
- Parkhill, Julian;
- Nazareth, Bernadette;
- Brown, Nicholas M.;
- Peacock, Sharon J.
Publication type:
Article
Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.
Published in:
Clinical Infectious Diseases, 2017, v. 64, n. 7, p. 886, doi. 10.1093/cid/ciw872
By:
- Raven, Kathy E.;
- Gouliouris, Theodore;
- Brodrick, Hayley;
- Coll, Francesc;
- Brown, Nicholas M.;
- Reynolds, Rosy;
- Reuter, Sandra;
- Török, M. Estée;
- Parkhill, Julian;
- Peacock, Sharon J.
Publication type:
Article
Evolution of mobile genetic element composition in an epidemic methicillinresistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.
Published in:
BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4065-z
By:
- Jamrozy, Dorota;
- Coll, Francesc;
- Mather, Alison E.;
- Harris, Simon R.;
- Harrison, Ewan M.;
- MacGowan, Alasdair;
- Karas, Andreas;
- Elston, Tony;
- Török, M. Estée;
- Parkhill, Julian;
- Peacock, Sharon J.
Publication type:
Article
The Loss of Landscape Ecological Functionality in the Barcelona Province (1956–2009): Could Land-Use History Involve a Legacy for Current Biodiversity?
Published in:
Sustainability (2071-1050), 2020, v. 12, n. 6, p. 2238, doi. 10.3390/su12062238
By:
- Tello, Enric;
- Marull, Joan;
- Padró, Roc;
- Cattaneo, Claudio;
- Coll, Francesc
Publication type:
Article
The composition, active components and bacteriostatic activity of propolis in dietetics.
Published in:
Journal of the American Oil Chemists' Society (JAOCS), 1994, v. 71, n. 5, p. 529, doi. 10.1007/BF02540666
By:
- Bonvehí, Josep;
- Coll, Francesc;
- Jordà, Rossend
Publication type:
Article
Long-term bio-cultural heritage: exploring the intermediate disturbance hypothesis in agro-ecological landscapes (Mallorca, c. 1850-2012).
Published in:
Biodiversity & Conservation, 2015, v. 24, n. 13, p. 3217, doi. 10.1007/s10531-015-0955-z
By:
- Marull, Joan;
- Tello, Enric;
- Fullana, Nofre;
- Murray, Ivan;
- Jover, Gabriel;
- Font, Carme;
- Coll, Francesc;
- Domene, Elena;
- Leoni, Veronica;
- Decolli, Trejsi
Publication type:
Article
Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites.
Published in:
PLoS Genetics, 2015, v. 11, n. 4, p. 1, doi. 10.1371/journal.pgen.1005131
By:
- Samad, Hanif;
- Coll, Francesc;
- Preston, Mark D.;
- Ocholla, Harold;
- Fairhurst, Rick M.;
- Clark, Taane G.
Publication type:
Article
Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0353-5
By:
- Harrison, Ewan M.;
- Ludden, Catherine;
- Brodrick, Hayley J.;
- Blane, Beth;
- Brennan, Gráinne;
- Morris, Dearbháile;
- Coll, Francesc;
- Reuter, Sandra;
- Brown, Nicholas M.;
- Holmes, Mark A.;
- O'Connell, Brian;
- Parkhill, Julian;
- Török, M. Estee;
- Cormican, Martin;
- Peacock, Sharon J.
Publication type:
Article
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.
Published in:
Genome Medicine, 2015, v. 7, n. 1, p. 1, doi. 10.1186/s13073-015-0164-0
By:
- Coll, Francesc;
- McNerney, Ruth;
- Preston, Mark D.;
- Guerra-Assunção, José Afonso;
- Warry, Andrew;
- Hill-Cawthorne, Grant;
- Mallard, Kim;
- Nair, Mridul;
- Miranda, Anabela;
- Alves, Adriana;
- Perdigão, João;
- Viveiros, Miguel;
- Portugal, Isabel;
- Hasan, Zahra;
- Hasan, Rumina;
- Glynn, Judith R.;
- Martin, Nigel;
- Pain, Arnab;
- Clark, Taane G.
Publication type:
Article
Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.
Published in:
2016
By:
- Phelan, Jody;
- Coll, Francesc;
- McNerney, Ruth;
- Ascher, David B.;
- Pires, Douglas E. V.;
- Furnham, Nick;
- Coeck, Nele;
- Hill-Cawthorne, Grant A.;
- Nair, Mridul B.;
- Mallard, Kim;
- Ramsay, Andrew;
- Campino, Susana;
- Hibberd, Martin L.;
- Pain, Arnab;
- Rigouts, Leen;
- Clark, Taane G.
Publication type:
journal article
Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-991
By:
- Perdigão, João;
- Silva, Hugo;
- Machado, Diana;
- Macedo, Rita;
- Maltez, Fernando;
- Silva, Carla;
- Jordao, Luisa;
- Couto, Isabel;
- Mallard, Kim;
- Coll, Francesc;
- Hill-Cawthorne, Grant A.;
- McNerney, Ruth;
- Pain, Arnab;
- Clark, Taane G.;
- Viveiros, Miguel;
- Portugal, Isabel
Publication type:
Article
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Published in:
Bioinformatics, 2012, v. 28, n. 22, p. 2991, doi. 10.1093/bioinformatics/bts544
By:
- Coll, Francesc;
- Mallard, Kim;
- Preston, Mark D.;
- Bentley, Stephen;
- Parkhill, Julian;
- McNerney, Ruth;
- Martin, Nigel;
- Clark, Taane G.
Publication type:
Article

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