Main Menu

Publications

Publications Highlights View all by category

Types of Publications


Journal Articles

Yau, C. Osdoit, M. van der Noordaa, M. Shad, S. Wei, J. de Croze, D. Hamy, A.-. Laé, M. Reyal, F. Sonke, G.S. Steenbruggen, T.G. van Seijen, M. Wesseling, J. Martín, M. del Monte-Millán, M. López-Tarruella, S. Boughey, J.C. Goetz, M.P. Hoskin, T. Gould, R. Valero, V. Edge, S.B. Abraham, J.E. Bartlett, J.M. Caldas, C. Dunn, J. Earl, H. Hayward, L. Hiller, L. Provenzano, E. Sammut, S.-. Thomas, J.S. Cameron, D. Graham, A. Hall, P. Mackintosh, L. Fan, F. Godwin, A.K. Schwensen, K. Sharma, P. DeMichele, A.M. Cole, K. Pusztai, L. Kim, M.-. van 't Veer, L.J. Esserman, L.J. Symmans, W.F. Adamson, K. Albain, K.S. Asare, A.L. Asare, S.M. Balassanian, R. Beckwith, H. Berry, S.M. Berry, D.A. Boughey, J.C. Buxton, M.B. Chen, Y.-. Chen, B. Chien, A.J. Chui, S.Y. Clark, A.S. Clennell, J.L. Datnow, B. DeMichele, A.M. Duan, X. Edmiston, K.K. Elias, A.D. Ellis, E.D. Esserman, L.L. Euhus, D.M. Fadare, O. Fan, F. Feldman, M.D. Forero-Torres, A. Haley, B.B. Han, H.S. Harada, S. Haugen, P. Helsten, T. Hirst, G.L. Hylton, N.M. Isaacs, C. Kemmer, K. Khan, Q.J. Khazai, L. Klein, M.E. Krings, G. Lang, J.E. LeBeau, L.G. Leyland-Jones, B. Liu, M.C. Lo, S. Lu, J. Magliocco, A. Matthews, J.B. Melisko, M.E. Mhawech-Fauceglia, P. Moulder, S.L. Murthy, R.K. Nanda, R. Northfelt, D.W. Ocal, I.T. Olopade, O. Pambuccian, S. Paoloni, M. Park, J.W. Parker, B.A. Perlmutter, J. Peterson, G. Pusztai, L. Rendi, M. Rugo, H.S. Sahoo, S. Sams, S. Sanil, A. Sattar, H. Schwab, R.B. Singhrao, R. Steeg, K. Stringer-Reasor, E. Symmans, W.F. Tawfik, O. Tripathy, D. Troxell, M.L. van't Veer, L.J. Venters, S.J. Vinh, T. Viscusi, R.K. Wallace, A.M. Wei, S. Wilson, A. Yau, C. Yee, D. Zeck, J.C. (2022). Residual cancer burden after neoadjuvant chemotherapy and long-term survival outcomes in breast cancer: a multicentre pooled analysis of 5161 patients. The lancet oncology, Vol.23 (1), pp. 149-160.

Pugh, T.J. Bell, J.L. Bruce, J.P. Doherty, G.J. Galvin, M. Green, M.F. Hunter-Zinck, H. Kumari, P. Lenoue-Newton, M.L. Li, M.M. Lindsay, J. Mazor, T. Ovalle, A. Sammut, S.-. Schultz, N. Yu, T.V. Sweeney, S.M. Bernard, B. (2022). AACR Project GENIE: 100,000 Cases and Beyond. Cancer discovery, Vol.12 (9), pp. 2044-2057.  show abstract

Sammut, S.-. Crispin-Ortuzar, M. Chin, S.-. Provenzano, E. Bardwell, H.A. Ma, W. Cope, W. Dariush, A. Dawson, S.-. Abraham, J.E. Dunn, J. Hiller, L. Thomas, J. Cameron, D.A. Bartlett, J.M. Hayward, L. Pharoah, P.D. Markowetz, F. Rueda, O.M. Earl, H.M. Caldas, C. (2022). Multi-omic machine learning predictor of breast cancer therapy response. Nature, Vol.601 (7894), pp. 623-629.  show abstract

Rueda, O.M. Sammut, S.-. Seoane, J.A. Chin, S.-. Caswell-Jin, J.L. Callari, M. Batra, R. Pereira, B. Bruna, A. Ali, H.R. Provenzano, E. Liu, B. Parisien, M. Gillett, C. McKinney, S. Green, A.R. Murphy, L. Purushotham, A. Ellis, I.O. Pharoah, P.D. Rueda, C. Aparicio, S. Caldas, C. Curtis, C. (2019). Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups. Nature, Vol.567 (7748), pp. 399-404.

De Mattos-Arruda, L. Sammut, S.-. Ross, E.M. Bashford-Rogers, R. Greenstein, E. Markus, H. Morganella, S. Teng, Y. Maruvka, Y. Pereira, B. Rueda, O.M. Chin, S.-. Contente-Cuomo, T. Mayor, R. Arias, A. Ali, H.R. Cope, W. Tiezzi, D. Dariush, A. Dias Amarante, T. Reshef, D. Ciriaco, N. Martinez-Saez, E. Peg, V. Ramon y Cajal, S. Cortes, J. Vassiliou, G. Getz, G. Nik-Zainal, S. Murtaza, M. Friedman, N. Markowetz, F. Seoane, J. Caldas, C. (2019). The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer. Cell reports, Vol.27 (9), pp. 2690-2708.e10.

Messaoudene, M. Mourikis, T.P. Michels, J. Fu, Y. Bonvalet, M. Lacroix-Trikki, M. Routy, B. Fluckiger, A. Rusakiewicz, S. Roberti, M.P. Cotteret, S. Flament, C. Poirier-Colame, V. Jacquelot, N. Ghiringhelli, F. Caignard, A. Eggermont, A.M. Kroemer, G. Marabelle, A. Arnedos, M. Vicier, C. Dogan, S. Jaulin, F. Sammut, S.-. Cope, W. Caldas, C. Delaloge, S. McGranahan, N. André, F. Zitvogel, L. (2019). T-cell bispecific antibodies in node-positive breast cancer: novel therapeutic avenue for MHC class I loss variants. Annals of oncology, Vol.30 (6), pp. 934-944.

McDonald, B.R. Contente-Cuomo, T. Sammut, S.-. Odenheimer-Bergman, A. Ernst, B. Perdigones, N. Chin, S.-. Farooq, M. Mejia, R. Cronin, P.A. Anderson, K.S. Kosiorek, H.E. Northfelt, D.W. McCullough, A.E. Patel, B.K. Weitzel, J.N. Slavin, T.P. Caldas, C. Pockaj, B.A. Murtaza, M. (2019). Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer. Science translational medicine, Vol.11 (504).  show abstract

Gao, M. Callari, M. Beddowes, E. Sammut, S.-. Grzelak, M. Biggs, H. Jones, L. Boumertit, A. Linn, S.C. Cortes, J. Oliveira, M. Baird, R. Chin, S.-. Caldas, C. (2019). Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA. Genome medicine, Vol.11 (1).

Chin, S.-. Santonja, A. Grzelak, M. Ahn, S. Sammut, S.-. Clifford, H. Rueda, O.M. Pugh, M. Goldgraben, M.A. Bardwell, H.A. Cho, E.Y. Provenzano, E. Rojo, F. Alba, E. Caldas, C. (2018). Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Experimental and molecular pathology, Vol.104 (3), pp. 161-169.

Callari, M. Batra, A.S. Batra, R.N. Sammut, S.-. Greenwood, W. Clifford, H. Hercus, C. Chin, S.-. Bruna, A. Rueda, O.M. Caldas, C. (2018). Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts. Bmc genomics, Vol.19 (1).

Beddowes, E. Sammut, S.J. Gao, M. Caldas, C. (2017). Predicting treatment resistance and relapse through circulating DNA. The breast, Vol.34, pp. S31-S35.

Maia, A.-. Sammut, S.-. Jacinta-Fernandes, A. Chin, S.-. (2017). Big data in cancer genomics. Current opinion in systems biology, Vol.4, pp. 78-84.

Callari, M. Sammut, S.-. De Mattos-Arruda, L. Bruna, A. Rueda, O.M. Chin, S.-. Caldas, C. (2017). Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome medicine, Vol.9 (1).

Janowitz, T. Williams, E.H. Marshall, A. Ainsworth, N. Thomas, P.B. Sammut, S.J. Shepherd, S. White, J. Mark, P.B. Lynch, A.G. Jodrell, D.I. Tavaré, S. Earl, H. (2017). New Model for Estimating Glomerular Filtration Rate in Patients With Cancer. Journal of clinical oncology, Vol.35 (24), pp. 2798-2805.  show abstract

Beumer, I.J. Persoon, M. Witteveen, A. Dreezen, C. Chin, S.-. Sammut, S.-. Snel, M. Caldas, C. Linn, S. van 't Veer, L.J. Bernards, R. Glas, A.M. (2016). Prognostic Value of MammaPrint® in Invasive Lobular Breast Cancer. Biomarker insights, Vol.11, pp. BMI.S38435-BMI.S38435.  show abstract

Bruna, A. Rueda, O.M. Greenwood, W. Batra, A.S. Callari, M. Batra, R.N. Pogrebniak, K. Sandoval, J. Cassidy, J.W. Tufegdzic-Vidakovic, A. Sammut, S.-. Jones, L. Provenzano, E. Baird, R. Eirew, P. Hadfield, J. Eldridge, M. McLaren-Douglas, A. Barthorpe, A. Lightfoot, H. O'Connor, M.J. Gray, J. Cortes, J. Baselga, J. Marangoni, E. Welm, A.L. Aparicio, S. Serra, V. Garnett, M.J. Caldas, C. (2016). A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Cell, Vol.167 (1), pp. 260-274.e22.  show abstract

Vollan, H.K. Rueda, O.M. Chin, S.-. Curtis, C. Turashvili, G. Shah, S. Lingjaerde, O.C. Yuan, Y. Ng, C.K. Dunning, M.J. Dicks, E. Provenzano, E. Sammut, S. McKinney, S. Ellis, I.O. Pinder, S. Purushotham, A. Murphy, L.C. Kristensen, V.N. Brenton, J.D. Pharoah, P.D. Børresen-Dale, A.-. Aparicio, S. Caldas, C. (2015). A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Molecular oncology, Vol.9 (1), pp. 115-127.

Sammut, S.J. Tomson, N. Corrie, P. (2014). Pyogenic Granuloma as a Cutaneous Adverse Effect of Vemurafenib. New england journal of medicine, Vol.371 (13), pp. 1265-1267.

Chen, L. Kostadima, M. Martens, J.H. Canu, G. Garcia, S.P. Turro, E. Downes, K. Macaulay, I.C. Bielczyk-Maczynska, E. Coe, S. Farrow, S. Poudel, P. Burden, F. Jansen, S.B. Astle, W.J. Attwood, A. Bariana, T. de Bono, B. Breschi, A. Chambers, J.C. Choudry, F.A. Clarke, L. Coupland, P. van der Ent, M. Erber, W.N. Jansen, J.H. Favier, R. Fenech, M.E. Foad, N. Freson, K. van Geet, C. Gomez, K. Guigo, R. Hampshire, D. Kelly, A.M. Kerstens, H.H. Kooner, J.S. Laffan, M. Lentaigne, C. Labalette, C. Martin, T. Meacham, S. Mumford, A. Nürnberg, S.T. Palumbo, E. van der Reijden, B.A. Richardson, D. Sammut, S.J. Slodkowicz, G. Tamuri, A.U. Vasquez, L. Voss, K. Watt, S. Westbury, S. Flicek, P. Loos, R. Goldman, N. Bertone, P. Read, R.J. Richardson, S. Cvejic, A. Soranzo, N. Ouwehand, W.H. Stunnenberg, H.G. Frontini, M. Rendon, A. (2014). Transcriptional diversity during lineage commitment of human blood progenitors. Science, Vol.345 (6204).  show abstract

Sammut, S.J. Mazhar, D. (2012). Management of febrile neutropenia in an acute oncology service. Qjm, Vol.105 (4), pp. 327-336.

de Bono, B. Grenon, P. Sammut, S.J. (2012). ApiNATOMY: A novel toolkit for visualizing multiscale anatomy schematics with phenotype-related information. Human mutation, Vol.33 (5), pp. 837-848.

Curtis, C. Shah, S.P. Chin, S.-. Turashvili, G. Rueda, O.M. Dunning, M.J. Speed, D. Lynch, A.G. Samarajiwa, S. Yuan, Y. Gräf, S. Ha, G. Haffari, G. Bashashati, A. Russell, R. McKinney, S. Langerød, A. Green, A. Provenzano, E. Wishart, G. Pinder, S. Watson, P. Markowetz, F. Murphy, L. Ellis, I. Purushotham, A. Børresen-Dale, A.-. Brenton, J.D. Tavaré, S. Caldas, C. Aparicio, S. (2012). The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, Vol.486 (7403), pp. 346-352.

Batra, R.N. Lifshitz, A. Vidakovic, A.T. Chin, S.-. Sati-Batra, A. Sammut, S.-. Provenzano, E. Ali, H.R. Dariush, A. Bruna, A. Murphy, L. Purushotham, A. Ellis, I. Green, A. Garrett-Bakelman, F.E. Mason, C. Melnick, A. Aparicio, S.A. Rueda, O.M. Tanay, A. Caldas, C. DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. Nature communications, Vol.12 (1).  show abstract

Pereira, B. Chin, S.-. Rueda, O.M. Vollan, H.-. Provenzano, E. Bardwell, H.A. Pugh, M. Jones, L. Russell, R. Sammut, S.-. Tsui, D.W. Liu, B. Dawson, S.-. Abraham, J. Northen, H. Peden, J.F. Mukherjee, A. Turashvili, G. Green, A.R. McKinney, S. Oloumi, A. Shah, S. Rosenfeld, N. Murphy, L. Bentley, D.R. Ellis, I.O. Purushotham, A. Pinder, S.E. Børresen-Dale, A.-. Earl, H.M. Pharoah, P.D. Ross, M.T. Aparicio, S. Caldas, C. The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes. Nature communications, Vol.7 (1).  show abstract

Pan, J.-. Zabidi, M.M. Ng, P.-. Meng, M.-. Hasan, S.N. Sandey, B. Sammut, S.-. Yip, C.-. Rajadurai, P. Rueda, O.M. Caldas, C. Chin, S.-. Teo, S.-. The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences. Nature communications, Vol.11 (1).  show abstract

De Mattos-Arruda, L. Cortes, J. Blanco-Heredia, J. Tiezzi, D.G. Villacampa, G. Gonçalves-Ribeiro, S. Paré, L. Souza, C.A. Ortega, V. Sammut, S.-. Cusco, P. Fasani, R. Chin, S.-. Perez-Garcia, J. Dienstmann, R. Nuciforo, P. Villagrasa, P. Rubio, I.T. Prat, A. Caldas, C. The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers. Npj breast cancer, Vol.7 (1).  show abstract

Michaut, M. Chin, S.-. Majewski, I. Severson, T.M. Bismeijer, T. de Koning, L. Peeters, J.K. Schouten, P.C. Rueda, O.M. Bosma, A.J. Tarrant, F. Fan, Y. He, B. Xue, Z. Mittempergher, L. Kluin, R.J. Heijmans, J. Snel, M. Pereira, B. Schlicker, A. Provenzano, E. Ali, H.R. Gaber, A. O’Hurley, G. Lehn, S. Muris, J.J. Wesseling, J. Kay, E. Sammut, S.J. Bardwell, H.A. Barbet, A.S. Bard, F. Lecerf, C. O’Connor, D.P. Vis, D.J. Benes, C.H. McDermott, U. Garnett, M.J. Simon, I.M. Jirström, K. Dubois, T. Linn, S.C. Gallagher, W.M. Wessels, L.F. Caldas, C. Bernards, R. Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer. Scientific reports, Vol.6 (1).  show abstract

Pereira, B. Chin, S.-. Rueda, O.M. Vollan, H.-. Provenzano, E. Bardwell, H.A. Pugh, M. Jones, L. Russell, R. Sammut, S.-. Tsui, D.W. Liu, B. Dawson, S.-. Abraham, J. Northen, H. Peden, J.F. Mukherjee, A. Turashvili, G. Green, A.R. McKinney, S. Oloumi, A. Shah, S. Rosenfeld, N. Murphy, L. Bentley, D.R. Ellis, I.O. Purushotham, A. Pinder, S.E. Børresen-Dale, A.-. Earl, H.M. Pharoah, P.D. Ross, M.T. Aparicio, S. Caldas, C. Erratum: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes. Nature communications, Vol.7 (1).  show abstract

Sammut, S.J. Finn, R.D. Bateman, A. Pfam 10 years on: 10 000 families and still growing. Briefings in bioinformatics, Vol.9 (3), pp. 210-219.

Finn, R.D. Tate, J. Mistry, J. Coggill, P.C. Sammut, S.J. Hotz, H.-. Ceric, G. Forslund, K. Eddy, S.R. Sonnhammer, E.L. Bateman, A. The Pfam protein families database. Nucleic acids research, Vol.36 (Database), pp. D281-D288.


Conferences

de Bono, B.Sammut, S.J.Grenon, P. (2011). Achieving Semantic Interoperability between Physiology Models and Clinical Data, Presented at 2011 IEEE Seventh International Conference on e-Science Workshops (eScienceW), 2011 IEEE Seventh International Conference on e-Science Workshops, .

In this section

Publications Research overview