Teaching Breast Cancer in Undergraduate Science Courses: Innovative approaches to stimulate research interest and engagement

Population structure, antimicrobial resistance, and virulence factors of diabetic foot-associated E. coli
Ajumobi, V., Tahir, Z., Hayes, P.M., McCormick, A.L. and Torraca, V. 2026. Population structure, antimicrobial resistance, and virulence factors of diabetic foot-associated E. coli. Microbiology Spectrum. 14 (2) e02837-25. https://doi.org/10.1128/spectrum.02837-25

Human Nucleic Acids and Inheritance
Tinworth, L. 2025. Human Nucleic Acids and Inheritance. in: Volpi, E. and Tinworth, L. (ed.) Medical Genetics and Genomics Oxford University Press (OUP).

Patterns of phosphorylated tau accumulation in a spectrum of acquired and developmental brain lesions associated with refractory epilepsy
Mrzyglod A., Mebrouk, A., Bartkiewicz, J., El Hachami, H., Ryniejska, M., deTisi, J., Coras, R., Blumcke, I., Xiao, F., Miserocchi, A., McEvoy, A., Koepp, M., Liu, J.Y.W. and Thom, M. 2025. Patterns of phosphorylated tau accumulation in a spectrum of acquired and developmental brain lesions associated with refractory epilepsy. Epilepsia. 66, pp. 3006-3021. https://doi.org/10.111/epi.18418

Evaluation of Antioxidant and Anti-Inflammatory Effects of a Nanoformulation Derived from Annurca Apple Callus Extract in an In Vitro Model of Iron Overload-Induced Inflammation
Gubitosa, F., Taramova, L., Chan, S., Liu, J.Y.W., Fraternale, D., Patel, V. B., Somavarapu, S., Potenza, L. and Zariwala, M. 2025. Evaluation of Antioxidant and Anti-Inflammatory Effects of a Nanoformulation Derived from Annurca Apple Callus Extract in an In Vitro Model of Iron Overload-Induced Inflammation. Antioxidants. 14 (6) 631. https://doi.org/10.3390/antiox14060631

Abstract 4550: Dried blood sot sampling as a minimally invasive and accessible method for investigating circulating tumor DNA in diverse cancer settings
Amit Roshan, Fazlur R. Talukdar, Angela An, Emma-Jane Ditter, Ze Zhou, Paulius D. Mennea, Linfang Wu, Maria C. Neofytou, Anita Balakrishnan, Claire M. Connell, Gabriel Funingana, Giovanni Codacci-Pisanelli, Girma Mulisa, Tamrat Abebe, Constanza Linossi, Hui Zhao, Wendy N. Cooper, Huiqi Yang, Rajesh Jena, James D. Brenton, Pippa Corrie, Rebecca C. Fitzgerald, Simon Pacey, Richard Baird and Nitzan Rosenfeld 2025. Abstract 4550: Dried blood sot sampling as a minimally invasive and accessible method for investigating circulating tumor DNA in diverse cancer settings. Cancer Research. 85 (8_Suppl_1), p. Abstract nr 4550. https://doi.org/10.1158/1538-7445.am2025-4550

A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.
Wang, H., Mennea, P.D., Chan, Y.K.E., Cheng, Z., Neofytou, M.C., Surani, A.A., Vijayaraghavan, A., Ditter, E.J., Bowers, R., Eldridge, M.D., Shcherbo, D.S., Smith, C.G., Markowetz, F., Cooper, W.N., Kaplan, T., Rosenfeld, N. and Zhao, H. 2025. A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data. Genome Biology. 26 141. https://doi.org/10.1186/s13059-025-03607-5

The prevalence of chronic traumatic encephalopathy in a historical epilepsy post‐mortem collection
Ryniejska, Maritchka, El‐Hachami, Hanaa, Mrzyglod, Alicja, Liu, Joan and Thom, M. 2025. The prevalence of chronic traumatic encephalopathy in a historical epilepsy post‐mortem collection. Brain Pathology. 35 (3), p. e13317. https://doi.org/10.1111/bpa.13317

The prevalence of chronic traumatic encephalopathy in a historical epilepsy post-mortem collection
Ryniejska, M., El-Hachami, H., Mrzyglod, A., Liu, J.Y.W. and Thom, M. 2025. The prevalence of chronic traumatic encephalopathy in a historical epilepsy post-mortem collection. Brain Pathology. 35 (3) e13317. https://doi.org/10.1111/bpa.13317

Microangiopathy in temporal lobe epilepsy with diffusion MRI alterations and cognitive decline
Joan Y.W. Liu, Lawrence Binding, Isha Puntambekar, Smriti Patodia, Yau Lim, Alicja Mrzyglod, Fenglai Xiao, Shengning Pan, Remika Mito, Jane deTisi, John S Duncan, Sallie Baxendale, Matthias Koepp and Maria Thom 2024. Microangiopathy in temporal lobe epilepsy with diffusion MRI alterations and cognitive decline. Acta Neuropathologica Communications. 148 49. https://doi.org/10.1007/s00401-024-02809-8

Doctors’ and nurses’ eating practices during shift work: Findings from a qualitative study
Sum, K., Cheshire, A., Ridge, Damien T., Sengupta, D. and Deb, D.S. 2024. Doctors’ and nurses’ eating practices during shift work: Findings from a qualitative study. Proceedings of the Nutrition Society. 83 (OCE2), p. E204. https://doi.org/10.1017/s0029665124004282

The Cavendish Living lab - a multidisciplinary, vertically integrated project focused on sustainability
Basnett, P., Percy, L., Sengupta, D. and Smith, C.L. 2023. The Cavendish Living lab - a multidisciplinary, vertically integrated project focused on sustainability. Westminster Learning and Teaching Symposium 2023: Better Than the Real Thing? Exploring Education Futures at the University of Westminster. University of Westminster 04 Sep 2023

Antiviral Drug Target Identification and Ligand Discovery
Patel, Hershna and Sengupta, Dipankar 2023. Antiviral Drug Target Identification and Ligand Discovery. in: Gore, M. and Jagtap, U.B. (ed.) Computational Drug Discovery and Design Springer.

Dual production of polyhydroxyalkanoates and antibacterial/antiviral gold nanoparticles
McCormick, A.L., Basnett, P., Vecchiato, V., Wright, E., Noble, B., Marcello, E. and Paxinou, A. 2023. Dual production of polyhydroxyalkanoates and antibacterial/antiviral gold nanoparticles. Frontiers in Nanotechnology. 5 1243056. https://doi.org/10.3389/fnano.2023.1243056

Smart Urban Metabolism: A Big-Data and Machine Learning Perspective
Ruchira Ghosh and Dipankar Sengupta 2023. Smart Urban Metabolism: A Big-Data and Machine Learning Perspective. in: Urban Metabolism and Climate Change Springer. pp. 325–344

Inhibiting CDK4/6 in pancreatic ductal adenocarcinoma via microRNA-21
Mortoglou, M., Miralles, F., Mould, R., Sengupta, D. and Uysal Onganer, P. 2023. Inhibiting CDK4/6 in pancreatic ductal adenocarcinoma via microRNA-21. European Journal of Cell Biology. 102 (2) 151318. https://doi.org/10.1016/j.ejcb.2023.151318

Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
Mueller, Stefanie H, Lai, Alvina G, Valkovskaya, Maria, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Lush, Michael, Abu-Ful, Zomoruda, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Baert, Thais, Freeman, Laura E Beane, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Brenner, Hermann, Brucker, Sara Y, Buys, Saundra S, Castelao, Jose E, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Choi, Ji-Yeob, Chung, Wendy K, NBCS Collaborators, Colonna, Sarah V, CTS Consortium, Cornelissen, Sten, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dossus, Laure, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Gago-Dominguez, Manuela, Gao, Yu-Tang, García-Closas, Montserrat, García-Sáenz, José A, Genkinger, Jeanine, Gentry-Maharaj, Aleksandra, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Harkness, Elaine F, Harrington, Patricia A, Hartikainen, Jaana M, Hartman, Mikael, Hein, Alexander, Ho, Weang-Kee, Hooning, Maartje J, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Hunter, David J, Huo, Dezheng, ABCTB Investigators, Ito, Hidemi, Iwasaki, Motoki, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Khusnutdinova, Elza K, Kim, Sung-Won, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Kwong, Ava, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Linet, Martha, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Matsuo, Keitaro, Mavroudis, Dimitrios, Menon, Usha, Muir, Kenneth, Murphy, Rachel A, Nevanlinna, Heli, Newman, William G, Niederacher, Dieter, O'Brien, Katie M, Obi, Nadia, Offit, Kenneth, Olopade, Olufunmilayo I, Olshan, Andrew F, Olsson, Håkan, Park, Sue K, Patel, Alpa V, Patel, Achal, Perou, Charles M, Peto, Julian, Pharoah, Paul D P, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Ramachandran, Dhanya, Rashid, Muhammad U, Rennert, Gad, Romero, Atocha, Ruddy, Kathryn J, Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Schneider, Michael O, Scott, Christopher, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Surowy, Harald, Tamimi, Rulla M, Tapper, William J, Taylor, Jack A, Teo, Soo Hwang, Teras, Lauren R, Toland, Amanda E, Tollenaar, Rob A E M, Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Vijai, Joseph, Weinberg, Clarice R, Wendt, Camilla, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Yamaji, Taiki, Yang, Xiaohong R, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, Dunning, Alison M, Easton, Douglas F, Hemingway, Harry, Hamann, Ute and Kuchenbaecker, K. 2023. Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry. Genome Medicine. 15 (1), p. 7. https://doi.org/10.1186/s13073-022-01152-5

Author Correction: A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex
Jones, A.R., Iacoangeli, A., Adey, B.N., Bowles, H., Shatunov, A., Troakes, C., Garson, J.A., McCormick, A.L. and Al‑Chalabi, A. 2022. Author Correction: A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Scientific Reports. 12 14171. https://doi.org/10.1038/s41598-022-18488-y

Physical activity, sedentary time and breast cancer risk: a Mendelian randomisation study.
Dixon-Suen, S., Lewis, Sarah J, Martin, Richard M, English, Dallas R, Boyle, T., Giles, Graham G, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Lush, Michael, Investigators, Abctb, Ahearn, Thomas U, Ambrosone, Christine B, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Auvinen, Päivi, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Brenner, Hermann, Brüning, Thomas, Buys, Saundra S, Camp, Nicola J, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Cessna, Melissa H, Chang-Claude, Jenny, Chanock, Stephen J, Clarke, Christine L, Conroy, Don M, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dwek, Miriam, Eccles, Diana M, Eliassen, A Heather, Engel, Christoph, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Goldberg, Mark S, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Häberle, Lothar, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N, Harvie, Michelle, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J, Hoppe, Reiner, Hopper, John, Howell, Anthony, Hunter, David J, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jung, Audrey, Kaaks, Rudolf, Keeman, Renske, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Loibl, Sibylle, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, Mavroudis, Dimitrios, Menon, Usha, Mulligan, Anna Marie, Murphy, Rachel A, Collaborators, Nbcs, Nevanlinna, Heli, Nevelsteen, Ines, Newman, William G, Offit, Kenneth, Olshan, Andrew F, Olsson, Håkan, Orr, Nick, Patel, Alpa, Peto, Julian, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Rees-Punia, Erika, Rennert, Gad, Rennert, Hedy S, Romero, A., Saloustros, Emmanouil, Sandler, Dale P, Schmidt, Marjanka K, Schmutzler, Rita K, Schwentner, Lukas, Scott, Christopher, Shah, Mitul, Shu, Xiao-Ou, Simard, Jacques, Southey, Melissa C, Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Taylor, Jack A, Terry, Mary Beth, Tollenaar, Rob A E M, Troester, Melissa A, Truong, Thérèse, Untch, Michael, Vachon, Celine M, Joseph, Vijai, Wappenschmidt, Barbara, Weinberg, Clarice R, Wolk, Alicja, Yannoukakos, Drakoulis, Zheng, Wei, Ziogas, Argyrios, Dunning, Alison M, Pharoah, Paul D P, Easton, Douglas F, Milne, Roger L, Lynch, B. and Breast Cancer Association Consortium 2022. Physical activity, sedentary time and breast cancer risk: a Mendelian randomisation study. British Journal of Sports Medicine. 56 (20), pp. 1157-1170. https://doi.org/10.1136/bjsports-2021-105132

Author Correction: A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex
Jones, Ashley R., Iacoangeli, Alfredo, Adey, Brett N., Bowles, Harry, Shatunov, Aleksey, Troakes, Claire, Garson, Jeremy A., McCormick, Adele L. and Al-Chalabi, Ammar 2022. Author Correction: A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Scientific Reports. 12 (1) 14171. https://doi.org/10.1038/s41598-022-18488-y

Serotonin transporter in the temporal lobe, hippocampus and amygdala in SUDEP
Patodia, S., Somani, A., Liu, J.Y.W., Cattaneo, A., Paradisco, B., Garcia, M., Othman, M., Diehl, B., Foong, J. and Thom, M. 2022. Serotonin transporter in the temporal lobe, hippocampus and amygdala in SUDEP. Brain Pathology. 32 (5) e13074. https://doi.org/10.1111/bpa.13074

Safety of intracranial electroencephalography during functional electromagnetic resonance imaging in humans at 1.5 tesla using a head transmit RF coil: Histopathological and heat-shock immunohistochemistry observations.
Liu, Joan Y W, Hawsawi, Hassan B, Sharma, Niraj, Carmichael, David W, Diehl, Beate, Thom, Maria and Lemieux, Louis 2022. Safety of intracranial electroencephalography during functional electromagnetic resonance imaging in humans at 1.5 tesla using a head transmit RF coil: Histopathological and heat-shock immunohistochemistry observations. NeuroImage. 254 119129. https://doi.org/10.1016/j.neuroimage.2022.119129

Renal tumouroids: challenges of manufacturing 3D cultures from patient derived primary cells.
Nyga, A., Stamati, Katerina, Redondo, Patricia A, Azimi, Tayebeh, Feber, Andrew, Neves, Joana B, Hamoudi, Rifat, Presneau, Nadège, El Sheikh, Soha, Tran, Maxine G B, Emberton, Mark, Loizidou, Marilena and Cheema, Umber 2022. Renal tumouroids: challenges of manufacturing 3D cultures from patient derived primary cells. Journal of Cell Communication and Signaling. 16, pp. 637-648. https://doi.org/10.1007/s12079-022-00666-2

A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex.
Jones, A.R., Iacoangeli, A., Adey, B.N., Bowles, H., Shatunov, A, Troakes, C., Garson, J.A., McCormick, A.L. and Al‑Chalabi, A. 2021. A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Scientific Reports. 11 14283. https://doi.org/10.1038/s41598-021-93742-3

Interpretable semisupervised classifier for predicting cancer stages
Grau, I., Sengupta, D. and Nowe, A. 2021. Interpretable semisupervised classifier for predicting cancer stages. in: Kumar, P., Kumar, Y. and Tawhid, M.A. (ed.) Machine Learning, Big Data, and IoT for Medical Informatics Academic Press. pp. 241-259

Artificial Intelligence in Precision Medicine: A Perspective in Biomarker and Drug Discovery
Sengupta, D. and Santoshi, S. 2021. Artificial Intelligence in Precision Medicine: A Perspective in Biomarker and Drug Discovery. in: Saxena, A. and Chandra, S. (ed.) Artificial Intelligence and Machine Learning in Healthcare Springer. pp. 71-88

An ensemble approach for evaluating the cognitive performance of human population at high altitude
Sengupta, D., Sharma, V.K., Hota, S.K., Srivastava, R.B. and Naik, P.K. 2021. An ensemble approach for evaluating the cognitive performance of human population at high altitude. in: Kumar, P., Kumar, Y. and Tawhid, M.A. (ed.) Machine Learning, Big Data, and IoT for Medical Informatics Academic Press. pp. 165-178

Machine learning in precision medicine
Sengupta, D. 2021. Machine learning in precision medicine. in: Kumar, P., Kumar, Y. and Tawhid, M.A. (ed.) Machine Learning, Big Data, and IoT for Medical Informatics Academic Press. pp. 405-419

Breast Cancer Risk Factors and Survival by Tumor Subtype: Pooled Analyses from the Breast Cancer Association Consortium
Morra, Anna, Jung, Audrey Y., Behrens, S., Keeman, R., Ahearn, T., Anton-Culver, Hoda, Arndt, V., Augustinsson, A., Auvinen, Päivi K., Beane Freeman, Laura E., Becher, Heiko, Beckmann, Matthias W., Blomqvist, Carl, Bojesen, Stig E., Bolla, Manjeet K., Brenner, H., Briceno, Ignacio, Brucker, Sara Y., Camp, N., Campa, Daniele, Canzian, F., Castelao, Jose E., Chanock, Stephen J., Choi, Ji-Yeob, Clarke, Christine L., Couch, Fergus J., Cox, A., Cross, Simon S., Czene, Kamila, Dörk, Thilo, Dunning, A., Dwek, Miriam, Easton, Douglas F., Eccles, Diana M., Egan, Kathleen M., Evans, D., Fasching, P., Flyger, Henrik, Gago-Dominguez, M., Gapstur, Susan M., Garcia-Saenz, J., Gaudet, M., Giles, G., Grip, Mervi, Guénel, P., Haiman, Christopher A., Håkansson, Niclas, Hall, P., Hamann, Ute, Han, Sileny N., Hart, S., Hartman, M., Heyworth, Jane S., Hoppe, Reiner, Hopper, John L., Hunter, David J., Ito, H., Jager, A., Jakimovska, Milena, Jakubowska, A., Janni, W., Kaaks, R., Kang, Daehee, Middha Kapoor, P., Kitahara, Cari M., Koutros, S., Kraft, Peter, Kristensen, Vessela N., Lacey, James V., Lambrechts, D., Le Marchand, Loic, Li, J., Lindblom, Annika, Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mariapun, Shivaani, Matsuo, K., Mavroudis, Dimitrios, Milne, R., Muranen, T., Newman, W., Noh, Dong-Young, Nordestgaard, Børge G., Obi, Nadia, Olshan, Andrew F., Olsson, Håkan, Park-Simon, T., Petridis, Christos, Pharoah, P., Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rashid, Muhammad U., Rennert, G., Rennert, H., Rhenius, V., Romero, A., Saloustros, E., Sawyer, Elinor J., Schneeweiss, A., Schwentner, Lukas, Scott, C., Shah, Mitul, Shen, Chen-Yang, Shu, Xiao-Ou, Southey, M., Stram, D., Tamimi, R., Tapper, William, Tollenaar, Rob A.E.M., Tomlinson, I., Torres, D., Troester, Melissa A., Truong, Thérèse, Vachon, C., Wang, Qin, Wang, Sophia S., Williams, Justin A., Winqvist, Robert, Wolk, A., Wu, Anna H., Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, A., Yang, Xiaohong R., Eliassen, A. Heather, Holmes, M., Garcia-Closas, M., Teo, S., Schmidt, M. and Chang-Claude, J. 2021. Breast Cancer Risk Factors and Survival by Tumor Subtype: Pooled Analyses from the Breast Cancer Association Consortium. Cancer Epidemiology, Biomarkers and Prevention. 30 (4), pp. 623-642. https://doi.org/10.1158/1055-9965.epi-20-0924

Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment.
Morra, Anna, Escala-Garcia, Maria, Beesley, Jonathan, Keeman, Renske, Canisius, Sander, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L, Augustinsson, Annelie, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Brüning, Thomas, Buys, Saundra S, Caan, Bette, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Cheng, Ting-Yuan David, Clarke, Christine L, Colonna, Sarah V, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Dörk, T., Dossus, Laure, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, García-Sáenz, José A, Giles, Graham G, Grip, Mervi, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N, Hartikainen, Jaana M, Hartmann, Arndt, He, Wei, Hooning, Maartje J, Hoppe, Reiner, Hopper, John L, Howell, Anthony, Hunter, David J, Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Keupers, Machteld, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Linet, Martha, Luben, Robert N, Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martens, John W M, Martinez, Maria Elena, Mavroudis, Dimitrios, Michailidou, Kyriaki, Milne, Roger L, Mulligan, Anna Marie, Muranen, Taru A, Nevanlinna, Heli, Newman, W., Nielsen, Sune F, Nordestgaard, Børge G, Olshan, Andrew F, Olsson, Håkan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa V, Peissel, Bernard, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Presneau, Nadege, Rack, Brigitte, Rennert, Gad, Rennert, Hedy S, Rhenius, Valerie, Romero, A., Roylance, Rebecca, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schneeweiss, Andreas, Scott, Christopher, Shah, Mitul, Smichkoska, Snezhana, Southey, Melissa C, Stone, J., Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Teras, Lauren R, Terry, Mary Beth, Tollenaar, Rob A E M, Tomlinson, Ian, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Wang, Qin, Hurson, Amber N, Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Brauch, Hiltrud, García-Closas, Montserrat, Pharoah, Paul D P, Easton, Douglas F, Chenevix-Trench, Georgia and Schmidt, M. 2021. Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment. Breast cancer research : BCR. 23 (1) 86. https://doi.org/10.1186/s13058-021-01450-7

Mendelian randomisation study of smoking exposure in relation to breast cancer risk.
Park, H., Neumeyer, Sonja, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, J., Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, A., Baten, Adinda, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, H., Brucker, Sara Y, Burwinkel, Barbara, Campa, Daniele, Canzian, F., Castelao, Jose E, Chanock, Stephen J, Chenevix-Trench, Georgia, Clarke, Christine L, NBCS Collaborators, Conroy, Don M, Couch, Fergus J, Cox, A., Cross, Simon S, Czene, Kamila, Daly, Mary B, Devilee, P., Dörk, Thilo, Dos-Santos-Silva, Isabel, Dwek, Miriam, Eccles, Diana M, Eliassen, A Heather, Engel, Christoph, Eriksson, Mikael, Evans, D Gareth, Fasching, P., Flyger, Henrik, Fritschi, Lin, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, Giles, Graham G, Glendon, Gord, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Grip, Mervi, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Han, Sileny, Harkness, E., Hart, S., He, Wei, Heemskerk-Gerritsen, B., Hopper, John L, Hunter, David J, ABCTB Investigators, kConFab Investigators, Jager, Agnes, Jakubowska, A., John, Esther M, Jung, Audrey, Kaaks, Rudolf, Middha Kapoor, P., Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M, Koppert, Linetta B, Koutros, Stella, Kristensen, Vessela N, Kurian, A., Lacey, James, Lambrechts, Diether, Le Marchand, Loic, Lo, Wing-Yee, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, Mavroudis, Dimitrios, Meindl, Alfons, Menon, Usha, Milne, Roger L, Muranen, Taru A, Nevanlinna, Heli, Newman, W., Nordestgaard, Børge G, Offit, Kenneth, Olshan, Andrew F, Olsson, Håkan, Park-Simon, Tjoung-Won, Peterlongo, P., Peto, J., Plaseska-Karanfilska, Dijana, Presneau, Nadege, Radice, Paolo, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Saloustros, Emmanouil, Sawyer, E., Schmidt, Marjanka K, Schmutzler, Rita K, Schoemaker, Minouk J, Schwentner, Lukas, Scott, C., Shah, Mitul, Shu, Xiao-Ou, Simard, Jacques, Smeets, A., Southey, Melissa C, Spinelli, John J, Stevens, Victoria, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Taylor, Jack A, Terry, Mary Beth, Tomlinson, I., Troester, Melissa A, Truong, T., Vachon, Celine M, van Veen, Elke M, Vijai, Joseph, Wang, Sophia, Wendt, Camilla, Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Dunning, Alison M, Pharoah, P., Easton, Douglas F, Zheng, Wei, Kraft, Peter and Chang-Claude, Jenny 2021. Mendelian randomisation study of smoking exposure in relation to breast cancer risk. British Journal of Cancer. https://doi.org/10.1038/s41416-021-01432-8

Glial regenerative cell types in the superficial cortex in cortical dysplasia subtypes
Liu, J., Reeves, C., van der Pijl, R. and Thom, M. 2021. Glial regenerative cell types in the superficial cortex in cortical dysplasia subtypes. Epilepsy Research. 169 106529. https://doi.org/10.1016/j.eplepsyres.2020.106529

Breast Cancer Detection and Treatment Monitoring Using a Noninvasive Prenatal Testing Platform: Utility in Pregnant and Nonpregnant Populations.
Lenaerts, L., Che, H., Brison, N., Neofytou, M., Jatsenko, T., Lefrère, H., Maggen, C., Villela, D., Verheecke, M., Dehaspe, L., Croitor, A., Hatse, S., Wildiers, H., Neven, P. and Amant, F. 2020. Breast Cancer Detection and Treatment Monitoring Using a Noninvasive Prenatal Testing Platform: Utility in Pregnant and Nonpregnant Populations. Clinical Chemistry. 66 (11), pp. 1414-1423. https://doi.org/10.1093/clinchem/hvaa196

Predicting fetoplacental mosaicism during cfDNA-based NIPT.
Neofytou, M. 2020. Predicting fetoplacental mosaicism during cfDNA-based NIPT. Current Opinion in Obstetrics and Gynecology. 32 (2), pp. 152-158. https://doi.org/10.1097/gco.0000000000000610

Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA
Huiwen Che, Darine Villela, Eftychia Dimitriadou, Cindy Melotte, Nathalie Brison, Maria Neofytou, Kris Van Den Bogaert, Olga Tsuiko, Koen Devriendt, Eric Legius, Masoud Zamani Esteki, Thierry Voet and Joris Robert Vermeesch 2020. Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA. Genetics in Medicine. 22 (5), pp. P962-973. https://doi.org/10.1038/s41436-019-0748-y

An interpretable semi-supervised classifier using rough sets for amended self-labeling
Grau, I., Sengupta, D., Garcia Lorenzo, M.M. and Nowe, A. 2020. An interpretable semi-supervised classifier using rough sets for amended self-labeling. IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2020). Glasgow, UK 19 - 24 Jul 2020 IEEE . https://doi.org/10.1109/fuzz48607.2020.9177549

Elevated microRNA expression could be diagnostic biomarker for PDAC
Mortoglou, M., Arisan, D., Ferreira, T., McCormick, A.L. and Uysal Onganer, P. 2020. Elevated microRNA expression could be diagnostic biomarker for PDAC. Pancreatology. 20 (8) e19. https://doi.org/10.1016/j.pan.2020.10.015

Granule Cell Dispersion in Human Temporal Lobe Epilepsy: Proteomics investigation of neurodevelopmental migratory pathways
Liu, J., Dzurova, N., Al-Kaaby, B., Millks, K., Sisodiya, S.M. and Thom, M. 2020. Granule Cell Dispersion in Human Temporal Lobe Epilepsy: Proteomics investigation of neurodevelopmental migratory pathways. Frontiers in Cellular Neuroscience. 14 53. https://doi.org/10.3389/fncel.2020.00053

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis
Maria Escala-Garcia, Jean Abraham, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Alan Ashworth, Paul L. Auer, Päivi Auvinen, Matthias W. Beckmann, Jonathan Beesley, Sabine Behrens, Javier Benitez, Marina Bermisheva, Carl Blomqvist, William Blot, Natalia V. Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Anne-Lise Børresen-Dale, Hiltrud Brauch, Hermann Brenner, Sara Y. Brucker, Barbara Burwinkel, Carlos Caldas, Federico Canzian, Jenny Chang-Claude, Stephen J. Chanock, Suet-Feung Chin, Christine L. Clarke, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Mary B. Daly, Joe Dennis, Peter Devilee, Janet A. Dunn, Alison M. Dunning, Miriam Dwek, Helena M. Earl, Diana M. Eccles, A. Heather Eliassen, Carolina Ellberg, D. Gareth Evans, Peter A. Fasching, Jonine Figueroa, Henrik Flyger, Manuela Gago-Dominguez, Susan M. Gapstur, Montserrat García-Closas, José A. García-Sáenz, Mia M. Gaudet, Angela George, Graham G. Giles, David E. Goldgar, Anna González-Neira, Mervi Grip, Pascal Guénel, Qi Guo, Christopher A. Haiman, Niclas Håkansson, Ute Hamann, Patricia A. Harrington, Louise Hiller, Maartje J. Hooning, John L. Hopper, Anthony Howell, Chiun-Sheng Huang, Guanmengqian Huang, David J. Hunter, Anna Jakubowska, Esther M. John, Rudolf Kaaks, Pooja Middha Kapoor, Renske Keeman, Cari M. Kitahara, Linetta B. Koppert, Peter Kraft, Vessela N. Kristensen, Diether Lambrechts, Loic Le Marchand, Flavio Lejbkowicz, Annika Lindblom, Jan Lubiński, Arto Mannermaa, Mehdi Manoochehri, Siranoush Manoukian, Sara Margolin, Maria Elena Martinez, Tabea Maurer, Dimitrios Mavroudis, Alfons Meindl, Roger L. Milne, Anna Marie Mulligan, Susan L. Neuhausen, Heli Nevanlinna, William G. Newman, Andrew F. Olshan, Janet E. Olson, Håkan Olsson, Nick Orr, Paolo Peterlongo, Christos Petridis, Ross L. Prentice, Nadege Presneau, Kevin Punie, Dhanya Ramachandran, Gad Rennert, Atocha Romero, Mythily Sachchithananthan, Emmanouil Saloustros, Elinor J. Sawyer, Rita K. Schmutzler, Lukas Schwentner, Christopher Scott, Jacques Simard, Christof Sohn, Melissa C. Southey, Anthony J. Swerdlow, Rulla M. Tamimi, William J. Tapper, Manuel R. Teixeira, Mary Beth Terry, Heather Thorne, Rob A. E. M. Tollenaar, Ian Tomlinson, Melissa A. Troester, Thérèse Truong, Clare Turnbull, Celine M. Vachon, Lizet E. van der Kolk, Qin Wang, Robert Winqvist, Alicja Wolk, Xiaohong R. Yang, Argyrios Ziogas, Paul D. P. Pharoah, Per Hall, Lodewyk F. A. Wessels, Georgia Chenevix-Trench, Gary D. Bader, Thilo Dörk, Douglas F. Easton, Sander Canisius & Marjanka K. Schmidt, Dwek, M. and Presneau, Nadège 2020. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. Nature Communications . 16 (11) 312. https://doi.org/10.1038/s41467-019-14100-6

Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors
L. Lenaerts, P. Vandenberghe, N. Brison, H. Che, M. Neofytou, M. Verheecke, L. Leemans, C. Maggen, B. Dewaele, L. Dehaspe, S. Vanderschueren, D. Dierickx, V. Vandecaveye, F. Amant and J. R. Vermeesch 2019. Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors. Annals of Oncology. 30 (1), pp. p85-95. https://doi.org/10.1093/annonc/mdy476

Response to the Letter from Garcia-Montojo and colleagues concerning our paper entitled, Quantitative analysis of human endogenous retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis.
Garson, J.A., Usher, L., Al-Chalabi, A., Huggett, J., Day, E. and McCormick, A.L. 2019. Response to the Letter from Garcia-Montojo and colleagues concerning our paper entitled, Quantitative analysis of human endogenous retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis. Acta Neuropathologica Communications. 7 102. https://doi.org/10.1186/s40478-019-0756-9

Quantitative analysis of Human Endogenous Retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis
Garson, J.A., Usher, L., Al-Chalabi, A., Huggett, J., Day, E.F. and McCormick, A.L. 2019. Quantitative analysis of Human Endogenous Retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis. Acta Neuropathologica Communications. 7 45. https://doi.org/10.1186/s40478-019-0698-2

Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer.
Ferreira, M.A., Gamazon, E.R., Al-Ejeh, F., Aittomäki, K., Andrulis, I.L., Anton-Culver, H., Arason, A., Arndt, V., Aronson, K.J., Arun, B.K., Asseryanis, E., Azzollini, J., Chenevix-Trench, G., Dwek, M. and Presneau, Nadège 2019. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nature Communications . 10, p. 1741. https://doi.org/10.1038/s41467-018-08053-5

Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes.
Mavaddat, N., Michailidou, K., Dennis, J., Lush, M., Fachal, L., Lee, A., Tyrer, J.P., Chen, T.H., Wang, Q., Bolla, M.K., Yang, X., Adank, M.A., Ahearn, T., Aittomäki, K., Allen, J., Easton, D.F., Dwek, M. and Presneau, Nadège 2019. Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes. American Journal of Human Genetics. 104 (1), pp. 21-34. https://doi.org/10.1016/j.ajhg.2018.11.002

Spatiotemporal dynamics of PDGFRβ expression in pericytes and glial scar formation in penetrating brain injuries in adults
Reeves, C., Jardim, A.P., Sisodiya, S.M., Thom, M. and Liu, J. 2019. Spatiotemporal dynamics of PDGFRβ expression in pericytes and glial scar formation in penetrating brain injuries in adults. Neuropathology and Applied Neurobiology. 45 (6), pp. 609-627 NAN-2018-0107.R1. https://doi.org/10.1111/nan.12539

Maternal Constitutional and Acquired Copy Number Variations
Maria Neofytou and Joris Robert Vermeesch 2018. Maternal Constitutional and Acquired Copy Number Variations. in: Noninvasive Prenatal Testing (NIPT): Applied Genomics in Prenatal Screening and Diagnosis Academic Press. pp. 179-188

Unbiased genomewide screening of circulating plasma DNA for cancer detection
L. Lenaerts, N. Brison, M. Neofytou, H. Che, L. Dehaspe, M. Verheecke, C. Maggen, B. Dewaele, S. Vanderschueren, V. Vandecaveye, P. Vandenberghe, J. Vermeesch and F. Amant 2018. Unbiased genomewide screening of circulating plasma DNA for cancer detection. Annals of Oncology. 29 (Supplement 8), p. viii479. https://doi.org/10.1093/annonc/mdy294

Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA.
Maria Neofytou, Nathalie Brison, Kris Van den Bogaert, Luc Dehaspe, Koen Devriendt, Anja Geerts and Joris R. Vermeesch 2018. Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA. Prenatal Diagnosis. 38 (2), pp. 148-150. https://doi.org/10.1002/pd.5194

MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT
Anna Keravnou, Marios Ioannides, Charalambos Loizides, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Elena Kypri, Michael D. Hadjidaniel, Maria Neofytou, Skevi Kyriacou, Carolina Sismani, George Koumbaris and Philippos C. Patsalis 2018. MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT. PLoS ONE. 13 (6) e0199010. https://doi.org/10.1371/journal.pone.0199010

Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing
Nathalie Brison, Maria Neofytou, Luc Dehaspe, Baran Bayindir, Kris Van Den Bogaert, Griet Van Buggenhout, Leila Dardour, Hilde Peeters, Hilde Van Esch, Annick Vogels, Thomy de Ravel, Eric Legius, Koen Devriendt and Joris R. Vermeesch 2018. Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing. Prenatal Diagnosis. 38 (4), pp. 258-266. https://doi.org/10.1002/pd.5223

Multinodular and vacuolating neuronal tumors in epilepsy: dysplasia or neoplasia?
Thom, M., Liu, J., Bongaarts, A., Reinten, R., Paradiso, B., Jäger, H., Reeves, C., Somani, A., An, S., Marsdon, D., McEvoy, A., Miserocchi, A., Thorne, L., Newman, F., Bucur, S., Honavar, M., Jacques, T. and Aronica, E. 2018. Multinodular and vacuolating neuronal tumors in epilepsy: dysplasia or neoplasia? Brain Pathology. 28 (2), pp. 155-171. https://doi.org/10.1111/bpa.12555

Characterising subtypes of hippocampal sclerosis and reorganization: correlation with pre and postoperative memory deficit
Prada Jardim, A., Liu, J., Baber, J., Michalak, Z., Reeves, C., Ellis, M., Novy, J., de Tisi, J., McEvoy, A., Miserocchi, A., Targas Yacubian, E., Sisodiya, S., Thompson, P. and Thom, M. 2018. Characterising subtypes of hippocampal sclerosis and reorganization: correlation with pre and postoperative memory deficit. Brain Pathology. 28 (2), pp. 143-154. https://doi.org/10.1111/BPA.12514

The ventrolateral medulla and medullary raphe in sudden unexpected death in epilepsy
Patodia, S., Somani, A., O’Hare, M., Venkateswaran, R., Liu, J., Michalak, Z., Ellis, M., Scheffer, I., Diehl, B., Sisodiya, S. and Thom, M. 2018. The ventrolateral medulla and medullary raphe in sudden unexpected death in epilepsy. Brain. 141 (6), pp. 1719-1733. https://doi.org/10.1093/brain/awy078

Doublecortin-expressing cell types in temporal lobe epilepsy
Liu, J.Y.W., Matarin, M., Reeves, C., McEvoy, A.W., Miserocchi, A., Thompson, P., Sisodiya, S.M. and Thom, M. 2018. Doublecortin-expressing cell types in temporal lobe epilepsy. Acta Neuropathologica Communications. 6, p. 60 60. https://doi.org/10.1186/s40478-018-0566-5

Nestin-expressing cell types in the temporal lobe and hippocampus: Morphology, differentiation, and proliferative capacity
Liu, J., Reeves, C., Thomas, J., McEvoy, A., Miserocchi, A., Thompson, P., Sisodiya, S. and Thom, M. 2018. Nestin-expressing cell types in the temporal lobe and hippocampus: Morphology, differentiation, and proliferative capacity. GLIA. 66 (1), pp. 62-77 23211. https://doi.org/10.1002/glia.23211

Targeted capture enrichment assay for non-invasive prenatal testing of large and small size sub-chromosomal deletions and duplications
Maria Neofytou, Kyriakos Tsangaras, Elena Kypri, Charalambos Loizides, Marios Ioannides, Achilleas Achilleos, Petros Mina, Anna Keravnou, Carolina Sismani, George Koumbaris and Philippos C. Patsalis 2017. Targeted capture enrichment assay for non-invasive prenatal testing of large and small size sub-chromosomal deletions and duplications. PLoS ONE. 12 (2) e0171319. https://doi.org/10.1371/journal.pone.0171319

Pathology-MRI correlations in diffuse low-grade epilepsy associated tumors
Al-Hajri, A., Al-Mughairi, S., Somani, A., An, S., Liu, J.Y.W., Miserocchi, A., McEvoy, A.W., Yousry, T., Hoskote, C. and Thom, M. 2017. Pathology-MRI correlations in diffuse low-grade epilepsy associated tumors. Journal of Neuropathology and Experimental Neurology. 76 (12), pp. 1023-1033. https://doi.org/10.1093/jnen/nlx090

Training set edition using Rough Set Theory for Semi-supervised Classification
Grau, I., Nápoles, G., Sengupta, D., García Lorenzo, M.M. and Nowe, A. 2017. Training set edition using Rough Set Theory for Semi-supervised Classification. 2nd International Symposium on Fuzzy and Rough Sets. Villa Clara, Cuba 24 - 26 Oct 2017 Editorial Feijoó.

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer.
Milne, R.L., Kuchenbaecker, K.B., Michailidou, K., Beesley, J., Kar, S., Lindström, S., Hui, S., Lemaçon, A., Soucy, P., Dennis, J., Jiang, X., Rostamianfar, A., Finucane, H., Simard, J., Dwek, M. and Presneau, Nadège 2017. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nature Genetics. 49, pp. 1767-1778. https://doi.org/10.1038/ng.3785

Association analysis identifies 65 new breast cancer risk loci
Michailidou, K., Lindström, S., Dennis, J., Beesley, J., Hui, S., Kar, S., Lemaçon, A., Soucy, P., Glubb, D., Rostamianfar, A., Bolla, M.K., Wang, Q., Tyrer, J., Dicks, E., Easton, D.F., Dwek, M. and Presneau, Nadège 2017. Association analysis identifies 65 new breast cancer risk loci. Nature. 551, pp. 92-94. https://doi.org/10.1038/nature24284

Ethnic differences in the +405 and −460 vascular endothelial growth factor polymorphisms and peripheral neuropathy in patients with diabetes residing in a North London, community in the United Kingdom
Zitouni, K., Tinworth, L. and Earle, K.A. 2017. Ethnic differences in the +405 and −460 vascular endothelial growth factor polymorphisms and peripheral neuropathy in patients with diabetes residing in a North London, community in the United Kingdom. BMC Neurology. 17, p. 125 125. https://doi.org/10.1186/s12883-017-0905-3

Post-translational regulation contributes to the loss of LKB1 expression through SIRT1 deacetylase in osteosarcomas
Presneau, Nadège, Duhamel, L.A., Ye, H., Tirabosco, R., Flanagan, A.M. and Eskandarpour, M. 2017. Post-translational regulation contributes to the loss of LKB1 expression through SIRT1 deacetylase in osteosarcomas. British Journal of Cancer. 117, pp. 398-408. https://doi.org/10.1038/bjc.2017.174

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions
Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D. Hadjidaniel, Elisavet a. Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George koumbaris and Philippos C. Patsalis 2016. Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions. Genetics Research. 98 e15. https://doi.org/10.1017/S0016672316000136

Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex
George Koumbaris, Elena Kypri, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Maria Neofytou, Voula Velissariou, Georgia Christopoulou, Ioannis Kallikas, Alicia González-Liñán, Egle Benusiene, Anna Latos-Bielenska, Pietryga Marek, Alfredo Santana, Nikoletta Nagy, Márta Széll, Piotr Laudanski, Elisavet A. Papageorgiou, Marios Ioannides and Philippos C. Patsalis 2016. Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex. Clinical Chemistry. 62 (6), pp. 848-855. https://doi.org/10.1373/clinchem.2015.252502

Correction: Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial.
Sutherland, K.A., Parry, C.M., McCormick, A.L., Kapaata, A., Lyagoba, F., Kaleebu, P., Gilks, C.F., Goodall, R., Spyer, M., Kityo, C., Pillay, D., Gupta, R.K. and DART Virology Group 2016. Correction: Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial. PLoS ONE. 11 (6) e0157094. https://doi.org/10.1371/journal.pone.0157094

PAX6, brain structure and function in human adults: Advanced MRI in aniridia
Yogarajah, M., Matarin, M., Vollmar, C., Thompson, P.J., Duncan, J.S., Symms, M., Moore, A.T., Liu, J.Y.W., Thom, M., van Heyningen, V. and Sisodiya, S.M. 2016. PAX6, brain structure and function in human adults: Advanced MRI in aniridia. Annals of Clinical and Translational Neurology. 3 (5), pp. 314-330. https://doi.org/10.1002/acn3.297

Combined Ex Vivo 9.4T MRI and Quantitative Histopathological Study in Normal and Pathological Neocortical Resections in Focal Epilepsy
Reeves, C., Tachrount, M., Thomas, D., Michalak, Z., Liu, J.Y.W., Ellis, M., Diehl, B., Miserocchi, A., McEvoy, A.W., Eriksson, S., Yousry, T. and Thom, M. 2016. Combined Ex Vivo 9.4T MRI and Quantitative Histopathological Study in Normal and Pathological Neocortical Resections in Focal Epilepsy. Brain Pathology. 26 (3), pp. 319-333. https://doi.org/10.1111/bpa.12298

Genomic Variant Classifier Tool
Grau, I., Sengupta, D., Farid, D.M., Manderick, B., Nowe, A., Garcia Lorenzo, M.M., Daneels, D., Bonduelle, M., Croes, D. and Van Dooren , S. 2016. Genomic Variant Classifier Tool. SAI Intelligent Systems Conference 2016. London 21 Sep 2016 Springer. https://doi.org/10.1007/978-3-319-56994-9_32

GeVaCT - Genomic Variant Classifier Tool
Daneels, D., Grau, I., Sengupta, D., Bonduelle, M.L., Farid, D., Croes, D., Nowé, A. and Van Dooren, S. 2016. GeVaCT - Genomic Variant Classifier Tool. European Journal of Human Genetics. 24 (E-Supplement 1), p. 341.

Grey-Box Model: An ensemble approach for addressing semi-supervised classification problems
Sengupta, D., Grau, I., Garcia Lorenzo, M.M. and Nowe, A. 2016. Grey-Box Model: An ensemble approach for addressing semi-supervised classification problems. Benelearn 2016: Belgian-Dutch Conference on Machine Learning. Katholieke Universiteit Leuven, Campus Kortrijk (KULAK) 12 - 13 Sep 2016

Hyperphosphorylated tau in patients with refractory epilepsy correlates with cognitive decline: a study of temporal lobe resections
Tai, X., Koepp, M., Duncan, J., Fox, N., Thompson, P., Baxendale, S., Liu, J., Reeves, C., Michalak, Z. and Thom, M. 2016. Hyperphosphorylated tau in patients with refractory epilepsy correlates with cognitive decline: a study of temporal lobe resections. Brain. 139 (9), pp. 2441-55. https://doi.org/10.1093/brain/aww187

Early lipofuscin accumulation in Frontal Lobe Epilepsy
Liu, J., Reeves, C., Diehl, B., Coppola, A., Al-Hajri, A., Hoskote, C., Mughairy, S., Tachrount, M., Groves, M., Michalak, Z., Mills, K., McEvoy, A., Miserocchi, A., Sisodiya, S. and Thom, M. 2016. Early lipofuscin accumulation in Frontal Lobe Epilepsy. Annals of Neurology. 80, pp. 882-895. https://doi.org/10.1002/ana.24803

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
Zeng, C., Guo, X., Long, J., Kuchenbaecker, K.B., Droit, A., Michailidou, K., Ghoussaini, M., Kar, S., Freeman, A., Hopper, J.L., Milne, R.L., Bolla, M.K., Wang, Q., Dennis, J., Agata, S., Ahmed, S., Aittomaki, K., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arason, A., Arndt, V., Arun, B.K., Arver, B., Bacot, F., Barrowdale, D., Baynes, C., Beeghly-Fadiel, A., Benitez, J., Bermisheva, M., Blomqvist, C., Blot, W.J., Bogdanova, N.V., Bojesen, S.E., Bonanni, B., Borresen-Dale, A.-L., Brand, J.S., Brauch, H., Brennan, P., Brenner, H., Broeks, A., Brüning, T., Burwinkel, B., Buys, S.S., Cai, Q., Caldes, T., Campbell, I., Carpenter, J., Chang-Claude, J., Choi, J.Y., Claes, K.B.M., Clarke, C., Cox, A., Cross, S.S., Czene, K., Daly, M.B., de la Hoya, M., De Leeneer, K., Devilee, P., Diez, O., Domchek, S.M., Doody, M.M., Dorfling, C.M., Dörk, T., Dos Santos Silva, I., Dumont, M., Dwek, M., Dworniczak, B., Egan, K.M., Eilber, U., Einbeigi, Z., Ejlertsen, B., Ellis, S., Frost, D., Lalloo, F., Fasching, P.A., Figueroa, J.D., Flyger, H., Friedlander, M., Friedman, E., Gambino, G., Gao, Y.T., Garber, J., Garcia-Closas, M., Gehrig, A., Damiola, F., Lesueur, F., Mazoyer, S., Stoppa-Lyonnet, D., Giles, G.G., Godwin, A.K., Goldgar, D.E., González-Neira, A., Greene, M.H., Guenel, P., Haeberle, L., Haiman, C.A., Hallberg, E., Hamann, U., Hansen, T.V.O., Hart, S., Hartikainen, J.M., Hartman, M., Hassan, N., Healey, S., Hogervorst, F.B.L., Verhoef, S., Hendricks, C.B., Hillemanns, P., Hollestelle, A., Hulick, P.J., Hunter, D.J., Imyanitov, E.N., Isaacs, C., Ito, H., Jakubowska, A., Janavicius, R., Jaworska-Bieniek, K., Jensen, U.B., John, E.M., Beauparlant, C.J., Jones, M., Kabisch, M., Kang, D., Karlan, B.Y., Kauppila, S., Kerin, M.J., Khan, S., Khusnutdinova, E., Knight, J.A., Konstantopoulou, I., Kraft, P., Kwong, A., Laitman, Y., Lambrechts, D., Lazaro, C., Le Marchand, L., Lee, C.N., Lee, M.H., Lester, J., Li, J., Liljegren, A., Lindblom, A., Lophatananon, A., Lubinski, J., Mai, P.L., Mannermaa, A., Manoukian, S., Margolin, S., Marme, F., Matsuo, K., McGuffog, L., Meindl, A., Menegaux, F., Montagna, M., Muir, K., Mulligan, A.M., Nathanson, K.L., Neuhausen, S.L., Nevanlinna, H., Newcomb, P.A., Nord, S., Nussbaum, R.L., Offit, K., Olah, E., Olopade, O.I., Olswold, C., Osorio, A., Papi, L., Park-Simon, T.W., Paulsson-Karlsson. Y., Peeters, S., Peissel, B., Peterlongo, P., Peto, J., Pfeiler, G., Phelan, C.M., Presneau, Nadège, Presneau, N., Radice, P., Rahman, N., Ramus, S.J., Rashid, M.U., Rennert, G., Rhiem, K., Rudolph, A., Salani, R., Sangrajrang, S., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Schoemaker, M.J., Schürmann, P., Seynaeve, C., Shen, C.Y., Shrubsole, M.J., Shu, X.O., Sigurdson, A., Singer, C.F., Slager, S., Soucy, P., Southey, M., Steinemann, D., Swerdlow, A., Szabo, C.I., Tchatchou, S., Teixeira, M.R., Teo, S.H., Terry, M.B., Tessier, D.C., Teulé, A., Thomassen, M., Tihomirova, L., Tischkowitz, M., Toland, A.E., Tung, N., Turnbull, C., van den Ouweland, A.M., van Rensburg, E.J., Ven den Berg, D., Vijai, J., Wang-Gohrke, S., Weitzel, J.N., Whittemore, A.S., Winqvist, R., Wong, T.Y., Wu, A.H., Yannoukakos, D., Yu, J.C., Pharoah, P.D., Hall, P., Chenevix-Trench, G., Dunning, A.M., Simard, J., Couch, F.J., Antoniou, A.C., Easton, D.F., Antoniou, A.C. and Zheng, W. 2016. Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. Breast Cancer Research. 18 (1), p. 64. https://doi.org/10.1186/s13058-016-0718-0

A cautionary note in the interpretation of human papillomavirus E6 immunohistochemistry in focal cortical dysplasia
Thom, M., Liu, J., Reeves, C., Stopps, V., Sisodiya, S.M. and Liu, J.Y.W. 2015. A cautionary note in the interpretation of human papillomavirus E6 immunohistochemistry in focal cortical dysplasia. Annals of Neurology. 77 (2), pp. 352-353. https://doi.org/10.1002/ana.24330

GEVACT: Genomic Variant Classifier Tool
Daneels, D., Grau, I., Sengupta, D., Bonduelle, M., Farid, D.M., Croes, D., Nowé, A. and Van Dooren, S. 2015. GEVACT: Genomic Variant Classifier Tool. BeSHG & NVHG First Joint Meeting “Genetics & Society”. Leuven, Belgium 04 - 05 Feb 2016

CliniPhenome: Clinical and Phenotypic Annotation Database
Sengupta, D., Croes, D., Van Dooren, S., Bonduelle, M. and Nowe, A. 2015. CliniPhenome: Clinical and Phenotypic Annotation Database. BeMGI Annual Meeting 2015. Ghent, Belgium

GeVaCT: Genomic Variant Classifier Tool
Grau, I., Daneels, D., Van Dooren, S., Bonduelle , M., Farid, D.M., Croes, D., Nowé, A. and Sengupta, D. 2015. GeVaCT: Genomic Variant Classifier Tool. 10th Benelux Bioinformatics Conference. University of Antwerp, Belgium 07 - 08 Dec 2015

CliniPhenome: Clinical and Phenotypic Annotation Database
Sengupta, D., Croes, D., Van Dooren, S., Bonduelle, M. and Nowe, A. 2015. CliniPhenome: Clinical and Phenotypic Annotation Database. 2nd International Conference on Health Informatics & Technology. Valencia, Spain 27 - 29 Jul 2015 OMICS Publishing Group.

Gag-Protease Sequence Evolution Following Protease Inhibitor Monotherapy Treatment Failure in HIV-1 Viruses Circulating in East Africa.
Sutherland, K.A., Goodall, R.L., McCormick, A.L., Kapaata, A., Lyagoba, F., Kaleebu, P., Thiltgen, G., Gilks, C.F., Spyer, M., Kityo, C., Pillay, D., Dunn, D. and Gupta, R.K. 2015. Gag-Protease Sequence Evolution Following Protease Inhibitor Monotherapy Treatment Failure in HIV-1 Viruses Circulating in East Africa. AIDS Research and Human Retroviruses. 31 (10), pp. 1032-1037. https://doi.org/10.1089/aid.2015.0138

Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial
Sutherland, K.A., Parry, C.M., McCormick, A.L., Kapaata, A., Lyagoba, F., Kaleebu, P., Gilks, C.F., Goodall, R., Spyer, M., Kityo, C., Pillay, D., Gupta, R.K. and DART Virology Group 2015. Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial. PLoS ONE. 10 (9) e0137834. https://doi.org/10.1371/journal.pone.0137834

IL28B genotype predicts response to chronic hepatitis C triple therapy with telaprevir or boceprevir in treatment naïve and treatment-experienced patients other than prior partial- and null-responders
Calisti, G., Tavares, A., Macartney, M.J., McCormick, A.L., Labbett, W., Jacobs, M., Dusheiko, G., Rosenberg, W.M. and Haque, T. 2015. IL28B genotype predicts response to chronic hepatitis C triple therapy with telaprevir or boceprevir in treatment naïve and treatment-experienced patients other than prior partial- and null-responders. SpringerPlus. 4 (1). https://doi.org/10.1186/s40064-015-1137-x

Evaluation of sequencing of HCV core/E1, NS5A and NS5B as a genotype predictive tool in comparison with commercial assays targeting 5′UTR
McCormick, A.L., Macartney, M.J., Abdi-Abshir, I., Labbett, W., Smith, C., Irish, D., Webster, D.P. and Haque, T. 2015. Evaluation of sequencing of HCV core/E1, NS5A and NS5B as a genotype predictive tool in comparison with commercial assays targeting 5′UTR. Journal of Clinical Virology. 66 (May), pp. 56-59. https://doi.org/10.1016/j.jcv.2015.03.006

Ultra-deep sequencing provides insights into the virology of hepatitis C super-infections in a case of three sequential infections with different genotypes
Chung, E., Ferns, R.B., He, M., Rigatti, R., Grant, P., McCormick, A.L., Bhagani, S., Webster, D.P., Nastouli, E. and Waters, L.J. 2015. Ultra-deep sequencing provides insights into the virology of hepatitis C super-infections in a case of three sequential infections with different genotypes. Journal of Clinical Virology. 70 (Sept), pp. 63-66. https://doi.org/10.1016/j.jcv.2015.06.105

Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses
Aitken, S.J., Presneau, Nadège, Dileo, P., Berisha, F., Tirabosco, R., Amary, M.F., Flanagan, A.M. and Kalimuthu Sangeetha 2015. Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses. Virchows Archiv. 467 (2), pp. 203-210. https://doi.org/10.1007/s00428-015-1765-0

The utility of genotypic tropism testing in clinical practice
Wyatt, H., Herman, O., Macartney, M.J., Conibear, T., Garcia-Diaz, A., Booth, C., McCormick, A.L., Smith, C., Johnson, M., Irish, D. and Webster, D. 2015. The utility of genotypic tropism testing in clinical practice. International Journal of STD and AIDS. 26 (8), pp. 593-594. https://doi.org/10.1177/0956462414546917

Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics
Presneau, Nadège, Baumhoer Daniel, Behjati Sam, Pillay Nischalan, Tarpey Patrick Campbell Peter, J., Jundt Gernot, Hamoudi Rifat Wedge David, C., Van Loo Peter Hassan A Bassim, Khatri, B., Ye Hongtao, Tirabosco, R., Flanagan, A.M., Campbell Peter J., Wedge David C., Hassan A. Bassim and Amary, M.F. 2015. Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics. The Journal of Pathology: Clinical Research. 1 (2), pp. 113-123. https://doi.org/10.1002/cjp2.13

Mutations in IDH1 and IDH2 are not present in sporadic ovarian sex cord-stromal tumours
Aitken, S.J., Presneau, Nadège, Khatri, B., Flanagan, A.M., Clarke, B. and McCluggage, W.G. 2015. Mutations in IDH1 and IDH2 are not present in sporadic ovarian sex cord-stromal tumours. Histopathology. 66 (6), pp. 897-898. https://doi.org/10.1111/his.12489

An NRAS mutation in a case of Erdheim-Chester disease
Aitken, S.J., Presneau, Nadège, Amary, M.F., O'Donnell, P., Flanagan, A.M. and Tirabosco, R. 2015. An NRAS mutation in a case of Erdheim-Chester disease. Histopathology . 66 (2), pp. 316-319. https://doi.org/10.1111/his.12443

Phenotypic and genotypic analyses to guide selection of reverse transcriptase inhibitors in second-line HIV therapy following extended virological failure in Uganda
R. L. Goodall, D. T. Dunn, T. Pattery, A. van Cauwenberge, P. Nkurunziza, P. Awio, N. Ndembi, P. Munderi, C. Kityo, C. F. Gilks, P. Kaleebu, D. Pillay, P. Kaleebu, D. Pillay, P. Awio, M. Chirara, D. Dunn, D. M. Gibb, C. Gilks, R. Goodall, A. Kapaata, M. Katuramur, F. Lyagoba, R. Magala, B. Magambo, K. Mataruka, A.L. McCormick, L. Mugarura, T. Musunga, M. Nabankkema, J. Nkalubo, P. Nkurunziza, C. Parry, V. Robertson, M. Spyer, D. Yirrell, H. Grosskurth, P. Munderi, G. Kabuye, D. Nsibambi, R. Kasirye, E. Zalwango, M. Nakazibwe, B. Kikaire, G. Nassuna, R. Massa, K. Fadhiru, M. Namyalo, A. Zalwango, L. Generous and P. Khauka 2014. Phenotypic and genotypic analyses to guide selection of reverse transcriptase inhibitors in second-line HIV therapy following extended virological failure in Uganda. Journal of Antimicrobial Chemotherapy. 69 (7), pp. 1938-1944. https://doi.org/10.1093/jac/dku052

Feasibility of testing and detection of HIV-1 drug resistance in proviral DNA
Booth, C., McCormick, A.L., Garcia-Diaz, A., Macartney, M., Youle, M., Johnson, M. and Webster, D. 2014. Feasibility of testing and detection of HIV-1 drug resistance in proviral DNA. BMC Infectious Diseases. 14 (Supplement 4) O25. https://doi.org/10.1186/1471-2334-14-s4-o25

Analysis of transmitted HIV-1 drug resistance using 454 ultra-deep-sequencing and the DeepChek(®)-HIV system.
Garcia-Diaz, A., McCormick, A.L., Booth, C., Gonzalez, D., Sayada, C., Haque, T., Johnson, M. and Webster, D. 2014. Analysis of transmitted HIV-1 drug resistance using 454 ultra-deep-sequencing and the DeepChek(®)-HIV system. Journal of the International AIDS Society. 17 (Suppl 3) 19752. https://doi.org/10.7448/ias.17.4.19752

A comparative study of the dentate gyrus in hippocampal sclerosis in epilepsy and dementia
Bandopadhyay, R., Liu, J.Y.W., Sisodiya, S.M. and Thom, M. 2014. A comparative study of the dentate gyrus in hippocampal sclerosis in epilepsy and dementia. Neuropathology and Applied Neurobiology. 40 (2), pp. 177-190. https://doi.org/10.1111/nan.12087

High-throughput, automated quantification of white matter neurons in mild malformation of cortical development in epilepsy
Liu, J.Y.W., Ellis, M., Brooke-Ball, H., de Tisi, J., Eriksson, S.H., Brandner, S., Sisodiya, S.M. and Thom, M. 2014. High-throughput, automated quantification of white matter neurons in mild malformation of cortical development in epilepsy. Acta Neuropathologica Communications. 2 72. https://doi.org/10.1186/2051-5960-2-72

Evidence for mTOR pathway activation in a spectrum of epilepsy-associated pathologies
Liu, J.Y.W., Reeves, C., Michalak, Z., Coppola, A., Diehl, B., Sisodiya, S.M. and Thom, M. 2014. Evidence for mTOR pathway activation in a spectrum of epilepsy-associated pathologies. Acta Neuropathologica Communications. 2 71. https://doi.org/10.1186/2051-5960-2-71

In vivo P-glycoprotein function before and after epilepsy surgery
Bauer, M., Karch, R., Zeitlinger, M., Liu, J.Y.W., Koepp, M.J., Asselin, M.-C., Sisodiya, S.M., Hainfellner, J.A., Wadsak, W., Mitterhauser, M., Müller, M., Pataraia, E. and Langer, O. 2014. In vivo P-glycoprotein function before and after epilepsy surgery. Neurology. 83 (15). https://doi.org/10.1212/wnl.0000000000000858

Interictal psychosis following temporal lobe surgery: dentate gyrus pathology
Thom, M., Kensche, M., Maynard, J., Liu, J.Y.W., Reeves, C., Goc, J., Marsdon, D., Fluegel, D. and Foong, J. 2014. Interictal psychosis following temporal lobe surgery: dentate gyrus pathology. Psychological Medicine. 44 (14), pp. 3037-3049. https://doi.org/10.1017/s0033291714000452

A spatiotemporal study of gliosis in relation to depth electrode tracks in drug-resistant epilepsy
Goc, J., Liu, J.Y.W., Sisodiya, S.M. and Thom, M. 2014. A spatiotemporal study of gliosis in relation to depth electrode tracks in drug-resistant epilepsy. European Journal of Neuroscience. 39 (12), pp. 2151-2162. https://doi.org/10.1111/ejn.12548

Benchmarking pre-processing and batch effect removal methods for Insilico DB: Genomics Big Data Infrastructure
De Clerck, Q., Nowe, A., Coletta, A. and Sengupta, D. 2014. Benchmarking pre-processing and batch effect removal methods for Insilico DB: Genomics Big Data Infrastructure. 9th Benelux Bioinformatics Conference (BBC 2014). Novotel-Kirchberg, Luxembourg 08 - 09 Dec 2014

Homology Modeling of Bacteriocins: From sequence alignments to structural models
Atri, P., Sengupta, D., Verma, S., Ali, S. and Dey, G. 2014. Homology Modeling of Bacteriocins: From sequence alignments to structural models. International Journal of Scientific & Engineering Research. 5 (5), pp. 123-126.

Telaprevir or boceprevir based therapy for chronic hepatitis C infection: Development of resistance-associated variants in treatment failure
Macartney, M.J., Irish, D., Bridge, S.H., Garcia-Diaz, A., Booth, C., McCormick, A.L., Labbett, W., Smith, C., Velazquez, C., Tanwar, S., Trembling, P., Jacobs, M., Dusheiko, G., Rosenberg, W.M. and Haque, T. 2014. Telaprevir or boceprevir based therapy for chronic hepatitis C infection: Development of resistance-associated variants in treatment failure. Antiviral Research. 105, pp. 112-7. https://doi.org/10.1016/j.antiviral.2014.02.019

Prevalence of baseline polymorphisms for potential resistance to NS5A inhibitors in drug-naive individuals infected with hepatitis C genotypes 1–4
McCormick, A.L., Wang, L., Garcia-Diaz, A., Macartney, M.J., Webster, D.P. and Haque, T. 2014. Prevalence of baseline polymorphisms for potential resistance to NS5A inhibitors in drug-naive individuals infected with hepatitis C genotypes 1–4 . Antiviral Therapy. 20 (1), pp. 81-85. https://doi.org/10.3851/IMP2763

The utility of different bioinformatics algorithms for genotypic HIV-1 tropism testing in a large clinical cohort with multiple subtypes
Bartlett, A., Macartney, M.J., Conibear, T., Feyertag, F., Smith, C., Johnson, M., Hyams, C., Garcia-Diaz, A., McCormick, A.L., Booth, C., Robertson, D. and Webster, D.P. 2014. The utility of different bioinformatics algorithms for genotypic HIV-1 tropism testing in a large clinical cohort with multiple subtypes. AIDS. 28 (11), pp. 1611-7. https://doi.org/10.1097/QAD.0000000000000288

Baseline drug-resistance mutations are detectable in HCV genes NS3 and NS5A but not NS5B in acute and chronic HIV-coinfected patients
McCormick, A.L., Moynihan, L., Macartney, M.J., Garcia-Diaz, A., Smith, C., Johnson, M., Rodger, A.J., Bhagani, S., Haque, T. and Webster, D. 2014. Baseline drug-resistance mutations are detectable in HCV genes NS3 and NS5A but not NS5B in acute and chronic HIV-coinfected patients. Antiviral Therapy. 20 (3), p. 2015. https://doi.org/10.3851/IMP2871

Fibroblastic growth factor receptor 1 amplification in osteosarcoma is associated with poor response to neo-adjuvant chemotherapy
Fernanda Amary, M., Ye, H., Berisha, F., Khatri, B., Forbes, G., Lehovsky, K., Frezza, A.M., Behjati, S., Tarpey, P., Pillay, N., Campbell, P.J., Tirabosco, R., Presneau, Nadège, Strauss, S.J. and Flanagan, A.M. 2014. Fibroblastic growth factor receptor 1 amplification in osteosarcoma is associated with poor response to neo-adjuvant chemotherapy. Cancer Medicine. 3 (4), pp. 980-987. https://doi.org/10.1002/cam4.268

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics
Guilhamon, P., Butcher, L.M., Presneau, Nadège, Wilson, G.A., Feber, A., Paul, D.S., Schütte, M., Haybaeck, J., Keilholz, U., Hoffman, J., Ross, M.T., Flanagan, A.M. and Beck, S. 2014. Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics. Genome Medicine. 6 (12), pp. 116-126. https://doi.org/10.1186/s13073-014-0116-0

A quantitative study of white matter hypomyelination and oligodendroglial maturation in focal cortical dysplasia type II
Shepherd, C., Liu, J., Goc, J., Martinian, L., Jacques, T.S., Sisodiya, S.M., Thom, M. and Liu, J.Y.W. 2013. A quantitative study of white matter hypomyelination and oligodendroglial maturation in focal cortical dysplasia type II. Epilepsia. 54 (5), pp. 898-908. https://doi.org/10.1111/epi.12143

P-glycoprotein expression and function in patients with temporal lobe epilepsy: A case-control study
Feldmann, M., Asselin, M.-C., Wang, S., McMahon, A., Anton-Rodriguez, J., Walker, M., Symms, M., Brown, G., Hinz, R., Matthews, J., Bauer, M., Langer, O., Thom, M., Jones, T., Vollmar, C., Duncan, J.S., Sisodiya, S.M., Koepp, M.J. and Liu, J.Y.W. 2013. P-glycoprotein expression and function in patients with temporal lobe epilepsy: A case-control study. The Lancet Neurology. 12 (8), pp. 777-785. https://doi.org/10.1016/s1474-4422(13)70109-1

Association rule mining based study for identification of clinical parameters akin to occurrence of brain tumor
Sengupta, D., Sood, M., Vijayvargia, P., Hota, S. and Naik, P.K. 2013. Association rule mining based study for identification of clinical parameters akin to occurrence of brain tumor. Bioinformation. 9 (11), pp. 555-559. https://doi.org/10.6026/97320630009555

Design of dimensional model for clinical data storage and analysis
Sengupta, D., Arora, P., Pant, S. and Naik, P.K. 2013. Design of dimensional model for clinical data storage and analysis. Applied Medical Informatics. 32 (2), pp. 47-53.

SN algorithm: analysis of temporal clinical data for mining periodic patterns and impending augury
Sengupta, D. and Naik, P.K. 2013. SN algorithm: analysis of temporal clinical data for mining periodic patterns and impending augury. Journal of Clinical Bioinformatics. 3 24. https://doi.org/10.1186/2043-9113-3-24

Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencingdrug resistance assay in a routine diagnostic laboratory
Garcia-Diaz, A., Guerrero-Ramos, A., McCormick, A.L., Macartney, M.J., Conibear, T., Johnson, M., Haque, T. and Webster, D.P. 2013. Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencingdrug resistance assay in a routine diagnostic laboratory. Journal of Clinical Virology. 58 (2), pp. 468-473. https://doi.org/10.1016/j.jcv.2013.07.009

Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone
Behjati Sam, Tarpey Patrick Campbell Peter, J., Presneau, Nadège, Pillay Nischalan, Van Loo Peter Hassan A Bassim, Wedge David C., Cooke, S.L., Gundem, G., Davies, H., Nik-Zainal, S., Martin, S., McLaren, S., Goody, V., Robinson, B., Butler, A., Teague, J.W., Halai, D., Khatri, B., Myklebost, O., Baumhoer Daniel, Jundt Gernot, Hamoudi Rifat Wedge David, C., Tirabosco, R., Amary, M.F., Futreal, P.A., Stratton, M.R., Campbell Peter J., Flanagan, A.M., Scheipl Susanne and Goodie Victoria 2013. Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nature Genetics. 45 (12), pp. 1479-1482. https://doi.org/10.1038/ng.2814

Neuropathology of 16p13.11 deletion in epilepsy
Liu, J.Y.W., Kasperavičiute, D., Martinian, L., Thom, M. and Sisodiya, S.M. 2012. Neuropathology of 16p13.11 deletion in epilepsy. PLoS ONE. 7 (4). https://doi.org/10.1371/journal.pone.0034813

Neuropathology of the blood-brain barrier and pharmaco-resistance in human epilepsy
Liu, J.Y.W., Thom, M., Catarino, C.B., Martinian, L., Figarella-Branger, D., Bartolomei, F., Koepp, M. and Sisodiya, S.M. 2012. Neuropathology of the blood-brain barrier and pharmaco-resistance in human epilepsy. Brain. 135 (10), p. 3115–3133. https://doi.org/10.1093/brain/aws147

Investigation of hypoxia-inducible factor-1α in hippocampal sclerosis: A postmortem study
Feast, A., Martinian, L., Liu, J.Y.W., Catarino, C.B., Thom, M. and Sisodiya, S.M. 2012. Investigation of hypoxia-inducible factor-1α in hippocampal sclerosis: A postmortem study. Epilepsia. 53 (8), pp. 1349-1359. https://doi.org/10.1111/j.1528-1167.2012.03591.x

Variability of sclerosis along the longitudinal hippocampal axis in epilepsy: A post mortem study
Thom, M., Liagkouras, I., Martinian, L., Catarino, C.B., Sisodiya, S.M. and Liu, J.Y.W. 2012. Variability of sclerosis along the longitudinal hippocampal axis in epilepsy: A post mortem study. Epilepsy Research. 102 (1-2), pp. 45-59. https://doi.org/10.1016/j.eplepsyres.2012.04.015

TpPred: A Tool for Hierarchical Prediction of Transport Proteins Using Cluster of Neural Networks and Sequence Derived Features
Jain, S., Ranjan, P., Sengupta, D. and Naik, P.K. 2012. TpPred: A Tool for Hierarchical Prediction of Transport Proteins Using Cluster of Neural Networks and Sequence Derived Features. International Journal for Computational Biology. 1 (1), pp. 28-36.

Neurofibrillary tangle pathology and Braak staging in chronic epilepsy in relation to traumatic brain injury and hippocampal sclerosis: A post-mortem study
Thom, M., Liu, J.Y.W., Thompson, P., Phadke, R., Narkiewicz, M., Martinian, L., Marsdon, D., Koepp, M., Caboclo, L., Catarino, C.B. and Sisodiya, S.M. 2011. Neurofibrillary tangle pathology and Braak staging in chronic epilepsy in relation to traumatic brain injury and hippocampal sclerosis: A post-mortem study. Brain. 134 (10), pp. 2969-2981. https://doi.org/10.1093/brain/awr209

Dravet syndrome as epileptic encephalopathy: Evidence from long-term course and neuropathology
Catarino, C.B., Liu, J.Y.W., Liagkouras, I., Gibbons, V.S., Labrum, R.W., Ellis, R., Woodward, C., Davis, M.B., Smith, S.J., Cross, J.H., Appleton, R.E., Yendle, S.C., McMahon, J.M., Bellows, S.T., Jacques, T.S., Zuberi, S.M., Koepp, M.J., Martinian, L., Scheffer, I.E., Thom, M. and Sisodiya, S.M. 2011. Dravet syndrome as epileptic encephalopathy: Evidence from long-term course and neuropathology. Brain. 134 (10), pp. 2982-3010. https://doi.org/10.1093/brain/awr129

Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix
Pathak, P., Naik, P.K., Sengupta, D., Singh, S.K. and Tandon, C. 2011. Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix. Journal of Biomedical Science and Engineering. 4 (9), pp. 591-598. https://doi.org/10.4236/jbise.2011.49075

Impact of the N348I Mutation in HIV-1 Reverse Transcriptase on Nonnucleoside Reverse Transcriptase Inhibitor Resistance in Non-Subtype B HIV-1
McCormick, A.L., Parry, C.M., Crombe, A., Goodall, R.L., Gupta, R.K., Kaleebu, P., Kityo, C., Chirara, M., Towers, G.J. and Pillay, D. 2011. Impact of the N348I Mutation in HIV-1 Reverse Transcriptase on Nonnucleoside Reverse Transcriptase Inhibitor Resistance in Non-Subtype B HIV-1. Antimicrobial Agents and Chemotherapy. 55 (4), pp. 1806-1809. https://doi.org/10.1128/AAC.01197-10

Immunolabeling recovery in archival, post-mortem, human brain tissue using modified antigen retrieval and the catalyzed signal amplification system
Liu, J.Y.W., Martinian, L., Thom, M. and Sisodiya, S.M. 2010. Immunolabeling recovery in archival, post-mortem, human brain tissue using modified antigen retrieval and the catalyzed signal amplification system. Journal of Neuroscience Methods. 190 (1), pp. 49-56. https://doi.org/10.1016/j.jneumeth.2010.04.020

Full length HIV-1 Gag determines protease inhibitor susceptibility within in vitro assays
Gupta, R.K., Kohli, A., McCormick, A.L., Towers, G.J., Pillay, D. and Parry, C.M. 2010. Full length HIV-1 Gag determines protease inhibitor susceptibility within in vitro assays. AIDS. 24 (11), p. 1651–1655. https://doi.org/10.1097/QAD.0b013e3283398216

Lack of Minority K65RResistant Viral Populations Detected After Repeated Treatment Interruptions of Tenofovir/Zidovudine and Lamivudine in a Resource-Limited Setting
McCormick, A.L., Goodall, R.L., Joyce, A., Ndembi, N., Chirara, M., Katunduk, P., Walker, A.S., Yirrell, D.L., Gilks, C.F. and Pillay, D. 2010. Lack of Minority K65RResistant Viral Populations Detected After Repeated Treatment Interruptions of Tenofovir/Zidovudine and Lamivudine in a Resource-Limited Setting. Journal of Acquired Immune Deficiency Syndromes. 54 (2), pp. 215-216. https://doi.org/10.1097/QAI.0b013e3181cc1058

Viral Rebound and Emergence of Drug Resistance in the Absence of Viral Load Testing: A Randomized Comparison between Zidovudine-Lamivudine plus Nevirapine and Zidovudine-Lamivudine plus Abacavir
Ndembi, N., Goodall, R.L., Dunn, D.T., McCormick, A.L., Burke, A., Lyagoba, F., Munderi, P., Katundu, P., Kityo, C., Robertson, V., Yirrell, D.L., Walker, A.S., Gibb, D.M., Gilks, C.F., Kaleebu, P. and Pillay, D. 2010. Viral Rebound and Emergence of Drug Resistance in the Absence of Viral Load Testing: A Randomized Comparison between Zidovudine-Lamivudine plus Nevirapine and Zidovudine-Lamivudine plus Abacavir. The Journal of Infectious Diseases. 201 (1), pp. 106-113. https://doi.org/10.1086/648590

Utilising mitochondrial DNA markers to identify insects for forensic applications: an investigation into how the preservation and storage of insect tissue can affect mtDNA yield
Thompson, A., Tinworth, L. and Smith, C.L. 2009. Utilising mitochondrial DNA markers to identify insects for forensic applications: an investigation into how the preservation and storage of insect tissue can affect mtDNA yield. in: Proceedings of the 5th National FORREST Conference 2009 (FORensic RESearch and Teaching), 30th June – 1st July 2009, Liverpool John Moores University Forensic Institute Research Network and The Higher Education Academy Physical Sciences Centre. pp. 45

Developmentally acquired PKA localisation in mouse oocytes and embryos
Webb, R.J., Tinworth, L., Thomas, G.M.H., Zaccolo, M. and Carroll, J. 2008. Developmentally acquired PKA localisation in mouse oocytes and embryos. Developmental Biology. 317 (1), pp. 36-45. https://doi.org/10.1016/j.ydbio.2008.01.045

Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues
Sengupta, D., Verma, D. and Naik, P.K. 2008. Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues. In Silico Biology. 8 (3-4), pp. 275-289.

Quantification of reverse transcriptase in ALS and elimination of a novel retroviral candidate
McCormick, A.L., Brown, R.H., Cudkowicz, M.E., Al-Chalabi, A. and Garson, J.A. 2008. Quantification of reverse transcriptase in ALS and elimination of a novel retroviral candidate. Neurology. 70 (4), pp. 278-283. https://doi.org/10.1212/01.wnl.0000297552.13219.b4

Binding Modes, binding Affinities and ADME Screening of HIV-1 NNRTI Inhibitor: Efavirnez and its analogues.
Sengupta, D. 2007. Binding Modes, binding Affinities and ADME Screening of HIV-1 NNRTI Inhibitor: Efavirnez and its analogues. Online Journal of Bioinformatics. 8 (1), pp. 99-114.

In-silico TAT-PTD prediction for cell penetrating peptides
Tandon, C., Aggarwal, A., Goel, P., Sengupta, D. and Naik, P.K. 2007. In-silico TAT-PTD prediction for cell penetrating peptides. Online Journal of Bioinformatics. 8 (1), pp. 115-138.

Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: Screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
Sengupta, D., Verma, D. and Naik, P.K. 2007. Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: Screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties. Journal of Biosciences. 32 (3), pp. 1307-1316. https://doi.org/10.1007/s12038-007-0140-y

Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
Sengupta, D., Verma, D. and Naik, P.K. 2007. Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties. Journal of Biosciences. 32, pp. 1307-1316. https://doi.org/10.1007/s12038-007-0124-y

Clustering of HIV-I Subtype: Study of Molecular Diversity using Phylogenetic Analysis
Sengupta, D., Verma, D., Mishra, V.S. and Naik, P.K. 2006. Clustering of HIV-I Subtype: Study of Molecular Diversity using Phylogenetic Analysis. Bioinformatics Trends: A Journal of Bioinformatics and its Applications. 1 (1), pp. 1-12.

A molecular map of mesenchymal tumors
Henderson, S.R., Guiliano, D.B., Presneau, N., McLean, S., Frow, R., Vujovic, S., Anderson, J., Sebire, N., Whelan, J., Athanasou, N., Flanagan, A.M. and Boshoff, C. 2005. A molecular map of mesenchymal tumors. Genome Biology. 6 R76. https://doi.org/10.1186/gb-2005-6-9-r76

An interferon gamma-gp120 fusion delivered as a DNA vaccine induces enhanced priming
Nimal, S., McCormick, A.L., Thomas, M.S. and Heath, A.W. 2005. An interferon gamma-gp120 fusion delivered as a DNA vaccine induces enhanced priming. Vaccine. 23 (10), pp. 3984-3990. https://doi.org/10.1016/j.vaccine.2005.01.160

CD40 antibody as an adjuvant induces enhanced T cell responses
Carlring, J., Barr, T.A., McCormick, A.L. and Heath, A.W. 2004. CD40 antibody as an adjuvant induces enhanced T cell responses. Vaccine. 22 (25-26), p. 3323–3328. https://doi.org/10.1016/j.vaccine.2004.02.043

A potent adjuvant effect of CD40 antibody attached to antigen
Barr, T.A., McCormick, A.L., Carlring, J. and Heath, A.W. 2003. A potent adjuvant effect of CD40 antibody attached to antigen. Immunology. 109 (1), pp. 87-92. https://doi.org/10.1046/j.1365-2567.2003.01634.x

Immunization with an Interferon-g–gp120 Fusion Protein Induces Enhanced Immune Responses to Human Immunodeficiency Virus gp120
McCormick, A.L., Thomas, M.S. and Heath, A.W. 2001. Immunization with an Interferon-g–gp120 Fusion Protein Induces Enhanced Immune Responses to Human Immunodeficiency Virus gp120. The Journal of Infectious Diseases. 184 (11), pp. 1423-1430. https://doi.org/10.1086/324371

Gag Determinants of Fitness and Drug Susceptibility in Protease Inhibitor-Resistant Human Immunodeficiency Virus Type 1
Parry, C.M., Kohli, A., Boinett, C.J., Towers, G.J., McCormick, A.L. and Pillay, D. 1999. Gag Determinants of Fitness and Drug Susceptibility in Protease Inhibitor-Resistant Human Immunodeficiency Virus Type 1. Journal of Virology. 83 (18), pp. 9094-9101. https://doi.org/10.1128/JVI.02356-08

Cell Surface Expression of CD154 Inhibits Alloantibody Responses: A Mechanism for the Prevention of Autoimmune Responses against Activated T Cells?
McCormick, A.L., Santos-Argumedo, L., Thomas, M.S. and Heath, A.W. 1999. Cell Surface Expression of CD154 Inhibits Alloantibody Responses: A Mechanism for the Prevention of Autoimmune Responses against Activated T Cells? Cellular Immunology. 195 (2), pp. 157-161. https://doi.org/10.1006/cimm.1999.1528

Enhancement of immunogenicity of recombinant antigens by production of a cytokine-antigen fusion protein for vaccination
McCormick, A.L., Thomas, M.S. and Heath, A.W. 1997. Enhancement of immunogenicity of recombinant antigens by production of a cytokine-antigen fusion protein for vaccination. Biochemical Society Transactions. 25, p. 297S. https://doi.org/10.1042/bst025297s