Computational Biology: Publications

  • Böttcher, JP; Bonavita, E; Chakravarty, P; Blees, H; Cabeza-Cabrerizo, M; Sammicheli, S; Rogers, NC; Sahai, E; Zelenay, S and Reis e Sousa, C (2018)
    NK cells stimulate recruitment of cDC1 into the tumor microenvironment promoting cancer immune control.
    Cell 172, 1022-1037 e1014 PubMed abstract
  • Denaxa, M; Neves, G; Rabinowitz, A; Kemlo, S; Liodis, P; Burrone, J and Pachnis, V (2018)
    Modulation of apoptosis controls inhibitory interneuron number in the cortex.
    Cell Reports 22, 1710-1721 PubMed abstract
  • Esmail, H; Lai, RP; Lesosky, M; Wilkinson, KA; Graham, CM; Horswell, S; Coussens, AK; Barry, CE, III; O'Garra, A and Wilkinson, RJ (2018)
    Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis.
    Proceedings of the National Academy of Sciences of the United States of America 115, E964-E973 PubMed abstract
  • Griessinger, E; Vargaftig, J; Horswell, S; Taussig, DC; Gribben, J and Bonnet, D (2018)
    Acute myeloid leukemia xenograft success prediction: saving time.
    Experimental Hematology 59, 66-71 e64 PubMed abstract
  • Khan, OM; Carvalho, J; Spencer-Dene, B; Mitter, R; Frith, D; Snijders, AP; Wood, SA and Behrens, A (2018)
    The deubiquitinase USP9X regulates FBW7 stability and suppresses colorectal cancer.
    Journal of Clinical Investigation 128, 1326-1337 PubMed abstract
  • Kümper, S; Gantke, T; Chen, C-S; Soneji, Y; Pattison, MJ; Chakravarty, P; Kjær, S; Thomas, D; Haslam, C; Leavens, BJ; House, D; Powell, DJ and Ley, SC (2018)
    Assaying kinase activity of the TPL-2/NF-κB1 p105/ABIN-2 complex using an optimal peptide substrate.
    Biochemical Journal 475, 329-340 PubMed abstract
  • León-Ortiz, AM; Panier, S; Sarek, G; Vannier, J-B; Patel, H; Campbell, PJ and Boulton, SJ (2018)
    A distinct class of genome rearrangements driven by heterologous recombination.
    Molecular Cell 69, 292-305 e296 PubMed abstract
  • Mitchell, TJ; Turajlic, S; Rowan, A; Nicol, D; Farmery, JHR; O'Brien, T; Martincorena, I; Tarpey, P; Angelopoulos, N; Yates, LR; Butler, AP; Raine, K; Stewart, GD; Challacombe, B; Fernando, A; Lopez, JI; Hazell, S; Chandra, A; Chowdhury, S; Rudman, S; Soultati, A; Stamp, G; Fotiadis, N; Pickering, L; Au, L; Spain, L; Lynch, J; Stares, M; Teague, J; Maura, F; Wedge, DC; Horswell, S; Chambers, T; Litchfield, K; Xu, H; Stewart, A; Elaidi, R; Oudard, S; McGranahan, N; Csabai, I; Gore, M; Futreal, PA; Larkin, J; Lynch, AG; Szallasi, Z; Swanton, C; Campbell, PJ and TRACERx Renal Consortium (2018)
    Timing the landmark events in the evolution of clear cell renal cell cancer: TRACERx Renal.
    Cell 173, 611-623.e617 PubMed abstract
  • Moretto, F; Wood, NE; Kelly, G; Doncic, A and van Werven, FJ (2018)
    A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast.
    Nature Communications 9, 780 PubMed abstract
  • Morini, MF; Giampietro, C; Corada, M; Pisati, F; Lavarone, E; Cunha, SI; Conze, LL; O'Reilly, N; Joshi, D; Kjaer, S; George, R; Nye, E; Ma, A; Jin, J; Mitter, R; Lupia, M; Cavallaro, U; Pasini, D; Calado, DP; Dejana, E and Taddei, A (2018)
    VE-cadherin-mediated epigenetic regulation of endothelial gene expression.
    Circulation Research 122, 231-245 PubMed abstract
  • Pearce, OMT; Delaine-Smith, R; Maniati, E; Nichols, S; Wang, J; Böhm, S; Rajeeve, V; Ullah, D; Chakravarty, P; Jones, RR; Montfort, A; Dowe, T; Gribben, J; Jones, JL; Kocher, HM; Serody, JS; Vincent, BG; Connelly, J; Brenton, JD; Chelala, C; Cutillas, PR; Lockley, M; Bessant, C; Knight, MM and Balkwill, FR (2018)
    Deconstruction of a metastatic tumor microenvironment reveals a common matrix response in human cancers.
    Cancer Discovery 8, 304-319 PubMed abstract
  • Ramachandran, A; Vizán, P; Das, D; Chakravarty, P; Vogt, J; Rogers, KW; Müller, P; Hinck, AP; Sapkota, GP and Hill, CS (2018)
    TGF-β uses a novel mode of receptor activation to phosphorylate SMAD1/5 and induce epithelial-to-mesenchymal transition.
    eLife 7, e31756 PubMed abstract
  • Turajlic, S; Xu, H; Litchfield, K; Rowan, A; Chambers, T; Lopez, JI; Nicol, D; O'Brien, T; Larkin, J; Horswell, S; Stares, M; Au, L; Jamal-Hanjani, M; Challacombe, B; Chandra, A; Hazell, S; Eichler-Jonsson, C; Soultati, A; Chowdhury, S; Rudman, S; Lynch, J; Fernando, A; Stamp, G; Nye, E; Jabbar, F; Spain, L; Lall, S; Guarch, R; Falzon, M; Proctor, I; Pickering, L; Gore, M; Watkins, TBK; Ward, S; Stewart, A; DiNatale, R; Becerra, MF; Reznik, E; Hsieh, JJ; Richmond, TA; Mayhew, GF; Hill, SM; McNally, CD; Jones, C; Rosenbaum, H; Stanislaw, S; Burgess, DL; Alexander, NR; Swanton, C; PEACE and Consortium, TR (2018)
    Tracking cancer evolution reveals constrained routes to metastases: TRACERx Renal.
    Cell 173, 581-594 e512 PubMed abstract
  • Turajlic, S; Xu, H; Litchfield, K; Rowan, A; Horswell, S; Chambers, T; O'Brien, T; Lopez, JI; Watkins, TBK; Nicol, D; Stares, M; Challacombe, B; Hazell, S; Chandra, A; Mitchell, TJ; Au, L; Eichler-Jonsson, C; Jabbar, F; Soultati, A; Chowdhury, S; Rudman, S; Lynch, J; Fernando, A; Stamp, G; Nye, E; Stewart, A; Xing, W; Smith, JC; Escudero, M; Huffman, A; Matthews, N; Elgar, G; Phillimore, B; Costa, M; Begum, S; Ward, S; Salm, M; Boeing, S; Fisher, R; Spain, L; Navas, C; Grönroos, E; Hobor, S; Sharma, S; Aurangzeb, I; Lall, S; Polson, A; Varia, M; Horsfield, C; Fotiadis, N; Pickering, L; Schwarz, RF; Silva, B; Herrero, J; Luscombe, NM; Jamal-Hanjani, M; Rosenthal, R; Birkbak, NJ; Wilson, GA; Pipek, O; Ribli, D; Krzystanek, M; Csabai, I; Szallasi, Z; Gore, M; McGranahan, N; Van Loo, P; Campbell, P; Larkin, J; Swanton, C and TRACERx Renal Consortium (2018)
    Deterministic evolutionary trajectories influence primary tumor growth: TRACERx Renal.
    Cell 173, 595-610.e511 PubMed abstract
  • Abbosh, C; Birkbak, NJ; Wilson, GA; Jamal-Hanjani, M; Constantin, T; Salari, R; Quesne, JL; Moore, DA; Veeriah, S; Rosenthal, R; Marafioti, T; Kirkizlar, E; Watkins, TBK; McGranahan, N; Ward, S; Martinson, L; Riley, J; Fraioli, F; Bakir, MA; Grönroos, E; Zambrana, F; Endozo, R; Bi, WL; Fennessy, FM; Sponer, N; Johnson, D; Laycock, J; Shafi, S; Czyzewska-Khan, J; Rowan, A; Chambers, T; Matthews, N; Turajlic, S; Hiley, C; Lee, SM; Forster, MD; Ahmad, T; Falzon, M; Borg, E; Lawrence, D; Hayward, M; Kolvekar, S; Panagiotopoulos, N; Janes, SM; Thakrar, R; Ahmed, A; Blackhall, F; Summers, Y; Hafez, D; Naik, A; Ganguly, A; Kareht, S; Shah, R; Joseph, L; Quinn, AM; Crosbie, P; Naidu, B; Middleton, G; Langman, G; Trotter, S; Nicolson, M; Remmen, H; Kerr, K; Chetty, M; Gomersall, L; Fennell, DA; Nakas, A; Rathinam, S; Anand, G; Khan, S; Russell, P; Ezhil, V; Ismail, B; Irvin-sellers, M; Prakash, V; Lester, JF; Kornaszewska, M; Attanoos, R; Adams, H; Davies, H; Oukrif, D; Akarca, AU; Hartley, JA; Lowe, HL; Lock, S; Iles, N; Bell, H; Ngai, Y; Elgar, G; Szallasi, Z; Schwarz, RF; Herrero, J; Stewart, A; Quezada, SA; Van Loo, P; Dive, C; Lin, CJ; Rabinowitz, M; Aerts, HJWL; Hackshaw, A; Shaw, JA; Zimmermann, BG; The TRACERx Consortium; The PEACE Consortium and Swanton, C (2017)
    Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.
    Nature 545, 446-451 PubMed abstract
  • Coda, DM; Gaarenstroom, T; East, P; Patel, H; Miller, DSJ; Lobley, A; Matthews, N; Stewart, A and Hill, CS (2017)
    Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling.
    eLife 6, e22474 PubMed abstract
  • Coelho, MA; de Carné Trécesson, S; Rana, S; Zecchin, D; Moore, C; Molina-Arcas, M; East, P; Spencer-Dene, B; Nye, E; Barnouin, K; Snijders, AP; Lai, WS; Blackshear, PJ and Downward, J (2017)
    Oncogenic RAS signaling promotes tumor immunoresistance by stabilizing PD-L1 mRNA.
    Immunity 47, 1083-1099 e1086 PubMed abstract
  • Crockford, A; Zalmas, LP; Grönroos, E; Dewhurst, SM; McGranahan, N; Cuomo, ME; Encheva, V; Snijders, AP; Begum, J; Purewal, S; Cerveira, J; Patel, H; Renshaw, MJ and Swanton, C (2017)
    Cyclin D mediates tolerance of genome-doubling in cancers with functional p53.
    Annals of Oncology 28, 149-156 PubMed abstract
  • Desai, R; Frazier, AE; Durigon, R; Patel, H; Jones, AW; Dalla Rosa, I; Lake, NJ; Compton, AG; Mountford, HS; Tucker, EJ; Mitchell, ALR; Jackson, D; Sesay, A; Di Re, M; van den Heuvel, LP; Burke, D; Francis, D; Lunke, S; McGillivray, G; Mandelstam, S; Mochel, F; Keren, B; Jardel, C; Turner, AM; Ian Andrews, P; Smeitink, J; Spelbrink, JN; Heales, SJ; Kohda, M; Ohtake, A; Murayama, K; Okazaki, Y; Lombès, A; Holt, IJ; Thorburn, DR and Spinazzola, A (2017)
    ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
    Brain 140, 1595-1610 PubMed abstract
  • Di Tullio, A; Rouault-Pierre, K; Abarrategi, A; Mian, S; Grey, W; Gribben, J; Stewart, A; Blackwood, E and Bonnet, D (2017)
    The combination of CHK1 inhibitor with G-CSF overrides cytarabine resistance in human acute myeloid leukemia.
    Nature Communications 8, 1679 PubMed abstract
  • Esnault, C; Gualdrini, F; Horswell, S; Kelly, G; Stewart, A; East, P; Matthews, N and Treisman, R (2017)
    ERK-induced activation of TCF family of SRF cofactors initiates a chromatin modification cascade associated with transcription.
    Molecular Cell 65, 1081-1095 e1085 PubMed abstract
  • Fogarty, NME; McCarthy, A; Snijders, KE; Powell, BE; Kubikova, N; Blakeley, P; Lea, R; Elder, K; Wamaitha, SE; Kim, D; Maciulyte, V; Kleinjung, J; Kim, J-S; Wells, D; Vallier, L; Bertero, A; Turner, JMA and Niakan, KK (2017)
    Genome editing reveals a role for OCT4 in human embryogenesis.
    Nature 550, 67-73 PubMed abstract
  • Gehrig, S; Macpherson, JA; Driscoll, PC; Symon, A; Martin, SR; MacRae, JI; Kleinjung, J; Fraternali, F and Anastasiou, D (2017)
    An engineered photoswitchable mammalian pyruvate kinase.
    FEBS Journal 284, 2955-2980 PubMed abstract
  • Helft, J; Anjos-Afonso, F; van der Veen, AG; Chakravarty, P; Bonnet, D and Reis e Sousa, C (2017)
    Dendritic cell lineage potential in human early hematopoietic progenitors.
    Cell Reports 20, 529-537 PubMed abstract
  • Jamal-Hanjani, M; Wilson, GA; McGranahan, N; Birkbak, NJ; Watkins, TBK; Veeriah, S; Shafi, S; Johnson, DH; Mitter, R; Rosenthal, R; Salm, M; Horswell, S; Escudero, M; Matthews, N; Rowan, A; Chambers, T; Moore, DA; Turajlic, S; Xu, H; Lee, S-M; Forster, MD; Ahmad, T; Hiley, CT; Abbosh, C; Falzon, M; Borg, E; Marafioti, T; Lawrence, D; Hayward, M; Kolvekar, S; Panagiotopoulos, N; Janes, SM; Thakrar, R; Ahmed, A; Blackhall, F; Summers, Y; Shah, R; Joseph, L; Quinn, AM; Crosbie, PA; Naidu, B; Middleton, G; Langman, G; Trotter, S; Nicolson, M; Remmen, H; Kerr, K; Chetty, M; Gomersall, L; Fennell, DA; Nakas, A; Rathinam, S; Anand, G; Khan, S; Russell, P; Ezhil, V; Ismail, B; Irvin-Sellers, M; Prakash, V; Lester, JF; Kornaszewska, M; Attanoos, R; Adams, H; Davies, H; Dentro, S; Taniere, P; O'Sullivan, B; Lowe, HL; Hartley, JA; Iles, N; Bell, H; Ngai, Y; Shaw, JA; Herrero, J; Szallasi, Z; Schwarz, RF; Stewart, A; Quezada, SA; Le Quesne, J; Van Loo, P; Dive, C; Hackshaw, A; Swanton, C and The TRACERx Consortium (2017)
    Tracking the evolution of non-small-cell lung cancer.
    New England Journal of Medicine 376, 2109-2121 PubMed abstract
  • Kalmar, B; Innes, A; Wanisch, K; Koyen Kolaszynska, A; Pandraud, A; Kelly, G; Abramov, AY; Reilly, MM; Schiavo, G and Greensmith, L (2017)
    Mitochondrial deficits and abnormal mitochondrial retrograde axonal transport play a role in the pathogenesis of mutant Hsp27 induced Charcot Marie Tooth Disease.
    Human Molecular Genetics 26, 3313-3326 PubMed abstract
  • Kannan, Y; Li, Y; Coomes, SM; Okoye, IS; Pelly, VS; Sriskantharajah, S; Gückel, E; Webb, L; Czieso, S; Nikolov, N; MacDonald, AS; Ley, SC and Wilson, MS (2017)
    Tumor progression locus 2 reduces severe allergic airway inflammation by inhibiting Ccl24 production in dendritic cells.
    Journal of Allergy and Clinical Immunology 139, 655-666.e657 PubMed abstract
  • Kurat, CF; Yeeles, JTP; Patel, H; Early, A and Diffley, JFX (2017)
    Chromatin controls DNA replication origin selection, lagging-strand synthesis, and replication fork rates.
    Molecular Cell 65, 117-130 PubMed abstract
  • Linch, M; Goh, G; Hiley, C; Shanmugabavan, Y; McGranahan, N; Rowan, A; Wong, YNS; King, H; Furness, A; Freeman, A; Linares, J; Akarca, A; Herrero, J; Rosenthal, R; Harder, N; Schmidt, G; Wilson, GA; Birkbak, NJ; Mitter, R; Dentro, S; Cathcart, P; Arya, M; Johnston, E; Scott, R; Hung, M; Emberton, M; Attard, G; Szallasi, Z; Punwani, S; Quezada, SA; Marafioti, T; Gerlinger, M; Ahmed, HU and Swanton, C (2017)
    Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters.
    Annals of Oncology 28, 2472-2480 PubMed abstract
  • López-Garcia, C; Sansregret, L; Domingo, E; McGranahan, N; Hobor, S; Birkbak, NJ; Horswell, S; Grönroos, E; Favero, F; Rowan, AJ; Matthews, N; Begum, S; Phillimore, B; Burrell, R; Oukrif, D; Spencer-Dene, B; Kovac, M; Stamp, G; Stewart, A; Danielsen, H; Novelli, M; Tomlinson, I and Swanton, C (2017)
    BCL9L dysfunction impairs caspase-2 expression permitting aneuploidy tolerance in colorectal cancer.
    Cancer Cell 31, 79-93 PubMed abstract
  • Montfort, A; Pearce, O; Maniati, E; Vincent, BG; Bixby, L; Böhm, S; Dowe, T; Wilkes, EH; Chakravarty, P; Thompson, R; Topping, J; Cutillas, PR; Lockley, M; Serody, JS; Capasso, M and Balkwill, FR (2017)
    A strong B-cell response is part of the immune landscape in human high-grade serous ovarian metastases.
    Clinical Cancer Research 23, 250-262 PubMed abstract
  • Navarro, FJ; Chakravarty, P and Nurse, P (2017)
    Phosphorylation of the RNA binding protein Zfs1 modulates sexual differentiation in fission yeast.
    Journal of Cell Science 130, 4144-4154 PubMed abstract
  • Passaro, D; Di Tullio, A; Abarrategi, A; Rouault-Pierre, K; Foster, K; Ariza-McNaughton, L; Montaner, B; Chakravarty, P; Bhaw, L; Diana, G; Lassailly, F; Gribben, J and Bonnet, D (2017)
    Increased vascular permeability in the bone marrow microenvironment contributes to disease progression and drug response in acute myeloid leukemia.
    Cancer Cell 32, 324-341 e326 PubMed abstract
  • Ros, S; Flöter, J; Kaymak, I; Da Costa, C; Houddane, A; Dubuis, S; Griffiths, B; Mitter, R; Walz, S; Blake, S; Behrens, A; Brindle, KM; Zamboni, N; Rider, MH and Schulze, A (2017)
    6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 is essential for p53-null cancer cells.
    Oncogene 36, 3287-3299 PubMed abstract
  • Sansregret, L; Patterson, JO; Dewhurst, S; López-García, C; Koch, A; McGranahan, N; Chao, WCH; Barry, DJ; Rowan, A; Instrell, R; Horswell, S; Way, M; Howell, M; Singleton, MR; Medema, RH; Nurse, P; Petronczki, M and Swanton, C (2017)
    APC/C dysfunction limits excessive cancer chromosomal instability.
    Cancer Discovery 7, 218-233 PubMed abstract
  • Weems, JC; Slaughter, BD; Unruh, JR; Boeing, S; Hall, SM; McLaird, MB; Yasukawa, T; Aso, T; Svejstrup, JQ; Conaway, JW and Conaway, RC (2017)
    Cockayne syndrome B protein regulates recruitment of the Elongin A ubiquitin ligase to sites of DNA damage.
    Journal of Biological Chemistry 292, 6431-6437 PubMed abstract
  • Williamson, L; Saponaro, M; Boeing, S; East, P; Mitter, R; Kantidakis, T; Kelly, GP; Lobley, A; Walker, J; Spencer-Dene, B; Howell, M; Stewart, A and Svejstrup, JQ (2017)
    UV irradiation induces a non-coding RNA that functionally opposes the protein encoded by the same gene.
    Cell 168, 843-855 PubMed abstract
  • Blaas, L; Pucci, F; Messal, HA; Andersson, AB; Ruiz, EJ; Gerling, M; Douagi, I; Spencer-Dene, B; Musch, A; Mitter, R; Bhaw, L; Stone, R; Bornhorst, D; Sesay, AK; Jonkers, J; Stamp, G; Malanchi, I; Toftgård, R and Behrens, A (2016)
    Lgr6 labels a rare population of mammary gland progenitor cells that are able to originate luminal mammary tumours.
    Nature Cell Biology 18, 1346-1356 PubMed abstract
  • Blake, SM; Stricker, SH; Halavach, H; Poetsch, AR; Cresswell, G; Kelly, G; Kanu, N; Marino, S; Luscombe, NM; Pollard, SM and Behrens, A (2016)
    Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation.
    eLife 5, e08711 PubMed abstract
  • Boeing, S; Williamson, L; Encheva, V; Gori, I; Saunders, RE; Instrell, R; Aygün, O; Rodriguez-Martinez, M; Weems, JC; Kelly, GP; Conaway, JW; Conaway, RC; Stewart, A; Howell, M; Snijders, AP and Svejstrup, JQ (2016)
    Multiomic analysis of the UV-induced DNA damage response.
    Cell Reports 15, 1597-1610 PubMed abstract
  • Böhm, S; Montfort, A; Pearce, OMT; Topping, J; Chakravarty, P; Everitt, GLA; Clear, A; McDermott, JR; Ennis, D; Dowe, T; Fitzpatrick, A; Brockbank, EC; Lawrence, AC; Jeyarajah, A; Faruqi, AZ; McNeish, IA; Singh, N; Lockley, M and Balkwill, FR (2016)
    Neoadjuvant chemotherapy modulates the immune microenvironment in metastases of tubo-ovarian high-grade serous carcinoma.
    Clinical Cancer Research 22, 3025-3036 PubMed abstract
  • Brown, PJ; Gascoyne, DM; Lyne, L; Spearman, H; Felce, SL; McFadden, N; Chakravarty, P; Barrans, S; Lynham, S; Calado, DP; Ward, M and Banham, AH (2016)
    N-terminally truncated FOXP1 protein expression and alternate internal FOXP1 promoter usage in normal and malignant B cells.
    Haematologica 101, 861-871 PubMed abstract
  • Castellano, E; Molina-Arcas, M; Krygowska, AA; East, P; Warne, P; Nicol, A and Downward, J (2016)
    RAS signalling through PI3-Kinase controls cell migration via modulation of Reelin expression.
    Nature Communications 7, 11245 PubMed abstract
  • Debaisieux, S; Encheva, V; Chakravarty, P; Snijders, AP and Schiavo, G (2016)
    Analysis of signaling endosome composition and dynamics using SILAC in embryonic stem cell-derived neurons.
    Molecular & Cellular Proteomics 15, 542-557 PubMed abstract
  • Di Marco Barros, R; Roberts, NA; Dart, RJ; Vantourout, P; Jandke, A; Nussbaumer, O; Deban, L; Cipolat, S; Hart, R; Iannitto, ML; Laing, A; Spencer-Dene, B; East, P; Gibbons, D; Irving, PM; Pereira, P; Steinhoff, U and Hayday, A (2016)
    Epithelia use butyrophilin-like molecules to shape organ-specific γδ T cell compartments.
    Cell 167, 203-218 e217 PubMed abstract
  • Elbediwy, A; Vincent-Mistiaen, ZI; Spencer-Dene, B; Stone, RK; Boeing, S; Wculek, SK; Cordero, J; Tan, EH; Ridgway, R; Brunton, VG; Sahai, E; Gerhardt, H; Behrens, A; Malanchi, I; Sansom, OJ and Thompson, BJ (2016)
    Integrin signalling regulates YAP and TAZ to control skin homeostasis.
    Development 143, 1674-1687 PubMed abstract
  • Gualdrini, F; Esnault, C; Horswell, S; Stewart, A; Matthews, N and Treisman, R (2016)
    SRF co-factors control the balance between cell proliferation and contractility.
    Molecular Cell 64, 1048-1061 PubMed abstract
  • Helft, J; Böttcher, JP; Chakravarty, P; Zelenay, S; Huotari, J; Schraml, BU; Goubau, D and Reis e Sousa, C (2016)
    Alive but confused: heterogeneity of CD11c+ MHC class II+ cells in GM-CSF mouse bone marrow cultures.
    Immunity 44, 3-4 PubMed abstract
  • Jamal-Hanjani, M; Wilson, GA; Horswell, S; Mitter, R; Sakarya, O; Constantin, T; Salari, R; Kirkizlar, E; Sigurjonsson, S; Pelham, R; Kareht, S; Zimmermann, B and Swanton, C (2016)
    Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer.
    Annals of Oncology 27, 862-867 PubMed abstract
  • Kantidakis, T; Saponaro, M; Mitter, R; Horswell, S; Kranz, A; Boeing, S; Aygün, O; Kelly, GP; Matthews, N; Stewart, A; Stewart, AF and Svejstrup, JQ (2016)
    Mutation of cancer driver MLL2 results in transcription stress and genome instability.
    Genes & Development 30, 408-420 PubMed abstract
  • Kulbe, H; Iorio, F; Chakravarty, P; Milagre, CS; Moore, R; Thompson, RG; Everitt, G; Canosa, M; Montoya, A; Drygin, D; Braicu, I; Sehouli, J; Saez-Rodriguez, J; Cutillas, PR and Balkwill, FR (2016)
    Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
    Oncotarget 7, 15648-15661 PubMed abstract
  • Ling, H; Pickard, K; Ivan, C; Isella, C; Ikuo, M; Mitter, R; Spizzo, R; Bullock, MD; Braicu, C; Pileczki, V; Vincent, K; Pichler, M; Stiegelbauer, V; Hoefler, G; Almeida, MI; Hsiao, A; Zhang, X; Primrose, JN; Packham, GK; Liu, K; Bojja, K; Gafà, R; Xiao, L; Rossi, S; Song, JH; Vannini, I; Fanini, F; Kopetz, S; Zweidler-McKay, P; Wang, X; Ionescu, C; Irimie, A; Fabbri, M; Lanza, G; Hamilton, SR; Berindan-Neagoe, I; Medico, E; Mirnezami, AH; Calin, GA and Nicoloso, MS (2016)
    The clinical and biological significance of MIR-224 expression in colorectal cancer metastasis.
    Gut 65, 977-989 PubMed abstract
  • McGranahan, N; Furness, AJS; Rosenthal, R; Ramskov, S; Lyngaa, R; Saini, SK; Jamal-Hanjani, M; Wilson, GA; Birkbak, NJ; Hiley, CT; Watkins, TBK; Shafi, S; Murugaesu, N; Mitter, R; Akarca, AU; Linares, J; Marafioti, T; Henry, JY; Van Allen, EM; Miao, D; Schilling, B; Schadendorf, D; Garraway, LA; Makarov, V; Rizvi, NA; Snyder, A; Hellmann, MD; Merghoub, T; Wolchok, JD; Shukla, SA; Wu, CJ; Peggs, KS; Chan, TA; Hadrup, SR; Quezada, SA and Swanton, C (2016)
    Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.
    Science 351, 1463-1469 PubMed abstract
  • Morales Torres, C; Biran, A; Burney, MJ; Patel, H; Henser-Brownhill, T; Cohen, A-HS; Li, Y; Ben-Hamo, R; Nye, E; Spencer-Dene, B; Chakravarty, P; Efroni, S; Matthews, N; Misteli, T; Meshorer, E and Scaffidi, P (2016)
    The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity.
    Science 353, aaf1644 PubMed abstract
  • Niavarani, A; Horswell, S; Sadri, R and Bonnet, D (2016)
    The Wilms Tumor-1 (WT1) rs2234593 variant is a prognostic factor in normal karyotype acute myeloid leukemia.
    Annals of Hematology 95, 179-190 PubMed abstract
  • Nitarska, J; Smith, JG; Sherlock, WT; Hillege, MMG; Nott, A; Barshop, WD; Vashisht, AA; Wohlschlegel, JA; Mitter, R and Riccio, A (2016)
    A functional switch of NuRD chromatin remodeling complex subunits regulates mouse cortical development.
    Cell Reports 17, 1683-1698 PubMed abstract
  • Pattison, MJ; Mitchell, O; Flynn, HR; Chen, C-S; Yang, H-T; Ben-Addi, H; Boeing, S; Snijders, AP and Ley, SC (2016)
    TLR and TNF-R1 activation of the MKK3/MKK6-p38α axis in macrophages is mediated by TPL-2 kinase.
    Biochemical Journal 473, 2845-2861 PubMed abstract
  • Peck, B; Schug, ZT; Zhang, Q; Dankworth, B; Jones, DT; Smethurst, E; Patel, R; Mason, S; Jiang, M; Saunders, R; Howell, M; Mitter, R; Spencer-Dene, B; Stamp, G; McGarry, L; James, D; Shanks, E; Aboagye, EO; Critchlow, SE; Leung, HY; Harris, AL; Wakelam, MJO; Gottlieb, E and Schulze, A (2016)
    Inhibition of fatty acid desaturation is detrimental to cancer cell survival in metabolically compromised environments.
    Cancer & Metabolism 4, 6 PubMed abstract
  • Ranes, M; Boeing, S; Wang, Y; Wienholz, F; Menoni, H; Walker, J; Encheva, V; Chakravarty, P; Mari, P-O; Stewart, A; Giglia-Mari, G; Snijders, AP; Vermeulen, W and Svejstrup, JQ (2016)
    A ubiquitylation site in Cockayne syndrome B required for repair of oxidative DNA damage, but not for transcription-coupled nucleotide excision repair.
    Nucleic Acids Research 44, 5246-5255 PubMed abstract
  • Srinivasan, N; Gordon, O; Ahrens, S; Franz, A; Deddouche, S; Chakravarty, P; Phillips, D; Yunus, AA; Rosen, MK; Valente, RS; Teixeira, L; Thompson, B; Dionne, MS; Wood, W and Reis e Sousa, C (2016)
    Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster.
    eLife 5, e19662 PubMed abstract
  • Swee, LK; Tan, ZW; Sanecka, A; Yoshida, N; Patel, H; Grotenbreg, G; Frickel, E-M and Ploegh, HL (2016)
    Peripheral self-reactivity regulates antigen-specific CD8 T-cell responses and cell division under physiological conditions.
    Open Biology 6, 160293 PubMed abstract
  • Vaidyanathan, A; Sawers, L; Gannon, A-L; Chakravarty, P; Scott, AL; Bray, SE; Ferguson, MJ and Smith, G (2016)
    ABCB1 (MDR1) induction defines a common resistance mechanism in paclitaxel- and olaparib-resistant ovarian cancer cells.
    British Journal of Cancer 115, 431-441 PubMed abstract
  • Wang, Y; Jones-Tabah, J; Chakravarty, P; Stewart, A; Muotri, A; Laposa, RR and Svejstrup, JQ (2016)
    Pharmacological bypass of Cockayne syndrome B function in neuronal differentiation.
    Cell Reports 14, 2554-2561 PubMed abstract
  • Amankwatia, EB; Chakravarty, P; Carey, FA; Weidlich, S; Steele, RJC; Munro, AJ; Wolf, CR and Smith, G (2015)
    MicroRNA-224 is associated with colorectal cancer progression and response to 5-fluorouracil-based chemotherapy by KRAS-dependent and -independent mechanisms.
    British Journal of Cancer 112, 1480-1490 PubMed abstract
  • Bullock, MD; Pickard, K; Mitter, R; Sayan, AE; Primrose, JN; Ivan, C; Calin, GA; Thomas, GJ; Packham, GK and Mirnezami, AH (2015)
    Stratifying risk of recurrence in stage II colorectal cancer using deregulated stromal and epithelial microRNAs.
    Oncotarget 6, 7262-7279 PubMed abstract
  • Cellura, D; Pickard, K; Quaratino, S; Parker, H; Strefford, JC; Thomas, GJ; Mitter, R; Mirnezami, AH and Peake, NJ (2015)
    miR-19-mediated inhibition of transglutaminase-2 leads to enhanced invasion and metastasis in colorectal cancer.
    Molecular Cancer Research 13, 1095-1105 PubMed abstract
  • Cheng, TMK; Heeger, S; Chaleil, RAG; Matthews, N; Stewart, A; Wright, J; Lim, C; Bates, PA and Uhlmann, F (2015)
    A simple biophysical model emulates budding yeast chromosome condensation.
    eLife 4, e05565 PubMed abstract
  • del Pozo Martin, Y; Park, D; Ramachandran, A; Ombrato, L; Calvo, F; Chakravarty, P; Spencer-Dene, B; Derzsi, S; Hill, CS; Sahai, E and Malanchi, I (2015)
    Mesenchymal cancer cell-stroma crosstalk promotes niche activation, epithelial reversion, and metastatic colonization.
    Cell Reports 13, 2456-2469 PubMed abstract
  • di Martino, E; Kelly, G; Roulson, J-A and Knowles, MA (2015)
    Alteration of cell-cell and cell-matrix adhesion in urothelial cells: an oncogenic mechanism for mutant FGFR3.
    Molecular Cancer Research 13, 138-148 PubMed abstract
  • Diefenbacher, ME; Chakraborty, A; Blake, SM; Mitter, R; Popov, N; Eilers, M and Behrens, A (2015)
    Usp28 counteracts Fbw7 in intestinal homeostasis and cancer.
    Cancer Research 75, 1181-1186 PubMed abstract
  • Ehrensberger, AH; Franchini, D-M; East, P; George, R; Matthews, N; Maslen, SL and Svejstrup, JQ (2015)
    Retention of the native epigenome in purified mammalian chromatin.
    PLOS ONE 10, e0133246 PubMed abstract
  • Favero, F; McGranahan, N; Salm, M; Birkbak, NJ; Sanborn, JZ; Benz, SC; Becq, J; Peden, JF; Kingsbury, Z; Grocok, RJ; Humphray, S; Bentley, D; Spencer-Dene, B; Gutteridge, A; Brada, M; Roger, S; Dietrich, P-Y; Forshew, T; Gerlinger, M; Rowan, A; Stamp, G; Eklund, AC; Szallasi, Z and Swanton, C (2015)
    Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome.
    Annals of Oncology 26, 880-887 PubMed abstract
  • Godin-Heymann, N; Brabetz, S; Murillo, MM; Saponaro, M; Santos, CR; Lobley, A; East, P; Chakravarty, P; Matthews, N; Kelly, G; Jordan, S; Castellano, E and Downward, J (2015)
    Tumour-suppression function of KLF12 through regulation of anoikis.
    Oncogene 35, 3324-3334 PubMed abstract
  • Goubau, D; van der Veen, AG; Chakravarty, P; Lin, R; Rogers, N; Rehwinkel, J; Deddouche, S; Rosewell, I; Hiscott, J and Reis e Sousa, C (2015)
    Mouse superkiller-2-like helicase DDX60 is dispensable for type I IFN induction and immunity to multiple viruses.
    European Journal of Immunology 45, 3386-3403 PubMed abstract
  • Helft, J; Böttcher, J; Chakravarty, P; Zelenay, S; Huotari, J; Schraml, BU; Goubau, D and Reis e Sousa, C (2015)
    GM-CSF mouse bone marrow cultures comprise a heterogeneous population of CD11c+MHCII+ macrophages and dendritic cells.
    Immunity 42, 1197-1211 PubMed abstract
  • Jamal-Hanjani, M; A'Hern, R; Birkbak, NJ; Gorman, P; Grönroos, E; Ngang, S; Nicola, P; Rahman, L; Thanopoulou, E; Kelly, G; Ellis, P; Barrett-Lee, P; Johnston, SRD; Bliss, J; Roylance, R and Swanton, C (2015)
    Extreme chromosomal instability forecasts improved outcome in ER-negative breast cancer: a prospective validation cohort study from the TACT trial.
    Annals of Oncology 26, 1340-1346 PubMed abstract
  • Joachim, J; Jefferies, HBJ; Razi, M; Frith, D; Snijders, AP; Chakravarty, P; Judith, D and Tooze, SA (2015)
    Activation of ULK kinase and autophagy by GABARAP trafficking from the centrosome is regulated by WAC and GM130.
    Molecular Cell 60, 899-913 PubMed abstract
  • Kanu, N; Grönroos, E; Martinez, P; Burrell, RA; Yi Goh, X; Bartkova, J; Maya-Mendoza, A; Mistrik, M; Rowan, AJ; Patel, H; Rabinowitz, A; East, P; Wilson, G; Santos, CR; McGranahan, N; Gulati, S; Gerlinger, M; Birkbak, NJ; Joshi, T; Alexandrov, LB; Stratton, MR; Powles, T; Matthews, N; Bates, PA; Stewart, A; Szallasi, Z; Larkin, J; Bartek, J and Swanton, C (2015)
    SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.
    Oncogene 34, 5699-5708 PubMed abstract
  • Kovac, M; Navas, C; Horswell, S; Salm, M; Bardella, C; Rowan, A; Stares, M; Castro-Giner, F; Fisher, R; de Bruin, EC; Kovacova, M; Gorman, M; Makino, S; Williams, J; Jaeger, E; Jones, A; Howarth, K; Larkin, J; Pickering, L; Gore, M; Nicol, DL; Hazell, S; Stamp, G; O'Brien, T; Challacombe, B; Matthews, N; Phillimore, B; Begum, S; Rabinowitz, A; Varela, I; Chandra, A; Horsfield, C; Polson, A; Tran, M; Bhatt, R; Terracciano, L; Eppenberger-Castori, S; Protheroe, A; Maher, E; El Bahrawy, M; Fleming, S; Ratcliffe, P; Heinimann, K; Swanton, C and Tomlinson, I (2015)
    Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution.
    Nature Communications 6, 6336 PubMed abstract
  • Lewis, CA; Brault, C; Peck, B; Bensaad, K; Griffiths, B; Mitter, R; Chakravarty, P; East, P; Dankworth, B; Alibhai, D; Harris, AL and Schulze, A (2015)
    SREBP maintains lipid biosynthesis and viability of cancer cells under lipid- and oxygen-deprived conditions and defines a gene signature associated with poor survival in glioblastoma multiforme.
    Oncogene 34, 5128-5140 PubMed abstract
  • McGarry, DJ; Chakravarty, P; Wolf, CR and Henderson, CJ (2015)
    Altered protein S-glutathionylation identifies a potential mechanism of resistance to acetaminophen-induced hepatotoxicity.
    Journal of Pharmacology and Experimental Therapeutics 355, 137-144 PubMed abstract
  • McGarry, DJ; Chen, W; Chakravarty, P; Lamont, DL; Wolf, CR and Henderson, CJ (2015)
    Proteome-wide identification and quantification of S-glutathionylation targets in mouse liver.
    Biochemical Journal 469, 25-32 PubMed abstract
  • Murugaesu, N; Wilson, GA; Birkbak, NJ; Watkins, TBK; McGranahan, N; Kumar, S; Abbassi-Ghadi, N; Salm, M; Mitter, R; Horswell, S; Rowan, A; Phillimore, B; Biggs, J; Begum, S; Matthews, N; Hochhauser, D; Hanna, GB and Swanton, C (2015)
    Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy.
    Cancer Discovery 5, 821-831 PubMed abstract
  • Niavarani, A; Currie, E; Reyal, Y; Anjos-Afonso, F; Horswell, S; Griessinger, E; Luis Sardina, J and Bonnet, D (2015)
    APOBEC3A is implicated in a novel class of G-to-A mRNA editing in WT1 transcripts.
    PLOS ONE 10, e0120089 PubMed abstract
  • Pender, A; Garcia-Murillas, I; Rana, S; Cutts, RJ; Kelly, G; Fenwick, K; Kozarewa, I; Gonzalez de Castro, D; Bhosle, J; O'Brien, M; Turner, NC; Popat, S and Downward, J (2015)
    Efficient genotyping of KRAS mutant non-small cell lung cancer using a multiplexed droplet digital PCR approach.
    PLOS ONE 10, e0139074 PubMed abstract
  • Ramasubramanyan, S; Osborn, K; Al-Mohammad, R; Perez-Fernandez, IBN; Zuo, J; Balan, N; Godfrey, A; Patel, H; Peters, G; Rowe, M; Jenner, RG and Sinclair, AJ (2015)
    Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression.
    Nucleic Acids Research 43, 3563-3577 PubMed abstract
  • Schmieg, N; Thomas, C; Yabe, A; Lynch, DS; Iglesias, T; Chakravarty, P and Schiavo, G (2015)
    Novel Kidins220/ARMS splice isoforms: potential specific regulators of neuronal and cardiovascular development.
    PLOS ONE 10, e0129944 PubMed abstract
  • Swamy, M; Abeler-Dörner, L; Chettle, J; Mahlakõiv, T; Goubau, D; Chakravarty, P; Ramsay, G; Reis e Sousa, C; Staeheli, P; Blacklaws, BA; Heeney, JL and Hayday, AC (2015)
    Intestinal intraepithelial lymphocyte activation promotes innate antiviral resistance.
    Nature Communications 6, 7090 PubMed abstract
  • Zelenay, S; van der Veen, AG; Böttcher, JP; Snelgrove, KJ; Rogers, N; Acton, SE; Chakravarty, P; Girotti, MR; Marais, R; Quezada, SA; Sahai, E and Reis e Sousa, C (2015)
    Cyclooxygenase-dependent tumor growth through evasion of immunity.
    Cell 162, 1257-1270 PubMed abstract
  • Andre, F; Mardis, E; Salm, M; Soria, JC; Siu, LL and Swanton, C (2014)
    Prioritizing targets for precision cancer medicine.
    Annals of Oncology 25, 2295-2303 PubMed abstract
  • Barfeld, SJ; East, P; Zuber, V and Mills, IG (2014)
    Meta-analysis of prostate cancer gene expression data identifies a novel discriminatory signature enriched for glycosylating enzymes.
    BMC Medical Genomics 7, 513 PubMed abstract
  • Bullock, MD; Mellone, M; Pickard, KM; Sayan, AE; Mitter, R; Primrose, JN; Packham, GK; Thomas, G and Mirnezami, AH (2014)
    Molecular profiling of the invasive tumor microenvironment in a 3-dimensional model of colorectal cancer cells and ex vivo fibroblasts.
    Journal of Visualized Experiments e51475 PubMed abstract
  • Chandler, H; Patel, H; Palermo, R; Brookes, S; Matthews, N and Peters, G (2014)
    Role of polycomb group proteins in the DNA damage response--a reassessment.
    PLOS ONE 9, e102968 PubMed abstract
  • de Bruin, EC; McGranahan, N; Mitter, R; Salm, M; Wedge, DC; Yates, L; Jamal-Hanjani, M; Shafi, S; Murugaesu, N; Rowan, AJ; Grönroos, E; Muhammad, MA; Horswell, S; Gerlinger, M; Varela, I; Jones, D; Marshall, J; Voet, T; Van Loo, P; Rassl, DM; Rintoul, RC; Janes, SM; Lee, S-M; Forster, M; Ahmad, T; Lawrence, D; Falzon, M; Capitanio, A; Harkins, TT; Lee, CC; Tom, W; Teefe, E; Chen, S-C; Begum, S; Rabinowitz, A; Phillimore, B; Spencer-Dene, B; Stamp, G; Szallasi, Z; Matthews, N; Stewart, A; Campbell, P and Swanton, C (2014)
    Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.
    Science 346, 251-256 PubMed abstract
  • Deddouche, S; Goubau, D; Rehwinkel, J; Chakravarty, P; Begum, S; Maillard, PV; Borg, A; Matthews, N; Feng, Q; van Kuppeveld, FJM and Reis e Sousa, C (2014)
    Identification of an LGP2-associated MDA5 agonist in picornavirus-infected cells.
    eLife 3, e01535 PubMed abstract
  • Ellis, RA; Horswell, S; Ness, T; Lumsdon, J; Tooze, SA; Kirkham, N; Armstrong, JL and Lovat, PE (2014)
    Prognostic impact of p62 expression in cutaneous malignant melanoma.
    Journal of Investigative Dermatology 134, 1476-1478 PubMed abstract
  • Esnault, C; Stewart, A; Gualdrini, F; East, P; Horswell, S; Matthews, N and Treisman, R (2014)
    Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts.
    Genes & Development 28, 943-958 PubMed abstract
  • Fisher, R; Horswell, S; Rowan, A; Salm, MP; de Bruin, EC; Gulati, S; McGranahan, N; Stares, M; Gerlinger, M; Varela, I; Crockford, A; Favero, F; Quidville, V; André, F; Navas, C; Grönroos, E; Nicol, D; Hazell, S; Hrouda, D; O'Brien, T; Matthews, N; Phillimore, B; Begum, S; Rabinowitz, A; Biggs, J; Bates, PA; McDonald, NQ; Stamp, G; Spencer-Dene, B; Hsieh, JJ; Xu, J; Pickering, L; Gore, M; Larkin, J and Swanton, C (2014)
    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
    Genome Biology 15, 433 PubMed abstract
  • Gerlinger, M; Horswell, S; Larkin, J; Rowan, AJ; Salm, MP; Varela, I; Fisher, R; McGranahan, N; Matthews, N; Santos, CR; Martinez, P; Phillimore, B; Begum, S; Rabinowitz, A; Spencer-Dene, B; Gulati, S; Bates, PA; Stamp, G; Pickering, L; Gore, M; Nicol, DL; Hazell, S; Futreal, PA; Stewart, A and Swanton, C (2014)
    Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.
    Nature Genetics 46, 225-233 PubMed abstract
  • Harding, JL; Horswell, S; Heliot, C; Armisen, J; Zimmerman, LB; Luscombe, NM; Miska, EA and Hill, CS (2014)
    Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.
    Genome Research 24, 96-106 PubMed abstract
  • Jamal-Hanjani, M; Hackshaw, A; Ngai, Y; Shaw, J; Dive, C; Quezada, S; Middleton, G; de Bruin, E; Le Quesne, J; Shafi, S; Falzon, M; Horswell, S; Blackhall, F; Khan, I; Janes, S; Nicolson, M; Lawrence, D; Forster, M; Fennell, D; Lee, S-M; Lester, J; Kerr, K; Muller, S; Iles, N; Smith, S; Murugaesu, N; Mitter, R; Salm, M; Stuart, A; Matthews, N; Adams, H; Ahmad, T; Attanoos, R; Bennett, J; Birkbak, NJ; Booton, R; Brady, G; Buchan, K; Capitano, A; Chetty, M; Cobbold, M; Crosbie, P; Davies, H; Denison, A; Djearman, M; Goldman, J; Haswell, T; Joseph, L; Kornaszewska, M; Krebs, M; Langman, G; MacKenzie, M; Millar, J; Morgan, B; Naidu, B; Nonaka, D; Peggs, K; Pritchard, C; Remmen, H; Rowan, A; Shah, R; Smith, E; Summers, Y; Taylor, M; Veeriah, S; Waller, D; Wilcox, B; Wilcox, M; Woolhouse, I; McGranahan, N and Swanton, C (2014)
    Tracking genomic cancer evolution for precision medicine: the lung TRACERx study.
    PLOS Biology 12, e1001906 PubMed abstract
  • Lönnstedt, IM; Caramia, F; Li, J; Fumagalli, D; Salgado, R; Rowan, A; Salm, M; Kanu, N; Savas, P; Horswell, S; Gade, S; Loibl, S; Neven, P; Sotiriou, C; Swanton, C; Loi, S and Speed, TP (2014)
    Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.
    Genome Biology 15, 470 PubMed abstract
  • Lopez-Serra, L; Kelly, G; Patel, H; Stewart, A and Uhlmann, F (2014)
    The Scc2-Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions.
    Nature Genetics 46, 1147-1151 PubMed abstract
  • Luxton, HJ; Barnouin, K; Kelly, G; Hanrahan, S; Totty, N; Neal, DE and Whitaker, HC (2014)
    Regulation of the localisation and function of the oncogene LYRIC/AEG-1 by ubiquitination at K486 and K491.
    Molecular Oncology 8, 633-641 PubMed abstract
  • Pemberton, H; Anderton, E; Patel, H; Brookes, S; Chandler, H; Palermo, R; Stock, J; Rodriguez-Niedenführ, M; Racek, T; de Breed, L; Stewart, A; Matthews, N and Peters, G (2014)
    Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts.
    Genome Biology 15, R23 PubMed abstract
  • Roden, DL; Sewell, GW; Lobley, A; Levine, AP; Smith, AM and Segal, AW (2014)
    ZODET: software for the identification, analysis and visualisation of outlier genes in microarray expression data.
    PLOS ONE 9, e81123 PubMed abstract
  • Rushworth, LK; Kidger, AM; Delavaine, L; Stewart, G; van Schelven, S; Davidson, J; Bryant, CJ; Caddye, E; East, P; Caunt, CJ and Keyse, SM (2014)
    Dual-specificity phosphatase 5 regulates nuclear ERK activity and suppresses skin cancer by inhibiting mutant Harvey-Ras (HRasQ61L)-driven SerpinB2 expression.
    Proceedings of the National Academy of Sciences of the United States of America 111, 18267-18272 PubMed abstract
  • Saponaro, M; Kantidakis, T; Mitter, R; Kelly, GP; Heron, M; Williams, H; Söding, J; Stewart, A and Svejstrup, JQ (2014)
    RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.
    Cell 157, 1037-1049 PubMed abstract
  • Sawers, L; Ferguson, MJ; Ihrig, BR; Young, HC; Chakravarty, P; Wolf, CR and Smith, G (2014)
    Glutathione S-transferase P1 (GSTP1) directly influences platinum drug chemosensitivity in ovarian tumour cell lines.
    British Journal of Cancer 111, 1150-1158 PubMed abstract
  • Wang, Y; Chakravarty, P; Ranes, M; Kelly, G; Brooks, PJ; Neilan, E; Stewart, A; Schiavo, G and Svejstrup, JQ (2014)
    Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease.
    Proceedings of the National Academy of Sciences of the United States of America 111, 14454-14459 PubMed abstract
  • Bullock, MD; Pickard, KM; Nielsen, BS; Sayan, AE; Jenei, V; Mellone, M; Mitter, R; Primrose, JN; Thomas, GJ; Packham, GK and Mirnezami, AH (2013)
    Pleiotropic actions of miR-21 highlight the critical role of deregulated stromal microRNAs during colorectal cancer progression.
    Cell Death & Disease 4, e684 PubMed abstract
  • Ehrensberger, AH; Kelly, GP and Svejstrup, JQ (2013)
    Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps.
    Cell 154, 713-715 PubMed abstract
  • Griffiths, B; Lewis, CA; Bensaad, K; Ros, S; Zhang, Q; Ferber, EC; Konisti, S; Peck, B; Miess, H; East, P; Wakelam, M; Harris, AL and Schulze, A (2013)
    Sterol regulatory element binding protein-dependent regulation of lipid synthesis supports cell survival and tumor growth.
    Cancer & Metabolism 1, 3 PubMed abstract
  • Hart, R; Stanley, P; Chakravarty, P and Hogg, N (2013)
    The kindlin 3 pleckstrin homology domain has an essential role in lymphocyte function-associated antigen 1 (LFA-1) integrin-mediated B cell adhesion and migration.
    Journal of Biological Chemistry 288, 14852-14862 PubMed abstract
  • Horswell, S; Matthews, N and Swanton, C (2013)
    Cancer heterogeneity and "the struggle for existence": diagnostic and analytical challenges.
    Cancer Letters 340, 220-226 PubMed abstract
  • Horswell, SD; Fryer, LGD; Hutchison, CE; Zindrou, D; Speedy, HE; Town, M-M; Duncan, EJ; Sivapackianathan, R; Patel, HN; Jones, EL; Braithwaite, A; Salm, MPA; Neuwirth, CKY; Potter, E; Anderson, JR; Taylor, KM; Seed, M; Betteridge, DJ; Crook, MA; Wierzbicki, AS; Scott, J; Naoumova, RP and Shoulders, CC (2013)
    CDKN2B expression in adipose tissue of familial combined hyperlipidemia patients.
    Journal of Lipid Research 54, 3491-3505 PubMed abstract
  • Jones, DT; Lechertier, T; Reynolds, LE; Mitter, R; Robinson, SD; Kirn-Safran, CB and Hodivala-Dilke, KM (2013)
    Endogenous ribosomal protein L29 (RPL29): a newly identified regulator of angiogenesis in mice.
    Disease Models & Mechanisms 6, 115-124 PubMed abstract
  • Lopez-Serra, L; Lengronne, A; Borges, V; Kelly, G and Uhlmann, F (2013)
    Budding yeast Wapl controls sister chromatid cohesion maintenance and chromosome condensation.
    Current Biology 23, 64-69 PubMed abstract
  • Rouault-Pierre, K; Lopez-Onieva, L; Foster, K; Anjos-Afonso, F; Lamrissi-Garcia, I; Serrano-Sanchez, M; Mitter, R; Ivanovic, Z; de Verneuil, H; Gribben, J; Taussig, D; Rezvani, HR; Mazurier, F and Bonnet, D (2013)
    HIF-2α protects human hematopoietic stem/progenitors and acute myeloid leukemic cells from apoptosis induced by endoplasmic reticulum stress.
    Cell Stem Cell 13, 549-563 PubMed abstract
  • Williamson, SC; Mitter, R; Hepburn, AC; Wilson, L; Mantilla, A; Leung, HY; Robson, CN and Heer, R (2013)
    Characterisations of human prostate stem cells reveal deficiency in class I UGT enzymes as a novel mechanism for castration-resistant prostate cancer.
    British Journal of Cancer 109, 950-956 PubMed abstract
  • Zhang, L; Pickard, K; Jenei, V; Bullock, MD; Bruce, A; Mitter, R; Kelly, G; Paraskeva, C; Strefford, J; Primrose, J; Thomas, GJ; Packham, G and Mirnezami, AH (2013)
    miR-153 supports colorectal cancer progression via pleiotropic effects that enhance invasion and chemotherapeutic resistance.
    Cancer Research 73, 6435-6447 PubMed abstract
  • Arthur-Farraj, PJ; Latouche, M; Wilton, DK; Quintes, S; Chabrol, E; Banerjee, A; Woodhoo, A; Jenkins, B; Rahman, M; Turmaine, M; Wicher, GK; Mitter, R; Greensmith, L; Behrens, A; Raivich, G; Mirsky, R and Jessen, KR (2012)
    c-Jun reprograms Schwann cells of injured nerves to generate a repair cell essential for regeneration.
    Neuron 75, 633-647 PubMed abstract
  • Close, P; East, P; Dirac-Svejstrup, AB; Hartmann, H; Heron, M; Maslen, S; Chariot, A; Söding, J; Skehel, M and Svejstrup, JQ (2012)
    DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.
    Nature 484, 386-389 PubMed abstract
  • Ferber, EC; Peck, B; Delpuech, O; Bell, GP; East, P and Schulze, A (2012)
    FOXO3a regulates reactive oxygen metabolism by inhibiting mitochondrial gene expression.
    Cell Death and Differentiation 19, 968-979 PubMed abstract
  • Gerlinger, M; Rowan, AJ; Horswell, S; Larkin, J; Endesfelder, D; Gronroos, E; Martinez, P; Matthews, N; Stewart, A; Tarpey, P; Varela, I; Phillimore, B; Begum, S; McDonald, NQ; Butler, A; Jones, D; Raine, K; Latimer, C; Santos, CR; Nohadani, M; Eklund, AC; Spencer-Dene, B; Clark, G; Pickering, L; Stamp, G; Gore, M; Szallasi, Z; Downward, J; Futreal, PA and Swanton, C (2012)
    Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
    New England Journal of Medicine 366, 883-892 PubMed abstract
  • Gerlinger, M; Santos, CR; Spencer-Dene, B; Martinez, P; Endesfelder, D; Burrell, RA; Vetter, M; Jiang, M; Saunders, RE; Kelly, G; Dykema, K; Rioux-Leclercq, N; Stamp, G; Patard, JJ; Larkin, J; Howell, M and Swanton, C (2012)
    Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target.
    Journal of Pathology 227, 146-156 PubMed abstract
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    Gene expression analysis in human breast cancer associated blood vessels.
    PLOS ONE 7, e44294 PubMed abstract
  • Kulbe, H; Chakravarty, P; Leinster, DA; Charles, KA; Kwong, J; Thompson, RG; Coward, JI; Schioppa, T; Robinson, SC; Gallagher, WM; Galletta, L; Salako, MA; Smyth, JF; Hagemann, T; Brennan, DJ; Bowtell, DD and Balkwill, FR (2012)
    A dynamic inflammatory cytokine network in the human ovarian cancer microenvironment.
    Cancer Research 72, 66-75 PubMed abstract
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    The GATA2 transcriptional network is requisite for RAS oncogene-driven non-small cell lung cancer.
    Cell 149, 642-655 PubMed abstract
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    CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction.
    Journal of Pathology 226, 482-494 PubMed abstract
  • Lewis, A; Davis, H; Deheragoda, M; Pollard, P; Nye, E; Jeffery, R; Segditsas, S; East, P; Poulsom, R; Stamp, G; Wright, N and Tomlinson, I (2012)
    The C-terminus of Apc does not influence intestinal adenoma development or progression.
    Journal of Pathology 226, 73-83 PubMed abstract
  • Ros, S; Santos, CR; Moco, S; Baenke, F; Kelly, G; Howell, M; Zamboni, N and Schulze, A (2012)
    Functional metabolic screen identifies 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 as an important regulator of prostate cancer cell survival.
    Cancer Discovery 2, 328-343 PubMed abstract
  • Salm, MPA; Horswell, SD; Hutchison, CE; Speedy, HE; Yang, X; Liang, L; Schadt, EE; Cookson, WO; Wierzbicki, AS; Naoumova, RP and Shoulders, CC (2012)
    The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.
    Genome Research 22, 1144-1153 PubMed abstract
  • Steckel, M; Molina-Arcas, M; Weigelt, B; Marani, M; Warne, PH; Kuznetsov, H; Kelly, G; Saunders, B; Howell, M; Downward, J and Hancock, DC (2012)
    Determination of synthetic lethal interactions in KRAS oncogene-dependent cancer cells reveals novel therapeutic targeting strategies.
    Cell Research 22, 1227-1245 PubMed abstract
  • Anglesio, MS; George, J; Kulbe, H; Friedlander, M; Rischin, D; Lemech, C; Power, J; Coward, J; Cowin, PA; House, CM; Chakravarty, P; Gorringe, KL; Campbell, IG; Australian Ovarian Cancer Study Group; Okamoto, A; Birrer, MJ; Huntsman, DG; de Fazio, A; Kalloger, SE; Balkwill, F; Gilks, CB and Bowtell, DD (2011)
    IL6-STAT3-HIF signaling and therapeutic response to the angiogenesis inhibitor sunitinib in ovarian clear cell cancer.
    Clinical Cancer Research 17, 2538-2548 PubMed abstract
  • Collazos, A; Michael, N; Whelan, RDH; Kelly, G; Mellor, H; Pang, LCH; Totty, N and Parker, PJ (2011)
    Site recognition and substrate screens for PKN family proteins.
    Biochemical Journal 438, 535-543 PubMed abstract
  • Coward, J; Kulbe, H; Chakravarty, P; Leader, D; Vassileva, V; Leinster, DA; Thompson, R; Schioppa, T; Nemeth, J; Vermeulen, J; Singh, N; Avril, N; Cummings, J; Rexhepaj, E; Jirstrom, K; Gallagher, WM; Brennan, DJ; McNeish, IA and Balkwill, FR (2011)
    Interleukin-6 as a therapeutic target in human ovarian cancer.
    Clinical Cancer Research 17, 6083-6096 PubMed abstract
  • Dodding, MP; Mitter, R; Humphries, AC and Way, M (2011)
    A kinesin-1 binding motif in vaccinia virus that is widespread throughout the human genome.
    EMBO Journal 30, 4523-4538 PubMed abstract
  • Gadaleta, E; Cutts, RJ; Kelly, GP; Crnogorac-Jurcevic, T; Kocher, HM; Lemoine, NR and Chelala, C (2011)
    A global insight into a cancer transcriptional space using pancreatic data: importance, findings and flaws.
    Nucleic Acids Research 39, 7900-7907 PubMed abstract
  • Henderson, CJ; Ritchie, KJ; McLaren, A; Chakravarty, P and Wolf, CR (2011)
    Increased skin papilloma formation in mice lacking glutathione transferase GSTP.
    Cancer Research 71, 7048-7060 PubMed abstract
  • Lawson, ARJ; Hindley, GFL; Forshew, T; Tatevossian, RG; Jamie, GA; Kelly, GP; Neale, GA; Ma, J; Jones, TA; Ellison, DW and Sheer, D (2011)
    RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology.
    Genome Research 21, 505-514 PubMed abstract
  • Mourão-Sá, D; Robinson, MJ; Zelenay, S; Sancho, D; Chakravarty, P; Larsen, R; Plantinga, M; Van Rooijen, N; Soares, MP; Lambrecht, B and Reis e Sousa, C (2011)
    CLEC-2 signaling via Syk in myeloid cells can regulate inflammatory responses.
    European Journal of Immunology 41, 3040-3053 PubMed abstract
  • Sanz-Moreno, V; Gaggioli, C; Yeo, M; Albrengues, J; Wallberg, F; Viros, A; Hooper, S; Mitter, R; Féral, CC; Cook, M; Larkin, J; Marais, R; Meneguzzi, G; Sahai, E and Marshall, CJ (2011)
    ROCK and JAK1 signaling cooperate to control actomyosin contractility in tumor cells and stroma.
    Cancer Cell 20, 229-245 PubMed abstract
  • Staresincic, L; Walker, J; Dirac-Svejstrup, AB; Mitter, R and Svejstrup, JQ (2011)
    GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein.
    Journal of Biological Chemistry 286, 35553-35561 PubMed abstract
  • Walker, J; Kwon, SY; Badenhorst, P; East, P; McNeill, H and Svejstrup, JQ (2011)
    Role of Elongator subunit Elp3 in Drosophila melanogaster larval development and immunity.
    Genetics 187, 1067-1075 PubMed abstract
  • Andreassi, C; Zimmermann, C; Mitter, R; Fusco, S; De Vita, S; Saiardi, A and Riccio, A (2010)
    An NGF-responsive element targets myo-inositol monophosphatase-1 mRNA to sympathetic neuron axons.
    Nature Neuroscience 13, 291-301 PubMed abstract
  • Ashrafian, H; O'Flaherty, L; Adam, J; Steeples, V; Chung, Y-L; East, P; Vanharanta, S; Lehtonen, H; Nye, E; Hatipoglu, E; Miranda, M; Howarth, K; Shukla, D; Troy, H; Griffiths, J; Spencer-Dene, B; Yusuf, M; Volpi, E; Maxwell, PH; Stamp, G; Poulsom, R; Pugh, CW; Costa, B; Bardella, C; Di Renzo, MF; Kotlikoff, MI; Launonen, V; Aaltonen, L; El-Bahrawy, M; Tomlinson, I and Pollard, PJ (2010)
    Expression profiling in progressive stages of fumarate-hydratase deficiency: the contribution of metabolic changes to tumorigenesis.
    Cancer Research 70, 9153-9165 PubMed abstract
  • Bilsland, LG; Sahai, E; Kelly, G; Golding, M; Greensmith, L and Schiavo, G (2010)
    Deficits in axonal transport precede ALS symptoms in vivo.
    Proceedings of the National Academy of Sciences of the United States of America 107, 20523-20528 PubMed abstract
  • Clear, AJ; Lee, AM; Calaminici, M; Ramsay, AG; Morris, KJ; Hallam, S; Kelly, G; Macdougall, F; Lister, TA and Gribben, JG (2010)
    Increased angiogenic sprouting in poor prognosis FL is associated with elevated numbers of CD163+ macrophages within the immediate sprouting microenvironment.
    Blood 115, 5053-5056 PubMed abstract
  • McDowall, A; Svensson, L; Stanley, P; Patzak, I; Chakravarty, P; Howarth, K; Sabnis, H; Briones, M and Hogg, N (2010)
    Two mutations in the KINDLIN3 gene of a new leukocyte adhesion deficiency III patient reveal distinct effects on leukocyte function in vitro.
    Blood 115, 4834-4842 PubMed abstract
  • Ribeiro, PS; Josué, F; Wepf, A; Wehr, MC; Rinner, O; Kelly, G; Tapon, N and Gstaiger, M (2010)
    Combined functional genomic and proteomic approaches identify a PP2A complex as a negative regulator of Hippo signaling.
    Molecular Cell 39, 521-534 PubMed abstract

[Page last updated 1 Jun 2018]

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