Computational Biology: Publications

  • 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
  • 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
  • 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
  • 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)
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    Science 346, 251-256 PubMed abstract
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    Prognostic impact of p62 expression in cutaneous malignant melanoma.
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    Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts.
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    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
    Genome Biology 15, 433 PubMed abstract
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    Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.
    Nature Genetics 46, 225-233 PubMed abstract
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    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
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    Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.
    Genome Biology 15, 470 PubMed abstract
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    The Scc2-Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions.
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    Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts.
    Genome Biology 15, R23 PubMed abstract
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    ZODET: software for the identification, analysis and visualisation of outlier genes in microarray expression data.
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    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
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    RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.
    Cell 157, 1037-1049 PubMed abstract
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    Glutathione S-transferase P1 (GSTP1) directly influences platinum drug chemosensitivity in ovarian tumour cell lines.
    British Journal of Cancer 111, 1150-1158 PubMed abstract
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    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
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    Pleiotropic actions of miR-21 highlight the critical role of deregulated stromal microRNAs during colorectal cancer progression.
    Cell Death & Disease 4, e684 PubMed abstract
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    Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps.
    Cell 154, 713-715 PubMed abstract
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    Sterol regulatory element binding protein-dependent regulation of lipid synthesis supports cell survival and tumor growth.
    Cancer & Metabolism 1, 3 PubMed abstract
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    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
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    Cancer heterogeneity and "the struggle for existence": diagnostic and analytical challenges.
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    CDKN2B expression in adipose tissue of familial combined hyperlipidemia patients.
    Journal of Lipid Research 54, 3491-3505 PubMed abstract
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    Endogenous ribosomal protein L29 (RPL29): a newly identified regulator of angiogenesis in mice.
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    Budding yeast Wapl controls sister chromatid cohesion maintenance and chromosome condensation.
    Current Biology 23, 64-69 PubMed abstract
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    HIF-2α protects human hematopoietic stem/progenitors and acute myeloid leukemic cells from apoptosis induced by endoplasmic reticulum stress.
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    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
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    miR-153 supports colorectal cancer progression via pleiotropic effects that enhance invasion and chemotherapeutic resistance.
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    c-Jun reprograms Schwann cells of injured nerves to generate a repair cell essential for regeneration.
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    FOXO3a regulates reactive oxygen metabolism by inhibiting mitochondrial gene expression.
    Cell Death and Differentiation 19, 968-979 PubMed abstract
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    Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
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    Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target.
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    Gene expression analysis in human breast cancer associated blood vessels.
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    A dynamic inflammatory cytokine network in the human ovarian cancer microenvironment.
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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
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    The C-terminus of Apc does not influence intestinal adenoma development or progression.
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    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
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    The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.
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    Interleukin-6 as a therapeutic target in human ovarian cancer.
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    A kinesin-1 binding motif in vaccinia virus that is widespread throughout the human genome.
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    RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology.
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    CLEC-2 signaling via Syk in myeloid cells can regulate inflammatory responses.
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    GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein.
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    Role of Elongator subunit Elp3 in Drosophila melanogaster larval development and immunity.
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    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 Nov 2017]

Aengus Stewart (Lead) 

aengus.stewart@crick.ac.uk
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