Search Results - "Samarajiwa, Shamith"

INTERFEROME: the database of interferon regulated genes by Samarajiwa, Shamith A, Forster, Sam, Auchettl, Katie, Hertzog, Paul J

“…INTERFEROME is an open access database of types I, II and III Interferon regulated genes (http://www.interferome.org) collected from analysing expression data…”
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Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes by Narita, Masako, Young, Andrew R. J., Arakawa, Satoko, Samarajiwa, Shamith A., Nakashima, Takayuki, Yoshida, Sei, Hong, Sungki, Berry, Lorraine S., Reichelt, Stefanie, Ferreira, Manuela, Tavaré, Simon, Inoki, Ken, Shimizu, Shigeomi, Narita, Masashi

“…Protein synthesis and autophagic degradation are regulated in an opposite manner by mammalian target of rapamycin (mTOR), whereas under certain conditions it…”
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Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape by Bidwell, Bradley N, Slaney, Clare Y, Withana, Nimali P, Forster, Sam, Cao, Yuan, Loi, Sherene, Andrews, Daniel, Mikeska, Thomas, Mangan, Niamh E, Samarajiwa, Shamith A, de Weerd, Nicole A, Gould, Jodee, Argani, Pedram, Möller, Andreas, Smyth, Mark J, Anderson, Robin L, Hertzog, Paul J, Parker, Belinda S

“…The authors identify Irf7 and associated interferon signaling as an important factor suppressing bone metastasis of breast cancers. Irf7 is lost in…”
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A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma by Syafruddin, Saiful E., Rodrigues, Paulo, Vojtasova, Erika, Patel, Saroor A., Zaini, M. Nazhif, Burge, Johanna, Warren, Anne Y., Stewart, Grant D., Eisen, Tim, Bihary, Dóra, Samarajiwa, Shamith A., Vanharanta, Sakari

“…Transcriptional networks are critical for the establishment of tissue-specific cellular states in health and disease, including cancer. Yet, the…”
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Type I Interferon Receptors: Biochemistry and Biological Functions by de Weerd, Nicole A., Samarajiwa, Shamith A., Hertzog, Paul J.

“…Minireviews: no abstract…”
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Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation by Chandra, Tamir, Kirschner, Kristina, Thuret, Jean-Yves, Pope, Benjamin D., Ryba, Tyrone, Newman, Scott, Ahmed, Kashif, Samarajiwa, Shamith A., Salama, Rafik, Carroll, Thomas, Stark, Rory, Janky, Rekin's, Narita, Masako, Xue, Lixiang, Chicas, Agustin, Nũnez, Sabrina, Janknecht, Ralf, Hayashi-Takanaka, Yoko, Wilson, Michael D., Marshall, Aileen, Odom, Duncan T., Babu, M. Madan, Bazett-Jones, David P., Tavaré, Simon, Edwards, Paul A.W., Lowe, Scott W., Kimura, Hiroshi, Gilbert, David M., Narita, Masashi

“…The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of…”
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SGK1 mutations in DLBCL generate hyperstable protein neoisoforms that promote AKT independence by Gao, Jie, Sidiropoulou, Eirini, Walker, Ieuan, Krupka, Joanna A., Mizielinski, Karol, Usheva, Zelvera, Samarajiwa, Shamith A., Hodson, Daniel J.

“…Serum and glucocorticoid-regulated kinase 1 (SGK1) is one of the most frequently mutated genes in diffuse large B-cell lymphoma (DLBCL). However, little is…”
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Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence by Olan, Ioana, Parry, Aled J., Schoenfelder, Stefan, Narita, Masako, Ito, Yoko, Chan, Adelyne S. L., Slater, Guy St.C., Bihary, Dóra, Bando, Masashige, Shirahige, Katsuhiko, Kimura, Hiroshi, Samarajiwa, Shamith A., Fraser, Peter, Narita, Masashi

“…Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue…”
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NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence by Parry, Aled J., Hoare, Matthew, Bihary, Dóra, Hänsel-Hertsch, Robert, Smith, Stephen, Tomimatsu, Kosuke, Mannion, Elizabeth, Smith, Amy, D’Santos, Paula, Russell, I. Alasdair, Balasubramanian, Shankar, Kimura, Hiroshi, Samarajiwa, Shamith A., Narita, Masashi

“…Senescent cells interact with the surrounding microenvironment achieving diverse functional outcomes. We have recently identified that NOTCH1 can drive…”
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The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer by Patel, Saroor A., Hirosue, Shoko, Rodrigues, Paulo, Vojtasova, Erika, Richardson, Emma K., Ge, Jianfeng, Syafruddin, Saiful E., Speed, Alyson, Papachristou, Evangelia K., Baker, David, Clarke, David, Purvis, Stephenie, Wesolowski, Ludovic, Dyas, Anna, Castillon, Leticia, Caraffini, Veronica, Bihary, Dóra, Yong, Cissy, Harrison, David J., Stewart, Grant D., Machiela, Mitchell J., Purdue, Mark P., Chanock, Stephen J., Warren, Anne Y., Samarajiwa, Shamith A., Carroll, Jason S., Vanharanta, Sakari

“…Large-scale human genetic data 1 – 3 have shown that cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here,…”
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Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis by Gong, Chun, Krupka, Joanna A., Gao, Jie, Grigoropoulos, Nicholas F., Giotopoulos, George, Asby, Ryan, Screen, Michael, Usheva, Zelvera, Cucco, Francesco, Barrans, Sharon, Painter, Daniel, Zaini, Nurmahirah Binte Mohammed, Haupl, Björn, Bornelöv, Susanne, Ruiz De Los Mozos, Igor, Meng, Wei, Zhou, Peixun, Blain, Alex E., Forde, Sorcha, Matthews, Jamie, Khim Tan, Michelle Guet, Burke, G.A. Amos, Sze, Siu Kwan, Beer, Philip, Burton, Cathy, Campbell, Peter, Rand, Vikki, Turner, Suzanne D., Ule, Jernej, Roman, Eve, Tooze, Reuben, Oellerich, Thomas, Huntly, Brian J., Turner, Martin, Du, Ming-Qing, Samarajiwa, Shamith A., Hodson, Daniel J.

“…DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the…”
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Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns by Newsham, Izzy, Sendera, Marcin, Jammula, Sri Ganesh, Samarajiwa, Shamith A

“…Cancer, a collection of more than two hundred different diseases, remains a leading cause of morbidity and mortality worldwide. Usually detected at the…”
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re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data by Barbosa-Morais, Nuno L, Dunning, Mark J, Samarajiwa, Shamith A, Darot, Jeremy F.J, Ritchie, Matthew E, Lynch, Andy G, Tavaré, Simon

“…Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the…”
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Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53 by Kirschner, Kristina, Samarajiwa, Shamith A, Cairns, Jonathan M, Menon, Suraj, Pérez-Mancera, Pedro A, Tomimatsu, Kosuke, Bermejo-Rodriguez, Camino, Ito, Yoko, Chandra, Tamir, Narita, Masako, Lyons, Scott K, Lynch, Andy G, Kimura, Hiroshi, Ohbayashi, Tetsuya, Tavaré, Simon, Narita, Masashi

“…The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been…”
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NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis by Rodrigues, Paulo, Patel, Saroor A, Harewood, Louise, Olan, Ioana, Vojtasova, Erika, Syafruddin, Saiful E, Zaini, M Nazhif, Richardson, Emma K, Burge, Johanna, Warren, Anne Y, Stewart, Grant D, Saeb-Parsy, Kourosh, Samarajiwa, Shamith A, Vanharanta, Sakari

“…Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been…”
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Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis by Xavier, Joana M., Magno, Ramiro, Russell, Roslin, de Almeida, Bernardo P., Jacinta-Fernandes, Ana, Besouro-Duarte, André, Dunning, Mark, Samarajiwa, Shamith, O’Reilly, Martin, Maia, António M., Rocha, Cátia L., Rosli, Nordiana, Ponder, Bruce A. J., Maia, Ana-Teresa

“…Understanding breast cancer genetic risk relies on identifying causal variants and candidate target genes in risk loci identified by genome-wide association…”
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Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease by Alcalá‐Vida, Rafael, Garcia‐Forn, Marta, Castany‐Pladevall, Carla, Creus‐Muncunill, Jordi, Ito, Yoko, Blanco, Enrique, Golbano, Arantxa, Crespí‐Vázquez, Kilian, Parry, Aled, Slater, Guy, Samarajiwa, Shamith, Peiró, Sandra, Di Croce, Luciano, Narita, Masashi, Pérez‐Navarro, Esther

“…Lamins are crucial proteins for nuclear functionality. Here, we provide new evidence showing that increased lamin B1 levels contribute to the pathophysiology…”
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Exploring the role of stromal osmoregulation in cancer and disease using executable modelling by Shorthouse, David, Riedel, Angela, Kerr, Emma, Pedro, Luisa, Bihary, Dóra, Samarajiwa, Shamith, Martins, Carla P., Shields, Jacqueline, Hall, Benjamin A.

“…Osmotic regulation is a vital homoeostatic process in all cells and tissues. Cells initially respond to osmotic stresses by activating transmembrane transport…”
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Soluble IFN receptor potentiates in vivo type I IFN signaling and exacerbates TLR4-mediated septic shock by Samarajiwa, Shamith A, Mangan, Niamh E, Hardy, Matthew P, Najdovska, Meri, Dubach, Daphne, Braniff, Susie-Jane, Owczarek, Catherine M, Hertzog, Paul J

“…Circulating levels of a soluble type I IFNR are elevated in diseases, such as chronic inflammation, infections, and cancer, but whether it functions as an…”
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Locus-specific induction of gene expression from heterochromatin loci during cellular senescence by Tomimatsu, Kosuke, Bihary, Dóra, Olan, Ioana, Parry, Aled J, Schoenfelder, Stefan, Chan, Adelyne S L, Slater, Guy St C, Ito, Yoko, Rugg-Gunn, Peter J, Kirschner, Kristina, Bermejo-Rodriguez, Camino, Seko, Tomomi, Kugoh, Hiroyuki, Shiraishi, Ken, Sayama, Koji, Kimura, Hiroshi, Fraser, Peter, Narita, Masako, Samarajiwa, Shamith A, Narita, Masashi

“…Senescence is a fate-determined state, accompanied by reorganization of heterochromatin. Although lineage-appropriate genes can be temporarily repressed…”
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