Search Results - "de Santiago, Ines"

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis by Sivakumar, Shivan, de Santiago, Ines, Chlon, Leon, Markowetz, Florian

“…KRAS is the most frequently mutated gene in pancreatic ductal adenocarcinoma (PDAC), but the mechanisms underlying the transcriptional response to oncogenic…”
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Analysis of ChIP-seq Data in R/Bioconductor by de Santiago, Ines, Carroll, Thomas

“…The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation…”
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RNA polymerase II primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation by Ferrai, Carmelo, Torlai Triglia, Elena, Risner‐Janiczek, Jessica R, Rito, Tiago, Rackham, Owen JL, de Santiago, Inês, Kukalev, Alexander, Nicodemi, Mario, Akalin, Altuna, Li, Meng, Ungless, Mark A, Pombo, Ana

“…Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co‐occupancy of RNA polymerase II (RNAPII) which is thought to…”
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Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier by Martins, Filipe C, Santiago, Ines de, Trinh, Anne, Xian, Jian, Guo, Anne, Sayal, Karen, Jimenez-Linan, Mercedes, Deen, Suha, Driver, Kristy, Mack, Marie, Aslop, Jennifer, Pharoah, Paul D, Markowetz, Florian, Brenton, James D

“…TP53 and BRCA1/2 mutations are the main drivers in high-grade serous ovarian carcinoma (HGSOC). We hypothesise that combining tissue phenotypes from image…”
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Complex multi-enhancer contacts captured by genome architecture mapping by Beagrie, Robert A., Scialdone, Antonio, Schueler, Markus, Kraemer, Dorothee C. A., Chotalia, Mita, Xie, Sheila Q., Barbieri, Mariano, de Santiago, Inês, Lavitas, Liron-Mark, Branco, Miguel R., Fraser, James, Dostie, Josée, Game, Laurence, Dillon, Niall, Edwards, Paul A. W., Nicodemi, Mario, Pombo, Ana

“…The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and…”
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Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells by Barbieri, Mariano, Xie, Sheila Q, Torlai Triglia, Elena, Chiariello, Andrea M, Bianco, Simona, de Santiago, Inês, Branco, Miguel R, Rueda, David, Nicodemi, Mario, Pombo, Ana

“…Homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber, rather than CTCF occupancy, explain the 3D HoxB…”
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Regulators of genetic risk of breast cancer identified by integrative network analysis by Castro, Mauro A A, de Santiago, Ines, Campbell, Thomas M, Vaughn, Courtney, Hickey, Theresa E, Ross, Edith, Tilley, Wayne D, Markowetz, Florian, Ponder, Bruce A J, Meyer, Kerstin B

“…Kerstin Meyer and colleagues analyze a breast cancer gene regulatory network generated using publicly available expression and ChIP-seq data sets. They…”
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Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data by Carroll, Thomas S, Liang, Ziwei, Salama, Rafik, Stark, Rory, de Santiago, Ines

“…With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality…”
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Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas by Hilvo, Mika, de Santiago, Ines, Gopalacharyulu, Peddinti, Schmitt, Wolfgang D, Budczies, Jan, Kuhberg, Marc, Dietel, Manfred, Aittokallio, Tero, Markowetz, Florian, Denkert, Carsten, Sehouli, Jalid, Frezza, Christian, Darb-Esfahani, Silvia, Braicu, Elena Ioana

“…Ovarian cancer is a heterogeneous disease of low prevalence, but poor survival. Early diagnosis is critical for survival, but it is often challenging because…”
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Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer by Martins, Filipe Correia, Couturier, Dominique-Laurent, de Santiago, Ines, Sauer, Carolin Margarethe, Vias, Maria, Angelova, Mihaela, Sanders, Deborah, Piskorz, Anna, Hall, James, Hosking, Karen, Amirthanayagam, Anumithra, Cosulich, Sabina, Carnevalli, Larissa, Davies, Barry, Watkins, Thomas B. K., Funingana, Ionut G., Bolton, Helen, Haldar, Krishnayan, Latimer, John, Baldwin, Peter, Crawford, Robin, Eldridge, Matthew, Basu, Bristi, Jimenez-Linan, Mercedes, Mcpherson, Andrew W., McGranahan, Nicholas, Litchfield, Kevin, Shah, Sohrab P., McNeish, Iain, Caldas, Carlos, Evan, Gerard, Swanton, Charles, Brenton, James D.

“…Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we…”
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Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs by Brookes, Emily, de Santiago, Inês, Hebenstreit, Daniel, Morris, Kelly J., Carroll, Tom, Xie, Sheila Q., Stock, Julie K., Heidemann, Martin, Eick, Dirk, Nozaki, Naohito, Kimura, Hiroshi, Ragoussis, Jiannis, Teichmann, Sarah A., Pombo, Ana

“…Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer. Polycomb silencing in embryonic stem…”
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Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk by de Biase, Maria Stella, Massip, Florian, Wei, Tzu-Ting, Giorgi, Federico M, Stark, Rory, Stone, Amanda, Gladwell, Amy, O'Reilly, Martin, Schütte, Daniel, de Santiago, Ines, Meyer, Kerstin B, Markowetz, Florian, Ponder, Bruce A J, Rintoul, Robert C, Schwarz, Roland F

“…Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in…”
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Eukaryotic gene regulation in three dimensions and its impact on genome evolution by Madan Babu, M, Janga, Sarath Chandra, de Santiago, Ines, Pombo, Ana

“…Recent advances in molecular techniques and high-resolution imaging are beginning to provide exciting insights into the higher order chromatin organization…”
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Data-Driven Medicine in the Diagnosis and Treatment of Infertility by de Santiago, Ines, Polanski, Lukasz

“…Infertility, although not a life-threatening condition, affects around 15% of couples trying for a pregnancy. The increasing availability of large datasets…”
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Master regulators of FGFR2 signalling and breast cancer risk by Fletcher, Michael N. C., Castro, Mauro A. A., Wang, Xin, de Santiago, Ines, O’Reilly, Martin, Chin, Suet-Feung, Rueda, Oscar M., Caldas, Carlos, Ponder, Bruce A. J., Markowetz, Florian, Meyer, Kerstin B.

“…The fibroblast growth factor receptor 2 (FGFR2) locus has been consistently identified as a breast cancer risk locus in independent genome-wide association…”
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Immunophenotypes of pancreatic ductal adenocarcinoma: Meta‐analysis of transcriptional subtypes by Santiago, Ines, Yau, Christopher, Heij, Lara, Middleton, Mark R., Markowetz, Florian, Grabsch, Heike I., Dustin, Michael L., Sivakumar, Shivan

“…Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a…”
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FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness by Campbell, Thomas M, Castro, Mauro A A, de Santiago, Ines, Fletcher, Michael N C, Halim, Silvia, Prathalingam, Radhika, Ponder, Bruce A J, Meyer, Kerstin B

“…The fibroblast growth factor receptor 2 (FGFR2) locus is consistently the top hit in genome-wide association studies for oestrogen receptor-positive (ER(+))…”
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Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation by Ghoussaini, Maya, Edwards, Stacey L., Hillman, Kristine M., Kaufmann, Susanne, Beesley, Jonathan, Dennis, Joe, Bolla, Manjeet K., Dicks, Ed, Guo, Qi, Schmidt, Marjanka K., Shah, Mitul, Luben, Robert, Darabi, Hatef, Eriksson, Mikael, Bojesen, Stig E., Nordestgaard, Børge G., Lambrechts, Diether, Neven, Patrick, Wildiers, Hans, Th Rutgers, Emiel J., Couch, Fergus J., Hallberg, Emily, Vachon, Celine, Seibold, Petra, Flesch-Janys, Dieter, dos-Santos-Silva, Isabel, Gibson, Lorna, Nevanlinna, Heli, Aittomäki, Kristiina, Blomqvist, Carl, Hall, Per, Kang, Daehee, Park, Sue K., Iwata, Hiroji, Truong, Thérèse, Menegaux, Florence, Burwinkel, Barbara, Marme, Frederik, Sohn, Christof, Tseng, Chiu-chen, Van Den Berg, David, Stram, Daniel O., Perez, Jose Ignacio Arias, Shu, Xiao-Ou, Cai, Qiuyin, Reed, Malcolm W. R., Tchatchou, Sandrine, Sawyer, Elinor J., Kerin, Michael J., Henderson, Brian E., YIP, Cheng Har, Wong, Tien Y., Martens, John W. M., Hopper, John L., Tsimiklis, Helen, Kapuscinski, Miroslav K., Shen, Chen-Yang, Giles, Graham G., Hartman, Mikael, Haeberle, Lothar, Ekici, Arif B., Ashworth, Alan, García-Closas, Montserrat, Lissowska, Jolanta, Simard, Jacques, Goldberg, Mark S., Labrèche, France, Dumont, Martine, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Brauch, Hiltrud, Brüning, Thomas, Radice, Paolo, Volorio, Sara, Helbig, Sonja, Mannermaa, Arto, Kataja, Vesa, Tollenaar, Robert A. E. M., Seynaeve, Caroline, Jaworska-Bieniek, Katarzyna, Toland, Amanda E., Ambrosone, Christine B., Yannoukakos, Drakoulis, Sangrajrang, Suleeporn, McKay, James, Long, Jirong, Anton-Culver, Hoda, Neuhausen, Susan L., Baynes, Caroline, Ahmed, Shahana, Maranian, Mel, González-Neira, Anna, Herrero, Daniel, Vincent, Daniel, Carroll, Jason, Caldas, Carlos, Brown, Melissa A., Lupien, Mathieu, Kristensen, Vessela N., Easton, Douglas F.

“…GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50…”
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BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes by de Santiago, Ines, Liu, Wei, Yuan, Ke, O'Reilly, Martin, Chilamakuri, Chandra Sekhar Reddy, Ponder, Bruce A J, Meyer, Kerstin B, Markowetz, Florian

“…Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their…”
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Genomic profiling in pancreatic cancer reveals spatial genetic heterogeneity but spatial transcriptomic homogeneity by Sivakumar, Shivan, Rana, Anas, Seth, Chandan, de Santiago, Ines, Soonawalla, Zahir, Morgan, Robert, Rendek, Aniko, Silva, Michael, Reddy, Srikanth, Jones, Stephanie, Nicod, Jerome, Turnquist, Casmir, Tandon, Ruchi, O’Neill, Eric, Lord, Simon, Dustin, Michael, Taylor, Jenny, Middleton, Mark, Yau, Christopher

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