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Tailored graphical lasso for data integration in gene network reconstruction
Abstract: Background: Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene...
Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance.
Ankur Chakravarthy, Ian Reddin, Stephen Henderson, Cindy Dong, Nerissa Kirkwood, Maxmilan Jeyakumar, Daniela Rothschild Rodriguez, Natalia Gonzalez Martinez, Jacqueline McDermott, Xiaoping Su, Nagayasau Egawa, Christina S Fjeldbo, Vilde Eide Skingen, Heidi Lyng, Mari Kyllesø Halle, Camilla Krakstad, Afschin Soleiman, Susanne Sprung, Matt Lechner, Peter JI Ellis, Mark Wass, Martin Michaelis, Heidi Fiegl, Helga Salvesen, Gareth J Thomas, John Doorbar, Kerry Chester, Andrew Feber, Tim R Fenton
Oct 07, 2022
Tailored graphical lasso for data integration in gene network reconstruction.
BACKGROUND: Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene association...
TCR and CD28 activate the transcription factor NF-κB in T-cells via distinct adaptor signaling complexes.
Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance.
Ankur Chakravarthy, Ian Reddin, Stephen Henderson, Cindy Dong, Nerissa Kirkwood, Maxmilan Jeyakumar, Daniela Rothschild Rodriguez, Natalia Gonzalez Martinez, Jacqueline McDermott, Xiaoping Su, Nagayasau Egawa, Christina S Fjeldbo, Vilde Eide Skingen, Heidi Lyng, Mari Kyllesø Halle, Camilla Krakstad, Afschin Soleiman, Susanne Sprung, Matt Lechner, Peter JI Ellis, Mark Wass, Martin Michaelis, Heidi Fiegl, Helga Salvesen, Gareth J Thomas, John Doorbar, Kerry Chester, Andrew Feber, Tim R Fenton
Nov 07, 2022
Human papillomavirus (HPV)-associated cervical cancer is a leading cause of cancer deaths in women. Here we present an integrated multi-omic analysis of 643 cervical squamous cell carcinomas (CSCC, the most common histological...
A Common Variant at the 14q32 Endometrial Cancer Risk Locus Activates AKT1 through YY1 Binding.
Jodie N Painter, Susanne Kaufmann, Tracy A O'Mara, Kristine M Hillman, Haran Sivakumaran, Hatef Darabi, Timothy Ht Cheng, John Pearson, Stephen Kazakoff, Nicola Waddell, Erling A Hoivik, Ellen L Goode, Rodney J Scott, Ian Tomlinson, Alison M Dunning, Douglas F Easton, Juliet D French, Helga B Salvesen, Pamela M Pollock, Deborah J Thompson, Amanda B Spurdle, Stacey L Edwards
May 17, 2016
Chromosomes Human Pair 14 Endometrial Neoplasms Female Genetic Loci Genetic Predisposition to Disease Genome-Wide Association Study Genotype Humans Phosphatidylinositol 3-Kinases Polymorphism Single Nucleotide Protein Binding Proto-Oncogene Proteins c-akt Risk Factors Signal Transduction Uterine Neoplasms YY1 Transcription Factor
Autofluorescence-Directed Confocal Endomicroscopy in Combination With a Three-Biomarker Panel Can Inform Management Decisions in Barrett's Esophagus.
Massimiliano di Pietro, Elizabeth L Bird-Lieberman, Xinxue Liu, Tara Nuckcheddy-Grant, Helga Bertani, Maria O'Donovan, Rebecca C Fitzgerald
Nov 16, 2015
Aged Algorithms Aneuploidy Barrett Esophagus Biomarkers Biopsy Cyclin A Disease Progression Esophagoscopy esophagus False Positive Reactions Female Humans Male Microscopy Confocal Middle Aged Narrow Band Imaging Optical Imaging Precancerous Conditions Sensitivity and Specificity Tumor Suppressor Protein p53 Watchful Waiting
Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma.
Joseph J Caumanns, Katrien Berns, G Bea A Wisman, Rudolf SN Fehrmann, Tushar Tomar, Harry Klip, Gert J Meersma, E Marielle Hijmans, Annemiek MC Gennissen, Evelien W Duiker, Desiree Weening, Hiroaki Itamochi, Roelof JC Kluin, Anna KL Reyners, Michael J Birrer, Helga B Salvesen, Ignace Vergote, Els Van Nieuwenhuysen, James Brenton, E Ioana Braicu, Jolanta Kupryjanczyk, Beata Spiewankiewicz, Lorenza Mittempergher, René Bernards, Ate GJ van der Zee, Steven de Jong
Sep 10, 2018
Purpose: Advanced-stage ovarian clear cell carcinoma (OCCC) is unresponsive to conventional platinum-based chemotherapy. Frequent alterations in OCCC include deleterious mutations in the tumor suppressor ARID1A and activating...
Adenocarcinoma Clear Cell Animals Cell Line Tumor Cell Proliferation Class I Phosphatidylinositol 3-Kinases DNA-Binding Proteins Female Gene Expression Regulation Neoplastic Heterografts Humans Mechanistic Target of Rapamycin Complex 1 Mechanistic Target of Rapamycin Complex 2 Mice Morpholines Mutation Nuclear Proteins Ovarian Neoplasms Signal Transduction Transcription Factors
Walking, cycling, and public transport for commuting and non-commuting travels across 5 European urban regions
H. Charreire, C. Roda, T. Feuillet, A. Piombini, Helga Bardos, H. Rutter, S. Compernolle, Joreintje D. Mackenbach, J. Lakerveld, Jean Michel Oppert
Oct 31, 2021
The objective of this study was to explore individual and contextual-level characteristics associated with active (walking and cycling) and public transport as main travel modes for both non-commuting and commuting purposes, in...
Modal choice Travel purposes motivations Multilevel approach European metropolitan areas /dk/atira/pure/sustainabledevelopmentgoals/sustainable_cities_and_communities name=SDG 11 - Sustainable Cities and Communities /dk/atira/pure/sustainabledevelopmentgoals/climate_action name=SDG 13 - Climate Action /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being
The Immune Adaptor SLP-76 Binds to SUMO-RANGAP1 at Nuclear Pore Complex Filaments to Regulate Nuclear Import of Transcription Factors in T Cells.
Hebin Liu, Helga Schneider, Asha Recino, Christine Richardson, Martin W Goldberg, Christopher E Rudd
Aug 18, 2015
Active Transport Cell Nucleus Adaptor Proteins Signal Transducing Animals Cell Line GTPase-Activating Proteins Humans Jurkat Cells Mice Microscopy Electron Transmission NFATC Transcription Factors Nuclear Pore Phosphoproteins Protein Binding Small Ubiquitin-Related Modifier Proteins T-Lymphocytes Transcription Factor RelA
Human Mitochondrial DNA-Protein Complexes Attach to a Cholesterol-Rich Membrane Structure.
Joachim M Gerhold, Şirin Cansiz-Arda, Madis Lõhmus, Oskar Engberg, Aurelio Reyes, Helga van Rennes, Alberto Sanz, Ian J Holt, Helen M Cooper, Johannes N Spelbrink
Nov 23, 2017
The helicase Twinkle is indispensable for mtDNA replication in nucleoids. Previously, we showed that Twinkle is tightly membrane-associated even in the absence of mtDNA, which suggests that Twinkle is part of a membrane-attached...
City-level climate change mitigation in China.
Yuli Shan, Dabo Guan, Klaus Hubacek, Bo Zheng, Steven J Davis, Lichao Jia, Jianghua Liu, Zhu Liu, Neil Fromer, Zhifu Mi, Jing Meng, Xiangzheng Deng, Yuan Li, Jintai Lin, Heike Schroeder, Helga Weisz, Hans Joachim Schellnhuber
Apr 12, 2019
As national efforts to reduce CO2 emissions intensify, policy-makers need increasingly specific, subnational information about the sources of CO2 and the potential reductions and economic implications of different possible...
Walking, cycling, and public transport for commuting and non-commuting travels across 5 European urban regions
H. Charreire, C. Roda, T. Feuillet, A. Piombini, Helga Bardos, H. Rutter, S. Compernolle, Joreintje D. Mackenbach, J. Lakerveld, Jean Michel Oppert
Oct 31, 2021
The objective of this study was to explore individual and contextual-level characteristics associated with active (walking and cycling) and public transport as main travel modes for both non-commuting and commuting purposes, in...
Modal choice Travel purposes motivations Multilevel approach European metropolitan areas /dk/atira/pure/sustainabledevelopmentgoals/sustainable_cities_and_communities name=SDG 11 - Sustainable Cities and Communities /dk/atira/pure/sustainabledevelopmentgoals/climate_action name=SDG 13 - Climate Action /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being
Development and Validation of Confocal Endomicroscopy Diagnostic Criteria for Low-Grade Dysplasia in Barrett's Esophagus.
Massimiliano di Pietro, Helga Bertani, Maria OʼDonovan, Patricia Santos, Hani Alastal, Richard Phillips, Jacobo Ortiz-Fernández-Sordo, Marietta Iacucci, Ines Modolell, Luca Reggiani Bonetti, Krish Ragunath, Lorenz Wernisch
Apr 15, 2019
Corrigendum
The helicase Twinkle is indispensable for mtDNA replication in nucleoids. Previously, we showed that Twinkle is tightly membrane-associated even in the absence of mtDNA, which suggests that Twinkle is part of a...
Joachim M Gerhold, Şirin Cansiz-Arda, Madis Lõhmus, Oskar Engberg, Aurelio Reyes, Helga van Rennes, Alberto Sanz, Ian J Holt, Helen M Cooper, Johannes N Spelbrink
Nov 23, 2017
Plasma Sulfur Amino Acids and Risk of Cerebrovascular Diseases
Kathrine J Vinknes, Helga Refsum, Cheryl Turner, Kay-Tee Khaw, Nicholas J Wareham, Nita G Forouhi, Fumiaki Imamura
Nov 16, 2020
Putatively novel serotypes and the potential for reduced vaccine effectiveness
Andries J van Tonder, James E Bray, Sigríður J Quirk, Gunnsteinn Haraldsson, Keith A Jolley, Martin CJ Maiden, Steen Hoffmann, Stephen D Bentley, Ásgeir Haraldsson, Helga Erlendsdóttir, Karl G Kristinsson, Angela B Brueggemann
Feb 24, 2020
Age Related Multiple Sclerosis Severity Score
Ali Manouchehrinia, Helga Westerlind, Elaine Kingwell, Feng Zhu, Robert Carruthers, Ryan Ramanujam, Maria Ban, Anna Glaser, Stephen Sawcer, Helen Tremlett, Jan Hillert
Mar 14, 2017
Evolutionary loss of inflammasomes in the Carnivora and implications for the carriage of zoonotic infections.
Zsofi Digby, Panagiotis Tourlomousis, James Rooney, Joseph P Boyle, Betsaida Bibo-Verdugo, Robert J Pickering, Steven J Webster, Thomas P Monie, Lee J Hopkins, Nobuhiko Kayagaki, Guy S Salvesen, Soren Warming, Lucy Weinert, Clare E Bryant
Aug 06, 2021
Zoonotic pathogens, such as COVID-19, reside in animal hosts before jumping species to infect humans. The Carnivora, like mink, carry many zoonoses, yet how diversity in host immune genes across species affect pathogen carriage...
Carnivora NLRC4 NLRP3 Caspase 1 caspase 11 caspase 4 inflammasome Animals Carnivora Caspase 1 Caspase 8 Caspases Initiator Cell Death Cell Line evolution Molecular Humans Inflammasomes Interleukin-1beta Lipopolysaccharides MACROPHAGES Mice Mice Inbred C57BL NLR proteins Recombinant Fusion Proteins Recombinant Proteins Salmonella typhi Zoonoses
Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci.
Dylan M Glubb, Sharon E Johnatty, Michael CJ Quinn, Tracy A O'Mara, Jonathan P Tyrer, Bo Gao, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Ignace Vergote, Digna R Velez Edwards, Alicia Beeghly-Fadiel, Javier Benitez, Maria J Garcia, Marc T Goodman, Pamela J Thompson, Thilo Dörk, Matthias Dürst, Francesmary Modungo, Kirsten Moysich, Florian Heitz, Andreas du Bois, Jacobus Pfisterer, Peter Hillemanns, AGO Study Group, Beth Y Karlan, Jenny Lester, Ellen L Goode, Julie M Cunningham, Stacey J Winham, Melissa C Larson, Bryan M McCauley, Susanne Krüger Kjær, Allan Jensen, Joellen M Schildkraut, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Helga B Salvesen, Line Bjorge, Penny M Webb, Peter Grant, Tanja Pejovic, Melissa Moffitt, Claus K Hogdall, Estrid Hogdall, James Paul, Rosalind Glasspool, Marcus Bernardini, Alicia Tone, David Huntsman, Michelle Woo, Aocs Group, Anna DeFazio, Catherine J Kennedy, Paul DP Pharoah, Stuart MacGregor, Georgia Chenevix-Trench
Nov 22, 2018
Local conditions and policy design determine whether ecological compensation can achieve No Net Loss goals.
Laura J Sonter, Jeremy S Simmonds, James EM Watson, Julia PG Jones, Joseph M Kiesecker, Hugo M Costa, Leon Bennun, Stephen Edwards, Hedley S Grantham, Victoria F Griffiths, Kendall Jones, Kei Sochi, Philippe Puydarrieux, Fabien Quétier, Helga Rainer, Hugo Rainey, Dilys Roe, Musnanda Satar, Britaldo S Soares-Filho, Malcolm Starkey, Kerry Ten Kate, Ray Victurine, Amrei von Hase, Jessie A Wells, Martine Maron
Apr 29, 2021
Comprehensive genetic assessment of the ESR1 locus identifies a risk region for endometrial cancer.
Tracy A O'Mara, Dylan M Glubb, Jodie N Painter, Timothy Cheng, Joe Dennis, Australian National Endometrial Cancer Study Group (ANECS), John Attia, Elizabeth G Holliday, Mark McEvoy, Rodney J Scott, Katie Ashton, Tony Proietto, Geoffrey Otton, Mitul Shah, Shahana Ahmed, Catherine S Healey, Maggie Gorman, Lynn Martin, National Study of Endometrial Cancer Genetics Group (NSECG), Shirley Hodgson, Peter A Fasching, Alexander Hein, Matthias W Beckmann, Arif B Ekici, Per Hall, Kamila Czene, Hatef Darabi, Jingmei Li, Matthias Dürst, Ingo Runnebaum, Peter Hillemanns, Thilo Dörk, Diether Lambrechts, Jeroen Depreeuw, Daniela Annibali, Frederic Amant, Hui Zhao, Ellen L Goode, Sean C Dowdy, Brooke L Fridley, Stacey J Winham, Helga B Salvesen, Tormund S Njølstad, Jone Trovik, Henrica MJ Werner, Emma Tham, Tao Liu, Miriam Mints, RENDOCAS, Manjeet K Bolla, Kyriaki Michailidou, Jonathan P Tyrer, Qin Wang, John L Hopper, AOCS Group, Julian Peto, Anthony J Swerdlow, Barbara Burwinkel, Hermann Brenner, Alfons Meindl, Hiltrud Brauch, Annika Lindblom, Jenny Chang-Claude, Fergus J Couch, Graham G Giles, Vessela N Kristensen, Angela Cox, Paul DP Pharoah, Alison M Dunning, Ian Tomlinson, Douglas F Easton, Deborah J Thompson, Amanda B Spurdle
Sep 03, 2015
ESR1 endometrial cancer fine-mapping analysis SINGLE-NUCLEOTIDE POLYMORPHISMS Breast Neoplasms Case-Control Studies Computational Biology Cytoskeletal Proteins Databases Genetic Endometrial Neoplasms Estrogen Receptor alpha Female Genetic Loci Genetic Predisposition to Disease Genotype Humans Meta-Analysis as Topic Nerve Tissue Proteins Nuclear Proteins Polymorphism Single Nucleotide Prognosis Promoter Regions Genetic Risk Factors
Genetic Risk Score Mendelian Randomization Shows that Obesity Measured as Body Mass Index, but not Waist
Jodie N Painter, Tracy A O'Mara, Louise Marquart, Penelope M Webb, John Attia, Sarah E Medland, Timothy Cheng, Joe Dennis, Elizabeth G Holliday, Mark McEvoy, Rodney J Scott, Shahana Ahmed, Catherine S Healey, Mitul Shah, Maggie Gorman, Lynn Martin, Shirley V Hodgson, Matthias W Beckmann, Arif B Ekici, Peter A Fasching, Alexander Hein, Matthias Rübner, Kamila Czene, Hatef Darabi, Per Hall, Jingmei Li, Thilo Dörk, Matthias Dürst, Peter Hillemanns, Ingo B Runnebaum, Frederic Amant, Daniela Annibali, Jeroen Depreeuw, Diether Lambrechts, Patrick Neven, Julie M Cunningham, Sean C Dowdy, Ellen L Goode, Brooke L Fridley, Stacey J Winham, Tormund S Njølstad, Helga B Salvesen, Jone Trovik, Henrica MJ Werner, Katie A Ashton, Geoffrey Otton, Anthony Proietto, Miriam Mints, Emma Tham, Manjeet K Bolla, Kyriaki Michailidou, Qin Wang, Jonathan P Tyrer, John L Hopper, Julian Peto, Anthony J Swerdlow, Barbara Burwinkel, Hermann Brenner, Alfons Meindl, Hiltrud Brauch, Annika Lindblom, Jenny Chang-Claude, Fergus J Couch, Graham G Giles, Vessela N Kristensen, Angela Cox, Paul DP Pharoah, Ian Tomlinson, Alison M Dunning, Douglas F Easton, Deborah J Thompson, Amanda B Spurdle, AOCS Group, for RENDOCAS, National Study of Endometrial Cancer Genetics Group (NSECG), Australian National Endometrial Cancer Study Group (ANECS)
Oct 04, 2016
CYP19A1 fine-mapping and Mendelian randomization
Deborah J Thompson, Tracy A O'Mara, Dylan M Glubb, Jodie N Painter, Timothy Cheng, Elizabeth Folkerd, Deborah Doody, Joe Dennis, Penelope M Webb, Australian National Endometrial Cancer Study Group (ANECS), Maggie Gorman, Lynn Martin, Shirley Hodgson, National Study of Endometrial Cancer Genetics Group (NSECG), Kyriaki Michailidou, Jonathan P Tyrer, Mel J Maranian, Per Hall, Kamila Czene, Hatef Darabi, Jingmei Li, Peter A Fasching, Alexander Hein, Matthias W Beckmann, Arif B Ekici, Thilo Dörk, Peter Hillemanns, Matthias Dürst, Ingo Runnebaum, Hui Zhao, Jeroen Depreeuw, Stefanie Schrauwen, Frederic Amant, Ellen L Goode, Brooke L Fridley, Sean C Dowdy, Stacey J Winham, Helga B Salvesen, Jone Trovik, Tormund S Njolstad, Henrica MJ Werner, Katie Ashton, Tony Proietto, Geoffrey Otton, Luis Carvajal-Carmona, Emma Tham, Tao Liu, Miriam Mints, for RENDOCAS, Rodney J Scott, Mark McEvoy, John Attia, Elizabeth G Holliday, Grant W Montgomery, Nicholas G Martin, Dale R Nyholt, Anjali K Henders, John L Hopper, Nadia Traficante, AOCS Group, Matthias Ruebner, Anthony J Swerdlow, Barbara Burwinkel, Hermann Brenner, Alfons Meindl, Hiltrud Brauch, Annika Lindblom, Diether Lambrechts, Jenny Chang-Claude, Fergus J Couch, Graham G Giles, Vessela N Kristensen, Angela Cox, Manjeet K Bolla, Qin Wang, Stig E Bojesen, Mitul Shah, Robert Luben, Kay-Tee Khaw, Paul DP Pharoah, Alison M Dunning, Ian Tomlinson, Mitch Dowsett, Douglas F Easton, Amanda B Spurdle
Dec 01, 2015
Five endometrial cancer risk loci identified through genome-wide association analysis.
Timothy Ht Cheng, Deborah J Thompson, Tracy A O'Mara, Jodie N Painter, Dylan M Glubb, Susanne Flach, Annabelle Lewis, Juliet D French, Luke Freeman-Mills, David Church, Maggie Gorman, Lynn Martin, National Study of Endometrial Cancer Genetics Group (NSECG), Shirley Hodgson, Penelope M Webb, Australian National Endometrial Cancer Study Group (ANECS), John Attia, Elizabeth G Holliday, Mark McEvoy, Rodney J Scott, Anjali K Henders, Nicholas G Martin, Grant W Montgomery, Dale R Nyholt, Shahana Ahmed, Catherine S Healey, Mitul Shah, Joe Dennis, Peter A Fasching, Matthias W Beckmann, Alexander Hein, Arif B Ekici, Per Hall, Kamila Czene, Hatef Darabi, Jingmei Li, Thilo Dörk, Matthias Dürst, Peter Hillemanns, Ingo Runnebaum, Frederic Amant, Stefanie Schrauwen, Hui Zhao, Diether Lambrechts, Jeroen Depreeuw, Sean C Dowdy, Ellen L Goode, Brooke L Fridley, Stacey J Winham, Tormund S Njølstad, Helga B Salvesen, Jone Trovik, Henrica MJ Werner, Katie Ashton, Geoffrey Otton, Tony Proietto, Tao Liu, Miriam Mints, Emma Tham, RENDOCAS, Chibcha Consortium, Mulin Jun Li, Shun H Yip, Junwen Wang, Manjeet K Bolla, Kyriaki Michailidou, Qin Wang, Jonathan P Tyrer, Malcolm Dunlop, Richard Houlston, Claire Palles, John L Hopper, AOCS Group, Julian Peto, Anthony J Swerdlow, Barbara Burwinkel, Hermann Brenner, Alfons Meindl, Hiltrud Brauch, Annika Lindblom, Jenny Chang-Claude, Fergus J Couch, Graham G Giles, Vessela N Kristensen, Angela Cox, Julie M Cunningham, Paul DP Pharoah, Alison M Dunning, Stacey L Edwards, Douglas F Easton, Ian Tomlinson, Amanda B Spurdle
May 18, 2016
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