bioconductor: beadarray | Projects

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: over 5 years ago

10.7554/eLife.58705

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: over 4 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: about 13 years ago

10.1186/s13059-016-0999-8

Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia
Cited by: 64
Author(s): Syed Haider, Alan McIntyre, Ruud G.P.M. van Stiphout, Laura Winchester, Simon Wigfield, Adrian L. Harris, Francesca M. Buffa
Software Mentions: 10
Published: over 8 years ago

10.3389/fgene.2020.586602

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types
Cited by: 13
Author(s): Bruno César Feltes, Joice de Faria Poloni, Itamar José Guimarães Nunes, Sara Socorro Faria, Márcio Dorn
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: almost 12 years ago

10.12688/f1000research.2-264.v1

illuminaio: An open source IDAT parsing tool for Illumina microarrays
Cited by: 59
Author(s): Mike L. Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Software Mentions: 9
Published: about 11 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: over 4 years ago

10.18632/oncotarget.6793

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A
Cited by: 12
Author(s): Nadine Rohwer, Fabian Bindel, Christina Grimm, Suling J. Lin, Jessica Wappler, Bertram Klinger, Nils Blüthgen, Ilona Du Bois, Bernd Schmeck, Hans Lehrach, Marjo de Graauw, Emanuel Gonçalvès, Julio Sáez-Rodríguez, Patrick Tan, Heike Grabsch, Alessandro Prigione, Stefan Kempa, Thorsten Cramer
Software Mentions: 8
Published: almost 9 years ago

10.1371/journal.pgen.1008482

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival
Cited by: 12
Author(s): Rodrigo Guarischi-Sousa, Jhonatas Sirino Monteiro, Lilian Costa Alecrim, Jussara S. Michaloski, Laura Beatriz da Silva Cardeal, Elisa Napolitano Ferreira, Dirce Maria Carraro, Diana Noronha Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C. Boutros, João Carlos Setúbal, Ricardo J. Giordano
Software Mentions: 7
Published: about 5 years ago

10.1534/g3.115.023739

argyle: An R Package for Analysis of Illumina Genotyping Arrays
Cited by: 34
Author(s): Andrew P. Morgan
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pone.0216793

Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes
Cited by: 4
Author(s): A. Borys, Michał Seweryn, Tomasz Gołąbek, Łukasz Bełch, Agnieszka Klimkowska, Justyna Totoń‐Żurańska, Julita Machlowska, Piotr Chłosta, Krzysztof Okoń, Paweł Wołkow
Software Mentions: 7
Published: over 5 years ago

10.1038/mt.2014.86

Characterizing Human Stem Cell–derived Sensory Neurons at the Single-cell Level Reveals Their Ion Channel Expression and Utility in Pain Research
Cited by: 105
Author(s): Gareth T. Young, Alex Gutteridge, Heather De Fox, Anna Wilbrey, Lishuang Cao, Lily T Cho, Adam R. Brown, Caroline Benn, Laura R Kammonen, Julia Friedman, Magda Bictash, Paul Whiting, James Bilsland, Edward B. Stevens
Software Mentions: 6
Published: over 10 years ago

10.1186/s13059-015-0605-5

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
Cited by: 61
Author(s): Santiago Uribe-Lewis, Rory Stark, Thomas Carroll, Mark J. Dunning, Martin Bachman, Yoko Itō, Lovorka Stojic, Silvia Halim, Sarah L. Vowler, Andy G. Lynch, Benjamin Delatte, Eric James de Bony, Laurence Colin, Matthieu Defrance, Felix Krueger, Ana Luísa Silva, Rogier ten Hoopen, Ashraf E.K. Ibrahim, François Fuks, Adele Murrell
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0156594

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data
Cited by: 94
Author(s): Christian Müller, Arne Schillert, Caroline Röthemeier, David‐Alexandre Trégouët, Carole Proust, Harald Binder, Norbert Pfeiffer, Manfred E. Beutel, Karl J. Lackner, Renate B. Schnabel, Laurence Tiret, Philipp S. Wild, Stefan Blankenberg, Tanja Zeller, Andreas Ziegler
Software Mentions: 5
Published: over 8 years ago

10.1186/1471-2164-14-930

RETRACTED ARTICLE: Gene expression analysis indicates CB1 receptor upregulation in the hippocampus and neurotoxic effects in the frontal cortex 3 weeks after single-dose MDMA administration in Dark Agouti rats
Cited by: 9
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: about 11 years ago

10.1186/s12967-020-02503-9

Genomic landscape of the immune microenvironments of brain metastases in breast cancer
Cited by: 11
Author(s): Wei-Cheng Lu, Hui Xie, Ce Yuan, Jinjiang Li, Zhaoyang Li, Andrew Wu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-018-4929-x

Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti rats
Cited by: 12
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0051013

A Measure of the Signal-to-Noise Ratio of Microarray Samples and Studies Using Gene Correlations
Cited by: 15
Author(s): David Venet, Vincent Detours, Hugues Bersini
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0035035

MAPK Signaling Determines Anxiety in the Juvenile Mouse Brain but Depression-Like Behavior in Adults
Cited by: 37
Author(s): Benedikt Wefers, Christiane Hitz, Sabine M. Hölter, Dietrich Trümbach, Jens Hansen, Peter Weber, Benno Pütz, Jan M. Deussing, Martin Hrabě de Angelis, Till Roenneberg, Fang Zheng, Christian Alzheimer, Alcino Silva, Wolfgang Wurst, Ralf Kühn
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0054961

Host Responses to Melioidosis and Tuberculosis Are Both Dominated by Interferon-Mediated Signaling
Cited by: 57
Author(s): Gavin Koh, M. Fernanda Schreiber, Rubén Bautista, Rapeephan R. Maude, Susanna Dunachie, Direk Limmathurotsakul, Nicholas P. J. Day, Gordon Dougan, Sharon J. Peacock
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0113662

Transcriptional Evidence for the Role of Chronic Venlafaxine Treatment in Neurotrophic Signaling and Neuroplasticity Including also Glutatmatergic- and Insulin-Mediated Neuronal Processes
Cited by: 52
Author(s): Viola Tamási, Péter Petschner, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, Gabriella Juhász, György Bagdy
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0214061

Expression of socially sensitive genes: The multi-ethnic study of atherosclerosis
Cited by: 7
Author(s): Kristen Brown, Ana V. Diez‐Roux, Jennifer A. Smith, Belinda L. Needham, Bhramar Mukherjee, Erin B. Ware, Yongmei Liu, Steven W. Cole, Teresa E. Seeman, Sharon L.R. Kardia
Software Mentions: 4
Published: over 5 years ago

10.1007/s00592-018-1223-y

Negative pressure wound therapy in the treatment of diabetic foot ulcers may be mediated through differential gene expression
Cited by: 12
Author(s): Sebastian Borys, Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Jerzy Hohendorff, Teresa Koblik, Julita Machlowska, Beata Kieć‐Wilk, Paweł Wołkow, Maciej Małecki
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-018-0403-5

Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers
Cited by: 12
Author(s): S Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm, Hans Neubauer
Software Mentions: 4
Published: over 6 years ago

10.5966/sctm.2016-0088

Directing Differentiation of Pluripotent Stem Cells Toward Retinal Pigment Epithelium Lineage
Cited by: 40
Author(s): Parul Choudhary, Heather Booth, Alex Gutteridge, Beata Surmacz, Irene Louca, Juliette Steer, Julie Kerby, Paul J. Whiting
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2121-14-43

In vitro three-dimensional modeling of fallopian tube secretory epithelial cells
Cited by: 39
Author(s): Kate Lawrenson, Maria Notaridou, Nathan Lee, E. Benjamin, Ian Jacobs, Christopher S. Jones, Simon A. Gayther
Software Mentions: 4
Published: about 11 years ago

10.18632/oncotarget.23065

Transcriptome evolution from breast epithelial cells to basal-like tumors
Cited by: 11
Author(s): Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-38310-y

Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium
Cited by: 5
Author(s): Monika Horázná, Lucie Janečková, Jiří Švec, Oľga Babošová, Dušan Hrčkulák, Martina Vojtěchová, Kateřina Galušková, Eva Šloncová, Michal Kolář, Hynek Strnad, Vladimír Kořínek
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep33956

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
Cited by: 19
Author(s): Alan Mueller, Simon R. Tew, Olga Vasieva, Peter Clegg, Elizabeth G. Canty‐Laird
Software Mentions: 4
Published: about 8 years ago

10.1016/j.ebiom.2015.07.017

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study
Cited by: 217
Author(s): Helen Ross-Adams, Alastair Lamb, Mark J. Dunning, Silvia Halim, Johan Lindberg, Charles E. Massie, Lars Egevad, Roslin Russell, Antonio Ramos-Montoya, Sarah L. Vowler, Naomi L. Sharma, Jonathan Kay, Hayley C. Whitaker, Jeremy Clark, Rachel Hurst, Vincent Gnanapragasam, Nimish Shah, Anne Y. Warren, Christopher S. Cooper, Andy G. Lynch, Rory Stark, Ian G. Mills, Henrik Grönberg, David E. Neal
Software Mentions: 4
Published: over 9 years ago

10.3390/diagnostics9020039

Mining Featured Biomarkers Linked with Epithelial Ovarian Cancer Based on Bioinformatics
Cited by: 2
Author(s): Varun Alur, Varshita Raju, Basavaraj Vastrad, Chanabasayya Vastrad
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-10-588

The pitfalls of platform comparison: DNA copy number array technologies assessed
Cited by: 94
Author(s): Christina Curtis, Andy G. Lynch, Mark J. Dunning, Inmaculada Spiteri, John C. Marioni, James Hadfield, Suet-Feung Chin, James D. Brenton, Simon Tavaré, Carlos Caldas
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2105-11-208

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data
Cited by: 8
Author(s): Mike L. Smith, Mark J. Dunning, Simon Tavaré, Andy G. Lynch
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-017-1511-5

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
Cited by: 261
Author(s): Andrew E. Teschendorff, Charles E. Breeze, Shiqing Zheng, Stephan Beck
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-11-280

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Cited by: 4
Author(s): Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panos Deloukas, Simon Tavaré
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2164-12-593

A co-ordinated interaction between CTCF and ER in breast cancer cells
Cited by: 56
Author(s): Caryn S. Ross-Innes, Gordon D. Brown, Jason S. Carroll
Software Mentions: 3
Published: about 13 years ago

10.1186/1756-0500-5-1

Peripheral blood gene expression: it all boils down to the RNA collection tubes
Cited by: 128
Author(s): Andreas Menke, Monika Rex‐Haffner, Torsten Klengel, Elisabeth B. Binder, Divya Mehta
Software Mentions: 3
Published: almost 13 years ago

10.1186/1752-0509-5-56

Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease
Cited by: 72
Author(s): Priyanka Pandey, Shan Qin, Jacqueline Ho, Jing Zhou, Jordan A. Kreidberg
Software Mentions: 3
Published: over 13 years ago

10.3390/microarrays2020131

Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes
Cited by: 10
Author(s): Daniel M. Johnstone, Carlos Riveros, Mohsen Heidari, Ross M. Graham, Debbie Trinder, Regina Berretta, John K. Olynyk, Rodney J. Scott, Pablo Moscato, Elizabeth A. Milward
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0082989

Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by Folic Acid
Cited by: 55
Author(s): Gioia Altobelli, Irina Bogdarina, Elia Stupka, Adrian Clark, Simon C. Langley‐Evans
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0051562

Prophylactic Valproic Acid Treatment Prevents Schizophrenia-Related Behaviour in Disc1-L100P Mutant Mice
Cited by: 23
Author(s): Tatiana V. Lipina, F. Nipa Haque, Alexander McGirr, Paul C. Boutros, Thorsten Berger, Tak W. Mak, John Roder, Albert H.C. Wong
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0097380

Genome-Wide Identification of Expression Quantitative Trait Loci (eQTLs) in Human Heart
Cited by: 45
Author(s): Tamara T. Koopmann, Michiel E. Adriaens, Perry D. Moerland, Roos F. Marsman, M.L. Westerveld, Sean Lal, Taifang Zhang, Christine Q. Simmons, István Baczkó, Cristobal dos Remedios, Nanette H. Bishopric, András Varró, Alfred L. George, Elisabeth M. Lodder, Connie R. Bezzina
Software Mentions: 3
Published: over 10 years ago

10.1016/j.cell.2012.04.011

Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development
Cited by: 389
Author(s): Martin A.M. Reijns, Björn Rabe, Rachel E. Rigby, Pleasantine Mill, Katy R. Astell, Laura A. Lettice, Shelagh Boyle, Andrea Leitch, Margaret Keighren, Fiona Kilanowski, Paul S. Devenney, David Sexton, Graeme R. Grimes, Ian Holt, Robert E. Hill, Martin S. Taylor, Kirstie A. Lawson, Julia R. Dorin, Andrew P. Jackson
Software Mentions: 3
Published: over 12 years ago

10.1186/1749-8546-7-19

Effects of alpha-mangostin on the expression of anti-inflammatory genes in U937 cells
Cited by: 39
Author(s): Szu-Hsiu Liu, Lain-Tze Lee, Nai-Yun Hu, Kuo-Kuei Huange, Ying-Chu Shih, Munekazu Iinuma, Jen-Ming Li, Ting-Yu Chou, Wei‐Hsin Wang, Ting-Shou Chen
Software Mentions: 3
Published: over 12 years ago

10.1016/j.dib.2015.05.007

Prenatal alcohol exposure alters gene expression in the rat brain: Experimental design and bioinformatic analysis of microarray data
Cited by: 2
Author(s): Alexandre A. Lussier, Katarzyna Stępień, Joanne Weinberg, Michæl S. Kobor
Software Mentions: 3
Published: over 9 years ago

10.3389/fendo.2021.628907

Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies
Cited by: 7
Author(s): Harish Joshi, Basavaraj Vastrad, Nidhi Joshi, Chanabasayya Vastrad, Anandkumar Tengli, Iranna Kotturshetti
Software Mentions: 3
Published: over 3 years ago

10.1126/sciadv.1501678

Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation
Cited by: 111
Author(s): Till F. M. Andlauer, Dorothea Buck, Gisela Antony, Antonios Bayas, Lukas Bechmann, Achim Berthele, Andrew T. Chan, Christiane Gasperi, Ralf Gold, Christiane Graetz, Jürgen Haas, Michael Hecker, Carmen Infante-Duarte, M. Knop, Tania Kümpfel, Volker Limmroth, Ralf A. Linker, Verena Loleit, Felix Luessi, Sven G. Meuth, Mark Mühlau, Sandra Nischwitz, Friedemann Paul, Michael Pütz, Tobias Ruck, Anke Salmen, Martin Stangel, Jan‐Patrick Stellmann, Klarissa Hanja Stürner, Björn Tackenberg, Florian Then Bergh, Hayrettin Tumani, Clemens Warnke, Frank Weber, Heinz Wiendl, Brigitte Wildemann, Uwe K. Zettl, Ulf Ziemann, Frauke Zipp, Janine Arloth, Peter Weber, Milena Radivojkov‐Blagojevic, Markus O. Scheinhardt, Theresa Dankowski, Peter Lichtner, Darina Czamara, Tania Carrillo-Roa, Elisabeth B. Binder, Klaus Berger, Lars Bertram, André Franke, Christian Gieger, Stefan Herms, Georg Homuth, Marcus Ising, Karl‐Heinz Jöckel, Tim Kacprowski, Stefan Kloiber, Matthias Laudes, Wolfgang Lieb, Christina M. Lill, Thomas Meitinger, Susanne Moebus, Martina Müller‐Nurasyid, Markus M. Nöthen, Astrid Petersmann, Rajesh Rawal, Ulf Schminke, Konstantin Strauch, Henry Völzke, Mélanie Waldenberger, Jürgen Wellmann, Eleonora Porcu, Antonella Mulas, Maristella Pitzalis, Carlo Sidore, Ilenia Zara, Francesco Cucca, Magdalena Żołędziewska, Andreas Ziegler, Bernhard Hemmer, Bertram Müller‐Myhsok
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.27746

Distinct SoxB1 networks are required for naïve and primed pluripotency
Cited by: 16
Author(s): Andrea Corsinotti, Frederick C K Wong, Tülin Tatar, Iwona Szczerbinska, Florian Halbritter, Douglas Colby, Sabine Gogolok, Raphaël Pantier, Kirsten Liggat, Elham Sadat Mirfazeli, Elisa Hall-Ponselé, Nicholas P. Mullin, Valerie Wilson, Ian Chambers
Software Mentions: 3
Published: about 7 years ago

10.1038/s42003-019-0716-8

NHC-gold compounds mediate immune suppression through induction of AHR-TGFβ1 signalling in vitro and in scurfy mice
Cited by: 14
Author(s): Xinlai Cheng, Stefanie Haeberle, Iart Luca Shytaj, Rodrigo A. Gama-Brambila, Jannick Theobald, Shahrouz Ghafoory, Jessica Wölker, Uttara Basu, Claudia Schmidt, Annika Timm, Katerina Taškova, Andrea S. Bauer, Jörg D. Hoheisel, Nikolaos Tsopoulidis, Oliver T. Fackler, Andrea Savarino, Miguel A. Andrade‐Navarro, Ingo Ott, Marina Lušić, Eva Hadaschik, Stefan Wölfl
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.devcel.2019.05.032

Id1 Stabilizes Epiblast Identity by Sensing Delays in Nodal Activation and Adjusting the Timing of Differentiation
Cited by: 11
Author(s): Mattias Malaguti, Rosa Portero Migueles, Guillaume Blin, Chia–Yi Lin, Sally Lowell
Software Mentions: 2
Published: over 5 years ago

10.1007/s11306-015-0838-z

Metabolomic changes during cellular transformation monitored by metabolite–metabolite correlation analysis and correlated with gene expression
Cited by: 15
Author(s): Basetti Madhu, Masako Narita, Alexandra Jauhiainen, Suraj Menon, Marion Stubbs, Simon Tavaré, Masashi Narita, John R. Griffiths
Software Mentions: 2
Published: over 9 years ago

10.1186/s12944-017-0641-0

Isoprenoids responsible for protein prenylation modulate the biological effects of statins on pancreatic cancer cells
Cited by: 26
Author(s): Helena Gbelcová, Silvie Rimpelová, Zdeněk Knejzlı́k, Jana Šáchová, Michal Kolář, Hynek Strnad, Vanda Repiská, Walter Cosimo D’Acunto, Tomáš Ruml, Libor Vı́tek
Software Mentions: 2
Published: about 7 years ago

10.1530/ERC-14-0454

HES5 silencing is an early and recurrent change in prostate tumourigenesis
Cited by: 10
Author(s): Charles E. Massie, Inmaculada Spiteri, Helen Ross-Adams, Hayley J. Luxton, Jonathan Kay, Hayley C. Whitaker, Mark J. Dunning, Alastair Lamb, Antonio Ramos-Montoya, Daniel Brewer, Christopher S. Cooper, Rosalind Eeles, _ _, Anne Y. Warren, Simon Tavaré, David E. Neal, Andy G. Lynch
Software Mentions: 2
Published: almost 10 years ago

10.1289/ehp.1509834

Genome-Wide Analysis of DNA Methylation and Cigarette Smoking in a Chinese Population
Cited by: 73
Author(s): Xiaoyan Zhu, Jun Li, Siyun Deng, Kuai Yu, Xuezhen Liu, Qifei Deng, Huizhen Sun, Xiaomin Zhang, Meian He, Huan Guo, Weihong Chen, Jing Yuan, Bing Zhang, Dan Kuang, Xiaosheng He, Yansen Bai, Xu Han, Bing Liu, Xiaoliang Li, Liangle Yang, Haijing Jiang, Yizhi Zhang, Jie Hu, Long Cheng, Xiaoting Luo, Wenhua Mei, Zhiming Zhou, Shan Sun, Liyun Zhang, Chuanyao Liu, Yanjun Guo, Zhihong Zhang, Frank B. Hu, Liming Liang, Tangchun Wu
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2156-11-25

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta
Cited by: 63
Author(s): Caroline Daelemans, Matthew E. Ritchie, Guillaume Smits, Sayeda Abu-Amero, Ian Sudbery, Matthew S. Forrest, Susana Campino, Taane G. Clark, Philip Stanier, Dominic P. Kwiatkowski, Panos Deloukas, Emmanouil T. Dermitzakis, Simon Tavaré, Gudrun E. Moore, Ian Dunham
Software Mentions: 2
Published: over 14 years ago

10.1093/carcin/bgw065

FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness
Cited by: 45
Author(s): Thomas M. Campbell, Mauro A. A. Castro, Inês de Santiago, Michael Fletcher, Silvia Halim, Radhika Prathalingam, Bruce A.J. Ponder, Kerstin B. Meyer
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2018.02893

Human Hookworm Infection Enhances Mycobacterial Growth Inhibition and Associates With Reduced Risk of Tuberculosis Infection
Cited by: 20
Author(s): Matthew K. O’Shea, Tom Fletcher, Julius Müller, Rachel Tanner, Magali Matsumiya, J. W. Bailey, Jayne Jones, Steven G. Smith, Gavin Koh, William Horsnell, Nicholas J. Beeching, James Dunbar, David E. Wilson, Adam F. Cunningham, Helen McShane
Software Mentions: 2
Published: about 6 years ago

10.3389/fphar.2018.01373

Downregulation of the Vitamin D Receptor Regulated Gene Set in the Hippocampus After MDMA Treatment
Cited by: 1
Author(s): Péter Petschner, Noemi Balogh, Csaba Ádori, Viola Tamási, S. Kumar, Gabriella Juhász, György Bagdy
Software Mentions: 2
Published: about 6 years ago

10.1002/cam4.4212

Treatment resistance analysis reveals GLUT‐1‐mediated glucose uptake as a major target of synthetic rocaglates in cancer cells
Cited by: 2
Author(s): Julia Sieber-Frank, Hans‐Jürgen Stark, Simon Kalteis, Elena-Sophie Prigge, Richard Köhler, Carolin Andresen, Thomas Henkel, Georg Casari, Tobias Schubert, Wolfgang Fischl, Min Li‐Weber, Peter H. Krammer, Magnus von Knebel Doeberitz, Jürgen Kopitz, Matthias Kloor, Aysel Ahadova
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-021-02262-w

Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes
Cited by: 19
Author(s): Leandro Balzano‐Nogueira, Ricardo N. Ramirez, Tatyana Zamkovaya, Jordan Dailey, Alexandria N. Ardissone, Srikar Chamala, Joan Serrano‐Quílez, Teresa Rubio, Michael J. Haller, Patrick Concannon, Mark A. Atkinson, Desmond Schatz, Eric W. Triplett, Ana Conesa
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-10-372

Illumina WG-6 BeadChip strips should be normalized separately
Cited by: 21
Author(s): Wei Shi, Aditi Banerjee, Matthew E. Ritchie, Steve Gerondakis, Gordon K. Smyth
Software Mentions: 2
Published: about 15 years ago

10.1038/s41598-020-80509-5

Nuclear IL-33 restrains the early conversion of fibroblasts to an extracellular matrix-secreting phenotype
Cited by: 16
Author(s): Francesca Gatti, Sobuj Mia, Clara Hammarström, Nadine Frerker, Bjarte Fosby, Junbai Wang, Wojciech Pietka, Olav Sundnes, Johanna Hol, Monika Kasprzycka, Guttorm Haraldsen
Software Mentions: 2
Published: almost 4 years ago

10.1186/1756-0500-1-18

Spike-in validation of an Illumina-specific variance-stabilizing transformation
Cited by: 14
Author(s): Mark J. Dunning, Matthew E. Ritchie, Nuno L. Barbosa‐Morais, Simon Tavaré, Andy G. Lynch
Software Mentions: 2
Published: over 16 years ago

10.1038/s41388-018-0368-z

Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer
Cited by: 23
Author(s): Rachel Brough, Aditi Gulati, Syed Haider, Rahul Kumar, James Campbell, Erik S. Knudsen, Stephen J. Pettitt, Colm J. Ryan, Christopher J. Lord
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0025946

Platelets in Patients with Premature Coronary Artery Disease Exhibit Upregulation of miRNA340* and miRNA624*
Cited by: 88
Author(s): Brigitte M. Sondermeijer, Annemieke Bakker, Amalia Halliani, Maurice W J de Ronde, Arnoud A. Marquart, Anke J. Tijsen, Ties A. Mulders, Maayke G.M. Kok, Suzanne Battjes, Stephanie Maiwald, Suthesh Sivapalaratnam, Mieke D. Trip, Perry D. Moerland, Joost C. M. Meijers, Esther E. Creemers, Sara‐Joan Pinto‐Sietsma
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0087850

Pharmacological Levels of Withaferin A (Withania somnifera) Trigger Clinically Relevant Anticancer Effects Specific to Triple Negative Breast Cancer Cells
Cited by: 66
Author(s): Katarzyna Szarc vel Szic, Ken Op de Beeck, Dariusz Ratman, An Wouters, Ilse Beck, Ken Declerck, Karen Heyninck, Erik Fransén, Marc Bracke, Karolien De Bosscher, Filip Lardon, Guy Van Camp, Wim Vanden Berghe
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0023604

Profiling Trait Anxiety: Transcriptome Analysis Reveals Cathepsin B (Ctsb) as a Novel Candidate Gene for Emotionality in Mice
Cited by: 46
Author(s): Ludwig Czibere, Laura A. Baur, Anke Wittmann, Katja Gemmeke, Andrea Steiner, Peter Weber, Benno Pütz, Nafees Ahmad, Mirjam Bunck, Cornelia Graf, Regina Widner, Claudia Kühne, Markus Panhuysen, Boris Hambsch, Gabriele Rieder, Thomas Reinheckel, Christoph Peters, Florian Holsboer, Rainer Landgraf, Jan M. Deussing
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1004453

Brg1 Loss Attenuates Aberrant Wnt-Signalling and Prevents Wnt-Dependent Tumourigenesis in the Murine Small Intestine
Cited by: 33
Author(s): Aliaksei Z. Holik, Madeleine A. Young, Joanna Krzystyniak, Geraint T. Williams, Daniel Metzger, Boris Shorning, Alan R. Clarke
Software Mentions: 2
Published: over 10 years ago

10.1186/1479-5876-10-115

Coculture with hematopoietic stem cells protects cardiomyocytes against apoptosis via paracrine activation of AKT
Cited by: 12
Author(s): Mark E. Rosenberg, Matthias Lutz, Constantin Kühl, Rainer Will, Volker Eckstein, Jutta Krebs, Hugo A. Katus, Norbert Frey
Software Mentions: 2
Published: over 12 years ago

10.14814/phy2.14416

An improvement in skeletal muscle mitochondrial capacity with short‐term aerobic training is associated with changes in Tribbles 1 expression
Cited by: 5
Author(s): Rick B. Vega, Bram Brouwers, Stephanie A. Parsons, Natalie Stephens, Maria F. Pino, Andrew Hodges, Fanchao Yi, Gongxin Yu, Richard E. Pratley, Steven R. Smith, Lauren M. Sparks
Software Mentions: 2
Published: over 4 years ago

10.1038/cddis.2014.542

The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape
Cited by: 124
Author(s): A. Modelska, Ernest Turro, Robert B. Russell, J Beaton, Thomas Sbarrato, Keith A. Spriggs, Jodi Miller, Stefan Gräf, Elena Provenzano, Fiona M. Blows, Paul D.P. Pharoah, Carlos Caldas, John Le Quesne
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.13130

TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection
Cited by: 47
Author(s): Hiroe Namba-Fukuyo, Sayaka Funata, Keisuke Matsusaka, Masaki Fukuyo, Bahityar Rahmutulla, Yasunobu Mano, Masashi Fukayama, Hiroyuki Aburatani, Atsushi Kaneda
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0094772

Melanoma Transition Is Frequently Accompanied by a Loss of Cytoglobin Expression in Melanocytes: A Novel Expression Site of Cytoglobin
Cited by: 19
Author(s): Yoshihiko Fujita, Satoshi Koinuma, Marco A. De Velasco, Jan Bolz, Yosuke Togashi, Masato Terashima, Hidetoshi Hayashi, Takuya Matsuo, Kazuto Nishio
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003240

Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes
Cited by: 56
Author(s): Sophie Garnier, Vinh Truong, Jessy Brocheton, Tanja Zeller, Maxime Rovital, Philipp S. Wild, Andreas Ziegler, Thomas Münzel, Laurence Tiret, Stefan Blankenberg, Panos Deloukas, Jeanette Erdmann, Christian Hengstenberg, Nilesh J. Samani, Heribert Schunkert, Willem H. Ouwehand, Alison H. Goodall, François Cambien, David‐Alexandre Trégouët
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.biopen.2017.02.003

Arborvitae ( Thuja plicata ) essential oil significantly inhibited critical inflammation- and tissue remodeling-related proteins and genes in human dermal fibroblasts
Cited by: 11
Author(s): Xuesheng Han, Tory L. Parker
Software Mentions: 1
Published: over 7 years ago

10.1016/j.biopen.2017.02.005

Anti-inflammatory, tissue remodeling, immunomodulatory, and anticancer activities of oregano ( Origanum vulgare ) essential oil in a human skin disease model
Cited by: 57
Author(s): Xuesheng Han, Tory L. Parker
Software Mentions: 1
Published: over 7 years ago

10.1016/j.biopen.2017.01.003

Biological activities of frankincense essential oil in human dermal fibroblasts
Cited by: 25
Author(s): Xuesheng Han, Damian Rodriguez, Tory L. Parker
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0022785

The UBC9 E2 SUMO Conjugating Enzyme Binds the PR-Set7 Histone Methyltransferase to Facilitate Target Gene Repression
Cited by: 13
Author(s): Tanya M. Spektor, Lauren M. Congdon, Chendhore S. Veerappan, Judd C. Rice
Software Mentions: 1
Published: over 13 years ago

10.1016/j.celrep.2014.07.034

IRF5:RelA Interaction Targets Inflammatory Genes in Macrophages
Cited by: 81
Author(s): David Saliba, Andreas Heger, Hayley L. Eames, Spyros Oikonomopoulos, Ana Teixeira, Katrina Blazek, Ariadne Androulidaki, Daniel Wong, Fui G. Goh, Miriam Weiss, Adam Byrne, Manolis Pasparakis, Jiannis Ragoussis, Irina A. Udalova
Software Mentions: 1
Published: over 10 years ago

10.1016/j.celrep.2018.06.066

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation
Cited by: 94
Author(s): James Monypenny, Hanna Milewicz, Fabián Flores-Borja, Gregory Weitsman, Anthony Cheung, R Chowdhury, Thomas Burgoyne, Appitha Arulappu, Katherine Lawler, Paul R. Barber, José M. Vicencio, Melanie D. Keppler, Wahyu Wulaningsih, Sean M. Davidson, Franca Fraternali, Natalie Woodman, Mark Turmaine, Cheryl Gillett, Dafne Franz, Sergio A. Quezada, Clare E. Futter, Alex von Kriegsheim, Walter Kölch, Borivoj Vojnovic, Jeremy G. Carlton, Tony Ng
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-10-556

Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells
Cited by: 369
Author(s): Bok Sil Hong, Ji-Hoon Cho, Hyun-Jung Kim, Eunjeong Choi, Sangchul Rho, Jongmin Kim, Ji Hyun Kim, Dong-Sic Choi, Eui Chong Kim, Daehee Hwang, Yong Song Gho
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-11-540

The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment
Cited by: 6
Author(s): Andy G. Lynch, James Hadfield, Mark J. Dunning, Michelle Osborne, Natalie Thorne, Simon Tavaré
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0113842

Ectopic MicroRNA-150-5p Transcription Sensitizes Glucocorticoid Therapy Response in MM1S Multiple Myeloma Cells but Fails to Overcome Hormone Therapy Resistance in MM1R Cells
Cited by: 35
Author(s): Ajay Palagani, Ken Op de Beeck, Stefan Naulaerts, Jolien Diddens, Chandra Sekhar Chirumamilla, Guy Van Camp, Kris Laukens, Karen Heyninck, Sarah Gerlo, Pieter Mestdagh, Jo Vandesompele, Wim Vanden Berghe
Software Mentions: 1
Published: about 10 years ago

10.1038/s41416-020-01113-y

Increased expression of glutamine transporter SNAT2/SLC38A2 promotes glutamine dependence and oxidative stress resistance, and is associated with worse prognosis in triple-negative breast cancer
Cited by: 43
Author(s): Matteo Morotti, Christos E. Zois, Rokaya El-Ansari, Madeleine L. Craze, Emad A. Rakha, Shih‐Jung Fan, Alessandro Valli, Syed Haider, Deborah C. I. Goberdhan, Andrew Green, Adrian L. Harris
Software Mentions: 1
Published: about 4 years ago

10.1016/j.biopen.2017.03.004

Lemongrass ( Cymbopogon flexuosus ) essential oil demonstrated anti-inflammatory effect in pre-inflamed human dermal fibroblasts
Cited by: 43
Author(s): Xuesheng Han, Tory L. Parker
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0056594

Prenatal Metformin Exposure in Mice Programs the Metabolic Phenotype of the Offspring during a High Fat Diet at Adulthood
Cited by: 69
Author(s): Henriikka Salomäki, Laura H. Vähätalo, Kirsti Laurila, Norma Jäppinen, Anna‐Maija Penttinen, Liisa Ailanen, Juan Ilyasizadeh, Ullamari Pesonen, Markku Koulu
Software Mentions: 1
Published: almost 12 years ago

10.15252/embj.201593339

Ribonuclease H2 mutations induce a <scp>cGAS</scp>/<scp>STING</scp>‐dependent innate immune response
Cited by: 188
Author(s): Karen J. Mackenzie, Paula Carroll, Laura A. Lettice, Žygimantė Tarnauskaitė, Kaalak Reddy, Flora Dix, Ailsa Revuelta, E. Abbondati, Rachel E. Rigby, Björn Rabe, Fiona Kilanowski, Graeme R. Grimes, Adeline Fluteau, Paul S. Devenney, Robert E. Hill, Martin A.M. Reijns, Andrew P. Jackson
Software Mentions: 1
Published: almost 9 years ago

10.1186/1477-5956-9-69

Proteomic and transcriptomic analysis of heart failure due to volume overload in a rat aorto-caval fistula model provides support for new potential therapeutic targets - monoamine oxidase A and transglutaminase 2
Cited by: 36
Author(s): Jiřı́ Petrák, Jana Pospisilova, Miroslava Šedinová, Petr Jedelský, Lucie Lorková, Ondřej Vít, Michal Kolář, Hynek Strnad, Jan Beneš, David Sedmera, Luděk Červenka, Vojtěch Melenovský
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0045863

Comprehensive Exploration of the Effects of miRNA SNPs on Monocyte Gene Expression
Cited by: 10
Author(s): Nicolas Greliche, Tanja Zeller, Philipp S. Wild, Maxime Rotival, Arne Schillert, Andreas Ziegler, Panos Deloukas, Jeanette Erdmann, Christian Hengstenberg, Willem H. Ouwehand, Nilesh J. Samani, Heribert Schunkert, Thomas Münzel, Karl J. Lackner, François Cambien, Alison H. Goodall, Laurence Tiret, Stefan Blankenberg, David‐Alexandre Trégouët
Software Mentions: 1
Published: over 12 years ago

10.1186/1476-511X-9-99

Genetic and diet effects on Ppar-α and Ppar-γ signaling pathways in the Berlin Fat Mouse Inbred line with genetic predisposition for obesity
Cited by: 10
Author(s): Asja Wagener, Helge Goessling, Armin O. Schmitt, Susanne Mauel, Achim D. Gruber, Richard Reinhardt, Gudrun A. Brockmann
Software Mentions: 1
Published: over 14 years ago

Projects: bioconductor: beadarray

Papers Mentioning beadarray 94