Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: lumi
https://packages.ecosyste.ms/registries/bioconductor.org/packages/lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
2 versions
Latest release: about 1 year ago
10 dependent packages
321,959 downloads total
Papers Mentioning lumi 238
10.1111/jcmm.12328
Extracellular matrix and cytochrome P450 gene expression can distinguish steatohepatitis from steatosis in miceCited by: 15
Author(s): Ewa E. Hennig, Michał Mikula, Krzysztof Goryca, Agnieszka Paziewska, Joanna K. Ledwon, Monika Nesteruk, Marek Woszczyński, Bożena Walewska-Zielecka, Kazimiera Pyśniak, Jerzy Ostrowski
Software Mentions: 1
Published: over 10 years ago
10.1016/j.cels.2017.08.009
Stem Cell Differentiation as a Non-Markov Stochastic ProcessCited by: 162
Author(s): Patrick S. Stumpf, R Smith, Michael Lenz, Andreas Schuppert, Franz‐Josef Müller, Ann C. Babtie, Thalia E. Chan, Michael Stumpf, Colin P. Please, Sam Howison, Fumio Arai, Ben D. MacArthur
Software Mentions: 1
Published: about 7 years ago
10.1186/1743-422X-10-361
Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapyCited by: 16
Author(s): Jing Qin Wu, Tara Ruth Sassé, Monica Miranda Saksena, Nitin K. Saksena
Software Mentions: 1
Published: almost 11 years ago
10.3390/cancers12010112
Cancer Associated Fibroblasts and Senescent Thyroid Cells in the Invasive Front of Thyroid CarcinomaCited by: 29
Author(s): Emanuela Minna, Silvia Brich, Katia Todoerti, Silvana Pilotti, Paola Collini, Elisa Bonaldi, Paola Romeo, Loris De Cecco, Matteo Dugo, Federica Perrone, Adele Busico, Andrea Vingiani, Ilaria Bersani, Andrea Anichini, Roberta Mortarini, Antonino Neri, Giancarlo Pruneri, Angela Greco, Maria Grazia Borrello
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12859-021-04381-4
DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantificationCited by: 3
Author(s): Clémentine Decamps, A Arnaud, Florent Petitprez, Mira Ayadi, Aurélia Baurès, Lucile Armenoult, Sérgio Escalera, Isabelle Guyon, Rémy Nicolle, Richard Tomasini, Aurélien de Reyniès, Jérôme Cros, Yuna Blum, Magali Richard
Software Mentions: 1
Published: about 3 years ago
10.1038/s41598-019-48204-2
Synergistic silencing of α-globin and induction of γ-globin by histone deacetylase inhibitor, vorinostat as a potential therapy for β-thalassaemiaCited by: 21
Author(s): Sachith Mettananda, Nirmani Yasara, Christopher A. Fisher, Stephen Taylor, Richard J. Gibbons, Deborah Higgs
Software Mentions: 1
Published: over 5 years ago
10.18632/oncotarget.18543
Novel tropolones induce the unfolded protein response pathway and apoptosis in multiple myeloma cellsCited by: 15
Author(s): Staci L. Haney, Cheryl Allen, Michelle L. Varney, Kaitlyn M. Dykstra, Eric R. Falcone, Sean Colligan, Qiang Hu, Alyssa M. Aldridge, Dennis L. Wright, Andrew J. Wiemer, Sarah A. Holstein
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pgen.1004160
Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin SecretionCited by: 389
Author(s): Tasnim Dayeh, Petr Volkov, Sofia Salö, Elin Hall, Erika Nilsson, Anna Olsson, Clare L. Kirkpatrick, Claes B. Wollheim, Lena Eliasson, Tina Rönn, Karl Bacos, Charlotte Ling
Software Mentions: 1
Published: over 10 years ago
10.4161/21624011.2014.958937
Local treatment of a pleural mesothelioma tumor with ONCOS-102 induces a systemic antitumor CD8<sup>+</sup>T-cell response, prominent infiltration of CD8<sup>+</sup>lymphocytes and Th1 type polarizationCited by: 38
Author(s): Tuuli Ranki, Timo Joensuu, Elke Jäger, Julia Karbach, Claudia Wahle, Kalevi Kairemo, Tuomo Alanko, Kaarina Partanen, Riku Turkki, Nina Linder, Johan Lundin, Ari Ristimäki, Matti Kankainen, Akseli Hemminki, Charlotta Backman, Kasper Dienel, Mikael von Euler, Elina Haavisto, Tiina Hakonen, Juuso Juhila, Magnus Jäderberg, Petri Priha, Lotta Vassilev, Antti Vuolanto, Sari Pesonen
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0071632
Notch Pathway Activation Contributes to Inhibition of C2C12 Myoblast Differentiation by EthanolCited by: 18
Author(s): Michelle A. Arya, Albert Tai, Eric C. Wooten, Christopher Parkin, Elena Kudryavtseva, Gordon S. Huggins
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0029985
PGC-1α Induces Mitochondrial and Myokine Transcriptional Programs and Lipid Droplet and Glycogen Accumulation in Cultured Human Skeletal Muscle CellsCited by: 41
Author(s): Emma Mormeneo, Cecilia Jiménez‐Mallebrera, Xavier Palomer, Valeria De Nigris, Manuel Vázquez‐Carrera, Anna Orozco, A. Nascimento, J. Colomer, Carles Lerín, Anna M. Gómèz-Foix
Software Mentions: 1
Published: almost 13 years ago
10.3390/cancers12061462
SPOP Deregulation Improves the Radiation Response of Prostate Cancer Models by Impairing DNA Damage RepairCited by: 7
Author(s): Rihan El Bezawy, Martina Tripari, Stefano Percio, A. Cicchetti, Monica Tortoreto, C. Stucchi, Stella Tinelli, Valentina Zuco, Valentina Doldi, Paolo Gandellini, Riccardo Valdagni, Nadia Zaffaroni
Software Mentions: 1
Published: over 4 years ago
10.18632/oncotarget.24743
Regulation of breast cancer induced bone disease by cancer-specific IKKβCited by: 6
Author(s): Silvia Marino, Ryan T. Bishop, Mattia Capulli, Antonia Sophocleous, John G. Logan, Patrick Mollat, Barbara Mognetti, Laura Ventura, Andrew H. Sims, Nadia Rucci, Stuart H. Ralston, Aymen I. Idris
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0010395
Using Canonical Correlation Analysis to Discover Genetic Regulatory VariantsCited by: 49
Author(s): Melissa Naylor, Xihong Lin, Scott T. Weiss, Benjamin A. Raby, Christoph Lange
Software Mentions: 1
Published: over 14 years ago
10.3389/fimmu.2020.00381
Discovery and Differential Processing of HLA Class II-Restricted Minor Histocompatibility Antigen LB-PIP4K2A-1S and Its Allelic Variant by Asparagine EndopeptidaseCited by: 6
Author(s): Anita N. Kremer, Judith Bausenwein, Ellie G.A. Lurvink, Andreas E. Kremer, Caroline E. Rutten, Cornelis A.M. van Bergen, Sascha Kretschmann, Edith van der Meijden, M. Willy Honders, Daniela Mazzeo, Colin Watts, Andréas Mackensen, J.H. Frederik Falkenburg, Marieke Griffioen
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2014.00280
DNA methylation changes in the postmortem dorsolateral prefrontal cortex of patients with schizophreniaCited by: 59
Author(s): Shusuke Numata, Tianzhang Ye, Mary M. Herman, Barbara K. Lipska
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0079051
Role of Tumor Necrosis Factor-α in the Human Systemic Endotoxin-Induced TranscriptomeCited by: 14
Author(s): Brendon P. Scicluna, Cornelis van ’t Veer, Max Nieuwdorp, Karen Felsmann, Britta Wlotzka, Erik S.G. Stroes, Tom van der Poll
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0042430
The Modular Nature of Dendritic Cell Responses to Commensal and Pathogenic FungiCited by: 11
Author(s): Lisa Rizzetto, Sonja I. Buschow, Luca Beltrame, Carl G. Figdor, Stephan Schierer, Gerold Schuler, Duccio Cavalieri
Software Mentions: 1
Published: over 12 years ago
10.1186/1755-8794-3-18
Molecular analysis of endothelial progenitor cell (EPC) subtypes reveals two distinct cell populations with different identitiesCited by: 280
Author(s): Reinhold J. Medina, Christina O'Neill, Mark Sweeney, Jasenka Guduric-Fuchs, Tom Gardiner, David Simpson, Alan W. Stitt
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2466-11-17
The CD4+ T-cell transcriptome and serum IgE in asthma: IL17RB and the role of sexCited by: 25
Author(s): Gary M. Hunninghake, Jen-Hwa Chu, Sunita Sharma, Michael H. Cho, Blanca E. Himes, Angela J. Rogers, Amy Murphy, Vincent J. Carey, Benjamin A. Raby
Software Mentions: 1
Published: over 13 years ago
10.1093/hmg/ddw072
The heritability and patterns of DNA methylation in normal human colorectumCited by: 9
Author(s): Amy Rowlatt, Gustavo Hernández-Suárez, María Carolina Sanabria‐Salas, M. L. Vidal López, Konrad Rawlik, Eva Hernández‐Illán, Cristina Alenda, Adela Castillejo, José Luis Viruez Soto, Chris Haley, Albert Tenesa
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0107166
The Effect of Freeze-Thaw Cycles on Gene Expression Levels in Lymphoblastoid Cell LinesCited by: 24
Author(s): Minal Çalışkan, Jonathan K. Pritchard, Carole Ober, Yoav Gilad
Software Mentions: 1
Published: about 10 years ago
10.1186/1756-0500-6-33
Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samplesCited by: 12
Author(s): Douglas W. Mahoney, Terry M. Therneau, S. Keith Anderson, Jin Jen, Jean Pierre A. Kocher, Monica M. Reinholz, Edith A. Perez, Jeanette E. Eckel‐Passow
Software Mentions: 1
Published: almost 12 years ago
10.1111/desc.12739
Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthoodCited by: 5
Author(s): Sarah J. Goodman, Danielle S. Roubinov, Nicole R. Bush, Mina Park, Pau Farré, Eldon Emberly, Clyde Hertzman, Marilyn J. Essex, Michæl S. Kobor, W. Thomas Boyce
Software Mentions: 1
Published: about 6 years ago
10.3390/biomedicines9010068
High Monopolar Spindle 1 Is Associated with Short Survival of Cholangiocarcinoma Patients and Enhances the Progression Via AKT and STAT3 Signaling PathwaysCited by: 1
Author(s): Piya Prajumwongs, Ratthaphong Phumphu, Orawan Waenphimai, Worachart Lert-itthiporn, Kulthida Vaeteewoottacharn, Sopit Wongkham, Yaovalux Chamgramol, Chawalit Pairojkul, Kanlayanee Sawanyawisuth
Software Mentions: 1
Published: almost 4 years ago
10.1186/1745-7580-6-10
DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cellsCited by: 24
Author(s): Duccio Cavalieri, Damaríz Rivero, Luca Beltrame, Sonja I. Buschow, Enrica Calura, Lisa Rizzetto, Sandra Gessani, Maria Cristina Gauzzi, Walter Reith, Andreas S. Baur, Roberto Bonaiuti, Marco Brandizi, Carlotta De Filippo, Ugo D’Oro, Sorin Drăghici, Isabelle Dunand-Sauthier, Evelina Gatti, Francesca Granucci, Michaela Gündel, Matthijs Kramer, Mirela Kuka, Árpád Lányi, Cornelis J.M. Melief, Nadine van Montfoort, Renato Ostuni, Philippe Pierre, Răzvan Popovici, Éva Rajnavölgyi, Stephan Schierer, Gerold Schuler, Vassili Soumelis, Andrea Splendiani, Irene Stefanini, Maria Gabriella Torcia, Ivan Zanoni, Raphaël Zollinger, Carl G. Figdor, Jonathan M. Austyn
Software Mentions: 1
Published: almost 15 years ago
10.1186/1471-2105-11-587
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysisCited by: 1,559
Author(s): Pan Du, Xiao Zhang, Chiang Ching Huang, Nadereh Jafari, Warren A. Kibbe, Lifang Hou, Simon Lin
Software Mentions: 1
Published: almost 14 years ago
10.1038/s41597-020-00592-1
Transcriptome analysis of blood and spleen in virulent and avirulent mouse malaria infectionCited by: 3
Author(s): Yuancun Zhao, Caroline Hosking, Deirdre Cunningham, Jean Langhorne, Jing-wen Lin
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0133738
Overlap Chronic Placental Inflammation Is Associated with a Unique Gene Expression PatternCited by: 18
Author(s): Kripa Raman, Huaqing Wang, Michael Troncone, Waliul I. Khan, Guillaume Paré, Jefferson Terry
Software Mentions: 1
Published: over 9 years ago
10.1186/s40425-016-0121-5
Phase I study with ONCOS-102 for the treatment of solid tumors – an evaluation of clinical response and exploratory analyses of immune markersCited by: 147
Author(s): Tuuli Ranki, Sari Pesonen, Akseli Hemminki, Kaarina Partanen, Kalevi Kairemo, Tuomo Alanko, Johan Lundin, Nina Linder, Riku Turkki, Ari Ristimäki, Elke Jäger, Julia Karbach, Claudia Wahle, Matti Kankainen, Charlotta Backman, Mikael von Euler, Elina Haavisto, Tiina Hakonen, Raita Heiskanen, Magnus Jäderberg, Juuso Juhila, Petri Priha, Laura Suoranta, Lotta Vassilev, Antti Vuolanto, Timo Joensuu
Software Mentions: 1
Published: over 8 years ago
10.1186/s13148-017-0435-2
An epigenome-wide study of obesity in African American youth and young adults: novel findings, replication in neutrophils, and relationship with gene expressionCited by: 32
Author(s): Xiaoling Wang, Yue Pan, Haidong Zhu, Guang Hao, Yisong Huang, Vernon A. Barnes, Huidong Shi, Harold Snieder, James S. Pankow, Kari E. North, Megan L. Grove, Weihua Guan, Ellen W. Demerath, Yanbin Dong, Shaoyong Su
Software Mentions: 1
Published: almost 7 years ago
10.18632/oncotarget.6899
Transcriptomic profiling of urine extracellular vesicles reveals alterations of CDH3 in prostate cancerCited by: 55
Author(s): Félix Royo, Patricia Zúñiga-García, Verónica Torrano, Ana Loizaga, Pilar Sánchez-Mosquera, Aitziber Ugalde-Olano, Esperanza González, Ana R. Cortazar, Laura Palomo, Sonia Fernández-Ruiz, Isabel Lacasa-Viscasillas, María Berdasco, James D. Sutherland, Rosa Barrio, Amaia Zabala-Letona, Natalia Martín-Martín, Amaia Arruabarrena-Aristorena, Lorea Valcárcel-Jiménez, Alfredo Caro‐Maldonado, J. González-Tampán, Guido Cachi-Fuentes, Manel Esteller, Ana M. Aransay, Miguel Unda, Juan Manuel Falcón‐Pérez, Arkaitz Carracedo
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep31068
Genome-Wide Transcriptome and Binding Sites Analyses Identify Early FOX Expressions for Enhancing Cardiomyogenesis Efficiency of hESC CulturesCited by: 7
Author(s): Hock Chuan Yeo, Sherwin Ting, Romulo M. Brena, Geoffrey Koh, Allen Chen, Siew Qi Toh, Yoon-Pin Lim, Steve Oh, Dong-Yup Lee
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1006033
A Syntenic Cross Species Aneuploidy Genetic Screen Links RCAN1 Expression to β-Cell Mitochondrial Dysfunction in Type 2 DiabetesCited by: 36
Author(s): Heshan Peiris, Michael Duffield, João Fadista, Claire F. Jessup, Vinder Kashmir, Amanda J Genders, Sean L. McGee, Alyce M. Martin, Madiha Saiedi, Nicholas M. Morton, Roderick Carter, Michael A. Cousin, Alexandros C. Kokotos, Nikolay Oskolkov, Petr Volkov, Tertius Hough, Elizabeth Fisher, Victor L. J. Tybulewicz, Jorge Busciglio, Pınar Coşkun, Ann Becker, Pavel V. Belichenko, William C. Mobley, Michael Ryan, Jeng Yie Chan, D. Ross Laybutt, P. Toby Coates, Shaofeng Yang, Charlotte Ling, Leif Groop, Melanie April Pritchard, Damien J. Keating
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1004418
Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem RepeatsCited by: 46
Author(s): Manisha Brahmachary, Audrey Guilmatre, Javier Quilez, Dan Hasson, Christelle Borel, Peter E. Warburton, Andrew J. Sharp
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1009189
Rare genetic variation at transcription factor binding sites modulates local DNA methylation profilesCited by: 26
Author(s): Alejandro Martin-Trujillo, Nihir Patel, Felix Richter, Bharati Jadhav, Paras Garg, Sarah U. Morton, David McKean, Steven R. DePalma, Elizabeth Goldmuntz, Dorota Gruber, Richard Kim, Jane W. Newburger, George A. Porter, Alessandro Giardini, Daniel Bernstein, Martin Tristani‐Firouzi, Jonathan G. Seidman, Christine E. Seidman, Wendy K. Chung, Bruce D. Gelb, Andrew J. Sharp
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pgen.1003000
The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression LevelsCited by: 101
Author(s): Athma A. Pai, Carolyn E. Cain, Orna Mizrahi-Man, Sherryl De Leon, Noah Lewellen, Jean‐Baptiste Veyrieras, Jacob F. Degner, Daniel J. Gaffney, Joseph K. Pickrell, Matthew Stephens, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 1
Published: about 12 years ago