bioconductor: lumi | Projects | Ecosyste.ms: Papers

10.1038/sdata.2015.68

Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes
Cited by: 40
Author(s): Wasco Wruck, Karl Kashofer, Samrina Rehman, Andriani Daskalaki, Daniela Berg, Ewa Gralka, Justyna Józefczuk, Katharina Drews, Vikash Pandey, Christian Regenbrecht, Christoph Wierling, Paola Turano, Ulrike Korf, Kurt Zatloukal, Hans Lehrach, Hans V. Westerhoff, James Adjaye
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13073-019-0674-2

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis
Cited by: 52
Author(s): Clara Lorente-Sorolla, Antonio García-Gómez, Francesc Català-Moll, Víctor Toledano, Laura Ciudad, José Avendaño-Ortíz, Charbel Maroun Eid, Alejandro Martín-Quirós, Mónica Martínez-Gallo, Adolfo Ruiz-Sanmartín, Álvaro García del Campo, Ricard Ferrer, Juan Carlos Ruiz‐Rodríguez, Damiana Álvarez-Errico, Eduardo López-Collazo, Esteban Ballestar
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-018-0440-0

DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling
Cited by: 29
Author(s): Leonardo De Boni, Gilles Gasparoni, Carolin Haubenreich, Sascha Tierling, Imke Schmitt, Michael Peitz, Philipp Koch, Jörn Walter, Ullrich Wüllner, Oliver Brüstle
Software Mentions: 3
Published: almost 7 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

10.1371/journal.pgen.1003459

SNF5 Is an Essential Executor of Epigenetic Regulation during Differentiation
Cited by: 44
Author(s): Jueng Soo You, Daniel D. De Carvalho, Chao Dai, Minmin Liu, Kurinji Pandiyan, Xianghong Jasmine Zhou, Gangning Liang, Peter A. Jones
Software Mentions: 3
Published: over 11 years ago

10.7150/thno.47938

Identification of a Tumor Microenvironment-relevant Gene set-based Prognostic Signature and Related Therapy Targets in Gastric Cancer
Cited by: 49
Author(s): Wangyu Cai, Zi-Nan Dong, Xiao-Teng Fu, Lingyun Lin, Lin Wang, Guodong Ye, Qin Luo, Yuchao Chen
Software Mentions: 3
Published: almost 5 years ago

10.1002/ctm2.458

Integrative multiomics analysis of human atherosclerosis reveals a serum response factor‐driven network associated with intraplaque hemorrhage
Cited by: 28
Author(s): Han Jin, Pieter Goossens, Péter Juhász, Wouter J. Eijgelaar, Marco Manca, Jöel Karel, Evgueni Smirnov, C.J.J.M. Sikkink, Barend Mees, Olivia J. Waring, Kim van Kuijk, Gregorio E. Fazzi, Marion J.J. Gijbels, Martina Kutmon, Chris T. Evelo, Ulf Hedin, M. J. A. P. Daemen, Judith C. Sluimer, Ljubica Matic, Erik A. L. Biessen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1003053

Network Analysis of a Pkd1-Mouse Model of Autosomal Dominant Polycystic Kidney Disease Identifies HNF4α as a Disease Modifier
Cited by: 72
Author(s): Luís F. Menezes, Fang Zhou, Andrew D. Patterson, Klaus Piontek, Kristopher W. Krausz, Frank J. Gonzalez, Gregory G. Germino
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13073-018-0557-y

Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells
Cited by: 27
Author(s): Ksenia S. Anufrieva, Victoria О. Shender, Georgij Arapidi, Marat S. Pavlyukov, M. I. Shakhparonov, Polina V. Shnaider, Ivan Butenko, Maria A. Lagarkova, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.1186/1742-4690-8-18

Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease
Cited by: 53
Author(s): Jing Qin Wu, Dominic E. Dwyer, Wayne B. Dyer, Jean Yee Hwa Yang, Binbin Wang, Nitin K. Saksena
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0015188

Genome-Wide Analysis of Glucocorticoid Receptor Binding Regions in Adipocytes Reveal Gene Network Involved in Triglyceride Homeostasis
Cited by: 151
Author(s): Chi-Yi Yu, Oleg Mayba, Joyce V. Lee, Joanna Tran, Charlie Harris, Terence P. Speed, Jen-Chywan Wang
Software Mentions: 3
Published: almost 14 years ago

10.1186/1465-9921-11-70

Response of the mouse lung transcriptome to welding fume: effects of stainless and mild steel fumes on lung gene expression in A/J and C57BL/6J mice
Cited by: 25
Author(s): Patti C. Zeidler-Erdely, Michael L. Kashon, Shengqiao Li, James M. Antonini
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0033542

Gene Expression Profile of Adult Human Olfactory Bulb and Embryonic Neural Stem Cell Suggests Distinct Signaling Pathways and Epigenetic Control
Cited by: 36
Author(s): Hany E. Marei, Ahmed Abd‐Elmaksoud, Fabrizio Michetti, Mario Pescatori, Roberto Pallini, Patricia Casalbore, Carlo Cenciarelli, Mohamed Elhadidy
Software Mentions: 3
Published: over 12 years ago

10.15252/emmm.201708047

The <scp>GPR</scp> 120 agonist <scp>TUG</scp> ‐891 promotes metabolic health by stimulating mitochondrial respiration in brown fat
Cited by: 75
Author(s): Maaike Schilperoort, Anke Dam, Geerte Hoeke, Irina G. Shabalina, Anthony Okolo, Aylin Hanyaloglu, Lea Dib, Isabel M. Mol, Natarin Caengprasath, Yi‐Wah Chan, Sami Damak, Anne Reifel Miller, Tamer Coşkun, Bharat Shimpukade, Trond Ulven, Sander Kooijman, Patrick C.N. Rensen, Mark Christian
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0070097

SIRT1 is a Direct Coactivator of Thyroid Hormone Receptor β1 with Gene-Specific Actions
Cited by: 56
Author(s): Ji Ho Suh, Douglas H. Sieglaff, Aijun Zhang, Xuefeng Xia, Aleksandra Čvoro, Glenn E. Winnier, Paul Webb
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-13-453

Microarray analysis revealing common and distinct functions of promyelocytic leukemia protein (PML) and tumor necrosis factor alpha (TNFα) signaling in endothelial cells
Cited by: 21
Author(s): Xiangguo Cheng, Hung‐Ying Kao
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.30496

The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1 lymphocytes
Cited by: 53
Author(s): Yasmina Serroukh, Chunyan Gu-Trantien, Baharak Hooshiar Kashani, Matthieu Defrance, Thien‐Phong Vu Manh, Abdulkader Azouz, Aurélie Detavernier, Alice Hoyois, Jishnu Das, Martin Bizet, Émeline Pollet, Tressy Tabbuso, Emilie Calonne, Klaas P. J. M. van Gisbergen, Marc Dalod, François Fuks, Stanislas Goriely, Arnaud Marchant
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0097780

Initiation of an Inflammatory Response in Resident Intestinal Lamina Propria Cells -Use of a Human Organ Culture Model
Cited by: 8
Author(s): Jutta Schröder–Braunstein, Judith Gras, Benedikt Brors, Sonja Schwarz, Timea Szikszai, Felix Lasitschka, Guido H. Wabnitz, Antje Heidtmann, Young-Seon Lee, Serin Schiessling, Christine Leowardi, Mohammed Al-Saeedi, Alexis Ulrich, Antonia Engelke, Johannes Winter, Yvonne Samstag, Thomas Giese, Stefan Meuer
Software Mentions: 3
Published: over 10 years ago

10.3389/fcimb.2017.00512

Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro
Cited by: 33
Author(s): Genevieve Syn, Denise Anderson, Jenefer M. Blackwell, Sarra E. Jamieson
Software Mentions: 3
Published: almost 7 years ago

10.3389/fonc.2020.574778

Comprehensive Characterization of Immunological Profiles and Clinical Significance in Hepatocellular Carcinoma
Cited by: 3
Author(s): Tao Peng, Liang Hong, Wenyi Tang, Qun Lü, Yanrong Zhao, Si Zhang, Li Ma, Ruyi Xue
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2012.00157

Detection of Expression Quantitative Trait Loci in Complex Mouse Crosses: Impact and Alleviation of Data Quality and Complex Population Substructure
Cited by: 6
Author(s): Ovidiu D. Iancu, Priscila Darakjian, Sunita Kawane, Daniel Bottomly, Robert Hitzemann, Shannon K. McWeeney
Software Mentions: 3
Published: almost 13 years ago

10.3389/fgene.2019.00800

Missense Pathogenic variants in KIF4A Affect Dental Morphogenesis Resulting in X-linked Taurodontism, Microdontia and Dens-Invaginatus
Cited by: 7
Author(s): Lord Jephthah Joojo Gowans, Sophia Cameron-Christie, Rebecca L. Slayton, Tamara Busch, Miguel Romero-Bustillos, Steven Eliason, Mason Sweat, Nara Sobreira, Wenjie Yu, Piranit Nik Kantaputra, Elizabeth Wohler, Wasiu Lanre Adeyemo, Salil A. Lachke, Deepti Anand, Colleen A. Campbell, Bernadette Drummond, David Markie, Wendy-Ann Jansen van Vuuren, Ludwig Jansen van Vuuren, Paul S. Casamassimo, Ronald L. Ettinger, Arwa I. Owais, I. van Staden, Brad A. Amendt, Adebowale Adeyemo, Jeffrey C. Murray, Stephen Robertson, Azeez Butali
Software Mentions: 3
Published: about 5 years ago

10.1186/s12920-015-0141-x

Extensive alterations of the whole-blood transcriptome are associated with body mass index: results of an mRNA profiling study involving two large population-based cohorts
Cited by: 21
Author(s): Georg Homuth, Simone Wahl, Christian Müller, Claudia Schurmann, Ulrike Mäder, Stefan Blankenberg, Maren Carstensen, Marcus Dörr, Karlhans Endlich, Christian Englbrecht, Stephan B. Felix, Christian Gieger, Harald Grallert, Christian Herder, Thomas Illig, Jochen Kruppa, Carola Marzi, Julia Mayerle, Thomas Meitinger, Andres Metspalu, Matthias Nauck, Annette Peters, Wolfgang Rathmann, Eva Reinmaa, Rainer Rettig, Michael Roden, Arne Schillert, Katharina Schramm, Leif Steil, Konstantin Strauch, Alexander Teumer, Henry Völzke, Henri Wallaschofski, Philipp S. Wild, Andreas Ziegler, Uwe Völker, Holger Prokisch, Tanja Zeller
Software Mentions: 3
Published: about 9 years ago

10.3389/fonc.2020.556018

Integrative Analysis of DNA Methylation Identified 12 Signature Genes Specific to Metastatic ccRCC
Cited by: 8
Author(s): Siwei Qian, Si Sun, Lei Zhang, Shengwei Tian, Kai Xu, Guangyuan Zhang, Ming Chen
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2105-13-329

Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays
Cited by: 12
Author(s): Sandra Plancade, Yves Rozenholc, Eiliv Lund
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13073-015-0227-2

Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis
Cited by: 12
Author(s): Nan Du, Kaiyu Jiang, Ashley Sawle, Mark Barton Frank, Carol A. Wallace, Aidong Zhang, James N. Jarvis
Software Mentions: 3
Published: about 9 years ago

10.1186/s13287-019-1209-x

Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature
Cited by: 76
Author(s): Lucas‐Sebastian Spitzhorn, Matthias Megges, Wasco Wruck, Shaifur Rahman, Jörg Otte, Özer Degistirici, Roland Meisel, Rüdiger V. Sorg, Richard O.C. Oreffo, James Adjaye
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1000781

Genome-Wide mRNA Expression Correlates of Viral Control in CD4+ T-Cells from HIV-1-Infected Individuals
Cited by: 166
Author(s): Margalida Rotger, Kristen K. Dang, Jacques Fellay, Erin L. Heinzen, Sheng Feng, Patrick Descombes, Kevin V. Shianna, Dongliang Ge, Huldrych F Günthard, David B. Goldstein, Amalio Telenti, Aids Immunology
Software Mentions: 3
Published: over 14 years ago

10.1186/2044-5040-2-7

miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells
Cited by: 36
Author(s): Kyle L. MacQuarrie, Zizhen Yao, Janet M. Young, Yi Cao, Stephen J. Tapscott
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0028761

A “Crossomics” Study Analysing Variability of Different Components in Peripheral Blood of Healthy Caucasoid Individuals
Cited by: 20
Author(s): Kristina Gruden, Matjaž Hren, Ana Herman, Andrej Blejec, Tanja Albrecht, Joachim Selbig, Chris Bauer, Jochannes Schuchardt, Michal Or-Guil, Klemen Zupančič, Urban Švajger, Borut Štabuc, Alojz Ihan, Andreja Nataša Kopitar, Maja Ravnikar, Miomir Knežević, Primož Rožman, Matjaž Jeras
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-32549-1

Integrative metabolic and transcriptomic profiling of prostate cancer tissue containing reactive stroma
Cited by: 45
Author(s): Maria Andersen, Kjersti Rise, Guro F. Giskeødegård, Elin Richardsen, Helena Bertilsson, Øystein Størkersen, Tone Frost Bathen, Morten Rye, May‐Britt Tessem
Software Mentions: 3
Published: about 6 years ago

10.1186/1743-8977-9-25

Type I interferon and pattern recognition receptor signaling following particulate matter inhalation
Cited by: 12
Author(s): Aaron Erdely, James M. Antonini, Rebecca Salmen‐Muniz, Angie Liston, Tracy Hulderman, Petia P. Simeonova, Michael L. Kashon, Shengqiao Li, Ja K. Gu, Samuel Stone, Bean T. Chen, David G. Frazer, Patti C. Zeidler-Erdely
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13073-015-0187-6

Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas
Cited by: 16
Author(s): Chulin Sha, Sharon Barrans, Matthew A. Care, David Cunningham, Reuben Tooze, Andrew Jack, David R. Westhead
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-16201-y

Cartilage intermediate layer protein 1 (CILP1): A novel mediator of cardiac extracellular matrix remodelling
Cited by: 34
Author(s): Frans A. van Nieuwenhoven, Chantal Munts, Roel C Op't Veld, Arantxa González, Javier Dı́ez, Stéphane Heymans, Blanche Schroen, Marc van Bilsen
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0060213

Microarray Analyses of Glucocorticoid and Vitamin D3 Target Genes in Differentiating Cultured Human Podocytes
Cited by: 13
Author(s): Xiangguo Cheng, Xuan Zhao, Simran Khurana, Leslie A. Bruggeman, Hung Ying Kao
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0190280

DNA methylation profiling of genomic DNA isolated from urine in diabetic chronic kidney disease: A pilot study
Cited by: 13
Author(s): Ashani Lecamwasam, Alexandra Sexton-Oates, Jake Carmody, Elif I Ekinci, Karen M. Dwyer, Richard Saffery
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0029429

Genomic Analysis of wig-1 Pathways
Cited by: 5
Author(s): Yalda Sedaghat, Curt Mazur, Mahyar Sabripour, Gene Hung, Brett P. Monia
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0052407

Gene Specific Actions of Thyroid Hormone Receptor Subtypes
Cited by: 27
Author(s): Jean Z. Lin, Douglas H. Sieglaff, Chaoshen Yuan, Jing Su, Anitha Christy S. Arumanayagam, Sharareh Firouzbakht, Jaime Javier Cantú Pompa, Frances Denoto Reynolds, Xixi Zhou, Aleksandra Čvoro, Paul Webb
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0023232

Age-Dependent Decline in Mouse Lung Regeneration with Loss of Lung Fibroblast Clonogenicity and Increased Myofibroblastic Differentiation
Cited by: 60
Author(s): Julia Paxson, Alisha M. Gruntman, Christopher Parkin, Melissa R. Mazan, Airiel M. Davis, Edward P. Ingenito, Andrew M. Hoffman
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0137103

Similarities and Distinctions in Actions of Surface-Directed and Classic Androgen Receptor Antagonists
Cited by: 5
Author(s): Ji Ho Suh, Arundhati Chattopadhyay, Douglas H. Sieglaff, Cheryl Samaniego, Marc B. Cox, Paul Webb
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0018276

DNMT3L Is a Regulator of X Chromosome Compaction and Post-Meiotic Gene Transcription
Cited by: 19
Author(s): Natasha Zamudio, Hamish S. Scott, Katja M. Wolski, Chi-Yi Lo, Charity W. Law, Dillon W. Leong, Sarah Kinkel, Suyinn Chong, Damien Jolley, Gordon K. Smyth, David de Kretser, Emma Whitelaw, Moira K O'Bryan
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0022856

Comprehensive Gene Expression Analysis of Human Embryonic Stem Cells during Differentiation into Neural Cells
Cited by: 52
Author(s): Ali Fathi, Maryam Hatami, Vahid Hajihosseini, Faranak Fattahi, Sahar Kiani, Hossein Baharvand, Ghasem Hosseini Salekdeh
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0006271

Drug and Cell Type-Specific Regulation of Genes with Different Classes of Estrogen Receptor β-Selective Agonists
Cited by: 63
Author(s): Sreenvinasan Paruthiyil, Aleksandra Čvoro, Xiaoyue Zhao, Zhijin Wu, Yunxia Sui, Richard E. Staub, Scott Baggett, Candice B. Herber, Chandi Griffin, Mary Tagliaferri, Heather A. Harris, Isaac Cohen, Leonard F. Bjeldanes, Terence P. Speed, Fred Schaufele, Dale C. Leitman
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0119275

Efficient Differentiation of Steroidogenic and Germ-Like Cells from Epigenetically-Related iPSCs Derived from Ovarian Granulosa Cells
Cited by: 19
Author(s): Raymond M. Anchan, Behzad Gerami‐Naini, J. Suzanne Lindsey, Joshua Wk Ho, Adam Kieżun, S.T. Lipskind, Nicholas Ng, Joseph A. LiCausi, Chloe S. Kim, Paul R. Brezina, Thomas Tuschl, Richard L. Maas, W.G. Kearns, Zev Williams
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1003572

A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue
Cited by: 499
Author(s): Tina Rönn, Petr Volkov, Cajsa Davegårdh, Tasnim Dayeh, Elin Hall, Anna Olsson, Erika Nilsson, Åsa Tornberg, Marloes Dekker Nitert, Karl-Fredrik Eriksson, Helena A. Jones, Leif Groop, Charlotte Ling
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0116807

Fetal-Adult Cardiac Transcriptome Analysis in Rats with Contrasting Left Ventricular Mass Reveals New Candidates for Cardiac Hypertrophy
Cited by: 5
Author(s): K Grabowski, Mona Riemenschneider, Leonard Schulte, Anika Witten, Angela Schulz, Monika Stoll, Reinhold Kreutz
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0040938

MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs
Cited by: 61
Author(s): Dong Lu, Matthew P Davis, Cei Abreu‐Goodger, Wei Wang, Lia S. Campos, Julia Siede, Elena Vigorito, William C. Skarnes, Ian Dunham, Anton J. Enright, Pentao Liu
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0083359

Peg3 Mutational Effects on Reproduction and Placenta-Specific Gene Families
Cited by: 64
Author(s): Joomyeong Kim, Wesley D. Frey, Hui He, Hana Kim, Muhammad B. Ekram, Arundhati Bakshi, Mohammad Faisal, Bambarendage P. U. Perera, An Ye, Ryoichi Teruyama
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0106289

Antiproliferative Effects and Mechanisms of Liver X Receptor Ligands in Pancreatic Ductal Adenocarcinoma Cells
Cited by: 43
Author(s): Nicholes R. Candelaria, Sridevi Addanki, Jine Zheng, Trang Nguyen-Vu, Husna Karaboga, Prasenjit Dey, Chiara Gabbi, Lise Lotte Vedin, Liu Ka, Weiqiang Wu, Philip Jonsson, Jean Z. Lin, Fei Su, Lakshmi Reddy Bollu, Sally E. Hodges, Amy L. McElhany, Mehdi A. Issazadeh, William E. Fisher, Michael Ittmann, Knut R. Steffensen, Jan Åke Gustafsson, Chin Yo Lin
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0033844

miR-34a Repression in Proneural Malignant Gliomas Upregulates Expression of Its Target PDGFRA and Promotes Tumorigenesis
Cited by: 107
Author(s): Joachim Silber, Anders Jacobsen, Tatsuya Ozawa, Girish Harinath, Alicia Pedraza, Chris Sander, Eric C. Holland, Jason T. Huse
Software Mentions: 2
Published: over 12 years ago

10.1186/s12989-014-0071-3

Short-term diesel exhaust inhalation in a controlled human crossover study is associated with changes in DNA methylation of circulating mononuclear cells in asthmatics
Cited by: 85
Author(s): Ruiwei Jiang, Meaghan J. Jones, Francesco Sava, Michæl S. Kobor, Christopher Carlsten
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0017848

Human Papillomavirus Deregulates the Response of a Cellular Network Comprising of Chemotactic and Proinflammatory Genes
Cited by: 131
Author(s): Rezaul Karim, Craig Meyers, Claude Backendorf, Kristina Ludigs, Rienk Offringa, G.J.B. van Ommen, Cornelis J.M. Melief, Sjoerd H. van der Burg, Judith M. Boer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0089750

Biomarkers of Histone Deacetylase Inhibitor Activity in a Phase 1 Combined-Modality Study with Radiotherapy
Cited by: 7
Author(s): Anne Hansen Ree, Marie Grøn Sælen, Erta Kalanxhi, Ingrid H.G. Østensen, Kristina Schee, Kathrine Røe, Torveig Weum Abrahamsen, Svein Dueland, Kjersti Flatmark
Software Mentions: 2
Published: over 10 years ago

10.1186/s12989-014-0034-8

Oxidative stress and reduced responsiveness of challenged circulating leukocytes following pulmonary instillation of metal-rich particulate matter in rats
Cited by: 18
Author(s): Aaron Erdely, James M. Antonini, Shih‐Houng Young, Michael L. Kashon, Ja K. Gu, Tracy Hulderman, Rebecca Salmen, Terence Meighan, Jenny R. Roberts, Patti C. Zeidler-Erdely
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.08711

Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation
Cited by: 16
Author(s): Sophia M. Blake, Stefan H. Stricker, Hanna Halavach, Anna R. Poetsch, George D Cresswell, Gavin Kelly, Nnennaya Kanu, Silvia Marino, Nicholas M. Luscombe, Steven M. Pollard, Axel Behrens
Software Mentions: 2
Published: over 8 years ago

10.1038/s41418-018-0100-0

cIAP1 regulates the EGFR/Snai2 axis in triple-negative breast cancer cells
Cited by: 15
Author(s): Maria Teresa Majorini, Giacomo Manenti, Miguel Mano, Loris De Cecco, Annalisa Conti, Patrizia Pinciroli, Enrico Fontanella, Elda Tagliabue, Claudia Chiodoni, Mario P. Colombo, Domenico Delia, Daniele Lecis
Software Mentions: 2
Published: over 6 years ago

10.1038/cddis.2016.359

A novel crosstalk between CCAR2 and AKT pathway in the regulation of cancer cell proliferation
Cited by: 22
Author(s): Michela Restelli, Martina Magni, Vincenzo Ruscica, Patrizia Pinciroli, Loris De Cecco, Giacomo Buscemi, Domenico Delia, Laura Zannini
Software Mentions: 2
Published: about 8 years ago

10.3390/cells9010099

Csf1 Deficiency Dysregulates Glial Responses to Demyelination and Disturbs CNS White Matter Remyelination
Cited by: 16
Author(s): Bartosz Wylot, Jakub Mieczkowski, Sylwia Niedziółka, Bożena Kamińska, Małgorzata Zawadzka
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13148-015-0112-2

DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations
Cited by: 59
Author(s): Ingo G. H. Schmidt‐Wolf, Muhammad Ahmer Jamil, Nicole Nuesgen, Felix Schreiner, Lutz Priebe, Per Hoffmann, Stefan Herns, Markus M. Nöthen, Holger Fröhlich, Johannes Oldenburg, Joachim Woelfle, Osman El‐Maarri
Software Mentions: 2
Published: over 9 years ago

10.1186/bcr3443

Liver × receptor ligands disrupt breast cancer cell proliferation through an E2F-mediated mechanism
Cited by: 66
Author(s): Trang Nguyen-Vu, Lise Lotte Vedin, Liu Ka, Philip Jonsson, Jean Z. Lin, Nicholes R. Candelaria, Lindsay P. Candelaria, Sridevi Addanki, Cecilia Williams, Jan‐Åke Gustafsson, Knut R. Steffensen, Chin Yo Lin
Software Mentions: 2
Published: over 11 years ago

10.1186/s13148-021-01150-1

Epigenetic age is associated with baseline and 3-year change in frailty in the Canadian Longitudinal Study on Aging
Cited by: 21
Author(s): Chris P. Verschoor, David T.S. Lin, Michæl S. Kobor, Oxana Mian, Jinhui Ma, Guillaume Paré, Gustavo Ybazeta
Software Mentions: 2
Published: over 3 years ago

10.1186/s13148-017-0339-1

Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns
Cited by: 23
Author(s): Olivia M. de Goede, Pascal M. Lavoie, Wendy P. Robinson
Software Mentions: 2
Published: over 7 years ago

10.1186/s13148-021-01034-4

Chromatin remodeling by the histone methyltransferase EZH2 drives lung pre-malignancy and is a target for cancer prevention
Cited by: 10
Author(s): Carmen S. Tellez, Maria A. Picchi, Daniel E. Juri, Kieu Do, Dhimant Desai, Shantu Amin, Julie A. Hutt, Piotr T. Filipczak, Steven A. Belinsky
Software Mentions: 2
Published: over 3 years ago

10.1186/s13148-015-0064-6

Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes
Cited by: 66
Author(s): Nathalie Acevedo, Lovisa E. Reinius, Morana Vitezic, Vittorio Fortino, Cilla Söderhäll, Hanna Honkanen, Riitta Veijola, Olli Simell, Jorma Toppari, Jorma Ilonen, Mikael Knip, Annika Scheynius, Heikki Hyöty, Dario Greco, Juha Kere
Software Mentions: 2
Published: over 9 years ago

10.1007/s12575-009-9012-1

MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interferon-Alpha-2a
Cited by: 20
Author(s): Fredy Siegrist, Thomas P. Singer, Ulrich Certa
Software Mentions: 2
Published: over 15 years ago

10.1242/bio.047290

<i>Greb1</i> is required for axial elongation and segmentation in vertebrate embryos
Cited by: 3
Author(s): Ravindra Singh Prajapati, Richard Mitter, Annalisa Vezzaro, David Ish‐Horowicz
Software Mentions: 2
Published: almost 5 years ago

10.1186/1752-0509-3-55

A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism
Cited by: 30
Author(s): Jen-Hwa Chu, Scott T. Weiss, Vincent J. Carey, Benjamin A. Raby
Software Mentions: 2
Published: over 15 years ago

10.1186/s13075-016-1059-1

Whole blood expression profiling from the TREAT trial: insights for the pathogenesis of polyarticular juvenile idiopathic arthritis
Cited by: 20
Author(s): Kaiyu Jiang, Lai-Ping Wong, Ashley Sawle, Mark Barton Frank, Yanmin Chen, Carol A. Wallace, James N. Jarvis
Software Mentions: 2
Published: over 8 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/ejhg.2014.139

Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents
Cited by: 67
Author(s): Sarah Voisin, Markus Sällman Almén, George Moschonis, George P. Chrousos, Yannis Μanios, Helgi B. Schiöth
Software Mentions: 2
Published: over 10 years ago

10.1186/s12868-015-0151-9

Implication of coronin 7 in body weight regulation in humans, mice and flies
Cited by: 13
Author(s): Anders Eriksson, Michael J. Williams, Sarah Voisin, Ingrid Hansson, Arunkumar Krishnan, Gaëtan Philippot, O. V. Yamskova, Florence M Herisson, Rohit Dnyansagar, George Moschonis, Yannis Μanios, George P. Chrousos, Pawel K. Olszewski, Robert Frediksson, Helgi B. Schiöth
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2021.735643

Tissue-Resident-Memory CD8+ T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes
Cited by: 14
Author(s): Tao Peng, Khamsone Phasouk, Catherine Sodroski, Sijie Sun, Yon Hwangbo, Erik D. Layton, Lei Jin, Alexis Klock, Kurt Diem, Amalia Magaret, Lichen Jing, Kerry J. Laing, Alvason Li, Meei‐Li Huang, Max E. Mertens, Christine Johnston, Keith R. Jerome, David M. Koelle, Anna Wald, David M. Knipe, Lawrence Corey, Jia Zhu
Software Mentions: 2
Published: about 3 years ago

10.1007/s00204-016-1865-x

Maintenance of drug metabolism and transport functions in human precision-cut liver slices during prolonged incubation for 5 days
Cited by: 33
Author(s): Viktoriia Starokozhko, Suresh Vatakuti, Bauke Schievink, Marjolijn T. Merema, Annika Asplund, Jane Synnergren, Anders Aspegren, Geny M. M. Groothuis
Software Mentions: 2
Published: about 8 years ago

10.3389/fimmu.2019.01535

IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function
Cited by: 14
Author(s): Laura A. Ridgley, Amy E. Anderson, Nicola J Maney, Najib Naamane, Andrew Skelton, Catherine A. Lawson, Paul Emery, John D. Isaacs, Ruaidhrı́ J. Carmody, Arthur G. Pratt
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2021.581030

Characterization of Tumor Microenvironment in Lung Adenocarcinoma Identifies Immune Signatures to Predict Clinical Outcomes and Therapeutic Responses
Cited by: 7
Author(s): Donglai Chen, Yifei Wang, Xi Zhang, Qifeng Ding, Xiaofan Wang, Yuhang Xue, Wei Wang, Yiming Mao, Chang Chen, Yongbing Chen
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2019.00385

DNMT Inhibitors Increase Methylation in the Cancer Genome
Cited by: 61
Author(s): Anil Giri, Tero Aittokallio
Software Mentions: 2
Published: over 5 years ago

10.3389/fphys.2018.01180

The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism – A Systems Biology Analysis Using Self-Organizing Maps
Cited by: 10
Author(s): Christiane Rennert, Sebastian Vlaic, Eugenia Marbach-Breitrück, Carlo Thiel, Susanne Sales, Andrej Shevchenko, Rolf Gebhardt, Madlen Matz‐Soja
Software Mentions: 2
Published: about 6 years ago

10.1186/gb-2014-15-3-r51

Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs
Cited by: 107
Author(s): Hilary C. Martin, Shivangi Wani, Anita L Steptoe, K. V. Krishnan, Kátia Nones, Ehsan Nourbakhsh, Alexander V. Vlassov, Sean M. Grimmond, Nicole Cloonan
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.30325

Injury-induced perivascular niche supports alternative differentiation of adult rodent CNS progenitor cells
Cited by: 24
Author(s): Justyna Ulanska-Poutanen, Jakub Mieczkowski, Chao Zhao, Katarzyna Konarzewska, Beata Kaza, Hartmut B.F. Pohl, Łukasz Bugajski, Bożena Kamińska, Robin J.M. Franklin, Małgorzata Zawadzka
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-017-4006-x

Fungal biomarker discovery by integration of classifiers
Cited by: 2
Author(s): J. Saraiva, Marcus Oswald, Antje Biering, Daniela Röll, Cora Assmann, Tilman E. Klassert, Markus Blaess, Kristin Czakai, Ralf A. Claus, Jürgen Löffler, Hortense Slevogt, Rainer König
Software Mentions: 2
Published: over 7 years ago

10.1038/srep10775

Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system
Cited by: 381
Author(s): Antonis Koussounadis, Simon P. Langdon, In Hwa Um, David J. Harrison, V. Anne Smith
Software Mentions: 2
Published: over 9 years ago

10.1038/srep08117

PhenomeExpress: A refined network analysis of expression datasets by inclusion of known disease phenotypes
Cited by: 26
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-13-190

Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks
Cited by: 19
Author(s): Monika Ray, Reem Yunis, Xiucui Chen, David M. Rocke
Software Mentions: 2
Published: over 12 years ago

10.18632/oncotarget.12859

Metformin treatment reduces temozolomide resistance of glioblastoma cells
Cited by: 53
Author(s): Seung Ho Yang, Shenglan Li, Guangrong Lu, Xue Han, Dong H. Kim, Jay‐Jiguang Zhu, Ying Liu
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-11-585

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse
Cited by: 56
Author(s): Ovidiu D. Iancu, Priscila Darakjian, Nicole A.R. Walter, Barry Malmanger, Denesa Oberbeck, John K. Belknap, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 2
Published: about 14 years ago

10.1038/srep39297

Unraveling gene expression profiles in peripheral motor nerve from amyotrophic lateral sclerosis patients: insights into pathogenesis
Cited by: 21
Author(s): Nilo Riva, Ferdinando Clarelli, Teuta Domi, Federica Cerri, Francesca Gallia, Amelia Trimarco, Paola Brambilla, Christian Lunetta, A. Lazzerini, Giuseppe Lauria, Carla Taveggia, Sandro Iannaccone, Eduardo Nobile‐Orazio, Giancarlo Comi, Maurizio D’Antonio, Filippo Martinelli Boneschi, Angelo Quattrini
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-019-44865-1

Overexpression of miRNA-25-3p inhibits Notch1 signaling and TGF-β-induced collagen expression in hepatic stellate cells
Cited by: 21
Author(s): Berit Genz, Miranda A. Coleman, Katharine M. Irvine, Jamie R. Kutasovic, Mariska Miranda, Francis D. Gratte, Janina E.E. Tirnitz–Parker, John K. Olynyk, Diego A. Calvopina, Anna Weis, Nicole Cloonan, Harley Robinson, Michelle M. Hill, Fares Al-Ejeh, Grant A. Ramm
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.22236

EphA2 signaling is impacted by carcinoembryonic antigen cell adhesion molecule 1-L expression in colorectal cancer liver metastasis in a cell context-dependent manner
Cited by: 4
Author(s): Azadeh Arabzadeh, Kevin McGregor, Valérie Breton, Lauren Van Der Kraak, Uri David Akavia, Celia M.T. Greenwood, Nicole Beauchemin
Software Mentions: 2
Published: about 7 years ago

10.1186/s13287-017-0602-6

Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress
Cited by: 7
Author(s): M. Barandalla, Hui Shi, Hui Xiao, Silvia Colleoni, Cesare Galli, Píetro Lió, Matthew Trotter, Giovanna Lazzari
Software Mentions: 2
Published: over 7 years ago

10.1186/s13287-018-1118-4

Sex influences DNA methylation and gene expression in human skeletal muscle myoblasts and myotubes
Cited by: 47
Author(s): Cajsa Davegårdh, Elin Hall, Christa Broholm, Tora Ida Henriksen, Maria Pedersen, Bente Klarlund Pedersen, Camilla Schéele, Charlotte Ling
Software Mentions: 2
Published: almost 6 years ago

10.3402/jev.v1i0.18396

Cellular stress conditions are reflected in the protein and RNA content of endothelial cell‐derived exosomes
Cited by: 470
Author(s): Olivier G. de Jong, Marianne C. Verhaar, Yong Chen, Pieter Vader, Hendrik Gremmels, George Posthuma, Raymond M. Schiffelers, Marjan Guček, Bas W. M. van Balkom
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12958-017-0273-2

Differentiating mouse embryonic stem cells express markers of human endometrium
Cited by: 13
Author(s): Parveen Parasar, Caitlin R. Sacha, Nicholas Ng, E. R. McGuirk, Sireesha Chinthala, Pınar Özcan, J. Suzanne Lindsey, Sophia Salas, Marc R. Laufer, Stacey A. Missmer, Raymond M. Anchan
Software Mentions: 2
Published: over 7 years ago

10.1186/s13045-014-0056-6

Mutated in colorectal cancer (MCC) is a novel oncogene in B lymphocytes
Cited by: 18
Author(s): Shanique Edwards, Jacqueline Baron, Cynthia Moore, Yan Liu, David H. Perlman, Ronald P. Hart, Ping Xie
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1007707

A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome
Cited by: 40
Author(s): Paras Garg, Ricky S. Joshi, Corey T. Watson, Andrew J. Sharp
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1004158

Genome-Wide DNA Methylation Analysis Predicts an Epigenetic Switch for GATA Factor Expression in Endometriosis
Cited by: 143
Author(s): Matthew T. Dyson, Damian Roqueiro, Diana Monsivais, Cihangir Mutlu Ercan, Mary Ellen Pavone, David Brooks, Toshiyuki Kakinuma, Masanori Ono, Nadereh Jafari, Yang Dai, Serdar E. Bulun
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.ppat.1007298

Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway
Cited by: 48
Author(s): Weijian Ye, Marvin Chew, Jue Hou, Fritz Lai, Stije J. Leopold, Hooi Linn Loo, Aniruddha Ghose, A. K. Dutta, Yi‐Ping Phoebe Chen, Eng Eong Ooi, Nicholas J. White, Arjen M. Dondorp, Peter R. Preiser, Jianzhu Chen
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0115778

Prenatal Metformin Exposure in a Maternal High Fat Diet Mouse Model Alters the Transcriptome and Modifies the Metabolic Responses of the Offspring
Cited by: 45
Author(s): Henriikka Salomäki, Merja Heinäniemi, Laura H. Vähätalo, Liisa Ailanen, Kim Eerola, Suvi T. Ruohonen, Ullamari Pesonen, Markku Koulu
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1003491

Irf8-Regulated Genomic Responses Drive Pathological Inflammation during Cerebral Malaria
Cited by: 41
Author(s): Joanne Berghout, David Langlais, Irena Radovanovic, Mifong Tam, John D. MacMicking, Mary M. Stevenson, Philippe Gros
Software Mentions: 2
Published: over 11 years ago

10.1186/s13148-015-0129-6

Nucleated red blood cells impact DNA methylation and expression analyses of cord blood hematopoietic cells
Cited by: 48
Author(s): Olivia M. de Goede, Hamid Reza Razzaghian, E. Magda Price, Meaghan J. Jones, Michæl S. Kobor, Wendy P. Robinson, Pascal M. Lavoie
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-3214-0

Transcription factor ZNF25 is associated with osteoblast differentiation of human skeletal stem cells
Cited by: 11
Author(s): Natalie A. Twine, Linda Harkness, Moustapha Kassem, Marc R. Wilkins
Software Mentions: 1
Published: about 8 years ago

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