bioconductor: lumi | Projects | Ecosyste.ms: Papers

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: about 14 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: over 3 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: almost 13 years ago

10.1186/1756-0500-4-546

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data
Cited by: 20
Author(s): Francesco Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma
Software Mentions: 11
Published: almost 13 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
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: about 4 years ago

10.1126/sciadv.1600760

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia
Cited by: 85
Author(s): S. Picaud, Katharina Leonards, Jean-Philippe Lambert, Oliver M. Dovey, Christopher Wells, Oleg Fedorov, Octovia Monteiro, Takao Fujisawa, Chenyi Wang, Hannah Lingard, C. Tallant, Nikzad Nikbin, Lucie Guetzoyan, Richard J. Ingham, Steven V. Ley, P.E. Brennan, Susanne Müller, Anastasia Samsonova, Anne‐Claude Gingras, Juerg Schwaller, George S. Vassiliou, Stefan Knapp, P. Filippakopoulos
Software Mentions: 10
Published: about 8 years ago

10.7717/peerj.1845

A molecular classification of human mesenchymal stromal cells
Cited by: 42
Author(s): Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim‐Anh Lê Cao, Christine A. Wells
Software Mentions: 10
Published: over 8 years ago

10.1002/embj.201386825

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells
Cited by: 48
Author(s): Fernando J. Calero-Nieto, Felicia Ng, Nicola K. Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 10
Published: over 10 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

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: about 9 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: almost 11 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0143970

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome
Cited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: almost 9 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: over 9 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: almost 8 years ago

10.1371/journal.pone.0164292

Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes
Cited by: 55
Author(s): T. Huibertus van Essen, Sake I. van Pelt, Inge H. G. Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J. van den Elsen, Pieter A. van der Velden, Didier Decaudin, Martine J. Jager
Software Mentions: 8
Published: about 8 years ago

10.7717/peerj.11233

Identification of a ferroptosis-related gene signature (FRGS) for predicting clinical outcome in lung adenocarcinoma
Cited by: 11
Author(s): Sheng Wang, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 8
Published: over 3 years ago

10.1186/1471-2164-11-349

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Cited by: 70
Author(s): RM Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel‐Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
Software Mentions: 7
Published: over 14 years ago

10.1371/journal.pone.0196836

Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: over 6 years ago

10.1016/j.jim.2016.02.023

Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1+ DCs in mouse and human and distinguishes them from Langerhans cells
Cited by: 44
Author(s): Sabrina Carpentier, Thien‐Phong Vu Manh, Rabie Chelbi, Sandrine Henri, Bernard Malissen, Muzlifah Haniffa, Florent Ginhoux, Marc Dalod
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0201751

Pancreatic cancer survival analysis defines a signature that predicts outcome
Cited by: 52
Author(s): Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydın Tözeren
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: almost 14 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

10.1038/s41398-020-0710-4

Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden
Cited by: 49
Author(s): Michael A. Mooney, Peter Ryabinin, Beth Wilmot, Priya Bhatt, Jonathan Mill, Joel T. Nigg
Software Mentions: 6
Published: almost 5 years ago

10.3390/jpm9020021

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.561086

Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes
Cited by: 6
Author(s): Elisabeth Findeiss, Sigrid C. Schwarz, Valentin Evsyukov, Thomas W. Rösler, Matthias Höllerhage, Tasnim Chakroun, Niko-Petteri Nykänen, Yimin Shen, Wolfgang Wurst, Michael Köhl, Jörg Tost, Günter U. Höglinger
Software Mentions: 6
Published: over 3 years ago

10.1002/1878-0261.12062

Methylation profiling of paediatric pilocytic astrocytoma reveals variants specifically associated with tumour location and predictive of recurrence
Cited by: 14
Author(s): Alexandra Sexton-Oates, Andrew Dodgshun, Volker Hovestadt, David Jones, David M. Ashley, Michael J. Sullivan, Duncan MacGregor, Richard Saffery
Software Mentions: 6
Published: over 6 years ago

10.1038/s41419-021-03738-0

A KDM4A-PAF1-mediated epigenomic network is essential for acute myeloid leukemia cell self-renewal and survival
Cited by: 18
Author(s): Matthew E. Massett, Laura Monaghan, Shaun Patterson, Niamh Mannion, Roderick P Bunschoten, Alex Hoose, Sandra Marmiroli, Rob M. J. Liskamp, Heather G. Jørgensen, David Vetrie, Alison M. Michie, Xu Huang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-19451-6

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma
Cited by: 20
Author(s): Nina P. Connolly, Amol C. Shetty, Jesse A. Stokum, Ina Hoeschele, Marni B. Siegel, C. Ryan Miller, Anthony J. Kim, Cheng‐Ying Ho, Eduardo Dávila, J. Marc Simard, Scott E. Devine, John H. Rossmeisl, Eric C. Holland, Jeffrey A. Winkles, Graeme F. Woodworth
Software Mentions: 6
Published: almost 7 years ago

10.1038/leu.2015.172

Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia
Cited by: 15
Author(s): Jonathan Sive, Silvia Basilico, Rebecca Hannah, Sarah Kinston, Fernando J. Calero-Nieto, Berthold Göttgens
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0075136

Synergistic Re-Activation of Epigenetically Silenced Genes by Combinatorial Inhibition of DNMTs and LSD1 in Cancer Cells
Cited by: 31
Author(s): Han Han, Xiaojing Yang, Kurinji Pandiyan, Gangning Liang
Software Mentions: 6
Published: about 11 years ago

10.1186/s13148-015-0097-x

DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array
Cited by: 15
Author(s): Cristina Gallego-Fábrega, Caty Carrera, Elena Muiño, Joan Montaner, Jurek Krupinski, Israel Fernández-Cadenas
Software Mentions: 6
Published: over 9 years ago

10.3390/jcm8010050

Efficacy of Integrating a Novel 16-Gene Biomarker Panel and Intelligence Classifiers for Differential Diagnosis of Rheumatoid Arthritis and Osteoarthritis
Cited by: 24
Author(s): Nguyen Phuoc Long, Seongoh Park, Nguyễn Hoàng Anh, Jung Eun Min, Sang Jun Yoon, Hyung Min Kim, Tran Diem Nghi, Dong Kyu Lim, Jeong Hill Park, Jong-Tae Lim, Sung Won Kwon
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2164-15-132

Major aging-associated RNA expressions change at two distinct age-positions
Cited by: 17
Author(s): Marius Gheorghe, M.M.J. Snoeck, Michael Emmerich, Thomas Bäck, Jelle J. Goeman, Vered Raz
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0044736

Brain Transcriptional and Epigenetic Associations with Autism
Cited by: 131
Author(s): Matthew R. Ginsberg, Robert A. Rubin, Tatiana Falcone, Angela H. Ting, Marvin R. Natowicz
Software Mentions: 5
Published: about 12 years ago

10.1186/s13059-015-0863-2

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
Cited by: 89
Author(s): Roser Vento‐Tormo, Carlos Company, Javier Rodríguez-Ubreva, Lorenzo de la Rica, José Urquiza, Biola M. Javierre, Radhakrishnan Sabarinathan, Ana Luque, Manel Esteller, Josep M. Aran, Damiana Álvarez-Errico, Esteban Ballestar
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pgen.1006643

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells
Cited by: 102
Author(s): Silva Kasela, Kai Kisand, Liina Tserel, Epp Kaleviste, Anu Remm, Krista Fischer, Tõnu Esko, Harm-Jan Westra, Benjamin P. Fairfax, Seiko Makino, Julian C. Knight, Lude Franke, Andres Metspalu, Pärt Peterson, Lili Milani
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0247669

Immune gene expression networks in sepsis: A network biology approach
Cited by: 13
Author(s): Kyung Soo Kim, Dong Wook Jekarl, Jaeeun Yoo, Seungok Lee, Myungshin Kim, Yonggoo Kim
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0230253

Comparing genome-scale DNA methylation and CNV marks between adult human cultured ITGA6+ testicular cells and seminomas to assess in vitro genomic stability
Cited by: 8
Author(s): Robert B. Struijk, Lambert C. J. Dorssers, Peter Henneman, Martin A. Rijlaarsdam, Andrea Venema, Aldo Jongejan, Marcel M.A.M. Mannens, Leendert H. J. Looijenga, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0024351

Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Cited by: 63
Author(s): Nancy Mah, Ying Wang, Mei-Chih Liao, Alessandro Prigione, Justyna Józefczuk, Björn Lichtner, Katharina Wolfrum, Manuela Haltmeier, Max Flöttmann, Martin H. Schaefer, Alexander Hahn, Ralf Mrowka, Edda Klipp, Miguel A. Andrade‐Navarro, James Adjaye
Software Mentions: 5
Published: about 13 years ago

10.1093/database/baaa012

CancerLivER: a database of liver cancer gene expression resources and biomarkers
Cited by: 19
Author(s): Harpreet Kaur, Sherry Bhalla, Dilraj Kaur, Gajendra P. S. Raghava
Software Mentions: 5
Published: almost 5 years ago

10.1038/s42003-021-02116-y

DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift
Cited by: 22
Author(s): Julia Franzen, Theodoros Georgomanolis, Anton Selich, Chao-Chung Kuo, Reinhard Stöger, Lilija Brant, Melita Sara Mulabdić, Eduardo Fernández-Rebollo, Clara Grezella, Alina Ostrowska, Matthias Begemann, Miloš Nikolić, Björn Rath, Anthony D. Ho, Michael Rothe, Axel Schambach, Argyris Papantonis, Wolfgang Wagner
Software Mentions: 5
Published: over 3 years ago

10.1038/srep31669

Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells
Cited by: 3
Author(s): Mariam El-Ashmawy, Melissa Coquelin, Krishna Luitel, Kimberly Batten, Jerry W. Shay
Software Mentions: 5
Published: over 8 years ago

10.1186/s13601-016-0105-z

Cow’s milk allergy in Dutch children: an epigenetic pilot survey
Cited by: 36
Author(s): Nicole C. M. Petrus, Peter Henneman, Andrea Venema, Adri N. Mul, Femke van Sinderen, Martin A. Haagmans, Olaf R.F. Mook, Raoul C. M. Hennekam, A. B. Sprikkelman, Marcel M.A.M. Mannens
Software Mentions: 5
Published: over 8 years ago

10.1186/1868-7083-6-4

Differences in smoking associated DNA methylation patterns in South Asians and Europeans
Cited by: 227
Author(s): Hannah R Elliott, Therese Tillin, Wendy L. McArdle, Karen Ho, Aparna Duggirala, Tim Frayling, George Davey Smith, Alun D. Hughes, Nish Chaturvedi, Caroline L Relton
Software Mentions: 5
Published: almost 11 years ago

10.1038/srep36055

Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions
Cited by: 28
Author(s): Betty Hebecker, Sebastian Vlaic, Theresia Conrad, Michael Bauer, Sascha Brunke, Mario Kapitan, Jörg Linde, Bernhard Hube, Ilse D. Jacobsen
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0174602

Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data
Cited by: 1
Author(s): Yunfeng Li, Jarrett Morrow, Benjamin A. Raby, Kelan G. Tantisira, Scott T. Weiss, Wei Huang, Weiliang Qiu
Software Mentions: 5
Published: over 7 years ago

10.1186/s12918-018-0671-x

Multi-omics integration reveals molecular networks and regulators of psoriasis
Cited by: 35
Author(s): Yuqi Zhao, Deepali Jhamb, Le Shu, Douglas Arneson, Deepak K. Rajpal, Xia Yang
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.07103

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0111819

Expression Analysis of All Protease Genes Reveals Cathepsin K to Be Overexpressed in Glioblastoma
Cited by: 39
Author(s): Urška Verbovšek, Helena Motaln, Ana Rotter, Nadia A. Atai, Kristina Gruden, C. J. F. Van Noorden, Tamara T. Lah
Software Mentions: 5
Published: about 10 years ago

10.1534/g3.116.028712

Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes
Cited by: 6
Author(s): Silvia N. Kariuki, John Blischak, Shigeki Nakagome, David B. Witonsky, Anna Di Rienzo
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-07238-0

T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders
Cited by: 32
Author(s): Jyoti Rani, Inna Mittal, Atreyi Pramanik, Namita Singh, Namita Dube, Smriti Sharma, Bhanwar Lal Puniya, Muthukurussi Varieth Raghunandanan, Ahmed Mobeen, Srinivasan Ramachandran
Software Mentions: 5
Published: over 7 years ago

10.1186/s13148-019-0637-x

Association of leukocyte DNA methylation changes with dietary folate and alcohol intake in the EPIC study
Cited by: 20
Author(s): Flavie Perrier, Vivian Viallon, Srikant Ambatipudi, Akram Ghantous, Cyrille Cuenin, Héctor Hernández-Vargas, Véronique Chajès, Laura Baglietto, Marco Matejcic, Hortensia Moreno-Macías, Tilman Kühn, Heiner Boeing, Anna Karakatsani, Αναστασία Κοτανίδου, Antonia Trichopoulou, Sabina Sieri, Salvatore Panico, Francesca Fasanelli, Martijn E.T. Dollé, N. Charlotte Onland‐Moret, Ivonne Sluijs, Elisabete Weiderpass, J. Ramón Quiŕos, Antonio Agudo, José María Huerta, Eva Ardanaz, Miren Dorronsoro, Tammy Y.N. Tong, Konstantinos K. Tsilidis, Elio Riboli, Marc J. Gunter, Zdenko Herceg, Pietro Ferrari, Isabelle Romieu
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2017.01351

Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16
Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2105-10-189

Platform dependence of inference on gene-wise and gene-set involvement in human lung development
Cited by: 3
Author(s): Rose Du, Kelan G. Tantisira, Vincent J. Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T. Kho, Barbara J. Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J. Mariani, J. Steven Leeder, Scott T. Weiss
Software Mentions: 4
Published: over 15 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

10.1186/1471-2407-13-58

Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients
Cited by: 79
Author(s): Liesbeth Hameetman, Suzan Commandeur, Jan Nico Bouwes Bavinck, Hermina C. Wisgerhof, Frank R. de Gruijl, Rein Willemze, Leon H.F. Mullenders, Cornelis P. Tensen, Harry Vrieling
Software Mentions: 4
Published: almost 12 years ago

10.3390/nu12123602

Epigenetic Patterns in Five-Year-Old Children Exposed to a Low Glycemic Index Dietary Intervention during Pregnancy: Results from the ROLO Kids Study
Cited by: 10
Author(s): Aisling A. Geraghty, A. Sexton-Oates, Eileen C. O’Brien, Richard Saffery, Fionnuala M. McAuliffe
Software Mentions: 4
Published: about 4 years ago

10.1186/1755-8794-6-51

Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia
Cited by: 26
Author(s): Eduardo Tejera, João Bernardes, Irene Rebelo
Software Mentions: 4
Published: about 11 years ago

10.3389/fcell.2021.717772

Human Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Acquire Rejuvenation and Reduced Heterogeneity
Cited by: 21
Author(s): Wasco Wruck, Nina Graffmann, Lucas‐Sebastian Spitzhorn, James Adjaye
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0029021

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Cited by: 72
Author(s): Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antònia Navarro, Diana Monsivais, John S. Coon, Julie Kim, Yang Dai, Serdar E. Bulun
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0111637

miR-27 Negatively Regulates Pluripotency-Associated Genes in Human Embryonal Carcinoma Cells
Cited by: 14
Author(s): Heiko Fuchs, Matthias Theuser, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 10 years ago

10.1186/1755-8794-7-39

Identification of Chiari Type I Malformation subtypes using whole genome expression profiles and cranial base morphometrics
Cited by: 22
Author(s): Christina A. Markunas, Eric F. Lock, Karen Soldano, Heidi Cope, Chien‐Kuang Cornelia Ding, David S. Enterline, Gerald A. Grant, Herbert E. Fuchs, Allison E. Ashley-Koch, Simon G. Gregory
Software Mentions: 4
Published: over 10 years ago

10.1186/s13045-017-0462-7

Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs
Cited by: 56
Author(s): Todd P. Knutson, Thu H. Truong, Shihong Ma, Nicholas J. Brady, Megan Sullivan, Ganesh V. Raj, Kathryn L. Schwertfeger, Carol A. Lange
Software Mentions: 4
Published: over 7 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

10.1038/s41598-020-80158-8

Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort
Cited by: 6
Author(s): Nikita Baiju, Torkjel M. Sandanger, Pål Sætrom, Therese Haugdahl Nøst
Software Mentions: 4
Published: almost 4 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

10.1371/journal.pone.0178151

Analysis of early mesothelial cell responses to Staphylococcus epidermidis isolated from patients with peritoneal dialysis-associated peritonitis
Cited by: 5
Author(s): Amanda L. McGuire, Kieran T. Mulroney, Christine Carson, Ram Ramesh, Grant Morahan, Aron Chakera
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-13-619

Molecular characterisation of cell line models for triple-negative breast cancers
Cited by: 63
Author(s): Anita Grigoriadis, Alan Mackay, Elodie Noël, Pei Jun Wu, Rachael Natrajan, Jessica Frankum, Jorge S. Reis‐Filho, Andrew Tutt
Software Mentions: 4
Published: almost 13 years ago

10.1186/1471-2164-14-475

Variable promoter methylation contributes to differential expression of key genes in human placenta-derived venous and arterial endothelial cells
Cited by: 30
Author(s): Jihoon E. Joo, Ursula Hiden, Luciana Lassance, Lavinia Gordon, David Martino, Gernot Desoyé, Richard Saffery
Software Mentions: 4
Published: over 11 years ago

10.1186/s12859-017-1915-2

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder
Cited by: 10
Author(s): Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chenglian Feng, Guang Fan
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-58779-w

A Group of Olfactory Receptor Alleles that Encode Full Length Proteins are Down-Regulated as Olfactory Sensory Neurons Mature
Cited by: 1
Author(s): Richard C. Krolewski, Brian M. Lin, Samuel D. Stampfer, Adam Packard, James E. Schwob
Software Mentions: 4
Published: almost 5 years ago

10.1186/1868-7083-4-20

Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease
Cited by: 41
Author(s): Justine A. Ellis, Jane Munro, Raul A Chavez, Lavinia Gordon, Jihoon E. Joo, Jonathan Akikusa, Roger C. Allen, Anne‐Louise Ponsonby, Jeffrey M Craig, Richard Saffery
Software Mentions: 4
Published: about 12 years ago

10.1038/srep29434

Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: over 8 years ago

10.1038/srep33752

Transcriptome meta-analysis reveals a dysregulation in extra cellular matrix and cell junction associated gene signatures during Dengue virus infection
Cited by: 27
Author(s): Sumbul Afroz, Jeevan Giddaluru, Mohd. Manzar Abbas, Nooruddin Khan
Software Mentions: 4
Published: about 8 years ago

10.1186/gb-2013-14-9-r99

PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
Cited by: 164
Author(s): Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul B.M.M.K. Islam, José Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar
Software Mentions: 4
Published: almost 12 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: about 6 years ago

10.1371/journal.pgen.1002604

Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
Cited by: 52
Author(s): Xiaojing Yang, Houtan Noushmehr, Han Han, Claudia Andreu-Vieyra, Gangning Liang, Peter A. Jones
Software Mentions: 4
Published: over 12 years ago

10.3390/cancers11020263

Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts
Cited by: 2
Author(s): Hanna Najgebauer, Andrew F. Jarnuczak, Andrea Varró, Christopher M. Sanderson
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1004642

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cited by: 80
Author(s): Alessio Iannetti, Adeline Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam J. Moore, Holger Hummerich, Benjamin E. Gewurz, Simon Cockell, Parmjit Jat, Elaine Willmore, Neil D. Perkins
Software Mentions: 4
Published: about 10 years ago

10.3390/cancers13112760

Follow-Up Study Confirms the Presence of Gastric Cancer DNA Methylation Hallmarks in High-Risk Precursor Lesions
Cited by: 3
Author(s): Antonio Gómez, Miguel L Pato, Luís Bujanda, Núria Sala, Osmel Companioni, Ángel Cosme, Martina Tufano, David Hanly, Nadia García, José Miguel Sanz‐Anquela, Javier P. Gisbert, Consuelo López, José Ignacio Elizalde, Míriam Cuatrecasas, Victòria Andreu, María José Paúles, María Dolores Martín-Arranz, Luís Ortega, Elvira Poves, Jesús Barrio, María Ángeles Torres, Guillermo Muñoz, Ángel Ferrández, María José Ramírez‐Lázaro, Sergio Lario, Carlos González, Manel Esteller, María Berdasco
Software Mentions: 4
Published: over 3 years ago

10.1002/reg2.48

Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in<i>Xenopus</i>embryos, axolotl regeneration, and human mesenchymal cell differentiation
Cited by: 51
Author(s): Vaibhav P. Pai, Christopher J. Martyniuk, Karen Echeverri, Sarah Sundelacruz, David L. Kaplan, Michael Levin
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.ppat.1009107

Mycolactone toxin induces an inflammatory response by targeting the IL-1β pathway: Mechanistic insight into Buruli ulcer pathophysiology
Cited by: 23
Author(s): Mélanie Foulon, Marie Robbe-Saule, Jérémy Manry, Lucille Esnault, Yan Boucaud, Alexandre Alcaïs, Marine Malloci, Martine Fanton d’Andon, Tiffany Beauvais, Nathalie Labarrière, Pascale Jeannin, Laurent Abel, Jean‐Paul Saint‐André, Anne Croué, Yves Delneste, Ivo Gomperts Boneca, Laurent Marsollier, Estelle Marion
Software Mentions: 4
Published: almost 4 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

10.3389/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/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/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/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/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

10.3389/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

10.3389/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

10.1186/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

10.18632/aging.101298

Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells
Cited by: 18
Author(s): Masaru Miyano, Rosalyn W. Sayaman, Marcus H. Stoiber, Chi‐Hui Lin, Martha R. Stampfer, James Brown, Mark A. LaBarge
Software Mentions: 3
Published: about 7 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

10.3389/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

10.1371/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

10.1186/1471-2407-10-126

The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer
Cited by: 54
Author(s): Robert Calaluce, Matthew M. Gubin, J. Wade Davis, Joseph Magee, Jing Chen, Yuki Kuwano, Myriam Gorospe, Ulus Atasoy
Software Mentions: 3
Published: over 14 years ago

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