bioconductor: biomaRt | Projects | Ecosyste.ms: Papers

10.3390/genes11040396

Domesticated gag Gene of Drosophila LTR Retrotransposons Is Involved in Response to Oxidative Stress
Cited by: 6
Author(s): Pavel A. Makhnovskii, Yevheniia Balakireva, Л. Н. Нефедова, А. Р. Лавренов, I. V. Kuzmin, Alexander Kim
Software Mentions: 3
Published: over 4 years ago

10.1016/j.csbj.2021.05.055

Genetic mapping of developmental trajectories for complex traits and diseases
Cited by: 1
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0203566

Epitranscriptomics: Correlation of N6-methyladenosine RNA methylation and pathway dysregulation in the hippocampus of HIV transgenic rats
Cited by: 8
Author(s): Yu Fu, Barry Zorman, Pavel Sumazin, Pietro Paolo Sanna, Vez Repunte‐Canonigo
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-2935-4

Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake
Cited by: 84
Author(s): Rebecca S. G. Kong, Guanxiang Liang, Yanhong Chen, Paul Stothard, Le Luo Guan
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-8-439

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets
Cited by: 38
Author(s): Claude Chelala, Stephan A. Hahn, Hannah J. Whiteman, Sayka Barry, Deepak Hariharan, Tomasz P. Radon, Nicholas R. Lemoine, Tatjana Crnogorac‐Jurčević
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2164-11-28

Regional regulation of transcription in the chicken genome
Cited by: 8
Author(s): Haisheng Nie, R.P.M.A. Crooijmans, J.W.M. Bastiaansen, Hendrik‐Jan Megens, Martien A. M. Groenen
Software Mentions: 3
Published: almost 15 years ago

10.3390/cancers12010200

Deep Sequencing Analysis Reveals Distinctive Non-Coding RNAs When Comparing Tumor Multidrug-Resistant Cells and Extracellular Vesicles with Drug-Sensitive Counterparts
Cited by: 13
Author(s): Diana Sousa, Rune Matthiesen, Raquel T. Lima, M. Helena Vasconcelos
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22179432

Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts
Cited by: 0
Author(s): Laurent Winckers, Chris T. Evelo, Egon Willighagen, Martina Kutmon
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0253864

The KrasG12D;Trp53fl/fl murine model of undifferentiated pleomorphic sarcoma is macrophage dense, lymphocyte poor, and resistant to immune checkpoint blockade
Cited by: 3
Author(s): Karys Hildebrand, Arvind K. Singla, Reid McNeil, Kayla L. Marritt, Kurt Hildebrand, Franz J. Zemp, Jahanara Rajwani, Doha Itani, Pinaki Bose, Douglas J. Mahoney, Frank R. Jirik, Michael J. Monument
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0076903

Genome-Wide Profiling of the Activity-Dependent Hippocampal Transcriptome
Cited by: 38
Author(s): Guido Hermey, Claudia Mahlke, Jakob J. Gutzmann, Jörg Schreiber, Nils Blüthgen, Dietmar Kuhl
Software Mentions: 3
Published: about 11 years ago

10.7554/eLife.46976

HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis
Cited by: 44
Author(s): Shuping Zhang, Alejandra Macias-Garcia, Jacob C. Ulirsch, Jason Velazquez, Vincent Butty, Stuart S. Levine, Vijay G. Sankaran, Jane-Jane Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-020-00905-1

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Cited by: 18
Author(s): Luisa Henkel, Benedikt Rauscher, Barbara Schmitt, J. Winter, Michael Boutros
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-021-07505-5

Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle
Cited by: 12
Author(s): Paulina G. Eusebi, Natalia Sevane, Thomas O’Rourke, Manuel Pizarro, Cédric Boeckx, S. Dunner
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-10-2

GenomeGraphs: integrated genomic data visualization with R
Cited by: 67
Author(s): Steffen Durinck, James Bullard, Paul T. Spellman, Sandrine Dudoit
Software Mentions: 3
Published: almost 16 years ago

10.7150/ijms.52256

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: <i>in silico</i> gene expression analysis
Cited by: 13
Author(s): Yen‐Hung Wu, I‐Jeng Yeh, Nam Nhut Phan, Meng‐Chi Yen, Hsin‐Liang Liu, Chih‐Yang Wang, Hui‐Ping Hsu
Software Mentions: 3
Published: almost 4 years ago

10.1093/gbe/evab160

Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis
Cited by: 2
Author(s): Megan Chan, Pranav S. Bhamidipati, Heather J. Goldsby, Arend Hintze, Hans A. Hofmann, Rebecca L. Young
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pntd.0008935

Dual RNAseq analyses at soma and germline levels reveal evolutionary innovations in the elephantiasis-agent Brugia malayi, and adaptation of its Wolbachia endosymbionts
Cited by: 3
Author(s): Germain Chevignon, Vincent Foray, Mercedes M. Pérez‐Jiménez, Silvia Libro, Matthew Chung, Jeremy M. Foster, Frédéric Landmann
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-017-3621-x

Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo
Cited by: 22
Author(s): Jesper L.V. Mååg, Dominik C. Kaczorowski, Debabrata Panja, Timothy J. Peters, Clive R. Bramham, Karin Wibrand, Marcel E. Dinger
Software Mentions: 3
Published: over 7 years ago

10.1186/s12920-019-0524-5

Exploiting orthology and de novo transcriptome assembly to refine target sequence information
Cited by: 3
Author(s): Julia F. Söllner, Germán Leparc, Matthias Zwick, Tanja Schönberger, Tobias Hildebrandt, Kay Nieselt, Eric J. Simon
Software Mentions: 3
Published: over 5 years ago

10.1093/emph/eoz015

Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication
Cited by: 6
Author(s): Samuel Pattillo Smith, Julie Baker Phillips, Maddison L Johnson, Patrick Abbot, John A. Capra, Antonis Rokas
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.33444

Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3
Cited by: 26
Author(s): Tiangong Lu, Armand Bankhead, Mats Ljungman, Nouri Neamati
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12987-019-0137-6

A perfusion bioreactor-based 3D model of the subarachnoid space based on a meningeal tissue construct
Cited by: 7
Author(s): Albert Neutzner, Laura Power, Markus Dürrenberger, Hendrik P. N. Scholl, Peter Meyer, Hanspeter E. Killer, David Wendt, Corina Kohler
Software Mentions: 3
Published: over 5 years ago

10.1186/s40364-018-0133-z

Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses
Cited by: 4
Author(s): Michelle E. Penney, Patrick S. Parfrey, Sevtap Savas, Yildiz E. Yilmaz
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giaa149

GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci
Cited by: 63
Author(s): Pablo Augusto de Souza Fonseca, Aroa Suárez-Vega, Gabriele Marras, Ángela Cánovas
Software Mentions: 3
Published: almost 4 years ago

10.1155/2015/146250

An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets
Cited by: 7
Author(s): Paolo Cremaschi, Roberta Carriero, Stefania Astrologo, Caterina Colì, Antonella Lisa, Silvia Parolo, Silvia Bione
Software Mentions: 3
Published: almost 10 years ago

10.1002/iid3.190

IL‐12 and IL‐15 induce the expression of CXCR6 and CD49a on peripheral natural killer cells
Cited by: 43
Author(s): Theresa Hydes, Angela Noll, Gabriela Salinas-Riester, Mohammed Abu-Hilal, Thomas Armstrong, Zaed Hamady, John Primrose, Arjun Takhar, Lutz Walter, Salim I. Khakoo
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1004383

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
Cited by: 1,738
Author(s): Claudia Giambartolomei, Damjan Vukcevic, Eric E. Schadt, Lude Franke, Aroon D. Hingorani, Chris Wallace, Vincent Plagnol
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-020-76026-0

Investigation of associations between Piezo1 mechanoreceptor gain-of-function variants and glaucoma-related phenotypes in humans and mice
Cited by: 6
Author(s): Sally L. Baxter, William T Keenan, Argus Athanas, James Proudfoot, Linda M. Zangwill, Radha Ayyagari, Jeffrey M. Liebmann, Christopher A. Girkin, Ardem Patapoutian, Robert N. Weinreb
Software Mentions: 3
Published: about 4 years ago

10.1172/jci.insight.125679

Angiocrine signals regulate quiescence and therapy resistance in bone metastasis
Cited by: 51
Author(s): Amit Singh, Vimal Veeriah, Pengjun Xi, Rossella Labella, Junyu Chen, Sara Romeo, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.97219

Unique features and clinical importance of acute alloreactive immune responses
Cited by: 8
Author(s): Charlotte Inman, Suzy Eldershaw, Joanne E. Croudace, Nathaniel J. Davies, Archana Sharma-Oates, Tanuja Rai, Hayden Pearce, Mirjana Sirovica, Y. L. Tracey Chan, Kriti Verma, Jianmin Zuo, Sandeep Nagra, Francesca Kinsella, Jane Nunnick, Rasoul Amel-Kashipaz, Charles Craddock, Ram Malladi, Paul Moss
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2019.10.131

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells
Cited by: 48
Author(s): Assaf Magen, Jia Nie, Thomas Ciucci, Samira Tamoutounour, Yongmei Zhao, Monika Mehta, Bao Tran, Dorian B. McGavern, Sridhar Hannenhalli, Rémy Bosselut
Software Mentions: 2
Published: almost 5 years ago

10.3390/cancers12082077

Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer
Cited by: 5
Author(s): Markus Glaß, Ágnes Dorn, Stefan Hüttelmaier, Monika Hämmerle, Tony Gutschner
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.688503

Response to Oxidative Burst-Induced Hypoxia Is Associated With Macrophage Inflammatory Profiles as Revealed by Cellular Genome-Wide Association
Cited by: 2
Author(s): Mehdi Emam, Saeid Tabatabaei, Mehdi Sargolzaei, Bonnie A. Mallard
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers12071808

Genomic and Transcriptomic Characterisation of Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer
Cited by: 12
Author(s): Sinéad Toomey, Jillian R. Gunther, Aoife Carr, David C. Weksberg, Valentina Thomas, Manuela Salvucci, Orna Bacon, El Masry Sherif, Joanna Fay, Elaine W. Kay, Katherine M. Sheehan, Deborah A. McNamara, Kevin E. Sanders, Geena Mathew, Oscar S. Breathnach, Liam Grogan, Patrick G. Morris, Wai Chin Foo, Yi Qian Nancy You, Jochen H M Prehn, Brian O’Neill, Sunil Krishnan, Bryan T. Hennessy, Simon J. Furney
Software Mentions: 2
Published: over 4 years ago

10.3389/fonc.2020.01206

Biological Landscape of Triple Negative Breast Cancers Expressing CTLA-4
Cited by: 20
Author(s): María G. C. Navarrete-Bernal, Mayte Guadalupe Cervantes-Badillo, José Fabián Martínez-Herrera, César Lara-Torres, Raquel Gerson-Cwilich, Alejandro Zentella‐Dehesa, Marı́a de Jesús Ibarra-Sánchez, José Esparza-López, Juan José Montesinos, Víctor Adrián Cortés-Morales, Diego Osorio-Pérez, Diana A. Villegas-Osorno, Eduardo Reyes-Sánchez, Pablo Salazar-Sojo, Luis F. Tallabs-Utrilla, Sandra Romero-Córdoba, Leticia Rocha‐Zavaleta
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22052622

TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues
Cited by: 359
Author(s): Áron Bartha, Balázs Győrffy
Software Mentions: 2
Published: over 3 years ago

10.3389/fvets.2021.662002

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course
Cited by: 5
Author(s): Kirsten E. McLoughlin, Carolina N. Correia, John A. Browne, David A. Magee, Nicolas C. Nalpas, Kévin Rue-Albrecht, Adam O. Whelan, Bernardo Villarreal‐Ramos, H. M. Vordermeier, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0028431

A Brain Region-Specific Predictive Gene Map for Autism Derived by Profiling a Reference Gene Set
Cited by: 19
Author(s): Ajay Kumar, Catherine Croft Swanwick, Nicole V. Johnson, Idan Menashe, Sharmila Basu, Michael E. Bales, Sharmila Banerjee-Basu
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0125934

Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples
Cited by: 41
Author(s): Sylvie Bourassa, Frédéric Fournier, Benjamin Nehmé, Isabelle Kelly, André Tremblay, Valéry Lemelin, Benoı̂t Lamarche, Patrick Couture, Arnaud Droit
Software Mentions: 2
Published: over 9 years ago

10.3390/genes10100770

A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity
Cited by: 3
Author(s): Sean M. Santos, Mert Icyuz, Ilya Pound, Doreen William, Jingyu Guo, Brett A. McKinney, Michael Niederweis, John W. Rodgers, John L. Hartman
Software Mentions: 2
Published: about 5 years ago

10.3390/genes11050535

Spatio-Temporal Roles of ASD-Associated Variants in Human Brain Development
Cited by: 3
Author(s): Yujin Kim, Joon Yong An
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0011990

Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates
Cited by: 20
Author(s): Haisheng Nie, R.P.M.A. Crooijmans, A. Lammers, Evert M. van Schothorst, Jaap Keijer, Pieter Neerincx, Jack A. M. Leunissen, Hendrik‐Jan Megens, Martien A. M. Groenen
Software Mentions: 2
Published: over 14 years ago

10.1186/gb-2006-7-7-r66

Cited by: 277
Author(s): Michael Boutros, Lı́gia P. Brás, Wolfgang Huber
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pone.0171661

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer
Cited by: 88
Author(s): Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1006225

Intra-patient Inter-metastatic Genetic Heterogeneity in Colorectal Cancer as a Key Determinant of Survival after Curative Liver Resection
Cited by: 55
Author(s): Anita Sveen, Inger Marie Løes, Sharmini Alagaratnam, Gro Nilsen, Maren Høland, Ole Christian Lingjærde, Halfdan Sørbye, Kaja Christine Graue Berg, Arild Horn, Jon Helge Angelsen, Stian Knappskog, Per Eystein Lønning, Ragnhild Lothe
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-9-26

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'
Cited by: 44
Author(s): Aléxandre Kuhn, Ruth Lüthi-Carter, Mauro Delorenzi
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pgen.1003514

Impact of Natural Genetic Variation on Gene Expression Dynamics
Cited by: 35
Author(s): Marit Ackermann, Weronika Sikora-Wohlfeld, Andreas Beyer
Software Mentions: 2
Published: over 11 years ago

10.3390/jcm8081160

Identification of Prognostic Candidate Genes in Breast Cancer by Integrated Bioinformatic Analysis
Cited by: 56
Author(s): Charles C.N. Wang, Chia‐Ying Li, Jia-Hua Cai, Phillip C.-Y. Sheu, Jeffrey J. P. Tsai, Meng‐Yu Wu, Chia-Jung Li, Ming‐Feng Hou
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1000121

Advanced Genomic Data Mining
Cited by: 12
Author(s): Xosé M. Fernández‐Suárez, Ewan Birney
Software Mentions: 2
Published: about 16 years ago

10.14814/phy2.13831

Effects of bone marrow-derived mesenchymal stromal cells on gene expression in human alveolar type II cells exposed to TNF-α , IL-1β , and IFN-γ
Cited by: 6
Author(s): Matthew Schwede, Erin M. Wilfong, Rachel L. Zemans, Patricia Lee, Claudia C. dos Santos, Xiaohui Fang, Michael A. Matthay
Software Mentions: 2
Published: over 6 years ago

10.1038/srep13629

RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli
Cited by: 37
Author(s): Nicolas C. Nalpas, David A. Magee, Kevin M. Conlon, John A. Browne, Claire Healy, Kirsten E. McLoughlin, Kévin Rue-Albrecht, Paul A. McGettigan, Kate E. Killick, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 2
Published: about 9 years ago

10.1038/srep24658

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2
Cited by: 27
Author(s): Bilge San, Naomi D. Chrispijn, Nadine Wittkopp, Simon J. van Heeringen, Anne Karine Lagendijk, Marco Aben, Jeroen Bakkers, René F. Ketting, Leonie M. Kamminga
Software Mentions: 2
Published: over 8 years ago

10.1038/srep25696

Principal components analysis and the reported low intrinsic dimensionality of gene expression microarray data
Cited by: 59
Author(s): Michael Lenz, Franz‐Josef Müller, Martin Zenke, Andreas Schuppert
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.11513

Epithelial-mesenchymal transition and nuclear β-catenin induced by conditional intestinal disruption of Cdh1 with Apc is E-cadherin EC1 domain dependent
Cited by: 4
Author(s): Julia Anne Helen Matheson, Claudia Bühnemann, Emma Carter, David Barnes, H. H. Hoppe, Judy Hughes, Stephen Cobbold, J. A. Harper, Hans Morreau, Mirvat Surakhy, A. Bassim Hassan
Software Mentions: 2
Published: about 8 years ago

10.1038/srep30975

Thermal fluctuations affect the transcriptome through mechanisms independent of average temperature
Cited by: 48
Author(s): Jesper Givskov Sørensen, Mads Fristrup Schou, Torsten Nygaard Kristensen, Volker Loeschcke
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-015-0455-x

Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets
Cited by: 1
Author(s): Umesh K. Nandal, Wytze J. Vlietstra, Carsten Byrman, Rienk E. Jeeninga, Jeffrey H. Ringrose, Antoine H. C. van Kampen, Dave Speijer, Perry D. Moerland
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-018-32146-2

A comprehensive manually-curated compendium of bovine transcription factors
Cited by: 15
Author(s): Marcela Maria de Souza, Adhemar Zerlotini, Ludwig Geistlinger, P. C. Tizioto, Taylor Jf, M. I. P. Rocha, Wellison J. S. Diniz, Luiz Lehmann Coutinho, Luciana Correia de Almeida Regitano
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-50592-4

The PAX3-FOXO1 oncogene alters exosome miRNA content and leads to paracrine effects mediated by exosomal miR-486
Cited by: 29
Author(s): Farah Ghamloush, Sandra E. Ghayad, Ghina Rammal, Assil Fahs, Abeer J. Ayoub, Zeina Merabi, Mohamad Harajly, Hassan Zalzali, Raya Saab
Software Mentions: 2
Published: about 5 years ago

10.1016/S2666-5247(21)00146-4

Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection: a nested, case-control diagnostic accuracy study
Cited by: 35
Author(s): Gupta Rk, Joshua Rosenheim, Lucy Bell, Aneesh Chandran, José Afonso Guerra‐Assunção, Gabriele Pollara, Matthew Whelan, Jessica Artico, George Joy, Hibba Kurdi, Daniel M. Altmann, Rosemary J. Boyton, Mala K. Maini, Áine McKnight, Jonathan Lambourne, Teresa Cutiño-Moguel, Charlotte Manisty, Thomas A. Treibel, James Moon, Benjamin M. Chain, Mahdad Noursadeghi, Hakam Abbass, Aderonke Abiodun, Mashael Alfarih, Zoe Alldis, Oliver E. Amin, Mervyn Andiapen, João Augusto, Georgiana Luisa Baca, Sasha N. L. Bailey, Anish Bhuva, Alex Boulter, Ruth Bowles, Olivia V Bracken, Ben O’Brien, Tim Brooks, Natalie Bullock, David K. Butler, Gabriella Captur, Nicola Champion, Carmen Chan, David Collier, Jorge Couto de Sousa, Xosé Couto-Parada, Rhodri H. Davies, Brooke Douglas, Cecilia Di Genova, Keenan Dieobi‐Anene, Mariana O. Diniz, Anaya Ellis, Karen Feehan, Malcolm Finlay, Marianna Fontana, Nasim Forooghi, Celia Gaier, Joseph M. Gibbons, Derek W. Gilroy, Matt Hamblin, Gabrielle Harker, Jacqueline Hewson, Lauren M. Hickling, Aroon D. Hingorani, Lee Howes, Alun Hughes, Gemma Hughes, Rebecca Hughes, Ivie Itua, Victor Jardim, Wing-Yiu Jason Lee, Melaniepetra Jensen, Jessica Jones, Meleri Jones, Vikas Kapil, Kai‐Min Lin, Sarah Louth, Vineela Mandadapu, Katia Menacho, Celina Mfuko, Oliver Mitchelmore, Christopher Moon, Diana Muñoz Sandoval, Sam M. Murray, Ashley Otter, Corinna Pade, Susana Palma, Ruth Parker, Kush Patel, Babita Pawarova, Steffen E. Petersen, Brian Piniera, Franziska P. Pieper, Daniel Pope, Maria Prossora, Lisa Rannigan, Alicja Rapala, Catherine J. Reynolds, Amy Richards, Matthew Robathan, Genine Sambile, Nathalie M. Schmidt, Amanda Semper, Andreas Seraphim, Mihaela Simion, Angelique Smit, Michelle A. Sugimoto, Leo Swadling, Stephen Taylor, Nigel Temperton, Stephen J. Thomas, George Thornton, Art Tucker, Jessry Veerapen, Mohit Vijayakumar, Sophie Welch, Theresa Wodehouse, Lucinda Wynne, Dan Zahedi
Software Mentions: 2
Published: about 3 years ago

10.1186/s12933-019-0918-x

Significance of circulating microRNAs in diabetes mellitus type 2 and platelet reactivity: bioinformatic analysis and review
Cited by: 103
Author(s): Justyna Pordzik, Daniel Jakubik, Joanna Jarosz-Popek, Zofia Wicik, Ceren Eyileten, Salvatore De Rosa, Ciro Indolfi, Jolanta M. Siller‐Matula, Pamela Czajka, Marek Postuła
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-017-1672-2

Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer
Cited by: 20
Author(s): Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
Software Mentions: 2
Published: over 7 years ago

10.1155/2016/5469371

Analyzing the miRNA-Gene Networks to Mine the Important miRNAs under Skin of Human and Mouse
Cited by: 5
Author(s): Jianghong Wu, Husile Gong, Yongsheng Bai, Wenguang Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-021-82522-8

Detection of selection signatures for response to Aleutian mink disease virus infection in American mink
Cited by: 13
Author(s): Karim Karimi, A. Farid, Sean Myles, Younes Miar
Software Mentions: 2
Published: almost 4 years ago

10.3390/biology10080760

Survival-Based Biomarker Module Identification Associated with Oral Squamous Cell Carcinoma (OSCC)
Cited by: 14
Author(s): Prithvi Singh, Arpita Rai, Amit Kumar Verma, Mohammed A Alsahli, Arshad Husain Rahmani, Saleh A. Almatroodi, Faris Alrumaihi, Kapil Dev, Anuradha Sinha, Shweta Sankhwar, Ravins Dohare
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.27083

CpG promoter hypo-methylation and up-regulation of microRNA-190b in hormone receptor-positive breast cancer
Cited by: 2
Author(s): Elisabet Alexandra Frick, Thorkell Gudjonsson, Jórunn E. Eyfjörd, Jón Gunnlaugur Jónasson, Laufey Tryggvadóttír, Olafur A. Stefansson, Stefan Sigurdsson
Software Mentions: 2
Published: over 5 years ago

10.1186/1752-0509-8-74

Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression
Cited by: 17
Author(s): Trish P Tran, Edison Ong, Andrew Hodges, Giovanni Paternostro, Carlo Piermarocchi
Software Mentions: 2
Published: over 10 years ago

10.1038/s41398-021-01231-y

Multi-omic and multi-species meta-analyses of nicotine consumption
Cited by: 12
Author(s): Rohan Palmer, Chelsie E. Benca-Bachman, Spencer B. Huggett, Jason A. Bubier, John E. McGeary, Nikhil Ramgiri, Jenani Srijeyanthan, Jingjing Yang, Peter M. Visscher, Jian Yang, Valerie S. Knopik, Elissa J. Chesler
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-11-547

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia
Cited by: 66
Author(s): Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, Laurent Duret, Aurélie Kapusta, Éric Meyer, Linda Sperling
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-9-443

Gene expression profiling of liver from dairy cows treated intra-mammary with lipopolysaccharide
Cited by: 57
Author(s): Li Jiang, Peter Sørensen, Christine M. Røntved, L. Vels, K.L. Ingvartsen
Software Mentions: 2
Published: about 16 years ago

10.3892/ijmm.2014.1843

Comprehensive identification of essential pathways and transcription factors related to epilepsy by gene set enrichment analysis on microarray datasets
Cited by: 8
Author(s): Kan He, Weizhong Xiao, Wen Lv
Software Mentions: 2
Published: over 10 years ago

10.1093/jhered/esaa021

X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone
Cited by: 6
Author(s): Marcella D. Baiz, Priscilla K. Tucker, Jacob L. Mueller, Liliana Cortés‐Ortiz
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-07202-9

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns
Cited by: 0
Author(s): Yuan Lu, Mikki Boswell, William Boswell, Raquel Y. Salinas, Markita Savage, José Carlos Castañeda Reyes, Sean M. Walter, R. William Marks, Trevor J. Gonzalez, Geraldo Medrano, Wesley C. Warren, Manfred Schartl, Ronald B. Walter
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-15-S12-S2

Time-course human urine proteomics in space-flight simulation experiments
Cited by: 22
Author(s): Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S. Tiys, В. А. Иванисенко, Н. А. Колчанов, Alexey Kononikhin, Igor Popov, E. N. Nikolaev, Л. Х. Пастушкова, И. М. Ларина
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-15-39

Integrated transcriptome analysis of mouse spermatogenesis
Cited by: 116
Author(s): Gennady Margolin, Pavel P. Khil, Joongbaek Kim, Marina A. Bellani, R. Daniel Camerini‐Otero
Software Mentions: 2
Published: almost 11 years ago

10.3390/nu13092923

Moringa Oleifera Seed Extract Concomitantly Supplemented with Chemotherapy Worsens Tumor Progression in Mice with Triple Negative Breast Cancer and Obesity
Cited by: 9
Author(s): Elizabeth R. M. Zunica, Shengping Yang, Ann A. Coulter, Christy L. White, John P. Kirwan, L Anne Gilmore
Software Mentions: 2
Published: about 3 years ago

10.3389/fgene.2018.00746

A Comprehensive Analysis of Fibroblast Growth Factor Receptor 2b Signaling on Epithelial Tip Progenitor Cells During Early Mouse Lung Branching Morphogenesis
Cited by: 36
Author(s): Matthew R. Jones, Salma Dilai, Arun Lingampally, Cho-Ming Chao, Soula Danopoulos, Gianni Carraro, Regina T. Mukhametshina, Jochen Wilhelm, Eveline Baumgart-Vogt, Denise Al Alam, Chengshui Chen, Parviz Minoo, Jin San Zhang, Savério Bellusci
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12863-019-0739-7

Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype
Cited by: 2
Author(s): Fang Shao, Yaqi Wang, Yang Zhao, Sheng Yang
Software Mentions: 2
Published: over 5 years ago

10.3389/fendo.2021.694893

New Insights Into Mitochondrial Dysfunction at Disease Susceptibility Loci in the Development of Type 2 Diabetes
Cited by: 5
Author(s): Hannah Maude, Winston Lau, Nikolas Maniatis, Toby Andrew
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2020.576604

Fgf10 Signaling-Based Evidence for the Existence of an Embryonic Stage Distinct From the Pseudoglandular Stage During Mouse Lung Development
Cited by: 7
Author(s): Sara Taghizadeh, Matthew R. Jones, Ruth Olmer, Saskia Ulrich, Soula Danopoulos, Chengguo Shen, Chaolei Chen, Jochen Wilhelm, Ulrich Martin, Chengshui Chen, Denise Al Alam, Savério Bellusci
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2021.694033

Lifespan-Associated Gene Expression Signatures of Recombinant BXD Mice Implicates Coro7 and Set in Longevity
Cited by: 7
Author(s): Davide Vitiello, Alexander Dakhovnik, Cyril Statzer, Collin Y. Ewald
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00160

Predicting Stage-Specific Recurrent Aberrations From Somatic Copy Number Dataset
Cited by: 2
Author(s): Chaima Aouiche, Bolin Chen, Xuequn Shang
Software Mentions: 2
Published: over 4 years ago

10.3390/cells9051274

Evidence for Overlapping and Distinct Biological Activities and Transcriptional Targets Triggered by Fibroblast Growth Factor Receptor 2b Signaling between Mid- and Early Pseudoglandular Stages of Mouse Lung Development
Cited by: 12
Author(s): Matthew R. Jones, Arun Lingampally, Jin Wu, Jamschid Sedighi, Negah Ahmadvand, Jochen Wilhelm, Ana Ivonne Vazquez‐Armendariz, Susanne Herold, Chengshui Chen, Jin‐San Zhang, Savério Bellusci, Cho-Ming Chao
Software Mentions: 2
Published: over 4 years ago

10.3390/cells9092143

miR-9-Mediated Inhibition of EFEMP1 Contributes to the Acquisition of Pro-Tumoral Properties in Normal Fibroblasts
Cited by: 12
Author(s): Giulia Cosentino, Sandra Romero-Córdoba, Ilaria Plantamura, Alessandra Cataldo, Marilena V. Iorio
Software Mentions: 2
Published: about 4 years ago

10.1007/s00018-019-03066-9

Stabilization of E2-EPF UCP protein is implicated in hepatitis B virus-associated hepatocellular carcinoma progression
Cited by: 5
Author(s): Jung Hwa Lim, Dae–Ghon Kim, Dae–Yeul Yu, Hyun Mi Kang, Kyung Hee Noh, Dae‐Soo Kim, Dongmin Park, Tae Kyung Chang, Dong-Soo Im, Cho‐Rok Jung
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.633812

Immunogenomic Profiling Demonstrate AC003092.1 as an Immune-Related eRNA in Glioblastoma Multiforme
Cited by: 11
Author(s): Xiaoyu Guo, Sheng Zhong, Zhenning Wang, Tian Xie, Hao Duan, Jiayu Zhang, Guanhua Zhang, Lingming Liang, Run Cui, Hongrong Hu, Jie Lü, Yi Hui Wu, Jiajun Dong, Zhenqiang He, Yonggao Mou
Software Mentions: 1
Published: over 3 years ago

10.1186/s13040-015-0063-3

DAPPER: a data-mining resource for protein-protein interactions
Cited by: 6
Author(s): Syed Haider, Zoltán Lipinszki, Marcin R. Przewloka, Yaseen Ladak, Pier Paolo D’Avino, Yuu Kimata, Píetro Lió, David M. Glover
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-020-0718-7

The pan-cancer landscape of prognostic germline variants in 10,582 patients
Cited by: 20
Author(s): Ajay Chatrath, Roza Przanowska, Shashi Kiran, Zhangli Su, Shekhar Saha, Briana Wilson, Tsunematsu Takemoto, Ji-Hye Ahn, Kyung Yong Lee, Teressa Paulsen, Ewelina Sobierajska, Manjari Kiran, Xiwei Tang, Tianxi Li, Pankaj Kumar, Aakrosh Ratan, Anindya Dutta
Software Mentions: 1
Published: almost 5 years ago

10.1186/1752-0509-8-83

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer
Cited by: 203
Author(s): Paola Paci, Teresa Colombo, Lorenzo Farina
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0177004

Gene expression of behaviorally relevant genes in the cerebral hemisphere changes after selection for tameness in Red Junglefowl
Cited by: 9
Author(s): Johan Bélteky, Beatrix Agnvall, Per Jensen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1008461

The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)
Cited by: 24
Author(s): Alexandra M. Sparks, Kathryn Watt, Rona Sinclair, Jill G. Pilkington, Josephine M. Pemberton, Tom N. McNeilly, Daniel H. Nussey, Susan E. Johnston
Software Mentions: 1
Published: about 5 years ago

10.1038/s41398-020-00866-7

The role of rare compound heterozygous events in autism spectrum disorder
Cited by: 1
Author(s): Bochao Lin, Fabrice Colas, Isaäc J. Nijman, Jelena Medic, William J. Brands, Jeremy Parr, Kristel R. van Eijk, Sabine M. Klauck, Andreas G. Chiocchetti, Christine M. Freitag, Elena Maestrini, Elena Bacchelli, Hilary Coon, Astrid M. Vicente, Guiomar Oliveira, Alistair T. Pagnamenta, Louise Gallagher, Sean Ennis, Richard Anney, Thomas Bourgeron, Jurjen J. Luykx, Jacob Vorstman
Software Mentions: 1
Published: over 4 years ago

10.3389/fnins.2021.704785

Early Life Adversity and Polygenic Risk for High Fasting Insulin Are Associated With Childhood Impulsivity
Cited by: 6
Author(s): Aashita Batra, Lawrence M. Chen, Zihan Wang, Carine Parent, Irina Pokhvisneva, Sachin Patel, Robert D. Levitan, Michael J. Meaney, Patrícia Pelufo Silveira
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2148-12-45

Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks
Cited by: 47
Author(s): Robert H. S. Kraus, Hindrik H. D. Kerstens, Pim van Hooft, Hendrik‐Jan Megens, Johan Elmberg, Arseny Tsvey, Dmitry Sartakov, S. A. Soloviev, R.P.M.A. Crooijmans, Martien A. M. Groenen, Ronald C. Ydenberg, Herbert H. T. Prins
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13073-018-0522-9

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels
Cited by: 26
Author(s): Timothy O’Brien, Peilin Jia, Neil E. Caporaso, Maria Teresa Landi, Zhongming Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2835-0

Cross-population analysis for functional characterization of type II diabetes variants
Cited by: 2
Author(s): Dalia Elmansy, Mehmet Koyutürk
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-532

Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs
Cited by: 47
Author(s): Xiaoling Zhang, Hinco J. Gierman, Daniel Levy, Andrew S. Plump, Radu Dobrin, Harald H.H. Göring, Joanne E. Curran, Matthew P. Johnson, John Blangero, Stuart K. Kim, Christopher J. O’Donnell, Valur Emilsson, Andrew D. Johnson
Software Mentions: 1
Published: over 10 years ago

10.1186/1756-9966-31-24

An integrated analysis of miRNA and gene copy numbers in xenografts of Ewing's sarcoma
Cited by: 32
Author(s): Neda Mosakhani, Mohamed Guled, Gayle Leen, Silvia Calabuig, Tarja Niini, Isidro Machado, Suvi Savola, Katia Scotlandi, José Antonio Löpez‐Guerrero, Antonio Llombart‐Bosch, Sakari Knuutila
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0169594

A Hypothesis Testing Based Method for Normalization and Differential Expression Analysis of RNA-Seq Data
Cited by: 8
Author(s): Yan Zhou, Guochang Wang, Jun Zhang, Han Li
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0001763

Transcriptomic Signature of Leishmania Infected Mice Macrophages: A Metabolic Point of View
Cited by: 99
Author(s): Imen Rabhi, Sameh Rabhi, Rym Ben‐Othman, Axel Rasche, Adriani Daskalaki, Bernadette Trentin, David Piquemal, Béatrice Regnault, Albert Descoteaux, Lamia Guizani-Tabbane
Software Mentions: 1
Published: over 12 years ago

10.3892/ijmm.2015.2220

Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset
Cited by: 13
Author(s): Kan He, Wen Lv, Qingqing Zhang, Yuqing Wang, Liming Tao, Dahai Liu
Software Mentions: 1
Published: over 9 years ago

Projects: bioconductor: biomaRt

Papers Mentioning biomaRt 446