bioconductor: affy | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.514363

Prognostic and Predictive Value of an Immunoscore Signature in Glioblastoma Multiform
Cited by: 8
Author(s): Xiangjun Tang, Pengfei Xu, Ann Chen, Gang Deng, Shenqi Zhang, Lun Gao, Long‐Jun Dai, Qianxue Chen
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

10.1186/1471-2105-13-56

'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences
Cited by: 5
Author(s): Michael Dannemann, Michael Lachmann, Anna Lorenc
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-021-86207-0

Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
Cited by: 17
Author(s): Peng-Fei Zheng, Lu-Zhu Chen, Yao-Zong Guan, Peng Liu
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.103172

Overexpression of miR-142-5p inhibits the progression of nonalcoholic steatohepatitis by targeting TSLP and inhibiting JAK-STAT signaling pathway
Cited by: 12
Author(s): Chao Zhou, Pu Wang, Lei Lei, Yi Huang, Yue Wu
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1003503

HDAC7 Is a Repressor of Myeloid Genes Whose Downregulation Is Required for Transdifferentiation of Pre-B Cells into Macrophages
Cited by: 55
Author(s): Bruna Barneda-Zahonero, Lidia Román-González, Olga Collazo, Hasan Rafati, Abul B.M.M.K. Islam, Lars H. Bussmann, Alessandro Di Tullio, Luisa I. De Andres, Thomas Graf, Núria López‐Bigas, Tokameh Mahmoudi, Maribel Parra
Software Mentions: 4
Published: over 11 years ago

10.1186/s12859-019-3140-7

Multiplatform biomarker identification using a data-driven approach enables single-sample classification
Cited by: 5
Author(s): Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola
Software Mentions: 4
Published: about 5 years ago

10.1186/s12916-017-0851-3

Comprehensive DNA methylation study identifies novel progression-related and prognostic markers for cutaneous melanoma
Cited by: 55
Author(s): Jasper Wouters, Miguel Vizoso, Anna Martínez-Cardús, Francesc Carmona, Olivier Govaere, Teresa Laguna, Jesuchristopher Joseph, Peter Dynoodt, Claudia Aura, Mona Foth, Roy H. E. Cloots, Karin van den Hurk, Balázs Bálint, Ian Murphy, Enda McDermott, Kieran Sheahan, Karin Jirström, Björn Nodin, Girish Mallya-Udupi, Joost J. van den Oord, William M. Gallagher, Manel Esteller
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-8-273

The utility of MAS5 expression summary and detection call algorithms
Cited by: 144
Author(s): Stuart D Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller
Software Mentions: 4
Published: over 17 years ago

10.3389/fgene.2021.608936

Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy
Cited by: 6
Author(s): Zhongchao Gai, Yujiao Wang, Lü Tian, Guoli Gong, Jieqiong Zhao
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.36998

Downregulation of ribosome biogenesis during early forebrain development
Cited by: 63
Author(s): Kevin F. Chau, Morgan L. Shannon, Ryann M. Fame, Erin Fonseca, Hillary Mullan, Matthew B. Johnson, Anoop K. Sendamarai, Mark W. Springel, Laurent Beaugerie, Maria K. Lehtinen
Software Mentions: 4
Published: over 6 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.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1002074

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex
Cited by: 53
Author(s): Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua Julie Zhu, Inmaculada M. Barrasa, Melissa M. Harrison, Robert Horvitz, Albertha J.M. Walhout, Kirsten Hagstrom
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pgen.1006593

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease
Cited by: 99
Author(s): Fiona Kerr, Oyinkan Sofola-Adesakin, Dobril Ivanov, Jemma Gatliff, Beatriz Gomez Perez‐Nievas, Hélène Bertrand, Pedro Martı́nez, Rebecca Callard, Inge Snoeren, Helena M. Cochemé, Jennifer Adcott, Mobina Khericha, Jorge Iván Castillo-Quan, Geoff Wells, Wendy Noble, Janet M. Thornton, Linda Partridge
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.631982

Integrated Protein–Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma
Cited by: 13
Author(s): Li Tian, Tong Chen, Jiaju Lü, Jing Yan, Yuting Zhang, Peifang Qin, Sentai Ding, Yali Zhou
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-10869-y

Functional prediction of long non-coding RNAs in ovarian cancer-associated fibroblasts indicate a potential role in metastasis
Cited by: 33
Author(s): Fatemeh Vafaee, Emily K. Colvin, Samuel C. Mok, Viive M. Howell, Goli Samimi
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-10-363

Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor
Cited by: 56
Author(s): Anita Zamboni, Pamela Gatto, Alessandro Cestaro, S. Pilati, Roberto Viola, Fulvio Mattivi, C. Moser, Riccardo Velasco
Software Mentions: 4
Published: over 15 years ago

10.1038/srep18616

Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer
Cited by: 15
Author(s): Ning An, Xue Yang, Shujun Cheng, Guiqi Wang, Kaitai Zhang
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0227193

Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth
Cited by: 22
Author(s): Aishwarya P. Yadama, Hooman Mirzakhani, Thomas F. McElrath, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-1964-8

A genetic framework for H2O2 induced cell death in Arabidopsis thaliana
Cited by: 40
Author(s): Eve Kaurilind, Enjun Xu, Mikael Brosché
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.ppat.1004635

IFNγ Signaling Endows DCs with the Capacity to Control Type I Inflammation during Parasitic Infection through Promoting T-bet+ Regulatory T Cells
Cited by: 24
Author(s): Hyang-Mi Lee, Anne Fleige, Ruth Forman, Sunglim Cho, Aly A. Khan, Ling-Li Lin, Duc T. Nguyen, Aisling O’Hara Hall, Zhinan Yin, Christopher A. Hunter, Werner Müller, Li-Fan Lu
Software Mentions: 4
Published: almost 10 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

10.1186/1471-2105-16-S17-S5

A computational method for drug repositioning using publicly available gene expression data
Cited by: 4
Author(s): K M Shabana, K. A. Abdul Nazeer, Meeta Pradhan, Mathew Palakal
Software Mentions: 4
Published: almost 9 years ago

10.1242/jcs.181248

Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells <i>via</i> p65 and H2B phosphorylation
Cited by: 11
Author(s): Jasmine Li, Kristine Hardy, Chansavath Phetsouphanh, Wen Juan Tu, Elissa L Sutcliffe, Robert McCuaig, Christopher R Sutton, Anjum Zafar, C. Mee Ling Munier, John Zaunders, Xu Yin, Angelo Theodoratos, Abel Tan, Pek Siew Lim, Tobias Knaute, Antonia Masch, Johannes Zerweck, Vedran Brezar, Peter J. Milburn, Jenny C. Dunn, Marco G. Casarotto, Stephen J. Turner, Nabila Seddiki, Anthony D. Kelleher, Sudha Rao
Software Mentions: 4
Published: almost 9 years ago

10.1289/ehp.1002546

Global Gene Expression Profiling of a Population Exposed to a Range of Benzene Levels
Cited by: 94
Author(s): Cliona M. McHale, Luoping Zhang, Qing Lan, Roel Vermeulen, Guilan Li, Alan Hubbard, Kristin E. Porter, Reuben Thomas, Christopher J. Portier, Min Shen, Stephen M. Rappaport, Shu Yin, Martyn T. Smith, Nathaniel Rothman
Software Mentions: 4
Published: over 13 years ago

10.1242/dmm.034850

Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis
Cited by: 21
Author(s): Soo-Hyun Kim, Richard P. Redvers, Lap Hing, Xiawei Ling, Andrew J. Lucke, Robert C. Reid, David P. Fairlie, Ángel G. Martín, Robin L. Anderson, Delphine Denoyer, Normand Pouliot
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2164-13-380

The carbon starvation response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome
Cited by: 107
Author(s): Benjamin Nitsche, Tina Jørgensen, Michiel Akeroyd, Vera Meyer, Arthur F. J. Ram
Software Mentions: 4
Published: almost 13 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

10.3389/fcell.2020.588368

A Novel Signature Constructed by RNA-Binding Protein Coding Genes to Improve Overall Survival Prediction of Glioma Patients
Cited by: 11
Author(s): Zewei Tu, Lei Shu, Jingying Li, Lei Wu, Chuming Tao, Minhua Ye, Xingen Zhu, Kai Huang
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.ppat.1002949

Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor
Cited by: 54
Author(s): Debrah A. Fine, Orit Rozenblatt-Rosen, Megha Padi, Anna Korkhin, Robert James, Guillaume Adelmant, Rosa Yoon, Lifei Guo, Christian Berrios, Ying Zhang, Michael A. Calderwood, Soundarapandian Velmurgan, Jingwei Cheng, Jarrod A. Marto, David E. Hill, Michael E. Cusick, Marc Vidal, Laurence Florens, Michael P. Washburn, Larisa Litovchick, James A. DeCaprio
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-018-27376-3

Transcriptional analysis of adipose tissue during development reveals depot-specific responsiveness to maternal dietary supplementation
Cited by: 16
Author(s): Hernan P. Fainberg, Mark Birtwistle, Reham I. Alagal, Ahmad Alhaddad, Mark Pope, Graeme R. Davies, Rachel Woods, Marcos Castellanos, Sean May, Catharine A. Ortori, David A. Barrett, V.E.A. Perry, Frank Wiens, Bernd Stahl, Eline van der Beek, Harold S. Sacks, Helen Budge, Michael Symonds
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-12-589

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments
Cited by: 30
Author(s): Robert Kitchen, Victoria Sabine, Arthur A. Simen, JM Dixon, John M.S. Bartlett, Andrew H. Sims
Software Mentions: 4
Published: almost 13 years ago

10.7717/peerj.9848

Identification of key modules and hub genes associated with lung function in idiopathic pulmonary fibrosis
Cited by: 5
Author(s): Yuechong Xia, Lei Cheng, Danhui Yang, Hong Luo
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.3509

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis
Cited by: 9
Author(s): Raquel L. Costa, Luiz M. R. Gadelha, Marcelo Ribeiro-Alves, Fábio Porto
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0038149

Transcriptional Profiling of Human Brain Endothelial Cells Reveals Key Properties Crucial for Predictive In Vitro Blood-Brain Barrier Models
Cited by: 164
Author(s): Eduard Urich, Stanley E. Lazic, Juliette Molnos, Isabelle Wells, Per Ola Freskgård
Software Mentions: 4
Published: over 12 years ago

10.1111/jcmm.16222

The pioneer and differentiation factor FOXA2 is a key driver of yolk‐sac tumour formation and a new biomarker for paediatric and adult yolk‐sac tumours
Cited by: 13
Author(s): Wasco Wruck, Felix Bremmer, Mara Kotthoff, Alexander Fichtner, Margaretha A. Skowron, Stefan Schönberger, Gabriele Calaminus, Christian Vokuhl, David Pfister, Axel Heidenreich, Peter Albers, James Adjaye, Daniel Nettersheim
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13071-015-0974-3

Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210
Cited by: 58
Author(s): Benjamin Frank, Ana Marcu, Antônio Luis de Oliveira Almeida Petersen, Heike Weber, Christian Stigloher, Jeremy C. Mottram, Claus‐Jürgen Scholz, Uta Schurigt
Software Mentions: 4
Published: over 9 years ago

10.1038/s42003-021-01651-y

Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival
Cited by: 9
Author(s): Sandeep K. Singhal, Jung S. Byun, Samson Park, Tingfen Yan, Ryan Yancey, Ambar Caban, Sara Gil Hernandez, Stephen M. Hewitt, Heike Boisvert, Stephanie Hennek, Mark Bobrow, Shakir Ahmed, Jason White, Clayton Yates, Andrew Aukerman, R. Vanguri, Rohan Bareja, Romina Lenci, Paula Lucía Farré, Adriana De Siervi, Anna María Nápoles, Nasreen A. Vohra, Kevin Gardner
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-11-138

Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland
Cited by: 114
Author(s): Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, Helmut Blum
Software Mentions: 4
Published: over 14 years ago

10.18632/aging.102275

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice
Cited by: 52
Author(s): Huimin Li, Xinhui Wang, Xinyue Lu, Hongxin Zhu, Sheng Li, Shiwei Duan, Xinzhi Zhao, Fuquan Zhang, Gil Alterovitz, Fudi Wang, Qiang Li, Xiao-Li Tian, Mingqing Xu
Software Mentions: 4
Published: about 5 years ago

10.3390/cells8101117

Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles
Cited by: 8
Author(s): Stefaan Verhulst, Tania Roskams, Pau Sancho–Bru, Leo A. van Grunsven
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: almost 18 years ago

10.7150/jca.39723

Weighted gene co-expression network analysis identified MYL9 and CNN1 are associated with recurrence in colorectal cancer
Cited by: 15
Author(s): Qiu Xiao, Shen-Hong Cheng, Fei Xu, Jinwen Yin, Liyang Wang, Xinyou Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41423-019-0218-0

Coexpression of CD163 and CD141 identifies human circulating IL-10-producing dendritic cells (DC-10)
Cited by: 45
Author(s): Michela Comi, Daniele Avancini, Francesca R. Santoni de Sio, Matteo Villa, Molly Javier Uyeda, Matteo Floris, Daniela Tomasoni, Alessandro Bulfone, Maria Grazia Roncarolo, Silvia Gregori
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-9-S2-S12

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Cited by: 30
Author(s): Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì Maria Victoria Grober, Maria Ravo, Angelo Facchiano, Claudia Angelini, Alessandro Weisz
Software Mentions: 4
Published: over 16 years ago

10.7150/jca.57225

Integrating 13 Microarrays to Construct a 6 RNA-binding proteins Prognostic Signature for Gastric Cancer patients
Cited by: 0
Author(s): Liqun Zhou, Qi Zhou, You Wu, Lin Xin
Software Mentions: 4
Published: almost 4 years ago

10.2478/intox-2014-0010

Systems toxicology approaches enable mechanistic comparison of spontaneous and cigarette smoke-related lung tumor development in the A/J mouse model
Cited by: 14
Author(s): Karsta Luettich, Yu‐Tao Xiang, Anita Iskandar, Alain Sewer, Florian Martin, Marja Talikka, Patrick Vanscheeuwijck, An Berges, Emilija Veljkovic, Ignacio González-Suárez, Walter K. Schlage, Walter K. Schlage, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.11995

The modulatory properties of <i>Astragalus membranaceus</i> treatment on endometrial cancer: an integrated pharmacological method
Cited by: 4
Author(s): Qianqian Zhang, Xianghua Huang
Software Mentions: 4
Published: about 3 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

10.1038/s41598-018-28185-4

Early alteration of epigenetic-related transcription in Huntington’s disease mouse models
Cited by: 35
Author(s): Irati Hervás-Corpión, Deisy Guiretti, Manuel Alcaráz-Iborra, Román Olivares, Antonio Campos‐Caro, Ángel Barco, Luis M. Valor
Software Mentions: 4
Published: over 6 years ago

10.1186/1476-4598-13-241

OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets
Cited by: 22
Author(s): Stephen F. Madden, Colin Clarke, Britta K. Stordal, Mark Carey, Russell Broaddus, William M. Gallagher, John Crown, Gordon B. Mills, Bryan T. Hennessy
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-016-1137-3

Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
Cited by: 106
Author(s): Xuan Li, Emily Speranza, César Muñoz‐Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel García-Dorival, Yongxiang Fang, Yper Hall, Elsa Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E. Diane Williamson, Thomas R. Laws, N’Faly Magassouba, David A. Matthews, Stephan Günther, Andrew R. Cossins, Armand Sprecher, John H. Connor, Miles W. Carroll, Julian A. Hiscox
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0137654

The Role of the Immune Response in the Pathogenesis of Thyroid Eye Disease: A Reassessment
Cited by: 15
Author(s): James T. Rosenbaum, Dongseok Choi, Amanda Wong, David J. Wilson, Hans E. Grossniklaus, Christina A. Harrington, Roger A. Dailey, John D. Ng, Eric A. Steele, Craig N. Czyz, Jill A. Foster, David T. Tse, Chris Alabiad, Sander R. Dubovy, Prashant K. Parekh, Gerald J. Harris, Michael Kazim, Payal Patel, Valerie A. White, Peter J. Dolman, Deepak P. Edward, Hind M. Alkatan, Hailah Al Hussain, Dinesh Selva, R. Patrick Yeatts, Bobby S. Korn, Don O. Kikkawa, Patrick Stauffer
Software Mentions: 4
Published: about 9 years ago

10.1186/gb-2014-15-3-r52

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis
Cited by: 120
Author(s): Hai Wu, Troy W. Whitfield, Jonathan A. R. Gordon, Jason R. Dobson, Phillip W. L. Tai, André J. van Wijnen, Janet L. Stein, Jane B. Lian
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0179265

Cancer cell redirection biomarker discovery using a mutual information approach
Cited by: 7
Author(s): Kimberly Roche, F. Alex Feltus, Jang Pyo Park, Marie–May Coissieux, Chenyan Chang, Vera B. S. Chan, Mohamed Bentires‐Alj, Brian W. Booth
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-7-511

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Cited by: 23
Author(s): Andrew Holloway, Alicia Oshlack, Dileepa S. Diyagama, David D.L. Bowtell, Gordon K. Smyth
Software Mentions: 4
Published: almost 18 years ago

10.3390/microarrays1020084

Quality Visualization of Microarray Datasets Using Circos
Cited by: 2
Author(s): Martin Koch, Michael Wiese
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0240120

Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia
Cited by: 7
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Roderick A.F. MacLeod, Hans G. Drexler
Software Mentions: 4
Published: about 4 years ago

10.1007/s12032-021-01464-3

Dual inhibition of TGFβ and AXL as a novel therapy for human colorectal adenocarcinoma with mesenchymal phenotype
Cited by: 6
Author(s): Davide Ciardiello, Bernadette Blauensteiner, Nunzia Matrone, Valentina Belli, Thomas Mohr, Pietro Paolo Vitiello, Giulia Martini, L. Poliero, Claudia Cardone, Stefania Napolitano, Vincenzo De Falco, Emilio Francesco Giunta, Vincenza Ciaramella, Carminia Della Corte, Giusi Barra, Francesco Selvaggi, Renato Franco, Federica Zito Marino, Antonio Cuomo, Teresa Troiani, Maria Sibilia, Fortunato Ciardiello, Erika Martinelli
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers13174250

Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways
Cited by: 10
Author(s): Antonio Ahn, Euan J. Rodger, Jyoti Motwani, Grégory Gimenez, Peter A. Stockwell, Matthew Parry, Peter Hersey, Aniruddha Chatterjee, Michael R. Eccles
Software Mentions: 4
Published: about 3 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

10.1371/journal.pone.0054144

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
Cited by: 139
Author(s): José M. Otero, Donatella Cimini, Kiran Raosaheb Patil, Simon Guldberg Poulsen, Lisbeth Olsson, Jens Nielsen
Software Mentions: 4
Published: almost 12 years ago

10.3390/genes11070815

Cortical Granule Distribution and Expression Pattern of Genes Regulating Cellular Component Size, Morphogenesis, and Potential to Differentiation are Related to Oocyte Developmental Competence and Maturational Capacity In Vivo and In Vitro
Cited by: 10
Author(s): Magdalena Kulus, Wiesława Kranc, Michal Ješeta, Patrycja Sujka‐Kordowska, Aneta Konwerska, Sylwia Ciesiółka, Piotr Celichowski, Lisa Moncrieff, Ievgeniia Kocherova, Małgorzata Józkowiak, Jakub Kulus, Maria Wieczorkiewicz, Hanna Piotrowska‐Kempisty, Mariusz T. Skowroński, Dorota Bukowska, Marie Machatková, Šárka Hanuláková, Paul Mozdziak, J. M. Jaśkowski, Bartosz Kempisty, Paweł Antosik
Software Mentions: 4
Published: over 4 years ago

10.1002/cam4.3854

Identification of MEG8/miR‐378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis
Cited by: 7
Author(s): Jiang Lei, Zhen-Yu He, Jun Wang, Min Hu, Ping Zhou, Chen-Lu Lian, Hua Li, San‐Gang Wu, Juan Zhou
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3654

Establishment of a prognostic model of four genes in gastric cancer based on multiple data sets
Cited by: 11
Author(s): Liqun Zhou, Shi H Li, You Wu, Lin Xin
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3833

The immune landscape during the tumorigenesis of cervical cancer
Cited by: 18
Author(s): Yiying Wang, Mengdi He, Guodong Zhang, Kankan Cao, Moran Yang, Hongwei Zhang, Haiou Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-10-389

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
Cited by: 18
Author(s): Herman M. J. Sontrop, Perry D. Moerland, René van den Ham, Marcel J. T. Reinders, Wim Verhaegh
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2105-8-146

Analysis of probe level patterns in Affymetrix microarray data
Cited by: 15
Author(s): A. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson
Software Mentions: 4
Published: over 17 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: almost 10 years ago

10.18632/genesandcancer.133

Genetically transforming human osteoblasts to sarcoma: development of an osteosarcoma model
Cited by: 21
Author(s): Yi Yuan Yang, Rui Yang, Michael Roth, Sajida Piperdi, Wendong Zhang, Howard D. Dorfman, Pulivarthi H. Rao, Amy Park, Sandeep Tripathi, Carrie Freeman, Yunjia Zhang, Rebecca Sowers, Jeremy Rosenblum, David S. Geller, Bang H. Hoang, Jonathan Gill, Richard Görlick
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0007556

An Eight-Gene Blood Expression Profile Predicts the Response to Infliximab in Rheumatoid Arthritis
Cited by: 92
Author(s): Antonio Julià, Alba Erra, Carles Palacio, Carlos Tomás, Xavier Sans, P Barceló, Sara Marsal
Software Mentions: 4
Published: about 15 years ago

10.3389/fphys.2021.651690

Identification of VCAN as Hub Gene for Diabetic Kidney Disease Immune Injury Using Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Qiannan Xu, Binjue Li, Yucheng Wang, Cuili Wang, Shi Feng, Xue Lü, Jianghua Chen, Hong Jiang
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0047107

Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos
Cited by: 12
Author(s): Elisa A. Casanova, Michał Okoniewski, Paolo Cinelli
Software Mentions: 4
Published: about 12 years ago

10.1007/s10549-021-06328-y

Increased gene expression variability in BRCA1-associated and basal-like breast tumours
Cited by: 2
Author(s): George A. R. Wiggins, Michael A. Black, Anita K. Dunbier, Arthur Morley‐Bunker, kConFab Investigators, John F. Pearson, Logan C. Walker
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-10-186

The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
Cited by: 6
Author(s): Daniela Eggle, Svenja Debey–Pascher, Marc Beyer, Joachim L. Schultze
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0031505

Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis
Cited by: 10
Author(s): Zhide Fang, Ruofei Du, Xiangqin Cui
Software Mentions: 4
Published: almost 13 years ago

10.3389/fphys.2018.00399

Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis
Cited by: 55
Author(s): Chen Liang, Lushun Yuan, Kaiyu Qian, Guofeng Qian, Yuan Zhu, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0187572

Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles
Cited by: 56
Author(s): Arsen Arakelyan, Lilit Nersisyan, David Poghosyan, Lusine Khondkaryan, Աննա Հակոբյան, Henry Löffler-Wirth, Evie Melanitou, Hans Binder
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-15-910

Transcriptomic portrait of human Mesenchymal Stromal/Stem cells isolated from bone marrow and placenta
Cited by: 50
Author(s): Beatriz Rosón-Burgo, Fermín Sánchez‐Guijo, Consuelo del Cañizo, Javier De Las Rivas
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0185682

Meta-analysis of peripheral blood gene expression modules for COPD phenotypes
Cited by: 15
Author(s): Dominik Reinhold, Jarrett Morrow, Sean Jacobson, Junxiao Hu, Benjamin Ringel, Max A. Seibold, Craig P. Hersh, Katerina Kechris, Russell P. Bowler
Software Mentions: 4
Published: about 7 years ago

10.3389/fphar.2016.00126

EP300 Protects from Light-Induced Retinopathy in Zebrafish
Cited by: 13
Author(s): Reiko Kawase, Yuhei Nishimura, Yoshifumi Ashikawa, Shota Sasagawa, Soichiro Murakami, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Hiroshi Yamamoto, Kazumi Moriyuki, Shinsaku Yamane, Kazuhiro Tsuruma, Masamitsu Shimazawa, Hideaki Hara, Toshio Tanaka
Software Mentions: 4
Published: over 8 years ago

10.3389/fphys.2018.00019

Comparison of Fatty Acid and Gene Profiles in Skeletal Muscle in Normal and Obese C57BL/6J Mice before and after Blunt Muscle Injury
Cited by: 6
Author(s): Jens-Uwe Werner, Klaus Tödter, Pengfei Xu, Lydia Lockhart, Markus Jähnert, Pascal Gottmann, Annette Schürmann, Ludger Scheja, Martin Wabitsch, Uwe Knippschild
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2013.00184

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways
Cited by: 13
Author(s): Alexander J. Trevarton, Michael B. Mann, Christoph Knapp, Hiromitsu Araki, Jonathan D. Wren, Steven Stones-Havas, Michael A. Black, Cristin G. Print
Software Mentions: 4
Published: almost 12 years ago

10.3389/fonc.2019.01030

Novel Biomarkers Associated With Progression and Prognosis of Bladder Cancer Identified by Co-expression Analysis
Cited by: 42
Author(s): Yejinpeng Wang, Changhong Liang, Lingao Ju, Kaiyu Qian, Xuefeng Li, Xinghuan Wang, Yu Xiao
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0247827

Identification of UBE2C as hub gene in driving prostate cancer by integrated bioinformatics analysis
Cited by: 12
Author(s): Yan Wu, Jili Wang, Qi Tang, Guoping Ren
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0004229

Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing
Cited by: 19
Author(s): Xiangqin Cui, Ann E. Loraine
Software Mentions: 4
Published: almost 16 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-15-341

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Cited by: 34
Author(s): Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cécile Segonzac, Graham J. Etherington, Kee Hoon Sohn, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: almost 12 years ago

10.1042/BSR20203020

Network-based approach to identify prognosis-related genes in tamoxifen-treated patients with estrogen receptor-positive breast cancer
Cited by: 4
Author(s): Yanyan Wang, Xiaonan Gong, Yujie Zhang
Software Mentions: 4
Published: about 3 years ago

10.1042/BSR20203812

An autophagy-related prognostic signature associated with immune microenvironment features of uveal melanoma
Cited by: 8
Author(s): Zhuotao Zheng, Lingyue Zhang, Zewei Tu, Yan Deng, Xingtian Yin
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0090322

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
Cited by: 29
Author(s): Philipp Schulz, Karel Jansseune, Thomas Degenkolbe, Michaël Méret, Hannes Claeys, Aleksandra Skirycz, Markus Teige, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 4
Published: over 10 years ago

10.3390/biom10091230

The Transcriptomic Evidence on the Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indians Indicates the Involvement of Both
Cited by: 6
Author(s): Anshul Kumar, Prabhat Tiwari, Aditya Saxena, Naincy Purwar, Nitin Wahi, Balram Sharma, Sandeep Kumar Mathur
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0137171

Discovery of a Novel Immune Gene Signature with Profound Prognostic Value in Colorectal Cancer: A Model of Cooperativity Disorientation Created in the Process from Development to Cancer
Cited by: 22
Author(s): Ning An, Xiaoyu Shi, Yueming Zhang, Ning Lv, Feng Li, Di Xia, Ning Han, Guiqi Wang, Shujun Cheng, Kaitai Zhang
Software Mentions: 4
Published: about 9 years ago

10.3389/fphys.2018.00674

Diet-Induced Obesity Affects Muscle Regeneration After Murine Blunt Muscle Trauma—A Broad Spectrum Analysis
Cited by: 19
Author(s): Pengfei Xu, Jens-Uwe Werner, Sebastian Milerski, Carmen M. Hamp, Tatjana Kuzenko, Markus Jähnert, Pascal Gottmann, Luisa de Roy, Daniela Warnecke, Alireza Abaei, Annette Palmer, Markus Huber‐Lang, Lutz Dürselen, Volker Rasche, Annette Schürmann, Martin Wabitsch, Uwe Knippschild
Software Mentions: 4
Published: over 6 years ago

10.1016/j.immuni.2019.12.007

Regulatory T Cells Restrain Interleukin-2- and Blimp-1-Dependent Acquisition of Cytotoxic Function by CD4+ T Cells
Cited by: 112
Author(s): Anna Śledzińska, Maria Vila de Mucha, Katharina Bergerhoff, Alastair Hotblack, Dafne Franz Demane, Ehsan Ghorani, Ayse U. Akarca, Maria A V Marzolini, Isabelle Solomon, Frederick Arce Vargas, Martin Pulé, Masahiro Ono, Benedict Seddon, George Kassiotis, Charlotte E. Ariyan, Thomas Korn, Teresa Marafioti, Graham M. Lord, Hans J. Stauss, Richard G. Jenner, Karl S. Peggs, Sergio A. Quezada
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-018-29077-3

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
Cited by: 58
Author(s): Franziska Liesecke, Dimitri Daudu, Rodolphe Dugé de Bernonville, Sébastien Besseau, Marc Clastre, Vincent Courdavault, Johan-Owen De Craene, Joël Crèche, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: over 6 years ago

10.1155/2013/512086

Systems Approaches Evaluating the Perturbation of Xenobiotic Metabolism in Response to Cigarette Smoke Exposure in Nasal and Bronchial Tissues
Cited by: 46
Author(s): Anita Iskandar, Florian Martin, Marja Talikka, Walter K. Schlage, Radina Kostadinova, Carole Mathis, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: almost 12 years ago

10.3389/fonc.2019.00812

Identification of a Specific Gene Module for Predicting Prognosis in Glioblastoma Patients
Cited by: 17
Author(s): Xiangjun Tang, Pengfei Xu, Bin Wang, Jie Luo, Rui Fu, Kuan‐Ming Huang, Long‐Jun Dai, Junti Lu, Gang Cao, Hao Peng, Li Zhang, Zhaohui Zhang, Qianxue Chen
Software Mentions: 3
Published: about 5 years ago

Projects: bioconductor: affy

Papers Mentioning affy 989