bioconductor: affyPLM | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.1186/s12920-015-0114-0

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: over 9 years ago

10.3389/fneur.2020.579683

Development and Validation of a Five-Gene Signature to Predict Relapse-Free Survival in Multiple Sclerosis
Cited by: 6
Author(s): Fei Ye, Jie Liang, Jiaoxing Li, Haiyan Li, Wenli Sheng
Software Mentions: 13
Published: about 4 years ago

10.3390/diagnostics10020066

Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis
Cited by: 22
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 12
Published: almost 5 years ago

10.1007/s12032-017-0963-9

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 7 years ago

10.1186/s12935-021-02041-4

Ten-gene signature reveals the significance of clinical prognosis and immuno-correlation of osteosarcoma and study on novel skeleton inhibitors regarding MMP9
Cited by: 17
Author(s): Weihang Li, Ziyi Ding, Dong Wang, Chengfei Li, Yikai Pan, Yingjing Zhao, Hongzhe Zhao, Tianxing Lu, Rui Xu, Shilei Zhang, Bin Yuan, Yunlong Zhao, Yanjiang Yin, Yuan Gao, Jing Li, Ming Yan
Software Mentions: 11
Published: over 3 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: almost 15 years ago

10.1371/journal.pone.0095224

Two-Stage, In Silico Deconvolution of the Lymphocyte Compartment of the Peripheral Whole Blood Transcriptome in the Context of Acute Kidney Allograft Rejection
Cited by: 18
Author(s): Casey P. Shannon, Robert Balshaw, Raymond T. Ng, J. Wilson-McManus, Paul Keown, Robert McMaster, Bruce M. McManus, David Landsberg, Nicole M. Isbel, Greg Knoll, Scott J. Tebbutt
Software Mentions: 9
Published: over 10 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: about 4 years ago

10.1186/s12950-020-00260-6

Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis
Cited by: 11
Author(s): Pedro A. Ruiz-Castro, Ulrike Kogel, Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, Bjoern Titz, Llenalia Garcia, Athanasios Kondylis, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 8
Published: over 4 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: about 6 years ago

10.7150/ijms.48244

Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis
Cited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pmed.1002223

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
Cited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41598-017-11110-6

A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies
Cited by: 29
Author(s): Gift Nyamundanda, Pawan Poudel, Yatish Patil, Anguraj Sadanandam
Software Mentions: 8
Published: over 7 years ago

10.1186/1471-2164-14-445

The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India
Cited by: 20
Author(s): R. Kimberley Cook, James R. Hennell, Samiuela Lee, Cheang Khoo, Maria Carles, Vincent J. Higgins, Suresh Govindaraghavan, Nikolaus J. Sucher
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0153355

Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates
Cited by: 20
Author(s): Julie M. Yabu, Janet Siebert, Holden T. Maecker
Software Mentions: 6
Published: over 8 years ago

10.1186/s12967-020-02597-1

Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass
Cited by: 8
Author(s): Bishnupriya Chhatriya, Moumita Mukherjee, Sukanta Ray, Barsha Saha, Somdatta Lahiri, Sandip Halder, Indranil Ghosh, Sujan Khamrui, Kshaunish Das, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra, Srikanta Goswami
Software Mentions: 6
Published: about 4 years ago

10.7150/ijms.61309

Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Ke Zhu, Aiqun Xu, Wanli Xia, Pulin Li, Rui Han, Enze Wang, Sijing Zhou, Ran Wang
Software Mentions: 6
Published: almost 4 years ago

10.1186/1743-422X-11-126

Reactive astrogliosis in response to hemorrhagic fever virus: microarray profile of Junin virus-infected human astrocytes
Cited by: 8
Author(s): Olga A. Kolokoltsova, Nadezhda E. Yun, Slobodan Paessler
Software Mentions: 6
Published: over 10 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium “ Candidatus Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: almost 6 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

10.1186/1471-2105-14-7

GSVA: gene set variation analysis for microarray and RNA-Seq data
Cited by: 6,480
Author(s): Sonja Hänzelmann, Robert Castelo, Justin Guinney
Software Mentions: 6
Published: almost 12 years ago

10.1186/s12872-021-02166-4

Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis
Cited by: 4
Author(s): Zhiyuan Fan, Wei Peng, Zhiwen Wang, Ling Zhang, Kuo Li
Software Mentions: 6
Published: over 3 years ago

10.3390/jpm10040210

Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease
Cited by: 3
Author(s): Ying Chun Chen, Mei Yi Wu, Zhi Yu, Wan Hsuan Chou, Yi Ting Lai, Chih-Chin Kao, Imaniar Noor Faridah, Mai Szu Wu, Wei Chiao Chang
Software Mentions: 6
Published: about 4 years ago

10.3389/fcell.2021.648856

Comprehensive Characterization of Cachexia-Inducing Factors in Diffuse Large B-Cell Lymphoma Reveals a Molecular Subtype and a Prognosis-Related Signature
Cited by: 5
Author(s): Zhixing Kuang, Xun Li, Rongqiang Liu, Shaoxing Chen, Jiannan Tu
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-018-4782-y

Gene expression profiling in the developing secondary palate in the absence of Tbx1 function
Cited by: 2
Author(s): Maria Zoupa, Guilherme M. Xavier, Stephanie Bryan, Ioannis Theologidis, Matthew Arno, Martyn T. Cobourne
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0096376

Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
Cited by: 38
Author(s): Daniel Nätt, Beatrix Agnvall, Per Jensen
Software Mentions: 6
Published: over 10 years ago

10.1186/s12920-015-0106-0

Integrated approaches to miRNAs target definition: time-series analysis in an osteosarcoma differentiative model
Cited by: 15
Author(s): Andrea Grilli, Marika Sciandra, Mario Terracciano, Piero Picci, Katia Scotlandi
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0041066

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis
Cited by: 25
Author(s): Federico Carlos Blanco, Marcelo Soria, María Verónica Bianco, Fabiana Bigi
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-016-2851-7

The application of transcriptomic data in the authentication of beef derived from contrasting production systems
Cited by: 6
Author(s): T. Sweeney, Alexandre Lejeune, A.P. Moloney, Frank J. Monahan, Paul M Gettigan, Gérard Downey, Stephen D. E. Park, M. F. Ryan
Software Mentions: 5
Published: over 8 years ago

10.18632/aging.202635

Transcriptome profiling reveals target in primary myelofibrosis together with structural biology study on novel natural inhibitors regarding JAK2
Cited by: 7
Author(s): Weihang Li, Bin Yuan, Yingjing Zhao, Tianxing Lu, Shilei Zhang, Ziyi Ding, Dong Wang, Sheng Zhong, Guangxun Gao, Ming Yan
Software Mentions: 5
Published: almost 4 years ago

10.1042/BSR20203231

Identification of an autophagy-related gene signature predicting overall survival for hepatocellular carcinoma
Cited by: 5
Author(s): Wenfang Xu, Wenxiu Guo, Ping Lü, Ding Ma, Lei Liu, Fudong Yu
Software Mentions: 5
Published: almost 4 years ago

10.1111/jcmm.15851

Prognostic and predictive value of a mRNA signature in peripheral T‐cell lymphomas: A mRNA expression analysis
Cited by: 6
Author(s): Jiannan Tu, Zhixing Kuang, Xiaoxiao Xie, Shizhen Wu, Ting Wu, Shengchi Chen
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0004481

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: almost 16 years ago

10.7554/eLife.06942

NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets
Cited by: 52
Author(s): Romaric Bouveret, Ashley J. Waardenberg, Nicole Schönrock, Mirana Ramialison, Tram Doan, Daniëlle de Jong, Antoine Bondue, Gurpreet Kaur, Mohamed Salim, Hananeh Fonoudi, Chiann-mun Chen, Merridee A. Wouters, Shoumo Bhattacharya, Nicolas Plachta, Sally L. Dunwoodie, Gavin Chapman, Cédric Blanpain, Richard P. Harvey
Software Mentions: 5
Published: over 9 years ago

10.3389/fonc.2021.705939

Identification of the Effects of Chondroitin Sulfate on Inhibiting CDKs in Colorectal Cancer Based on Bioinformatic Analysis and Experimental Validation
Cited by: 1
Author(s): Yingyu Zhou, Xuyang Li, Yuki Morita, Satoshi Hachimura, Takuya Miyakawa, Sachiko Takahashi, Masaru Tanokura
Software Mentions: 5
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

10.18632/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: over 5 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

10.1186/1471-2105-8-449

A comparison of Affymetrix gene expression arrays
Cited by: 59
Author(s): Mark D. Robinson, Terence P. Speed
Software Mentions: 4
Published: about 17 years ago

10.1186/1471-2164-11-26

1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1
Cited by: 80
Author(s): Pavlo L. Kovalenko, Zhentao Zhang, Min Cui, S. Clinton, James C. Fleet
Software Mentions: 4
Published: almost 15 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: almost 15 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

10.1186/1471-2164-10-363

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

10.1093/bioinformatics/btu027

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Cited by: 15
Author(s): Marta Rosikiewicz, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 11 years ago

10.1155/2013/848952

Integration of Data from Omic Studies with the Literature-Based Discovery towards Identification of Novel Treatments for Neovascularization in Diabetic Retinopathy
Cited by: 4
Author(s): Aleš Maver, Dimitar Hristovski, Thomas C. Rindflesch, Borut Peterlin
Software Mentions: 4
Published: almost 12 years ago

10.1155/2020/4980609

The Important Role of Perituberal Tissue in Epileptic Patients with Tuberous Sclerosis Complex by the Transcriptome Analysis
Cited by: 3
Author(s): Shuqiang Li, Huijie Shao, Liansheng Chang
Software Mentions: 4
Published: about 4 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: over 4 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

10.1371/journal.pone.0001061

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Cited by: 52
Author(s): Caitlin B. Conboy, Christiana Spyrou, Natalie Thorne, Elizabeth J. Wade, Nuno L. Barbosa‐Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
Software Mentions: 4
Published: about 17 years ago

10.3389/fimmu.2021.704655

An Immune-Associated Genomic Signature Effectively Predicts Pathologic Complete Response to Neoadjuvant Paclitaxel and Anthracycline-Based Chemotherapy in Breast Cancer
Cited by: 4
Author(s): Changfang Fu, Yu Liu, Xinghua Han, Yueyin Pan, Hongqiang Wang, Hongzhi Wang, Haiming Dai, Wulin Yang
Software Mentions: 4
Published: over 3 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

10.7150/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

10.1093/jxb/eru119

Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences
Cited by: 81
Author(s): Salma Balazadeh, Jörg Schildhauer, Wagner L. Araújo, Sergi Munné‐Bosch, Alisdair R. Fernie, Sebastian Proost, Klaus Humbeck, Bernd Mueller‐Roeber
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.ppat.1009773

CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice
Cited by: 15
Author(s): Deniz Koyuncu, M. Khalid Khan Niazi, Thomas E. Tavolara, Claudia Abeijón, Melanie Ginese, Yanghui Liao, Carolyn Mark, Aubrey G. Specht, Adam C. Gower, Blanca I. Restrepo, Daniel M. Gatti, Igor Kramnik, Metin N. Gürcan, Bülent Yener, Gillian Beamer
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-62578-8

Detecting qualitative changes in biological systems
Cited by: 5
Author(s): Cristina Mitrea, Aliccia Bollig‐Fischer, Călin Voichiţa, Michèle Donato, Roberto Romero, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-82853-6

Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia
Cited by: 19
Author(s): Kornphimol Kulthong, Guido Hooiveld, Loes P. M. Duivenvoorde, Ignacio Miro Estruch, Victor Augustus Marin, Meike van der Zande, Hans Bouwmeester
Software Mentions: 4
Published: almost 4 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: almost 4 years ago

10.1038/s41598-021-91864-2

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Cited by: 2
Author(s): Parastoo Modarres, Farzaneh Mohamadi Farsani, Amir Abas Nekouie, Sadeq Vallian
Software Mentions: 4
Published: over 3 years ago

10.1186/s13395-019-0196-z

Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field
Cited by: 8
Author(s): Apostolos Malatras, Stéphanie Duguez, William Duddy
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1007802

Strength of T cell signaling regulates HIV-1 replication and establishment of latency
Cited by: 20
Author(s): Matthew Gagné, Daniel Michaels, Gillian M. Schiralli Lester, Suryaram Gummuluru, Wilson Wong, Andrew J. Henderson
Software Mentions: 3
Published: over 5 years ago

10.1016/j.isci.2021.102848

Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana
Cited by: 10
Author(s): Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, C.-L. Jen, William Duddy, Γεράσιμος Δάρας, Polydefkis Hatzopoulos, David Westhead, Ioannis Michalopoulos
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0009983

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis
Cited by: 100
Author(s): Manasa Ramakrishna, Lauren Williams, Samantha E. Boyle, Jennifer L. Bearfoot, Anita Sridhar, Terence P. Speed, Kylie L. Gorringe, Ian Campbell
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0121730

Gene Expression Profiles Associated with Pediatric Relapsed AML
Cited by: 23
Author(s): Costa Bachas, Gerrit Jan Schuurhuis, C. Michel Zwaan, Marry M. van den Heuvel‐Eibrink, Monique L. den Boer, Eveline S.J.M. de Bont, Zinia J. Kwidama, Dirk Reinhardt, Ursula Creutzig, Valérie de Haas, Gertjan J. L. Kaspers, Jacqueline Cloos
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.67358

Drosophila STING protein has a role in lipid metabolism
Cited by: 22
Author(s): Katarina Akhmetova, Maxim Balasov, Igor Chesnokov
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-015-0583-7

Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma
Cited by: 77
Author(s): Sebastian Kurscheid, Pierre Bady, Davide Sciuscio, Ivana Samaržija, Tal Shay, Irene Vassallo, Wim Van Criekinge, Roy Thomas Daniel, Martin J. van den Bent, Christine Marosi, Michael Weller, Warren P. Mason, Eytan Domany, Roger Stupp, Mauro Delorenzi, Monika E. Hegi
Software Mentions: 3
Published: almost 10 years ago

10.1186/gb-2007-8-6-r125

Correcting for sequence biases in present/absent calls
Cited by: 29
Author(s): Eugene F. Schuster, Eric Blanc, Linda Partridge, Janet M. Thornton
Software Mentions: 3
Published: almost 18 years ago

10.1186/s12885-021-07950-1

APE1 may influence CD4+ naïve T cells on recurrence free survival in early stage NSCLC
Cited by: 9
Author(s): Yanping Li, Xiaolong Zhao, He Xiao, Bo Yang, Jie Liu, Wenwang Rao, Xiaoyan Dai, Mengxia Li, Nan Dai, Yuxin Yang, Dong Wang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.0030217

Localization of Candidate Regions Maintaining a Common Polymorphic Inversion (2La) in Anopheles gambiae
Cited by: 76
Author(s): Bradley J. White, Matthew W. Hahn, Marco Pombi, Bryan J. Cassone, Neil F. Lobo, Frédéric Simard, Nora J. Besansky
Software Mentions: 3
Published: about 17 years ago

10.1186/s40462-016-0069-6

Gene expression in the brain of a migratory songbird during breeding and migration
Cited by: 19
Author(s): John Boss, Miriam Liedvogel, Max Lundberg, Peter Olsson, Nils Reischke, Sara Naurin, Susanne Åkesson, Dennis Hasselquist, Anthony P. H. Wright, Mats Grahn, Staffan Bensch
Software Mentions: 3
Published: almost 9 years ago

10.3389/fimmu.2019.00094

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro
Cited by: 70
Author(s): Olaf Perdijk, Peter van Baarlen, Marcela M. Fernandez-Gutierrez, Frank Schuren, Sylvia Brugman, H.F.J. Savelkoul, Michiel Kleerebezem, R. J. Joost van Neerven
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-5000-7

Murine host response to Neisseria gonorrhoeae upper genital tract infection reveals a common transcriptional signature, plus distinct inflammatory responses that vary between reproductive cycle phases
Cited by: 11
Author(s): Ian Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik‐Dasthagirisaheb, Scott D. Gray-Owen, Lee M. Wetzler
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0230905

Identification of human peripheral blood monocyte gene markers for early screening of solid tumors
Cited by: 11
Author(s): Siyang Chen, Menghan Liu, Bowen Liang, Shanghua Ge, Jie Peng, Haiyue Huang, Ye Xu, Xiaoli Tang, Libin Deng
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0024235

In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs
Cited by: 45
Author(s): Piotr Bielecki, Jacek Puchałka, Melissa L. Wos‐Oxley, Holger Loessner, Justyna Glik, Marek Kawecki, Mariusz Nowak, Burkhard Tümmler, Siegfried Weiß, Vítor A. P. Martins dos Santos
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.0010026

A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana
Cited by: 384
Author(s): Matthew A. Hannah, Arnd G. Heyer, Dirk K. Hincha
Software Mentions: 3
Published: over 19 years ago

10.1186/1756-0500-3-255

Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway
Cited by: 48
Author(s): Christiane Katja Kleindt, Ralf Stracke, Marcus Frank, Bernd Weißhaar
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pgen.0040014

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Cited by: 481
Author(s): Todd P. Michael, Todd C. Mockler, Ghislaı̀n Breton, Connor McEntee, Amanda Byer, Jonathan D. Trout, Samuel P. Hazen, Rongkun Shen, Henry D. Priest, Christopher Sullivan, Scott A. Givan, Marcelo J. Yanovsky, Fangxin Hong, Steve A. Kay, Joanne Chory
Software Mentions: 3
Published: almost 17 years ago

10.1111/j.1365-313X.2008.03727.x

The transcriptome of syncytia induced by the cyst nematodeHeterodera schachtiiin Arabidopsis roots
Cited by: 197
Author(s): Dagmar Szakasits, Petra Heinen, Krzysztof Wieczorek, Julia Hofmann, Florian Wagner, David P. Kreil, Peter Sykacek, Florian M. W. Grundler, Holger Bohlmann
Software Mentions: 3
Published: almost 16 years ago

10.1016/j.omtn.2021.03.001

lncRNA LOC102724169 plus cisplatin exhibit the synergistic anti-tumor effect in ovarian cancer with chronic stress
Cited by: 6
Author(s): Xiaofang Zhou, Mu Liu, Guanming Deng, Le Chen, Lijuan Sun, Yun Zhang, Chenhui Luo, Jie Tang
Software Mentions: 3
Published: over 3 years ago

10.1039/c3mb25485b

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster
Cited by: 5
Author(s): Dobril Ivanov, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Software Mentions: 3
Published: almost 12 years ago

10.1111/j.1365-2141.2006.06342.x

Gene expression profiling reveals consistent differences between clinical samples of human leukaemias and their model cell lines
Cited by: 15
Author(s): Nicolas Leupin, Aléxandre Kuhn, Barbara Hügli, Tobias Grob, Rolf Jaggi, Andreas Tobler, Mauro Delorenzi, Martin F. Fey
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.pone.0204438

Loss of the Spinocerebellar Ataxia type 3 disease protein ATXN3 alters transcription of multiple signal transduction pathways
Cited by: 22
Author(s): Li Zeng, David Zhang, Hayley S. McLoughlin, Annie J. Zalon, L. Aravind, Henry L. Paulson
Software Mentions: 3
Published: over 6 years ago

10.1186/s12967-019-1790-x

Bioinformatic gene analysis for potential biomarkers and therapeutic targets of atrial fibrillation-related stroke
Cited by: 60
Author(s): Rongjun Zou, Dingwen Zhang, Lei Lv, Wu Shi, Zilin Song, Bin Yi, Bingjia Lai, Qian Chen, Shiming Yang, Peng Hua
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-79235-9

Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba
Cited by: 32
Author(s): Hua Ma, Zhijun He, Jing Chen, Xu Zhang, Pingping Song
Software Mentions: 3
Published: almost 4 years ago

10.1002/pld3.123

Identification of gene expression logical invariants in Arabidopsis
Cited by: 8
Author(s): Sonalisa Pandey, Debashis Sahoo
Software Mentions: 3
Published: almost 6 years ago

10.7150/ijms.63402

Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer
Cited by: 8
Author(s): Chang Liu, Yu Pan, Qinyu Li, Yifan Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-10-191

Unsupervised assessment of microarray data quality using a Gaussian mixture model
Cited by: 4
Author(s): Brian E. Howard, Beate Sick, Steffen Heber
Software Mentions: 3
Published: over 15 years ago

10.1038/sdata.2018.306

Transcriptomic profiles of tissues from rats treated with anticancer drug combinations
Cited by: 0
Author(s): Myrtle A. Davis, Enid M. Knight, Sandy Eldridge, Jianying Li, Pierre R. Bushel
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0106054

Extracellular Matrix Defects in Aneurysmal Fibulin-4 Mice Predispose to Lung Emphysema
Cited by: 17
Author(s): Natasja W. M. Ramnath, Koen M. van de Luijtgaarden, Ingrid van der Pluijm, Menno van Nimwegen, Paula M. van Heijningen, Sigrid Swagemakers, Bibi S. van Thiel, Ruziedi Y. Ridwan, Nicole van Vliet, Marcel Vermeij, Lukas J.A.C. Hawinkels, Anne de Munck, Oleh Dzyubachyk, Erik Meijering, Peter van der Spek, Robbert J. Rottier, Hiromi Yanagisawa, Rudi W. Hendriks, Roland Kanaar, Ellen V. Rouwet, Alex KleinJan, Jeroen Essers
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1002929

Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses
Cited by: 41
Author(s): Y. Dufour, Saheed Imam, Bon Chul Koo, Heather A. Green, Timothy J. Donohue
Software Mentions: 2
Published: over 12 years ago

10.1155/2013/458278

Transcriptional Response of Bovine Monocyte-Derived Macrophages after the Infection with Different ArgentineanMycobacterium bovisIsolates
Cited by: 7
Author(s): Karina Caimi, Federico Carlos Blanco, Marcelo Soria, Fabiana Bigi
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0040275

Molecular Profiles of HCV Cirrhotic Tissues Derived in a Panel of Markers with Clinical Utility for Hepatocellular Carcinoma Surveillance
Cited by: 7
Author(s): Ricardo C. Gehrau, Kellie J. Archer, Valeria R. Mas, Daniel G. Maluf
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0069082

Utilization of Never-Medicated Bipolar Disorder Patients towards Development and Validation of a Peripheral Biomarker Profile
Cited by: 29
Author(s): Catherine L. Clelland, Laura L. Read, Laura J. Panek, Robert H. Nadrich, Carter Bancroft, James D. Clelland
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-9-489

Determining gene expression on a single pair of microarrays
Cited by: 7
Author(s): Robert W. Reid, Anthony A. Fodor
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0069768

Hippocampal Gene Expression Meta-Analysis Identifies Aging and Age-Associated Spatial Learning Impairment (ASLI) Genes and Pathways
Cited by: 18
Author(s): Raihan K. Uddin, Shiva M. Singh
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0042297

Distinct Cardiac Transcriptional Profiles Defining Pregnancy and Exercise
Cited by: 34
Author(s): Eunhee Chung, Joseph Heimiller, Leslie A. Leinwand
Software Mentions: 2
Published: over 12 years ago

10.1186/s13075-017-1237-9

Epstein-Barr virus lytic infection promotes activation of Toll-like receptor 8 innate immune response in systemic sclerosis monocytes
Cited by: 56
Author(s): Antonella Farina, Giovanna Peruzzi, Valentina Lacconi, Stefania Lenna, Silvia Quarta, Edoardo Rosato, Anna Rita Vestri, Michael York, David H. Dreyfus, Alberto Faggioni, Stefania Morrone, Maria Trojanowska, Giuseppina Farina
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1004050

Angiogenic Activity of Breast Cancer Patients’ Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches
Cited by: 18
Author(s): Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene‐Treboux, Eveline Faes-van’t Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, F. Majo, Michaël Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans‐Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xénarios, Marie‐Agnès Doucey
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0201929

Nutrient supply alters transcriptome regulation in adipose tissue of pre-weaning Holstein calves
Cited by: 9
Author(s): L.N. Leal, Josué Moura Romão, Guido Hooiveld, F. Soberon, H. Berends, Mark V. Boekshoten, M.E. Van Amburgh, J. Martín-Tereso, M.A. Steele
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0026465

Identification of Hypoxia-Induced Genes in Human SGBS Adipocytes by Microarray Analysis
Cited by: 50
Author(s): Kathrin Geiger, Andreas Leiherer, Axel Muendlein, Nicole M. Stark, Simone Geller-Rhomberg, Christoph H. Saely, Martin Wabitsch, Peter Fraunberger
Software Mentions: 2
Published: about 13 years ago

Projects: bioconductor: affyPLM

Papers Mentioning affyPLM 162