bioconductor: affy | Projects | Ecosyste.ms: Papers

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 2 years ago

10.1155/2021/6648093

Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 16
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: about 3 years ago

10.1186/1741-7007-7-70

Genetical genomic determinants of alcohol consumption in rats and humans
Cited by: 136
Author(s): Boris Tabakoff, Laura Saba, Morton P. Printz, Pam Flodman, Colin A. Hodgkinson, David Goldman, George F. Koob, H. G. Richardson, Katerina Kechris, Richard L. Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, M Dongier, Katherine M. Conigrave, John B. Whitfield, John B. Saunders, Bridget F. Grant, Paula L. Hoffman
Software Mentions: 5
Published: over 14 years ago

10.1016/j.molp.2020.07.010

The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense
Cited by: 25
Author(s): Roland E. Schwarzenbacher, Grace Wardell, Joost H. M. Stassen, Emily Guest, Peijun Zhang, Estrella Luna, Jurriaan Ton
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0042678

The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Cited by: 19
Author(s): Karol Baca-López, M. Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández‐Lemus
Software Mentions: 5
Published: over 11 years ago

10.18632/oncotarget.26929

Deregulated expression of NKL homeobox genes in T-cell lymphomas
Cited by: 10
Author(s): Stefan Nagel, Claudia Pommerenke, Roderick A.F. MacLeod, Corinna Meyer, Maren Kaufmann, Silke Fähnrich, Hans Drexler
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2019.01716

Enhanced Immunomodulation in Inflammatory Environments Favors Human Cardiac Mesenchymal Stromal-Like Cells for Allogeneic Cell Therapies
Cited by: 3
Author(s): Falk Diedrichs, Meaghan Stolk, Karsten Jürchott, Marion Haag, Michael Sittinger, Martina Seifert
Software Mentions: 5
Published: almost 5 years ago

10.1155/2021/2042114

Identification of Prognostic Metabolism-Related Genes in Clear Cell Renal Cell Carcinoma
Cited by: 8
Author(s): Yusa Chen, Yumei Liang, Ying Chen, Shan Ouyang, Kanghan Liu, Yin Wu
Software Mentions: 5
Published: over 2 years ago

10.3389/fimmu.2021.695865

Prognosis and Characterization of Immune Microenvironment in Acute Myeloid Leukemia Through Identification of an Autophagy-Related Signature
Cited by: 19
Author(s): Denggang Fu, Biyu Zhang, Shiyong Wu, Yinghua Zhang, Jingwu Xie, Wangbin Ning, Hua Jiang
Software Mentions: 5
Published: almost 3 years ago

10.3892/mmr.2014.3006

Analysis of the protein-protein interaction networks of differentially expressed genes in pulmonary embolism
Cited by: 5
Author(s): Hao Wang, Chen Wang, Lei Zhang, Yinghua Lu, Qianglin Duan, Zhu Gong, Aibin Liang, Haoming Song, Lemin Wang
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0156594

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data
Cited by: 94
Author(s): Christian Müller, Arne Schillert, Caroline Röthemeier, David‐Alexandre Trégouët, Carole Proust, Harald Binder, Norbert Pfeiffer, Manfred E. Beutel, Karl J. Lackner, Renate B. Schnabel, Laurence Tiret, Philipp S. Wild, Stefan Blankenberg, Tanja Zeller, Andreas Ziegler
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms21218016

Enhancer of Zeste Homolog 2 (EZH2) Mediates Glucolipotoxicity-Induced Apoptosis in β-Cells
Cited by: 3
Author(s): Tina Dahlby, Christian Simon, Marie Balslev Backe, Mattias Salling Dahllöf, Edward B. Holson, Bridget K. Wagner, Marianne Böni-Schnetzler, Michał Marzec, Morten Lundh, Thomas Mandrup‐Poulsen
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.22169

Immunological landscape of consensus clusters in colorectal cancer
Cited by: 49
Author(s): Paweł Karpiński, Joanna Rossowska, Maria M. Sasiadek
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2229-10-150

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
Cited by: 129
Author(s): Dennis Janz, Katja Behnke, Jörg‐Peter Schnitzler, Basem Kanawati, Philippe Schmitt‐Kopplin, Andrea Polle
Software Mentions: 5
Published: almost 14 years ago

10.1186/s12920-019-0519-2

A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies
Cited by: 7
Author(s): Joshua Mannheimer, Dawn L. Duval, Ashok Prasad, Daniel L. Gustafson
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0065267

Zinc Finger Nuclease Mediated Knockout of ADP-Dependent Glucokinase in Cancer Cell Lines: Effects on Cell Survival and Mitochondrial Oxidative Metabolism
Cited by: 14
Author(s): Susan Richter, Shona Morrison, Timothy Connor, Jiechuang Su, Cristin G. Print, Ron S. Ronimus, Sean L. McGee, William R. Wilson
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12859-021-04095-7

Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression
Cited by: 5
Author(s): Qinghong Dai, Tao Liu, Yongchao Gao, Honghao Zhou, Xiong Li, Wei Zhang
Software Mentions: 5
Published: about 3 years ago

10.1515/med-2020-0114

CCTs as new biomarkers for the prognosis of head and neck squamous cancer
Cited by: 11
Author(s): Yanbo Dong, Siyu Lu, Zhenxiao Wang, Liangfa Liu
Software Mentions: 5
Published: over 4 years ago

10.1186/gb-2007-8-9-r190

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data
Cited by: 29
Author(s): Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P. King, Paul Britton
Software Mentions: 5
Published: over 17 years ago

10.3390/ijms21030751

Effect of Bortezomib on Global Gene Expression in PC12-Derived Nerve Cells
Cited by: 10
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Bogusław Machaliński
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms21186499

MiR-581/SMAD7 Axis Contributes to Colorectal Cancer Metastasis: A Bioinformatic and Experimental Validation-Based Study
Cited by: 12
Author(s): Xiaojuan Zhao, Shuzhen Liu, Bianbian Yan, Jin Yang, Erfei Chen
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-6-306

WebArray: an online platform for microarray data analysis
Cited by: 72
Author(s): Xiaoqin Xia, Michael McClelland, Yipeng Wang
Software Mentions: 5
Published: over 18 years ago

10.1186/1471-2164-10-63

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes
Cited by: 16
Author(s): Steven P. Wilder, Pamela J. Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 5
Published: over 15 years ago

10.7554/eLife.34042

Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types
Cited by: 21
Author(s): Saša Jereb, Hun‐Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John Fak, Yuan Yuan, Mary E. Hatten, Robert B. Darnell
Software Mentions: 5
Published: about 6 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: almost 9 years ago

10.1155/2019/9651380

Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas
Cited by: 14
Author(s): Xueren Gao, Jianguo Wang, Shulong Zhang
Software Mentions: 5
Published: over 5 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 7 years ago

10.1371/journal.pone.0208982

Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) RNAi is associated with cell cycle inhibition, apoptosis, DNA damage response and drug sensitivity in breast cancer
Cited by: 11
Author(s): Şahika Cıngır Köker, Ermira Jahja, Huma Shehwana, Ayşe Gökçe Keşküş, Özlen Konu
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-14-263

Ontology based molecular signatures for immune cell types via gene expression analysis
Cited by: 12
Author(s): Terrence F. Meehan, Nicole Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2164-11-263

Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities
Cited by: 47
Author(s): Ivy D. Moffat, Paul C. Boutros, Hanbo Chen, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 5
Published: about 14 years ago

10.1371/journal.pone.0247669

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

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13395-017-0144-8

Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells
Cited by: 29
Author(s): Natalia Pietrosemoli, Sébastien Mella, Siham Yennek, Meryem B. Baghdadi, Hiroshi Sakai, Ramkumar Sambasivan, Francesca Pala, Daniela Di Girolamo, Shahragim Tajbakhsh
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-76404-8

Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy
Cited by: 67
Author(s): Abul B.M.M.K. Islam, A. A. Khan
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-81538-4

Clinical implications of intrinsic molecular subtypes of breast cancer for sentinel node status
Cited by: 12
Author(s): Maria Rossing, Christina Bligaard Pedersen, Tove Filtenborg Tvedskov, Ilse Vejborg, Maj Lis Møller Talman, Lars Rønn Olsen, Niels Kroman, Finn Cilius Nielsen, Maj Britt Jensen, Bent Ejlertsen
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0111819

Expression Analysis of All Protease Genes Reveals Cathepsin K to Be Overexpressed in Glioblastoma
Cited by: 39
Author(s): Urška Verbovšek, Helena Motaln, Ana Rotter, Nadia A. Atai, Kristina Gruden, C. J. F. Van Noorden, Tamara T. Lah
Software Mentions: 5
Published: over 9 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2105-10-11

Filtering for increased power for microarray data analysis
Cited by: 218
Author(s): Amber J. Hackstadt, Ann Hess
Software Mentions: 5
Published: over 15 years ago

10.1186/1471-2105-9-422

SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
Cited by: 32
Author(s): Raj Chari, Bradley P. Coe, Craig Wedseltoft, Marie Benetti, Ian M. Wilson, Emily A. Vucic, Calum MacAulay, Raymond T. Ng, Wan L. Lam
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pone.0154531

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq
Cited by: 63
Author(s): Shiva Marthandan, Mario Baumgart, Stefan Priebe, Marco Groth, Jonas Schaer, Christoph Kaether, Reinhard Guthke, Alessandro Cellerino, Matthias Platzer, Stephan Diekmann, Peter Hemmerich
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0248650

Elucidating the immune infiltration in acne and its comparison with rosacea by integrated bioinformatics analysis
Cited by: 14
Author(s): Lu Yang, Yanhong Shou, Yue Yang, Jianhua Xu
Software Mentions: 5
Published: about 3 years ago

10.1038/s41398-019-0666-4

Hepatic gene expression explains primary drug toxicity in bipolar disorder
Cited by: 0
Author(s): Anna Maria Birkl-Toeglhofer, Christoph Birkl, Ida C. Llenos, Serge Weis, Johannes Haybaeck
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.39188

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury
Cited by: 27
Author(s): Jordan W. Squair, Seth Tigchelaar, Kyung‐Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K. Kwon, Andrei V. Krassioukov, Christopher R. West, Leonard J. Foster, Michael A. Skinnider
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0067907

Gene-Metabolite Expression in Blood Can Discriminate Allergen-Induced Isolated Early from Dual Asthmatic Responses
Cited by: 18
Author(s): Amrit Singh, Masatsugu Yamamoto, Sarah Kam, Jian Ruan, Gail M. Gauvreau, Paul M. O'Byrne, J. Mark FitzGerald, R. Robert Schellenberg, Louis‐Philippe Boulet, Gabriella Wojewodka, Cynthia Kanagaratham, Juan B. De Sanctis, Danuta Radzioch, Scott J. Tebbutt
Software Mentions: 5
Published: almost 11 years ago

10.3389/fnagi.2021.686066

Significant Difference of Immune Cell Fractions and Their Correlations With Differential Expression Genes in Parkinson’s Disease
Cited by: 13
Author(s): Yilin Huang, Huisheng Liu, Jiaqi Hu, Chongyin Han, Zhenggang Zhong, Wei Luo, Yuhu Zhang, Fei Ling
Software Mentions: 5
Published: almost 3 years ago

10.1186/1471-2105-6-98

ProGenExpress: Visualization of quantitative data on prokaryotic genomes
Cited by: 6
Author(s): Michael Watson
Software Mentions: 5
Published: about 19 years ago

10.1371/journal.pone.0129610

Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: almost 9 years ago

10.1002/cam4.2927

Identification of key lncRNAs in the tumorigenesis of intraductal pancreatic mucinous neoplasm by coexpression network analysis
Cited by: 11
Author(s): Jun Ding, Yang Li, Yong Zhang, Bin Fan, Qinghe Li, Jian Zhang
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2164-15-132

Major aging-associated RNA expressions change at two distinct age-positions
Cited by: 17
Author(s): Marius Gheorghe, M.M.J. Snoeck, Michael Emmerich, Thomas Bäck, Jelle J. Goeman, Vered Raz
Software Mentions: 5
Published: over 10 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2164-11-723

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
Cited by: 66
Author(s): José M. Otero, Wanwipa Vongsangnak, Mohammad Ali Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark, Jens Nielsen
Software Mentions: 5
Published: over 13 years ago

10.1093/jxb/eraa108

Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions
Cited by: 16
Author(s): Tai‐Hsi Wu, Shalini Krishnamoorthi, Honzhen Goh, Richalynn Leong, Amy Catherine Sanson, Daisuke Urano
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-017-07238-0

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

10.1038/s41598-019-48589-0

Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells
Cited by: 7
Author(s): Juan Bautista Menendez-Gonzalez, Samantha Sinnadurai, Alex Gibbs, Leigh-anne Thomas, Maria Konstantinou, Alfonso Garcia-Valverde, Magali Boyer, Zhengke Wang, Ashleigh S. Boyd, Allison Blair, Rhys G. Morgan, Neil P. Rodrigues
Software Mentions: 5
Published: over 4 years ago

10.7150/jca.42736

TOP2A Promotes Tumorigenesis of High-grade Serous Ovarian Cancer by Regulating the TGF-β/Smad Pathway
Cited by: 23
Author(s): Yan Gao, Hongyu Zhao, Meng Ren, Qi Chen, Jie Li, Zhefeng Li, Chenghong Yin, Wentao Yue
Software Mentions: 5
Published: over 4 years ago

10.1186/s13058-016-0714-4

Intermittent energy restriction induces changes in breast gene expression and systemic metabolism
Cited by: 33
Author(s): Michelle Harvie, Andrew H. Sims, Mary Pegington, Katherine Spence, Adam Mitchell, Andrew A. Vaughan, J. William Allwood, Yun Xu, Nicholas J. W. Rattray, Royston Goodacre, D. Gareth Evans, Ellen Sullivan Mitchell, Debbie McMullen, Robert B. Clarke, Anthony Howell
Software Mentions: 5
Published: almost 8 years ago

10.7150/jca.37637

Tumour-Infiltrating Immune Cell-Based Subtyping and Signature Gene Analysis in Breast Cancer Based on Gene Expression Profiles
Cited by: 15
Author(s): Jingxin Jiang, Weiwei Pan, Yazhang Xu, Chao Ni, Dan Xue, Zhigang Chen, Wuzhen Chen, Jian Huang
Software Mentions: 5
Published: over 4 years ago

10.1186/s13073-016-0315-y

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p
Cited by: 34
Author(s): Zsolt Czimmerer, Tamás Varga, Máté Kiss, Cesaré Ovando Vázquez, Quang Minh Doan‐Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna Nagy, Bence Dániel, Szilárd Póliska, Attila Horváth, Gergely Nagy, Éva Várallyay, Matthew N. Poy, Judith E. Allen, Zsolt Bacsó, Cei Abreu‐Goodger, László Nagy
Software Mentions: 5
Published: almost 8 years ago

10.1016/j.gpb.2019.02.003

Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma
Cited by: 12
Author(s): Jun Wang, Xueying Xie, Junchao Shi, Wenjun He, Qi Chen, Liang Chen, Wanjun Gu, Tong Zhou
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.0040006

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
Cited by: 45
Author(s): Michał Okoniewski, Crispin Miller
Software Mentions: 5
Published: about 16 years ago

10.1186/s13058-017-0814-9

DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms
Cited by: 28
Author(s): David J. Lemler, Miranda L. Lynch, Lia Tesfay, Zhiyong Deng, Bibbin T. Paul, Xiaohong Wang, Poornima Hegde, David H. Manz, Suzy V. Torti, Frank M. Torti
Software Mentions: 5
Published: about 7 years ago

10.3390/cancers11010053

Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning
Cited by: 34
Author(s): Kelvin Wong, Robert Rostomily, Stephen T.C. Wong
Software Mentions: 5
Published: over 5 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: over 3 years ago

10.3389/fimmu.2021.657162

Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness
Cited by: 3
Author(s): Eléna Gonçalves, Yolanda Guillén, Javier R. Lama, Jorge Sánchez, Christian Berthou, Roger Paredes, Béhazine Combadière
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-015-0750-x

A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status
Cited by: 164
Author(s): Sanjana Sood, Iain J. Gallagher, Katie Lunnon, Eric Rullman, Aoife Keohane, Hannah Crossland, Bethan E. Phillips, Tommy Cederholm, Thomas E. Jensen, Luc J. C. van Loon, Lars Lannfelt, William E. Kraus, Philip J. Atherton, Robert Howard, Thomas Gustafsson, Angela Hodges, James A. Timmons
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-016-1097-7

Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
Cited by: 64
Author(s): Andrée Delahaye‐Duriez, Prashant K. Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno‐Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafał M. Kamiński, Enrico Petretto, Michael R. Johnson
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.58716

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
Cited by: 210
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Francesca Luca, Yi Xu, Adnan Alazizi, Yaozhu Leng, Chaur Dong Hsu, Nardhy Gomez-López
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-213X-9-30

Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation
Cited by: 17
Author(s): Daniel Hughes, Roger J. Keynes, David Tannahill
Software Mentions: 4
Published: almost 15 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: over 9 years ago

10.1186/1471-2105-9-164

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Cited by: 32
Author(s): Richard D. Pearson
Software Mentions: 4
Published: about 16 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: almost 4 years ago

10.1155/2020/8604340

MCM2andNUSAP1Are Potential Biomarkers for the Diagnosis and Prognosis of Pancreatic Cancer
Cited by: 16
Author(s): Yajun Deng, Hanyun Ma, Jinyong Hao, Qiqi Xie, Rui Zhao
Software Mentions: 4
Published: about 4 years ago

10.1186/s12872-020-01819-0

Integrative transcriptomic, proteomic, and machine learning approach to identifying feature genes of atrial fibrillation using atrial samples from patients with valvular heart disease
Cited by: 14
Author(s): Yaozhong Liu, Fan Bai, Zhenwei Tang, Na Liu, Qiming Liu
Software Mentions: 4
Published: over 3 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 3 years ago

10.1155/2020/2137319

Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Dengyong Xu, Yuzi Xu, Yiming Lv, Fei Wu, Yunlong Liu, Ming Zhu, Dake Chen, Bingjun Bai
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.202153

Upregulation of KIF20A promotes tumor proliferation and invasion in renal clear cell carcinoma and is associated with adverse clinical outcome
Cited by: 30
Author(s): Xiaohan Ren, Xinglin Chen, Yisheng Ji, Liang-In Lin, Yunxin Li, Chao Qin, Kai Fang
Software Mentions: 4
Published: over 3 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: almost 6 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: over 11 years ago

10.7717/peerj.11995

The modulatory properties of Astragalus membranaceus treatment on endometrial cancer: an integrated pharmacological method
Cited by: 4
Author(s): Qianqian Zhang, Xianghua Huang
Software Mentions: 4
Published: over 2 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: over 14 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: over 10 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: over 6 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: 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: about 8 years ago

10.1186/1471-2105-7-335

AMDA: an R package for the automated microarray data analysis
Cited by: 35
Author(s): Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi‐Castagnoli
Software Mentions: 4
Published: almost 18 years ago

10.1186/s12885-016-2948-z

Conservation of immune gene signatures in solid tumors and prognostic implications
Cited by: 62
Author(s): Julia Chifman, Ashok Pullikuth, Jeff W. Chou, Davide Bedognetti, Lance D. Miller
Software Mentions: 4
Published: over 7 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: over 2 years ago

10.1186/s12918-014-0121-3

Understanding disease mechanisms with models of signaling pathway activities
Cited by: 42
Author(s): Patricia Sebastián-León, Enrique Vidal, Pablo Mínguez, Ana Conesa, Sonia Tarazona, Alicia Amadoz, Leandro Pardo, Francisco Salavert, António Vidal-Puig, David Montaner, Joaquín Dopazo
Software Mentions: 4
Published: over 9 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: almost 9 years ago

10.1186/s12918-016-0280-5

DNetDB: The human disease network database based on dysfunctional regulation mechanism
Cited by: 21
Author(s): Jing Yang, Sujuan Wu, Shaoyou Yang, Jiawei Peng, Shi-Nuo Wang, Fu-Yan Wang, Yu-Xing Song, Ting Qi, Yixue Li, Yuanyuan Li
Software Mentions: 4
Published: almost 8 years ago

10.1186/1752-0509-6-54

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
Cited by: 96
Author(s): Florian Martin, Timothy M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 4
Published: almost 12 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: almost 7 years ago

10.1136/annrheumdis-2020-217646

Unique expansion of IL-21+ Tfh and Tph cells under control of ICOS identifies Sjögren’s syndrome with ectopic germinal centres and MALT lymphoma
Cited by: 75
Author(s): Elena Pontarini, William Murray-Brown, Cristina Croia, Davide Lucchesi, James Conway, Felice Rivellese, Liliane Fossati-Jimack, Elisa Astorri, Edoardo Prediletto, Elisa Corsiero, Francesca Romana Delvecchio, Rachel Coleby, Eva Gelbhardt, Aurora Bono, Chiara Baldini, Ilaria Puxeddu, Piero Ruscitti, Roberto Giacomelli, Francesca Barone, Benjamin A Fisher, Simon Bowman, Serena Colafrancesco, Roberta Priori, Nurhan Sutcliffe, S. J. Challacombe, Gianluca Carlesso, Anwar R. Tappuni, Costantino Pitzalis, Michèle Bombardieri
Software Mentions: 4
Published: over 3 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: over 6 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: over 12 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: about 6 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: over 15 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2019.01181

Circular RNA-Associated Competing Endogenous RNA Network and Prognostic Nomogram for Patients With Colorectal Cancer
Cited by: 42
Author(s): Wei Song, Tao Fu
Software Mentions: 4
Published: over 4 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: over 11 years ago

Projects: bioconductor: affy

Papers Mentioning affy 989