bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-42485-3

Comparison of multi-tissue aging between human and mouse
Cited by: 13
Author(s): Jujuan Zhuang, Lijun Zhang, Shuang Dai, Lingyu Cui, Cheng Guo, Laura Sloofman, Jialiang Yang
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-13-296

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data
Cited by: 167
Author(s): James R. Perkins, J. D. K. Dawes, Stephen B. McMahon, David L.H. Bennett, Christine A. Orengo, Matthias Kohl
Software Mentions: 4
Published: over 14 years ago

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.10458

Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods
Cited by: 13
Author(s): Gao Li, Yu‐Yan Pang, Xian-yu Guo, Jingjing Zeng, Zhong-Qing Tang, Dandan Xiong, Xia Yang, Ying Liu, Fuchao Ma, Lang Pan, Zhaoyong Feng
Software Mentions: 4
Published: almost 6 years ago

10.1042/BSR20203235

Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Cited by: 2
Author(s): Li Zhao, Yajun Xiao, Li Xu, Qingxiu Wang
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203505

Transcriptomic analysis of elderly women with low muscle mass: association with immune system pathway
Cited by: 1
Author(s): Levi H. Jales Neto, Bidossessi Wilfried Hounkpe, Geórgea Hermogenes Fernandes, Liliam Takayama, Valéria F. Caparbo, Neuza Lopes, Alexandre C. Pereira, Rosa Maria Rodrigues Pereira
Software Mentions: 4
Published: about 5 years ago

10.3390/jcm8050639

The Role of MicroRNAs in the Regulation of Gastric Cancer Stem Cells: A Meta-Analysis of the Current Status
Cited by: 22
Author(s): Vitalba Ruggieri, Sabino Russi, Pietro Zoppoli, Francesco La Rocca, Tiziana Angrisano, Geppino Falco, Giovanni Calice, Simona Laurino
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2020.529386

Integrative Analysis of DNA Methylation and Gene Expression to Determine Specific Diagnostic Biomarkers and Prognostic Biomarkers of Breast Cancer
Cited by: 17
Author(s): Ming Zhang, Yilin Wang, Yan Wang, Longyang Jiang, Xueping Li, Hua Gao, Minjie Wei, Lin Zhao
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/4612158

CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: about 6 years ago

10.3390/pathogens9050380

Inhibition of Asaia in Adult Mosquitoes Causes Male-Specific Mortality and Diverse Transcriptome Changes
Cited by: 12
Author(s): Maria Vittoria Mancini, Claudia Damiani, Sarah M. Short, Alessia Cappelli, Ulisse Ulissi, Aida Capone, Aurelio Serrao, Paolo Rossi, Augusto Amici, Cristina Kalogris, George Dimopoulos, Irene Ricci, Guido Favia
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: almost 9 years ago

10.7717/peerj.7705

The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma
Cited by: 30
Author(s): Jieling Li, Wang Xiao, Kai Zheng, Ying Liu, Junjun Li, Shaoqi Wang, Kaisheng Liu, Xianrang Song, Nan Li, Shouqi Xie, Shaoxiang Wang
Software Mentions: 4
Published: almost 7 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: over 11 years ago

10.1186/1471-2105-14-188

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
Cited by: 14
Author(s): George Y. Wu, Hongkai Ji
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2164-15-300

Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer
Cited by: 81
Author(s): Wei-Chun Chou, An‐Lin Cheng, Marco Brotto, Chun‐Yu Chuang
Software Mentions: 4
Published: over 12 years ago

10.3390/ijms21041518

The Molecular Mechanism of Perillaldehyde Inducing Cell Death in Aspergillus flavus by Inhibiting Energy Metabolism Revealed by Transcriptome Sequencing
Cited by: 18
Author(s): Chao Pan, Yongxin Li, Kunlong Yang, Famous Erhunmwunsee, Yan Ma, Xiaona He, Qingru Geng, Man Liu, Jun Tian
Software Mentions: 4
Published: over 6 years ago

10.3389/fmolb.2021.729789

Development of a Toll-Like Receptor-Based Gene Signature That Can Predict Prognosis, Tumor Microenvironment, and Chemotherapy Response for Hepatocellular Carcinoma
Cited by: 4
Author(s): Lixia Liu, Bin Liu, Jie Yu, Dongyun Zhang, Jing Shi, Ping Liang
Software Mentions: 4
Published: almost 5 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: about 5 years ago

10.3389/fcell.2021.691676

A Novel Risk Model Based on Lipid Metabolism-Associated Genes Predicts Prognosis and Indicates Immune Microenvironment in Breast Cancer
Cited by: 13
Author(s): Zhimin Ye, Shengmei Zou, Zhiyuan Niu, Zhijie Xu, Yongbin Hu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-021-08111-0

A novel 10 glycolysis-related genes signature could predict overall survival for clear cell renal cell carcinoma
Cited by: 20
Author(s): Qianwei Xing, Taidui Zeng, Shouyong Liu, Hong Cheng, Limin Ma, Yi Wang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-16747-x

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Cited by: 193
Author(s): Peter W. Eide, Jarle Bruun, Ragnhild Lothe, Anita Sveen
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms21062249

AHR Signaling Dampens Inflammatory Signature in Neonatal Skin γδ T Cells
Cited by: 11
Author(s): Katja Merches, Alfonso Schiavi, Heike Weighardt, Swantje Steinwachs, Nadine Teichweyde, Irmgard Förster, K Hochrath, Beatrix Schumak, Natascia Ventura, Patrick Petzsch, Karl Köhrer, Charlotte Esser
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1009390

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition
Cited by: 11
Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-40992-x

A comparison between the abdominal and femoral adipose tissue proteome of overweight and obese women
Cited by: 18
Author(s): Max Vogel, Ping Wang, Freek G. Bouwman, Nicole Hoebers, Ellen E. Blaak, Johan Renes, E.C.M. Mariman, Gijs H. Goossens
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21082966

Differential Expression and Function of Bicellular Tight Junctions in Skin and Oral Wound Healing
Cited by: 20
Author(s): Trevor R. Leonardo, Junhe Shi, Dandan Chen, Harsh M. Trivedi, Lin Chen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-20856-6

A cleavage product of Polycystin-1 is a mitochondrial matrix protein that affects mitochondria morphology and function when heterologously expressed
Cited by: 68
Author(s): Cheng-Chao Lin, Mahiro Kurashige, Yi Liu, Takeshi Terabayashi, Yu Ishimoto, Tanchun Wang, Vineet Choudhary, Ryan P. Hobbs, Li-Ka Liu, Ping-Hsien Lee, Patricia Outeda, Fang Zhou, Nicholas P. Restifo, Terry Watnick, Haruna Kawano, Shigeo Horie, William A. Prinz, Hong Xu, Luís F. Menezes, Gregory G. Germino
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.104134

The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis prediction
Cited by: 12
Author(s): Zhen Tan, Yubin Lei, Jin Xu, Si Shi, Jie Hua, Bo Zhang, Qingcai Meng, Jiang Liu, Yiyin Zhang, Miaoyan Wei, Xianjun Yu, Chen Liang
Software Mentions: 4
Published: almost 6 years ago

10.1590/1678-4685-GMB-2019-0090

Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma
Cited by: 4
Author(s): Yongwei Wang, Yaxian Gao, Sen Guo, Zhihong Chen
Software Mentions: 4
Published: over 6 years ago

10.1002/advs.202003504

Cytosolic Delivery of Thiolated Neoantigen Nano‐Vaccine Combined with Immune Checkpoint Blockade to Boost Anti‐Cancer T Cell Immunity
Cited by: 28
Author(s): Da Zhang, Zongming Lin, Ming Wu, Zhixiong Cai, Youshi Zheng, Lei He, Zhenli Li, Jie Zhou, Liqin Sun, Geng Chen, Yongyi Zeng, Juan Li, Jingfeng Liu, Huanghao Yang, Xiaolong Liu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1003188

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene
Cited by: 29
Author(s): Dario Nicetto, Matthias Hahn, Julia Jeannine Jung, Tobias D. Schneider, Tobias Straub, Róbert Dávid, Gunnar Schotta, Ralph A.W. Rupp
Software Mentions: 4
Published: over 13 years ago

10.1007/s00401-020-02230-x

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
Cited by: 21
Author(s): Sheila Mansouri, Suganth Suppiah, Yasin Mamatjan, Irene Paganini, Jeffrey Liu, Shirin Karimi, Vikas Patil, Farshad Nassiri, Olivia Singh, Yogi Sundaravadanam, Pramod C. Rath, Roberta Sestini, Francesca Gensini, Sameer Agnihotri, Jaishri O. Blakeley, Kimberly Laskie Ostrow, David A. Largaespada, Scott R. Plotkin, Anat Stemmer‐Rachamimov, Marcela Maria Ferrer, Trevor J. Pugh, Kenneth Aldape, Laura Papi, Gelareh Zadeh
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.102459

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma
Cited by: 13
Author(s): Song Jing, Fangzhou Song, Kun Liu, Wanfeng Zhang, Ruihan Luo, Yongyao Tang
Software Mentions: 4
Published: almost 7 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: almost 19 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: over 6 years ago

10.1186/bcr3684

Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer
Cited by: 45
Author(s): Bojana Jovanović, J. Scott Beeler, Michael W. Pickup, Anna Chytil, Agnieszka E. Gorska, William J. Ashby, Brian D. Lehmann, Andries Zijlstra, Jennifer A. Pietenpol, Harold L. Moses
Software Mentions: 4
Published: about 12 years ago

10.1038/celldisc.2017.13

Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
Cited by: 7
Author(s): Miriam Landfors, Jostein Johansen, Jan Magnus Aronsen, Cathrine Broberg Vågbø, Louis C. Doré, Chuan He, Ivar Sjaastad, Pål Sætrom, Péter Fedorcsák, John Arne Dahl, Håvard Aanes, Markus Fußer, Arne Klungland
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.202365

Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinoma
Cited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: over 5 years ago

10.7150/ijms.50491

Multi‐omics analysis of tumor mutational burden combined with prognostic assessment in epithelial ovarian cancer based on TCGA database
Cited by: 18
Author(s): Jinhui Liu, Wei Xu, Siyue Li, Rui Sun, Wenjun Cheng
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2021.695533

Identification of a Costimulatory Molecule Gene Signature to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Ling Aye, Xiaole Song, Jingyi Yang, Li Hu, Xicai Sun, Jiaju Zhou, Quan Liu, Hongmeng Yu, Dehui Wang
Software Mentions: 4
Published: about 5 years ago

10.3389/fmolb.2020.571641

Identification of a Novel Tumor Microenvironment–Associated Eight-Gene Signature for Prognosis Prediction in Lung Adenocarcinoma
Cited by: 36
Author(s): Chi Ma, Huan Luo, Jing Cao, Xiangyu Zheng, Jinjun Zhang, Yanmin Zhang, Zongqiang Fu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-39733-x

HER2 and p95HER2 differentially regulate miRNA expression in MCF-7 breast cancer cells and downregulate MYB proteins through miR-221/222 and miR-503
Cited by: 15
Author(s): Andrej Gorbatenko, Rolf Søkilde, Ester E. Sørensen, Inga Newie, Helena Persson, Beatriz Morancho, Joaquı́n Arribas, Thomas Litman, Carlos Rovira, Stine Falsig Pedersen
Software Mentions: 4
Published: over 7 years ago

10.3390/pathogens9070524

The Effect of Natural Feline Coronavirus Infection on the Host Immune Response: A Whole-Transcriptome Analysis of the Mesenteric Lymph Nodes in Cats with and without Feline Infectious Peritonitis
Cited by: 5
Author(s): Alexandra Malbon, Giancarlo Russo, Carole Burgener, Emi Barker, Marina L. Meli, Séverine Tasker, Anja Kipar
Software Mentions: 4
Published: about 6 years ago

10.1155/2021/8848227

A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma
Cited by: 10
Author(s): Yi Ding, Li Tian, Min Li, Tuersong Tayier, Meilin Zhang, Long Chen, Shumei Feng
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.01549

Inference of Subpathway Activity Profiles Reveals Metabolism Abnormal Subpathway Regions in Glioblastoma Multiforme
Cited by: 0
Author(s): Xudong Han, Donghua Wang, Ping Zhao, Chonghui Liu, Yilong Hao, Lulu Chang, Jian Zhao, Wei Zhao, Lili Mu, Jinghua Wang, Hulun Li, Qingfei Kong, Junwei Han
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 11 years ago

10.1172/JCI96138

REVERBa couples the circadian clock to hepatic glucocorticoid action
Cited by: 69
Author(s): Giorgio Caratti, Mudassar Iqbal, Louise Hunter, Dong Hwan Kim, Ping Wang, Ryan Vonslow, Nicola Begley, Abigail J. Tetley, Joanna Woodburn, Marie Pariollaud, Robert Maidstone, Ian J. Donaldson, Zhenguang Zhang, Louise Ince, Gareth Kitchen, Matthew Baxter, Toryn Poolman, Dion A. Daniels, David R. Stirling, Chad Brocker, Frank J. Gonzalez, A. S. I. Loudon, David A. Bechtold, Magnus Rattray, Laura Matthews, David Ray
Software Mentions: 4
Published: about 8 years ago

10.1155/2020/3416807

Identification of Hub Genes as Biomarkers Correlated with the Proliferation and Prognosis in Lung Cancer: A Weighted Gene Co-Expression Network Analysis
Cited by: 2
Author(s): Xuting Xu, Limin Xu, Huilian Huang, Jing Li, Shunli Dong, Lili Jin, Zhiyong Ma, Liqin Li
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.58597

The leukocyte non-coding RNA landscape in critically ill patients with sepsis
Cited by: 28
Author(s): Brendon P. Scicluna, Fabrice Uhel, Lonneke A. van Vught, Maryse A. Wiewel, Arie J. Hoogendijk, Ingelore Baessman, Marek Franitza, Peter Nürnberg, Janneke Horn, Olaf L. Cremer, Marc J. M. Bonten, Marcus J. Schultz, Tom van der Poll
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-38965-1

Initial findings of striatum tripartite model in OCD brain samples based on transcriptome analysis
Cited by: 14
Author(s): Bianca Cristina Garcia Lisbôa, Kátia C. Oliveira, Ana Carolina Tahira, André Rocha Barbosa, Arthur Sant’Anna Feltrin, Gisele Rodrigues Gouveia, Luzia Carreira Lima, Ana Cecília Feio dos Santos, David Martins, Renato Puga, Ariane Cristine Moretto, Carlos Alberto de Bragança Pereira, Beny Lafer, Renata Elaine Paraízo Leite, Renata Eloah de Lucena Ferretti‐Rebustini, José Marcelo Farfel, Lea T. Grinberg, Wilson Jacob‐Filho, Eurípedes Constantino Miguel, Marcelo Q. Hoexter, Helena Brentani
Software Mentions: 4
Published: over 7 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: over 6 years ago

10.1038/s41419-021-04144-2

LncRNA PCBP1-AS1-mediated AR/AR-V7 deubiquitination enhances prostate cancer enzalutamide resistance
Cited by: 19
Author(s): Boya Zhang, Mingpeng Zhang, Chunyi Shen, Guancong Liu, Fan Zhang, Jingyu Hou, Weitao Yao
Software Mentions: 4
Published: almost 5 years ago

10.1042/BSR20194337

Mining TCGA database for tumor mutation burden and their clinical significance in bladder cancer
Cited by: 71
Author(s): Jia Lv, Yongze Zhu, Alin Ji, Qi Zhang, Guodong Liao
Software Mentions: 4
Published: over 6 years ago

10.1155/2019/1093815

Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis
Cited by: 9
Author(s): Yao Ma, Xiaofei Feng, Wan-Xia Yang, Chongge You
Software Mentions: 4
Published: about 7 years ago

10.1042/BSR20201261

Construction of a novel prognostic-predicting model correlated to ovarian cancer
Cited by: 3
Author(s): Wei-Chun Tang, Jie Li, Xinxia Chang, Lizhou Jia, Qi Tang, Ying Wang, Yanli Zheng, Lichao Sun, Zhenqing Feng
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21228749

Dysregulation of Transcription Factor Activity during Formation of Cancer-Associated Fibroblasts
Cited by: 6
Author(s): Przemysław Kapusta, Joanna Dulińska-Litewka, Justyna Totoń‐Żurańska, A. Borys, Paweł Konieczny, Paweł Wołkow, Michał Seweryn
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcell.2021.699212

A Novel Six Metastasis-Related Prognostic Gene Signature for Patients With Osteosarcoma
Cited by: 12
Author(s): Di Zheng, Kezhou Xia, Ling Yu, Changtian Gong, Yubo Shi, Wěi Li, Yonglong Qiu, Jian Yang, Weichun Guo
Software Mentions: 4
Published: about 5 years ago

10.1155/2013/167915

Correction of Spatial Bias in Oligonucleotide Array Data
Cited by: 2
Author(s): Philippe Serhal, Sébastien Lemieux
Software Mentions: 4
Published: over 13 years ago

10.1186/s12859-020-3366-4

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Cited by: 4
Author(s): Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich A. Maus, Thomas Illig, David S. DeLuca
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.7135

Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis
Cited by: 31
Author(s): Fangcao Lei, Han Zhang, Xiaoli Xie
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.670184

A Novel Ferroptosis-Related Gene Signature for Overall Survival Prediction in Patients With Breast Cancer
Cited by: 18
Author(s): Lizhe Zhu, Qiang Tian, Siyuan Jiang, Huan Gao, Shibo Yu, Yifeng Zhou, Yan Yu, Yu Ren, Jianjun He, Bin Wang
Software Mentions: 4
Published: over 5 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: almost 9 years ago

10.3390/ijms22010275

The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function
Cited by: 8
Author(s): Yashwanth Subbannayya, Markus Haug, Sneha M. Pinto, Varshasnata Mohanty, Hany Zakaria Meås, Trude Helen Flo, T. S. Keshava Prasad, Richard K. Kandasamy
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cmet.2020.09.001

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy
Cited by: 107
Author(s): Dorian Forte, María García-Fernández, Abel Sánchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martín-Pérez, Juan Antonio López, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, M. Barber, Paolo Gallipoli, Ludovica Marando, Carlos L.F. de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michèle Cavo, Lucia Catani, Antonio Curti, Jesús Vázquez, Christian Frezza, Brian J. P. Huntly, Juerg Schwaller, Simón Méndez-Ferrer
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmolb.2021.633951

Identification of Epithelial-Mesenchymal Transition-Related lncRNAs that Associated With the Prognosis and Immune Microenvironment in Colorectal Cancer
Cited by: 6
Author(s): Chuan Liu, Chuan Hu, Jianyi Li, Liqing Jiang, Chengliang Zhao
Software Mentions: 4
Published: over 5 years ago

10.3389/pore.2021.1609868

Screening and Validation of Independent Predictors of Poor Survival in Pancreatic Cancer
Cited by: 6
Author(s): Lingling Shui, Yan Cai, E Changyong, Jiyao Sheng, Xuewen Zhang
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.102824

Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of osteosarcoma
Cited by: 103
Author(s): Chi Zhang, Jinghui Zheng, Zong-Han Lin, Haoyuan Lv, Zhuo-Miao Ye, Yueping Chen, Xiaoyun Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008076

Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures
Cited by: 57
Author(s): Dirk Schumacher, Geoffroy Andrieux, Karsten Boehnke, Marlen Keil, Alessandra Silvestri, Maxine Silvestrov, Ulrich Keilholz, Johannes Haybaeck, Gerrit Erdmann, Christoph Sachse, Markus F. Templin, Jens Hoffmann, Melanie Boerries, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 4
Published: over 7 years ago

10.1186/s13045-014-0089-x

Splicing factor 3b subunit 1 (Sf3b1) haploinsufficient mice display features of low risk Myelodysplastic syndromes with ring sideroblasts
Cited by: 20
Author(s): Valeria Visconte, Ali Tabarroki, Li Zhang, Yvonne Parker, Edy Hasrouni, R. Mahfouz, Kyoichi Isono, Haruhiko Koseki, Mikkael A. Sekeres, Yogen Saunthararajah, John Barnard, Daniel J. Lindner, Heesun J. Rogers, Ramon V. Tiu
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.64680

Urocortin-3 neurons in the mouse perifornical area promote infant-directed neglect and aggression
Cited by: 23
Author(s): Anita E. Autry, Wu Zheng, Vikrant Kapoor, Johannes Kohl, Dhananjay Bambah-Mukku, Nimrod D. Rubinstein, Brenda Marin-Rodriguez, Ilaria Carta, Victoria Sedwick, Ming Tang, Catherine Dulac
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22031332

The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling
Cited by: 4
Author(s): Daniel Pensold, Julia Gehrmann, Georg Pitschelatow, Asa Walberg, Kai Braunsteffer, Julia Reichard, Amin Ravaei, Jenice Linde, Angelika Lampert, Ivan G. Costa, Geraldine Zimmer-Bensch
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/5974350

A Prognostic Model Based on Six Metabolism-Related Genes in Colorectal Cancer
Cited by: 14
Author(s): Yuanlin Sun, Yang Zhang, Yuchen Guo, Zihao Yang, You Xu
Software Mentions: 4
Published: about 6 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 13 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22041632

Construction and Validation of a Prognostic Gene-Based Model for Overall Survival Prediction in Hepatocellular Carcinoma Using an Integrated Statistical and Bioinformatic Approach
Cited by: 8
Author(s): Eskezeia Y. Dessie, Siang-Jyun Tu, Hui-Shan Chiang, Jeffrey J. P. Tsai, Ya‐Sian Chang, Jan-Gowth Chang, Ka-Lok Ng
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9452

Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells
Cited by: 6
Author(s): Nanjue Cao, Henan Liu, Feng Dong, Wei Wang, Wei Sun, Gang Wang
Software Mentions: 4
Published: about 6 years ago

10.1042/BSR20193349

Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma
Cited by: 5
Author(s): Yu Jin, Xing Qin
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-06789-3

Distinctions between sex and time in patterns of DNA methylation across puberty
Cited by: 11
Author(s): Sarah R. Moore, Kathryn L. Humphreys, Natalie L. Colich, Elena Goetz Davis, David Lin, Julia L. MacIsaac, Michæl S. Kobor, Ian H. Gotlib
Software Mentions: 4
Published: over 6 years ago

10.1186/s13223-021-00584-9

Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells
Cited by: 1
Author(s): Jan Krzysztof Nowak, Marzena Dworacka, Nazgul Gubaj, Arystan Dossimov, Zhumabek Dossimov, Jarosław Walkowiak
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22052679

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model
Cited by: 15
Author(s): Fábio Pértille, Manuel Álvarez‐Rodríguez, Arthur Nery da Silva, Isabel Barranco, Jordi Roca, Carlos Guerrero-Bosagna, Heriberto Rodríguez-Martinez
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/9143695

Identification of Prognosis-Related Genes in Bladder Cancer Microenvironment across TCGA Database
Cited by: 7
Author(s): Xin Zhao, Yu Tang, Haoyu Ren, Yi Lei
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-96149-2

Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes
Cited by: 2
Author(s): V. D. Yakushina, В. В. Стрельников, А. С. Танас, А. В. Лавров
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2695-1

Improving microRNA target prediction with gene expression profiles
Cited by: 22
Author(s): Cesaré Ovando-Vázquez, Daniel Lepe-Soltero, Cei Abreu‐Goodger
Software Mentions: 4
Published: over 10 years ago

10.1186/s13195-018-0394-7

Alzheimer’s disease master regulators analysis: search for potential molecular targets and drug repositioning candidates
Cited by: 62
Author(s): Daiani Machado de Vargas, Marco Antônio De Bastiani, Eduardo R. Zimmer, Fábio Klamt
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-020-03935-2

H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection
Cited by: 9
Author(s): Nan Zhou, Ji Bao, Yuping Ning
Software Mentions: 4
Published: over 5 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: over 6 years ago

10.7554/eLife.18312

PDZD7-MYO7A complex identified in enriched stereocilia membranes
Cited by: 37
Author(s): Clive P. Morgan, Jocelyn F. Krey, M’hamed Grati, Bo Zhao, Shannon Fallen, Abhiraami Kannan-Sundhari, Xue Zhong Liu, Dongseok Choi, Ulrich Müller, Peter G. Barr-Gillespie
Software Mentions: 4
Published: about 10 years ago

10.1074/mcp.RA119.001392

Cathepsin L Regulates Metabolic Networks Controlling Rapid Cell Growth and Proliferation
Cited by: 7
Author(s): Tommy Weiss-Sadan, Gal Itzhak, Farnusch Kaschani, Zhanru Yu, Mohamed Mahameed, Adi Anaki, Yael Ben-Nun, Emmanuelle Merquiol, Boaz Tirosh, Benedikt M. Kessler, Markus Kaiser, Galia Blum
Software Mentions: 4
Published: about 7 years ago

10.1136/jitc-2020-001610

Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer
Cited by: 17
Author(s): Incheol Seo, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min, Sung Hwan Lee, Ju-Seog Lee, Shin Kim, Sung Uk Bae
Software Mentions: 4
Published: over 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 7 years ago

10.3389/fneur.2021.576382

Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome
Cited by: 6
Author(s): Hui Xie, Ce Yuan, Jinjiang Li, Zhaoyang Li, Wei-Cheng Lu
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.560229

A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related Genes
Cited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: over 11 years ago

10.18632/aging.203352

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer
Cited by: 8
Author(s): Yongfeng Wang, Kaili Lin, Tianchun Xu, Liuli Wang, Liangyin Fu, Guangming Zhang, Jing Ai, Yajun Jiao, Rongrong Zhu, Xiaoyong Han, Hui Cai
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/5549298

Bioinformatic Analysis of Prognostic and Immune-Related Genes in Pancreatic Cancer
Cited by: 2
Author(s): Ziang Li, Chang Hu, Zhiqiang Yang, Minlan Yang, Jiayu Fang, Xuhong Zhou
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-38310-y

Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium
Cited by: 5
Author(s): Monika Horázná, Lucie Janečková, Jiří Švec, Oľga Babošová, Dušan Hrčkulák, Martina Vojtěchová, Kateřina Galušková, Eva Šloncová, Michal Kolář, Hynek Strnad, Vladimír Kořínek
Software Mentions: 4
Published: over 7 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776