bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1155/2020/8867019

Development of an Autophagy Score Signature for Predicting Overall Survival in Papillary Renal Cell Carcinoma
Cited by: 2
Author(s): Xiang Gu, Xiaojun Chen, Lei Zhu, Wenbo Song, Ali Wang, Junfeng Chu, Tao Wang, Peng Jiang, Yuxiang Ge
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-11-280

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Cited by: 4
Author(s): Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panos Deloukas, Simon Tavaré
Software Mentions: 3
Published: over 16 years ago

10.3389/fmolb.2021.691602

HTR2B and SLC5A3 Are Specific Markers in Age-Related Osteoarthritis and Involved in Apoptosis and Inflammation of Osteoarthritis Synovial Cells
Cited by: 6
Author(s): Xin Lu, Yu Fan, Mingxia Li, Xiao Chang, Jun Qian
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-9-502

Microarray-based gene set analysis: a comparison of current methods
Cited by: 68
Author(s): Sarah Song, Michael A. Black
Software Mentions: 3
Published: almost 18 years ago

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 8 years ago

10.1155/2021/8886897

Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer
Cited by: 7
Author(s): Shuyan Zhang, Shanshan Li, Jiuxin Guo, Ningyi Li, Caining Zhang, Jie Liu
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-12-480

GC-Content Normalization for RNA-Seq Data
Cited by: 656
Author(s): Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
Software Mentions: 3
Published: almost 15 years ago

10.1155/2021/8839747

A 5-lncRNA Signature Associated with Smoking Predicts the Overall Survival of Patients with Muscle-Invasive Bladder Cancer
Cited by: 2
Author(s): Haoyue Sheng, Guiming Zhang, Yao Qi Huang, Lili Sun, Guohai Shi, Dingwei Ye
Software Mentions: 3
Published: over 5 years ago

10.3389/fmolb.2021.645388

Mining TCGA Data for Key Biomarkers Related to Immune Microenvironment in Endometrial cancer by Immune Score and Weighted Correlation Network Analysis
Cited by: 18
Author(s): Chengbin Guo, Yuqin Tang, Yongqiang Zhang, Gen Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s13046-019-1202-3

FOXM1 promotes hepatocellular carcinoma progression by regulating KIF4A expression
Cited by: 85
Author(s): Guohui Hu, Zheng Yan, Cheng Zhang, Minzhang Cheng, Yizhong Yan, Yiting Wang, Libin Deng, Quqin Lu, Shuhong Luo
Software Mentions: 3
Published: over 7 years ago

10.1155/2021/8849977

A Risk Signature with Autophagy-Related Long Noncoding RNAs for Predicting the Prognosis of Clear Cell Renal Cell Carcinoma: Based on the TCGA Database and Bioinformatics
Cited by: 14
Author(s): Yundong Xuan, Wei-Hao Chen, Kan Liu, Yu Tang Gao, Shidong Zuo, Baojun Wang, Xin Ma, Xu Zhang
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.10578

Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation
Cited by: 49
Author(s): Abdelnaby Khalyfa, Isaac Almendros, Alex Gileles‐Hillel, Mahzad Akbarpour, Wojciech Trzépizur, Babak Mokhlesi, Lei Huang, Jorge Andrade, Ramón Farré, David Gozal
Software Mentions: 3
Published: about 10 years ago

10.3389/fmolb.2020.565173

IGFLR1 as a Novel Prognostic Biomarker in Clear Cell Renal Cell Cancer Correlating With Immune Infiltrates
Cited by: 8
Author(s): Wenjing Song, You-Cheng Shao, Xin He, Peng Gong, Yan Yang, Shu‐Chun Huang, Yifan Zeng, Lei Wei, Jingwei Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1004293

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
Cited by: 22
Author(s): Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand
Software Mentions: 3
Published: over 11 years ago

10.1186/s12885-021-08541-w

Molecular identification of an immunity- and Ferroptosis-related gene signature in non-small cell lung Cancer
Cited by: 10
Author(s): Taisheng Liu, Honglian Luo, Jinye Zhang, Xiaoshan Hu, Jian Zhang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13046-019-1092-4

LPCAT1 promotes brain metastasis of lung adenocarcinoma by up-regulating PI3K/AKT/MYC pathway
Cited by: 86
Author(s): Chunhua Wei, Xiaomin Dong, Hui Lü, Fan Tong, Lingjuan Chen, Ruiguang Zhang, Jing Dong, Yu Hu, Gang Wu, Xiaorong Dong
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-021-08358-7

Identification of novel hub genes associated with gastric cancer using integrated bioinformatics analysis
Cited by: 17
Author(s): Xin Lu, Jiaqian Zhang, Sheng‐Xiao Zhang, Jun Qiao, Mengting Qiu, Xiangrong Liu, Xiaoxia Chen, Chong Gao, Huan-Hu Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-021-08356-9

Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology
Cited by: 9
Author(s): Yutao Wang, Kexin Yan, Linhui Wang, Jianbin Bi
Software Mentions: 3
Published: about 5 years ago

10.1242/dmm.010975

Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice
Cited by: 105
Author(s): Benjamin I. Laufer, Katarzyna Mantha, Morgan L. Kleiber, Eric J. Diehl, Sean M. F. Addison, Shiva M. Singh
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2020.00734

Analysis of Differentially Expressed Genes and Molecular Pathways in Familial Hypercholesterolemia Involved in Atherosclerosis: A Systematic and Bioinformatics Approach
Cited by: 75
Author(s): Sanjit Kumar, Dhirendra Kumar, R. Bithia, Srivarshini Sankar, R. Magesh, Mariem Sidenna, George Priya Doss C, Hatem Zayed
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2021.698570

Comprehensive Bioinformatics Analysis Identifies POLR2I as a Key Gene in the Pathogenesis of Hypertensive Nephropathy
Cited by: 4
Author(s): Shilong You, Jiaqi Xu, Boquan Wu, Shaojun Wu, Ying Zhang, Yingxian Sun, Naijin Zhang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.01410

A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes
Cited by: 3
Author(s): Qifei Wang, Haojian Zhang, Yuqing Liang, Huichuan Jiang, Siqiao Tan, Feng Luo, Zheming Yuan, Yuan Chen
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00970

Hub Genes Identification in a Murine Model of Allergic Rhinitis Based on Bioinformatics Analysis
Cited by: 5
Author(s): Chen Le, Le Shi, Yue Ma, Cheng Zheng
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.503256

Construction and Analysis of a ceRNA Network in Cardiac Fibroblast During Fibrosis Based on in vivo and in vitro Data
Cited by: 7
Author(s): Qingyuan Gao, Haifeng Zhang, Zhi-Teng Chen, Yuewei Li, Shaohua Wang, Zheng Wen, Yong Xie, Jing-Ting Mai, Jingfeng Wang, Yangxin Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-4385-z

Transcriptional effects of a positive feedback circuit in Drosophila melanogaster
Cited by: 5
Author(s): Jarosław Bryk, R. Guy Reeves, Floyd A. Reed, Jai A. Denton
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-15-1176

Distinct gene signatures in aortic tissue from ApoE-/-mice exposed to pathogens or Western diet
Cited by: 8
Author(s): Carolyn D. Kramer, Ellen O. Weinberg, Adam C. Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M. Beaulieu, Lee M. Wetzler, Yuriy O. Alekseyev, Frank C. Gibson, Jane E. Freedman, Robin R. Ingalls, Caroline A. Genco
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2021.709666

Establishment of an Endocytosis-Related Prognostic Signature for Patients With Low-Grade Glioma
Cited by: 4
Author(s): Dawei Wang, Shiguang Liu, Guangxin Wang
Software Mentions: 3
Published: about 5 years ago

10.7150/ijbs.57802

Downregulation of ACE2 expression by SARS-CoV-2 worsens the prognosis of KIRC and KIRP patients via metabolism and immunoregulation
Cited by: 14
Author(s): Qian Tang, Yue Wang, Ling Ou, Jieling Li, Kai Zheng, Hui Zhan, Jiayu Gu, Guibao Zhou, Shouqi Xie, Jianping Zhang, Wei Huang, Shaoxiang Wang, Wang Xiao
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.12063

Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia
Cited by: 30
Author(s): Farzaneh Ghazavi, Barbara De Moerloose, Wouter Van Loocke, Annelynn Wallaert, Hetty Helsmoortel, Alina Ferster, Marleen Bâkkus, Geneviève Plat, Éric Delabesse, Anne Uyttebroeck, Filip Van Nieuwerburgh, Dieter Deforce, Nadine Van Roy, Frank Speleman, Yves Benoît, Tim Lammens, Pieter Van Vlierberghe
Software Mentions: 3
Published: about 10 years ago

10.18632/oncotarget.6678

Genetic deletion of osteopontin in TRAMP mice skews prostate carcinogenesis from adenocarcinoma to aggressive human-like neuroendocrine cancers
Cited by: 8
Author(s): Giorgio Mauri, Elena Jachetti, Barbara Comuzzi, Matteo Dugo, Ivano Arioli, Silvia Miotti, Sabina Sangaletti, Emma Di Carlo, Claudio Tripodo, Mario P. Colombo
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 10 years ago

10.1186/s12885-021-08319-0

Identification of 4-genes model in papillary renal cell tumor microenvironment based on comprehensive analysis
Cited by: 4
Author(s): Lun Luo, Haiyi Zhou, Hao Su
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-6589-x

Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments
Cited by: 2
Author(s): Jeffrey Thompson, Devin C. Koestler
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-019-6470-y

Gene signature characteristic of elevated stromal infiltration and activation is associated with increased risk of hematogenous and lymphatic metastasis in serous ovarian cancer
Cited by: 36
Author(s): Huiran Yue, Jieyu Wang, Ruifang Chen, Xiaoman Hou, Jun Li, Xin Lu
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07977-5

Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes
Cited by: 4
Author(s): Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati, Claire Wathes
Software Mentions: 3
Published: almost 5 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2021.689801

A Prognostic Autophagy-Related Gene Pair Signature and Small-Molecule Drugs for Hepatocellular Carcinoma
Cited by: 2
Author(s): Ze-bing Song, GuoPei Zhang, Yang Yu, shaoqiang li
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.739509

Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients
Cited by: 1
Author(s): Quan Jiang, Lingli Chen, Hao Chen, Zhaoqing Tang, Fenglin Liu, Yihong Sun
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2021.580190

Identification of Infertility-Associated Topologically Important Genes Using Weighted Co-expression Network Analysis
Cited by: 2
Author(s): Jingni Wu, Xiaomeng Xia, Ye Hu, Xiaoling Fang, Sandra Oršulić
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00905

Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis
Cited by: 10
Author(s): Huiying Yang, Yukun Wang, Ziyi Zhang, Hua Li
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-021-07935-1

A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis
Cited by: 4
Author(s): Tejaswi V. S. Badam, Hendrik A de Weerd, David Martínez-Enguita, Tomas Olsson, Lars Alfredsson, Ingrid Kockum, Maja Jagodic, Zelmina Lubovac-Pilav, Mika Gustafsson
Software Mentions: 3
Published: about 5 years ago

10.1186/s12885-020-07216-2

Comprehensive analysis of prognostic tumor microenvironment-related genes in osteosarcoma patients
Cited by: 19
Author(s): Chuan Hu, Chuan Liu, Shaoqi Tian, Yuanhe Wang, Rui Shen, Huili Rao, Jianyi Li, Yu Xu, Bo Chen, Ye Lin
Software Mentions: 3
Published: about 6 years ago

10.3389/fcell.2020.584232

HS-5 and HS-27A Stromal Cell Lines to Study Bone Marrow Mesenchymal Stromal Cell-Mediated Support to Cancer Development
Cited by: 24
Author(s): Annalisa Adamo, Pietro Delfino, Alessandro Gatti, Alice Bonato, Paul Takam Kamga, Ilaria Tanasi, Stefano Ugel, Angela Mercuri, Simone Caligola, Mauro Krampera
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12957-020-01921-9

Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms
Cited by: 8
Author(s): Sihan Chen, Guodong Cao, Wei Wu, Yida Lu, Xueling He, Lei Yang, Ke Chen, Bo Chen, Mao Ming Xiong
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.11524

Subclones in B-lymphoma cell lines: isogenic models for the study of gene regulation
Cited by: 6
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Ole Ammerpohl, Robert Geffers, Vivien Hauer, Roderick A.F. MacLeod, Stefan Nagel, Julia Romani, Emanuela Rosati, Anders Rosén, Cord C. Uphoff, Margarete Zaborski, Hans Drexler
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2407-10-126

The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer
Cited by: 54
Author(s): Robert Calaluce, Matthew M. Gubin, J. Wade Davis, Joseph Magee, Jing Chen, Yuki Kuwano, Myriam Gorospe, Ulus Atasoy
Software Mentions: 3
Published: over 16 years ago

10.1186/s12967-016-0886-9

Serum microRNA-1233 is a specific biomarker for diagnosing acute pulmonary embolism
Cited by: 33
Author(s): Thorsten Kessler, Jeanette Erdmann, Baiba Vilne, Petra Bruse, Volkhard Kurowski, Patrick Diemert, Heribert Schunkert, Hendrik B. Sager
Software Mentions: 3
Published: over 10 years ago

10.3389/fgene.2021.648111

Identification and Functional Prediction of Long Non-Coding RNAs in Dilated Cardiomyopathy by Bioinformatics Analysis
Cited by: 15
Author(s): Yuxiao Chen, Jie Ding, Wei-Er Zhou, Xuan Zhang, Xiaotong Sun, Xiying Wang, Chi Zhang, Li Ni, Guofeng Shao, Shen‐Jiang Hu, Jian Yang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-020-07628-0

Analyses of metastasis-associated genes in IDH wild-type glioma
Cited by: 4
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00716

m6A RNA Methylation Regulators Contribute to Eutopic Endometrium and Myometrium Dysfunction in Adenomyosis
Cited by: 21
Author(s): Junyu Zhai, Shang Li, Sushmita Sen, Jessica Opoku‐Anane, Yanzhi Du, Zi‐Jiang Chen, Linda C. Giudice
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2021.620740

Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People
Cited by: 5
Author(s): Zhenhua Lu, Ling‐Bing Meng, Zhen Sun, Xiaolei Shi, Weiwei Shao, Yangyang Zheng, Xinglei Yao, Jianguo Song
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0116704

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice
Cited by: 241
Author(s): Aaron C. Ericsson, J. Wade Davis, William G. Spollen, Nathan J. Bivens, Scott A. Givan, Catherine E. Hagan, Mark A. McIntosh, Craig L. Franklin
Software Mentions: 3
Published: over 11 years ago

10.1186/s12885-021-08456-6

Elevated TYROBP expression predicts poor prognosis and high tumor immune infiltration in patients with low-grade glioma
Cited by: 20
Author(s): Jiajie Lu, Yün Peng, Rihong Huang, Zejia Feng, Yongyang Fan, Haojian Wang, Zhiyong Zeng, Yunxiang Ji, Yezhong Wang, Zhaotao Wang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0054664

Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways
Cited by: 31
Author(s): Alejandra Idan Valencia-Cruz, Laura Uribe-Figueroa, Rodrigo Galindo‐Murillo, Karol Baca-López, Anllely Grizett Gutiérrez, Adriana Vázquez-Aguirre, Lena Ruíz-Azuara, Enrique Hernández‐Lemus, Carmen Mejía
Software Mentions: 3
Published: over 13 years ago

10.18632/aging.102365

Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients
Cited by: 21
Author(s): Haojie Yang, Lun Hua, Hong-Cheng Lin, Dan Gan, Wei Jin, Can Cui, Yixin Yan, Yiming Qian, Changpeng Han, Zhenyi Wang
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2020.501376

Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans
Cited by: 10
Author(s): M.G. Sterken, R. Bevers, Rita J. M. Volkers, J.A.G. Riksen, J.E. Kammenga, L. Basten Snoek
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00594

Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data
Cited by: 11
Author(s): Pierre R. Bushel, Stephen S. G. Ferguson, Sreenivasa Ramaiahgari, Richard S. Paules, Scott S. Auerbach
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-15-879

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples
Cited by: 13
Author(s): Alberto Risueño, Beatriz Rosón-Burgo, Anna Dolnik, Jesús María Hernández-Rivas, Lars Bullinger, Javier De Las Rivas
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2018.00083

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
Cited by: 57
Author(s): Emily Price, Wendy P. Robinson
Software Mentions: 3
Published: over 8 years ago

10.3390/v11060549

Lnc-ITM2C-1 and GPR55 Are Proviral Host Factors for Hepatitis C Virus
Cited by: 14
Author(s): Pan Hu, Jochen Wilhelm, Gesche K. Gerresheim, Lyudmila Shalamova, Michael Niepmann
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2021.718638

Identification of ARHGEF38, NETO2, GOLM1, and SAPCD2 Associated With Prostate Cancer Progression by Bioinformatic Analysis and Experimental Validation
Cited by: 8
Author(s): Zhuolun Sun, Yunfei Mao, Xu Zhang, Shuo Lu, Hua Wang, Chi Zhang, Chutian Xiao, Yinghao Cao, Yunhao Qing, Yu Wang, Ké Li
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.7262

miR-451a is underexpressed and targets AKT/mTOR pathway in papillary thyroid carcinoma
Cited by: 72
Author(s): Emanuela Minna, Paola Romeo, Matteo Dugo, Loris De Cecco, Katia Todoerti, Silvana Pilotti, Francesco Perrone, Ettore Seregni, Luca Agnelli, Antonino Neri, Angela Greco, Maria Grazia Borrello
Software Mentions: 3
Published: over 10 years ago

10.1186/1756-0500-5-1

Peripheral blood gene expression: it all boils down to the RNA collection tubes
Cited by: 128
Author(s): Andreas Menke, Monika Rex‐Haffner, Torsten Klengel, Elisabeth B. Binder, Divya Mehta
Software Mentions: 3
Published: over 14 years ago

10.3389/fgene.2020.00777

Integrative Analysis Revealing Human Heart-Specific Genes and Consolidating Heart-Related Phenotypes
Cited by: 4
Author(s): Jinsoo Ahn, Huiguang Wu, Kichoon Lee
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-14-371

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor
Cited by: 34
Author(s): Franc Llorens, Manuela Hummel, Lorena Pantano, Xavier Pastor, Ana Vivancos, Ester Castillo, Heidi Mattlin, Anna Ferrer, Matthew Ingham, María Noguera, Robert Kofler, Juliane C. Dohm, Raquel Pluvinet, Mònica Bayés, Heinz Himmelbauer, José Antonio del Río, Eulàlia Martı́, Lauro Sumoy
Software Mentions: 3
Published: over 13 years ago

10.18632/aging.103056

USP22 promotes development of lung adenocarcinoma through ubiquitination and immunosuppression
Cited by: 15
Author(s): Bing Han, Yue Sun, Dongdong Yang, Huijuan Zhang, Steven Mo, Xuesong Chen, Hui Lu, Xueyan Mao, Jing Hu
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00411

Identification and Validation of Potential Biomarkers and Their Functions in Acute Kidney Injury
Cited by: 19
Author(s): Jianwen Chen, Yalei Chen, Alberto Olivero, Xiangmei Chen
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphereDirect.00454-18

Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions
Cited by: 15
Author(s): Claus Lang, Melanie J. Barnett, Robert F. Fisher, Liane Smith, Michelle E. Diodati, Sharon R. Long
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-7-126

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
Cited by: 97
Author(s): Roland J. Siezen, Jos Boekhorst, Lidia Muscariello, Douwe Molenaar, Bernadet Renckens, Michiel Kleerebezem
Software Mentions: 3
Published: over 20 years ago

10.1128/mBio.00215-20

Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Cited by: 56
Author(s): Myra Hosmillo, Yasmin Chaudhry, Komal Nayak, Frédéric Sorgeloos, Bon‐Kyoung Koo, Alessandra Merenda, Reidun Lillestøl, Lydia N Drumright, Matthias Zilbauer, Ian Goodfellow
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0135284

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1
Cited by: 20
Author(s): Swanhild U. Meyer, Steffen Sass, Nikola S. Mueller, Stefan Krebs, Stefan Bauersachs, Sebastian Kaiser, Helmut Blum, Christian Thirion, Sabine Krause, Fabian J. Theis, Michael W. Pfaffl
Software Mentions: 3
Published: about 11 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0199392

Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period
Cited by: 17
Author(s): Julian Rothen, Carl Murie, Jason Carnes, Atashi Anupama, Salim Abdulla, Mwajuma Chemba, Maxmillian Mpina, Marcel Tanner, B. Kim Lee Sim, Stephen L. Hoffman, Raphaël Gottardo, Claudia Daubenberger, Ken Stuart
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2021.737598

Editorial: Predicting High-Risk Individuals for Common Diseases Using Multi-Omics and Epidemiological Data
Cited by: 1
Author(s): Debajyoti Chowdhury, Xin Zhou, Bailiang Li, Yuanwei Zhang, William K. Cheung, Aiping Lü, Lu Zhang
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.8907

Weighted gene correlation network analysis reveals novel biomarkers associated with mesenchymal stromal cell differentiation in early phase
Cited by: 9
Author(s): Bin Xiao, Guozhu Wang, Weiwei Li
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00429

Construction and Validation of a 13-Gene Signature for Prognosis Prediction in Medulloblastoma
Cited by: 3
Author(s): L. Chang, Han Zou, Zujian Xiong, Yi Xiong, Danielle F Miyagishima, Siyi Wanggou, Xuejun Li
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00647

Identification of a Hypoxia-Associated Signature for Lung Adenocarcinoma
Cited by: 49
Author(s): Zhuomao Mo, Ling Yu, Zhirui Cao, Hao Hu, Shaoju Luo, Shijun Zhang
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.00727

Integrative Bioinformatics Approaches to Screen Potential Prognostic Immune-Related Genes and Drugs in the Cervical Cancer Microenvironment
Cited by: 14
Author(s): Zitong Zhao, Jigang Li, He Li, Na-Yi Yuan Wu, Peilin Ouyang, Shan Liu, Jifeng Cai, Jing Wang
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2021.650213

Predicting the Key Genes Involved in Aortic Valve Calcification Through Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Dinghui Wang, Tianhua Xiong, Wenlong Yu, Bin Liu, Jing Wang, Kaihu Xiao, Sheng Qiang
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00024-18

In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction
Cited by: 49
Author(s): Florent Masson, Sandra Calderon Copete, Fanny Schüpfer, Mario Gonzalo Garcia-Arraez, Bruno Lemaître
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00453

Weighted Gene Co-expression Network Analysis of Endometriosis and Identification of Functional Modules Associated With Its Main Hallmarks
Cited by: 58
Author(s): Mohammad Reza Bakhtiarizadeh, Batool Hosseinpour, Maryam Shahhoseini, Arthur Korte, Peyman Gifani
Software Mentions: 3
Published: almost 8 years ago

10.1128/mBio.00301-18

TgTKL1 Is a Unique Plant-Like Nuclear Kinase That Plays an Essential Role in Acute Toxoplasmosis
Cited by: 15
Author(s): Joseph M. Varberg, Isabelle Coppens, Gustavo Arrizabalaga, Rajshekhar Y. Gaji
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-960

Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Cited by: 27
Author(s): Ignacio Caballero, Judy Yen, Lisa E. Hensley, Anna N. Honko, Arthur J. Goff, John H. Connor
Software Mentions: 3
Published: over 12 years ago

10.3389/fcell.2021.668738

Screening for Core Genes Related to Pathogenesis of Alzheimer’s Disease
Cited by: 3
Author(s): Long-Xiu Yang, Yuan Qin, Chongdong Jian
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00684-13

Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae
Cited by: 96
Author(s): Matthew J. Bush, Maureen J. Bibb, Govind Chandra, Kim Findlay, Mark J. Buttner
Software Mentions: 3
Published: almost 13 years ago

10.18632/oncotarget.8148

Challenges in detecting pre-malignant pancreatic lesions during acute pancreatitis using a serum microRNA assay: a study based on KrasG12D transgenic mice
Cited by: 8
Author(s): Xiafei Hong, Jie Zhang, Qiao Wu, Wenze Wang, Adam Yongxin Ye, Wei Song, Hongmei Dai, Xiaohong Wang, Fan Wu, Lei You, Wenming Wu, Yupei Zhao
Software Mentions: 3
Published: over 10 years ago

10.3389/fcell.2020.602174

A Prognostic Model for Colon Cancer Patients Based on Eight Signature Autophagy Genes
Cited by: 26
Author(s): Jiasheng Xu, Siqi Dai, Ying Yuan, Qian Xiao, Kefeng Ding
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0038602

Gene Expression Changes in the Septum: Possible Implications for MicroRNAs in Sculpting the Maternal Brain
Cited by: 19
Author(s): Changjiu Zhao, Michael C. Saul, Terri M. Driessen, Stephen C. Gammie
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-015-1972-8

Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Cited by: 14
Author(s): Rossana Sussarellu, Arnaud Huvet, Sylvie Lapègue, Virgile Quillen, Christophe Lelong, Florence Cornette, Lasse Fast Jensen, Nicolas Bierne, Pierre Boudry
Software Mentions: 3
Published: almost 11 years ago

10.3389/fgene.2016.00137

Gene Coexpression Analyses Differentiate Networks Associated with Diverse Cancers Harboring TP53 Missense or Null Mutations
Cited by: 19
Author(s): Kathleen Klein, Karim Oualkacha, Marie-Hélène Lafond, Sahir Bhatnagar, Patricia N. Tonin, Celia M.T. Greenwood
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-9-390

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: about 18 years ago

10.1186/1471-2164-15-852

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models
Cited by: 10
Author(s): Sophie Rodius, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Céline Jeanty, Juan Manuel González‐Rosa, Mark Ibberson, Ricardo Costa, Ioannis Xénarios, Nadia Mercader, Francisco Azuaje
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pcbi.1002568

MC EMiNEM Maps the Interaction Landscape of the Mediator
Cited by: 14
Author(s): Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin Maier, Dietmar E. Martin, Holger Fröhlich, Patrick Cramer, Achim Tresch
Software Mentions: 3
Published: about 14 years ago

10.1111/ppl.13086

Blue light induces major changes in the gene expression profile of the cyanobacterium<scp>Synechocystis</scp>sp. PCC 6803
Cited by: 14
Author(s): Veerle M. Luimstra, J. Merijn Schuurmans, Klaas J. Hellingwerf, H.C.P. Matthijs, Jef Huisman
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.566024

Novel Gene Signature Reveals Prognostic Model in Acute Myeloid Leukemia
Cited by: 8
Author(s): Ying Qu, Shuying Zhang, Yanzhang Qu, Heng Guo, Suling Wang, Xuemei Wang, Tianjiao Huang, Hong Zhou
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5900-1

Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data
Cited by: 5
Author(s): Fernando Carazo, Marian Gimeno, Juan A Ferrer-Bonsoms, Ángel Rubio
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.8713

Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma
Cited by: 43
Author(s): Naiara da Costa Cinegaglia, Sónia C. S. Andrade, Tomáš Tokár, Maísa Pinheiro, Fabio Severino, Rogério Antônio de Oliveira, Érica Nishida Hasimoto, Daniele Cristina Catâneo, Antônio José Maria Catâneo, Júlio Defaveri, Cleonilson Protásio de Souza, Márcia Maria Chiquitelli Marques, Robson Francisco Carvalho, Luiz Lehmann Coutinho, Jefferson Luiz Gross, Sílvia Regina Rogatto, Wan L. Lam, Igor Jurišica, Patrícia P. Reis
Software Mentions: 3
Published: over 10 years ago

10.1038/s41398-021-01565-7

Intrauterine hyperglycemia impairs memory across two generations
Cited by: 9
Author(s): Kexin Zou, Jun Ren, Shuai Luo, Junyu Zhang, Chuanpeng Zhou, Chengxi Tan, Peng Lv, Xiao Sun, Jian‐Zhong Sheng, Xinmei Liu, He‐Feng Huang, Guo‐Lian Ding
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0113529

Genetic Insights into Graminella nigrifrons Competence for Maize fine streak virus Infection and Transmission
Cited by: 10
Author(s): Bryan J. Cassone, Fiorella M. Cisneros Carter, Andrew P. Michel, Lucy R. Stewart, Margaret G. Redinbaugh
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2019.00932

Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis
Cited by: 25
Author(s): Aftab Alam, Nikhat Imam, Mohd Murshad Ahmed, Safiya Tazyeen, Naaial Tamkeen, Anam Farooqui, Md. Zubbair Malik, Romana Ishrat
Software Mentions: 3
Published: almost 7 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776