Ecosyste.ms: Papers

10.1007/s12032-017-0963-9

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

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: almost 15 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 10 years ago

10.1038/srep26136

SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer
Cited by: 25
Author(s): Huidi Liu, Emilio Mastriani, Zi-Qiao Yan, Shuai Yin, Zheng Zeng, Hong Wang, Qinghai Li, Hongyu Liu, Xiaoyu Wang, Hongchu Bao, Yujie Zhou, Junjie Kou, Dongsheng Li, Ting Li, Jianrui Liu, Yongfang Liu, Lin Yin, Li Qiu, Liling Gong, Shulin Liu
Software Mentions: 6
Published: over 8 years ago

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2020.581789

Integrated Analysis of Key Genes and Pathways Involved in Fetal Growth Restriction and Their Associations With the Dysregulation of the Maternal Immune System
Cited by: 2
Author(s): Xue Wang, Hong Zhu, Lei Lei, Yang Zhang, Chao Tang, Jingyi Wu, Jing Zhou, Xirong Xiao
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-14-770

The periodontal pathogen Porphyromonas gingivalis changes the gene expression in vascular smooth muscle cells involving the TGFbeta/Notch signalling pathway and increased cell proliferation
Cited by: 28
Author(s): Boxi Zhang, Ali Ateia Elmabsout, Hazem Khalaf, Vladimir Basic, Kartheyaene Jayaprakash, Robert L. Kruse, Torbjörn Bengtsson, Allan Sirsjö
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2164-13-453

Microarray analysis revealing common and distinct functions of promyelocytic leukemia protein (PML) and tumor necrosis factor alpha (TNFα) signaling in endothelial cells
Cited by: 21
Author(s): Xiangguo Cheng, Hung‐Ying Kao
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12944-018-0798-1

Peripheral-blood gene expression profiling studies for coronary artery disease and its severity in Xinjiang population in China
Cited by: 6
Author(s): Meng Li, Shubin Jiang, Yu Ma, Ma Jun, Waseem Hassan, Jing Shang
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0052493

Anti-Inflammatory Lactobacillus rhamnosus CNCM I-3690 Strain Protects against Oxidative Stress and Increases Lifespan in Caenorhabditis elegans
Cited by: 134
Author(s): Gianfranco Grompone, Patricia Martorell, Silvia Llopis, Núria González, Salvador Genovés, Ana Paula Mulet, Tamara Fernández-Calero, Inés Tiscornia, Mariela Bollati-Fogolín, Isabelle Chambaud, Benoît Foligné, Agustín Montserrat, Daniel Ramón
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0245046

Liver epigenome changes in patients with hepatopulmonary syndrome: A pilot study
Cited by: 4
Author(s): Núria Mendoza, Eva Rivas, Roberto Rodríguez-Roisin, Tamara García, Miquel Bruguera, Àlvar Agustí, Rosa Faner
Software Mentions: 3
Published: over 3 years ago

10.1016/j.celrep.2017.08.003

Alloimmune Responses of Humanized Mice to Human Pluripotent Stem Cell Therapeutics
Cited by: 29
Author(s): Nigel G. Kooreman, Patrícia E. de Almeida, J. Stack, Raman Nelakanti, Sebastian Diecke, Ning‐Yi Shao, Rutger-Jan Swijnenburg, Verónica Sánchez-Freire, Elena Matsa, Chun Li, Andrew J. Connolly, Jaap F. Hamming, Paul H.A. Quax, Michael A. Brehm, Dale L. Greiner, Leonard D. Shultz, Joseph C. Wu
Software Mentions: 3
Published: about 7 years ago

10.1038/srep44232

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue
Cited by: 73
Author(s): Jarrett Morrow, Xiaobo Zhou, Taotao Lao, Zhiqiang Jiang, Dawn L. DeMeo, Michael H. Cho, Weiliang Qiu, Suzanne M. Cloonan, Víctor Pinto-Plata, B Celli, Nathaniel Marchetti, Gerard J. Criner, Raphael Bueno, George R. Washko, Kimberly Glass, John Quackenbush, Augustine M.K. Choi, Edwin K. Silverman, Craig P. Hersh
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-21065-x

RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment
Cited by: 25
Author(s): Kuo‐Hua Lin, Ming‐Yii Huang, Wei‐Chung Cheng, Shu-Chi Wang, Shih-Hua Fang, Hung-Pin Tu, Chin-Chuan Su, Yung-Li Hung, Po-Len Liu, Chi-Shuo Chen, Yuting Wang, Chia-Yang Li
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-60466-9

Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives
Cited by: 17
Author(s): Hye Yeong Jo, Hyo Won Han, Il Bong Jung, Ji Hyeon Ju, Soon‐Jung Park, Sung-Hwan Moon, Dongho Geum, Hye Min Kim, Han-Jin Park, Sun Kim, Glyn Stacey, Soo Kyung Koo, Mi-Hyun Park, Jung Hyun Kim
Software Mentions: 3
Published: over 4 years ago

10.1186/s12920-014-0072-y

Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods
Cited by: 49
Author(s): Jarrett Morrow, Weiliang Qiu, Divya Chhabra, Stephen I. Rennard, Paula Belloni, Anton Belousov, Sreekumar Pillai, Craig P. Hersh
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.7436

Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis
Cited by: 21
Author(s): Ze-Kun Liu, Renyu Zhang, Yu‐Le Yong, Zhiyun Zhang, Can Li, Zhi‐Nan Chen, Huijie Bian
Software Mentions: 2
Published: about 5 years ago

10.3892/ijmm.2015.2064

Sex-related gene expression profiles in the adrenal cortex in the mature rat: Microarray analysis with emphasis on genes involved in steroidogenesis
Cited by: 29
Author(s): Marcin Trejter, Anna Hochól, Marianna Tyczewska, Agnieszka Ziółkowska, Karol Jopek, Marta Szyszka, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 2
Published: over 9 years ago

10.1155/2016/1634730

Rapid Identification of Potential Drugs for Diabetic Nephropathy Using Whole-Genome Expression Profiles of Glomeruli
Cited by: 6
Author(s): Jingsong Shi, Song Jiang, Dandan Qiu, Weibo Le, Xiao Wang, Yinhui Lu, Zhihong Liu
Software Mentions: 2
Published: almost 9 years ago

10.1093/bioinformatics/btz039

InterMineR: an R package for InterMine databases
Cited by: 19
Author(s): Konstantinos Kyritsis, Bing Wang, Julie Sullivan, Rachel Lyne, Gos Micklem
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0063656

Protective Effects of Andrographolide Analogue AL-1 on ROS-Induced RIN-mβ Cell Death by Inducing ROS Generation
Cited by: 16
Author(s): Guang-Rong Yan, Hui-Hua Zhou, Yang Wang, Yin Zhong, Zi-Lu Tan, Yuqiang Wang, Qing-Yu He
Software Mentions: 2
Published: over 11 years ago

10.1038/s41389-018-0093-z

Development and evaluation of a novel series of Nitroxoline-derived BET inhibitors with antitumor activity in renal cell carcinoma
Cited by: 8
Author(s): Wei Chen, Hao Zhang, Zhifeng Chen, Hao Jiang, Liping Liao, Shijie Fan, Jing Xing, Yiqian Xie, Shijie Chen, Hong Ding, Kaixian Chen, Hualiang Jiang, Cheng Luo, Mingyue Zheng, Zhiyi Yao, Yiran Huang, Yuanyuan Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0086051

Mining Gene Expression Data for Pollutants (Dioxin, Toluene, Formaldehyde) and Low Dose of Gamma-Irradiation
Cited by: 23
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, А. В. Снежкина, V. R. Kogan, Ekaterina Plyusnina, Darya Peregudova, Nataliya V. Melnikova, Л. А. Урошлев, S. V. Mylnikov, Alexey A. Dmitriev, Sergey Plusnin, П. О. Федичев, Anna V. Kudryavtseva
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0070176

Transcriptional Events during the Recovery from MRSA Lung Infection: A Mouse Pneumonia Model
Cited by: 12
Author(s): Jiwang Chen, Gang Feng, Qiang Guo, Juliane Bubeck Wardenburg, Simon Lin, Ichiro Inoshima, Ryan Deaton, Jason X.‐J. Yuan, Joe G.N. Garcia, Roberto F. Machado, Michael Otto, Richard G. Wunderink
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0067994

Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: A Mouse MRSA Pneumonia Model
Cited by: 6
Author(s): Jiwang Chen, Gang Feng, Yang Song, Juliane Bubeck Wardenburg, Simon Lin, Ichiro Inoshima, Michael Otto, Richard G. Wunderink
Software Mentions: 1
Published: over 11 years ago

10.1016/j.stemcr.2019.01.017

Calpain Inhibition Restores Autophagy and Prevents Mitochondrial Fragmentation in a Human iPSC Model of Diabetic Endotheliopathy
Cited by: 33
Author(s): Sang‐Bing Ong, Won Hee Lee, Ning Shao, Nur Izzah Ismail, Khairunnisa Katwadi, Mim Mim Lim, Xiu Yi Kwek, Nathaly Anto Michel, Jiajun Li, Jordan Newson, Soroush Tahmasebi, Jalees Rehman, Kazuki Kodo, Hye Ryoun Jang, Sang Ging Ong
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.6194

Amplification of ACK1 promotes gastric tumorigenesis via ECD-dependent p53 ubiquitination degradation
Cited by: 22
Author(s): Songhui Xu, Jinzhou Huang, Min Chen, Ming Zeng, Feiyan Zou, De Chen, Guang-Rong Yan
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13054-015-1127-y

Improvement of prognostic performance in severely injured patients by integrated clinico-transcriptomics: a translational approach
Cited by: 16
Author(s): Daniel Rittirsch, Veit Schoenborn, Sandro Lindig, Elisabeth Wanner, Kai Sprengel, Sebastian Günkel, Barbara Schaarschmidt, Sonja Märsmann, Hans‐Peter Simmen, Paolo Cinelli, Michael Bauer, Ralf A. Claus, Guido A. Wanner
Software Mentions: 1
Published: almost 9 years ago

10.1186/1476-069X-13-94

Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study
Cited by: 49
Author(s): Juan J. Carmona, Tamar Sofer, John N. Hutchinson, Laura Cantone, Brent A. Coull, Arnab Maity, Pantel Vokonas, Xihong Lin, Joel Schwartz, Andrea Baccarelli
Software Mentions: 1
Published: almost 10 years ago

10.3389/fneur.2017.00152

Molecular Taxonomy of Sporadic Amyotrophic Lateral Sclerosis Using Disease-Associated Genes
Cited by: 20
Author(s): Giovanna Morello, Antonio Gianmaria Spampinato, Sebastiano Cavallaro
Software Mentions: 1
Published: over 7 years ago

10.3389/fonc.2019.01570

Overexpression of IGF2BP3 as a Potential Oncogene in Ovarian Clear Cell Carcinoma
Cited by: 24
Author(s): Huidi Liu, Zheng Zeng, Mitra Afsharpad, Caiji Lin, Siwen Wang, Hao Yang, Shuhong Liu, Linda E. Kelemen, Wenwen Xu, Wenqing Ma, Qing Xiang, Emilio Mastriani, Pengfei Wang, Jiali Wang, Shulin Liu, Randal N. Johnston, Martin Köbel
Software Mentions: 1
Published: over 4 years ago

10.1007/s00380-018-1158-9

Vascular restenosis in coronary artery bypass grafting might be associated with VEGF-C/VEGFR-3 signaling pathway
Cited by: 8
Author(s): Zuzanna Podemska-Jedrzejczak, Agnieszka Malińska, Patrycja Sujka‐Kordowska, Michał Nowicki, Mateusz Puślecki, Marek Jemielity, Bartłomiej Perek
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1005308

The SMC Loader Scc2 Promotes ncRNA Biogenesis and Translational Fidelity
Cited by: 8
Author(s): Musinu Zakari, Rhonda Trimble Ross, Allison Peak, Marco Blanchette, Chris Seidel, Jennifer L. Gerton
Software Mentions: 1
Published: about 9 years ago