Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: edgeR

https://packages.ecosyste.ms/registries/bioconductor.org/packages/edgeR

Empirical Analysis of Digital Gene Expression Data in R
3 versions
Latest release: about 1 year ago
166 dependent packages
2,704,225 downloads total

Papers Mentioning edgeR 6,568

10.1186/s12864-015-1731-x
Daytime soybean transcriptome fluctuations during water deficit stress
Cited by: 38
Author(s): Fabiana Aparecida Rodrigues, Renata Fuganti-Pagliarini, Juliana Marcolino-Gomes, Thiago Jonas Nakayama, Hugo Bruno Correa Molinari, Francisco Pereira Lobo, Frank G. Harmon, Alexandre Lima Nepomuceno
Software Mentions: 1
Published: over 9 years ago
10.3390/genes12050618
Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda
Cited by: 7
Author(s): Yue Jin, Shihao Li, Yang Yu, Chengsong Zhang, Xiaojun Zhang, Fuhua Li
Software Mentions: 1
Published: over 3 years ago
10.1128/mSystems.00275-18
Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum
Cited by: 3
Author(s): Jake J. Flood, Shelley D. Copley
Software Mentions: 1
Published: about 6 years ago
10.1186/1471-2164-14-412
Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production
Cited by: 29
Author(s): Sara J. Hanson, Claus‐Peter Stelzer, David Welch, John M. Logsdon
Software Mentions: 1
Published: over 11 years ago
10.1186/s12865-021-00439-3
Differential long non-coding RNA expression profile and function analysis in primary Sjogren’s syndrome
Cited by: 7
Author(s): Xiaochan Chen, Qi Cheng, Yan Du, Lei Liu, Huaxiang Wu
Software Mentions: 1
Published: over 3 years ago
10.3389/fphar.2021.607379
17β-Estradiol Promotes Apoptosis of HepG2 Cells Caused by Oxidative Stress by Increasing Foxo3a Phosphorylation
Cited by: 5
Author(s): Yusheng Guo, Xiangsheng Cai, Hong-Yang Lu, Qiqi Li, Ying Zheng, Zefang Lin, Zexiong Cheng, Maoxiang Yang, Li Zhang, Lei Xiang, Xiaorong Yang
Software Mentions: 1
Published: over 3 years ago
10.3390/genes12060944
Expression of Wnt and TGF-Beta Pathway Components during Whole-Body Regeneration from Cell Aggregates in Demosponge Halisarca dujardinii
Cited by: 6
Author(s): Ilya Borisenko, Fyodor Bolshakov, Alexander Ereskovsky, Andrey Lavrov
Software Mentions: 1
Published: over 3 years ago
10.3390/genes12070985
CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression
Cited by: 8
Author(s): Francesca Maria Rossi, Alvaro Centrón-Broco, Dario Dattilo, Gaia Di Timoteo, Marco Guarnacci, Alessio Colantoni, Manuel Beltran Nebot, Irene Bozzoni
Software Mentions: 1
Published: over 3 years ago
10.3389/fphar.2020.529553
The Target MicroRNAs and Potential Underlying Mechanisms of Yiqi-Bushen-Tiaozhi Recipe against‐Non-Alcoholic Steatohepatitis
Cited by: 9
Author(s): Hong Wang, Songsong Li, Yan Cai, Tingting Zhang, Qingrou Yang, Beihui He, Jianshun Yu, Zhiyun Chen
Software Mentions: 1
Published: about 4 years ago
10.3389/fphar.2020.584450
IQGAP3 Overexpression Correlates With Poor Prognosis and Radiation Therapy Resistance in Breast Cancer
Cited by: 10
Author(s): Xin Hua, Zhi‐Qing Long, Lanwei Guo, Wen Wen, Xin Huang, Wen Zhang
Software Mentions: 1
Published: almost 4 years ago
10.3389/fonc.2019.01348
7-lncRNA Assessment Model for Monitoring and Prognosis of Breast Cancer Patients: Based on Cox Regression and Co-expression Analysis
Cited by: 32
Author(s): Huayao Li, Chundi Gao, Lijuan Liu, Jing Zhuang, Jing Yang, Cun Liu, Chao Zhou, Fubin Feng
Software Mentions: 1
Published: almost 5 years ago
10.3389/fonc.2017.00135
Ror2 Signaling and Its Relevance in Breast Cancer Progression
Cited by: 38
Author(s): Michaela Bayerlová, Kerstin Menck, Florian Klemm, Alexander Wolff, Tobias Pukrop, Claudia R. Binder, Tim Beißbarth, Annalen Bleckmann
Software Mentions: 1
Published: over 7 years ago
10.3389/fonc.2019.00448
Integrated Bioinformatic Analysis of a Competing Endogenous RNA Network Reveals a Prognostic Signature in Endometrial Cancer
Cited by: 20
Author(s): Leilei Xia, Ye Wang, Meng Qi, Xiaoling Su, Jizi Shen, Jing Wang, Haiwei He, Biwei Wen, Caihong Zhang, Man Xu
Software Mentions: 1
Published: over 5 years ago
10.3390/genes12091437
Metformin Triggers Apoptosis and Induction of the G0/G1 Switch 2 Gene in Macrophages
Cited by: 5
Author(s): Xuming Hu, Huai‐Rong Luo, Chunfeng Dou, Xujing Chen, Yi Huang, Liping Wang, Song Xue, Zhen Sun, Shihao Chen, Qi Xu, Tuoyu Geng, Xin Zhao, Hengmi Cui
Software Mentions: 1
Published: about 3 years ago
10.3389/fonc.2021.587548
A 15-Gene Signature and Prognostic Nomogram for Predicting Overall Survival in Non-Distant Metastatic Oral Tongue Squamous Cell Carcinoma
Cited by: 3
Author(s): Muyuan Liu, Litian Tong, Bin Liang, Xuhong Song, Lingzhu Xie, Hanwei Peng, Dongyang Huang
Software Mentions: 1
Published: over 3 years ago
10.3389/fonc.2021.687208
LINC00346 Sponges miR-30c-2-3p to Promote the Development of Lung Adenocarcinoma by Targeting MYBL2 and Regulating CELL CYCLE Signaling Pathway
Cited by: 10
Author(s): Qinying Xu, Zuo-Feng Xu, Kai Zhu, Jinlan Lin, Bo Ye
Software Mentions: 1
Published: about 3 years ago
10.3389/fonc.2021.699625
Circular RNA hsa_circ_0007507 May Serve as a Biomarker for the Diagnosis and Prognosis of Gastric Cancer
Cited by: 5
Author(s): Weiwei Zhang, Ming Zheng, Shan Kong, Xian Li, Shuting Meng, Xudong Wang, Feng Wang, Chenxue Tang, Shaoqing Ju
Software Mentions: 1
Published: about 3 years ago
10.1590/1678-4685-GMB-2018-0033
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana
Cited by: 7
Author(s): Suhong Fu, Ming Lei, Zhang YongQun, Zhaomin Deng, Jing Shi, Doudou Hao
Software Mentions: 1
Published: over 5 years ago
10.3389/fonc.2021.736620
A Phase II Trial of Adjuvant Durvalumab Following Trimodality Therapy for Locally Advanced Esophageal and Gastroesophageal Junction Adenocarcinoma: A Big Ten Cancer Research Consortium Study
Cited by: 20
Author(s): Hirva Mamdani, Bryan J. Schneider, Susan M. Perkins, Heather N. Burney, Pashtoon Murtaza Kasi, Laith Abushahin, Thomas J. Birdas, Kenneth A. Kesler, Tracy M. Watkins, Sunil Badve, Milan Radovich, Shadia I. Jalal
Software Mentions: 1
Published: about 3 years ago
10.1590/1678-4685-GMB-2019-0377
Transcriptomic evidences of local thermal adaptation for the native fish Colossoma macropomum (Cuvier, 1818)
Cited by: 6
Author(s): Luciana Mara Fé-Gonçalves, José Deney Alves Araújo, Carlos dos Anjos dos Henrique Santos, Vera Maria Fonseca de Almeida-Val
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-021-08003-4
Early life and adult stress promote sex dependent changes in hypothalamic miRNAs and environmental enrichment prevents stress-induced miRNA and gene expression changes in rats
Cited by: 7
Author(s): Lauren McKibben, Yogesh K. Dwivedi
Software Mentions: 1
Published: about 3 years ago
10.1186/s12864-019-5823-x
Understanding the liver under heat stress with statistical learning: an integrated metabolomics and transcriptomics computational approach
Cited by: 15
Author(s): Allen Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh, Carl J. Schmidt
Software Mentions: 1
Published: over 5 years ago
10.3389/fonc.2020.581985
Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma
Cited by: 9
Author(s): Yanjie Han, Xinxin Li, Jiliang Yan, Chunyan Ma, Xin Wang, Hong Pan, Xiaoli Zheng, Zhen Zhang, Biao Gao, Xin‐Ying Ji
Software Mentions: 1
Published: about 4 years ago
10.1186/s12864-021-07825-6
Maternal cold exposure induces distinct transcriptome changes in the placenta and fetal brown adipose tissue in mice
Cited by: 3
Author(s): Sujoy Ghosh, Chul‐Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jenny L. Sones, Heike Münzberg, Leanne M. Redman, Jason Y. Chang
Software Mentions: 1
Published: over 3 years ago
10.3389/fonc.2021.626858
Genome-Wide Analyses of Prognostic and Therapeutic Alternative Splicing Signatures in Bladder Urothelial Carcinoma
Cited by: 1
Author(s): Zhongru Fan, Zhe Zhang, Chiyuan Piao, Zhuona Liu, Ze‐Shu Wang, Chuize Kong
Software Mentions: 1
Published: over 3 years ago
10.1534/genetics.117.300103
Developmental Restriction of Retrotransposition Activated in <i>Arabidopsis</i> by Environmental Stress
Cited by: 21
Author(s): Hervé Gaubert, Diego H. Sánchez, Hajk-Georg Drost, Jerzy Paszkowski
Software Mentions: 1
Published: over 7 years ago
10.3389/fonc.2020.00850
CircCSPP1 Functions as a ceRNA to Promote Colorectal Carcinoma Cell EMT and Liver Metastasis by Upregulating COL1A1
Cited by: 19
Author(s): Qingyuan Wang, Li Shi, Kui Shi, Bo Yuan, Gang Cao, Chenchen Kong, Jun Fu, Zhongsong Man, Xu Li, Xuanfeng Zhang, Yifei Feng, Xinglu Jiang, Xinhui Zhang, Jun Yan, Xiaohu Wu, Yueming Sun
Software Mentions: 1
Published: over 4 years ago
10.3389/fimmu.2021.705253
Targeted Transcriptomics of Frog Virus 3 in Infected Frog Tissues Reveal Non-Coding Regulatory Elements and microRNAs in the Ranaviral Genome and Their Potential Interaction with Host Immune Response
Cited by: 5
Author(s): Yun Tian, Collins N. Khwatenge, Jiuyi Li, Francisco De Jesús Andino, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2019.00265
Transcriptome Profiles of Human Visceral Adipocytes in Obesity and Colorectal Cancer Unravel the Effects of Body Mass Index and Polyunsaturated Fatty Acids on Genes and Biological Processes Related to Tumorigenesis
Cited by: 23
Author(s): Manuela Del Cornò, Antonella Baldassarre, Enrica Calura, Lucia Conti, Paolo Martini, Chiara Romualdi, Rosaria Varı́, Beatrice Scazzocchio, Massimo D’Archivio, Andrea Masotti, Sandra Gessani
Software Mentions: 1
Published: almost 6 years ago
10.3389/fimmu.2014.00396
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis
Cited by: 48
Author(s): Kirsten E. McLoughlin, Nicolas C. Nalpas, Kévin Rue-Albrecht, John A. Browne, David A. Magee, Kate E. Killick, Stephen D. E. Park, Karsten Hokamp, Kieran G. Meade, Cliona O’Farrelly, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 1
Published: about 10 years ago
10.1186/gb-2010-11-3-r25
A scaling normalization method for differential expression analysis of RNA-seq data
Cited by: 5,530
Author(s): Mark D. Robinson, Alicia Oshlack
Software Mentions: 1
Published: almost 15 years ago
10.1186/s12864-017-3515-y
Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress
Cited by: 7
Author(s): Juanxia Wu, Huabin Zhao, Dan Yu, Xinglong Xu
Software Mentions: 1
Published: almost 8 years ago
10.3389/fimmu.2020.01240
Neonatal Diet Impacts Circulatory miRNA Profile in a Porcine Model
Cited by: 4
Author(s): Laura E. Carr, Anne K. Bowlin, Ahmed A. Elolimy, Stephanie D. Byrum, Charity L. Washam, Christopher E. Randolph, Stewart L. MacLeod, Laxmi Yeruva
Software Mentions: 1
Published: over 4 years ago
10.3389/fimmu.2020.01602
Systemic Sclerosis Perturbs the Architecture of the Immunome
Cited by: 10
Author(s): Bhairav Paleja, Andrea Low, Pavanish Kumar, Suzan Saidin, Ahmad Lajam, Sharifah Nur Hazirah, Camillus Chua, Lai Li Yun, Salvatore Albani
Software Mentions: 1
Published: over 4 years ago
10.3389/fimmu.2019.02888
Mycobacterium abscessus—Bronchial Epithelial Cells Cross-Talk Through Type I Interferon Signaling
Cited by: 15
Author(s): Chongxu Zhang, Huda Asif, Gregory E. Holt, Anthony J. Griswold, Michael Campos, P.A. Bejarano, Nevis Fregien, Mehdi Mirsaeidi
Software Mentions: 1
Published: almost 5 years ago
10.3389/fimmu.2020.592569
Helpless Priming Sends CD8+ T Cells on the Road to Exhaustion
Cited by: 23
Author(s): Julia Busselaar, Sun Tian, Hans van Eenennaam, Jannie Borst
Software Mentions: 1
Published: about 4 years ago
10.1186/s12864-020-06869-4
Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects of 56Fe, 16O, and 28Si irradiation on the induction of murine hepatocellular carcinoma
Cited by: 5
Author(s): Anna M. Nia, Kamil Khanipov, Brooke L. Barnette, Robert L. Ullrich, George Golovko
Software Mentions: 1
Published: over 4 years ago
10.3389/fimmu.2016.00670
Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a
Cited by: 22
Author(s): Jennifer K. King, Nolan Ung, May Paing, Jorge R. Contreras, Michael O. Alberti, Thilini R. Fernando, Kelvin Zhang, Matteo Pellegrini, Dinesh S. Rao
Software Mentions: 1
Published: almost 8 years ago
10.3389/fimmu.2021.729776
The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis
Cited by: 15
Author(s): Miao Zou, Xiaoyun Su, Luoying Wang, Xingcheng Yi, Yue Qiu, Xirui Yin, Xuan Zhou, Xinhui Niu, Liuli Wang, Manman Su
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2021.688294
Macrophage Polarization Modulated by Porcine Circovirus Type 2 Facilitates Bacterial Coinfection
Cited by: 6
Author(s): Wen Zhang, Zhendong Fu, Hongyan Yin, Qin Han, Wenhui Fan, Fangkun Wang, Yue Shang
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2164-14-400
The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants
Cited by: 43
Author(s): Yvonne Weiss, Sylvain Forêt, David C. Hayward, Tracy D. Ainsworth, Rob King, Eldon E. Ball, David J. Miller
Software Mentions: 1
Published: over 11 years ago
10.1186/s12864-019-6082-6
A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression
Cited by: 13
Author(s): Stewart T. G. Burgess, Edward J Marr, Kathryn Bartley, Francesca Nunn, Rachel E. Down, Robert J. Weaver, Jessica C. Prickett, J. A. Dunn, Stéphane Rombauts, Thomas Van Leeuwen, Yves Van de Peer, Alasdair J. Nisbet
Software Mentions: 1
Published: about 5 years ago
10.1186/gb-2013-14-12-r149
Staged miRNA re-regulation patterns during reprogramming
Cited by: 16
Author(s): Christine Henzler, Zhonghan Li, Jason Dang, Mary Luz Arcila, Hongjun Zhou, Jingya Liu, Kung Yen Chang, Danielle S. Bassett, Tariq M. Rana, Kenneth S. Kosik
Software Mentions: 1
Published: almost 12 years ago
10.3389/fimmu.2021.703632
A Biological Circuit Involving Mef2c, Mef2d, and Hdac9 Controls the Immunosuppressive Functions of CD4+Foxp3+ T-Regulatory Cells
Cited by: 4
Author(s): Eros Di Giorgio, Liqing Wang, Yan Xiong, Lanette M Christensen, Tatiana Akimova, Rongxiang Han, Arabinda Samanta, Matteo Trevisanut, Claudio Brancolini, Ulf H. Beier, Wayne W. Hancock
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2020.02191
Human Chondrocyte Activation by Toxins From Premolis semirufa, an Amazon Rainforest Moth Caterpillar: Identifying an Osteoarthritis Signature
Cited by: 4
Author(s): Isadora Maria Villas-Boas, Giselle Pidde, Flávio Lichtenstein, Ana Tung Ching Ching, Inácio L.M. Junqueira-de-Azevedo, Carlos DeOcesano-Pereira, Carlos Eduardo Madureira Trufen, Ana Marisa Chudzinski‐Tavassi, Kátia L.P. Morais, Denise V. Tambourgi
Software Mentions: 1
Published: about 4 years ago
10.3389/fimmu.2020.01064
Different Exosomal microRNA Profile in Aquaporin-4 Antibody Positive Neuromyelitis Optica Spectrum Disorders
Cited by: 7
Author(s): Chen Chen, Yunting Wu, Miaochang Li, Chun-Ping Chu, Yipeng Zhao, Xiaobo Sun, Yuge Wang, Chunxin Liu, Haotian Wu, Xiaonan Zhong, Allan G. Kermode, Lisheng Peng
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-017-3644-3
High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production
Cited by: 20
Author(s): Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu, Diyan Li
Software Mentions: 1
Published: over 7 years ago
10.3389/fimmu.2021.722500
Transcriptional Changes in Pulmonary Phagocyte Subsets Dictate the Outcome Following Interaction With The Fungal Pathogen Cryptococcus neoformans
Cited by: 4
Author(s): Ashlee Hawkins, Brenden F. Determann, Benjamin N. Nelson, Karen L. Wozniak
Software Mentions: 1
Published: about 3 years ago
10.3389/fgene.2021.698983
Comparative Transcriptomic Analysis Reveals the Immunosuppressive Targets of Mesalazine in Dextran Sulfate Sodium-Induced Ulcerative Colitis
Cited by: 1
Author(s): Rong Li, Lin Cheng, Qi Wang, Liming Zhou
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2021.635599
Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation
Cited by: 6
Author(s): Yuqing Liu, Xudong Wang, Leyi Yuan, Yuxiang Liu, Tong Shen, Yunhua Zhang
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2021.667877
Leveraging Methylation Alterations to Discover Potential Causal Genes Associated With the Survival Risk of Cervical Cancer in TCGA Through a Two-Stage Inference Approach
Cited by: 7
Author(s): Jinhui Zhang, Haojie Lu, Shuo Zhang, Ting Wang, Huashuo Zhao, Fengjun Guan, Ping Zeng
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2020.617872
Transcriptome Analyses Identify an RNA Binding Protein Related Prognostic Model for Clear Cell Renal Cell Carcinoma
Cited by: 8
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 1
Published: almost 4 years ago
10.3389/fgene.2021.607238
The TP53-Related Signature Predicts Immune Cell Infiltration, Therapeutic Response, and Prognosis in Patients With Esophageal Carcinoma
Cited by: 7
Author(s): Hongpan Zhang, Zheng Huang, Yangguang Song, Zhihao Yang, Qi Shi, Kaige Wang, Zhiyu Zhang, Zheng Lv, Xiaobin Cui, Feng Li
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2021.674856
LncRNA SOX2-OT/miR-30d-5p/PDK1 Regulates PD-L1 Checkpoint Through the mTOR Signaling Pathway to Promote Non-small Cell Lung Cancer Progression and Immune Escape
Cited by: 14
Author(s): Zhoumiao Chen, Zhao Chun-hua, Shaohua Xu, Qiang Zhang
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2020.00273
HSD17B4, ACAA1, and PXMP4 in Peroxisome Pathway Are Down-Regulated and Have Clinical Significance in Non-small Cell Lung Cancer
Cited by: 12
Author(s): Xiuzhi Zhang, Hongmei Yang, Jinzhong Zhang, Fenglan Gao, Liping Dai
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2019.00409
Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig
Cited by: 8
Author(s): Yalan Yang, Rong Zhou, Wentong Li, Ying Liu, Yanmin Zhang, Ai Hong, Hua Li, Kui Li
Software Mentions: 1
Published: over 5 years ago
10.1186/s13059-015-0632-2
The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution
Cited by: 212
Author(s): Krystyna Cwiklinski, John P. Dalton, Philippe J. Dufresne, James La Course, Diana Williams, Jane E. Hodgkinson, Steve Paterson
Software Mentions: 1
Published: over 9 years ago
10.3389/fgene.2016.00191
Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case
Cited by: 9
Author(s): Adam G. Marsh, Matthew T. Cottrell, Morton F. Goldman
Software Mentions: 1
Published: about 8 years ago
10.3390/ijms21124252
Micro-Transcriptome Analysis Reveals Immune-Related MicroRNA Regulatory Networks of Paralichthys olivaceus Induced by Vibrio anguillarum Infection
Cited by: 11
Author(s): Xianhui Ning, Li Sun
Software Mentions: 1
Published: over 4 years ago
10.1128/mSystems.00819-20
Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
Cited by: 16
Author(s): Jiawei He, Xu‐jie Zhou, Yafeng Li, Yan-Na Wang, Lijun Liu, Sufang Shi, Xu Xin, Rongshan Li, Mario Falchi, Jicheng Lv, Hong Zhang
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2020.577000
Exploration of Sorafenib Influences on Gene Expression of Hepatocellular Carcinoma
Cited by: 0
Author(s): Huancheng Wang, Jia Liu
Software Mentions: 1
Published: about 4 years ago
10.1002/2211-5463.13059
Quantitative comparison of the mRNA content of human iPSC‐derived motor neurons and their extracellular vesicles
Cited by: 4
Author(s): Kentaro Otake, Keiko Adachi-Tominari, Hiroaki Nagai, Masayo Saito, Osamu Sano, Yoshihiko Hirozane, Hidehisa Iwata
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12864-021-07879-6
Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development
Cited by: 5
Author(s): Yun Tang, Jing-Yi Chen, Guohua Ding, Lin Zhen-shan
Software Mentions: 1
Published: over 3 years ago
10.1096/fj.201701558R
Macrophage‐derived extracellular vesicles mediate smooth muscle hyperplasia: role of altered miRNA cargo in response to HIV infection and substance abuse
Cited by: 45
Author(s): Himanshu Sharma, Mahendran Chinnappan, Stuti Agarwal, Pranjali Dalvi, Sumedha Gunewardena, Amy O’Brien-Ladner, Navneet K. Dhillon
Software Mentions: 1
Published: over 6 years ago
10.1186/s13059-015-0780-4
The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures
Cited by: 37
Author(s): Oksung Chung, Shil Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, JeHoon Jun, Hye-Jin Lee, Alvin Chon, Junsu Ko, Jeremy S. Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O’Brien, Andrea Manica, Jong Bhak, Woon Kee Paek
Software Mentions: 1
Published: about 9 years ago
10.1186/s13059-015-0813-z
Erratum to: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 11
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 1
Published: about 9 years ago
10.12688/f1000research.9094.2
Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury
Cited by: 6
Author(s): Liam M. Koehn, Natassya M. Noor, Qing Dong, Sing-Yan Er, Lachlan D. Rash, Glenn F. King, Katarzyna M. Dzięgielewska, NR Saunders, Mark D. Habgood
Software Mentions: 1
Published: almost 8 years ago
10.12688/f1000research.3928.2
edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Cited by: 68
Author(s): Zhiyin Dai, Julie Sheridan, Linden J. Gearing, Darcy Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O’Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 1
Published: about 10 years ago
10.1186/s12864-020-6494-3
Transcriptomic analysis of the testicular fusion in Spodoptera litura
Cited by: 5
Author(s): Yaqing Chang, Jun Ou, Yucheng Liu, Qiong Wu, Liang Wen, Sichun Zheng, Li Sheng, Qili Feng, Lin Liu
Software Mentions: 1
Published: almost 5 years ago
10.1186/s40164-021-00230-5
Blocking siglec-10hi tumor-associated macrophages improves anti-tumor immunity and enhances immunotherapy for hepatocellular carcinoma
Cited by: 26
Author(s): Nan Xiao, Xiao‐Dong Zhu, Kangshuai Li, Yifan Chen, Xuefeng Li, Bin Xu, Ming Lei, Jiejie Xu, Hui–Chuan Sun
Software Mentions: 1
Published: over 3 years ago
10.1093/emph/eow010
Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee
Cited by: 5
Author(s): Alexander S. Advani, Annie Y. Chen, Courtney C. Babbitt
Software Mentions: 1
Published: almost 9 years ago
10.1111/eva.13024
Age‐dependent expression of cancer‐related genes in a long‐lived seabird
Cited by: 4
Author(s): Richard Meitern, Jérôme Fort, Mathieu Giraudeau, Kalev Rattiste, Elin Sild, Tuul Sepp
Software Mentions: 1
Published: over 4 years ago
10.1186/s13227-016-0050-x
Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Cited by: 42
Author(s): Jesús F. Peña, Alexandre Alié, Daniel J. Richter, Lingyu Wang, Noriko Funayama, Scott Nichols
Software Mentions: 1
Published: over 8 years ago
10.1186/s13227-016-0044-8
HOX gene complement and expression in the planarian Schmidtea mediterranea
Cited by: 73
Author(s): Ko W. Currie, David D. R. Brown, Shujun Zhu, Changjiang Xu, Véronique Voisin, Gary D. Bader, Bret J. Pearson
Software Mentions: 1
Published: over 8 years ago
10.1155/2020/8591892
Fuzheng Huayu Recipe Prevented and Treated CCl4-Induced Mice Liver Fibrosis through Regulating Polarization and Chemotaxis of Intrahepatic Macrophages via CCL2 and CX3CL1
Cited by: 14
Author(s): Man Zhang, Hongliang Liu, Kai Huang, Yuan Peng, Tao Yue, Changqing Zhao, Xudong Hu, Chenghai Liu
Software Mentions: 1
Published: almost 4 years ago
10.1155/2021/5584099
Transcriptomic Analysis Exploring the Molecular Mechanisms of Hanchuan Zupa Granules in Alleviating Asthma in Rat
Cited by: 2
Author(s): Hai-Long Yin, Yanbo Fan, Dandan Mu, Fei Song, Fang Tian, Qiang Yin
Software Mentions: 1
Published: over 3 years ago
10.1186/s13072-018-0241-x
Physiological effects of KDM5C on neural crest migration and eye formation during vertebrate development
Cited by: 17
Author(s): Youni Kim, Youngeun Jeong, Kujin Kwon, Tayaba Ismail, Hyun-Kyung Lee, Chowon Kim, Jeen‐Woo Park, Oh Nam Kwon, Beom‐Sik Kang, Dong‐Seok Lee, Tae Joo Park, Taejoon Kwon, Hyun‐Shik Lee
Software Mentions: 1
Published: almost 6 years ago
10.1186/s13072-015-0013-9
Modelling the conditional regulatory activity of methylated and bivalent promoters
Cited by: 7
Author(s): David Budden, Daniel Hurley, Edmund J. Crampin
Software Mentions: 1
Published: over 9 years ago
10.1289/ehp.1408188
Effects of the Endocrine-Disrupting Chemical DDT on Self-Renewal and Differentiation of Human Mesenchymal Stem Cells
Cited by: 53
Author(s): Amy L. Strong, Zhenzhen Shi, Michael J. Strong, David F. Miller, Douglas B. Rusch, Aaron Buechlein, Erik K. Flemington, John A. McLachlan, Kenneth P. Nephew, Matthew E. Burow, Bruce A. Bunnell
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12864-015-2150-8
The comprehensive immunomodulation of NeurimmiRs in haemocytes of oyster Crassostrea gigas after acetylcholine and norepinephrine stimulation
Cited by: 25
Author(s): Hao Chen, Lingling Wang, Zhi Zhou, Zujun Hou, Zhaoqun Liu, Weilin Wang, Dahai Gao, Qiang Gao, Mengqiang Wang, Linsheng Song
Software Mentions: 1
Published: about 9 years ago
10.1186/s12940-017-0288-3
Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment
Cited by: 18
Author(s): Zhao‐Xi Wang, Birgit Claus Henn, Chaolong Wang, Yongyue Wei, Su Li, Ryan Sun, Han Chen, Peter J. Wagner, Quan Lu, Xihong Lin, Robert O. Wright, David C. Bellinger, Molly L. Kile, Maitreyi Mazumdar, Martha María Téllez‐Rojo, Lourdes Schnaas, David C. Christiani
Software Mentions: 1
Published: over 7 years ago
10.1186/s12940-020-00666-y
Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease
Cited by: 12
Author(s): Jennifer L. M. Thorson, Daniel Beck, Millissia Ben Maamar, Eric Nilsson, Michael K. Skinner
Software Mentions: 1
Published: about 4 years ago
10.1093/eep/dvaa022
Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells
Cited by: 12
Author(s): Steven K. Huang, Priya Tripathi, Lada A. Koneva, Raymond G. Cavalcante, N. Craig, Anne M. Scruggs, Maureen A. Sartor, Furong Deng, Yahong Chen
Software Mentions: 1
Published: almost 4 years ago
10.1093/eep/dvy026
Fatherhood alters gene expression within the MPOA
Cited by: 7
Author(s): Adele M. H. Seelke, Jessica Bond, Trent C Simmons, Nikhil Joshi, Matthew L. Settles, Danielle S. Stolzenberg, Mijke Rhemtulla, Karen L. Bales
Software Mentions: 1
Published: about 6 years ago
10.1002/ece3.7581
Comparative transcriptomics of albino and warningly‐coloured caterpillars
Cited by: 4
Author(s): Juan A. Galarza
Software Mentions: 1
Published: over 3 years ago
10.1002/ece3.7889
Transcriptomic response of <i>Daphnia magna</i> to nitrogen‐ or phosphorus‐limited diet
Cited by: 3
Author(s): Zhimeng Xu, Yingdong Li, Meng Li, Hongbin Liu
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-018-5318-1
Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis
Cited by: 13
Author(s): Qianqian Dong, Luye Shi, Yangwei Li, Mengwan Jiang, Hong Sun, Baishi Wang, Han Cheng, Yifeng Zhang, Tian Shao, Yuhua Shi, Zhenlong Wang
Software Mentions: 1
Published: almost 6 years ago
10.15252/embr.202051660
Plasmodium transcription repressor AP2‐O3 regulates sex‐specific identity of gene expression in female gametocytes
Cited by: 21
Author(s): Zhenkui Li, Huiting Cui, Jiepeng Guan, Cong Liu, Zhengang Yang, Jing Yuan
Software Mentions: 1
Published: over 3 years ago
10.15252/embr.201744853
The dynamic recruitment of <scp>TRBP</scp> to neuronal membranes mediates dendritogenesis during development
Cited by: 22
Author(s): Anna Antoniou, Sharof Khudayberdiev, Agata Idziak, Silvia Bicker, Ralf Jacob, Gerhard Schratt
Software Mentions: 1
Published: almost 7 years ago
10.15252/embr.201949942
SMaRT lncRNA controls translation of a G‐quadruplex‐containing mRNA antagonizing the DHX36 helicase
Cited by: 18
Author(s): Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Software Mentions: 1
Published: over 4 years ago
10.1038/s41420-020-00328-5
A defined N6-methyladenosine (m6A) profile conferred by METTL3 regulates muscle stem cell/myoblast state transitions
Cited by: 35
Author(s): Brandon Gheller, Jamie Blum, Ern Hwei Hannah Fong, Olga Malysheva, Benjamin D. Cosgrove, Anna Thalacker‐Mercer
Software Mentions: 1
Published: about 4 years ago
10.1038/s41420-021-00440-0
Dysregulation of miR-23b-5p promotes cell proliferation via targeting FOXM1 in hepatocellular carcinoma
Cited by: 9
Author(s): Xiaopei Yang, Shuguang Yang, Jun Song, Wenjie Yang, Jicheng Yang, Feng Zhang, Jianhua Rao
Software Mentions: 1
Published: over 3 years ago
10.1038/s41420-019-0152-z
The whole transcriptome and proteome changes in the early stage of myocardial infarction
Cited by: 15
Author(s): Yanfei Li, Cuiping Wang, Tingting Li, Linlin Ma, Fangzhou Fan, Yueling Jin, Junwei Shen
Software Mentions: 1
Published: over 5 years ago
10.1038/s41419-018-1025-8
IGF1R upregulation confers resistance to isoform-specific inhibitors of PI3K in PIK3CA-driven ovarian cancer
Cited by: 30
Author(s): Jonathan Zorea, Manu Prasad, Limor Cohen, Nan Li, Roman Schefzik, Susmita Ghosh, Barak Rotblat, Benedikt Brors, Moshe Elkabets
Software Mentions: 1
Published: about 6 years ago
10.1186/s12864-017-4037-3
Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
Cited by: 50
Author(s): Risheng Chen, Yunfeng Cheng, Sang‐Mi Han, Ben Van Handel, Lü Dong, Xinmin Li, Xiaoqing Xie
Software Mentions: 1
Published: over 7 years ago
10.1038/s41419-021-04126-4
Non-apoptotic function of caspase-8 confers prostate cancer enzalutamide resistance via NF-κB activation
Cited by: 6
Author(s): Jia Xia, Jiahui Zhang, Liangzhe Wang, Hailong Liu, Jie Wang, Junyan Liu, Zhao‐Qian Liu, Yingke Zhu, Yingjie Xu, Wen Yang, Yu Yan
Software Mentions: 1
Published: about 3 years ago
10.1038/s41419-019-1887-4
Direct neuronal reprogramming of olfactory ensheathing cells for CNS repair
Cited by: 15
Author(s): Xiaoyan Sun, Zijian Tan, Xu Huang, Xueyan Cheng, Yihang Yuan, Shangyao Qin, Dan Wang, Xiangyou Hu, Yakun Gu, Wen-Jing Qian, Zhongfeng Wang, Cheng He, Zhida Su
Software Mentions: 1
Published: about 5 years ago
10.1038/s41419-021-03510-4
Suppression of steroid 5α-reductase type I promotes cellular apoptosis and autophagy via PI3K/Akt/mTOR pathway in multiple myeloma
Cited by: 12
Author(s): Renjie Dou, Jinjun Qian, Wei Wu, Yanxin Zhang, Ye Yuan, Mengjie Guo, Rongfang Wei, Shu Yang, Artur Jurczyszyn, Siegfried Janz, Meral Beksaç, Chunyan Gu, Ye Yang
Software Mentions: 1
Published: over 3 years ago
10.1038/cddis.2015.392
Hemoglobinuria-related acute kidney injury is driven by intrarenal oxidative reactions triggering a heme toxicity response
Cited by: 96
Author(s): Jeremy Deuel, Christian A. Schaer, Felicitas S Boretti, Lennart Opitz, Inés García-Rubio, Jin Hyen Baek, Donat R. Spahn, Paul W. Buehler, Dominik J. Schaer
Software Mentions: 1
Published: almost 9 years ago
10.1128/mSystems.01190-20
Juvenile Hormone-Sensitive Ribosomal Activity Enhances Viral Replication in Aedes aegypti
Cited by: 7
Author(s): Zuo-Kun Shi, Dan Wen, Mengmeng Chang, Xiaomei Sun, Yanhong Wang, Chihang Cheng, Liqin Zhang, Ai Zheng, Zhen Zou
Software Mentions: 1
Published: over 3 years ago