bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7717/peerj.10654

Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
Cited by: 9
Author(s): Chelsea Hall, Sara Camilli, Henry Dwaah, Benjamin Kornegay, Christie A. Lacy, Malcolm Hill, Andrew P. Hill
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.1591

The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission
Cited by: 54
Author(s): Eugene V. Ryabov, Jessica Fannon, Jonathan D. Moore, Graham R. Wood, David J. Evans
Software Mentions: 1
Published: almost 9 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

10.3389/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

10.1186/1471-2164-11-282

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
Cited by: 136
Author(s): James R. Bradford, Yvonne Hey, Timothy Yates, Yaoyong Li, Stuart D Pepper, Crispin Miller
Software Mentions: 1
Published: over 14 years ago

10.3390/ijms22126218

Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy
Cited by: 8
Author(s): Canan Kuscu, Manjari Kiran, Akram Mohammed, Cem Kuscu, Sarthak Satpathy, Aaron R. Wolen, Elissa Bardhi, Amandeep Bajwa, James D. Eason, Daniel G. Maluf, Valeria R. Mas, Enver Akalin
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-015-2082-3

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer
Cited by: 51
Author(s): Manuel Saiselet, David Gacquer, Alex Spinette, Ligia Craciun, Myriam Decaussin‐Petrucci, Guy Andry, Vincent Detours, Carine Maenhaut
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-018-5128-5

Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-κB pathway in porcine intestinal epithelial cell line
Cited by: 37
Author(s): Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang, Dewen Tong
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-80837-6

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium
Cited by: 6
Author(s): Aboozar Soorni, Amir Mohammad Akrami, Reza Abolghasemi, Maryam Vahedi
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-14-682

Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake
Cited by: 31
Author(s): Jian Xu, Qiang Li, Liming Xu, Shaolin Wang, Yanliang Jiang, Zixia Zhao, Yan Zhang, Jiong-Tang Li, Chuanju Dong, Peng Xu, Xin Sun
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-1453-0

Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.)
Cited by: 26
Author(s): Zaijun Yang, Zhengsong Peng, Shuhong Wei, Mingli Liao, Yan Yu, Zeyan Jang
Software Mentions: 1
Published: over 9 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

10.1186/s12864-020-6539-7

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings
Cited by: 11
Author(s): Feng‐Yao Wu, Fengying Lu, Xin Fan, Chao Jin, Chuanmin Liu, Qunxing Pan, Huawei Sun, Xiaofei Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-80280-7

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae
Cited by: 15
Author(s): He Meng, Mingming Sun, Zipeng Jiang, Yutong Liu, Yu Sun, Dan Liŭ, Caihong Jiang, Min Ren, Guangdi Yuan, Wenlong Yu, Qi Sheng Feng, Aiguo Yang, Lei Cheng, Yuanying Wang
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-017-3674-x

The predictive nature of transcript expression levels on protein expression in adult human brain
Cited by: 46
Author(s): Amy L. Bauernfeind, Courtney C. Babbitt
Software Mentions: 1
Published: over 7 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

10.1186/s12864-020-07214-5

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus
Cited by: 10
Author(s): Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin, Bowen Chen
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0242179

MiR-424-5p regulates cell cycle and inhibits proliferation of hepatocellular carcinoma cells by targeting E2F7
Cited by: 24
Author(s): Yichao Zhao, Chaoqian Zhu, Qing Chang, Peng Peng, Jie Yang, Chunmei Liu, Yang Liu, Xiaonan Chen, Yuanguang Liu, Ran Cheng, Yijie Wu, Xiaotang Wu, Liang Hu, Jun Yin
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0103567

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy
Cited by: 44
Author(s): Jacqueline D. Farrell, Stephen Byrne, Cristiana Paina, Torben Asp
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-016-2472-1

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis
Cited by: 31
Author(s): Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Grégory Jubelin, Carl J. Yeoman, Margret E. Berg Miller, Christopher J. Fields, Nicolas Terrapon, Carine Le Bourvellec, Cathérine M.G.C. Renard, Bernard Henrissat, Bryan A. White, Pascale Mosoni
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.8609

Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation
Cited by: 4
Author(s): Wenmin Qiu, Jingen Li, Wei Yi, Fan Feng, Jing Jiang, Mingying Liu, Xiaojiao Han, Chaoguang Tian, Shihong Zhang, Renying Zhuo
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-017-3961-6

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi–SlPH tomato line with reduced fruit acidity and higher pH
Cited by: 9
Author(s): Shiri Barad, Noa Sela, Amit Dubey, Dilip Kumar, Neta Luria, Dana Ment, Shahar Cohen, Arthur A. Schaffer, Dov Prusky
Software Mentions: 1
Published: over 7 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

10.1186/1471-2164-13-28

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA
Cited by: 53
Author(s): Anastasios Mastrokolias, Johan T. den Dunnen, Gert‐Jan B. van Ommen, Peter A C ‘t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-016-2540-6

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions
Cited by: 72
Author(s): Yuta Yoshida, Takuya Tomiyama, Takanori Maruta, Masaru Tomita, Takahiro Ishikawa, Kazuharu Arakawa
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.59469

Adrenergic activation modulates the signal from the Reissner fiber to cerebrospinal fluid-contacting neurons during development
Cited by: 20
Author(s): Yasmine Cantaut-Belarif, Adeline Orts-Del’Immagine, Margot Penru, Guillaume Pézeron, Claire Wyart, Pierre-Luc Bardet
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-81164-0

Androgen receptor and its splice variant, AR-V7, differentially induce mRNA splicing in prostate cancer cells
Cited by: 9
Author(s): Manjul Rana, Jianrong Dong, Matthew J. Robertson, Cristian Coarfa, Nancy L. Weigel
Software Mentions: 1
Published: almost 4 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

10.7717/peerj.10668

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis
Cited by: 4
Author(s): Juan Wang, Xiongfei Wu, Yue Tu, Jianzhong Dang, Zhitao Cai, Wenjing Liao, Weili Quan, Yaxun Wei
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-80680-9

GATA3 somatic mutations are associated with clinicopathological features and expression profile in TCGA breast cancer patients
Cited by: 14
Author(s): Fahimeh Afzaljavan, Ayeh Sadat Sadr, Sevtap Savas, Alireza Pasdar
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots
Cited by: 1
Author(s): Wang Wei, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Ye, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Software Mentions: 1
Published: over 5 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

10.7717/peerj.8776

Physiological parameters and differential expression analysis of N-phenyl-N′-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis
Cited by: 4
Author(s): Lejun Ouyang, Zechen Wang, Limei Li, Baoling Chen
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-017-4095-6

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses
Cited by: 19
Author(s): Totta Ehret, Simone Spork, Christoph Dieterich, Richard Lucius, Emanuel Heitlinger
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.8379

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis
Cited by: 12
Author(s): Xuhui Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jianbin Guo
Software Mentions: 1
Published: almost 5 years ago

10.3390/microorganisms5010003

Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae
Cited by: 8
Author(s): Ryan M. Ames
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-07024-9

Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages
Cited by: 20
Author(s): Jing Yang, Ling Su, Dandan Li, Lixin Luo, Kai Sun, Meng Yang, Fengwei Gu, Aoyun Xia, Yongzhu Liu, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 1
Published: about 4 years ago

10.1186/s40478-019-0750-2

Restoration of histone acetylation ameliorates disease and metabolic abnormalities in a FUS mouse model
Cited by: 53
Author(s): Elisabeth Rossaert, Eveliina Pollari, Tom Jaspers, Lawrence Van Helleputte, Matthew Jarpe, Philip Van Damme, Katrien De Bock, Matthieu Moisse, Ludo Van Den Bosch
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22126430

Null cyp1b1 Activity in Zebrafish Leads to Variable Craniofacial Defects Associated with Altered Expression of Extracellular Matrix and Lipid Metabolism Genes
Cited by: 5
Author(s): Susana Alexandre-Moreno, Juan-Manuel Bonet-Fernández, Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar, Julio Escribano
Software Mentions: 1
Published: over 3 years ago

10.1111/acel.12373

Circulating micro <scp>RNA</scp> signature of genotype‐by‐age interactions in the long‐lived <scp>A</scp> mes dwarf mouse
Cited by: 50
Author(s): Berta Victoria, Joseph M. Dhahbi, Yury O. Nunez Lopez, Lina Spinel, Hani Atamna, Stephen R. Spindler, Michał M. Masternak
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4723-9

Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential
Cited by: 19
Author(s): Nicky‐Lee Willson, R. E. A. Forder, Rick Tearle, J. L. Williams, Robert J. Hughes, G. S. Nattrass, P. I. Hynd
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1502-8

Metatranscriptomic profiles of Eastern subterranean termites, Reticulitermes flavipes (Kollar) fed on second generation feedstocks
Cited by: 15
Author(s): Swapna Priya Rajarapu, Jacob Shreve, Ketaki P. Bhide, Jyothi Thimmapuram, Michael E. Scharf
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-81856-7

Freshwater mussels (Unionidae) brought into captivity exhibit up-regulation of genes involved in stress and energy metabolism
Cited by: 10
Author(s): Ieva Roznere, Brandon T. Sinn, Marymegan Daly, G. Thomas Watters
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-82284-3

Notch signaling-modified mesenchymal stem cells improve tissue perfusion by induction of arteriogenesis in a rat hindlimb ischemia model
Cited by: 7
Author(s): Shigeru Miyagawa, Shigeru Miyagawa, Takuji Kawamura, Takashi Shibuya, Kenichi Watanabe, Tomoya Nakagawa, Akira Harada, Dai Chida, Yoshiki Sawa
Software Mentions: 1
Published: almost 4 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.2019.01348

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

10.1186/1471-2164-15-269

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)
Cited by: 47
Author(s): Hiroko Ohmiya, Morana Vitezic, Martin C. Frith, Masayoshi Itoh, Piero Carninci, Alistair R.R. Forrest, Yoshihide Hayashizaki, Timo Lassmann
Software Mentions: 1
Published: over 10 years ago

10.1002/cam4.3963

Pivotal factors associated with the immunosuppressive tumor microenvironment and melanoma metastasis
Cited by: 21
Author(s): Chuan Zhang, Dan Dang, Lele Cong, Hongyan Sun, Xianling Cong
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-82509-5

Long non-coding RNAs as novel therapeutic targets in juvenile myelomonocytic leukemia
Cited by: 7
Author(s): Mattias Hofmans, Tim Lammens, Barbara Depreter, Ying Wu, Miriam Erlacher, Aurélie Cayé, Hélène Cavé, Christian Flotho, Valérie de Haas, Charlotte M. Niemeyer, Jan Starý, Filip Van Nieuwerburgh, Dieter Deforce, Wouter Van Loocke, Pieter Van Vlierberghe, Jan Philippé, Barbara De Moerloose
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-83074-7

Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat
Cited by: 13
Author(s): Haipei Liu, Amanda J. Able, Jason A. Able
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-14-110

Differential expression analysis for paired RNA-seq data
Cited by: 18
Author(s): Lisa Chung, John Ferguson, Wei Zheng, Feng Qian, Vincent M. Bruno, Ruth R. Montgomery, Hongyu Zhao
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-021-82848-3

A transcriptomic view to wounding response in young Scots pine stems
Cited by: 9
Author(s): Kean‐Jin Lim, Tanja Paasela, Anni Harju, Martti Venäläinen, Lars Paulín, Petri Auvinen, Katri Kärkkäinen, Teemu H. Teeri
Software Mentions: 1
Published: almost 4 years ago

10.1186/s40478-018-0555-8

Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients
Cited by: 22
Author(s): Daniel A. Mordes, Mercedes Prudencio, Lindsey D. Goodman, Joseph R. Klim, Rob Moccia, Francesco Limone, Olli Pietiläinen, Kaitavjeet Chowdhary, Dennis W. Dickson, Rosa Rademakers, Nancy M. Bonini, Leonard Petrucelli, Kevin Eggan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0039914

A Retinoblastoma Orthologue Is a Major Regulator of S-Phase, Mitotic, and Developmental Gene Expression in Dictyostelium
Cited by: 11
Author(s): Kimchi Strasser, Gareth Bloomfield, Asa MacWilliams, Adriano Ceccarelli, Harry K. MacWilliams, Adrian Tsang
Software Mentions: 1
Published: over 12 years ago

10.26508/lsa.202000688

IL-36 signaling in keratinocytes controls early IL-23 production in psoriasis-like dermatitis
Cited by: 33
Author(s): Jack Goldstein, Esen Yonca Bassoy, Assunta Caruso, Jennifer Palomo, Emiliana Rodriguez, Sylvain Lemeille, Cem Gabay
Software Mentions: 1
Published: over 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/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

10.1038/s41598-021-83835-4

Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain
Cited by: 12
Author(s): Thanida Laopanupong, Pinidphon Prombutara, Phongthon Kanjanasirirat, Salisa Benjaskulluecha, Atsadang Boonmee, Tanapat Palaga, Stéphane Méresse, Jiraporn Paha, Tegar Adriansyah Putra Siregar, Tanawadee Khumpanied, Suparerk Borwornpinyo, Angkana Chaiprasert, Pongsak Utaisincharoen, Marisa Ponpuak
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13568-020-01076-6

Comprehensive transcriptomic and proteomic analyses of antroquinonol biosynthetic genes and enzymes in Antrodia camphorata
Cited by: 4
Author(s): Xiaofeng Liu, Yongjun Xia, Yao Zhang, Caiyun Yang, Zhiqiang Xiong, Xin Song, Lianzhong Ai
Software Mentions: 1
Published: over 4 years ago

10.1111/acel.13466

Altered sperm tsRNAs in aged male contribute to anxiety‐like behavior in offspring
Cited by: 14
Author(s): Yi Guo, Dandan Bai, Wenqiang Liu, Yingdong Liu, Yalin Zhang, Xiaochen Kou, Jiayu Chen, Hong Wang, Xiaoming Teng, Ji Zuo, Shaorong Gao
Software Mentions: 1
Published: about 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

10.1186/s12864-016-2546-0

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
Cited by: 20
Author(s): María Fernanda Torres, Noushin Ghaffari, Ester Alvarenga Santos Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson, Lisa J. Vaillancourt
Software Mentions: 1
Published: over 8 years ago

10.3389/fphar.2019.00986

Transcriptional Analysis of the Effects of Gambogic Acid and Neogambogic Acid on Methicillin-Resistant Staphylococcus aureus
Cited by: 13
Author(s): Xin Hua, Yue Jia, Qin Yang, Wanjiang Zhang, Zhimin Dong, Siguo Liu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3751-1

Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes
Cited by: 44
Author(s): Navneet Kaur, Wenbo Chen, Yanyan Zheng, Daniel K. Hasegawa, Kai‐Shu Ling, Zhangjun Fei, William M. Wintermantel
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2019.00150

Analysis of lncRNA-Mediated ceRNA Crosstalk and Identification of Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 27
Author(s): Yunbao Pan, Guohong Liu, Dujuan Wang, Yirong Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s40478-019-0739-x

c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism
Cited by: 5
Author(s): Ashirwad Merve, Xinyu Zhang, Nicola Pomella, Serena Acquati, Joerg D. Hoeck, Anaëlle Dumas, Gabriel Rosser, Yichen Li, Jennie N. Jeyapalan, Silvia Vicenzi, Qianhai Fan, Zeng Jie Yang, Arianna Sabò, Denise Sheer, Axel Behrens, Silvia Marino
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4177-5

Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types
Cited by: 29
Author(s): Guillem Ylla, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 1
Published: about 7 years ago

10.3389/fphar.2020.621054

HIF Prolyl Hydroxylase Inhibitors for COVID-19 Treatment: Pros and Cons
Cited by: 17
Author(s): Andrey Poloznikov, Stepan Nersisyan, Dmitry M. Hushpulian, Eliot H. Kazakov, Alexander G. Tonevitsky, С. В. Казаков, В.И. Вечорко, С. В. Никулин, J. A. Makarova, Irina G. Gazaryan
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-84355-x

The role of gut microbiota and amino metabolism in the effects of improvement of islet β-cell function after modified jejunoileal bypass
Cited by: 9
Author(s): Cai Tan, Zhihua Zheng, Xiaogang Wan, Jiaqing Cao, Ran Wei, Jinyuan Duan
Software Mentions: 1
Published: over 3 years ago

10.3389/fphar.2018.00619

Antibacterial Activity and Mechanism of Action of Aspidinol Against Multi-Drug-Resistant Methicillin-Resistant Staphylococcus aureus
Cited by: 24
Author(s): Xin Hua, Qin Yang, Wanjiang Zhang, Zhimin Dong, Shen-Ye Yu, Štefan Schwarz, Siguo Liu
Software Mentions: 1
Published: over 6 years ago

10.3389/fphar.2021.647084

Research on the Species Difference of the Hepatotoxicity of Medicine Based on Transcriptome
Cited by: 11
Author(s): Ziying Xu, Qianjun Kang, Zihui Yu, Lichun Tian, Jingxuan Zhang, Ting Wang
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0149067

Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton
Cited by: 27
Author(s): Hisao Koga, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko Shibata, Masahiro Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, Hiroshi Wada
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-021-84402-7

Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos
Cited by: 3
Author(s): Ryoma Ota, Makoto Hayashi, Shumpei Morita, Hideharu Miura, Satoru Kobayashi
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-84519-9

Comparative transcriptome profiles of large and small bodied large-scale loaches cultivated in paddy fields
Cited by: 3
Author(s): Liulan Zhao, Kuo He, Qing Xiao, Qiao Li, Wei Luo, Jie Luo, Hongmei Fu, Jiayao Li, Xugan Wu, Jun Du, Quan Gong, Xun Wang
Software Mentions: 1
Published: over 3 years ago

10.3389/fphys.2020.579296

Extracellular Vesicles From High Glucose-Treated Podocytes Induce Apoptosis of Proximal Tubular Epithelial Cells
Cited by: 9
Author(s): Ying Huang, Ruizhao Li, Li Zhang, Yuanhan Chen, Wei Dong, Xingchen Zhao, Huan Yang, Shu Zhang, Zhiyong Xie, Zhiming Ye, Weidong Wang, Chunling Li, Zhilian Li, Shuangxin Liu, Zheng Dong, Xueqing Yu, Xinling Liang
Software Mentions: 1
Published: about 4 years ago

10.3389/fphys.2016.00170

Gene Expression Changes during the Gummosis Development of Peach Shoots in Response to Lasiodiplodia theobromae Infection Using RNA-Seq
Cited by: 22
Author(s): Lei Gao, Yuting Wang, Zhi Li, He Zhang, Junli Ye, Guohuai Li
Software Mentions: 1
Published: over 8 years ago

10.3389/fphys.2018.00429

Circulating miRNAs as Putative Biomarkers of Exercise Adaptation in Endurance Horses
Cited by: 9
Author(s): Katia Cappelli, Stefano Capomaccio, A. Viglino, Maurizio Silvestrelli, Francesca Beccati, Livia Moscati, Elisabetta Chiaradia
Software Mentions: 1
Published: over 6 years ago

10.3389/fphys.2017.00056

Increased Hemodynamic Load in Early Embryonic Stages Alters Endocardial to Mesenchymal Transition
Cited by: 27
Author(s): Madeline Midgett, Clàudia López, Larry L. David, Alina Maloyan, Sandra Rugonyi
Software Mentions: 1
Published: almost 8 years ago

10.1111/acel.13115

A lncRNA survey finds increases in neuroprotective LINC‐PINT in Parkinson’s disease substantia nigra
Cited by: 37
Author(s): Alon Simchovitz, Mor Hanan, Nadav Yayon, Songhua Lee, Estelle R. Bennett, David Greenberg, Sebastián Kadener, Hermona Soreq
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.8394

LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
Cited by: 11
Author(s): Zhou Wei, Kang Huang, Qiuyan Zhang, Shaojun Ye, Zibiao Zhong, Cheng Zeng, Guizhu Peng, Ling Li, Qifa Ye
Software Mentions: 1
Published: almost 5 years ago

10.3389/fphys.2021.687654

Airway Epithelial Cells Drive Airway Smooth Muscle Cell Phenotype Switching to the Proliferative and Pro-inflammatory Phenotype
Cited by: 6
Author(s): Michael J. O’Sullivan, Jinho Jang, Alice Panariti, Amina Bedrat, Gijs Ijpma, Bernardo Lemos, J. A. Park, Anne‐Marie Lauzon, James G. Martin
Software Mentions: 1
Published: over 3 years ago

10.3389/fphys.2019.00631

Mixed Diets Reduce the Oxidative Stress of Common Carp (Cyprinus carpio): Based on MicroRNA Sequencing
Cited by: 9
Author(s): Song Yang, Jie Luo, Yalan Long, Jie Du, Gaosi Xu, Zongjun Du, Wei Luo, Yan Wang, Zhi He
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.10223

Transcriptome and gene expression analysis ofRhynchophorus ferrugineus(Coleoptera: Curculionidae) during developmental stages
Cited by: 8
Author(s): Hui Yang, Danping Xu, Zhihang Zhuo, Jingjing Hu, Binfeng Lu
Software Mentions: 1
Published: about 4 years ago

10.3389/fphys.2021.633301

IAPs Gene Expansion in the Scallop Patinopecten yessoensis and Their Expression Profiles After Exposure to the Toxic Dinoflagellate
Cited by: 4
Author(s): Xiaomei Zhu, Fengmei Zhang, Shanshan Lian, Yinghui Wang, Naina Hu, Xiaomei Chen, Xiaoting Dai, Xiaoli Hu, Shi Wang, Zhenmin Bao
Software Mentions: 1
Published: almost 4 years ago

10.3389/fphys.2019.00872

Transcriptomic Responses of Skeletal Muscle to Acute Exercise in Diabetic Goto-Kakizaki Rats
Cited by: 6
Author(s): Shuang Fu, Yuhuan Meng, Wenlu Zhang, Jiajian Wang, Yuting He, Lizhen Huang, Hongmei Chen, Jian Kuang, Hongli Du
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 3 years ago

10.1111/acel.12743

<scp>NHR</scp>‐49/<scp>HNF</scp>4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting
Cited by: 61
Author(s): Grace Ying Shyen Goh, Johnathan J Winter, Forum Bhanshali, Kelsie R. S. Doering, Regina Lai, Kayoung Lee, Elizabeth A. Veal, Stefan Taubert
Software Mentions: 1
Published: over 6 years ago

10.3389/fphys.2019.00171

Effects of Early Intervention With Maternal Fecal Bacteria and Antibiotics on Liver Metabolome and Transcription in Neonatal Pigs
Cited by: 16
Author(s): Jiajia Wan, Chun-Hui Lin, Erdu Ren, Yong Su, Weiyun Zhu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.2520

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
Cited by: 26
Author(s): Moshtaghi Azam, Md. Lifat Rahi, Tuan Viet Nguyen, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.9262

Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas
Cited by: 8
Author(s): Wenjing Zeng, Yang Yi, Zhipeng Wen, Peng Chen, Xiaoping Chen, Zhicheng Gong
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms8071020

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil
Cited by: 16
Author(s): Nikola Major, Jasper Schierstaedt, Sven Jechalke, Joseph Nesme, Smiljana Goreta Ban, Marko Černe, Søren J. Sørensen, Dean Ban, Adam Schikora
Software Mentions: 1
Published: over 4 years ago

10.3389/fphys.2017.00631

Increased Hemodynamic Load in Early Embryonic Stages Alters Myofibril and Mitochondrial Organization in the Myocardium
Cited by: 15
Author(s): Madeline Midgett, Clàudia López, Larry L. David, Alina Maloyan, Sandra Rugonyi
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.28415

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions
Cited by: 54
Author(s): Jason A. Morrison, Rebecca McLennan, Lauren A. Wolfe, Madelaine Gogol, Samuel R. Meier, Mary Cathleen McKinney, Jessica M. Teddy, Laura Holmes, Craig L. Semerad, Andrew Box, Hua Li, Kathryn Hall, Anoja Perera, Paul M. Kulesa
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.4276

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A
Cited by: 17
Author(s): Shelby Calkins, Nicole C. Elledge, Katherine E. Mueller, Stephen M. Marek, Matthew Brian Couger, Mostafa S. Elshahed, Noha H. Youssef
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-021-07520-6

Assessment of the mechanism of drug resistance in Trichophyton mentagrophytes in response to various substances
Cited by: 3
Author(s): Chi Xiao, Jiaoyu Wang, Zhenfeng Liao, Yee Huang, Quanan Ji, Yan Liu, Fei Su, Lijun Xu, Qiang Wang, Yao Pan, Ké Li, Guolian Bao
Software Mentions: 1
Published: over 3 years ago

10.1155/2020/1384907

Proteome and Transcriptome Analysis of the Antioxidant Mechanism in Chicken Regulated by Eucalyptus Leaf Polyphenols Extract
Cited by: 2
Author(s): Wei Li, Zeqi He, Xiaoying Zhang, Yunjiao Chen, Jianjun Zuo, Yong Cao
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.50346

Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway
Cited by: 2
Author(s): Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kayoko Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Katsuyuki Murata, Masafumi Muratani, Masatsugu Ema, Jun-Dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken‐ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568