bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.18632/aging.103772

ARHGEF11 promotes proliferation and epithelial-mesenchymal transition of hepatocellular carcinoma through activation of &#x3B2;-catenin pathway
Cited by: 9
Author(s): Dingjun Hao, Zexin Zhu, Xu Lin, Xing Chen, Xuefeng Li, Tian Lan, Wei Li, Kefei Yuan, Yong Zeng
Software Mentions: 1
Published: about 4 years ago

10.7150/jca.37267

Overexpression of DUSP6 enhances chemotherapy-resistance of ovarian epithelial cancer by regulating the ERK signaling pathway
Cited by: 17
Author(s): Yan Gao, Hui Li, Qing Han, Yuan Li, Tongxia Wang, Cuiyu Huang, Youdong Mao, Xi Wang, Qun Zhang, Tian Jing, David M. Irwin, Tan H, Hongyan Guo
Software Mentions: 1
Published: almost 5 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

10.1111/pbi.13484

GhARF16‐1 modulates leaf development by transcriptionally regulating theGhKNOX2‐1gene in cotton
Cited by: 13
Author(s): Guanghui Xiao, Yuzhou Zhang, Hongbin Li, Xuan Fu, Hǎihóng Shāng, Changsong Zou, Jiřı́ Friml, Gao Xiao
Software Mentions: 1
Published: about 4 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

10.1111/pbi.13058

Os<scp>ACL</scp>‐A2 negatively regulates cell death and disease resistance in rice
Cited by: 43
Author(s): Banpu Ruan, Zhihua Hua, Juan Zhao, Bin Zhang, Deyong Ren, Chaolei Liu, Shenglong Yang, Anpeng Zhang, Hongzhen Jiang, Haiping Yu, Jiang Hu, Li Zhu, Guang Chen, Lan Shen, Guojun Dong, Guangheng Zhang, Dali Zeng, Longbiao Guo, Qian Qian, Zhenyu Gao
Software Mentions: 1
Published: almost 6 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

10.7150/jca.47902

Clinical significance of long non-coding RNA DUXAP8 and its protein coding genes in hepatocellular carcinoma
Cited by: 10
Author(s): Xiangkun Wang, Xiwen Liao, Rui Huang, Jianlu Huang, Zijun Chen, Xin Zhou, Chengkun Yang, Chuangye Han, Guangzhi Zhu, Tao Peng
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

10.1111/pbi.12960

Transgenic creeping bentgrass overexpressing Osa‐miR393a exhibits altered plant development and improved multiple stress tolerance
Cited by: 63
Author(s): Junlong Zhao, Shuangrong Yuan, Man Zhou, Nannan Yuan, Zhigang Li, Qian Hu, Frank Bethea, Haibo Liu, Shigui Li, Hong Luo
Software Mentions: 1
Published: over 6 years ago

10.1111/pbi.12754

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth
Cited by: 40
Author(s): Qiang Lu, Fenjuan Shao, Colleen MacMillan, Iain W. Wilson, Karen Van der Merwe, Steven G. Hussey, Alexander Andrew Myburg, Xiaomei Dong, Deyou Qiu
Software Mentions: 1
Published: over 7 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/s12864-017-3751-1

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

10.1186/s40478-020-01099-x

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer’s disease
Cited by: 116
Author(s): Akira Sobue, Okiru Komine, Yuichiro Hara, Fumito Endo, Hideaki Mizoguchi, Seiji Watanabe, Shigeo Murayama, Takashi Saito, Takaomi C. Saido, Naruhiko Sahara, Makoto Higuchi, Tomoo Ogi, Koji Yamanaka
Software Mentions: 1
Published: almost 4 years ago

10.7150/jca.46084

UXT antisense RNA 1 sever as a novel prognostic long non-coding RNA in early stage pancreatic ductal adenocarcinoma patients after receiving pancreaticoduodenectomy
Cited by: 1
Author(s): Xiwen Liao, Rui Huang, Xiangkun Wang, Ketuan Huang, Chengkun Yang, Xin Zhou, Chuangye Han, Hao Su, Xinping Ye, Kang Liu, Guangzhi Zhu, Tao Peng
Software Mentions: 1
Published: almost 4 years ago

10.1111/pbi.12913

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat
Cited by: 27
Author(s): Elodie Rey, Michaël Abrouk, Gabriel Keeble‐Gagnère, Miroslava Karafiátová, Jan Vrána, Sandrine Balzergue, Ludivine Soubigou‐Taconnat, Véronique Brunaud, Marie‐Laure Martin‐Magniette, Takashi R. Endo, Jan Bartoš, R. Appels, Jaroslav Doležel
Software Mentions: 1
Published: over 6 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

10.1007/s00425-020-03424-z

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach
Cited by: 3
Author(s): Izabela Sierocka, Sylwia Alaba, Artur Jarmołowski, Wojciech M. Karłowski, Zofia Szweykowska-Kulińska
Software Mentions: 1
Published: over 4 years ago

10.14814/phy2.14344

Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia
Cited by: 9
Author(s): Matthew W. Gorr, Krishna Sriram, Amy M. Chinn, Abinaya Muthusamy, Paul A. Insel
Software Mentions: 1
Published: almost 5 years ago

10.14814/phy2.12473

The effect of acute and long-term physical activity on extracellular matrix and serglycin in human skeletal muscle
Cited by: 43
Author(s): Marit Hjorth, Frode Norheim, Astri Jeanette Meen, Shirin Pourteymour, Sindre Lee, Torgeir Holen, Jørgen Jensen, Kåre I. Birkeland, Vladimir Martinov, Torgrim M. Langleite, Kristin Eckardt, Christian A. Drevon, Svein Olav Kolset
Software Mentions: 1
Published: over 9 years ago

10.14814/phy2.14289

Prostaglandin D2signaling is not involved in the recovery of rat hind limb tendons from injury
Cited by: 3
Author(s): Dylan C. Sarver, Kristoffer B. Sugg, Jeffrey R Talarek, Jacob B. Swanson, David J. Oliver, Aaron C. Hinken, Henning F. Kramer, Christopher L. Mendias
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-018-5081-3

Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species
Cited by: 4
Author(s): Bing Huang, Yingtong Lin, Chih-Wei Huang, Hsin Pei Lu, Min Xin Luo, Pei Chun Liao
Software Mentions: 1
Published: about 6 years ago

10.1111/jcmm.14048

MCLPMDA: A novel method for miRNA-disease association prediction based on matrix completion and label propagation
Cited by: 50
Author(s): Shengsheng Yu, Cheng Liang, Qiu Xiao, Guanghui Li, Pingjian Ding, Jiawei Luo
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-3747-x

Transcriptome profiling of litchi leaves in response to low temperature reveals candidate regulatory genes and key metabolic events during floral induction
Cited by: 13
Author(s): Hongna Zhang, Jiyuan Shen, Yongzan Wei, Houbin Chen
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.14567

MicroRNA‐transcriptome networks in whole blood and monocytes of women undergoing preterm labour
Cited by: 12
Author(s): Alison G. Paquette, Oksana Shynlova, Xiaogang Wu, Mark Kibschull, Kai Wang, Nathan D. Price, Stephen J. Lye
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.14627

Long non‐coding RNA LINC01225 promotes proliferation, invasion and migration of gastric cancer via Wnt/β‐catenin signalling pathway
Cited by: 13
Author(s): Ying Xü, Guohua Zhang, Chen Zou, Wenliang Qi, Zhigang Gong, Guoliang Zhang, Guansheng Ma, Wenbo Zhang, Pengcheng Jiang
Software Mentions: 1
Published: over 5 years ago

10.14814/phy2.12750

RNA-sequencing of WFS1-deficient pancreatic islets
Cited by: 17
Author(s): Marilin Ivask, Alison Hugill, Sulev Kõks
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.9849

Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat
Cited by: 0
Author(s): Junhao Huang, Lesha Zhang, Yang Fang, Wan Jiang, Juan Du, Jiaquan Zhu, Min Hu, Bing Shen
Software Mentions: 1
Published: about 4 years ago

10.1111/jcmm.14719

Systematic construction and validation of an immune prognostic model for lung adenocarcinoma
Cited by: 43
Author(s): Chenghan Luo, Mengyuan Lei, Yixia Zhang, Qian Zhang, Lifeng Li, Jingyao Lian, Shasha Li, Liping Wang, Guofu Pi
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.4140

Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
Cited by: 18
Author(s): Jinge Ma, Linmiao Li, Haiying Jiang, Xiujuan Zhang, Juan Li, Guanyu Li, Lihong Yuan, Jun Wu, Jinping Chen
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2898-5

Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells
Cited by: 7
Author(s): Ao Zhou, Meng Li, Bo He, Weixing Feng, Fei Huang, Bing Xu, A. Keith Dunker, Curt Balch, Bai‐Yan Li, Yunlong Liu, Yue Wang
Software Mentions: 1
Published: over 8 years ago

10.1111/jcmm.15090

Hedgehog signalling mediates drug resistance through targeting TAP1 in hepatocellular carcinoma
Cited by: 22
Author(s): Xiaotian Zhou, Jia Ding, Hui‐Yan Li, Jie‐Liang Zuo, Shengyang Ge, Hongyan Jia, Jian Wu
Software Mentions: 1
Published: almost 5 years ago

10.1111/jcmm.15161

LncRNA ADAMTS9‐AS2 suppresses the proliferation of gastric cancer cells and the tumorigenicity of cancer stem cells through regulating SPOP
Cited by: 18
Author(s): Feiran Wang, Chong Tang, Dong Xu, Yijie Tang, Yasu Jiang, Xuesong Gao, Jiacheng Xu
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.5681

De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis
Cited by: 19
Author(s): Li Li, Mimi Li, Xiwu Qi, Tang Xingli, Yunshan Zhou
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.9021

Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing
Cited by: 14
Author(s): Yue Zhang, Di Wang, Di Shen, Yang Luo, Yi‐Qun Che
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.11781

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris
Cited by: 5
Author(s): Sandra Cervantes, Jaana Vuosku, Tanja Pyhäjärvi
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.10976

Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots
Cited by: 2
Author(s): Liangchen Su, Shuai Liu, Xing Liu, Baihong Zhang, Meijuan Li, Lidan Zeng, Ling Li
Software Mentions: 1
Published: over 3 years ago

10.1111/jcmm.15242

Characterization of the prognostic values and response to immunotherapy/chemotherapy of Krüppel‐like factors in prostate cancer
Cited by: 20
Author(s): Jialin Meng, Xiaofan Lu, Yu Jie Zhou, Meng Zhang, Lei Gao, Shenglin Gao, Fangrong Yan, Chaozhao Liang
Software Mentions: 1
Published: over 4 years ago

10.1111/jcmm.15244

Analysis of deep sequencing exosome‐microRNA expression profile derived from CP‐II reveals potential role of gga‐miRNA‐451 in inflammation
Cited by: 12
Author(s): Yabo Zhao, Yali Fu, Meiling Zou, Yingfei Sun, Xun Yin, Liangjie Niu, Yanzhang Gong, Xiuli Peng
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.10249

Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes
Cited by: 2
Author(s): Xiaoping Li, Qihe Yu, Jishang Chen, Hui Huang, Zhuangsheng Liu, Chengxing Wang, Yuan He, Xin Zhang, Weiwen Li, Chao Li, Jinglin Zhao, Wansheng Long
Software Mentions: 1
Published: about 4 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

10.7717/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

10.7717/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

10.18632/oncotarget.6859

Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs
Cited by: 92
Author(s): Chunjie Jiang, Yongsheng Li, Zheng Zhao, Jianping Lu, Hong Chen, Na Ding, Guangjuan Wang, Juan Xu, Xia Li
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-3831-2

Gene expression and adaptive noncoding changes during human evolution
Cited by: 14
Author(s): Courtney C. Babbitt, Ralph Haygood, William Nielsen, Gregory A. Wray
Software Mentions: 1
Published: over 7 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

10.7717/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

10.1186/s12864-019-6247-3

Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Cited by: 13
Author(s): Vinicius Vilperte, Calin Rares Lucaciu, Heidi Halbwirth, Robert Boehm, Thomas Rattei, Thomas Debener
Software Mentions: 1
Published: about 5 years ago

10.1111/jcmm.16381

Theragnostic chromosomal rearrangements in treatment‐naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound
Cited by: 0
Author(s): Stephen J. Murphy, Michael J. Levy, James B. Smadbeck, Giannoula Karagouga, Alexa McCune, Frances Harris, Julia Udell, Sarah H. Johnson, Sarah E. Kerr, John C. Cheville, Benjamin R. Kipp, George Vasmatzis, Ferga C. Gleeson
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-016-2680-8

Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level
Cited by: 60
Author(s): Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Grégory Jubelin, Christophe Chambon, Carl J. Yeoman, Margret E. Berg Miller, Christopher J. Fields, Eric C. Martens, Nicolas Terrapon, Bernard Henrissat, Bryan A. White, Pascale Mosoni
Software Mentions: 1
Published: over 8 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

10.1111/jcmm.16760

The subtype‐specific molecular function of SPDEF in breast cancer and insights into prognostic significance
Cited by: 4
Author(s): Ting Ye, Jingyuan Li, June Feng, Jinglan Guo, Xue Wan, Dan Xie, Jinbo Liu
Software Mentions: 1
Published: over 3 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

10.1111/jcmm.16700

LncRNA PVT1 promotes the progression of ovarian cancer by activating TGF‐β pathway via miR‐148a‐3p/AGO1 axis
Cited by: 13
Author(s): Yuxian Wu, Wenqian Gu, Xiao Han, Zhendong Jin
Software Mentions: 1
Published: over 3 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

10.1111/jcmm.16825

MicroRNA‐205‐5p targets E2F1 to promote autophagy and inhibit pulmonary fibrosis in silicosis through impairing SKP2‐mediated Beclin1 ubiquitination
Cited by: 7
Author(s): Qian Qin, Qinghua Ma, Bin Wang, Qingqiang Qian, Changsong Zhao, Feng Fang, Xiaona Dong
Software Mentions: 1
Published: over 3 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

10.7717/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

10.1186/s12863-021-00973-4

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes
Cited by: 9
Author(s): Lin Yuan, Kun Pan, Yonghui Li, Bo Yi, Bingmiao Gao
Software Mentions: 1
Published: over 3 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

10.7717/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

10.7717/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

10.7554/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

10.7717/peerj.11755

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Cited by: 2
Author(s): Mengjun Huang, Haitao Xing, Zhexin Li, Honglei Li, Lin Wu, Yi Jiang
Software Mentions: 1
Published: over 3 years ago

10.3390/jcm8070963

Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder
Cited by: 15
Author(s): Min Young Lee, David Baxter, Kelsey Scherler, Taek‐Kyun Kim, Xiaogang Wu, Duna Abu‐Amara, Janine D. Flory, Rachel Yehuda, Charles R. Marmar, Marti Jett, Inyoul Lee, Kai Wang, Leroy Hood
Software Mentions: 1
Published: over 5 years ago

10.3390/jcm8091440

Surface Pre-Reacted Glass Filler Contributes to Tertiary Dentin Formation through a Mechanism Different Than That of Hydraulic Calcium-Silicate Cement
Cited by: 13
Author(s): Masakazu Okamoto, Muslim Ali, Shungo Komichi, Masakatsu Watanabe, Haozhang Huang, Yuki Ito, Jiro Miura, Yujiro Hirose, Manabu Mizuhira, Yusuke Takahashi, Daisuke Okuzaki, Shigetada Kawabata, Satoshi Imazato, Mikako Hayashi
Software Mentions: 1
Published: about 5 years ago

10.1186/s12863-020-00893-9

A novel mouse model expressing human forms for complement receptors CR1 and CR2
Cited by: 6
Author(s): Harriet M. Jackson, Kate E. Foley, Rita O’Rourke, Timothy M. Stearns, Dina Fathalla, B. Paul Morgan, Gareth R. Howell
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj.5307

A novel long non-coding RNA, AC012456.4, as a valuable and independent prognostic biomarker of survival in oral squamous cell carcinoma
Cited by: 11
Author(s): Xuegang Hu, Zailing Qiu, Jianchai Zeng, Tingting Xiao, Zhihong Ke, Hongbing Lyu
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.10328

Deregulation of lysophosphatidic acid metabolism in oral cancer promotes cell migration via the up-regulation of COX-2
Cited by: 3
Author(s): Mariati Abdul Rahman, Malcolm Tan, Steven P. Johnson, Robert Hollows, Wen Lin Chai, Jason Peter Mansell, Lee Fah Yap, Ian C. Paterson
Software Mentions: 1
Published: about 4 years ago

10.3390/jcm10102110

Plasma Exosomal miRNA Levels after Radiotherapy Are Associated with Early Progression and Metastasis of Cervical Cancer: A Pilot Study
Cited by: 5
Author(s): Oyeon Cho, Do Wan Kim, J.Y. Cheong
Software Mentions: 1
Published: over 3 years ago

10.3390/jcm10112227

miRNAs and Genes Involved in the Interplay between Ocular Hypertension and Primary Open-Angle Glaucoma. Oxidative Stress, Inflammation, and Apoptosis Networks
Cited by: 16
Author(s): J. Raga-Cervera, José Miguel Bolarín, José María Millán, Manuel García-Medina, Laia Pedrola, Javier Abellán-Abenza, Mar Valero-Velló, Silvia M. Sanz-González, José Enrique O’Connor, David Galarreta, Elena Bendala-Tufanisco, Aloma Mayordomo-Febrer, María Dolores Pinazo-Durán, Vicente Zanón‐Moreno
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.11135

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem
Cited by: 0
Author(s): Gina A. Garzón-Martínez, Francy Liliana García Arias, Felix E. Enciso-Rodríguez, Mauricio Soto‐Suárez, Carolina González, Aureliano Bombarely, Luz Stella Barrero, Jaime A. Osorio Guarín
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2156-15-S2-S6

Male-specific phosphorylated SR proteins in adult flies of the Mediterranean Fruitfly Ceratitis capitata
Cited by: 4
Author(s): Giuseppe Saccone, Christos Louis, Hongyou Zhang, Valeria Petrella, Michele Di Natale, Maria Perri, Marco Salvemini
Software Mentions: 1
Published: almost 10 years ago

10.7717/peerj.7442

Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
Cited by: 4
Author(s): Feng Pang, Mengmeng Zhang, Guohua Li, Zhenxing Zhang, Haifeng Huang, Baobao Li, Chengqiang Wang, Xiaohong Yang, Yiying Zheng, Q. An, Luyin Zhang, Lijun Du, Fengyang Wang
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3959

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
Cited by: 37
Author(s): Jiuqiang Guan, Keren Long, Jideng Ma, Jinwei Zhang, Dafang He, Long Jin, Qianzi Tang, Anan Jiang, Xun Wang, Yaodong Hu, Shilin Tian, Zhi Jiang, Mingzhou Li, Xiaolin Luo
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.8368

Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma
Cited by: 12
Author(s): Xun Shi, You Li, Yehuan Sun, Xu Zhao, Xin Sun, Tuotuo Gong, Zhinan Liang, Yuan Ma, Xiaozhi Zhang
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.4500

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq
Cited by: 30
Author(s): Liuxin Xiang, Chaowei Cai, Jieru Cheng, Lu Wang, Chaofeng Wu, Yùzhēn Shí, Jingzhi Luo, Lin He, Yushan Deng, Xiao Zhang, Yǒulù Yuán, Yingfan Cai
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.2977

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genusMacrobrachium: identification and expression validation in a model species (M. koombooloomba)
Cited by: 26
Author(s): Rahi Lifat, Shorash Amin, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: almost 8 years ago

10.1038/sdata.2016.89

Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases
Cited by: 312
Author(s): Mariet Allen, Minerva M. Carrasquillo, Cory C. Funk, Benjamin D. Heavner, Fanggeng Zou, Curtis S. Younkin, Jeremy D. Burgess, High Seng Chai, Julia E. Crook, James A. Eddy, Hongdong Li, Ben Logsdon, Mette A. Peters, Kristen K. Dang, Xue Wang, Daniel J. Serie, Chen Wang, Thuy Nguyen, Sarah Lincoln, Kimberly G. Malphrus, Gina Bisceglio, Li Ma, Todd E. Golde, Lara M. Mangravite, Yan W. Asmann, Nathan D. Price, Ronald C. Petersen, Neill R. Graff‐Radford, Dennis W. Dickson, Steven G. Younkin, Nilüfer Ertekin-Taner
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.6402

In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis
Cited by: 7
Author(s): Yashoda Ghanekar, Subhashini Sadasivam
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.7261

Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus
Cited by: 10
Author(s): Ying Xue, Jun Ma, Yehua He, Shuang Yu, Zhen Yuan Lin, Yingyuan Xiong, Fatima Rafique, Fuxing Jiang, Lina Sun, Min Ma, Yujue Zhou, Xi Li, Zhuo Huang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12863-016-0439-5

C14orf132 gene is possibly related to extremely low birth weight
Cited by: 3
Author(s): Airi Tiirats, Triin Viltrop, Margit Nõukas, Ene Reimann, Andres Salumets, Sulev Kõks
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.1549

In plantacomparative transcriptomics of host-adapted strains ofRalstonia solanacearum
Cited by: 25
Author(s): Florent Ailloud, Tiffany M. Lowe, Isabelle Robène, Stéphane Cruveiller, Caitilyn Allen, Philippe Prior
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.8035

Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis
Cited by: 0
Author(s): Jin Li, Juan Perucho, Yuanyuan Liu, Wenwen Xia, Fengfeng Cheng, Wenhui Tian, Lin Zhang, Jianbo Zhu, Aiying Wang
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.8403

Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
Cited by: 12
Author(s): Yue Li, Xiaoyan Zhou, Jiali Liu, Yin Yang, Xin Yuan, Rui Yang, Qi Wang, Jing Ji, Qian He
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12863-020-00862-2

RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers
Cited by: 3
Author(s): Hellenn Cardoso Oliveira, A. M. G. Ibelli, Simone Eliza Facioni Guimarães, Maurício Egídio Cantão, J. de O. Peixoto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.7743

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
Cited by: 3
Author(s): Shuang Fu, Yuhuan Meng, Shudai Lin, Wenlu Zhang, Yuting He, Lizhen Huang, Hongli Du
Software Mentions: 1
Published: about 5 years ago

10.1186/s12863-018-0700-1

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium
Cited by: 8
Author(s): Lijun Wu, Tao Liu, Yongsheng Xu, Wenjie Chen, Baolong Liu, Lianquan Zhang, Dengcai Liu, Huaigang Zhang, Bo Zhang
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11239

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
Cited by: 9
Author(s): Lanya Shui, Kaisen Huo, Yan Chen, Zilin Zhang, Yanfang Li, Jun Niu
Software Mentions: 1
Published: over 3 years ago

10.1038/sdata.2019.24

Long noncoding RNA and mRNA expression profiles following igf3 knockdown in common carp, Cyprinus carpio
Cited by: 29
Author(s): Fei Song, Lanmei Wang, Wenbin Zhu, Zaijie Dong
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.3529

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
Cited by: 11
Author(s): Michael Gerth, Gregory D. D. Hurst
Software Mentions: 1
Published: over 7 years ago

10.1016/j.patter.2021.100246

Quantum processor-inspired machine learning in the biomedical sciences
Cited by: 14
Author(s): Richard Y. Li, Sharvari Gujja, Sweta R. Bajaj, Omar Gamel, Nicholas A. Cilfone, Jeffrey R. Gulcher, Daniel A. Lidar, Thomas Chittenden
Software Mentions: 1
Published: over 3 years ago

10.3390/pathogens6040068

Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection
Cited by: 20
Author(s): Poyin Chen, Taylor Reiter, Bihua C. Huang, Nguyet Kong, Bart C. Weimer
Software Mentions: 1
Published: almost 7 years ago

10.1007/s11418-021-01505-1

Curcumin suppresses LGR5(+) colorectal cancer stem cells by inducing autophagy and via repressing TFAP2A-mediated ECM pathway
Cited by: 27
Author(s): Xiaohong Mao, Xin Zhang, Xiaowei Zheng, Yongwu Chen, Zixue Xuan, Ping Huang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12862-019-1362-y

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation
Cited by: 6
Author(s): Kristin Franke, Isabell Karl, Tonatiuh Peña Centeno, Barbara Feldmeyer, Christian Lassek, Vicencio Oostra, Katharina Riedel, Mario Stanke, Christopher W. Wheat, Klaus Fischer
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41597-019-0193-4

The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways
Cited by: 77
Author(s): Scott A. Ochsner, David Abraham, Kirt Martin, Wei Ding, Apollo McOwiti, Wasula H. Kankanamge, Zichen Wang, Kaitlyn J. Andreano, Ross A. Hamilton, Yue Chen, Angelica Hamilton, Marin L. Gantner, Michael Dehart, Shijing Qu, Susan G. Hilsenbeck, Lauren B. Becnel, Dave Bridges, Avi Ma’ayan, Janice M. Huss, Fabio Stossi, Charles E. Foulds, Anastasia Kralli, Donald P. McDonnell, Neil J. McKenna
Software Mentions: 1
Published: about 5 years ago

10.1186/s13071-020-3914-9

Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis
Cited by: 6
Author(s): Lucas Gentil Azevedo, Artur T. L. Queiroz, Aldina Barral, Luciane Amorim Santos, Pablo Ivan Pereira Ramos
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.7963

Comparative analysis of human and mouse transcriptomes of Th17 cell priming
Cited by: 39
Author(s): Soile Tuomela, Sini Rautio, Helena Ahlfors, Viveka Öling, Verna Salo, Ubaid Ullah, Zhi Chen, Saara Hämälistö, Subhash Tripathi, Tarmo Äijö, Omid Rasool, Hayssam Soueidan, Lodewyk Wessels, Brigitta Stockinger, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2148-13-165

Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei
Cited by: 14
Author(s): Jianbo Yuan, Xiaojun Zhang, Cheng-Zhang Liu, Jiankai Wei, Fuhua Li, Jianhai Xiang
Software Mentions: 1
Published: over 11 years ago

10.1186/s13071-020-3910-0

Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport
Cited by: 3
Author(s): Marziyeh Anari, Andreas J. Stroehlein, Ross S. Hall, Bill C.H. Chang, Robin B. Gasser, Neil D. Young
Software Mentions: 1
Published: almost 5 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568