bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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 6 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: over 6 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: about 5 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: almost 7 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: about 5 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: about 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: about 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: about 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: about 7 years ago

10.1084/jem.20190450

Tumor-derived IL-6 and trans-signaling among tumor, fat, and muscle mediate pancreatic cancer cachexia
Cited by: 76
Author(s): Joseph E. Rupert, Ashok Narasimhan, Daenique H. Jengelley, Yanlin Jiang, Jianguo Liu, Ernie D. Au, Libbie M Silverman, George E. Sandusky, Andrea Bonetto, Sha Cao, Xiaoyu Lu, Thomas M. O’Connell, Yunlong Liu, Leonidas G. Koniaris, Teresa A. Zimmers
Software Mentions: 1
Published: over 5 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: almost 8 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: over 5 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: over 6 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: over 5 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: over 6 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: about 7 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: almost 7 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: over 6 years ago

10.7150/jca.33157

Establishment and Characterization of a CTC Cell Line from Peripheral Blood of Breast Cancer Patient
Cited by: 19
Author(s): Pan Zhao, Weiping Zhou, Chang Liu, Huirong Zhang, Zhiqiang Cheng, Weiqing Wu, Kaisheng Liu, Hong Hu, Caineng Zhong, Yayuan Zhang, Dongxian Zhou, Feiyuan Liu, Yong Dai, Jianhong Wang, Chang Zou
Software Mentions: 1
Published: over 7 years ago

10.1186/s12929-018-0477-6

Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
Cited by: 7
Author(s): Ya Xu, Ying Qing Li, Na Liu, Qiuming He, Xin Tang, Xin Wen, Xiao Yang, Ying Sun, Ling TANG
Software Mentions: 1
Published: almost 8 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 5 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 5 years ago

10.1016/j.jbc.2021.101156

Iron loading induces cholesterol synthesis and sensitizes endothelial cells to TNFα-mediated apoptosis
Cited by: 9
Author(s): Allison L. Fisher, Daniel N. Srole, Nicolaos Palaskas, David Meriwether, Srinivasa T. Reddy, Tomas Ganz, Elizabeta Nemeth
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: over 10 years ago

10.1016/j.jbc.2021.100403

Targeting primary and metastatic uveal melanoma with a G protein inhibitor
Cited by: 20
Author(s): Michael D. Onken, Carol M. Makepeace, Kevin M. Kaltenbronn, Joelle Choi, Leonel F. Hernandez‐Aya, Katherine N. Weilbaecher, Kisha Piggott, P. Kumar Rao, Carla M. Yuede, Alethia J. Dixon, Patrick Osei‐Owusu, John A. Cooper, Kendall J. Blumer
Software Mentions: 1
Published: over 5 years ago

10.1074/jbc.RA120.015877

Elongin A associates with actively transcribed genes and modulates enhancer RNA levels with limited impact on transcription elongation rate in vivo
Cited by: 13
Author(s): M. Behfar Ardehali, Manashree Damle, Carlos Perea-Resa, Michael D. Blower, Robert E. Kingston
Software Mentions: 1
Published: over 5 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: over 5 years ago

10.1074/jbc.M116.733733

miR-30 Family Controls Proliferation and Differentiation of Intestinal Epithelial Cell Models by Directing a Broad Gene Expression Program That Includes SOX9 and the Ubiquitin Ligase Pathway
Cited by: 33
Author(s): Bailey C. E. Peck, John Sincavage, Sydney Feinstein, Amanda T. Mah, James G. Simmons, P. Kay Lund, Praveen Sethupathy
Software Mentions: 1
Published: about 10 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: about 5 years ago

10.1093/jxb/ert428

Global and local perturbation of the tomato microRNA pathway by atrans-activatedDICER-LIKE 1mutant
Cited by: 26
Author(s): Michael Kravchik, Ramanjulu Sunkar, Subha Damodharan, Ran Stav, Matat Zohar, Tal Isaacson, Tzahi Arazi
Software Mentions: 1
Published: over 12 years ago

10.1093/jac/dkaa296

A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems
Cited by: 13
Author(s): A. Keith Turner, Muhammad Yasir, Sarah Bastkowski, Andrea Telatin, Andrew J. Page, Ian G. Charles, Mark A. Webber
Software Mentions: 1
Published: about 6 years ago

10.1186/s40104-017-0202-4

Evaluation of fatty acid metabolism and innate immunity interactions between commercial broiler, F1 layer × broiler cross and commercial layer strains selected for different growth potentials
Cited by: 8
Author(s): Nicky‐Lee Willson, R. E. A. Forder, Rick Tearle, G. S. Nattrass, Robert J. Hughes, P. I. Hynd
Software Mentions: 1
Published: about 9 years ago

10.1016/j.jaci.2016.05.031

Tumor progression locus 2 reduces severe allergic airway inflammation by inhibiting Ccl24 production in dendritic cells
Cited by: 9
Author(s): Yashaswini Kannan, Yanda Li, Stephanie M. Coomes, Isobel Okoye, Victoria S. Pelly, Srividya Sriskantharajah, Eva Gückel, Lauren M. Webb, Stephanie Czieso, Nikolay P. Nikolov, Andrew S. MacDonald, Steven C. Ley, Mark S. Wilson
Software Mentions: 1
Published: over 9 years ago

10.1093/jxb/erw131

Up-regulating the abscisic acid inactivation geneZmABA8ox1bcontributes to seed germination heterosis by promoting cell expansion
Cited by: 16
Author(s): Yangyang Li, Cheng Wang, Xinye Liu, Jian Song, Hongjian Li, Zhipeng Sui, Ming Zhang, S. S. Fang, Jinfang Chu, Mingming Xin, Chaojie Xie, Yirong Zhang, Qixin Sun, Zhongfu Ni
Software Mentions: 1
Published: over 10 years ago

10.1093/jxb/erw338

Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis
Cited by: 34
Author(s): Long Jiang, Liduan Zheng, Xiaomeng Wu, Yan-Ni Fang, Hui-Hui Jia, Zongzhou Xie, Xiuxin Deng, Wen‐Wu Guo
Software Mentions: 1
Published: almost 10 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 8 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: about 8 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: almost 6 years ago

10.1093/jxb/erx057

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris
Cited by: 22
Author(s): James D. Stone, Pavla Koloušková, Daniel B. Sloan, Helena Štorchová
Software Mentions: 1
Published: over 9 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 5 years ago

10.1021/acs.jafc.1c00130

1H NMR Metabolomics and Full-Length RNA-Seq Reveal Effects of Acylated and Nonacylated Anthocyanins on Hepatic Metabolites and Gene Expression in Zucker Diabetic Fatty Rats
Cited by: 8
Author(s): Kang Chen, Xuetao Wei, Raghunath Pariyani, Maaria Kortesniemi, Yumei Zhang, Baoru Yang
Software Mentions: 1
Published: over 5 years ago

10.1172/jci.insight.143023

Shifting osteogenesis in vascular calcification
Cited by: 11
Author(s): Jiayi Yao, Xinhui Wu, Xuguang Qiao, Daoqin Zhang, Li Zhang, Jocelyn Ma, Xinjiang Cai, Kristina I. Boström, Yucheng Yao
Software Mentions: 1
Published: over 5 years ago

10.1093/jxb/erw391

Photosynthesis in C3–C4intermediateMoricandiaspecies
Cited by: 52
Author(s): Urte Schlüter, Andrea Bräutigam, Udo Gowik, Michael Melzer, Pascal‐Antoine Christin, Samantha Kurz, Tabea Mettler‐Altmann, Andreas P.M. Weber
Software Mentions: 1
Published: almost 10 years ago

10.3390/jof7050373

Transcriptome Analysis of the Japanese Pine Sawyer Beetle, Monochamus alternatus, Infected with the Entomopathogenic Fungus Metarhizium anisopliae JEF-197
Cited by: 4
Author(s): Jong-Cheol Kim, Mi-Rong Lee, Sihyeon Kim, So-Eun Park, Se-Jin Lee, Tae‐Young Shin, Woo Jin Kim, Jaesu Kim
Software Mentions: 1
Published: over 5 years ago

10.3390/jof7070493

Transcriptional Responses of Sclerotinia sclerotiorum to the Infection by SsHADV-1
Cited by: 17
Author(s): Zhong Qu, Yànpíng Fù, Yang Lin, Zhenzhen Zhao, Xuekun Zhang, Jiāsēn Chéng, Jiǎtāo Xiè, Tao Chen, Bo Li, Dàohóng Jiāng
Software Mentions: 1
Published: about 5 years ago

10.1093/jxb/erw343

C3cotyledons are followed by C4leaves: intra-individual transcriptome analysis ofSalsola soda(Chenopodiaceae)
Cited by: 19
Author(s): Maximilian Lauterbach, Kumari Billakurthi, Gudrun Kadereit, Martha Ludwig, Peter Westhoff, Udo Gowik
Software Mentions: 1
Published: almost 10 years ago

10.1172/jci.insight.89631

Plasma vesicle miRNAs for therapy response monitoring in Hodgkin lymphoma patients
Cited by: 113
Author(s): Monique A.J. van Eijndhoven, Josée M. Zijlstra, Nils J. Groenewegen, Esther E.E. Drees, Stuart van Niele, S. Rubina Baglio, Danijela Koppers-Lalić, Hans van der Voorn, Sten F. W. M. Libregts, Marca H. M. Wauben, Renée X. de Menezes, Jan R.T. van Weering, Rienk Nieuwland, Lydia Visser, Anke van den Berg, Daphne de Jong, D. Michiel Pegtel
Software Mentions: 1
Published: almost 10 years ago

10.3390/insects12030209

Antennal Transcriptome Analysis and Identification of Candidate Chemosensory Genes of the Harlequin Ladybird Beetle, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae)
Cited by: 11
Author(s): Gabriele Rondoni, Alessandro Roman, Camille Meslin, Nicolas Montagné, Eric Conti, Emmanuelle Jacquin‐Joly
Software Mentions: 1
Published: over 5 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: about 7 years ago

10.1093/gerona/glx101

The Effects of Graded Levels of Calorie Restriction: X. Transcriptomic Responses of Epididymal Adipose Tissue
Cited by: 19
Author(s): Davina Derous, Sharon E. Mitchell, Cara L Green, Yingchun Wang, Jing Han, Luonan Chen, Daniel E. L. Promislow, David Lusseau, Alex Douglas, John R. Speakman
Software Mentions: 1
Published: over 9 years ago

10.1093/jxb/ery077

GCN5 contributes to stem cuticular wax biosynthesis by histone acetylation of CER3 in Arabidopsis
Cited by: 34
Author(s): Tianya Wang, Jiewen Xing, Xinye Liu, Yingyin Yao, Zhaorong Hu, Huiru Peng, Mingming Xin, Dao‐Xiu Zhou, Yirong Zhang, Zhongfu Ni
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/ery189

Differential response to heat stress in outer and inner onion bulb scales
Cited by: 13
Author(s): Ortal Galsurker, Adi Doron‐Faigenboim, Paula Teper‐Bamnolker, Avinoam Daus, Amnon Lers, Dani Eshel
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/erz533

ATBS1-INTERACTING FACTOR 2 negatively regulates dark- and brassinosteroid-induced leaf senescence through interactions with INDUCER OF CBF EXPRESSION 1
Cited by: 19
Author(s): Yonggyun Kim, Park Min Su, Shin Dm, Giang Pham, Yong-Jin Jeong, Kim Sh
Software Mentions: 1
Published: almost 7 years ago

10.3390/insects11110816

Chemosensory-Related Gene Family Members of the Horn Fly, Haematobia irritans irritans (Diptera: Muscidae), Identified by Transcriptome Analysis
Cited by: 5
Author(s): Pia U. Olafson, Christopher Saski
Software Mentions: 1
Published: almost 6 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: almost 9 years ago

10.3390/insects10080245

Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Cited by: 30
Author(s): Dafu Chen, Huazhi Chen, Yuguang Du, Dingding Zhou, Suxia Geng, Haipeng Wang, Jieqi Wan, Chuan Xiong, Yusheng Zheng, Rui Guo
Software Mentions: 1
Published: about 7 years ago

10.1093/jxb/eraa221

Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling
Cited by: 17
Author(s): Ilana Lambert, Marjorie Pervent, Antoine Le Quéré, Gilles Clément, Marc Tauzin, Dany Séverac, Claire Benezech, Pascal Tillard, Marie‐Laure Martin‐Magniette, Stefano Colella, Marc Lepetit
Software Mentions: 1
Published: over 6 years ago

10.1093/jxb/eraa581

Restriction of cytosolic sucrose hydrolysis profoundly alters development, metabolism, and gene expression in Arabidopsis roots
Cited by: 12
Author(s): Cristina Pignocchi, Alexander Ivakov, Regina Feil, Martin Trick, Marilyn J. Pike, Trevor L. Wang, John E. Lunn, Alison M. Smith
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1002470

Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma
Cited by: 281
Author(s): Elaine M. Morazzani, Michael R. Wiley, Marta G. Murreddu, Zach N. Adelman, K.M. Myles
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.ppat.1003186

Epstein - Barr Virus Transforming Protein LMP-1 Alters B Cells Gene Expression by Promoting Accumulation of the Oncoprotein ΔNp73α
Cited by: 19
Author(s): Rosita Accardi, Ikbal Fathallah, Henri Gruffat, Giuseppe Mariggiò, Florence Le Calvez-Kelm, Catherine Voegele, Birke Bartosch, Héctor Hernandez-Vargas, James McKay, Bakary S. Sylla, Évelyne Manet, Massimo Tommasino
Software Mentions: 1
Published: over 13 years ago

10.1016/j.xinn.2020.100052

Regulatory Role of Retinoic Acid in Male Pregnancy of the Seahorse
Cited by: 8
Author(s): Chunyan Li, Yongxin Li, Geng Qin, Zelin Chen, Meng Qu, Bo Zhang, Xue Han, Xin Wang, Pei‐Yuan Qian, Qiang Lin
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-015-1667-1

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways
Cited by: 46
Author(s): Bas Verbruggen, Lisa K. Bickley, Eduarda M. Santos, Charles R. Tyler, Grant D. Stentiford, Kelly S. Bateman, Ronny van Aerle
Software Mentions: 1
Published: about 11 years ago

10.1186/s13018-021-02508-0

Cornuside I promoted osteogenic differentiation of bone mesenchymal stem cells through PI3K/Akt signaling pathway
Cited by: 5
Author(s): Feng Gao, Shuhua Xia, Xiuhui Wang, Xiaoxiao Zhou, Jun Wang
Software Mentions: 1
Published: about 5 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: over 6 years ago

10.1371/journal.ppat.1004443

Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid
Cited by: 85
Author(s): Shuji Asai, Ghanasyam Rallapalli, Sophie J. M. Piquerez, Marie‐Cécile Caillaud, Oliver J. Furzer, Naveed Ishaque, Lennart Wirthmueller, Georgina Fabro, Ken Shirasu, Jonathan D. G. Jones
Software Mentions: 1
Published: almost 12 years ago

10.1155/2020/9369182

The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001
Cited by: 11
Author(s): Kejian Tian, Fanjuan Meng, Meng Qi, Yan Gao, Lili Zhang, Le Wang, Yuqing Wang, Xue Li, Hongliang Huo
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.ppat.1004994

IFNγ and IL-12 Restrict Th2 Responses during Helminth/Plasmodium Co-Infection and Promote IFNγ from Th2 Cells
Cited by: 41
Author(s): Stephanie M. Coomes, Victoria S. Pelly, Yashaswini Kannan, Isobel Okoye, Stephanie Czieso, Lewis J. Entwistle, Jimena Perez-Lloret, Nikolay P. Nikolov, Alexandre J. Potocnik, Judit Bíró, Jean Langhorne, Mark S. Wilson
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.ppat.1005160

The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation
Cited by: 76
Author(s): Dan Drecktrah, Meghan Lybecker, Niko Popitsch, Philipp Rescheneder, Laura S. Hall, D. Scott Samuels
Software Mentions: 1
Published: almost 11 years ago

10.1128/IAI.00426-20

An Ixodes scapularis Protein Disulfide Isomerase Contributes to Borrelia burgdorferi Colonization of the Vector
Cited by: 4
Author(s): Yongguo Cao, Connor Rosen, Gunjan Arora, Akash Gupta, Carmen J. Booth, Kristen E. Murfin, Jiří Černý, Alejandro Marín López, Yu-Min Chuang, Xiao‐Tian Tang, Utpal Pal, Aaron M. Ring, Sukanya Narasimhan, Erol Fikrig
Software Mentions: 1
Published: almost 6 years ago

10.1002/path.5551

Large‐scale analysis of <scp>BAP1</scp> expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma
Cited by: 22
Author(s): Assunta De Rienzo, Lucian R. Chirieac, Yin P. Hung, David T. Severson, Samuel Freyaldenhoven, Corinne E. Gustafson, Nhien Dao, Claire Meyerovitz, Michela E Oster, Roderick V. Jensen, Beow Y. Yeap, Raphael Bueno, William G. Richards
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13059-019-1830-0

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
Cited by: 152
Author(s): Ciara H. O’Flanagan, Kieran R Campbell, Allen W. Zhang, Farhia Kabeer, Jamie Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham, Nicholas Ceglia, Richard A. Moore, Andrew J. Mungall, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-14-763

Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis strains reveals similar gene expression changes through attenuation
Cited by: 50
Author(s): Monica J. Pedroni, Kerry S. Sondgeroth, Gina M Gallego-López, Ignacio Echaide, Audrey O.T. Lau
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.ppat.1005697

The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis
Cited by: 63
Author(s): Marie Tollot, Assmann Daniela, Christian Becker, Janine Altmüller, Julien Y. Dutheil, Carl‐Eric Wegner, Regine Kahmann
Software Mentions: 1
Published: about 10 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: almost 11 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: almost 6 years ago

10.1371/journal.ppat.1006097

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis
Cited by: 40
Author(s): Melania Abrahamian, Audrey M. V. Ah‐Fong, Carol Davis, Kalina Andreeva, Howard S. Judelson
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-13-278

Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers
Cited by: 86
Author(s): Ying Wang, Vinayak Brahmakshatriya, Blanca Lupiani, Sanjay M. Reddy, Benjamin Soibam, Ashley Benham, Preethi H. Gunaratne, Hsiao‐Ching Liu, Nares Trakooljul, Nancy H. Ing, Ron Okimoto, Huaijun Zhou
Software Mentions: 1
Published: about 14 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: almost 11 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 11 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 8 years ago

10.1186/s12864-015-1555-8

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
Cited by: 10
Author(s): Yejun Wang, Keith D. MacKenzie, Aaron P. White
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1006847

Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster
Cited by: 100
Author(s): Katia Troha, Joo Hyun Im, Jonathan Revah, Brian P. Lazzaro, Nicolas Buchon
Software Mentions: 1
Published: over 8 years ago

10.1155/2019/4025747

A Full-Length Reference Floral Transcriptome ofBoehmeria tricuspisProvides Insights into Apomeiosis and Polyploidy
Cited by: 2
Author(s): Qing Tang, Ying Xu, Canhui Deng, Chaohua Cheng, Zhigang Dai, Zemao Yang, Chan Lee, Jianguang Su
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1007221

An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model
Cited by: 20
Author(s): James C. Romero-Masters, Makoto Ohashi, Reza Djavadian, Mark R. Eichelberg, Mitchell Hayes, Jillian A. Bristol, Shidong Ma, Erik A. Ranheim, Jenny E. Gumperz, Eric Johannsen, Shannon C. Kenney
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1007388

Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response
Cited by: 20
Author(s): Liam F. Fitzsimmons, Lin Liu, Steffen Porwollik, Sangeeta Chakraborty, Prerak Desai, Timothy Tapscott, Calvin A. Henard, Michael McClelland, Andrés Vázquez‐Torres
Software Mentions: 1
Published: almost 8 years ago

10.1186/1129-2377-15-S1-B24

HMTI-0197. Whole blood transcriptome analysis in migraine with aura patients: a case control study
Cited by: 0
Author(s): Agustı́n Oterino, María Toriello, Anna Esteve‐Codina, Simon Heath, J. Castillo, Jenifer Fernandez, Enar Pons, Sílvia Gutiérrez, Enrique Palacio, VG Quintanilla
Software Mentions: 1
Published: almost 12 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 9 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: over 13 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: over 9 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: over 7 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: over 16 years ago

10.1534/genetics.117.300103

Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress
Cited by: 21
Author(s): Hervé Gaubert, Diego H. Sánchez, Hajk-Georg Drost, Jerzy Paszkowski
Software Mentions: 1
Published: about 9 years ago

10.7150/ijms.49997

Research on the circadian clock gene HNF4a in different malignant tumors
Cited by: 0
Author(s): Mengjun Qiu, Li Zhang, Xiefan Fang, Qiuting Li, Lisheng Zhu, Bin Zhang, Shengli Yang, Zhifan Xiong
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2552-2

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)
Cited by: 43
Author(s): Ming Li, Zhaoxu Liang, Yuan Zeng, Yan Ji, Kai–Chao Wu, Jun Liang, Shikun He, Guanyu Wang, Zhanghong Mo, Feiquan Tan, Li Song, Wang LunWang
Software Mentions: 1
Published: over 10 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: over 6 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 7 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: almost 5 years ago

10.1038/s41368-019-0070-1

Transcriptome analysis of ankylosed primary molars with infraocclusion
Cited by: 3
Author(s): Annie Tong, Yuh-Lit Chow, Katie Xu, Rita Hardiman, Paul M. Schneider, Seong‐Seng Tan
Software Mentions: 1
Published: over 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: about 7 years ago

10.1098/rsob.140024

Sex-biased expression of microRNAs inDrosophila melanogaster
Cited by: 38
Author(s): A. De Marco
Software Mentions: 1
Published: over 12 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568