bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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: almost 7 years ago

10.1186/s12864-017-4053-3

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)
Cited by: 26
Author(s): Ming Li, Zhaoxu Liang, Shikun He, Yuan Zeng, Yan Ji, Fang Wei, Kai–Chao Wu, Guanyu Wang, Ning Xia, Wang LunWang, Song Li, Huachun Tan, Feiquan Tan
Software Mentions: 1
Published: about 9 years ago

10.1128/mSphere.00620-19

Global Transcriptomic Analysis of the Candida albicans Response to Treatment with a Novel Inhibitor of Filamentation
Cited by: 16
Author(s): Jesús A. Romo, Hao Zhang, Hong Cai, David Kadosh, Julia Koehler, Stephen P. Saville, Yufeng Wang, José L. Lopez-Ribot
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms221910435

Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis
Cited by: 3
Author(s): Yingning Wang, Fang Ma, Jixian Yang, Haijuan Guo, Delin Su, Liping Yu
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms221910696

RNA-Seq and Electrical Penetration Graph Revealed the Role of Grh1-Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper (Nephotettix cincticeps Uhler) Resistance in Rice (Oryza sativa L.)
Cited by: 1
Author(s): Young Ho Kwon, Nkulu Rolly Kabange, Ji-Yoon Lee, Bo Yoon Seo, Dongjin Shin, So-Myeong Lee, Jin-Kyung Cha, Jun-Hyeon Cho, Ju-Won Kang, Dong-Soo Park, Jong-Min Ko, Jonghee Lee
Software Mentions: 1
Published: about 5 years ago

10.1186/s41065-020-00122-4

Comparative transcriptome analysis reveals gene expression differences between two peach cultivars under saline-alkaline stress
Cited by: 9
Author(s): Shouqin Sun, Haiyan Song, Jing Li, Dong Chen, Tu MeiYan, Guanghong Jia, Guoqing Yu, Zhiqin Zhou
Software Mentions: 1
Published: over 6 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 10 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 10 years ago

10.1016/j.heliyon.2021.e06307

Cellular and molecular profiles of anterior nervous system regeneration in Diopatra claparedii Grube, 1878 (Annelida, Polychaeta)
Cited by: 0
Author(s): Mohd Ulul Ilmie Ahmad Nazri, Mohd Hafizi Mahmud, Basri Saidi, Mohd-Noor Mat-Isa, Zolkapli Ehsak, Bin Haji Ross Othman, Izwandy Idris, Wan Iryani Wan Ismail
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-018-0054-x

VlbZIP30 of grapevine functions in dehydration tolerance via the abscisic acid core signaling pathway
Cited by: 20
Author(s): Mingxing Tu, Xianhang Wang, Yanxun Zhu, Dejun Wang, Xuechuan Zhang, Ye Cui, Yajuan Li, Min Gao, Zhi Li, Yuejin Wang
Software Mentions: 1
Published: about 8 years ago

10.1128/mSphere.00983-19

20-Hydroxyecdysone Primes Innate Immune Responses That Limit Bacterial and Malarial Parasite Survival in Anopheles gambiae
Cited by: 28
Author(s): Richard A. K. Reynolds, Hyeogsun Kwon, Ryan C. Smith
Software Mentions: 1
Published: over 6 years ago

10.1038/s41438-020-00372-3

Grapevine VlbZIP30 improves drought resistance by directly activating VvNAC17 and promoting lignin biosynthesis through the regulation of three peroxidase genes
Cited by: 47
Author(s): Mingxing Tu, Xianhang Wang, Wuchen Yin, Wang Ya, Yajuan Li, Guofeng Zhang, Zhi Li, Junyang Song
Software Mentions: 1
Published: about 6 years ago

10.1002/hed.26089

MicroRNA‐based risk scoring system to identify early‐stage oral squamous cell carcinoma patients at high‐risk for cancer‐specific mortality
Cited by: 23
Author(s): Angela J. Yoon, Shuang Wang, David I. Kutler, Richard D. Carvajal, Elizabeth Philipone, Tian Wang, Dominic LaRoche, Brenda Y. Hernandez, Bradley D. McDowell, Claire Stewart, Fatemeh Momen‐Heravi, Regina M. Santella
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41438-019-0130-x

MicroRNA396-mediated alteration in plant development and salinity stress response in creeping bentgrass
Cited by: 58
Author(s): Shuangrong Yuan, Junlong Zhao, Zhigang Li, Qian Hu, Nannan Yuan, Man Zhou, Xiao-Xia Xia, Rooksana E. Noorai, Christopher Saski, Shigui Li, Hong Luo
Software Mentions: 1
Published: over 7 years ago

10.1038/hortres.2017.32

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy
Cited by: 6
Author(s): Jie Arro, José Cuenca, Yingzhen Yang, Zhenchang Liang, Peter Cousins, Gan-Yuan Zhong
Software Mentions: 1
Published: over 9 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 6 years ago

10.1186/s13099-020-00390-5

Transcriptome changes and polymyxin resistance of acid-adapted Escherichia coli O157:H7 ATCC 43889
Cited by: 2
Author(s): Daekeun Hwang, Seung Min Kim, Hyun Jung Kim
Software Mentions: 1
Published: almost 6 years ago

10.1080/19490976.2021.1887720

Gut microbiota shape the inflammatory response in mice with an epithelial defect
Cited by: 11
Author(s): Ran Wang, Md. Moniruzzaman, Kuan Yau Wong, Percival Wiid, Alexa Harding, Rabina Giri, Wendy Hui Tong, Jacqueline Creagh, Jakob Begun, Michael A. McGuckin, Sumaira Z. Hasnain
Software Mentions: 1
Published: almost 6 years ago

10.1080/19490976.2020.1862612

Dietary betaine prevents obesity through gut microbiota-drived microRNA-378a family
Cited by: 42
Author(s): Jing Du, Peiwen Zhang, Jiang Luo, Linyuan Shen, Shunhua Zhang, Hao Gu, Jin He, Linghui Wang, Xue Zhao, Mailing Gan, Yang Liu, Lili Niu, Ye Zhao, Qianzi Tang, Guoqing Tang, Dongmei Jiang, Yanzhi Jiang, Mingzhou Li, Anan Jiang, Long Jin, Jideng Ma, Surong Shuai, Lin Bai, Jinyong Wang, Bo Zeng, De Wu, Xuewei Li, Li Zhu
Software Mentions: 1
Published: almost 6 years ago

10.1128/mSphere.00179-21

The pH-Responsive Transcription Factors YlRim101 and Mhy1 Regulate Alkaline pH-Induced Filamentation in the Dimorphic Yeast Yarrowia lipolytica
Cited by: 8
Author(s): Tao Shu, Xinyu He, Jia-Wen Chen, Yi-Sheng Mao, Xiang-Dong Gao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-4437-z

Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass
Cited by: 13
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.immuni.2021.03.021

The CD94/NKG2A inhibitory receptor educates uterine NK cells to optimize pregnancy outcomes in humans and mice
Cited by: 39
Author(s): Norman Shreeve, Delphine Depierreux, Dean Hawkes, James A. Traherne, Ulla Sovio, Oisín Huhn, Jyothi Jayaraman, Amir Horowitz, Hormas Ghadially, John R. B. Perry, Ashley Moffett, John G. Sled, Andrew Sharkey, Francesco Colucci
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/giaa160

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense
Cited by: 25
Author(s): Shubo Jin, Chao Bian, Sufei Jiang, Kai Han, Yiwei Xiong, Wenyi Zhang, Chengcheng Shi, Hui Qiao, Zijian Gao, Ruihan Li, Yu Huang, Yongsheng Gong, Xinxin You, Guangyi Fan, Qiong Shi, Hongtuo Fu
Software Mentions: 1
Published: almost 6 years ago

10.1093/gigascience/giz157

Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation
Cited by: 21
Author(s): Gaosi Xu, Chao Bian, Zhou Nie, Jia Li, Yuyu Wang, Donghui Xu, Xinxin You, Hongbo Liu, Jiancao Gao, Hongxia Li, Kai Liu, Jian Yang, Quanjie Li, Nailin Shao, Yanbing Zhuang, Di‐An Fang, Tao Jiang, Yunyun Lv, Yu Huang, Ruobo Gu, Junmin Xu, Wei Ge, Qiong Shi, Pao Xu
Software Mentions: 1
Published: almost 7 years ago

10.1093/gigascience/gix031

Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects
Cited by: 15
Author(s): Feng Jiang, Qing Liu, Yanli Wang, Jie Zhang, Huimin Wang, Tianqi Song, Meiling Yang, Xianhui Wang, Le Kang
Software Mentions: 1
Published: over 9 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 10 years ago

10.1186/2047-217X-3-20

miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation
Cited by: 17
Author(s): Regina Z. Cer, J. Enrique Herrera-Galeano, Joseph J. Anderson, Kimberly A. Bishop‐Lilly, Vishwesh Mokashi
Software Mentions: 1
Published: about 12 years ago

10.1186/s13073-021-00968-x

Deep learning in cancer diagnosis, prognosis and treatment selection
Cited by: 197
Author(s): Khoa Tran, Olga Kondrashova, Andrew P. Bradley, Elizabeth D. Williams, John V. Pearson, Nicola Waddell
Software Mentions: 1
Published: about 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: about 9 years ago

10.1186/s13073-018-0548-z

Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers
Cited by: 76
Author(s): Ju Chien Cheng, Dongkai Wei, Yuan Ji, Lingli Chen, Liguang Yang, Guang Li, Leilei Wu, Ting Hou, Lu Xie, Guohui Ding, Hong Li, Yixue Li
Software Mentions: 1
Published: over 8 years ago

10.1093/gbe/evab023

Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species
Cited by: 3
Author(s): Xianqiong Zhong, Max Lundberg, Lars Råberg
Software Mentions: 1
Published: over 5 years ago

10.1093/gbe/evaa206

The Evolution of Phenotypic Plasticity in Response to Temperature Stress
Cited by: 27
Author(s): François Mallard, Viola Nolte, Christian Schlötterer
Software Mentions: 1
Published: about 6 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 9 years ago

10.1093/gbe/evv132

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees
Cited by: 40
Author(s): Amy L. Bauernfeind, Erik J. Soderblom, Meredith Turner, M. Arthur Moseley, John J. Ely, Patrick R. Hof, Chet C. Sherwood, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 1
Published: over 11 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 8 years ago

10.1093/gbe/evu035

Complete Dosage Compensation and Sex-Biased Gene Expression in the Moth Manduca sexta
Cited by: 51
Author(s): G. Troy Smith, Yun‐Ru Chen, Gary W. Blissard, Adriana D. Briscoe
Software Mentions: 1
Published: over 12 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: over 7 years ago

10.3389/fpls.2017.00971

Transcriptome Analysis of Genes Associated with the Artemisinin Biosynthesis by Jasmonic Acid Treatment under the Light in Artemisia annua
Cited by: 49
Author(s): Xiaolong Hao, Yijun Zhong, Xueqing Fu, Zongyou Lv, Qian Shen, Tingxiang Yan, Shi Pu, Yong Ma, Ming‐Hui Chen, Xueying Lv, Zhangkuanyu Wu, Jingya Zhao, Xiaofen Sun, Ling Li, Kexuan Tang
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2016.02031

Cellular and Molecular Changes Associated with Onion Skin Formation Suggest Involvement of Programmed Cell Death
Cited by: 15
Author(s): Ortal Galsurker, Adi Doron‐Faigenboim, Paula Teper‐Bamnolker, Avinoam Daus, Yael Fridman, Amnon Lers, Dani Eshel
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2021.687799

Assessing Dynamic Changes of Taste-Related Primary Metabolism During Ripening of Durian Pulp Using Metabolomic and Transcriptomic Analyses
Cited by: 13
Author(s): Lalida Sangpong, Gholamreza Khaksar, Pinnapat Pinsorn, Akira Oikawa, Ryosuke Sasaki, Alexander Erban, Mutsumi Watanabe, Karan Wangpaiboon, Takayuki Tohge, Joachim Kopka, Rainer Hoefgen, Kazuki Saito, Supaart Sirikantaramas
Software Mentions: 1
Published: over 5 years ago

10.26508/lsa.202000651

The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targets
Cited by: 10
Author(s): Ivan V. Litvinov, Pingxing Xie, Scott R. Gunn, Denis Sasseville, Philippe Lefrançois
Software Mentions: 1
Published: over 5 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 15 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: almost 7 years ago

10.3389/fpls.2021.659645

Seasonal Variation in Transcriptomic Profiling of Tetrastigma hemsleyanum Fully Developed Tuberous Roots Enriches Candidate Genes in Essential Metabolic Pathways and Phytohormone Signaling
Cited by: 10
Author(s): Qian-Qian Xiang, Siyuan Hu, Ayalew Ligaba-Osena, Jiayao Yang, Fan Tong, Wanli Guo
Software Mentions: 1
Published: over 5 years ago

10.1128/mSystems.00275-18

Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum
Cited by: 3
Author(s): Jake J. Flood, Shelley D. Copley
Software Mentions: 1
Published: almost 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 11 years ago

10.3389/fpls.2016.00637

Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis
Cited by: 7
Author(s): Libin Zhang, Yan Long, Chunhua Fu, Jun Xiang, Jianping Gan, Gang Wu, Haibo Jia, Liang Yu, Maoteng Li
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2020.588994

Multi-Omics Analyses Reveal the Molecular Mechanisms Underlying the Adaptation of Wheat (Triticum aestivum L.) to Potassium Deprivation
Cited by: 12
Author(s): Yong Zhao, Ruoxi Sun, Haodong Liu, Xiaowei Liu, Ke Xu, Kai Xiao, Shuhua Zhang, Xueju Yang, Cheng Xue
Software Mentions: 1
Published: about 6 years ago

10.3389/fphys.2019.00318

Transcriptome and Proteome Response of Rhipicephalus annulatus Tick Vector to Babesia bigemina Infection
Cited by: 23
Author(s): Sandra Antunes, Joana Couto, Joana Ferrolho, Gustavo Seron Sanches, Octávio Merino, Ned De la Cruz Hernández, Monica L. Mazuz, Margarita Villar, Varda Shkap, José de la Fuente, Ana Domingos
Software Mentions: 1
Published: over 7 years ago

10.1038/s41597-020-00751-4

Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes
Cited by: 4
Author(s): Laura Payton, Céline Noirot, Claire Hoede, Lukas Hüppe, Kim S. Last, David Wilcockson, E. A. Ershova, Sophie Valière, Bettina Meyer
Software Mentions: 1
Published: almost 6 years ago

10.3389/fphys.2020.00721

Transcriptome Profile Changes Associated With Heat Shock Reaction in the Entomopathogenic Nematode, Steinernema carpocapsae
Cited by: 1
Author(s): Yifei Xie, Xiu-Dan Wang, Wu-Hong Zhong, Dao‐Hong Zhu, Zhen He
Software Mentions: 1
Published: over 6 years ago

10.1038/srep02101

Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu
Cited by: 104
Author(s): Kuihua Han, Zhifeng Li, Rui Peng, Liping Zhu, Tao Zhou, Luguang Wang, Shuguang Li, Xiaobo Zhang, Wei Hu, Zhihong Wu, Nan Qin, Yuezhong Li
Software Mentions: 1
Published: over 13 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 9 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 7 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 6 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 5 years ago

10.1038/srep11136

Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera
Cited by: 50
Author(s): Abdullah M. Khamis, Adam R. Hamilton, Yulia A. Medvedeva, Tanvir Alam, Intikhab Álam, Magbubah Essack, Boris Umylny, Boris R. Janković, Nicholas L. Naeger, Makoto Suzuki, Matthias Harbers, Gene E. Robinson, Vladimir B. Bajic
Software Mentions: 1
Published: over 11 years ago

10.1038/srep12165

Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection
Cited by: 26
Author(s): Hai Peng, Zheng Chen, Zhiwei Fang, Jian Zhou, Xia Zhang, Lifen Gao, Lihong Chen, Lili Li, Tiantian Li, Wenxue Zhai, Weixiong Zhang
Software Mentions: 1
Published: over 11 years ago

10.1038/srep12620

Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine
Cited by: 32
Author(s): Hua Bao, Arun Kommadath, Guanxiang Liang, Xinwei Sun, Adriano S. Arantes, Christopher K. Tuggle, Shawn M. D. Bearson, Graham Plastow, Paul Stothard, Le Luo Guan
Software Mentions: 1
Published: about 11 years ago

10.1038/srep12946

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)
Cited by: 62
Author(s): Quanyuan Wan, Jian Su
Software Mentions: 1
Published: about 11 years ago

10.1038/srep13413

Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types
Cited by: 102
Author(s): Peng Li, Xiu Wu Bian, Di Kang Li, Chuan Xu, Guang Ming Wang, Qing Xia, Qing Xiong
Software Mentions: 1
Published: about 11 years ago

10.26508/lsa.201800036

Serine catabolism is essential to maintain mitochondrial respiration in mammalian cells
Cited by: 53
Author(s): Stéphanie Lucas, Guohua Chen, Siddhesh Aras, Jian Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep13608

Evidence for the expression of abundant microRNAs in the locust genome
Cited by: 23
Author(s): Yanli Wang, Feng Jiang, Huimin Wang, Tianqi Song, Yuanyuan Wei, Meiling Yang, Jianzhen Zhang, Le Kang
Software Mentions: 1
Published: about 11 years ago

10.1038/srep13980

Hyperinsulinemia shifted energy supply from glucose to ketone bodies in early nonalcoholic steatohepatitis from high-fat high-sucrose diet induced Bama minipigs
Cited by: 28
Author(s): Shulin Yang, Ji‐Han Xia, Yuanyuan Zhang, Jian‐Gao Fan, Hua Wang, Jing Yuan, Zhan-zhao Zhao, Qin Pan, Yulian Mu, Leilei Xin, Yao-xing Chen, Kui Li
Software Mentions: 1
Published: about 11 years ago

10.26508/lsa.202000985

The AXL-PYK2-PKCα axis as a nexus of stemness circuits in TNBC
Cited by: 5
Author(s): Lohit Khera, Yaron Vinik, Flavio Maina, Sima Lev
Software Mentions: 1
Published: over 5 years ago

10.1186/2049-3002-1-11

Respiratory complex I is essential to induce a Warburg profile in mitochondria-defective tumor cells
Cited by: 74
Author(s): Claudia Calabrese, Luisa Iommarini, Ivana Kurelac, Maria Antonietta Calvaruso, Mariantonietta Capristo, Pier‐Luigi Lollini, Patrizia Nanni, Christian Bergamini, Giordano Nicoletti, Carla De Giovanni, Anna Ghelli, Valentina Giorgio, Mariano Francesco Caratozzolo, Flaviana Marzano, Caterina Manzari, Christine M. Betts, Valerio Carelli, Claudio Ceccarelli, Marcella Attimonelli, Giovanni Romeo, Romana Fato, Michela Rugolo, Apollonia Tullo, Giuseppe Gasparre, Anna Maria Porcelli
Software Mentions: 1
Published: over 13 years ago

10.1038/srep15407

Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis
Cited by: 12
Author(s): Bin Luo, Wei Gu, Jiayong Zhong, Ying Wang, Gong Zhang
Software Mentions: 1
Published: about 11 years ago

10.1186/s40170-021-00270-9

Targeting MYC-enhanced glycolysis for the treatment of small cell lung cancer
Cited by: 19
Author(s): Kasey R. Cargill, C. Allison Stewart, Elizabeth M. Park, Kavya Ramkumar, Robert J. Cardnell, Qi Wang, Lixia Diao, Ли Шен, You-Hong Fan, Wai Kin Chan, Philip L. Lorenzi, Trudy G. Oliver, Lauren A. Byers
Software Mentions: 1
Published: about 5 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 7 years ago

10.1002/cam4.2099

Identification of competitive endogenous RNAs network in breast cancer
Cited by: 13
Author(s): Xiaojin Wang, Jiahui Wan, Zhanxiang Xu, Jiangbo Shu, Lin Ji, Yutian Liu, Shuwen Zhai, Rongjun Cui
Software Mentions: 1
Published: over 7 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: over 5 years ago

10.1002/cam4.432

<scp>HER2</scp> as a target in invasive urothelial carcinoma
Cited by: 35
Author(s): Joaquim Bellmunt, Lillian Werner, Aristotle Bamias, André P. Fay, Rachel S. Park, Markus Riester, Shamini Selvarajah, Justine A. Barletta, David M. Berman, Silvia de Muga, Marta Salido, Enrique Gallardo, Federico Rojo, Elizabeth A. Guancial, Richard Bambury, Stephanie A. Mullane, Toni K. Choueiri, Massimo Loda, Edward C. Stack, Jonathan E. Rosenberg
Software Mentions: 1
Published: over 11 years ago

10.1038/srep17643

Lactic acid is a sperm motility inactivation factor in the sperm storage tubules
Cited by: 42
Author(s): Mei Matsuzaki, Shusei Mizushima, Gen Hiyama, Noritaka Hirohashi, Kogiku Shiba, Kazuo Inaba, Tomohiro Suzuki, Hideo Dohra, Toshiyuki Ohnishi, Yoshikatsu Sato, Tetsuya Kohsaka, Yoshinobu Ichikawa, Yusuke Atsumi, Takashi Yoshimura, Tomohiro Sasanami
Software Mentions: 1
Published: almost 11 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 7 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 5 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: over 9 years ago

10.1038/srep17480

Reference genes for accessing differential expression among developmental stages and analysis of differential expression of OBP genes in Anastrepha obliqua
Cited by: 39
Author(s): Aline Minali Nakamura, Samira Chahad‐Ehlers, André Luís A. Lima, Cristiane Hayumi Taniguti, Iderval Sobrinho, Felipe Rafael Torres, Reinaldo Alves de Brito
Software Mentions: 1
Published: over 10 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 8 years ago

10.1038/srep20245

Transcriptome analysis of Glomus mosseae/Medicago sativa mycorrhiza on atrazine stress
Cited by: 21
Author(s): Fuqiang Song, Jize Li, Xiaoxu Fan, Quan Zhang, Wei Chang, Yang Fang, Gui Geng
Software Mentions: 1
Published: over 10 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 10 years ago

10.1038/srep21849

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast
Cited by: 38
Author(s): F. Salinas, Carl G. de Boer, Valentina Abarca, Verónica García, Mara Cuevas, Sebastián Araos, Luis F. Larrondo, Claudio Martı́nez, Francisco A. Cubillos
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22051

Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis
Cited by: 18
Author(s): Yao Wang, Rohit R. Jadhav, Joseph K. Liu, Desiree Wilson, Yidong Chen, Ian M. Thompson, Dean A. Troyer, Javier Hernández, Huidong Shi, Robin J. Leach, Tim Hui-Ming Huang, Victor X. Jin
Software Mentions: 1
Published: over 10 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: almost 6 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 10 years ago

10.1038/srep22896

Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis
Cited by: 23
Author(s): Seong Hyuk Lee, Min‐Sik Kim, Jae-Hak Lee, Tae Wan Kim, Seung Seob Bae, Sung-Mok Lee, Hae Chang Jung, Tae-Jun Yang, Arum Choi, Yong‐Jun Cho, Jung-Hyun Lee, Kae Kyoung Kwon, Hyun Sook Lee, Sung Gyun Kang
Software Mentions: 1
Published: over 10 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 5 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 8 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: over 5 years ago

10.21307/jofnem-2019-055

Identification of Suitable Meloidogyne spp. Housekeeping Genes
Cited by: 1
Author(s): Weiming Hu, Peter DiGennaro
Software Mentions: 1
Published: almost 8 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 7 years ago

10.1038/srep24869

Identifying Reproducible Molecular Biomarkers for Gastric Cancer Metastasis with the Aid of Recurrence Information
Cited by: 16
Author(s): Mengyao Li, Hong Guan, Jun Cheng, Jing Li, Hao Cai, Xiangyu Li, Qingzhou Guan, Man‐Li Tong, Hongdong Li, Zheng Guo
Software Mentions: 1
Published: over 10 years ago

10.1128/mSystems.00819-20

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
Cited by: 16
Author(s): Jiawei He, Xu‐jie Zhou, Yafeng Li, Yan-Na Wang, Lijun Liu, Sufang Shi, Xu Xin, Rongshan Li, Mario Falchi, Jicheng Lv, Hong Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/srep25333

Modeling Doxorubicin-Induced Cardiotoxicity in Human Pluripotent Stem Cell Derived-Cardiomyocytes
Cited by: 120
Author(s): Agnès Maillet, Kim Peng Tan, Xiaoran Chai, Singh N. Sadananda, Ashish Mehta, Jolene Ooi, Michael R. Hayden, Mahmoud A. Pouladi, Sujoy Ghosh, Winston Shim, Liam R. Brunham
Software Mentions: 1
Published: over 10 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 7 years ago

10.1002/cam4.2089

SIRT3 elicited an anti‐Warburg effect through HIF1α/PDK1/PDHA1 to inhibit cholangiocarcinoma tumorigenesis
Cited by: 37
Author(s): Lei Xu, Li Yang, Lixing Zhou, Robert Dorfman, Li Liu, Rui Cai, Chenfei Jiang, Dehua Tang, Yuming Wang, Xiaoping Zou, Lei Wang, Mingming Zhang
Software Mentions: 1
Published: over 7 years ago

10.1038/srep25635

Transcriptomic profile of tobacco in response to Alternaria longipes and Alternaria alternata infections
Cited by: 16
Author(s): Shengchang Duan, Xiao Ma, Wei Chen, Wenting Wan, Yuqi He, Xiaoxuan Ma, Yan Ma, Ni Long, Yuntao Tan, Yangzi Wang, Yujie Hou, Yang Dong
Software Mentions: 1
Published: over 10 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 5 years ago

10.1002/cam4.2097

Circulating PD‐1 (+) cells may participate in immune evasion in peripheral T‐cell lymphoma and chidamide enhance antitumor activity of PD‐1 (+) cells
Cited by: 10
Author(s): Wei Zhang, Haorui Shen, Yan Zhang, Wei Wang, Shaoxuan Hu, Dongmei Zou, Daobin Zhou
Software Mentions: 1
Published: over 7 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: almost 6 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 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568