bioconductor: DEGseq | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1093/database/bay027

Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: almost 7 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: almost 13 years ago

10.1186/1471-2105-12-267

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Cited by: 39
Author(s): Xutao Deng
Software Mentions: 7
Published: over 13 years ago

10.1155/2014/248090

MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control
Cited by: 49
Author(s): Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng, Yu Shyr
Software Mentions: 6
Published: almost 11 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-016-3199-8

Identification of novel targets of diabetic nephropathy and PEDF peptide treatment using RNA-seq
Cited by: 29
Author(s): Ana Rubín, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
Software Mentions: 6
Published: about 8 years ago

10.1155/2013/203681

Time Series Expression Analyses Using RNA-seq: A Statistical Approach
Cited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pcbi.1007869

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Cited by: 8
Author(s): Magali Richard, Clémentine Decamps, Florent Chuffart, Élisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost
Software Mentions: 6
Published: over 4 years ago

10.1186/s12920-019-0513-8

Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine
Cited by: 7
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Francesca Vitali, Helen Hao Zhang, Yves A. Lussier
Software Mentions: 6
Published: over 5 years ago

10.7150/jca.55570

Upregulating <i>KTN1</i> promotes Hepatocellular Carcinoma progression
Cited by: 1
Author(s): Jian Pan, Naixia Chao, Yao‐Yao Zhang, Tianyi Huang, Chengxiao Chen, Qiuhong Qin, Jinhong Guo, Rongshi Huang, Guopei Luo
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms17060956

Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes
Cited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0124564

Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)
Cited by: 45
Author(s): David Behringer, Heike Zimmermann, Birgit Ziegenhagen, Sascha Liepelt
Software Mentions: 5
Published: over 9 years ago

10.1093/bioinformatics/btz089

How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in <i>Arabidopsis thaliana</i>
Cited by: 9
Author(s): Kimon Froussios, Nicholas J. Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 5
Published: almost 6 years ago

10.1186/s40064-016-2743-y

Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis
Cited by: 9
Author(s): Jun Fan, Xiuping Chen, Wen-shun Hu, Shaoquan Zheng
Software Mentions: 5
Published: over 8 years ago

10.3390/ijms22020787

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri
Cited by: 13
Author(s): Ziqing He, Yingjuan Su, Ting Wang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-07313-3

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Cited by: 7
Author(s): Longsheng Xing, Yu X, Xi Qiao, Cong Huang, Qiang Wu, Yang Ni, Jiao Guo, Wan‐Xue Liu, Wei Fan, Fang‐Hao Wan, Wanqiang Qian
Software Mentions: 5
Published: almost 4 years ago

10.18632/aging.101565

Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging
Cited by: 38
Author(s): Hong-Cai Cai, Yamin Li, Huimin Li, Jean Damascene Niringiyumukiza, Mengdi Zhang, Li Chen, Gang Chen, Wenpei Xiang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07710-2

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China
Cited by: 11
Author(s): Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Junzheng Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang, Lizhi Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/s12943-018-0833-x

RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas
Cited by: 57
Author(s): Cheng Hsien Lu, Xi Su, Amanda Y. Wang, Tao Yuan, Zhenxiao Wang, Chaoping Huang, Yuehua Qiao, Hongyi Hu, Liangfa Liu
Software Mentions: 4
Published: over 6 years ago

10.1186/s13578-018-0227-1

Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages
Cited by: 9
Author(s): Xinyu Feng, Jia-Tong Wu, Shui-Sen Zhou, Jingwen Wang, Wei Hu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41419-017-0173-6

Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation
Cited by: 22
Author(s): Yanjian Li, Yi He, Zhengyu Liang, Yang Wang, Fengling Chen, Mohamed Nadhir Djekidel, Guipeng Li, Xu Zhang, Shuqin Xiang, Zejun Wang, Juntao Gao, Michael Q. Zhang, Chen Yang
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2164-15-676

De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties
Cited by: 58
Author(s): Qianqian Guo, Xiaojun Ma, Shugen Wei, Deyou Qiu, Iain W. Wilson, Ping Wu, Qi Tang, Lijun Liu, Shoukun Dong, Zimin Wei
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0181061

Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq
Cited by: 22
Author(s): Chunbao Zhang, Chunjing Lin, Fuyou Fu, Xiaofang Zhong, Bao Peng, Hao Yan, Jingyong Zhang, Weilong Zhang, Pengnian Wang, Xiaoyang Ding, Wei Zhang, Limei Zhao
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-020-01233-4

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model
Cited by: 28
Author(s): Yuhua Fu, Jingya Xu, Zhenshuang Tang, Lu Wang, Yin Ding, Yu Fan, Dongdong Zhang, Fei Deng, Yanping Zhang, Haohao Zhang, Haiyan Wang, Wenhui Xing, Lilin Yin, Shilin Zhu, Mengjin Zhu, Mei Yu, Xinyun Li, Xiaolei Liu, Xiaohui Yuan, Zhao Song
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: almost 9 years ago

10.3389/fcimb.2020.561761

LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes
Cited by: 12
Author(s): Xue Yang, Li Na Niu, Yaping Pan, Xiaodong Feng, Jie Liu, Yan Guo, Chunyu Pan, Fei Geng, Xiaolin Tang
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0152610

Human Milk Cells and Lipids Conserve Numerous Known and Novel miRNAs, Some of Which Are Differentially Expressed during Lactation
Cited by: 59
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0109262

De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Cited by: 48
Author(s): Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0033933

Identification of Early Zygotic Genes in the Yellow Fever Mosquito Aedes aegypti and Discovery of a Motif Involved in Early Zygotic Genome Activation
Cited by: 46
Author(s): James K. Biedler, Wanqi Hu, Hongseok Tae, Zhijian Tu
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2164-14-S8-S2

Evaluation of read count based RNAseq analysis methods
Cited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0235763

Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Cited by: 17
Author(s): Juan Jin, Lei Yang, Dingyu Fan, Xuxin Liu, Qing Hao
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0115740

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression
Cited by: 10
Author(s): Carol Soderlund, William M. Nelson, Stephen A. Goff
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12870-015-0632-0

Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0242382

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand
Cited by: 0
Author(s): Arin Ngamniyom
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.102228

Prognostic value of a hypoxia-related microRNA signature in patients with colorectal cancer
Cited by: 31
Author(s): Yongmei Yang, Ailin Qu, Qi Wu, Xin Zhang, Lili Wang, Chen Li, Zhaogang Dong, Du Li, Chuanxin Wang
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0146447

Transcriptome Analysis of Honeybee (Apis Mellifera) Haploid and Diploid Embryos Reveals Early Zygotic Transcription during Cleavage
Cited by: 30
Author(s): Camilla Valente Pires, Flávia Cristina de Paula Freitas, Alexandre S. Cristino, Peter K. Dearden, Zilá Luz Paulino Simões
Software Mentions: 4
Published: almost 9 years ago

10.18632/aging.102754

The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegans
Cited by: 9
Author(s): Yuanjian Song, Yuechen Wang, Ying Liu, Liang Wang, WenDa Zhang, Jing Cheng, Yushan Zhu, Haoyu Zhang, Qiang Zhang, Haichen Niu, Yingwei Zheng, Mengyu Liang, Mengqiong Deng, Hao Shi, Hao Wang, Fang Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12870-019-2087-1

Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka)
Cited by: 34
Author(s): Xing-Zheng Fu, Xiaoyong Zhang, Jie-Ya Qiu, Xue Zhou, Meng Yuan, Yuan He, Chun ChangPin, Li Cao, Lili Li, Peng LiangZhi
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0069401

TCW: Transcriptome Computational Workbench
Cited by: 16
Author(s): Carol Soderlund, William M. Nelson, Mark R. Willer, David R. Gang
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-015-1799-3

RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress
Cited by: 67
Author(s): Longxing Hu, Huiying Li, Liang Chen, Yanhong Lou, Erick Amombo, Jinmin Fu
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms19010245

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review
Cited by: 106
Author(s): Arun Sudhagar, Gokhlesh Kumar, Mansour El-Matbouli
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0143742

Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine
Cited by: 11
Author(s): Zhonghua Sheng, Yi Sun, Ruixin Zhu, Na Jiao, Kailin Tang, Zhen Cao, Chao Ma
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-020-02022-2

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Cited by: 28
Author(s): Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Li Pan, Bao‐Fa Sun, Ying Yang, Ning Zhang, Yongliang Zhao, Hailin Wang, Feng Liu, Qiangfeng Cliff Zhang, Yun‐Gui Yang
Software Mentions: 4
Published: over 4 years ago

10.1007/s12035-020-02128-5

Molecular Regulatory Mechanism and Toxicology of Neurodegenerative Processes in MPTP/Probenecid-Induced Progressive Parkinson’s Disease Mice Model Revealed by Transcriptome
Cited by: 12
Author(s): Weiwei Yang, Wenwen Hao, Zhen Meng, Shuizi Ding, Xiaodi Li, Tao Zhang, Weixiao Huang, Liang Xu, Yu Zhang, Jian Yang, Xiaosong Gu
Software Mentions: 4
Published: about 4 years ago

10.1186/s13578-017-0138-6

Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae
Cited by: 20
Author(s): Dan Yang, Changlong Chen, Qian Liu, Heng Jian
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-015-1825-5

Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates
Cited by: 124
Author(s): Nan Zhang, Dongqing Yang, Dandan Wang, Youzhi Miao, Jiahui Shao, Xuan Zhou, Zhihui Xu, Qing Li, Haichao Feng, Shuqing Liu, Qirong Shen, Ruifu Zhang
Software Mentions: 4
Published: about 9 years ago

10.3389/fonc.2021.636632

Long Noncoding RNA NONHSAT079852.2 Contributes to GBM Recurrence by Functioning as a ceRNA for has-mir-10401-3p to Facilitate HSPA1A Upregulation
Cited by: 3
Author(s): Ningning Zhao, Jiajie Zhang, Lili Zhao, Xiaoni Fu, Qian Zhao, Min Chao, Haiyan Cao, Yang Jiao, Yibo Hu, Chao Chen, Liang Wang, Huijuan Wang
Software Mentions: 4
Published: over 3 years ago

10.3390/md17030181

Comparative Transcriptome Analyses Provide Potential Insights into the Molecular Mechanisms of Astaxanthin in the Protection against Alcoholic Liver Disease in Mice
Cited by: 12
Author(s): Huilin Liu, Huimin Liu, Liang Zhu, Ziqi Zhang, Xin Zheng, Jingsheng Liu, Xueqi Fu
Software Mentions: 4
Published: over 5 years ago

10.1186/1748-7188-7-5

A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0058294

Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome
Cited by: 128
Author(s): Dapeng Bao, Ming Gong, Huajun Zheng, Mingjie Chen, Liang Zhang, Hong Wang, Jianping Jiang, Lin Wu, Yaping Zhu, Gang Zhu, Yan Zhou, Chuanhua Li, Shengyue Wang, Yan Zhao, Guoping Zhao, Qian Tan
Software Mentions: 4
Published: over 11 years ago

10.3389/fnmol.2021.639145

Post-stroke Delivery of Valproic Acid Promotes Functional Recovery and Differentially Modifies Responses of Peri-Infarct Microglia
Cited by: 6
Author(s): Tung‐Tai Kuo, Vicki Wang, Jui-Sheng Wu, Yuan-Hao Chen, Kuan-Yin Tseng
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-86821-y

Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach
Cited by: 3
Author(s): Momoko Hamano, Seitaro Nomura, Midori Iida, Issei Komuro, Yoshihiro Yamanishi
Software Mentions: 4
Published: over 3 years ago

10.1155/2021/3524571

RNA-Seq Expression Analysis of Chronic Asthmatic Mice with Bu-Shen-Yi-Qi Formula Treatment and Prediction of Regulated Gene Targets of Anti-Airway Remodeling
Cited by: 3
Author(s): Jie Cui, Zexi Lv, Fangzhou Teng, Yi Liu, Weifeng Tang, WenQian Wang, Tulake Wuniqiemu, Jingjing Qin, Xueyi Zhu, Ying Wei, Jingcheng Dong
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-019-5650-0

Selective translational usage of TSS and core promoters revealed by translatome sequencing
Cited by: 2
Author(s): Hua Li, Longchuan Bai, Hongmei Li, Xinhui Li, Yani Kang, Ningbo Zhang, Jingyong Sun, Zongshu Shao
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-015-0208-0

A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production
Cited by: 22
Author(s): Bang Wang, Pengli Cai, Wenliang Sun, Jingen Li, Chaoguang Tian, Yanhe Ma
Software Mentions: 3
Published: almost 10 years ago

10.1093/bib/bbx149

Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
Cited by: 20
Author(s): Francesca Vitali, Haiquan Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, Yves A. Lussier
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2021.655900

Genome-Wide DNA Methylation and Transcriptome Analyses Reveal Epigenetic and Genetic Mechanisms Underlying Sex Maintenance of Adult Chinese Alligator
Cited by: 4
Author(s): Jianqing Lin, Jun Yu, Li Sun, Sheng‐Guo Fang
Software Mentions: 3
Published: over 3 years ago

10.1042/BSR20171208

Bioinformatics analysis of microRNAs related to blood stasis syndrome in diabetes mellitus patients
Cited by: 10
Author(s): Ruixue Chen, Minghao Chen, Ye Xiao, Qiuer Liang, Yunfei Cai, Liguo Chen, Ming Fang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-11-422

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
Cited by: 677
Author(s): Thomas J. Hardcastle, Krystyna A. Kelly
Software Mentions: 3
Published: over 14 years ago

10.1038/s41421-021-00302-0

Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo
Cited by: 43
Author(s): Zhaoyong Zhang, Eric Zeng, Lu Zhang, Weiming Wang, Yingkang Jin, Jun Sun, Shuxiang Huang, Wenguang Yin, Jun Dai, Zhen Zhuang, Chen Zhao, Jing Sun, Airu Zhu, Fang Li, Weitao Cao, Xiaobo Li, Yongxia Shi, Mian Gan, Shengnan Zhang, Peilan Wei, Jicheng Huang, Nanshan Zhong, Guocai Zhong, Jingxian Zhao, Yanqun Wang, Wei Shao, Jincun Zhao
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00321

Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach
Cited by: 4
Author(s): Yangyang Pang, Long He, Yameng Song, Xiaozhe Song, Jiahuan Lv, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 3
Published: over 4 years ago

10.3390/biology10090885

Metabolic Regulation of Sugar Assimilation for Lipid Production in Aspergillus oryzae BCC7051 through Comparative Transcriptome Perspective
Cited by: 5
Author(s): Tayvich Vorapreeda, Bhimabol Khongto, Chinae Thammarongtham, Tanawut Srisuk, Kobkul Laoteng
Software Mentions: 3
Published: about 3 years ago

10.1186/s12885-017-3860-x

Gene expression, regulation of DEN and HBx induced HCC mice models and comparisons of tumor, para-tumor and normal tissues
Cited by: 18
Author(s): Qin Tang, Qi Wang, Qiong Zhang, Sheng‐Yan Lin, Yanhong Zhu, Xiangliang Yang, An‐Yuan Guo
Software Mentions: 3
Published: almost 7 years ago

10.18632/aging.103293

Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis
Cited by: 25
Author(s): Shaolin Ma, Jinhong Qin, Yongqiang Hao, Lei Fu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0067974

Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe
Cited by: 60
Author(s): Shuangyan Chen, Xin Huang, Xiaohong Yan, Yong Liang, Yuezhu Wang, Xiaofeng Li, Xianjun Peng, Xiaojun Ma, Lexin Zhang, Yueyue Cai, Tian Ma, Long Cheng, Dongmei Qi, Huajun Zheng, Xiaohan Yang, Xiaoxia Li, Gongshe Liu
Software Mentions: 3
Published: over 11 years ago

10.3390/cancers11101482

An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer
Cited by: 13
Author(s): Stephen Wan Leung, Chia Jung Chou, Tsui-Chin Huang, Pei Ming Yang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-017-1165-5

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)
Cited by: 27
Author(s): Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J. King, Kede Liu
Software Mentions: 3
Published: about 7 years ago

10.1186/1753-6561-5-S7-P20

Detection of genes involved in bud phenology in sessile oak (Quercus petraeaMatt. Liebl) combining digital expression analysis and Q-PCR
Cited by: 3
Author(s): S. Ueno, Christophe Klopp, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: about 13 years ago

10.1186/s12935-021-02170-w

RNA sequencing analysis reveals the competing endogenous RNAs interplay in resected hepatocellular carcinoma patients who received interferon-alpha therapy
Cited by: 5
Author(s): Yibin Wu, Longrong Wang, Xiaoshuang Wang, Yiming Zhao, Anrong Mao, Ning Zhang, Jiamin Zhou, Qi Pan, Weiping Zhu
Software Mentions: 3
Published: about 3 years ago

10.1186/s13578-019-0308-9

Zika virus antagonizes interferon response in patients and disrupts RIG-I–MAVS interaction through its CARD-TM domains
Cited by: 34
Author(s): Yiwen Hu, Xinhuai Dong, Zhenjian He, Yun Wu, Shihao Zhang, Jiajie Lin, Yi Yang, Jiahui Chen, Shu An, Yingxian Yin, Zhiyong Shen, Gucheng Zeng, Han Tian, Junchao Cai, Hongyu Guan, Jueheng Wu, Mengfeng Li, Xun Zhu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41419-020-2333-3

UHRF1-repressed 5’-hydroxymethylcytosine is essential for the male meiotic prophase I
Cited by: 9
Author(s): Hongjie Pan, Ning Jiang, Shenfei Sun, Hanwei Jiang, Jianze Xu, Xiaohua Jiang, Qian Gao, Liang Li, Haili Wu, Huajun Zheng, Qi Qi, Tianqi Li, Meixing Zhang, Lingling Zhang, Xiaofeng Wan, Xinhua Lin, Jiemin Wong, Qinghua Shi, Li R
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2018.00340

Integrative Analyses of Transcriptome Sequencing Identify Functional miRNAs in the Chicken Embryo Fibroblasts Cells Infected With Reticuloendotheliosis Virus
Cited by: 6
Author(s): Jie Zhai, Chang Gao, Lisheng Fu, Long Jiang, Shengyuan Dang, Shangen Zheng
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0218938

Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii
Cited by: 11
Author(s): Yang Wei, Min Yu, Changsong Zou, Changming Lu, Daoqian Yu, Hongyan Cheng, Pengfei Jiang, Feng Xu, Youping Zhang, Qiaolian Wang, Hong Zhang, Guoli Song, Zhuqing Zhou
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0173974

Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus
Cited by: 35
Author(s): Wei Chi, Yu Gao, Qing Hu, Wei Guo, Dapeng Li
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-721

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
Cited by: 75
Author(s): Tingting Lu, Chuanrang Zhu, Lu Gui, Yunli Guo, Yan Zhou, Zhiyong Zhang, Yan Zhao, Wenjun Li, Ying Lu, Weihua Tang, Qi Feng, Bin Han
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12870-021-03051-0

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique
Cited by: 3
Author(s): Huangwei Zhang, Meng Li, Min Jung Kong, Jim M. Dunwell, Yuyan Zhang, Chao Yue, Juyou Wu, Shaoling Zhang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0209061

Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)
Cited by: 14
Author(s): Jinjun Ren, Changsen Sun, Li Chen, Jianhong Hu, Xuetao Huang, Xiaolin Liu, Lizhi Liu
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0018493

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Cited by: 62
Author(s): Valerio Costa, Claudia Angelini, Luciana D’Apice, Margherita Mutarelli, Amelia Casamassimi, Linda Sommese, Maria Gallo, Marianna Aprile, Roberta Esposito, Luigi Leone, Aldo Donizetti, Stefania Crispi, Monica Rienzo, Berardo Sarubbi, Raffaele Calabrò, Marco Picardi, Paola Salvatore, Teresa Infante, Piergiuseppe De Berardinis, Claudio Napoli, Alfredo Ciccodicola
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0187966

RNA-seq reveals transcriptome changes in goats following myostatin gene knockout
Cited by: 24
Author(s): Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Qu Liu, Xiaolong Wang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-4778-7

Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck
Cited by: 10
Author(s): Jing Yang, Yanhua Qu, Yuan Huang, Fumin Lei
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0210650

LncRNA expression profile and ceRNA analysis in tomato during flowering
Cited by: 24
Author(s): Zhenchao Yang, Chengcheng Yang, Zhengyan Wang, Yang Zhao, Danyan Chen, Yongjun Wu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4900-x

Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)
Cited by: 24
Author(s): Zhiqiang Tian, Lina Sun, Yanyan Li, Linfa Quan, Huaijiang Zhang, Wentao Yan, Qiang Yue, Qiu GuiSheng
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0036234

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]
Cited by: 140
Author(s): Tao Xiang, Yinghong Gu, Haiyan Wang, Wen Zheng, Xiao Li, Chuan-Wu Zhao, Yizheng Zhang
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0031526

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis
Cited by: 55
Author(s): Gabor Gyetvai, Mads Sønderkær, Ulrike Göbel, Rico Basekow, Agim Ballvora, Maren Imhoff, Birgit Kersten, Kåre Lehmann Nielsen, Christiane Gebhardt
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12920-014-0071-z

PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders
Cited by: 10
Author(s): Zheng Zhao, Yongsheng Li, Hong Chen, Jianping Lu, Peter M. Thompson, Juan Chen, Zishan Wang, Juan Xu, Xu Chun, Xia Li
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0147147

Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori
Cited by: 94
Author(s): Yuqian Wu, Tingcai Cheng, Chun Li, Duolian Liu, Quan Zhang, Rodney Long, Ping Zhao, Qingyou Xia
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-021-03195-z

LncRNA TCONS_00021861 is functionally associated with drought tolerance in rice (Oryza sativa L.) via competing endogenous RNA regulation
Cited by: 30
Author(s): Jiajia Chen, Yuqing Zhong, Xin Qi
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0094187

ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells
Cited by: 19
Author(s): Lin Jiang, Ola Wallerman, Shady Younis, Carl-Johan Rubin, Elizabeth R. Gilbert, Elisabeth Sundström, Awaisa Ghazal, Xiaolan Zhang, Li Wang, Tarjei S. Mikkelsen, Gerhard Andersson, Leif Andersson
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0231376

Exploring differentially expressed genes between anagen and telogen secondary hair follicle stem cells from the Cashmere goat (Capra hircus) by RNA-Seq
Cited by: 14
Author(s): Nimantana He, Rui Su, Zhiying Wang, Yanjun Zhang, Jinquan Li
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008675

Tryptamine accumulation caused by deletion of MrMao-1 in Metarhizium genome significantly enhances insecticidal virulence
Cited by: 19
Author(s): Xiaowei Tong, Yundan Wang, Pengcheng Yang, Chengshu Wang, Le Kang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-5760-8

Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application
Cited by: 19
Author(s): Tianlun Zhao, Xiaojian Xu, Min Wang, Li Cheng, Cong Liu, Zhao RuBing, Shuijin Zhu, Qiuling He, Jinhong Chen
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: DEGseq

Papers Mentioning DEGseq 697