10.1186/1471-2164-15-1071

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi
Cited by: 20
Author(s): Raúl Castanera, Gúmer Pérez, Leticia Rodríguez López, Rubén Sancho, Francisco Santoyo, Manuel Alfaro, Toni Gabaldón, Antonio G. Pisabarro, José A. Oguiza, Lucı́a Ramı́rez
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-12-516

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach
Cited by: 36
Author(s): Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazuhira Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-018-5239-z

Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra
Cited by: 27
Author(s): Odile Rogier, Aurélien Chateigner, Souhila Amanzougarene, Marie-Claude Lesage-Descauses, Sandrine Balzergue, Véronique Brunaud, José Caïus, Ludivine Soubigou‐Taconnat, Véronique Jorge, Vincent Segura
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-20435-9

Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma
Cited by: 30
Author(s): Puya Gharahkhani, Kathryn P. Burdon, Jessica N. Cooke Bailey, Alex W. Hewitt, Matthew Law, Louis R. Pasquale, Jae H. Kang, Jonathan L. Haines, Emmanuelle Souzeau, Tiger Zhou, Owen M. Siggs, John Landers, Mona S Awadalla, Shilpi Sharma, Richard A. Mills, Bronwyn Ridge, David J. Lynn, Robert J. Casson, Stuart Graham, Ivan Goldberg, Andrew White, Paul R. Healey, John Grigg, Mitchell Lawlor, Paul Mitchell, Jonathan B Ruddle, Michael Coote, Mark J Walland, Stephen Best, Andrea L. Vincent, Jesse Gale, Graham Radford‐Smith, David C. Whiteman, Grant W. Montgomery, Nicholas G. Martin, David A. Mackey, Janey L. Wiggs, Stuart MacGregor, Jamie E Craig, R. Rand Allingham, Murray H. Brilliant, Donald L. Budenz, John H. Fingert, Douglas E. Gaasterland, Teresa Gaasterland, Lisa A Hark, Michael A. Hauser, Robert P. Igo, Peter Kraft, Richard K. Lee, Paul R. Lichter, Yutao Liu, Sayoko E. Moroi, Margaret A. Pericak‐Vance, Anthony Realini, Doug Rhee, Julia E. Richards, Robert Ritch, Joel S. Schuman, William K. Scott, Kuldev Singh, Arthur J. Sit, Douglas Vollrath, Gadi Wollstein, Donald J. Zack
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-016-1251-y

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori
Cited by: 32
Author(s): Qi Zhou, Bindan Zhang, Qiuhan Yu, Ze Zhang
Software Mentions: 1
Published: about 10 years ago

10.3390/ijms21176438

FRUITFULL Is a Repressor of Apical Hook Opening in Arabidopsis thaliana
Cited by: 4
Author(s): Miriam Führer, Angelika Gaidora, Peter Venhuizen, Jędrzej Dobrogojski, Chloé Béziat, Mugurel I. Feraru, Jürgen Kleine‐Vehn, Maria Kalyna, Elke Barbez
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-15-1026

Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress
Cited by: 100
Author(s): Liying Huang, Fan Zhang, Wensheng Wang, Yongli Zhou, Binying Fu, Zhikang Li
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-018-21835-7

HDAC4 regulates satellite cell proliferation and differentiation by targeting P21 and Sharp1 genes
Cited by: 33
Author(s): Nicoletta Marroncelli, Marzia Bianchi, Marco Bertin, Silvia Consalvi, Valentina Saccone, Marco De Bardi, Pier Lorenzo Puri, Daniela Palacios, Sergio Adamo, Viviana Moresi
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-13-S6-S11

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
Cited by: 48
Author(s): Boyko Kakaradov, Hui Xiong, Leo J. Lee, Nebojša Jojić, Brendan J. Frey
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-15-204

Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum
Cited by: 73
Author(s): Andrei Stecca Steindorff, Marcelo Henrique Soller Ramada, Alexandre Siqueira Guedes Coelho, Robert G. Miller, George J. Pappas, Cirano José Ulhôa, Eliane Ferreira Noronha
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-19564-y

Thyroid Dysfunction, Neurological Disorder and Immunosuppression as the Consequences of Long-term Combined Stress
Cited by: 8
Author(s): Jingping Zhang, Jingjing Huang, Kasimujiang Aximujiang, Chao-Jiang Xu, Abulaiti Ahemaiti, Guangxin Wu, Li Zhong, Kurexi Yunusi
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-5830-y

Transcriptome analysis reveals differential immune related genes expression in bovine viral diarrhea virus-2 infected goat peripheral blood mononuclear cells (PBMCs)
Cited by: 24
Author(s): Wenliang Li, Mao Li, Xin Shu, Runxia Liu, Hao Fei, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Cheng Zhong, Jiang Ji
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-24039-1

A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms
Cited by: 7
Author(s): Wen Jiang, Zhanyong Guo, Nuno Lages, W. Jim Zheng, Denis Féliers, Fangyuan Zhang, Degeng Wang
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-12-503

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes
Cited by: 119
Author(s): Matthew G. Links, Eric B. Holub, Rays H. Y. Jiang, Andrew Sharpe, Dwayne D. Hegedus, Elena Beynon, D. Sillito, Wayne E. Clarke, Shihomi Uzuhashi, M. Hossein Borhan
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-018-24813-1

Transcriptomic analysis of the liver of cholesterol-fed rabbits reveals altered hepatic lipid metabolism and inflammatory response
Cited by: 12
Author(s): Weirong Wang, Yulong Chen, Liang Bai, Zhao Song, Rong Wang, Baoning Liu, Yali Zhang, Jianglin Fan, Enqi Liu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24903-0

JIB-04, A Small Molecule Histone Demethylase Inhibitor, Selectively Targets Colorectal Cancer Stem Cells by Inhibiting the Wnt/β-Catenin Signaling Pathway
Cited by: 43
Author(s): Min Seong Kim, Hye In Cho, Hee Jung Yoon, Yeong Hee Ahn, Eun Jung Park, Yan Jin, Yong Suk Jang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1692-0

Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Cited by: 44
Author(s): Chui Yoke Chin, Yuka Hara, Ahmad Kamal Ghazali, Soon Joo Yap, Cin Kong, Yee Chin Wong, Naufal Rozali, Seng Fook Koh, Chee Choong Hoh, S. D. Puthucheary, Sheila Nathan
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms21186703

The Expression Profile of mRNA and tRNA Genes in Splenocytes and Neutrophils after In Vivo Delivery of Antitumor Short Hairpin RNA of Indoleamine 2,3- Dioxygenase
Cited by: 0
Author(s): Ming-Shyan Huang, Ya‐Ling Hsu, I‐Jeng Yeh, Kuan‐Ting Liu, Meng‐Chi Yen
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-3619-4

Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale
Cited by: 19
Author(s): Birgitt Oeser, Sabine Kind, Selma Schurack, Thomas Schmutzer, Paul Tudzynski, Janine Hinsch
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.202550

LncRNA Sirt1-AS upregulates Sirt1 to attenuate aging related deep venous thrombosis
Cited by: 12
Author(s): Zhenkai Lou, Jinwen Zhu, Xing Li, Xingguo Li, Kaili Du, Bing Wang, Fan Zhang, Chi Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-25743-8

Integrated analysis of hepatic mRNA and miRNA profiles identified molecular networks and potential biomarkers of NAFLD
Cited by: 26
Author(s): Meizhen Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-020-06983-3

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites
Cited by: 23
Author(s): Jiangfeng Song, Changming Chen, Shuanglin Zhang, Juntao Wang, Zhong Huang, Muxi Chen, Bihao Cao, Zhiwen Zhu, Jing Liu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-26499-x

Toxicity and Transcriptome Sequencing (RNA-seq) Analyses of Adult Zebrafish in Response to Exposure Carboxymethyl Cellulose Stabilized Iron Sulfide Nanoparticles
Cited by: 35
Author(s): Min Zheng, Jianguo Lü, Dongye Zhao
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-26753-2

Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle ‘degradome’ of rainbow trout
Cited by: 34
Author(s): Bam Paneru, Ali R. Ali, Rafet Al-Tobasei, Brett Kenney, Mohamed Salem
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-26084-2

Ameliorative effect of Sedum sarmentosum Bunge extract on Tilapia fatty liver via the PPAR and P53 signaling pathway
Cited by: 20
Author(s): Lida Huang, Yuan Cheng, Kai Huang, Yu Zhou, Yanqun Ma, Mengci Zhang
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21207520

The Lethal(2)-Essential-for-Life [L(2)EFL] Gene Family Modulates Dengue Virus Infection in Aedes aegypti
Cited by: 6
Author(s): Lucky Ronald Runtuwene, Seiichiro Kawashima, Victor D. Pijoh, Josef S. B. Tuda, Kyoko Hayashida, Junya Yamagishi, Chihiro Sugimoto, Shoko Nishiyama, Michihito Sasaki, Yasuko Orba, Hirofumi Sawa, Tomohiko Takasaki, Anthony A. James, Takashi Kobayashi, Yuki Eshita
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-017-3874-4

Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
Cited by: 15
Author(s): Xiaobo Luo, Liang Xu, Dongyi Liang, Yan Wang, Wei Zhang, Xiaoming Zhu, Yuelin Zhu, Haiyan Jiang, Mingjia Tang, Liwang Liu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-015-1793-9

A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues
Cited by: 50
Author(s): Isha Sethi, Rose‐Anne Romano, Christian Gluck, Kirsten Smalley, Bořivoj Vojtěšek, Michael Buck, Satrajit Sinha
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0066511

Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray
Cited by: 60
Author(s): Noam Leviatan, Noam Alkan, Dena Leshkowitz, Robert Fluhr
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0211773

Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle
Cited by: 35
Author(s): Sajad Ahmad Bhat, Syed Mudasir Ahmad, Eveline M. Ibeagha‐Awemu, Basharat Ahmad Bhat, Muneer Ahmad Dar, Peerzada Tajamul Mumtaz, Riaz Ahmad Shah, Nazir Ahmad Ganai
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-27220-8

Suppression of mitochondrial oxygen metabolism mediated by the transcription factor HIF-1 alleviates propofol-induced cell toxicity
Cited by: 21
Author(s): Chisato Sumi, Akihisa Okamoto, Hiromasa Tanaka, Munenori Kusunoki, Tomohiro Shoji, Takeo Uba, Takehiko Adachi, Teppei Iwai, Kenichiro Nishi, Hiroshi Harada, Hidemasa Bono, Yoshiyuki Matsuo, Kiichi Hirota
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.102778

Functional lncRNA-miRNA-mRNA networks in rabbit carotid atherosclerosis
Cited by: 12
Author(s): Yingnan Wu, Feng Zhang, Rui Lu, Feng Yin, Xiaoying Li, Shuang Zhang, Wen-ying Hou, Jiawei Tian, Xiangdong Kong, Lei Sun
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0127883

Whole Transcriptome of the Venom Gland from Urodacus yaschenkoi Scorpion
Cited by: 55
Author(s): Karen Luna-Ramírez, Verónica Quintero-Hernández, Víctor Rivelino Juárez-González, Lourival D. Possani
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0170652

Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests
Cited by: 5
Author(s): Akira Ishikawa
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0172491

Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis
Cited by: 49
Author(s): Lea Weber, Klaudia Al-Refae, Juliane Ebbert, Peter Jägers, Janine Altmüller, Christian Becker, Stephan A. Hahn, Günter Gisselmann, Hanns Hatt
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-27050-8

Intraflagellar transport 46 (IFT46) is essential for trafficking IFT proteins between cilia and cytoplasm in Paramecium
Cited by: 10
Author(s): Lei Shi, Xuefei Shi, Yuan Shen
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0094604

Acupuncture Promotes Angiogenesis after Myocardial Ischemia through H3K9 Acetylation Regulation at VEGF Gene
Cited by: 62
Author(s): Shu-ping Fu, Su-Yun He, Bin Xu, Chenyao Hu, Lu Shen, Weixing Shen, Yan Huang, Hao Hong, Qian Li, Ning Wang, Xuan-Liang Liu, Fanrong Liang, Bing-Mei Zhu
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-27664-y

Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness
Cited by: 19
Author(s): Xiang Luo, Da Cao, Jianfeng Zhang, Li Chen, Xiaocong Xia, Haoxian Li, Dan Zhao, Fuhong Zhang, Hui Xue, Lina Chen, Yongzhou Li, Shangyin Cao
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0156439

Topoisomerase 1 Regulates Gene Expression in Neurons through Cleavage Complex-Dependent and -Independent Mechanisms
Cited by: 35
Author(s): Angela M. Mabb, Jeremy M. Simon, Ian King, Hyeong-Min Lee, L. An, Benjamin D. Philpot, Mark J. Zylka
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-27826-y

Exon Junction Complexes can have distinct functional flavours to regulate specific splicing events
Cited by: 26
Author(s): Zhen Wang, Lionel Ballut, Isabelle Barbosa, Hervé Le Hir
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0162013

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae
Cited by: 15
Author(s): Raja Kaliyappan, Viswanathan Sriram, S. Backiyarani, S. Uma, Saraswathi Marimuthu Somasundram, M. Mayilvaganan
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0129598

Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening
Cited by: 74
Author(s): Wangshu Mou, Dongdong Li, Zisheng Luo, Linchun Mao, Tiejin Ying
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0077951

Identification of Differentially Expressed Transcripts and Pathways in Blood One Week and Six Months Following Implant of Left Ventricular Assist Devices
Cited by: 9
Author(s): Adam Mitchell, Weihua Guan, Rodney Staggs, A. Hamel, Sameh Hozayen, Neeta Adhikari, Suzanne Grindle, Snider Desir, Ranjit John, Jennifer L. Hall, Peter Eckman
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0147273

A Genome-Wide mRNA Expression Profile in Caenorhabditis elegans under Prolonged Exposure to 1750MHz Radiofrequency Fields
Cited by: 7
Author(s): Yan Gao, Yiming Lu, Jianming Yi, Zhihui Li, Dawen Gao, Zhoulong Yu, Tongning Wu, Chenggang Zhang
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms21217986

Role of AT1G72910, AT1G72940, and ADR1-LIKE 2 in Plant Immunity under Nonsense-Mediated mRNA Decay-Compromised Conditions at Low Temperatures
Cited by: 7
Author(s): Zeeshan Nasim, Muhammad Fahim, Katarzyna Gawarecka, Hendry Susila, Suhyun Jin, Geummin Youn, Ji Hoon Ahn
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0052506

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species
Cited by: 138
Author(s): Elsa Góngora-Castillo, Kevin L. Childs, Greg Fedewa, John Hamilton, David K. Liscombe, Maria Magallanes‐Lundback, Kranthi K. Mandadi, Ezekiel Nims, Weerawat Runguphan, Brieanne Vaillancourt, Marina Varbanova-Herde, Dean DellaPenna, Thomas D. McKnight, Sarah E. O’Connor, C. Robin Buell
Software Mentions: 1
Published: almost 14 years ago

10.3390/ijms22010037

Restoration of Sarcoplasmic Reticulum Ca2+ ATPase (SERCA) Activity Prevents Age-Related Muscle Atrophy and Weakness in Mice
Cited by: 24
Author(s): Rizwan Qaisar, Gavin Pharaoh, Shylesh Bhaskaran, Hongyang Xu, Rojina Ranjit, Jan Bian, Bumsoo Ahn, Constantin Georgescu, Jonathan D. Wren, Holly Van Remmen
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0092720

A Designed Experiments Approach to Optimization of Automated Data Acquisition during Characterization of Bacteria with MALDI-TOF Mass Spectrometry
Cited by: 22
Author(s): Lin Zhang, Connie M. Borror, Todd R. Sandrin
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0208766

A transcriptomics analysis of the Tbx5 paralogues in zebrafish
Cited by: 10
Author(s): Erin A.T. Boyle Anderson, Ruoya Ho
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0058598

RNA-Seq Reveals Activation of Both Common and Cytokine-Specific Pathways following Neutrophil Priming
Cited by: 88
Author(s): Helen L. Wright, Huw B. Thomas, Robert J. Moots, Steven W. Edwards
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0187424

Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity
Cited by: 23
Author(s): Reuben L. Smith, Josephine M.E. Tan, Martijs J. Jonker, Aldo Jongejan, Thomas Buissink, Steve Veldhuijzen, Antoine H. C. van Kampen, Stanley Brul, Hans van der Spek
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0124877

RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model
Cited by: 20
Author(s): Rebecca A. Brady, Vincent M. Bruno, Drusilla L Burns
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-310

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome
Cited by: 5
Author(s): Chi Yang, Michael Buck, Min-Hsuan Chen, Yun-Fan Chen, Hsin-Chi Lan, Jeremy J.W. Chen, Chao Cheng, Chun-Chi Liu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0076572

RNA-Seq Reveals Differential Gene Expression in Staphylococcus aureus with Single-Nucleotide Resolution
Cited by: 16
Author(s): Joseph Osmundson, Scott Dewell, Seth A. Darst
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0208538

Transcriptome-wide responses of adult melon thrips (Thrips palmi) associated with capsicum chlorosis virus infection
Cited by: 20
Author(s): Shirani M. K. Widana Gamage, Dorith Rotenberg, Derek J. Schneweis, Chang‐Her Tsai, Ralf G. Dietzgen
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0113141

Long-Term Reduction of T-Cell Intracellular Antigens Reveals a Transcriptome Associated with Extracellular Matrix and Cell Adhesion Components
Cited by: 4
Author(s): M. Nunez, Carmen Sánchez-Jiménez, José Alcalde, José M. Izquierdo
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-018-28371-4

Eosinophils support adipocyte maturation and promote glucose tolerance in obesity
Cited by: 54
Author(s): Eun Hui Lee, Michal Itan, Jae‐Dong Jang, Hyeon-Jung Gu, Perri Rozenberg, Melissa K. Mingler, Ting Wen, Ji-Young Yoon, Shi-Young Park, Joo Young Roh, Cheol Soo Choi, Woo‐Jae Park, Ariel Munitz, YunJae Jung
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0149702

Comparative Transcriptomic Analysis of Primary Duck Hepatocytes Provides Insight into Differential Susceptibility to DHBV Infection
Cited by: 5
Author(s): Yan Liang, Su Qu, Gang Liu, Lei Liu, Yao Yu, Guohui Ding, Yanfeng Zhao, Yixue Li, Youhua Xie, Junqi Zhang, Di Qu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0097814

Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus
Cited by: 14
Author(s): Xuecheng Wu, Bin Zhou, Chang Yin, Yong Guo, Ying Lin, Li Pan, Bin Wang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0180478

PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses
Cited by: 12
Author(s): Amr R.A. Kataya, Maria T. Creighton, Toga Pangihotan Napitupulu, Christine Sætre, Behzad Shiroud Heidari, Peter Ruoff, Cathrine Lillo
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0149373

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle
Cited by: 27
Author(s): Kate Keogh, David A. Kenny, Paul Cormican, Matthew S. McCabe, A. K. Kelly, Sinéad M. Waters
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0068907

Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing
Cited by: 40
Author(s): Karin Tamm-Rosenstein, Jaak Simm, Marina Suhorutshenko, Andres Salumets, Madis Metsis
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-018-28509-4

Gene expression profile in peripheral blood mononuclear cells of postpartum depression patients
Cited by: 17
Author(s): Danqing Pan, Yang Xu, Lei Zhang, Su Qizhu, Manman Chen, Bing Li, Qian Xiao, Qi Gao, Xinjun Peng, Binfei Jiang, Yuqing Gu, Ying Du, Pengfei Gao
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0152824

Involvement of Alternative Splicing in Barley Seed Germination
Cited by: 40
Author(s): Qisen Zhang, Xiaoqi Zhang, Songbo Wang, Cong Tan, Gaofeng Zhou, Chengdao Li
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0139134

Comparisons of the Effects of Elevated Vapor Pressure Deficit on Gene Expression in Leaves among Two Fast-Wilting and a Slow-Wilting Soybean
Cited by: 14
Author(s): Mura Jyostna Devi, Thomas R. Sinclair, Earl Taliercio
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0033071

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing
Cited by: 143
Author(s): Candice N. Hansey, Brieanne Vaillancourt, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler, C. Robin Buell
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-14-193

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
Cited by: 28
Author(s): Cheng‐Lin Liu, Jinwen Ma, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0164041

The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro
Cited by: 34
Author(s): Suzanne Miller, Amanda Henry, Emily Hodge, Alexander K. Kheirallah, Charlotte K. Billington, Tracy L. Rimington, Sangita Bhaker, Ma’en Obeidat, Erik Melén, Simon Kebede Merid, Caroline Swan, Catherine Gowland, Carl P. Nelson, Ceri E. Stewart, Charlotte E Bolton, Iain Kilty, Anders Mälarstig, Stuart G. Parker, Miriam F. Moffatt, Andrew J. Wardlaw, Ian P. Hall, Ian Sayers
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0205878

Next-Generation Sequencing and Quantitative Proteomics of Hutchinson-Gilford progeria syndrome-derived cells point to a role of nucleotide metabolism in premature aging
Cited by: 15
Author(s): Jesús Mateos, Juan Fafián-Labora, Miriam Morente-López, Iván Lesende-Rodríguez, Lorenzo Monserrat, María Antonia Odena, Eliandre de Oliveira, Javier de Toro, M.C. Arufe
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0171858

Endometrial factors similarly induced by IFNT2 and IFNTc1 through transcription factor FOXS1
Cited by: 15
Author(s): Kaoru Kusama, Rulan Bai, Keigo Nakamura, Sayaka Okada, Jiro Yasuda, Kazuhiko Imakawa
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0160197

Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
Cited by: 3
Author(s): Jingwen Wang, Liselotte Vesterlund, Juha Kere, Hong Jiao
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-017-1732-7

ISVASE: identification of sequence variant associated with splicing event using RNA-seq data
Cited by: 0
Author(s): Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0183163

Identification and analysis of differentially expressed long non-coding RNAs between multiparous and uniparous goat (Capra hircus) ovaries
Cited by: 23
Author(s): Yinghui Ling, Lei Xu, Long Zhu, Menghua Sui, Qi Zheng, Wenyong Li, Yong Liu, Fugui Fang, Xiaorong Zhang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0080597

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells
Cited by: 107
Author(s): Michael S. Humphrys, Todd Creasy, Yan Sun, Amol C. Shetty, Marcus C. Chibucos, Elliott F. Drábek, Claire M. Fraser, Umar Farooq, Naomi Sengamalay, Sandy Ott, Huizhong Shou, Patrik M. Bavoil, Anup Mahurkar, Garry Myers
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-018-27820-4

Transcriptional profiling and genes involved in acquired thermotolerance in Banana: a non-model crop
Cited by: 14
Author(s): S. M. Vidya, Himansu Kumar, R. M. Bhatt, R. H. Laxman, K. V. Ravishankar
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-27643-3

The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma
Cited by: 18
Author(s): Martina Sanlorenzo, Igor Vujic, Rosaura Esteve-Puig, Kevin Lai, Marin Vujic, Kevin Lin, Christian Posch, Michelle Dimon, Adrian Moy, Mitchell Zekhtser, Katia Johnston, Deborah Gho, Won‐Kyung Ho, Abhinay Gajjala, Juan Oses Prieto, Alma L. Burlingame, Adil Daud, Klemens Rappersberger, Susana Ortiz‐Urda
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0067531

RNA Sequencing of the Human Milk Fat Layer Transcriptome Reveals Distinct Gene Expression Profiles at Three Stages of Lactation
Cited by: 160
Author(s): Danielle G. Lemay, Olivia Ballard, Maria Hughes, Ardythe L. Morrow, Nelson D. Horseman, Laurie Nommsen‐Rivers
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-018-29278-w

Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development
Cited by: 14
Author(s): Maritz Laubscher, Katrien Brown, Libert Brice Tonfack, Alexander Andrew Myburg, Eshchar Mizrachi, Steven G. Hussey
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-29365-y

Integrated mRNA, sRNA, and degradome sequencing reveal oilseed rape complex responses to Sclerotinia sclerotiorum (Lib.) infection
Cited by: 15
Author(s): Hongju Jian, Jinqi Ma, Lijuan Wei, Aoxiang Zhang, Bo Yang, Jiana Li, Xinhua Xu, Liezhao Liu
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0071820

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression
Cited by: 65
Author(s): Peter A. Combs, Michael B. Eisen
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0031229

RNA-seq Reveals Novel Transcriptome of Genes and Their Isoforms in Human Pulmonary Microvascular Endothelial Cells Treated with Thrombin
Cited by: 44
Author(s): Liqin Zhang, Dilyara Cheranova, Margaret Gibson, Shinghua Ding, Daniel P. Heruth, Deyu Fang, Shui Qing Ye
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0061005

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays
Cited by: 142
Author(s): Rajandeep S. Sekhon, Roman Briskine, Candice N. Hirsch, Chad L. Myers, Nathan M. Springer, C. Robin Buell, Natalia de León, Shawn M. Kaeppler
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0096435

Expression of Olfactory Signaling Genes in the Eye
Cited by: 37
Author(s): Alexey Pronin, Konstantin Levay, Dmitry Velmeshev, Mohammad Ali Faghihi, Valery I. Shestopalov, Vladlen Z. Slepak
Software Mentions: 1
Published: over 12 years ago

10.18632/aging.202696

Fibroblasts from different body parts exhibit distinct phenotypes in adult progeria Werner syndrome
Cited by: 9
Author(s): Hisaya Kato, Yoshiro Maezawa, Nobuki Takayama, Yasuo Ouchi, Hiromi Kaneko, Daisuke Kinoshita, Aki Takada-Watanabe, Motohiko Oshima, Masaya Koshizaka, Hideyuki Ogata, Yoshitaka Kubota, Nobuyuki Mitsukawa, Koji Eto, Atsushi Iwama, Koutaro Yokote
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0073071

Mining RNA–Seq Data for Infections and Contaminations
Cited by: 14
Author(s): Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0116028

Large-Scale SNP Discovery through RNA Sequencing and SNP Genotyping by Targeted Enrichment Sequencing in Cassava (Manihot esculenta Crantz)
Cited by: 41
Author(s): Wirulda Pootakham, Jeremy R. Shearman, Panthita Ruang-areerate, Chutima Sonthirod, Duangjai Sangsrakru, Nukoon Jomchai, Thippawan Yoocha, Kanokporn Triwitayakorn, Somvong Tragoonrung, Sithichoke Tangphatsornruang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0135616

Dynein Heavy Chain, Encoded by Two Genes in Agaricomycetes, Is Required for Nuclear Migration in Schizophyllum commune
Cited by: 9
Author(s): Melanie Brunsch, Daniela Schubert, Matthias Gube, Christiane Ring, Lisa Hänisch, Jörg Linde, Katrin Krause, Erika Kothe
Software Mentions: 1
Published: about 11 years ago

10.18632/oncotarget.17208

Identification of the miRNA-mRNA regulatory network of small cell osteosarcoma based on RNA-seq
Cited by: 19
Author(s): Lin Xie, Yedan Liao, Lida Shen, Fengdi Hu, Sunlin Yu, Yonghong Zhou, Zhang Ya, Yihao Yang, Dongqi Li, Minyan Ren, Zhongqin Yuan, Zuozhang Yang
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms22031226

Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure
Cited by: 10
Author(s): Laura Pérez‐Martín, John Danku, Roser Tolrà, Charlotte Poschenrieder
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-14-150

Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach
Cited by: 38
Author(s): Nathaniel K. Jue, Michael Murphy, Seth D. Kasowitz, Sohaib M Qureshi, Craig Obergfell, Sahar Elsisi, Robert J. Foley, Rachel J. O’Neill, Michael O’Neill
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0141138

Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue
Cited by: 61
Author(s): Zhixiu Wang, Qinggang Li, Yangzom Chamba, Bo Zhang, Peng Shang, Changxin Wu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0199774

RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.)
Cited by: 65
Author(s): Keyvan Mahdavi Mashaki, Vanika Garg, Ali Asghar Nasrollahnezhad Ghomi, Himabindu Kudapa, Annapurna Chitikineni, Khalil Zaynali Nezhad, Ahad Yamchi, Hassan Soltanloo, Rajeev K. Varshney, Mahendar Thudi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0067252

Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study
Cited by: 21
Author(s): Jasmin Bavarva, Hongseok Tae, Robert E. Settlage, Harold R. Garner
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-018-30451-4

Mechanisms of wheat (Triticum aestivum) grain storage proteins in response to nitrogen application and its impacts on processing quality
Cited by: 31
Author(s): Ting Zheng, Pengfei Qi, Yong-Li Cao, Yanan Han, Hongling Ma, Zhen-Ru Guo, Yan Wang, Yu Qiao, Shi-Yu Hua, Haiyue Yu, Wang Jiang-ping, Jing Zhu, Cai-Yi Zhou, Yazhou Zhang, Qing Chen, Li Kong, Jirui Wang, Qiantao Jiang, Zehong Yan, Xiujin Lan, Guoquan Fan, Yuming Wei, Youliang Zheng
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-29812-w

Resistance to retinopathy development in obese, diabetic and hypertensive ZSF1 rats: an exciting model to identify protective genes
Cited by: 3
Author(s): Vincenza Caolo, Quentin Roblain, J Lecomte, Paolo Carai, Linsey J. F. Peters, Ilona Cuijpers, Emma Robinson, Kasper Derks, Jurgen Sergeys, Agnès Noël, Elizabeth A. V. Jones, Lieve Moons, Stéphane Heymans
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0104283

Reduction of Systematic Bias in Transcriptome Data from Human Peripheral Blood Mononuclear Cells for Transportation and Biobanking
Cited by: 13
Author(s): Hideki Ohmomo, Tsuyoshi Hachiya, Yu Shiwa, Ryo Furukawa, Kanako Ono, Shigeki Ito, Yoshiteru Ishida, Mamoru Satoh, Jiro Hitomi, Kenji Sobue, Atsushi Shimizu
Software Mentions: 1
Published: about 12 years ago

10.3390/ijms22031387

Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato
Cited by: 9
Author(s): Qi Wang, Xin Xu, Xiaoyu Cao, Tixu Hu, Dongnan Xia, Jianhua Zhu, Xiangqiang Zhan
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0207407

Aging-associated patterns in the expression of human endogenous retroviruses
Cited by: 21
Author(s): Tapio Nevalainen, Arttu Autio, Binisha H. Mishra, Saara Marttila, Marja Jylhä, Mikko Hurme
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0134939

Genome-Wide Analysis of Hypoxia-Responsive Genes in the Rice Blast Fungus, Magnaporthe oryzae
Cited by: 16
Author(s): Jaehyuk Choi, Hyun‐Jung Chung, Gir-Won Lee, Sun-Ki Koh, Suhn-Kee Chae, Yong-Hwan Lee
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-13-S12-A3

Regulation of cell proliferation and apoptosis by growth hormone during zebrafish auditory hair cell regeneration
Cited by: 1
Author(s): Gopinath Rajadinakaran, Huifang Sun, Claire A. Rinehart, Eric C. Rouchka, Michael E. Smith
Software Mentions: 1
Published: over 14 years ago