Ecosyste.ms: Papers

10.1371/journal.pone.0061768

RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats
Cited by: 53
Author(s): B. Alex Merrick, Dhiral Phadke, Scott S. Auerbach, Deepak Mav, Suzy M. Stiegelmeyer, Ruchir Shah, Raymond R. Tice
Software Mentions: 1
Published: over 11 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 6 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 11 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: almost 13 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 7 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: about 10 years ago

10.1371/journal.pone.0100989

A Comparison of Transcriptional Patterns and Mycological Phenotypes following Infection of Fusarium graminearum by Four Mycoviruses
Cited by: 50
Author(s): Kyung-Mi Lee, Won Kyong Cho, Jisuk Yu, Moonil Son, Hoseong Choi, Kyung-Hee Min, Yin-Won Lee, Kook‐Hyung Kim
Software Mentions: 1
Published: over 10 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 6 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 11 years ago

10.1371/journal.pone.0144540

Dysregulation of the DNA Damage Response and KMT2A Rearrangement in Fetal Liver Hematopoietic Cells
Cited by: 11
Author(s): Mai Nanya, Masaki Satō, Kousuke Tanimoto, Minoru Tozuka, Shuki Mizutani, Motoki Takagi
Software Mentions: 1
Published: almost 9 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 10 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 6 years ago

10.1038/s41598-017-19114-y

Efficient differentiation of human pluripotent stem cells into skeletal muscle cells by combining RNA-based MYOD1-expression and POU5F1-silencing
Cited by: 24
Author(s): Tasuku Akiyama, Saeko Sato, Nana Chikazawa-Nohtomi, Atsumi Soma, Hiromi Kimura, Shokichi Wakabayashi, Shigeru B. H. Ko, Minoru S.H. Ko
Software Mentions: 1
Published: almost 7 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: about 11 years ago

10.1038/s41598-018-19950-6

Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation
Cited by: 48
Author(s): Dandan Feng, Qi Li, Hong Yu, Lingfeng Kong, Shao Jun Du
Software Mentions: 1
Published: almost 7 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 10 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 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 5 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: about 13 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 8 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 9 years ago

10.1371/journal.pone.0146809

Virulent Diuraphis noxia Aphids Over-Express Calcium Signaling Proteins to Overcome Defenses of Aphid-Resistant Wheat Plants
Cited by: 9
Author(s): Deepak K. Sinha, Predeesh Chandran, Alicia E. Timm, Lina Maria Aguirre-Rojas, C. Michael Smith
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0196663

A comprehensive phylogeny of auxin homeostasis genes involved in adventitious root formation in carnation stem cuttings
Cited by: 10
Author(s): Ana Belén Sánchez-García, Sergio Ibáñez, Antonio Caño, Manuel Acosta, José Manuel Pérez-Pérez
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0131669

Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle
Cited by: 19
Author(s): Sarah W. Keenan, Craig A. Hill, Cyriac Kandoth, Leslie T. Buck, Daniel E. Warren
Software Mentions: 1
Published: over 9 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: almost 7 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: almost 6 years ago

10.1080/20002297.2019.1643205

<i>Staphylococcus aureus</i> induces COX-2-dependent proliferation and malignant transformation in oral keratinocytes
Cited by: 16
Author(s): Yuxia Wang, Shiyu Liu, Bolei Li, Yaling Jiang, Xinxuan Zhou, Jing Chen, Mingyun Li, Biao Ren, Xian Peng, Xuedong Zhou, Lei Cheng
Software Mentions: 1
Published: almost 6 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 11 years ago

10.1371/journal.pone.0246801

Comparative transcriptome analysis of leaves during early stages of chilling stress in two different chilling-tolerant brown-fiber cotton cultivars
Cited by: 1
Author(s): Shouwu Tang, Yajie Xian, Fei Wang, Cheng Luo, Song Wu, Shuangquan Xie, Xifeng Chen, Aiping Cao, Hongbin Li, Haifeng Liu
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0079298

An Integrated Model of the Transcriptome of HER2-Positive Breast Cancer
Cited by: 18
Author(s): Krishna R. Kalari, Brian M. Necela, Xiaojia Tang, Kevin J. Thompson, Melissa Lau, Jeanette E. Eckel‐Passow, Jennifer M. Kachergus, S. Keith Anderson, Zhifu Sun, Saurabh Baheti, Jennifer M. Carr, Tiffany R. Baker, Poulami Barman, Derek C. Radisky, Richard W. Joseph, Sarah A. McLaughlin, High Seng Chai, Carsten Stephan, David Rossell, Yan W. Asmann, E. Aubrey Thompson, Edith A. Perez
Software Mentions: 1
Published: about 11 years ago

10.1186/s12859-020-03824-8

Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq
Cited by: 8
Author(s): Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert C. Barber, Gang Huang
Software Mentions: 1
Published: almost 4 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 9 years ago

10.1371/journal.pone.0204506

Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress
Cited by: 20
Author(s): Xiaohui Li, Xuexia Xing, Shaohua Xu, Mingzhen Zhang, Yuan Wang, Hengyan Wu, Zhihao Sun, Zhaoguang Huo, Fang Chen, Yang Tiezhao
Software Mentions: 1
Published: about 6 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: almost 8 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 7 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 6 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 10 years ago

10.18632/aging.101082

Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential
Cited by: 12
Author(s): Qian Dong, Hui Gao, Yuanshuo Shi, Fuchuang Zhang, Xiang Gu, Anqi Wu, Danhan Wang, Yuanhong Chen, Abhik Bandyopadhyay, I‐Tien Yeh, Benjamin J. Daniel, Yidong Chen, Yi Zou, Vivienne I. Rebel, Christi A. Walter, Jianxin Lü, Changjiang Huang, LuZhe Sun
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0215039

Dual RNA-seq of Xanthomonas oryzae pv. oryzicola infecting rice reveals novel insights into bacterial-plant interaction
Cited by: 26
Author(s): Zhou-Xiang Liao, Ni Zhe, Xinli Wei, Long Chen, Jianyuan Li, Yu Yi, Wei Jiang, Bo-Le Jiang, Yanan He, Sheng Huang
Software Mentions: 1
Published: over 5 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 7 years ago

10.1371/journal.pone.0170571

RNA-Sequencing Reveals Biological Networks during Table Grapevine (‘Fujiminori’) Fruit Development
Cited by: 21
Author(s): Lingfei Shangguan, Qian Mei, Xiang Fang, Kekun Zhang, Haifeng Jia, Xiaoying Li, Yiqun Bao, Jinggui Fang
Software Mentions: 1
Published: almost 8 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 9 years ago

10.1371/journal.pone.0023356

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders
Cited by: 225
Author(s): Mingyan Lin, Erika Pedrosa, Abhishek Shah, Anastasia Hrabovsky, Shahina Maqbool, Deyou Zheng, Herbert M. Lachman
Software Mentions: 1
Published: about 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: almost 9 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 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 12 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 4 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 10 years ago

10.1371/journal.pone.0137394

A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis)
Cited by: 19
Author(s): Greta Carmona‐Antoñanzas, Stephen Carmichael, Jan Heumann, John B. Taggart, Karim Gharbi, James E. Bron, Michaël Bekaert, Armin Sturm
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0122493

Transcriptional Profiling of Ectoderm Specification to Keratinocyte Fate in Human Embryonic Stem Cells
Cited by: 13
Author(s): Ana Tadeu, Samantha Lin, Lin Hou, Lisa Chung, Ming Zhong, Hongyu Zhao, Valerie Horsley
Software Mentions: 1
Published: over 9 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: about 7 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 9 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 6 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: about 11 years ago

10.1371/journal.pone.0137087

A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth
Cited by: 35
Author(s): Biao Chen, Jiguo Xu, Xiaomei He, Haiping Xu, Guihuan Li, Hongwu Du, Qinghua Nie, Xiquan Zhang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0204124

Defense responses of lentil (Lens culinaris) genotypes carrying non-allelic ascochyta blight resistance genes to Ascochyta lentis infection
Cited by: 24
Author(s): Ehsan Sari, Vijai Bhadauria, Larissa Ramsay, M. Hossein Borhan, Judith Lichtenzveig, Kirstin E. Bett, Albert Vandenberg, Sabine Banniza
Software Mentions: 1
Published: about 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 7 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 8 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 10 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: over 7 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: almost 9 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: over 11 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 6 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 8 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 9 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 12 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 6 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: about 8 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: about 6 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: almost 8 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: over 8 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: over 9 years ago

10.1371/journal.pone.0137391

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data
Cited by: 68
Author(s): Vimal Rawat, Ahmed Abdelsamad, Björn Pietzenuk, Danelle Seymour, Daniel Koenig, Detlef Weigel, Aleš Pečinka, Korbinian Schneeberger
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 11 years ago

10.1186/s13048-020-00664-1

Circular RNA hsa_circ_0078607 suppresses ovarian cancer progression by regulating miR-518a-5p/Fas signaling pathway
Cited by: 29
Author(s): Nan Zhang, Yue Jin, Qiubo Hu, Shanshan Cheng, Chao Wang, Zhiyou Yang, Yu Wang
Software Mentions: 1
Published: over 4 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 11 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: over 11 years ago

10.1186/s13048-016-0213-3

Genome-wide transcriptional regulation of estrogen receptor targets in fallopian tube cells and the role of selective estrogen receptor modulators
Cited by: 20
Author(s): Georgette Moyle-Heyrman, Matthew J. Schipma, Matthew Dean, David A. Davis, Joanna E. Burdette
Software Mentions: 1
Published: almost 9 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 6 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: over 11 years ago

10.1371/journal.pone.0054196

Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni
Cited by: 49
Author(s): Didier Socquet-Juglard, Tim Kamber, Joël F. Pothier, Danilo Christen, C. Gessler, Brion Duffy, Andrea Patocchi
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0156424

Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics
Cited by: 57
Author(s): Takeshi Takeuchi, Lixy Yamada, Chuya Shinzato, Hitoshi Sawada, Noriyuki Satoh
Software Mentions: 1
Published: over 8 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 10 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 11 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 11 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 10 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: over 9 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 6 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 6 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 6 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: about 9 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 6 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 11 years ago

10.1186/1757-2215-7-17

Novel three-dimensional in vitro models of ovarian endometriosis
Cited by: 35
Author(s): Doerthe Brueggmann, Claire Templeman, Anna Starzinski‐Powitz, Nagesh Rao, Simon A. Gayther, Kate Lawrenson
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-017-4108-5

Genome-wide analysis of rice cis-natural antisense transcription under cadmium exposure using strand-specific RNA-Seq
Cited by: 8
Author(s): Youko Oono, Takayuki Yazawa, Hajime Kanamori, Harumi Sasaki, Satomi Mori, Takashi Matsumoto
Software Mentions: 1
Published: about 7 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: over 10 years ago

10.1186/1471-2164-15-578

Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha
Cited by: 35
Author(s): Chuan-Hung Chen, Tony Kuo, Ming Yang, Ting-Ying Chien, Mei-Ju Chu, Li-Chun Huang, Chien‐Yu Chen, Hsiao-Feng Lo, Shih‐Tong Jeng, Long‐Fang O. Chen
Software Mentions: 1
Published: almost 11 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 6 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: over 9 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 6 years ago