bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: over 7 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: about 6 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.47835

Epigenetic silencing of a multifunctional plant stress regulator
Cited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.644350

Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers
Cited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-017-0142-4

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2018.00330

Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes
Cited by: 7
Author(s): Ruidong Xiang, Jody McNally, J. J. Bond, David J. Tucker, Cameron McCarthy, A. J. Donaldson, K. L. Austin, Suzanne Rowe, Arjan Jonker, C. S. Pinares-Patiño, John C. McEwan, Phil Vercoe, V. H. Oddy, Brian P. Dalrymple
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2016.01744

Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals
Cited by: 17
Author(s): Erich M. Schwarz, Adrienne Roeder
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.21052

Embryonic origin of adult stem cells required for tissue homeostasis and regeneration
Cited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: almost 8 years ago

10.3389/fimmu.2021.667177

CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer
Cited by: 20
Author(s): Enhao Li, Xiaobao Yang, Yuzhang Du, Guanzheng Wang, David Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.53127

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity
Cited by: 23
Author(s): Nairita Maitra, Chi He, Heidi M. Blank, Mitsuhiro Tsuchiya, Birgit Schilling, Matt Kaeberlein, Rodolfo Aramayo, Brian K. Kennedy, Michael Polymenis
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 4 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: almost 4 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-68373-9

Increased predominance of the matured ventricular subtype in embryonic stem cell-derived cardiomyocytes in vivo
Cited by: 22
Author(s): Hajime Ichimura, Shin Kadota, Toshihide Kashihara, Mitsuhiko Yamada, Kyoko Ito, Hideki Kobayashi, Yuki Tanaka, Naoko Shiba, Shinichiro Chuma, Shugo Tohyama, Takashi Seto, Kenji Okada, Koichiro Kuwahara, Yuji Shiba
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2018.00049

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen
Cited by: 28
Author(s): Coraline R. Praz, Fabrizio Menardo, Mark D. Robinson, Marion Müller, Thomas Wicker, Salim Bourras, Beat Keller
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep45125

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Cited by: 42
Author(s): Matthew D. MacManes, Suzanne H. Austin, Andrew S. Lang, April M. Booth, Victoria S. Farrar, Rebecca M. Calisi
Software Mentions: 4
Published: over 7 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: over 4 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-019-1851-1

Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia
Cited by: 17
Author(s): Zi‐jun Xu, Ji‐chun Ma, Jing‐Dong Zhou, Xiang‐mei Wen, Dong‐ming Yao, Wei Zhang, Runbi Ji, Dehong Wu, Li‐Juan Tang, Zhaoqun Deng, Jun Qian, Lin Jiang
Software Mentions: 4
Published: over 5 years ago

10.1155/2015/862130

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library
Cited by: 29
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian D. Lehmann, Jennifer A. Pietenpol, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: almost 10 years ago

10.1155/2020/6784138

Identification of FOS as a Candidate Risk Gene for Liver Cancer by Integrated Bioinformatic Analysis
Cited by: 10
Author(s): Jinwu Hu, Guangyu Ding, Pei-Yao Fu, Wei‐Guo Tang, Qiqing Sun, Xiao‐Dong Zhu, Ying‐Hao Shen, Ji Zhou, Jia Fan, Hui–Chuan Sun, Cheng Huang
Software Mentions: 4
Published: over 4 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-021-07790-0

A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
Cited by: 4
Author(s): Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu, Guo‐Liang Tian
Software Mentions: 4
Published: over 3 years ago

10.3390/biomedicines9060646

Identification of MicroRNAs as Viable Aggressiveness Biomarkers for Prostate Cancer
Cited by: 11
Author(s): Luis Javier Martínez-González, Victor Sánchez-Conde, Jose María González-Cabezuelo, Alba Antúnez-Rodríguez, Eduardo Andrés-León, Inmaculada Robles-Fernández, José A. Lorente, Fernando Vázquez-Alonso, María Jesús Álvarez-Cubero
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0125224

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
Cited by: 31
Author(s): Nysia I. George, John F. Bowyer, Nathaniel M. Crabtree, Ching‐Wei Chang
Software Mentions: 4
Published: over 9 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: almost 4 years ago

10.3389/fpls.2016.01661

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation
Cited by: 13
Author(s): Igor Fesenko, A. V. Seredina, Georgij Arapidi, Vasily V. Ptushenko, Anatoly S. Urban, Ivan Butenko, Sergey I. Kovalchuk, Konstantin Babalyan, Andrey Knyazev, Regina Khazigaleeva, Elena N. Pushkova, Nikolay Anikanov, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Cited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.8917

Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma
Cited by: 131
Author(s): Ikhlak Ahmed, Thasni Karedath, Simeon Andrews, Iman K. Al-Azwani, Yasmin Ali Mohamoud, Denis Querleu, Arash Rafii, Joel A. Malek
Software Mentions: 4
Published: over 8 years ago

10.1038/s12276-020-00538-y

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Cited by: 39
Author(s): Hye Hyeon Eum, Minsuk Kwon, Daeun Ryu, Areum Jo, Wingyan Chung, Nayoung Kim, Yourae Hong, Dae‐Soon Son, Seung Tae Kim, Jeeyun Lee, Hae‐Ock Lee, Woong-Yang Park
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07889-4

Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Cited by: 6
Author(s): Rachel Smith, Amelia Goddard, Arun K. Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew L. Leisewitz, Hans Ackerman
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0164461

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 3 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0230566

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0190456

Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolism
Cited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12983-020-00366-w

Gut transcriptomic changes during hibernation in the greater horseshoe bat (Rhinolophus ferrumequinum)
Cited by: 4
Author(s): Haijian Sun, Jiaying Wang, Yanfeng Xing, Yi-Hsuan Pan, Xiuguang Mao
Software Mentions: 4
Published: over 4 years ago

10.1186/s12865-021-00428-6

Transcriptomics of type 2 diabetic and healthy human neutrophils
Cited by: 8
Author(s): Sarah E. Kleinstein, Jamison McCorrison, A. Razzaque Ahmed, Hatice Hastürk, Thomas E. Van Dyke, Marcelo Freire
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-67432-5

Differential expression of polyamine biosynthetic pathways in skin lesions and in plasma reveals distinct profiles in diffuse cutaneous leishmaniasis
Cited by: 7
Author(s): Hayna Malta‐Santos, Jaqueline França‐Costa, Amanda Ferreira Macedo, Artur T. L. Queiroz, Kiyoshi F. Fukutani, Sandra Márcia Muxel, Ricardo Khouri, Johan Van Weyenbergh, Viviane Boaventura, Aldina Barral, Jackson Maurício Lopes Costa, Eny Iochevet Segal Floh, Bruno B. Andrade, Lucile Maria Floeter‐Winter, Valéria M. Borges
Software Mentions: 4
Published: over 4 years ago

10.1098/rsob.200253

The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression
Cited by: 3
Author(s): Abdalla Elbialy
Software Mentions: 4
Published: about 4 years ago

10.12688/f1000research.16005.3

MSF: Modulated Sub-graph Finder
Cited by: 0
Author(s): Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: over 4 years ago

10.1186/s12967-020-02679-0

Development of nomogram based on immune-related gene FGFR4 for advanced non-small cell lung cancer patients with sensitivity to immune checkpoint inhibitors
Cited by: 13
Author(s): Li Wang, Zhixuan Ren, Bentong Yu, Jian Tang
Software Mentions: 4
Published: almost 4 years ago

10.3389/fpls.2016.01416

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing
Cited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: about 8 years ago

10.1093/biostatistics/kxu038

Joint analysis of differential gene expression in multiple studies using correlation motifs
Cited by: 29
Author(s): Yingying Wei, Toyoaki Tenzen, Hongkai Ji
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2021.667013

The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses
Cited by: 11
Author(s): José Ribamar Costa Ferreira‐Neto, Artemisa Nazaré da Costa Borges, Manassés Daniel da Silva, David Anderson de Lima Morais, João Pacífico Bezerra-Neto, Guillaume Bourque, Éderson Akio Kido, Ana Maria Benko‐Iseppon
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2020.587185

Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris
Cited by: 9
Author(s): Zhihua Wu, Wen Huang, Erdai Qin, Shuo Liu, Huan Liu, Aleel K. Grennan, Hong Liu, Rui Qin
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-01997-2

Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts
Cited by: 29
Author(s): Benjamin H. Mullin, Jennifer Tickner, Kun Zhu, Jacob Kenny, Shelby Mullin, Suzanne J. Brown, Frank Dudbridge, Nathan J. Pavlos, Edward S. Mocarski, John P. Walsh, Jiake Xu, Scott G. Wilson
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.00235

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs
Cited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.53704

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Cited by: 41
Author(s): Anastasia A. Minervina, Mikhail V. Pogorelyy, Ekaterina A. Komech, В. К. Карнаухов, Petra Bächer, Elisa Rosati, André Franke, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M. Walczak
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-021-00884-0

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice
Cited by: 14
Author(s): Jessica L Haigh, Anna Adhikari, Nycole A Copping, Tyler W. Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh B Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J Kreun, Jasmine Carter, Andrea Gompers, Jason T. Lambert, Cesar P Canales, L Pennacchio, Axel Visel, Diane E. Dickel, Jill L. Silverman, A. Nord
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: almost 13 years ago

10.1096/fj.201600675R

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration
Cited by: 22
Author(s): Svitlana Pasteuning-Vuhman, Johanna W Boertje-van der Meulen, Maaike van Putten, Maurice Overzier, Peter ten Dijke, Szymon M. Kiełbasa, Wibowo Arindrarto, Ron Wolterbeek, Ksenia Lezhnina, Ivan V. Ozerov, Aleksandr M Aliper, Willem M.H. Hoogaars, Annemieke Aartsma‐Rus, Cindy J.M. Loomans
Software Mentions: 4
Published: about 8 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.22878

Identification of cancer prognosis-associated functional modules using differential co-expression networks
Cited by: 10
Author(s): Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-17996-6

Identification of long non-coding RNAs in the immature and mature rat anterior pituitary
Cited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2021.709466

Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes
Cited by: 15
Author(s): Lauren J. Johnson, Siavash Azari, Amy Webb, Xiaoli Zhang, Mikhail A. Gavrilin, James L. Marshall, Kara M. Rood, Stéphanie Seveau
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: almost 5 years ago

10.1002/2211-5463.13062

Chondroitin polymerizing factor promotes breast carcinoma cell proliferation, invasion and migration and affects expression of epithelial‐mesenchymal transition‐related markers
Cited by: 6
Author(s): Li Yang, Hui Gong, Lei Feng, Dan Mao, Yujie Xiao, Yunqi Wang, Huang Li-zhong
Software Mentions: 4
Published: almost 4 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0081809

Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: about 11 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12987-021-00269-w

Characterization of the blood–brain barrier in genetically diverse laboratory mouse strains
Cited by: 16
Author(s): Johanna Schaffenrath, Sheng‐Fu Huang, Tania Wyss, Mauro Delorenzi, Annika Keller
Software Mentions: 4
Published: over 3 years ago

10.1186/1479-5876-12-159

An eight-miRNA signature as a potential biomarker for predicting survival in lung adenocarcinoma
Cited by: 95
Author(s): Xuelian Li, Yunrui Shi, Zhihua Yin, Xiaoxia Xue, Baosen Zhou
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-66309-x

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin
Cited by: 35
Author(s): Andrés Lamsfus‐Calle, Alberto Daniel‐Moreno, Justin S. Antony, Thomas Epting, Lukas Heumos, Praveen Baskaran, Jakob Admard, Nicolas Casadei, Ngadhnjim Latifi, Darina M. Siegmund, Michael Kormann, Rupert Handgretinger, Markus Mezger
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-81689-4

Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression
Cited by: 19
Author(s): Hollis Wright, Carlos F. Aylwin, Carlos A. Toro, Sergio R. Ojeda, Alejandro Lomniczi
Software Mentions: 4
Published: almost 4 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in <i>Drosophila melanogaster</i>
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: about 8 years ago

10.3389/fsurg.2021.717084

Identification of a Novel Signature Predicting Overall Survival in Head and Neck Squamous Cell Carcinoma
Cited by: 4
Author(s): Haige Zheng, Huixian Liu, Yumin Lu, Li Hengguo
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2019.00210

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle
Cited by: 23
Author(s): Wellison J. S. Diniz, Gianluca Mazzoni, Luiz Lehmann Coutinho, Priyanka Banerjee, Ludwig Geistlinger, Francesca Bertolini, Juliana Afonso, P. S. N. Oliveira, P. C. Tizioto, Haja N. Kadarmideen, Luciana Correia de Almeida Regitano
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.45310

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
Cited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 4 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2021.663736

MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Cited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: about 9 years ago

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 5 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: over 7 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

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: almost 7 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568