bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/biom11091395

A Set of 17 microRNAs Common for Brain and Cerebrospinal Fluid Differentiates Primary Central Nervous System Lymphoma from Non-Malignant Brain Tumors
Cited by: 3
Author(s): Maria Sromek, Grzegorz Rymkiewicz, Agnieszka Paziewska, Lukasz Szafron, Maria Kulecka, Michalina Zajdel, Mariusz Kulińczak, Michalina Dąbrowska, Aneta Bałabas, Zbigniew Bystydzieński, Magdalena Chechlińska, Jan Konrad Siwicki
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.103205

Chestnut polysaccharides benefit spermatogenesis through improvement in the expression of important genes
Cited by: 10
Author(s): Shuai Yu, Yong Zhao, Fa‐Li Zhang, Ya-Qi Li, Wei Shen, Zhongyi Sun
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2709-5

A likelihood ratio test for changes in homeolog expression bias
Cited by: 8
Author(s): Ronald D. Smith, Taliesin J Kinser, Gregory D. Smith, Joshua R. Puzey
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.42068

Analysis of the genomic architecture of a complex trait locus in hypertensive rat models links Tmem63c to kidney damage
Cited by: 18
Author(s): Angela Schulz, Nicola Victoria Müller, Nina A. van de Lest, Andreas Eisenreich, Martina Schmidbauer, Andrei Barysenka, Bettina Purfürst, Anje Sporbert, Theodor Lorenzen, Alexander M Meyer, Laura Herlan, Anika Witten, Frank Rühle, Weibin Zhou, Emile de Heer, Marion Scharpfenecker, Daniela Panáková, Monika Stoll, Reinhold Kreutz
Software Mentions: 1
Published: over 7 years ago

10.3390/biom11081206

Sex-Biased Expression of Pharmacogenes across Human Tissues
Cited by: 6
Author(s): Maria Laura Idda, Ilaria Campesi, Giovanni Fiorito, Andrea Vecchietti, Silvana Anna Maria Urru, Giuliana Solinas, Flavia Franconi, Matteo Floris
Software Mentions: 1
Published: over 5 years ago

10.3390/biom10010150

Identification of miRNAs Enriched in Extracellular Vesicles Derived from Serum Samples of Breast Cancer Patients
Cited by: 33
Author(s): Patrícia Midori Murobushi Ozawa, Evelyn Vieira, Débora S. Lemos, Ingrid L.M. Souza, Sı́lvio M. Zanata, Vânia C. S. Pankievicz, Thalita Regina Tuleski, Emanuel Maltempi de Souza, Pryscilla Fanini Wowk, Cı́cero de Andrade Urban, Fusakuni Kuroda, Rubens Silveira de Lima, Rodrigo Coutinho de Almeida, Daniela Fiori Gradia, Iglenir João Cavalli, Luciane R. Cavalli, Danielle Malheiros, Enilze M.S.F. Ribeiro
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.43570

Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression
Cited by: 14
Author(s): Yumin Qi, Yang Wu, Randy Saunders, Xiaoguang Chen, Chunhong Mao, James K. Biedler, Zhijian Tu
Software Mentions: 1
Published: over 7 years ago

10.3390/biom11091265

Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression
Cited by: 0
Author(s): Zihao Liu, Yu Shi, Qun Lin, Wenqian Yang, Qing Luo, Yinghuan Cen, Juanmei Li, Xiaolin Fang, Wen Guo Jiang, Chang Gong
Software Mentions: 1
Published: about 5 years ago

10.3390/biom10040501

BET Inhibitors Synergize with Carfilzomib to Induce Cell Death in Cancer Cells via Impairing Nrf1 Transcriptional Activity and Exacerbating the Unfolded Protein Response
Cited by: 18
Author(s): Janakiram R. Vangala, Ajay Potluri, Senthil K. Radhakrishnan
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.40448

H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes
Cited by: 33
Author(s): Itamar Lev, Hila Gingold, Oded Rechavi
Software Mentions: 1
Published: over 7 years ago

10.3390/biom9120823

Genome-Wide Analysis of Abscisic Acid Biosynthesis, Catabolism, and Signaling in Sorghum Bicolor under Saline-Alkali Stress
Cited by: 12
Author(s): Siqi Ma, Li-Yun Lin, Chen Meng, Chao Zhou, Jie Fu, Xiangling Shen, Chengsheng Zhang, Yiqiang Li
Software Mentions: 1
Published: almost 7 years ago

10.3390/biom11010041

isomiRs–Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?
Cited by: 10
Author(s): Ilias Glogovitis, Galina Yahubyan, Thomas Würdinger, Danijela Koppers-Lalić, Vesselin Baev
Software Mentions: 1
Published: almost 6 years ago

10.3390/biomedicines8040088

A Non-Coding RNA Landscape of Bronchial Epitheliums of Lung Cancer Patients
Cited by: 12
Author(s): Yanli Luo, V.K. Holden, Pushpawallie Dhilipkannah, Janaki Deepak, Nevins W. Todd, Feng Jiang
Software Mentions: 1
Published: over 6 years ago

10.3390/biomedicines8060147

Transcriptome-Wide Analysis of CXCR5 Deficient Retinal Pigment Epithelial (RPE) Cells Reveals Molecular Signatures of RPE Homeostasis
Cited by: 11
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Huang Hu
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.19386

Implications of PI3K/AKT inhibition on REST protein stability and neuroendocrine phenotype acquisition in prostate cancer cells
Cited by: 33
Author(s): Ruiqui Chen, Yinan Li, Ralph Buttyan, Xuesen Dong
Software Mentions: 1
Published: over 9 years ago

10.3390/biomedicines9080949

Evaluation of β-Catenin Inhibition of Axitinib and Nitazoxanide in Human Monocyte-Derived Dendritic Cells
Cited by: 1
Author(s): Waqas Azeem, Ragnhild Maukon Bakke, Benjamin Gabriel, Silke Appel, Anne Margrete Øyan, Karl‐Henning Kalland
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines9070719

miR-208b Reduces the Expression of Kcnj5 in a Cardiomyocyte Cell Line
Cited by: 4
Author(s): Julia Hupfeld, Maximilian Ernst, Maria Knyrim, Stephanie Binas, Udo Kloeckner, Sindy Rabe, Katja Quarch, Danny Misiak, Matthew Fuszard, Claudia Großmann, Michael Gekle, Barbara Schreier
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines8110450

Modulation of Small RNA Signatures in Schwann-Cell-Derived Extracellular Vesicles by the p75 Neurotrophin Receptor and Sortilin
Cited by: 12
Author(s): Nádia Pereira Gonçalves, Yan Yan, Maj Ulrichsen, Morten T. Venø, Ebbe Toftgaard Poulsen, Jan J. Enghild, Jørgen Kjems, Christian Bjerggaard Vægter
Software Mentions: 1
Published: about 6 years ago

10.1051/bmdcn/2019090427

The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis
Cited by: 13
Author(s): Nen Chung Chang, Yiping Huang
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms17081324

Genes Expressed Differentially in Hessian Fly Larvae Feeding in Resistant and Susceptible Plants
Cited by: 7
Author(s): Ming‐Shun Chen, Sanzhen Liu, Haiyan Wang, Xiaoyan Cheng, Mustapha El Bouhssini, R. Jeff Whitworth
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms17101758

Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita
Cited by: 12
Author(s): Parthiban Subramanian, Inchan Choi, Vimalraj Mani, Jun Hyung Park, Sathiyamoorthy Subramaniyam, Kang-Hyun Choi, Ji Hyun Sim, Chang-Muk Lee, Jun Mo Koo, Bum-Soo Hahn
Software Mentions: 1
Published: about 10 years ago

10.1155/2019/7149296

miRNA and mRNA Integration Network Construction Reveals Novel Key Regulators in Left-Sided and Right-Sided Colon Adenocarcinoma
Cited by: 15
Author(s): Likun Yang, Li Lin, Jing Ma, Shimin Yang, Chao Zou, Xiaozhou Yu
Software Mentions: 1
Published: over 7 years ago

10.1155/2017/4585213

MicroRNA Mediating Networks in Granulosa Cells Associated with Ovarian Follicular Development
Cited by: 9
Author(s): Bao-Yun Zhang, Long Chen, Guangde Feng, Xu Wei, Ke Zhang, Mingxing Chu, Pingqing Wang
Software Mentions: 1
Published: almost 10 years ago

10.18632/oncotarget.20166

The IDO inhibitor 1-methyl tryptophan activates the aryl hydrocarbon receptor response in mesenchymal stromal cells
Cited by: 23
Author(s): Christopher N. Lewis, Raghavan Chinnadurai, Steven E. Bosinger, Jacques Galipeau
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms18091977

Deep Circular RNA Sequencing Provides Insights into the Mechanism Underlying Grass Carp Reovirus Infection
Cited by: 44
Author(s): Libo He, Aidi Zhang, Lv Xiong, Yongming Li, Rong Huang, Lanjie Liao, Zhu Zhang, And Yaping Wang
Software Mentions: 1
Published: about 9 years ago

10.1155/2021/6681925

Identification of Critical Genes and lncRNAs in Osteolysis after Total Hip Arthroplasty and Osteoarthritis by RNA Sequencing
Cited by: 2
Author(s): Guang Yang, Kai Tang, Qiao Li, Yixin Li, Shui Sun
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/8890176

Transcriptomic Analyses Reveal Gene Expression Profiles and Networks in Nasopharyngeal Carcinoma
Cited by: 3
Author(s): Yuwen Zhou, Weiqiang Yang, Xueshuang Mei, Hongyi Hu
Software Mentions: 1
Published: almost 6 years ago

10.1155/2019/2365416

Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets
Cited by: 1
Author(s): Shuaifei Feng, Xiaoyong Du, Chao Wang, Dengdeng Ye, Guanjun Ma, Shuhong Zhao, Haiyan Wang, Xiangdong Liu
Software Mentions: 1
Published: about 7 years ago

10.1186/s12859-018-2434-5

Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks
Cited by: 13
Author(s): Peizhuo Wang, Lin Gao, Yuxuan Hu, Feng Li
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.21577

Tamoxifen sensitivity-related microRNA-342 is a useful biomarker for breast cancer survival
Cited by: 37
Author(s): Joseph C. Young, Tsutomu Kawaguchi, Li Yan, Qianya Qi, Song Liu, Kazuaki Takabe
Software Mentions: 1
Published: about 9 years ago

10.18632/aging.202640

Suppression of p16 alleviates the senescence-associated secretory phenotype
Cited by: 28
Author(s): Raquel Buj, Kelly E. Leon, Marlyn A Anguelov, Katherine M. Aird
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms19051467

Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome
Cited by: 19
Author(s): Kind-Leng Tong, Ahmad Syadi Mahmood Zuhdi, Wan Azman Wan Ahmad, Paul M. Vanhoutte, João Pedro de Magalhães, Mohd Rais Mustafa, Pooi-Fong Wong
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.22216

GEJ cancers: gastric or esophageal tumors? searching for the answer according to molecular identity
Cited by: 14
Author(s): Williams Fernandes Barra, Fabiano Cordeiro Moreira, Aline Cruz, André Salim Khayat, Danielle Queiroz Calcagno, Ney Pereira Carneiro dos Santos, Rui Wanderley Mascarenhas, Taíssa Maíra Thomaz Araújo, Geraldo Ishak, Sâmia Demachki, Rommel Rodrı́guez Burbano, Ândrea Ribeiro-dos-Santos, Sidney Emanuel Batista dos Santos, Gregory J. Riggins, Paulo Pimentel de Assumpção
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.21877

Azacitidine combined with the selective FLT3 kinase inhibitor crenolanib disrupts stromal protection and inhibits expansion of residual leukemia-initiating cells in FLT3-ITD AML with concurrent epigenetic mutations
Cited by: 14
Author(s): Anne-Kathrin Garz, Saskia Wolf, Sonja Grath, Verena I. Gaidzik, Stefan Habringer, Binje Vick, Martina Rudelius, Christoph Ziegenhain, Sylvia Herold, Marie‐Theresa Weickert, Martha Smets, Christian Peschel, Robert A.J. Oostendorp, Sebastian Bultmann, Irmela Jeremias, Christian Thiede, Konstanze Döhner, Ulrich Keller, Katharina Götze
Software Mentions: 1
Published: about 9 years ago

10.3390/ijms19092631

Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-acyl-l-homoserine Lactone Accumulation
Cited by: 8
Author(s): Haijun Lu, Yili Huang
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19102924

Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules
Cited by: 47
Author(s): Yingbin Xue, Q. J. Zhuang, Shengnan Zhu, Bi-Xian Xiao, Chaojie Liang, Hong Liao, Jichun Tian
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19103158

Comparative Analysis of the Integument Transcriptomes between stick Mutant and Wild-Type Silkworms
Cited by: 3
Author(s): Tan D, Hai Hu, Xiaoling Tong, Minjin Han, Songyuan Wu, Xin Ding, Fangyin Dai, Cheng Lü
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/5762932

Transcriptome Analysis Reveals the Negative Effect of 16 T High Static Magnetic Field on Osteoclastogenesis of RAW264.7 Cells
Cited by: 3
Author(s): Ting Huyan, Hourong Peng, Suna Cai, Qi Li, Di Dong, Zhouqi Yang, Peng Shang
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/9958745

The Potential Genes Mediate the Pathogenicity of Allogeneic CD4+T Cell in aGVHD Mouse Model
Cited by: 2
Author(s): Zhengyu Yu, Chenchen Qin, Min Cao, Xiaoya He, Hanyun Ren, Huihui Liu
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.22724

Optimizing prognosis-related key miRNA-target interactions responsible for cancer metastasis
Cited by: 1
Author(s): Hongying Zhao, Huating Yuan, Jing Hu, Chaohan Xu, Gaoming Liao, Wenkang Yin, Liwen Xu, Li Wang, Xinxin Zhang, Shi Ai, Jing Li, Yun Xiao
Software Mentions: 1
Published: almost 9 years ago

10.1155/2019/2951427

Transcriptome Analysis Reveals the Effect of Long Intergenic Noncoding RNAs on Pig Muscle Growth and Fat Deposition
Cited by: 9
Author(s): Guoting Chen, Xiangdong Cheng, Gaoli Shi, Cheng Zou, Lin Chen, Jingxuan Li, Mengxun Li, Fang Cui, Changchun Li
Software Mentions: 1
Published: over 7 years ago

10.1186/s40478-021-01231-5

Protein farnesylation is upregulated in Alzheimer’s human brains and neuron-specific suppression of farnesyltransferase mitigates pathogenic processes in Alzheimer’s model mice
Cited by: 11
Author(s): Angela Jeong, Shaowu Cheng, Rui Zhong, David A. Bennett, Martin O. Bergö, Li L
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/2043785

Extraction and Hypolipidemic Activity of Low Molecular Weight Polysaccharides Isolated from Rosa Laevigata Fruits
Cited by: 6
Author(s): Xuejiao Zhang, Hu Y, Chenzhong Jin, Weiguo Wu
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms19123892

Distinct Patterns of PPARγ Promoter Usage, Lipid Degradation Activity, and Gene Expression in Subcutaneous Adipose Tissue of Lean and Obese Swine
Cited by: 5
Author(s): Bowen Song, Shengwei Di, Shiquan Cui, Na Chen, Huan Wang, Xuan Wang, Qian Gao, Guizhi Tong, Hongbao Wang, Xuankai Huang, Liyan Ding, Ying Gao, Jun Li, Xibiao Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-020-3346-8

Ensemble disease gene prediction by clinical sample-based networks
Cited by: 5
Author(s): Ping Luo, Li Tian, Bolin Chen, Qianghua Xiao, Fang‐Xiang Wu
Software Mentions: 1
Published: over 6 years ago

10.3390/biology10090875

Intersex Plays a Role in Microbial Homeostasis in the Brown Planthopper
Cited by: 1
Author(s): Hou‐Hong Zhang, Hanjing Li, Yuxuan Ye, Ji-Chong Zhuo, Chuan-Xi Zhang
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20030720

Transcriptomic Analysis of Planarians under Simulated Microgravity or 8 g Demonstrates That Alteration of Gravity Induces Genomic and Cellular Alterations That Could Facilitate Tumoral Transformation
Cited by: 5
Author(s): Nídia de Sousa, Gustavo Rodríguez-Esteban, Ivan Colagè, Paolo D’Ambrosio, Jack J. W. A. van Loon, Emili Saló, Teresa Adell, Gennaro Auletta
Software Mentions: 1
Published: almost 8 years ago

10.3390/biology10090867

The Genetic Network of Forkhead Gene Family in Development of Brown Planthoppers
Cited by: 3
Author(s): Haiyan Lin, Cheng-Qi Zhu, Hou‐Hong Zhang, Zhicheng Shen, Chuan-Xi Zhang, Yuxuan Ye
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20040852

Transcriptome Profiling Reveals Effects of Drought Stress on Gene Expression in Diploid Potato Genotype P3-198
Cited by: 27
Author(s): Xiaohui Yang, Jie Liu, Jianfei Xu, Shaoguang Duan, Qianru Wang, Guangcun Li, Liping Jin
Software Mentions: 1
Published: over 7 years ago

10.3390/biology10080753

Identification of Riptortus pedestris Salivary Proteins and Their Roles in Inducing Plant Defenses
Cited by: 7
Author(s): Hai‐Jian Huang, Xiaotian Yan, Zhongyan Wei, Yi-Zhe Wang, Jianping Chen, Junmin Li, Zongtao Sun, Chuan‐Xi Zhang
Software Mentions: 1
Published: over 5 years ago

10.3390/biology9070153

A First Insight into North American Plant Pathogenic Fungi Armillaria sinapina Transcriptome
Cited by: 6
Author(s): Narimene Fradj, Nicolas de Montigny, Natacha Mérindol, Fatima Awwad, Yacine Boumghar, Hugo Germain, Isabel Desgagné‐Penix
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms20061338

Transcriptome Profile of the Variegated Ficus microcarpa c.v. Milky Stripe Fig Leaf
Cited by: 11
Author(s): Tin-Han Shih, Szu-Hsien Lin, Meng‐Yuan Huang, W. Huang, Chi-Ming Yang
Software Mentions: 1
Published: over 7 years ago

10.3390/biology10050440

Integrated Signals of Jasmonates, Sugars, Cytokinins and Auxin Influence the Initial Growth of the Second Buds of Chrysanthemum after Decapitation
Cited by: 9
Author(s): Daojin Sun, Luyao Zhang, Qi Yu, Jiali Zhang, Peiling Li, Yu Zhang, Xiangzhuo Xing, Lian Ding, Weimin Fang, Fadi Chen, Aiping Song
Software Mentions: 1
Published: over 5 years ago

10.1007/s10142-020-00732-1

UNAGI: an automated pipeline for nanopore full-length cDNA sequencing uncovers novel transcripts and isoforms in yeast
Cited by: 6
Author(s): Mohamad Al Kadi, Nicolas Jung, Shingo Ito, Shoichiro Kameoka, Takashi Hishida, Daisuke Motooka, Shota Nakamura, Tetsuya Iida, Daisuke Okuzaki
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.fgb.2016.04.005

Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression
Cited by: 25
Author(s): Paul Daly, Jolanda M. van Munster, Matthew Kokolski, Fei Sang, Martin Blythe, Sunir Malla, Juliana Velasco de Castro Oliveira, Gustavo H. Goldman, David B. Archer
Software Mentions: 1
Published: over 9 years ago

10.1186/s13293-021-00387-y

Sexual dimorphism of monocyte transcriptome in individuals with chronic low-grade inflammation
Cited by: 10
Author(s): Jisun So, Albert Tai, Alice H. Lichtenstein, Dayong Wu, Stefania Lamon‐Fava
Software Mentions: 1
Published: over 5 years ago

10.1007/s10142-020-00750-z

Comparative de novo transcriptome analysis of barley varieties with different malting qualities
Cited by: 3
Author(s): Leona Leišová‐Svobodová, Vratislav Psota, Štěpán Stočes, Petr Vácha, L. Kučera
Software Mentions: 1
Published: about 6 years ago

10.1534/g3.115.017632

X Chromosome and Autosome Dosage Responses in Drosophila melanogaster Heads
Cited by: 17
Author(s): Zhenxia Chen, Brian Oliver
Software Mentions: 1
Published: over 11 years ago

10.1186/s12983-021-00424-x

Mitonuclear mismatch alters nuclear gene expression in naturally introgressed Rhinolophus bats
Cited by: 3
Author(s): Yuting Ding, Wenli Chen, Qianqian Li, Stephen J. Rossiter, Xiuguang Mao
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms20071708

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)
Cited by: 4
Author(s): Delara Akhter, Ran Qin, Ujjal Kumar Nath, Jamal Eshag, Xiaogang Jin, Chao Shi
Software Mentions: 1
Published: over 7 years ago

10.3389/fvets.2021.668158

Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq
Cited by: 4
Author(s): Liang Yu, Marta Gòdia, Anna Castelló, Joan E. Rodríguez‐Gil, Sam Balasch, Armand Sánchez, Alex Clop
Software Mentions: 1
Published: over 5 years ago

10.1186/s13293-020-00305-8

Transcriptional analysis of the multiple Sry genes and developmental program at the onset of testis differentiation in the rat
Cited by: 5
Author(s): Jeremy W. Prokop, Surya B. Chhetri, J. Edward Van Veen, Xuqi Chen, Adam Underwood, Katie Uhl, Melinda R. Dwinell, Aron M. Geurts, Stephanie M. Correa, Arthur P. Arnold
Software Mentions: 1
Published: over 6 years ago

10.3389/fvets.2020.00492

RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection
Cited by: 8
Author(s): Fanfan Zhang, Weifeng Yuan, Zhiquan Li, Yuhan Zhang, Yang Yu, Kai Li, Zhen Ding, Yunyan Chen, Ting Cheng, Qiong Wu, Yuxin Tang, Deping Song
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2641-8

Shambhala: a platform-agnostic data harmonizer for gene expression data
Cited by: 30
Author(s): Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, А А Пулин, И И Еремин, Anton Buzdin
Software Mentions: 1
Published: almost 8 years ago

10.1534/g3.117.041053

NuA4 Lysine Acetyltransferase Complex Contributes to Phospholipid Homeostasis inSaccharomyces cerevisiae
Cited by: 7
Author(s): Louis Dacquay, Annika Flint, James Butcher, Danny Salem, Michael A. Kennedy, Mads Kærn, Alain Stintzi, Kristin Baetz
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms20092212

Molecular Signature of Prospero Homeobox 1 (PROX1) in Follicular Thyroid Carcinoma Cells
Cited by: 6
Author(s): Magdalena Rudzińska, Małgorzata Grzanka, Anna Stachurska, Michał Mikula, Katarzyna Paczkowska, Tomasz Stępień, Agnieszka Paziewska, Jerzy Ostrowski, Barbara Czarnocka
Software Mentions: 1
Published: over 7 years ago

10.1155/2021/5529430

Exosomal miR-218-5p/miR-363-3p from Endothelial Progenitor Cells Ameliorate Myocardial Infarction by Targeting the p53/JMY Signaling Pathway
Cited by: 29
Author(s): Xiaoyan Ke, Rongfeng Yang, Fang Wu, Xing Wang, Jiawen Liang, Xun Hu, Chengping Hu
Software Mentions: 1
Published: over 5 years ago

10.1242/bio.030254

Re-evaluating functional landscape of the cardiovascular system during development
Cited by: 6
Author(s): Norio Takada, Madoka Omae, Fumihiko Sagawa, C. Neil, Satsuki Endo, Satoshi Kozawa, Thomas N. Sato
Software Mentions: 1
Published: almost 10 years ago

10.1534/g3.117.300165

Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation inSaccharomyces cerevisiae
Cited by: 1
Author(s): Maia Segura-Wang, Megumi Onishi-Seebacher, Adrian M. Stütz, Balca R. Mardin, Jan Korbel
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.24269

RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line
Cited by: 21
Author(s): Agata Lichawska-Cieślar, Roza Pietrzycka, Janusz Ligęza, Maria Kulecka, Agnieszka Paziewska, Agata Kalita, Dobrochna Dolicka, Mateusz Wilamowski, Katarzyna Miękus, Jerzy Ostrowski, Michał Mikula, Jolanta Jura
Software Mentions: 1
Published: almost 9 years ago

10.1002/art.40545

Functional Characterization of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies rs12915901 as a Key Target Variant
Cited by: 41
Author(s): Colin Shepherd, Dongxing Zhu, Andrew Skelton, Jennifer Combe, Harrison Threadgold, Longji Zhu, Tonia L. Vincent, Paul Stuart, Louise N. Reynard, John Loughlin
Software Mentions: 1
Published: about 8 years ago

10.1534/g3.118.200174

Identification of General Patterns of Sex-Biased Expression in Daphnia, a Genus with Environmental Sex Determination
Cited by: 8
Author(s): Cécile Molinier, Céline Reisser, Peter D. Fields, Adeline Ségard, Yan R. Galimov, Christoph R. Haag
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms20133321

Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis
Cited by: 25
Author(s): Zifeng Yang, Li Wen, Xiao Dong Su, Pingfei Ge, Yan Zhou, Yuanyuan Hao, Huangying Shu, Chonglun Gao, Shanhan Cheng, Guopeng Zhu, Zhiwei Wang
Software Mentions: 1
Published: over 7 years ago

10.1242/bio.046474

Combinatorial genetic replenishments in myocardial and outflow tract tissues restore heart function in tnnt2 mutant zebrafish
Cited by: 5
Author(s): Lian Liu, Fei Fei, Ranran Zhang, Fang Wu, Qian Yang, Feng Wang, Song Sun, Hui Zhao, Qiang Li, Lei Wang, Youhua Wang, Yonghao Gui, Xu Wang
Software Mentions: 1
Published: almost 8 years ago

10.1242/bio.049684

Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation
Cited by: 13
Author(s): Tamsin J Samuels, Yoav Arava, Aino I Järvelin, Francesca Robertson, Young Seok Lee, Yang Lu, Ching-Po Yang, Tzumin Lee, David Ish‐Horowicz, Ilan Davis
Software Mentions: 1
Published: almost 7 years ago

10.1534/g3.118.200270

Tissue-Specific Transcriptome for Poeciliopsis prolifica Reveals Evidence for Genetic Adaptation Related to the Evolution of a Placental Fish
Cited by: 9
Author(s): Nathaniel K. Jue, Robert J. Foley, David N. Reznick, Rachel J. O’Neill, Michael O’Neill
Software Mentions: 1
Published: over 8 years ago

10.3389/fvets.2020.552251

The Effect of Atopic Dermatitis and Diet on the Skin Transcriptome in Staffordshire Bull Terriers
Cited by: 8
Author(s): Johanna Anturaniemi, Sara Zaldívar‐López, H.F.J. Savelkoul, Kari Elo, Anna Hielm‐Björkman
Software Mentions: 1
Published: about 6 years ago

10.1155/2020/1634270

High Throughput Approaches to Unravel the Mechanism of Action of a New Vanadium-Based Compound against Trypanosoma cruzi
Cited by: 13
Author(s): M. Florencia Mosquillo, Pablo Smircich, Analı́a Lima, Sérgio Alexandre Gehrke, Gonzalo Scalese, Ignacio Machado, Dinorah Gambino, Beatríz Garat, Leticia Pérez-Díaz
Software Mentions: 1
Published: over 6 years ago

10.1186/s13075-019-1988-6

Cartilage endoplasmic reticulum stress may influence the onset but not the progression of experimental osteoarthritis
Cited by: 12
Author(s): Louise H. W. Kung, Lorna Mullan, Jamie Soul, Ping Wang, Kazutoshi Mori, John F. Bateman, Michael D. Briggs, Raymond P. Boot-Handford
Software Mentions: 1
Published: about 7 years ago

10.3389/fvets.2021.650732

Exploring With Transcriptomic Approaches the Underlying Mechanisms of an Essential Oil-Based Phytogenic in the Small Intestine and Liver of Pigs
Cited by: 1
Author(s): Jérémy Le Coz, Suzana Ilic, Silvia Fibi-Smetana, Gerd Schatzmayr, Mathias Zaunschirm, Bertrand Grenier
Software Mentions: 1
Published: over 5 years ago

10.1093/bioinformatics/bty998

TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators
Cited by: 0
Author(s): Asa Thibodeau, Dong-Guk Shin
Software Mentions: 1
Published: almost 8 years ago

10.3389/fpls.2016.01905

RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense
Cited by: 16
Author(s): Stanford Kwenda, Tshepiso V. Motlolometsi, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2021.690857

Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode
Cited by: 12
Author(s): Inês Modesto, Lieven Sterck, Vicent Arbona, Isabel Carrasquinho, Yves Van de Peer, Celia María Gonzalo Miguel
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2019.00562

GmMYB176 Regulates Multiple Steps in Isoflavonoid Biosynthesis in Soybean
Cited by: 20
Author(s): Arun Kumaran Anguraj Vadivel, Justin B. Renaud, Sateesh Kagale, Sangeeta Dhaubhadel
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2018.01791

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus
Cited by: 26
Author(s): Azahara C. Martín, Philippa Borrill, Janet Higgins, Abdul Kader Alabdullah, Ricardo H. Ramírez-González, David Swarbreck, Cristóbal Uauy, Peter Shaw, Graham Moore
Software Mentions: 1
Published: almost 8 years ago

10.1534/g3.118.200805

The Role of UV-B light on Small RNA Activity During Grapevine Berry Development
Cited by: 28
Author(s): Sukumaran Sunitha, Rodrigo Loyola, José Antonio Alcalde, Patricio Arce‐Johnson, José Tomás Matus, Christopher D. Rock
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2020.00747

Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica
Cited by: 17
Author(s): Alexander Kirbis, Manuel Waller, Mariana Ricca, Zoe Bont, Anna Neubauer, Bernard Goffinet, Péter Szövényi
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2019.01141

Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic Response
Cited by: 17
Author(s): Eoghan King, Adrian Wallner, Isabelle Rimbault, Célia Barrachina, Agnieszka Klonowska, Lionel Moulin, Pierre Czernic
Software Mentions: 1
Published: about 7 years ago

10.1093/bioinformatics/bty553

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
Cited by: 10
Author(s): Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz
Software Mentions: 1
Published: about 8 years ago

10.1534/g3.119.400167

Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach
Cited by: 23
Author(s): Fei Shen, Zhenyu Huang, Baoguo Zhang, Yi Wang, Xi Zhang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2018.01450

Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales)
Cited by: 13
Author(s): Erin M. Sigel, Eric Schuettpelz, Kathleen M. Pryer, Joshua P. Der
Software Mentions: 1
Published: about 8 years ago

10.3389/fpls.2018.01300

MYBA From Blueberry (Vaccinium Section Cyanococcus) Is a Subgroup 6 Type R2R3MYB Transcription Factor That Activates Anthocyanin Production
Cited by: 48
Author(s): Blue Plunkett, Richard V. Espley, Andrew P. Dare, Ben Warren, Ella Grierson, Sarah Cordiner, Janice L. Turner, Andrew C. Allan, Nick W. Albert, Kevin Davies, Kathy E. Schwinn
Software Mentions: 1
Published: about 8 years ago

10.1534/g3.119.400077

Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts
Cited by: 13
Author(s): David C. Stieg, Kai-Ti Chang, Katrina F. Cooper, Randy Strich
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2016.01861

Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics
Cited by: 48
Author(s): Nirin Udomsom, Amit Rai, Hideyuki Suzuki, Jun Okuyama, Ryōsuke Imai, Tetsuya Mori, Ryo Nakabayashi, Kazuki Saito, Mami Yamazaki
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2019.01529

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight
Cited by: 36
Author(s): Raúl Herranz, Joshua P. Vandenbrink, Alicia Villacampa, Aránzazu Manzano, William L. Poehlman, F. Alex Feltus, John Z. Kiss, F. Javier Medina
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.bioflm.2019.100002

Interkingdom interactions on the denture surface: Implications for oral hygiene
Cited by: 13
Author(s): Christopher Delaney, Lindsay E. O’Donnell, Ryan Kean, Leighann Sherry, Jason L. Brown, Gareth Calvert, Christopher J. Nile, Laura J. Cross, David J. Bradshaw, Bernd W. Brandt, Douglas Robertson, Gordon Ramage
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms20184586

The miRNA–mRNA Networks Involving Abnormal Energy and Hormone Metabolisms Restrict Tillering in a Wheat Mutant dmc
Cited by: 9
Author(s): Junhang An, Hao Niu, Yongjing Ni, Yumei Jiang, Yong-Xing Zheng, Ruishi He, Junchang Li, Zhixin Jiao, Jing Zhang, Huijuan Li, Qiaoyun Li, Jishan Niu
Software Mentions: 1
Published: about 7 years ago

10.3389/fpls.2021.681166

Functional Characterization of the EMBRYONIC FLOWER 2 Gene Involved in Flowering in Ginkgo biloba
Cited by: 4
Author(s): Xian Zhou, Lanlan Wang, Janping Yan, Jiabao Ye, Shuiyuan Cheng, Feng Xu, Guiyuan Wang, Weiwei Zhang, Yongling Liao, Xiaomeng Liu
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2020.01186

Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant
Cited by: 31
Author(s): Kihyuck Choi, Jae-Hun Choi, Pyeong An Lee, Nazish Roy, Raees Khan, Hyoung Ju Lee, Hang-Yeon Weon, Hyun Gi Kong, Seon-Woo Lee
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2020.01276

SgRVE6, a LHY-CCA1-Like Transcription Factor From Fine-Stem Stylo, Upregulates NB-LRR Gene Expression and Enhances Cold Tolerance in Tobacco
Cited by: 9
Author(s): Shu Chen, Huai-An Huang, Jianhui Chen, Chengcheng Fu, Penglin Zhan, Shanwen Ke, Xiangqian Zhang, Tao Zhong, Xuewen Xie
Software Mentions: 1
Published: about 6 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583