bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fcell.2021.641618

Implementation of CRISPR/Cas9 Genome Editing to Generate Murine Lung Cancer Models That Depict the Mutational Landscape of Human Disease
Cited by: 18
Author(s): Oliver Hartmann, Michaela Reissland, Carina R. Maier, Thomas Fischer, Cristian Prieto-Garcia, Apoorva Baluapuri, Jessica Denise Schwarz, W. Schmitz, Martín Garrido‐Rodriguez, Nikolett Pahor, Clare C. Davies, Florian Bassermann, Amir Orian, Elmar Wolf, Almut Schulze, Marco A. Calzado, Mathias T. Rosenfeldt, Markus E. Diefenbacher
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1555-8

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
Cited by: 10
Author(s): Yejun Wang, Keith D. MacKenzie, Aaron P. White
Software Mentions: 1
Published: over 11 years ago

10.3389/fcell.2021.631413

Role of VEGFR2 in Mediating Endoplasmic Reticulum Stress Under Glucose Deprivation and Determining Cell Death, Oxidative Stress, and Inflammatory Factor Expression
Cited by: 2
Author(s): Bohan Xu, Leocadia Zhou, Qishan Chen, Jianing Zhang, Lijuan Huang, Shasha Wang, Zhimin Ye, Xianyue Ren, Yu Cai, Lasse D. Jensen, Weirong Chen, Xuri Li, Rong Ju
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.46551

NRG1 is a critical regulator of differentiation in TP63-driven squamous cell carcinoma
Cited by: 9
Author(s): Ganapati V. Hegde, Cecile de la Cruz, Jennifer M. Giltnane, Lisa Crocker, Avinashnarayan Venkatanarayan, Gabriele Schaefer, Debra Dunlap, Joerg D. Hoeck, Robert Piskol, Florian Gnad, Zora Modrušan, Frédéric J. de Sauvage, Christian W. Siebel, Erica Jackson
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-62507-9

Genetic and genomic analysis for cocoon yield traits in silkworm
Cited by: 11
Author(s): Shou-Min Fang, Qi Zhou, Qiuhan Yu, Ze Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-6247-3

Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Cited by: 13
Author(s): Vinicius Vilperte, Calin Rares Lucaciu, Heidi Halbwirth, Robert Boehm, Thomas Rattei, Thomas Debener
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcell.2020.00527

Transcriptome Characterization of Repressed Embryonic Myogenesis Due to Maternal Calorie Restriction
Cited by: 2
Author(s): Jun He, Ying He, Bing Yu, Xuelian Wang, Shuai Chen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0158711

Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis
Cited by: 14
Author(s): Joachim von Wulffen, RecogNice-Team, Oliver Sawodny, Ronny Feuer
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.713503

Establishment of Mouse Primed Stem Cells by Combination of Activin and LIF Signaling
Cited by: 2
Author(s): Mengyi Wei, Yanglin Chen, Chaoyue Zhao, Zheng Li, Baojiang Wu, Chen Chen, Xihe Li, Siqin Bao
Software Mentions: 1
Published: about 5 years ago

10.1111/jcmm.16381

Theragnostic chromosomal rearrangements in treatment‐naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound
Cited by: 0
Author(s): Stephen J. Murphy, Michael J. Levy, James B. Smadbeck, Giannoula Karagouga, Alexa McCune, Frances Harris, Julia Udell, Sarah H. Johnson, Sarah E. Kerr, John C. Cheville, Benjamin R. Kipp, George Vasmatzis, Ferga C. Gleeson
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms16010840

Identification of Retinopathy of Prematurity Related miRNAs in Hyperoxia-Induced Neonatal Rats by Deep Sequencing
Cited by: 12
Author(s): Ran Zhao, Lijuan Qian, Li Jiang
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41380-019-0493-2

Early-life stress impairs postnatal oligodendrogenesis and adult emotional behaviour through activity-dependent mechanisms
Cited by: 92
Author(s): Anne Teissier, Corentin Le Magueresse, Jimmy Olusakin, Belmira L. S. Andrade da Costa, Angela Michela De Stasi, A. Bacci, Yuka Imamura Kawasawa, Vidita A. Vaidya, Patricia Gaspar
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.9779

Chemotherapy-related cachexia is associated with mitochondrial depletion and the activation of ERK1/2 and p38 MAPKs
Cited by: 131
Author(s): Rafael Barreto, David L. Waning, Hongyu Gao, Yunlong Liu, Teresa A. Zimmers, Andrea Bonetto
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms16059152

Expression Profiling Reveals Genes Involved in the Regulation of Wool Follicle Bulb Regression and Regeneration in Sheep
Cited by: 19
Author(s): Guangbin Liu, Ruize Liu, Xiaohui Tang, Jianhua Cao, Zhao Song, Mei Yu
Software Mentions: 1
Published: over 11 years ago

10.3389/fcell.2019.00337

mTORC1-Rps15 Axis Contributes to the Mechanisms Underlying Global Translation Reduction During Senescence of Mouse Embryonic Fibroblasts
Cited by: 4
Author(s): Su Wu, Siyao Xu, Ruofei Li, Kecheng Li, Xiaoqin Zhong, Yingying Li, Zhifen Zhou, Yi Liu, Ran Feng, Jianfei Zheng, Zhou Songyang, Feng Liu
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms160613959

Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration
Cited by: 11
Author(s): Jun Cui, Jian Xu, Songhao Zhang, Kai Wang, Yanliang Jiang, Shahid Mahboob, Khalid A. Al‐Ghanim, Peng Xu
Software Mentions: 1
Published: over 11 years ago

10.1111/acel.12373

Circulating micro <scp>RNA</scp> signature of genotype‐by‐age interactions in the long‐lived <scp>A</scp> mes dwarf mouse
Cited by: 50
Author(s): Berta Victoria, Joseph M. Dhahbi, Yury O. Nunez Lopez, Lina Spinel, Hani Atamna, Stephen R. Spindler, Michał M. Masternak
Software Mentions: 1
Published: over 11 years ago

10.1111/jcmm.16760

The subtype‐specific molecular function of SPDEF in breast cancer and insights into prognostic significance
Cited by: 4
Author(s): Ting Ye, Jingyuan Li, June Feng, Jinglan Guo, Xue Wan, Dan Xie, Jinbo Liu
Software Mentions: 1
Published: over 5 years ago

10.3389/fcell.2021.704341

NAT10-Mediated N4-Acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation in vitro
Cited by: 11
Author(s): Yuting Xiang, Chuanchuan Zhou, Yanyan Zeng, Qi Guo, Jiana Huang, Taibao Wu, Jiawen Liu, Qiqi Liang, Haitao Zeng, Xiaoyan Liang
Software Mentions: 1
Published: about 5 years ago

10.1007/s00204-021-03092-2

New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids
Cited by: 17
Author(s): Daniela Rodrigues, Terezinha de Souza, Luke Coyle, Matteo Piazza, Bram Herpers, Sofia Ferreira, Mian Zhang, Johanna Vappiani, Daniel C. Sévin, Attila Gábor, Anthony M. Lynch, Seung‐Wook Chung, Julio Sáez-Rodríguez, Danyel Jennen, Jos Kleinjans, Theo M. de Kok
Software Mentions: 1
Published: over 5 years ago

10.3389/fcell.2021.727353

Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations
Cited by: 2
Author(s): Milda Narmontė, Povilas Gibas, Kristina Daniūnaitė, Juozas Gordevičius, Edita Kriukienė
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-2552-2

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)
Cited by: 43
Author(s): Ming Li, Zhaoxu Liang, Yuan Zeng, Yan Ji, Kai–Chao Wu, Jun Liang, Shikun He, Guanyu Wang, Zhanghong Mo, Feiquan Tan, Li Song, Wang LunWang
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.593677

The Cancer-Testis Long Non-coding RNA PCAT6 Facilitates the Malignant Phenotype of Ovarian Cancer by Sponging miR-143-3p
Cited by: 6
Author(s): Xiaofang Tan, Yang Shao, Yue Teng, Siyu Liu, Weijian Li, Lu Xue, Yuepeng Cao, Chongqi Sun, Jinhong Zhang, Jing Han, Xiaoli Wu, Hanzi Xu, Kaipeng Xie
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.16700

LncRNA PVT1 promotes the progression of ovarian cancer by activating TGF‐β pathway via miR‐148a‐3p/AGO1 axis
Cited by: 13
Author(s): Yuxian Wu, Wenqian Gu, Xiao Han, Zhendong Jin
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.8609

Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation
Cited by: 4
Author(s): Wenmin Qiu, Jingen Li, Wei Yi, Fan Feng, Jing Jiang, Mingying Liu, Xiaojiao Han, Chaoguang Tian, Shihong Zhang, Renying Zhuo
Software Mentions: 1
Published: over 6 years ago

10.1111/acel.13466

Altered sperm tsRNAs in aged male contribute to anxiety‐like behavior in offspring
Cited by: 14
Author(s): Yi Guo, Dandan Bai, Wenqiang Liu, Yingdong Liu, Yalin Zhang, Xiaochen Kou, Jiayu Chen, Hong Wang, Xiaoming Teng, Ji Zuo, Shaorong Gao
Software Mentions: 1
Published: about 5 years ago

10.1111/jcmm.16825

MicroRNA‐205‐5p targets E2F1 to promote autophagy and inhibit pulmonary fibrosis in silicosis through impairing SKP2‐mediated Beclin1 ubiquitination
Cited by: 7
Author(s): Qian Qin, Qinghua Ma, Bin Wang, Qingqiang Qian, Changsong Zhao, Feng Fang, Xiaona Dong
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-2680-8

Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level
Cited by: 60
Author(s): Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Grégory Jubelin, Christophe Chambon, Carl J. Yeoman, Margret E. Berg Miller, Christopher J. Fields, Eric C. Martens, Nicolas Terrapon, Bernard Henrissat, Bryan A. White, Pascale Mosoni
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2020.579708

Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period
Cited by: 6
Author(s): Xiaoyun Wu, Xiaofang Zhou, Lin Xiong, Jie Pei, Xixi Yao, Chunnian Liang, Pengjia Bao, Min Chen, Xian Guo, Ping Yan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40168-020-00812-1

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.
Cited by: 1
Author(s): Nathan D. Olson, M. S. Binoj Kumar, Shan Li, Domenick J. Braccia, Stephanie Hao, Winston Timp, Marc Salit, O. Colin Stine, Héctor Corrada Bravo
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms17010012

Identification of the Avian Pasteurella multocida phoP Gene and Evaluation of the Effects of phoP Deletion on Virulence and Immunogenicity
Cited by: 16
Author(s): Kangpeng Xiao, Qing Liu, Xueyan Liu, Yunlong Hu, Xinxin Zhao, Qingke Kong
Software Mentions: 1
Published: almost 11 years ago

10.1186/s40168-020-00888-9

Gut microbiome composition differences among breeds impact feed efficiency in swine
Cited by: 91
Author(s): Matteo Bergamaschi, Francesco Tiezzi, Jeremy Howard, Yongjun Huang, Kent Gray, Constantino Schillebeeckx, Nathan P. McNulty, Christian Maltecca
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.10668

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis
Cited by: 4
Author(s): Juan Wang, Xiongfei Wu, Yue Tu, Jianzhong Dang, Zhitao Cai, Wenjing Liao, Weili Quan, Yaxun Wei
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07402-x

Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum
Cited by: 6
Author(s): Akeem Owolabi Taiwo, Lincoln A. Harper, Mark Derbyshire
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots
Cited by: 1
Author(s): Wang Wei, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Ye, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Software Mentions: 1
Published: over 7 years ago

10.1099/mic.0.000579

Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390
Cited by: 15
Author(s): Maria Guillermina Casabona, Holger Kneuper, Daniela Alferes De Lima, Catriona P. Harkins, Martin Zoltner, Erik Hjerde, Matthew T. G. Holden, Tracy Palmer
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-4053-3

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)
Cited by: 26
Author(s): Ming Li, Zhaoxu Liang, Shikun He, Yuan Zeng, Yan Ji, Fang Wei, Kai–Chao Wu, Guanyu Wang, Ning Xia, Wang LunWang, Song Li, Huachun Tan, Feiquan Tan
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-018-4437-z

Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass
Cited by: 13
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-13-322

Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species
Cited by: 6
Author(s): Claudia Voelckel, Nicole Gruenheit, Patrick J. Biggs, Oliver Deusch, Peter J. Lockhart
Software Mentions: 1
Published: almost 15 years ago

10.3389/fcimb.2017.00045

Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Cited by: 30
Author(s): Xiaoting Hua, Lilin Liu, Youhong Fang, Qiucheng Shi, Xi Li, Qiong Chen, Kezhang Shi, Yan Jiang, Hua Zhou, Yunsong Yu
Software Mentions: 1
Published: over 9 years ago

10.15252/msb.20145470

An organ boundary‐enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
Cited by: 92
Author(s): Caihuan Tian, Xiaoni Zhang, Jun He, Haopeng Yu, Ying Wang, Bihai Shi, Yingying Han, Guoxun Wang, Xiaoming Feng, Cui Zhang, Jin Wang, Jiyan Qi, Rong Yu, Yuling Jiao
Software Mentions: 1
Published: about 12 years ago

10.7717/peerj.8776

Physiological parameters and differential expression analysis of N-phenyl-N′-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis
Cited by: 4
Author(s): Lejun Ouyang, Zechen Wang, Limei Li, Baoling Chen
Software Mentions: 1
Published: over 6 years ago

10.3390/jcm8070963

Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder
Cited by: 15
Author(s): Min Young Lee, David Baxter, Kelsey Scherler, Taek‐Kyun Kim, Xiaogang Wu, Duna Abu‐Amara, Janine D. Flory, Rachel Yehuda, Charles R. Marmar, Marti Jett, Inyoul Lee, Kai Wang, Leroy Hood
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-4646-5

Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle
Cited by: 22
Author(s): Jason Ioannidis, F.X. Donadeu
Software Mentions: 1
Published: over 8 years ago

10.3390/jcm8091440

Surface Pre-Reacted Glass Filler Contributes to Tertiary Dentin Formation through a Mechanism Different Than That of Hydraulic Calcium-Silicate Cement
Cited by: 13
Author(s): Masakazu Okamoto, Muslim Ali, Shungo Komichi, Masakatsu Watanabe, Haozhang Huang, Yuki Ito, Jiro Miura, Yujiro Hirose, Manabu Mizuhira, Yusuke Takahashi, Daisuke Okuzaki, Shigetada Kawabata, Satoshi Imazato, Mikako Hayashi
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms17030283

Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava
Cited by: 73
Author(s): Lili Fu, Zehong Ding, Bingying Han, Wei Hu, Yajun Li, Jiaming Zhang
Software Mentions: 1
Published: over 10 years ago

10.3389/fcimb.2021.662563

Transcriptome Signatures Predict Phenotypic Variations of Candida auris
Cited by: 11
Author(s): Sabrina Jenull, Michael Tscherner, Nataliia D. Kashko, Raju Shivarathri, Anton Stoiber, Manju Chauhan, Andriy Petryshyn, Neeraj Chauhan, Karl Kuchler
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-3756-9

Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii
Cited by: 26
Author(s): Fengming Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qin Xu, Dan Huang, Chenkai Zhao
Software Mentions: 1
Published: over 9 years ago

10.1002/mbo3.899

Shared and unique microbes between Small hive beetles (Aethina tumida) and their honey bee hosts
Cited by: 9
Author(s): Qiang Huang, Dawn Lopez, Jay D. Evans
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.10216

Desmoglein 2 promotes vasculogenic mimicry in melanoma and is associated with poor clinical outcome
Cited by: 36
Author(s): Lih Y. Tan, Chris Mintoff, M. Zahied Johan, Brenton Ebert, Clare G. Fedele, You Fang Zhang, Pacman Szeto, Karen E. Sheppard, Grant A. McArthur, Erwin Foster‐Smith, Andrew Ruszkiewicz, Michael P. Brown, Claudine S. Bonder, Mark Shackleton, Lisa M. Ebert
Software Mentions: 1
Published: over 10 years ago

10.3389/fcimb.2020.575630

Comparative Transcriptomics of Shiga Toxin-Producing and Commensal Escherichia coli and Cytokine Responses in Colonic Epithelial Cell Culture Infections
Cited by: 2
Author(s): Lisa M. Harrison, David W. Lacher, Mark K. Mammel, Susan R. Leonard
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms17050689

Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC2 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol
Cited by: 10
Author(s): Qun Li, Fanglan Ge, Yunya Tan, Guangxiang Zhang, Wei Li
Software Mentions: 1
Published: over 10 years ago

10.1186/s12863-021-00973-4

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes
Cited by: 9
Author(s): Lin Yuan, Kun Pan, Yonghui Li, Bo Yi, Bingmiao Gao
Software Mentions: 1
Published: over 5 years ago

10.3389/fcimb.2020.00097

RNA-Seq Revealed a Circular RNA-microRNA-mRNA Regulatory Network in Hantaan Virus Infection
Cited by: 64
Author(s): Shuang Lu, Ni Zhu, Weiwei Guo, Xin Wang, Kaiji Li, Jie Yan, Cuiping Jiang, Han Shi-yu, Hanmin Xiang, Xiaohan Wu, Yuanyuan Liu, Hairong Xiong, Liangjun Chen, Zuojiong Gong, Fan Luo, Wei Hou
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2017.00004

Repurposing Approach Identifies Auranofin with Broad Spectrum Antifungal Activity That Targets Mia40-Erv1 Pathway
Cited by: 64
Author(s): Shankar Thangamani, Matthew C. Maland, Haroon Mohammad, Pete E. Pascuzzi, Larisa Avramova, Carla M. Koehler, Tony R. Hazbun, Mohamed N. Seleem
Software Mentions: 1
Published: almost 10 years ago

10.3389/fcimb.2020.00066

Isoforms of Cathepsin B1 in Neurotropic Schistosomula of Trichobilharzia regenti Differ in Substrate Preferences and a Highly Expressed Catalytically Inactive Paralog Binds Cystatin
Cited by: 3
Author(s): Hana Dvořáková, Roman Leontovyč, Tomáš Macháček, Anthony J. O’Donoghue, Ondřej Šedo, Zbyněk Zdráhal, Charles S. Craik, Conor R. Caffrey, Petr Horák, Libor Mikeš
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2018.00231

The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi
Cited by: 20
Author(s): Dan Drecktrah, Laura S. Hall, Philipp Rescheneder, Meghan Lybecker, D. Scott Samuels
Software Mentions: 1
Published: over 8 years ago

10.3390/jcm10102110

Plasma Exosomal miRNA Levels after Radiotherapy Are Associated with Early Progression and Metastasis of Cervical Cancer: A Pilot Study
Cited by: 5
Author(s): Oyeon Cho, Do Wan Kim, J.Y. Cheong
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2435-6

Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis
Cited by: 27
Author(s): Lisa Zondag, Kim Rutherford, Neil J. Gemmell, Megan J. Wilson
Software Mentions: 1
Published: over 10 years ago

10.3390/jcm10112227

miRNAs and Genes Involved in the Interplay between Ocular Hypertension and Primary Open-Angle Glaucoma. Oxidative Stress, Inflammation, and Apoptosis Networks
Cited by: 16
Author(s): J. Raga-Cervera, José Miguel Bolarín, José María Millán, Manuel García-Medina, Laia Pedrola, Javier Abellán-Abenza, Mar Valero-Velló, Silvia M. Sanz-González, José Enrique O’Connor, David Galarreta, Elena Bendala-Tufanisco, Aloma Mayordomo-Febrer, María Dolores Pinazo-Durán, Vicente Zanón‐Moreno
Software Mentions: 1
Published: over 5 years ago

10.1186/s12863-020-00893-9

A novel mouse model expressing human forms for complement receptors CR1 and CR2
Cited by: 6
Author(s): Harriet M. Jackson, Kate E. Foley, Rita O’Rourke, Timothy M. Stearns, Dina Fathalla, B. Paul Morgan, Gareth R. Howell
Software Mentions: 1
Published: about 6 years ago

10.3389/fncel.2020.566148

Pioglitazone Ameliorates Gentamicin Ototoxicity by Affecting the TLR and STAT Pathways in the Early Postnatal Organ of Corti
Cited by: 3
Author(s): Marijana Sekulic-Jablanovic, Matthew B. Wright, Vesna Petkovic, Daniel Bodmer
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-6156-5

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection
Cited by: 10
Author(s): Xuelian Ma, Xiaomin Zhao, Kaili Wang, Xiaoyi Tang, Jianxiong Guo, Mi Mi, Yanping Qi, Lingling Chang, Yong Huang, Dewen Tong
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8379

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis
Cited by: 12
Author(s): Xuhui Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jianbin Guo
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-14-19

Transcriptome analysis of rice root heterosis by RNA-Seq
Cited by: 118
Author(s): Rongrong Zhai, Feng Yue, Huimin Wang, Xiaodeng Zhan, Xihong Shen, Weiming Wu, Yingxin Zhang, Daibo Chen, Gaoxing Dai, Yang Zhou, Shifeng Cheng
Software Mentions: 1
Published: almost 14 years ago

10.18632/oncotarget.10333

Dual tumor suppressing and promoting function of Notch1 signaling in human prostate cancer
Cited by: 24
Author(s): Karine Lefort, Paola Ostano, Maurizia Mello-Grand, Valérie Calpini, Maria Scatolini, Antonella Farsetti, G. Paolo Dotto, Giovanna Chiorino
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0186382

Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions
Cited by: 14
Author(s): Boon Huat Cheah, Sudhir Jadhao, Madavan Vasudevan, R Wickneswari V Ratnam, Kalaivani K. Nadarajah
Software Mentions: 1
Published: about 9 years ago

10.3389/fendo.2021.743155

Identification of mRNA Prognostic Markers for TGCT by Integration of Co-Expression and CeRNA Network
Cited by: 3
Author(s): Fang Zhu, Zhizhong Liu, Qianyin Zhou, Jingyu Fan, Dai Zhou, Xing Liu, Hao Bo, Le Tang, Liqing Fan
Software Mentions: 1
Published: about 5 years ago

10.3389/fendo.2021.650625

Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells
Cited by: 1
Author(s): Rajitha Indukuri, Linnea Hases, Amena Archer, Cecilia Williams
Software Mentions: 1
Published: over 5 years ago

10.3389/fendo.2019.00553

Identification of a New Theca/Interstitial Cell-Specific Gene and Its Biological Role in Growth of Mouse Ovarian Follicles at the Gonadotropin-Independent Stage
Cited by: 6
Author(s): Masato Aoyama, Akira Shiraishi, Shin Matsubara, Kazuyuki Horie, Tomohiro Osugi, Toru Kawada, Keiko Yasuda, Honoo Satake
Software Mentions: 1
Published: about 7 years ago

10.3389/fendo.2018.00574

Leptin Selectively Regulates Nutrients Metabolism in Nile Tilapia Fed on High Carbohydrate or High Fat Diet
Cited by: 33
Author(s): Caizhi Liu, Anbang He, Lei Ning, Yuan Luo, Dongliang Li, Meiling Zhang, Liqiao Chen, Zhen‐Yu Du
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-017-3596-7

Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress
Cited by: 88
Author(s): Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, R. S. Tomar, Ashish Chaturvedi, Kishor Gaikwad, Madan Pal
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms17050690

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction
Cited by: 19
Author(s): Hyungtaek Jung, Byung-Ha Yoon, Woo Jin Kim, Dong-Wook Kim, David A. Hurwood, Russell E. Lyons, Krishna R. Salin, Heui‐Soo Kim, Ilseon Baek, Vincent Chand, Peter B. Mather
Software Mentions: 1
Published: over 10 years ago

10.3389/fendo.2016.00165

Muscle Contraction Induces Acute Hydroxymethylation of the Exercise-Responsive Gene Nr4a3
Cited by: 28
Author(s): Pattarawan Pattamaprapanont, Christian Garde, Odile Fabre, Romain Barrès
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2156-15-S2-S6

Male-specific phosphorylated SR proteins in adult flies of the Mediterranean Fruitfly Ceratitis capitata
Cited by: 4
Author(s): Giuseppe Saccone, Christos Louis, Hongyou Zhang, Valeria Petrella, Michele Di Natale, Maria Perri, Marco Salvemini
Software Mentions: 1
Published: almost 12 years ago

10.1038/srep09836

Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to Changes in Water Salinity
Cited by: 21
Author(s): Jie Gu, Jing Woei Li, William Ka Fai Tse, Ting‐Fung Chan, Keng Po Lai, Chris K C Wong
Software Mentions: 1
Published: over 11 years ago

10.1186/s12863-016-0439-5

C14orf132 gene is possibly related to extremely low birth weight
Cited by: 3
Author(s): Airi Tiirats, Triin Viltrop, Margit Nõukas, Ene Reimann, Andres Salumets, Sulev Kõks
Software Mentions: 1
Published: about 10 years ago

10.1186/s12863-020-00862-2

RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers
Cited by: 3
Author(s): Hellenn Cardoso Oliveira, A. M. G. Ibelli, Simone Eliza Facioni Guimarães, Maurício Egídio Cantão, J. de O. Peixoto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-3585-x

RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development
Cited by: 70
Author(s): Audrey M. V. Ah‐Fong, Kyoung Su Kim, Howard S. Judelson
Software Mentions: 1
Published: over 9 years ago

10.3389/fendo.2021.687586

Metabolic Syndrome Is Associated With Altered mRNA and miRNA Content in Human Circulating Extracellular Vesicles
Cited by: 3
Author(s): Yongxin Li, Yijun Meng, Xiangyang Zhu, André J. van Wijnen, Alfonso Eirin, Lilach O. Lerman
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-00481-5

Transcriptomic profile of tobacco in response to Phytophthora nicotianae infection
Cited by: 21
Author(s): Jiankang Yang, Zhijun Tong, Dunhuang Fang, Xuejun Chen, Ke‐Qin Zhang, Bingguang Xiao
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-00914-1

In vitro biomimetic platforms featuring a perfusion system and 3D spheroid culture promote the construction of tissue-engineered corneal endothelial layers
Cited by: 7
Author(s): Shanyi Li, Yuting Han, Hao Lei, Yu‐Rong Zeng, Zekai Cui, Qiaolang Zeng, Deliang Zhu, Ruiling Lian, Jun Zhang, Zhe Chen, Jiansu Chen
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2020.00881

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height
Cited by: 4
Author(s): Xiaolin Liu, Wencai Yang, Jing Wang, Ming Yang, Kai Wei, Xiaoyan Liu, Zhengkun Qiu, Tong van Giang, Xiaoxuan Wang, Yanmei Guo, Junming Li, Lei Liu, Jinshuai Shu, Yan Du, Zejun Huang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-00893-3

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C
Cited by: 100
Author(s): Ruth Schmidt, Victor de Jager, Daniela Zühlke, Christian Wolff, Jörg Bernhardt, Katarina Cankar, Jules Beekwilder, Wilfred F. J. van IJcken, Frank Sleutels, Wietse de Boer, Katharina Riedel, Paolina Garbeva
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-6370-1

Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes
Cited by: 14
Author(s): Ruihong Wang, Pengda Ma, Chen Li, Lingang Xiao, Zongsuo Liang, Juane Dong
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12863-018-0700-1

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium
Cited by: 8
Author(s): Lijun Wu, Tao Liu, Yongsheng Xu, Wenjie Chen, Baolong Liu, Lianquan Zhang, Dengcai Liu, Huaigang Zhang, Bo Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1002/mbo3.836

Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris
Cited by: 14
Author(s): Ahmad Suparmin, Tatsuya Kato, Hiroyuki Takemoto, Enoch Y. Park
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-2082-3

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer
Cited by: 51
Author(s): Manuel Saiselet, David Gacquer, Alex Spinette, Ligia Craciun, Myriam Decaussin‐Petrucci, Guy Andry, Vincent Detours, Carine Maenhaut
Software Mentions: 1
Published: about 11 years ago

10.3389/fgene.2020.00534

Novel Insights Into Triple-Negative Breast Cancer Prognosis by Comprehensive Characterization of Aberrant Alternative Splicing
Cited by: 8
Author(s): Shasha Gong, Zhijian Song, David Ethan Spezia-Lindner, Feilong Meng, Tingting Ruan, Guangzhi Ying, Changhong Lai, Qianqian Wu, Yong Liang
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2020.00494

Quantitative Estimation of Oxidative Stress in Cancer Tissue Cells Through Gene Expression Data Analyses
Cited by: 6
Author(s): Liyang Liu, Haining Cui, Ying Xu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-5128-5

Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-κB pathway in porcine intestinal epithelial cell line
Cited by: 37
Author(s): Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang, Dewen Tong
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-14-682

Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake
Cited by: 31
Author(s): Jian Xu, Qiang Li, Liming Xu, Shaolin Wang, Yanliang Jiang, Zixia Zhao, Yan Zhang, Jiong-Tang Li, Chuanju Dong, Peng Xu, Xin Sun
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-015-1453-0

Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.)
Cited by: 26
Author(s): Zaijun Yang, Zhengsong Peng, Shuhong Wei, Mingli Liao, Yan Yu, Zeyan Jang
Software Mentions: 1
Published: over 11 years ago

10.3389/fgene.2019.00929

Transcriptome Analysis Reveals That Alfalfa Promotes Rumen Development Through Enhanced Metabolic Processes and Calcium Transduction in Hu Lambs
Cited by: 9
Author(s): Bin Yang, Hongwei Chen, Jiawen Cao, Bo He, Shanshan Wang, Yang Luo, Jiakun Wang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-020-6539-7

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings
Cited by: 11
Author(s): Feng‐Yao Wu, Fengying Lu, Xin Fan, Chao Jin, Chuanmin Liu, Qunxing Pan, Huawei Sun, Xiaofei Zhang
Software Mentions: 1
Published: over 6 years ago

10.1002/aps3.1206

Transcriptome analysis of maca (Lepidium meyenii ) root at different developmental stages
Cited by: 3
Author(s): Ruiguang Shang, Pu Yang, Bingyi Wang, Zhihui Zhao
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-07214-5

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus
Cited by: 10
Author(s): Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin, Bowen Chen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2018.01372

CD19+CD24hiCD38hi B Cells Are Expanded in Juvenile Dermatomyositis and Exhibit a Pro-Inflammatory Phenotype After Activation Through Toll-Like Receptor 7 and Interferon-α
Cited by: 60
Author(s): Christopher Piper, Meredyth G Ll Wilkinson, Claire T. Deakin, G. Otto, S Dowle, Chantal L. Duurland, Stuart Adams, Emiliano Marasco, Elizabeth C. Rosser, Anna Radziszewska, Rita Carsetti, Yiannis Ioannou, Philip L. Beales, Daniel Kelberman, David Isenberg, Claudia Mauri, Kiran Nistala, Lucy R. Wedderburn
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0231206

Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113
Cited by: 30
Author(s): Mukesh Kumar Malviya, Changning Li, Manoj Kumar Solanki, Rajesh Kumar Singh, Reemon Htun, Pratiksha Singh, Krishan K. Verma, Li‐Tao Yang, Yang–Rui Li
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms17101612

Elevated Expression of Calpain-4 Predicts Poor Prognosis in Patients with Gastric Cancer after Gastrectomy
Cited by: 5
Author(s): Peike Peng, Lingqiang Min, Shushu Song, Junjie Zhao, Lili Li, Caiting Yang, Miaomiao Shao, Mingming Zhang, Hao Wu, Jie Zhang, Can Li, Xuefei Wang, Hongshan Wang, Jing Qin, Yuanyuan Ruan, Jianxin Gu
Software Mentions: 1
Published: about 10 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568