bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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/s12866-017-1066-7

Transcriptome profiling analysis reveals metabolic changes across various growth phases in Bacillus pumilus BA06
Cited by: 19
Author(s): Han Liang, Huanhuan Shao, Yongcheng Liu, Gang Liu, Chunming Xie, Xiaoyu Cheng, Haiyan Wang, Xuemei Tan, Feng Hong
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-24509-6

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
Cited by: 69
Author(s): Sugata Roy, Sebastian Schmeier, Bogumił Kaczkowski, Peter Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Reto Guler, Vladimir B. Bajic, Frank Brombacher, Harukazu Suzuki
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25611-5

Ca2+ imaging and gene expression profiling of Lonicera Confusa in response to calcium-rich environment
Cited by: 10
Author(s): Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25103-6

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis
Cited by: 35
Author(s): Lingbin Liu, Qihai Xiao, Elizabeth R. Gilbert, Zhifu Cui, Xiaoling Zhao, Yan Wang, Huadong Yin, Diyan Li, Haihan Zhang, Qing Zhu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25516-3

Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Cited by: 18
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24999-4

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant
Cited by: 18
Author(s): Qianqian Shi, Zhenchuan Mao, Xi Zhang, Xiaoping Zhang, Yunsheng Wang, Jian Ling, Runmao Lin, Denghui Li, Xincong Kang, Wenxian Sun, Bingyan Xie
Software Mentions: 1
Published: over 8 years ago

10.3390/biomedicines9030280

Role of RGMc as a Neogenin Ligand in Follicular Development in the Ovary
Cited by: 0
Author(s): Yu Jin Kim, Young Joon Park, Yeo Reum Park, Young Sang Kim, Hye Ran Lee, Sang Jin Lee, Myung‐Joo Kim, KyuBum Kwack, Jung Jae Ko, Jae Ho Lee
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines9040388

Pharmacological Inhibition of WIP1 Sensitizes Acute Myeloid Leukemia Cells to the MDM2 Inhibitor Nutlin-3a
Cited by: 6
Author(s): Maria Chiara Fontana, Jacopo Nanni, Andrea Ghelli Luserna di Rorà, Elisabetta Petracci, Antonella Padella, Martina Ghetti, Anna Ferrari, Giovanni Marconi, Simona Soverini, Ilaria Iacobucci, Cristina Papayannidis, Antonio Curti, Ernesta Audisio, Maria Benedetta Giannini, Michela Rondoni, Francesco Lanza, Michèle Cavo, Giovanni Martinelli, Giorgia Simonetti
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-26738-1

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells
Cited by: 18
Author(s): Agnes P. Chan, Yongwook Choi, Lauren Brinkac, R. Krishnakumar, Jessica DePew, Maria Kim, Mary Hinkle, Emil Lesho, Derrick E. Fouts
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2180-14-47

There is a specific response to pH by isolates of Haemophilus influenzae and this has a direct influence on biofilm formation
Cited by: 14
Author(s): Nadiah Ishak, Alexandra Tikhomirova, Stephen J. Bent, Garth D. Ehrlich, Fang Hu, Stephen P. Kidd
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms22158197

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)
Cited by: 8
Author(s): Kinga Kęska, Michał Wojciech Szcześniak, Adela Adamus, Małgorzata Czernicka
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-27628-2

Molecular chaperoning helps safeguarding mitochondrial integrity and motor functions in the Sahara silver ant Cataglyphis bombycina
Cited by: 12
Author(s): Quentin Willot, Patrick Mardulyn, Matthieu Defrance, Cyril Gueydan, Serge Aron
Software Mentions: 1
Published: about 8 years ago

10.1155/2017/4352450

The miRNA Expression Profile in Acute Myocardial Infarct Using Sheep Model with Left Ventricular Assist Device Unloading
Cited by: 4
Author(s): Xiaoqian Yan, Yu Gan, Haibo Chen, Guang-Mao Liu, Shengshou Hu, Jianye Zhou
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-27527-6

Presymptomatic change in microRNAs modulates Tau pathology
Cited by: 6
Author(s): Salil Sharma, Inès Khadimallah, Adam Williamson Corya, Yousuf Ali, Xi Rao, Yunlong Liu, Hui Lü
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/7871918

De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser
Cited by: 8
Author(s): Shugen Wei, Lingyun Wan, Lili He, Ying Wei, Hairong Long, Xiaowen Ji, Jine Fu, Limei Pan
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-28297-x

Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo
Cited by: 31
Author(s): Chang Li, Veronika Rezov, Emmi I. Joensuu, Ville Vartiainen, Mikko Rönty, Miao Yin, Marjukka Myllärniemi, Katri Koli
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-28916-7

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets
Cited by: 41
Author(s): Pablo Ivan Pereira Ramos, Darío Augusto Fernández Do Porto, Esteban Lanzarotti, Ezequiel Sosa, Germán Burguener, Agustín Pardo, Cecília C. Klein, Marie‐France Sagot, Ana Tereza Ribeiro de Vasconcelos, Ana Cristina Gales, Marcelo A. Martí, Adrián Turjanski, Marisa Fabiana Nicolás
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-29662-6

An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide
Cited by: 22
Author(s): Tiago Simões, Sara C. Novais, Tiago Natal-da-Luz, Bart Devreese, Tjalf de Boer, Dick Roelofs, José Paulo Sousa, Nico M. van Straalen, Marco F.L. Lemos
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/4830847

The ceRNA Network Has Potential Prognostic Value in Clear Cell Renal Cell Carcinoma: A Study Based on TCGA Database
Cited by: 3
Author(s): Haosheng Liu, Zhaowen Zhu, Jianxiong Fang, Tianqi Liu, Zhenhui Zhang, Chao Zhao, Xiao‐Yong Pu, Jiumin Liu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-30147-9

Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau
Cited by: 8
Author(s): Yanyan Guo, Yongqiang Zhang, Guoqiang Zhang, Laiqiang Huang, Zhong‐Jian Liu
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-30262-7

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng
Cited by: 35
Author(s): Kyo Bin Kang, Murukarthick Jayakodi, Yun Sun Lee, Van Binh Nguyen, Hyun-Seung Park, Hyun Jo Koo, Ik‐Young Choi, Dae Hyun Kim, You Jin Chung, Byeol Ryu, Dong Hoon Lee, Sang Hyun Sung, Tae-Jin Yang
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/9502560

The YTH Domain Family of N6-Methyladenosine “Readers” in the Diagnosis and Prognosis of Colonic Adenocarcinoma
Cited by: 17
Author(s): Dian Xu, Jun Shao, Huan Song, Jianming Wang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-31592-2

Expression profiling of ubiquitin-related genes in LKB1 mutant lung adenocarcinoma
Cited by: 3
Author(s): Guanghui Wang, Fenglong Bie, Xiao Qu, Xudong Yang, Shaorui Liu, Yu Wang, Can Huang, Kai Wang, Jiajun Du
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-31719-5

Changes in circRNA expression profiles related to the antagonistic effects of Escherichia coli F17 in lamb spleens
Cited by: 9
Author(s): Chengyan Jin, Jianjun Bao, Yue Wang, Wei-Hao Chen, Shuangxia Zou, Tianyi Wu, Lihong Wang, Xiaoyang Lv, Wen Gao, Buzhong Wang, Guoqiang Zhu, Guojun Dai, Dongfang Shi, Wei Sun
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-33100-y

Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota
Cited by: 49
Author(s): Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Fabio Marongiu, Mauro Serra, Daniela Pagnozzi, Ezio Laconi, Sergio Uzzau
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-33597-3

Comparative transcriptomic analysis reveals common molecular factors responsive to heat and drought stress in Agrostis stolonifera
Cited by: 30
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12920-020-0727-9

Mitochondrial tRNA methylation in Alzheimer’s disease and progressive supranuclear palsy
Cited by: 9
Author(s): Talisa Silzer, Gita A. Pathak, Nicole Phillips
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/5597135

A New Lectin from Auricularia auricula Inhibited the Proliferation of Lung Cancer Cells and Improved Pulmonary Flora
Cited by: 2
Author(s): Zhendong Liu, Liang Li, Bei Xue, Dandan Zhao, Yanlong Zhang, Xiufeng Yan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-33899-6

Small non-coding RNA landscape of extracellular vesicles from human stem cells
Cited by: 50
Author(s): Sippy Kaur, Ahmed G. Abu-Shahba, Riku O. Paananen, Heidi Hongisto, Hanna Hiidenmaa, Heli Skottman, Riitta Seppänen‐Kaijansinkko, Bettina Mannerström
Software Mentions: 1
Published: almost 8 years ago

10.1155/2021/8875971

High FAM189B Expression and Its Prognostic Value in Patients with Gastric Cancer
Cited by: 3
Author(s): Changliang Wu, Quan-Xiao Tan, Dan Liŭ, Jun-E Jiang, Ting Lu, Zu-Mei Huang, Yingjie Su
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-34256-3

Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling
Cited by: 13
Author(s): Riccardo Lorrai, Francesco Gandolfi, Alessandra Boccaccini, Veronica Ruta, Marco Possenti, Anna Tramontano, Paolo Costantino, Rosalba Lepore, Paola Vittorioso
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-34333-7

Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species
Cited by: 7
Author(s): Hui Wang, Hanbo Zhao, Xiaobin Huang, Keping Sun, Feng Jiang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12866-016-0792-6

Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions
Cited by: 22
Author(s): Valeria R. Parreira, Kay Russell, Spiridoula Athanasiadou, John F. Prescott
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-34575-5

Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis
Cited by: 38
Author(s): Ikuko Yuyama, Masakazu Ishikawa, Masahiro Nozawa, Masa‐aki Yoshida, Kazuho Ikeo
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-35531-z

The presence of extracellular microRNAs in the media of cultured Drosophila cells
Cited by: 14
Author(s): Stijn Van den Brande, M. J. M. Gijbels, Niels Wynant, Dulce Santos, Lina Mingels, Yannick Gansemans, Filip Van Nieuwerburgh, Jozef Vanden Broeck
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-36376-2

Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii)
Cited by: 20
Author(s): Nan Jiang, Yuding Fan, Yong Zhou, Weiling Wang, Jie Ma, Lingbing Zeng
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37177-3

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome
Cited by: 15
Author(s): Heidi H. Pak, Nicole E. Cummings, Cara L Green, Jacqueline A. Brinkman, Deyang Yu, Jay L. Tomasiewicz, Shany E. Yang, Colin Boyle, Elizabeth N. Konon, Irene M. Ong, Dudley W. Lamming
Software Mentions: 1
Published: over 7 years ago

10.1155/2017/2503847

Fish Oil Feeding Modulates the Expression of Hepatic MicroRNAs in a Western-Style Diet-Induced Nonalcoholic Fatty Liver Disease Rat Model
Cited by: 11
Author(s): Hualin Wang, Yang Shao, Fahu Yuan, Na Li, Hongyu Zhang, Chaodong Wu, Zhiguo Liu
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms22189868

Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice
Cited by: 2
Author(s): Peng Hu, Yi Wen, Yueying Wang, Hao Wu, Junge Wang, Kaixiong Wu, Bingze Chai, Zhu LiXin, Guangheng Zhang, Zhenyu Gao, Deyong Ren, Lu Zhu, Longbiao Guo, Dali Zeng, Jing Xu, Song Yan, Qian Qian, Yuchun Rao, Jiang Hu
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-36726-0

Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues
Cited by: 17
Author(s): Songqian Huang, Yūki Ichikawa, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-35891-6

De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms
Cited by: 34
Author(s): Muhammad Sarwar, Zarnab Ahmad, Bushra Rashid, Sahar Hassan, Per L. Gregersen, Maria De la O. Leyva, István Nagy, Torben Asp, Tayyab Husnain
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37422-9

Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa
Cited by: 51
Author(s): Won Ju Hwang, Sang Sun Yoon
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22189668

Ginsenoside Prolongs the Lifespan of C. elegans via Lipid Metabolism and Activating the Stress Response Signaling Pathway
Cited by: 16
Author(s): Xiaoxuan Yu, Hui Li, Dongfa Lin, Weizhuo Guo, Zhihao Xu, Liping Wang, Shuwen Guan
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-37763-5

Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy
Cited by: 2
Author(s): Ryan Sprissler, Robert W. Bina, Willard S. Kasoff, Marlys H. Witte, Michael Bernas, C. Walter, David M. Labiner, Branden Lau, Michael F. Hammer, Martin E. Weinand
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37609-0

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone
Cited by: 20
Author(s): Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Jennifer Tickner, Nathan J. Pavlos, Frank Dudbridge, Jiake Xu, John P. Walsh, Scott G. Wilson
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/7340312

Pediococcus acidilactici P25 Protected Caenorhabditis elegans against Enterotoxigenic Escherichia coli K88 Infection and Transcriptomic Analysis of Its Potential Mechanisms
Cited by: 9
Author(s): Keqin Tan, Dun Deng, Xianyong Ma, Yiyan Cui, Zhonghuan Tian
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-37755-5

Reference assembly and gene expression analysis of Apostichopus japonicus larval development
Cited by: 9
Author(s): Alexey V. Boyko, Alexander S. Girich, М. Г. Елисейкина, С. И. Масленников, Igor Yu. Dolmatov
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-38368-8

Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Cited by: 31
Author(s): Ki Wook Kim, Jessica L. Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A. Bull, Fabio Luciani, Marc R. Wilkins, Jacki Catteau, W. Ian Lipkin, William D. Rawlinson, Thomas Briese, Maria E. Craig
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-38628-1

Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Cited by: 38
Author(s): Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/9426204

Effects of Cardiac Sympathetic Neurodegeneration and PPARγ Activation on Rhesus Macaque Whole Blood miRNA and mRNA Expression Profiles
Cited by: 1
Author(s): Jeanette M. Metzger, Mary S. Lopez, Jenna Kropp Schmidt, Megan E. Murphy, Raghu Vemuganti, Marina E. Emborg
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-39273-4

A RNA sequencing-based six-gene signature for survival prediction in patients with glioblastoma
Cited by: 41
Author(s): Shuguang Zuo, Xinhong Zhang, Liping Wang
Software Mentions: 1
Published: over 7 years ago

10.1155/2019/6763596

Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer
Cited by: 8
Author(s): Anna Pačínková, Vlad Popovici
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39100-w

Early responses given distinct tactics to infection of Peronophythora litchii in susceptible and resistant litchi cultivar
Cited by: 10
Author(s): Jun Sun, Liangjing Cao, L Huanling, Wenbin Guo, Shujun Wang, Fang Li, Xuefeng Zou, Jiabao Wang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12920-016-0212-7

A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer
Cited by: 35
Author(s): Hsiao-Rong Chen, David H. Sherr, Zhenjun Hu, Charles DeLisi
Software Mentions: 1
Published: about 10 years ago

10.1155/2020/3801748

Four Autophagy-Related lncRNAs Predict the Prognosis of HCC through Coexpression and ceRNA Mechanism
Cited by: 23
Author(s): Hao Wu, Tiantian Liu, Jianni Qi, Chengyong Qin, Qing Zhu
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-39852-5

Suppression of glioblastoma by a drug cocktail reprogramming tumor cells into neuronal like cells
Cited by: 19
Author(s): Lei Gao, Shichao Huang, Hong Zhang, Wei Hua, Shunmei Xin, Lin Cheng, Wuqiang Guan, Yongchun Yu, Ying Mao, Gang Pei
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-40227-z

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development
Cited by: 2
Author(s): Vikram S. Shivakumar, Gabriel Johnson, Elizabeth A. Zimmer
Software Mentions: 1
Published: over 7 years ago

10.1155/2019/7505260

RNA-Sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Prefrontal Cortex of Mice Following Repeated Social Defeat Stress
Cited by: 4
Author(s): Xian Wang, Shaolei Ma, Mao Mao, Caijuan Li, Xiaofeng Shen, Shunqing Xu, Jianjun Yang
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/2671281

Identification and Analysis of Novel Biomarkers Involved in Chromophobe Renal Cell Carcinoma by Integrated Bioinformatics Analyses
Cited by: 2
Author(s): Wei Zhang, Yin Xu, Jinghan Zhang, Jun Wu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-42010-6

A Network-guided Association Mapping Approach from DNA Methylation to Disease
Cited by: 16
Author(s): Yandan Lin, De-Shuang Huang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-42025-z

Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians
Cited by: 11
Author(s): Kiyono Sekii, Shunta Yorimoto, Hikaru Okamoto, Nanna Nagao, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryo Furukawa, Shuji Shigenobu, Kazuya Kobayashi
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms221910435

Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis
Cited by: 3
Author(s): Yingning Wang, Fang Ma, Jixian Yang, Haijuan Guo, Delin Su, Liping Yu
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms221910696

RNA-Seq and Electrical Penetration Graph Revealed the Role of Grh1-Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper (Nephotettix cincticeps Uhler) Resistance in Rice (Oryza sativa L.)
Cited by: 1
Author(s): Young Ho Kwon, Nkulu Rolly Kabange, Ji-Yoon Lee, Bo Yoon Seo, Dongjin Shin, So-Myeong Lee, Jin-Kyung Cha, Jun-Hyeon Cho, Ju-Won Kang, Dong-Soo Park, Jong-Min Ko, Jonghee Lee
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12870-018-1307-4

Parallel evolution of storage roots in morning glories (Convolvulaceae)
Cited by: 14
Author(s): Lauren A. Eserman, Robert L. Jarret, James H. Leebens‐Mack
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-018-1237-1

Resistance to Plum Pox Virus (PPV) in apricot (Prunus armeniaca L.) is associated with down-regulation of two MATHd genes
Cited by: 30
Author(s): Elena Zuriaga, Carlos Romero, José Blanca, M. L. Badenes
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-018-1356-8

Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata)
Cited by: 11
Author(s): Jiaoying Huang, Xuehong Hao, Ye Jin, Xiaohuan Guo, Qing Shao, Krishna B. Kumar, Yogesh Ahlawat, David E. Harry, Chandrashekhar P. Joshi, Youliang Zheng
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-2244-6

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum
Cited by: 22
Author(s): Donghong Chen, Han-Lin Qiu, Yong Huang, Lei Zhang, Jinping Si
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02375-7

High post-anthesis temperature effects on bread wheat (Triticum aestivum L.) grain transcriptome during early grain-filling
Cited by: 10
Author(s): Richard Ian Kino, Till K. Pellny, Rachel Mitchell, Asier Gonzalez-Uriarte, Paola Tosi
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03172-6

De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma
Cited by: 6
Author(s): Jyoti Devi, Ekjot Kaur, Mohit Kumar Swarnkar, Vishal Acharya, Shashi Bhushan
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12870-019-1742-x

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)
Cited by: 25
Author(s): Yuanyuan Cui, Ziran Wang, Shangwu Chen, Alexander Vainstein, Huiqin Ma
Software Mentions: 1
Published: over 7 years ago

10.1007/s11418-021-01505-1

Curcumin suppresses LGR5(+) colorectal cancer stem cells by inducing autophagy and via repressing TFAP2A-mediated ECM pathway
Cited by: 27
Author(s): Xiaohong Mao, Xin Zhang, Xiaowei Zheng, Yongwu Chen, Zixue Xuan, Ping Huang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-87991-5

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea
Cited by: 9
Author(s): Debasish B. Krishnatreya, Pooja Moni Baruah, Bhaskar Dowarah, Soni Chowrasia, Tapan Kumar Mondal, Niraj Agarwala
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-02330-6

Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud
Cited by: 16
Author(s): Jingjing Wang, Chunlei An, Hailin Guo, Xiangyang Yang, Jingbo Chen, Jingfeng Zong, Li Jianjian, Jianxiu Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-019-2067-5

Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng
Cited by: 22
Author(s): Xuejiao Li, Jianli Yang, Bin Hao, Yingchun Lu, Zhi-Long Qian, Ying Liu, Shuang Ye, Junrong Tang, Mo Chen, Guangqiang Long, Yan Zhao, Guanghui Zhang, Junwen Chen, Wei Fan, Shengchao Yang
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-021-88874-5

ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds
Cited by: 3
Author(s): Rocío Soledad Tognacca, Monica Carabelli, Giorgio Morelli, Ida Ruberti, Javier Francisco Botto
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-1824-9

Analysis of metabolic pathways related to fertility restoration and identification of fertility candidate genes associated with Aegilops kotschyi cytoplasm in wheat (Triticum aestivum L.)
Cited by: 7
Author(s): Sha Li, Zihan Liu, Yulin Jia, Jiali Ye, Xiaohong R. Yang, Lingli Zhang, Xiyue Song
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-021-89948-0

The chemical defensome of five model teleost fish
Cited by: 15
Author(s): Marta Eide, Xiaokang Zhang, Odd André Karlsen, Jeffrey Goldstone, John J. Stegeman, Inge Jonassen, Anders Goksøyr
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-02827-8

Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers
Cited by: 5
Author(s): Yu Qiao, Qiming Cheng, Yutong Zhang, Yan Wang, Fengyan Yi, Fengling Shi
Software Mentions: 1
Published: over 5 years ago

10.21307/jofnem-2019-055

Identification of Suitable Meloidogyne spp. Housekeeping Genes
Cited by: 1
Author(s): Weiming Hu, Peter DiGennaro
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-90982-1

Analysis of the role of Purα in the pathogenesis of Alzheimer's disease based on RNA-seq and ChIP-seq
Cited by: 4
Author(s): Xiaoguang Shi, Shuanglai Ren, Bingying Zhang, Shanshan Guo, Wenxin He, Chengmin Yuan, Xiaofan Yang, Kevin Ig-lzevbekhai, Tao Sun, Qinwen Wang, Jianqi Cui
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-92489-1

Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis
Cited by: 2
Author(s): Xinyi Gu, Bo Jin, Zhidan Qi, Xiaofeng Yin
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-93128-5

Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)
Cited by: 5
Author(s): Michaël Pierrelée, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, Bianca Habermann
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-018-1336-z

Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications
Cited by: 51
Author(s): Hangxiao Zhang, Huihui Wang, Qiang Zhu, Yanfeng Gao, Huiyuan Wang, Liangzhen Zhao, Yongsheng Wang, Feihu Xi, Wenfei Wang, Yanqiu Yang, Chentao Lin, Lianfeng Gu
Software Mentions: 1
Published: about 8 years ago

10.1186/s12870-020-02638-3

Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species
Cited by: 8
Author(s): Gerardo Alejo‐Jacuinde, Sandra Isabel González-Morales, Araceli Oropeza-Aburto, June Simpson, Luis Herrera-Estrella
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-021-03119-x

The core autophagy machinery is not required for chloroplast singlet oxygen-mediated cell death in the Arabidopsis thaliana plastid ferrochelatase two mutant
Cited by: 16
Author(s): Matthew D. Lemke, Karen E. Fisher, Marta A. Kozlowska, David W. Tano, Jesse D. Woodson
Software Mentions: 1
Published: about 5 years ago

10.21307/jofnem-2020-041

De novo transcriptome sequencing and analysis of Anisakis pegreffii (Nematoda: Anisakidae) third-stage and fourth stage larvae
Cited by: 5
Author(s): U‐Hwa Nam, Jong‐Oh Kim, Jeong-Ho Kim
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2229-11-177

Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
Cited by: 38
Author(s): Li Xiao, Hui Wang, Wan Park, Tingyun Kuang, Yulong He
Software Mentions: 1
Published: almost 15 years ago

10.21307/jofnem-2020-047

Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)
Cited by: 3
Author(s): Zhen F. Fu, Paula Agudelo, Christina E. Wells
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-018-1564-2

Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos
Cited by: 17
Author(s): Andreia S. Rodrigues, Jose J De Vega, Celia María Gonzalo Miguel
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-93381-8

The coordination of major events in C4 photosynthesis evolution in the genus Flaveria
Cited by: 12
Author(s): Ming‐Ju Amy Lyu, Udo Gowik, Steven Kelly, Sarah Covshoff, Julian M. Hibberd, Rowan F. Sage, Martha Ludwig, Gane Ka Shu Wong, Peter Westhoff, Xin Guang Zhu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-018-1428-9

Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack
Cited by: 33
Author(s): Xihui Liu, Ronghua Zhang, Hesheng Ou, Yiyun Gui, Jizhen Wei, Hui Zhou, Huachun Tan, Yang–Rui Li
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-95403-x

Identification of intima-to-media signals for flow-induced vascular remodeling using correlative gene expression analysis
Cited by: 4
Author(s): John Kolega, Kerry E. Poppenberg, Hee‐Woong Lim, Liza Gutierrez, Sricharan S. Veeturi, Adnan H. Siddiqui, Hamidreza Rajabzadeh-Oghaz, Vincent M. Tutino
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-96046-8

Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator
Cited by: 4
Author(s): Shukria Akbar, D. Cole Stevens
Software Mentions: 1
Published: about 5 years ago

10.1186/1755-8794-6-43

Association of candidate single nucleotide polymorphisms with somatic mutation of the epidermal growth factor receptor pathway
Cited by: 9
Author(s): Samuel Wormald, Liz Milla, Liam O’Connor
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-021-95938-z

Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells
Cited by: 3
Author(s): Hongyu Chen, Xi Chen, Yifei Shen, Xinxin Yin, FangJie Liu, Lu Liu, Jie Yao, Qinjie Chu, Yaqin Wang, Hongyan Qi, Michael P. Timko, Weijia Fang, Longjiang Fan
Software Mentions: 1
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568