Ecosyste.ms: Papers

10.1186/s12864-016-2716-0

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance
Cited by: 39
Author(s): Yadong Huang, Lin Li, Kevin P. Smith, Gary J. Muehlbauer
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.21460

Identification of <i>SPOP</i> related metabolic pathways in prostate cancer
Cited by: 12
Author(s): Min Yan, Huan Qi, Jia Li, Guozhu Ye, Yaping Shao, Tongming Li, Jing Liu, Hulin Piao, Guowang Xu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-019-6044-z

NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors
Cited by: 13
Author(s): Ji Hoon Phi, Chuanbowen Sun, Se‐Hoon Lee, Seungmook Lee, Inho Park, Seung Ah Choi, Shin Young Park, Ji Yeoun Lee, Kyu Chang Wang, Seung Ki Kim, Hong Seok Yun
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-513

Transcriptomics of differential vector competence: West Nile virus infection in two populations of Culex pipiens quinquefasciatus linked to ovary development
Cited by: 30
Author(s): Dong Ho Shin, Ayse Civana, Carolina Acevedo, Chelsea T. Smartt
Software Mentions: 1
Published: over 10 years ago

10.1038/srep29554

The Synthetic Elicitor DPMP (2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol) Triggers Strong Immunity in Arabidopsis thaliana and Tomato
Cited by: 21
Author(s): Yasemin Bektaş, Melinda Rodriguez-Salus, Mercedes Schroeder, Adilene Gomez, Isgouhi Kaloshian, Thomas Eulgem
Software Mentions: 1
Published: over 8 years ago

10.1038/srep29889

Phenotypically distinct helper NK cells are required for gp96-mediated anti-tumor immunity
Cited by: 18
Author(s): Abigail L. Sedlacek, Laurén B. Kinner-Bibeau, Robert J. Binder
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.17200

The exon junction complex regulates the splicing of cell polarity gene dlg1 to control Wingless signaling in development
Cited by: 11
Author(s): Min Liu, Yajuan Li, Aiguo Liu, Ruifeng Li, Ying Su, Juan Du, Cheng Li, Alan Jian Zhu
Software Mentions: 1
Published: over 8 years ago

10.1038/srep30953

microRNA-132/212 deficiency enhances Aβ production and senile plaque deposition in Alzheimer’s disease triple transgenic mice
Cited by: 95
Author(s): Julia Hernandez-Rapp, Sara Rainone, Claudia Goupil, Véronique Dorval, Pascal Y. Smith, Martine Saint-Pierre, Maxime Vallée, Emmanuel Planel, Arnaud Droit, Frédéric Calon, Francesca Cicchetti, Sébastien S. Hébert
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1560-y

Transcriptional events co-regulated by hypoxia and cold stresses in Zebrafish larvae
Cited by: 78
Author(s): Yong Long, Junjun Yan, Guangliang Song, Xiaohui Li, Xixi Li, Qing Li
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-020-07064-1

Hair follicle regional specificity in different parts of bay Mongolian horse by histology and transcriptional profiling
Cited by: 1
Author(s): Ruoyang Zhao, Yihan Wu, Yiping Zhao, Bei Li, Haitang Han, Togtokh Mongke, Tugeqin Bao, Wenxing Wang, Manglai Dugarjaviin, Ding Bai
Software Mentions: 1
Published: over 4 years ago

10.1038/srep31316

An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column
Cited by: 28
Author(s): Alberto Scoma, Marta Barbato, Sara Borin, Daniele Daffonchio, Nico Boon
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-020-07781-6

Low incidence of ABL-class and JAK-STAT signaling pathway alterations in uniformly treated pediatric and adult B-cell acute lymphoblastic leukemia patients using MRD risk-directed approach – a population-based study
Cited by: 4
Author(s): Rimvydas Norvilas, Vaidas Dirse, Rūta Semaškevičienė, Orinta Mickevičiūtė, Eglė Gineikienė, Mindaugas Stoškus, Goda Vaitkevičienė, Jelena Rascon, Laimonas Griškevičius
Software Mentions: 1
Published: almost 4 years ago

10.1038/srep31603

Immune cell-specific transcriptional profiling highlights distinct molecular pathways controlled by Tob1 upon experimental autoimmune encephalomyelitis
Cited by: 8
Author(s): Alessandro Didonna, Egle Cekanaviciute, Jorge R. Oksenberg, Sergio E. Baranzini
Software Mentions: 1
Published: over 8 years ago

10.1038/srep31602

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
Cited by: 131
Author(s): Spyros Oikonomopoulos, Yu Chang Wang, Haïg Djambazian, Dunarel Badescu, Jiannis Ragoussis
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-15-714

Olive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance
Cited by: 22
Author(s): Efthimia Sagri, Martin Reczko, Maria‐Eleni Gregoriou, Konstantina T. Tsoumani, Nikolaos E Zygouridis, Klelia D. Salpea, Frank G. Zalom, Jiannis Ragoussis, Kostas D. Mathiopoulos
Software Mentions: 1
Published: over 10 years ago

10.1038/srep32255

Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18
Cited by: 27
Author(s): Caroline Flegel, Felix C. E. Vogel, Adrian Hofreuter, Sebastian Wojcik, Clara T. Schoeder, Katarzyna Kieć‐Kononowicz, Norbert H. Brockmeyer, Christa E. Müller, Christian Becker, Janine Altmüller, Hanns Hatt, Günter Gisselmann
Software Mentions: 1
Published: over 8 years ago

10.1038/srep32249

Cell types differ in global coordination of splicing and proportion of highly expressed genes
Cited by: 16
Author(s): Ephraim F. Trakhtenberg, Nam Pho, Kristina M. Holton, Thomas Chittenden, Jeffrey L. Goldberg, Lingsheng Dong
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-018-4737-3

Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens
Cited by: 18
Author(s): Xiaoyan Cui, Huanxian Cui, Lu Liu, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng, Jie Wen
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep32952

NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation
Cited by: 35
Author(s): Verónica García-Carpizo, Jacinto Sarmentero, Baek Soo Han, Osvaldo Graña, Sergio Ruiz‐Llorente, David G. Pisano, Manuel Serrano, Harold B. Brooks, Robert M. Campbell, María J. Barrero
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-11-683

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)
Cited by: 78
Author(s): Hiroshi Mizuno, Yoshihiro Kawahara, Hiroaki Sakai, Hajime Kanamori, Hironobu Wakimoto, Harumi Yamagata, Youko Oono, Jianzhong Wu, Hiroshi Ikawa, Takeshi Itoh, Takashi Matsumoto
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-15-759

Systematic transcriptome analysis of the zebrafish model of diamond-blackfan anemia induced by RPS24 deficiency
Cited by: 15
Author(s): Binfeng Song, Qian Zhang, Zhaojun Zhang, Yang Wan, Qiong Jia, Xiaomin Wang, Xiaofan Zhu, Anskar Y. H. Leung, Tao Cheng, Xiangdong Fang, Weiping Yuan, Haibo Jia
Software Mentions: 1
Published: over 10 years ago

10.1038/srep33605

Identification of antisense long noncoding RNAs that function as SINEUPs in human cells
Cited by: 53
Author(s): Aleks Schein, S. Zucchelli, Sakari Kauppinen, Stefano Gustincich, Piero Carninci
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.02948

Two-signal requirement for growth-promoting function of Yap in hepatocytes
Cited by: 51
Author(s): Tian Su, Tanya Bondar, Xu Zhou, Cuiling Zhang, Hang He, Ruslan Medzhitov
Software Mentions: 1
Published: about 10 years ago

10.1038/srep34308

Comparative Secretome Analysis Reveals Perturbation of Host Secretion Pathways by a Hypovirus
Cited by: 15
Author(s): Jinzi Wang, Liming Shi, He XiPu, Lidan Lu, Xiaoping Li, Baoshan Chen
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34669

Maternal Fructose Exposure Programs Metabolic Syndrome-Associated Bladder Overactivity in Young Adult Offspring
Cited by: 9
Author(s): Wei‐Chia Lee, You‐Lin Tain, Kay L. H. Wu, Steve Leu, Julie Y.H. Chan
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34727

Lateralization of gene expression in the honeybee brain during olfactory learning
Cited by: 16
Author(s): Yu Guo, Zilong Wang, You Li, Guifeng Wei, Jiao Yuan, Yu Sun, Huan Wang, Qiuhong Qin, Zhen Zeng, Shao Wu Zhang, Runsheng Chen
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.21553

Genome-wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand-specific RNA-seq
Cited by: 3
Author(s): Qi-Lin Zhang, Zhengqing Xie, Mingzhu Liang, Bang Luo, Xiuqiang Wang, Jun-Yuan Chen
Software Mentions: 1
Published: over 7 years ago

10.1038/srep34957

AML1/ETO accelerates cell migration and impairs cell-to-cell adhesion and homing of hematopoietic stem/progenitor cells
Cited by: 13
Author(s): Marco Saia, Alberto Termanini, Nicoletta Rizzi, M. Mazza, Elisa Barbieri, Debora Valli, Paolo Ciana, Alicja M. Gruszka-Westwood, Myriam Alcalay
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34542

p21Cip1 plays a critical role in the physiological adaptation to fasting through activation of PPARα
Cited by: 12
Author(s): Elena Lopez-Guadamillas, Pablo J. Fernández-Marcos, Cristina Pantoja, Maribel Muñoz‐Martín, Dolores Fernández Martínez, Gonzalo Goméz-López, Ramón Campos-Olivas, Ángela M. Valverde, Manuel Serrano
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-018-4215-y

Helicase-like transcription factor expression is associated with a poor prognosis in Non-Small-Cell Lung Cancer (NSCLC)
Cited by: 3
Author(s): Ludovic Dhont, Melania Pintilie, Ethan Kaufman, Roya Navab, Susan H. Tam, Arsène Burny, Frances A. Shepherd, Alexandra Belayew, Ming‐Sound Tsao, Céline Mascaux
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep35305

A proteogenomic approach for protein-level evidence of genomic variants in cancer cells
Cited by: 12
Author(s): Jeonghun Yeom, Mohammad Humayun Kabir, Byungho Lim, Hee‐Sung Ahn, Seon‐Young Kim, Cheolju Lee
Software Mentions: 1
Published: over 8 years ago

10.1038/srep35550

Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1
Cited by: 18
Author(s): Jimena Giudice, Zheng Xia, Wei Li, Thomas A. Cooper
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.19573

Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana
Cited by: 44
Author(s): Urszula Piskurewicz, Mayumi Iwasaki, Daichi Susaki, Christian Megies, Tetsu Kinoshita, Luis Lopez‐Molina
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.22552

Glucose impairs tamoxifen responsiveness modulating connective tissue growth factor in breast cancer cells
Cited by: 30
Author(s): Maria Rosaria Ambrosio, Vittoria D’Esposito, Valerio Costa, Domenico Liguoro, Francesca Collina, Monica Cantile, Nella Prevete, Carmela Passaro, G. Mosca, Michelino De Laurentiis, Maurizio Di Bonito, Gerardo Botti, Renato Franco, Francesco Béguinot, Alfredo Ciccodicola, Pietro Formisano
Software Mentions: 1
Published: about 7 years ago

10.1186/s12885-015-1510-8

Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas
Cited by: 19
Author(s): Sunniva Bjørklund, Vessela N. Kristensen, Michael Seiler, Surendra Kumar, Grethe I.G. Alnæs, Ming Yao, John E. Kerrigan, Bjørn Naume, Ravi Sachidanandam, Gyan Bhanot, Anne Lise Børresen-Dale, Shridar Ganesan
Software Mentions: 1
Published: over 9 years ago

10.1111/acel.12598

Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study
Cited by: 13
Author(s): Robert Häsler, Geetha Venkatesh, Qihua Tan, Friederike Flachsbart, Anupam Sinha, Philip Rosenstiel, Wolfgang Lieb, Stefan Schreiber, Kaare Christensen, Lene Christiansen, Almut Nebel
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep36966

The molecular bases of floral scent evolution under artificial selection: insights from a transcriptome analysis in Brassica rapa
Cited by: 15
Author(s): Jing Cai, Pengjuan Zu, Florian P. Schiestl
Software Mentions: 1
Published: over 8 years ago

10.1038/srep36916

Sex-Specific Effects of Testosterone on the Sexually Dimorphic Transcriptome and Epigenome of Embryonic Neural Stem/Progenitor Cells
Cited by: 39
Author(s): Éric Vilain, Lara Roach, Allen Lipson, Neerja Vashist, Ascia Eskin, Tuck C Ngun, Jason E. Gosschalk, Stephen P. Klein, Hayk Barseghyan, Valerie A. Arboleda, Éric Vilain
Software Mentions: 1
Published: over 8 years ago

10.1186/s12915-016-0273-2

A de novo silencer causes elimination of MITF-M expression and profound hearing loss in pigs
Cited by: 49
Author(s): Lei Chen, Weiwei Guo, Lili Ren, Mingyao Yang, Yaofeng Zhao, Zhanbao Guo, Haijin Yi, Mingzhou Li, Yiqing Hu, Xi Long, Boyuan Sun, Jinxiu Li, Shumei Zhai, Tinghuan Zhang, Shilin Tian, Qingyong Meng, Ning Yu, Dan Zhu, Guoqing Tang, Qianzi Tang, Liming Ren, Ke Liu, Shihua Zhang, Tiandong Che, Zhengquan Yu, Nan Wu, Jing Lan, Ran Zhang, Tao Cong, Siqing Chen, Yaofeng Zhao, Yue Zhang, Bai XiaoQing, Ying Guo, Ling Zhao, Fengming Zhang, Hui Zhao, Zhen Liang, Zeng-Guang Hou, Jianmin Zhao, Jianan Li, Lijuan Zhang, Wei Sun, Xiangang Zou, Tao Wang, Liangpeng Ge, Zuohua Liu, Xiaoxiang Hu, Jingyong Wang, Shiming Yang, Ning Li
Software Mentions: 1
Published: over 8 years ago

10.1186/s40478-018-0625-y

Nicotine promotes neuron survival and partially protects from Parkinson’s disease by suppressing SIRT6
Cited by: 52
Author(s): Justin W. Nicholatos, Adam B. Francisco, Carolyn A. Bender, Tiffany Yeh, Fraz J. Lugay, Jairo E. Salazar, Christin Glorioso, Sergiy Libert
Software Mentions: 1
Published: over 6 years ago

10.1038/srep36993

mRNA changes in nucleus accumbens related to methamphetamine addiction in mice
Cited by: 39
Author(s): Li Zhu, Jiaqi Li, Nan Dong, Fanglin Guan, Yufeng Liu, Dongliang Ma, Eyleen L. K. Goh, Chih‐Ching Teng
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.23274

Dihydroartemisinin-regulated mRNAs and lncRNAs in chronic myeloid leukemia
Cited by: 5
Author(s): Xiang Li, Yue Gao, Qiang Zhang, Nan Hu, Dong Han, Shangwei Ning, Zhuo Ao
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.27706

Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis
Cited by: 30
Author(s): Stephin J. Vervoort, Olivier G. de Jong, M. Guy Roukens, Cynthia L Frederiks, Jeroen F. Vermeulen, Ana Rita Lourenço, Laura Bella, Ana Tufegdžić Vidaković, José Luís Sandoval, Cathy B. Moelans, Miranda van Amersfoort, Margaret J. Dallman, Alejandra Bruna, Carlos Caldas, Edward E. S. Nieuwenhuis, Elsken van der Wall, Patrick W.B. Derksen, Paul van Diest, Marianne C. Verhaar, Eric Lam, Michal Mokrý, Paul J. Coffer
Software Mentions: 1
Published: about 6 years ago

10.1038/srep38063

The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity
Cited by: 114
Author(s): Samer G. Alam, Qiao Zhang, Nripesh Prasad, Yuan Li, Srikar Chamala, Ram Anirudh Kuchibhotla, Birendra Kc, Varun Aggarwal, Shristi Shrestha, Angela L. Jones, Shawn Levy, Kyle J. Roux, Jeffrey A. Nickerson, Tanmay P. Lele
Software Mentions: 1
Published: about 8 years ago

10.1186/s12915-017-0402-6

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species
Cited by: 215
Author(s): Stephen L. Pearce, David F. Clarke, Peter D. East, Samia Elfékih, Karl Gordon, Lars S. Jermiin, Angela McGaughran, John G. Oakeshott, Αλέξιος Παπανικολάου, Omaththage P. Perera, Rahul Rane, Stephen Richards, Wee Tek Tay, Tom Walsh, Alisha Anderson, C. A. Anderson, Sassan Asgari, Philip G. Board, Anne Bretschneider, Pamela M. Campbell, Thomas Chertemps, John T. Christeller, Chris Coppin, Sharon Downes, Guowen Duan, Claire A Farnsworth, Robert T. Good, Linxiao Han, Yi Han, Klas Hatje, Irene Horne, Yongping Huang, Daniel Hughes, Emmanuelle Jacquin‐Joly, William James, Shalini N. Jhangiani, Martin Kollmar, Suyog Kuwar, S. Li, N-Y. Liu, Martine Maı̈bèche, Jason R. Miller, Nicolas Montagné, Trent Perry, Jiaxin Qu, Sue Song, Granger Sutton, Heiko Vogel, Brian P. Walenz, Wei Xü, Zhang Hj, Zhen Zou, Philip Batterham, Owain Edwards, René Feyereisen, Richard A. Gibbs, David G. Heckel, Annette McGrath, Charles Robin, Steven E. Scherer, Kim C. Worley, Yingliang Wu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-4123-6

The dynamic landscape of gene regulation during Bombyx mori oogenesis
Cited by: 10
Author(s): Qiang Zhang, Wei Sun, Bangyong Sun, Yang Xiao, Ze Zhang
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.14330

A feedback amplification loop between stem cells and their progeny promotes tissue regeneration and tumorigenesis
Cited by: 51
Author(s): Jun Chen, Na Xu, Huagnwei Huang, Tao Cai, Rongwen Xi
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.23694

Transcriptome profiling identified differentially expressed genes and pathways associated with tamoxifen resistance in human breast cancer
Cited by: 21
Author(s): Xin Men, Ma Jun, Tong Wu, Junyi Pu, Shaojia Wen, Jianfeng Shen, Xun Wang, Yamin Wang, Chao Chen, Peng Dai
Software Mentions: 1
Published: about 7 years ago

10.1038/srep39178

Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis
Cited by: 6
Author(s): Vivek Raj Senthivel, Marc Sturrock, Gabriel Piedrafita, Mark Isalan
Software Mentions: 1
Published: about 8 years ago

10.1038/srep39493

Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake
Cited by: 52
Author(s): P. C. Tizioto, Luiz Lehmann Coutinho, P. S. N. Oliveira, Wellison J. S. Diniz, A. O. de Lima, M. I. P. Rocha, Jared E. Decker, Robert D. Schnabel, Gérson Barreto Mourão, R. R. Túllio, Adhemar Zerlotini, Jeremy F. Taylor, Luciana Correia de Almeida Regitano
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-15-287

Species-specific alternative splicing leads to unique expression of sno-lncRNAs
Cited by: 44
Author(s): Xiao‐Ou Zhang, Qingrui Yin, Haibin Wang, Yang Zhang, Chen Tian, Ping Zheng, Xuhua Lu, Lingling Chen, Li Yang
Software Mentions: 1
Published: almost 11 years ago

10.18632/aging.101029

An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans
Cited by: 25
Author(s): Masaomi Kato, Mohammed A. Kashem, Chao Cheng
Software Mentions: 1
Published: over 8 years ago

10.1038/srep39516

Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network
Cited by: 39
Author(s): Qianlan Yao, Leilei Wu, Jia Li, Li Yang, Yidi Sun, Zhen Li, Sheng He, Fangyoumin Feng, Hong Li, Yixue Li
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-015-1598-x

The Eucalyptus terpene synthase gene family
Cited by: 115
Author(s): Carsten Külheim, Amanda Padovan, Charles A. Hefer, Sandra T. Krause, Tobias G. Köllner, Alexander Andrew Myburg, Jörg Degenhardt, William J. Foley
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-6062-x

‘Candidatus Phytoplasma solani’ interferes with the distribution and uptake of iron in tomato
Cited by: 16
Author(s): Sara Buoso, Laura Pagliari, Rita Musetti, Marta Martini, Fabio Marroni, Wolfgang Schmidt, Simonetta Santi
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-4857-9

Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes
Cited by: 105
Author(s): Eiichi Shoguchi, Girish Beedessee, Isao Tada, Kanako Hisata, Takeshi Kawashima, Takeshi Takeuchi, Nana Arakaki, Manabu Fujie, Ryo Koyanagi, Michael C. Roy, Masanobu Kawachi, Michio Hidaka, Noriyuki Satoh, Chuya Shinzato
Software Mentions: 1
Published: over 6 years ago

10.1038/srep40819

Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress
Cited by: 50
Author(s): Huan Zhang, Qian Zhang, Hong Zhai, Yán Li, Xiangfeng Wang, Qingchang Liu, Shaozhen He
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-015-1813-9

Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones
Cited by: 33
Author(s): Yuchen Yang, Shuhuan Yang, Jianfang Li, Yunfei Deng, Zhang Zhang, Shaohua Xu, Wuxia Guo, Cairong Zhong, Renchao Zhou, Suhua Shi
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-014-0109-x

Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers
Cited by: 11
Author(s): Tao Yu, Weisheng Zheng, Yonghua Jiang, Guitao Ding, Xinfeng Hou, Yitao Tang, Yueying Li, Shuai Gao, Gang Chang, Xiaobai Zhang, Wenqiang Liu, Xiaochen Kou, Hong Wang, Cizhong Jiang, Shaorong Gao
Software Mentions: 1
Published: about 10 years ago

10.1038/srep41008

The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury
Cited by: 43
Author(s): Raquel Cuevas-Diaz Duran, Han Yan, Yiyan Zheng, Xingfan Huang, Raymond J. Grill, Dong H. Kim, Qilin Cao, Jia Qian Wu
Software Mentions: 1
Published: about 8 years ago

10.1038/srep41040

Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production
Cited by: 42
Author(s): Xian Yin, Hyun‐Dong Shin, Jianghua Li, Guocheng Du, Long Liu, Jian Chen
Software Mentions: 1
Published: about 8 years ago

10.1038/srep40780

Zika virus disrupts molecular fingerprinting of human neurospheres
Cited by: 99
Author(s): Patrícia P. Garcez, Juliana Nascimento, Janaína Mota de Vasconcelos, Rodrigo Madeiro da Costa, Rodrigo Delvecchio, Pablo Trindade, Erick Correia Loiola, Luiza M. Higa, Juliana S. Cassoli, Gabriela Vitória, Patrícia Carvalho de Sequeira, Jaroslaw Sochacki, Renato Santana Aguiar, Hellen Thaís Fuzii, Ana María Bispo de Filippis, João Lídio da Silva Gonçalves Vianez Júnior, Amílcar Tanuri, Daniel Martins-de-Souza, Stevens K. Rehen
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.10567

Embryonic attenuated Wnt/β-catenin signaling defines niche location and long-term stem cell fate in hair follicle
Cited by: 51
Author(s): Zijian Xu, Wenjie Wang, Kaiju Jiang, Yu Zhou, Huagnwei Huang, Fengchao Wang, Bin Zhou, Ting Chen
Software Mentions: 1
Published: about 9 years ago

10.1038/srep41517

RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis
Cited by: 16
Author(s): Claire Mooney, Eva M. Jiménez-Mateos, Tobías Engel, Catherine Mooney, Mairéad Diviney, Morten T. Venø, Jørgen Kjems, Michael Farrell, Donncha F. O’Brien, Norman Delanty, David C. Henshall
Software Mentions: 1
Published: about 8 years ago

10.1038/srep41561

Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.)
Cited by: 12
Author(s): Xiang Luo, Zhenyi Xue, Chaozhi Ma, Kaining Hu, Ziru Zeng, Shengwei Dou, Jinxing Tu, Jinxiong Shen, Tingdong Fu
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-017-4367-1

Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance
Cited by: 52
Author(s): Phil Hyun Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
Software Mentions: 1
Published: about 7 years ago

10.1186/s12915-015-0121-9

The development and maintenance of the mononuclear phagocyte system of the chick is controlled by signals from the macrophage colony-stimulating factor receptor
Cited by: 53
Author(s): Valérie Garceau, Adam Balic, Carla García‐Morales, Kristin A. Sauter, Mike McGrew, Jacqueline Smith, Lonneke Vervelde, Adrian Sherman, Troy E. Fuller, Theodore Oliphant, John A Shelley, Raksha Tiwari, Thomas L. Wilson, Cosmin Chintoan-Uta, David W. Burt, Mark P. Stevens, Helen Sang, David Hume
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12915-015-0151-3

Lhx8 regulates primordial follicle activation and postnatal folliculogenesis
Cited by: 63
Author(s): Yu Ren, Hitomi Suzuki, Krishna Jagarlamudi, Kayla Golnoski, Megan McGuire, R N V R Lopes, Vassilis Pachnis, Aleksandar Rajkovic
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-016-0309-7

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
Cited by: 319
Author(s): Tofazzal Islam, Daniel Croll, Pierre Gladieux, Darren M. Soanes, Antoine Persoons, Pallab Bhattacharjee, Md. Shaid Hossain, Dipali Rani Gupta, Mohammad Mafizur Rahman, M. Golam Mahboob, Nicola Cook, Moin U. Salam, Musrat Zahan Surovy, Vanessa Bueno-Sancho, João Leodato Nunes Maciel, Antonio NhaniJúnior, Vanina Lilián Castroagudín, Juliana Teodora de Assis Reges, Paulo Cézar Ceresini, Sébastien Ravel, Ronny Kellner, Elisabeth Fournier, Didier Tharreau, Marc-Henri Lebrun, Bruce A. McDonald, Timothy Stitt, Daniel Swan, Nicholas J. Talbot, Diane G. O. Saunders, Joe Win, Sophien Kamoun
Software Mentions: 1
Published: over 8 years ago

10.1038/srep43226

Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.)
Cited by: 39
Author(s): Chenyang Wang, Shengrui Liu, Xiaoyu Zhang, Ma Yin, Chun-Gen Hu, Jinzhi Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep43598

Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53
Cited by: 27
Author(s): Ishwarya Venkata Narayanan, Michelle T. Paulsen, Karan Bedi, Nathaniel K. Berg, Emily A. Ljungman, Sofia Francia, Artur Veloso, Brian Magnuson, Fabrizio d’Adda di Fagagna, Thomas E. Wilson, Mats Ljungman
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep42795

REST is a crucial regulator for acquiring EMT-like and stemness phenotypes in hormone-refractory prostate cancer
Cited by: 34
Author(s): Yi Ting Chang, Tzu Ping Lin, Mel Campbell, Chin Chen Pan, Shu Hui Lee, Hsin Chen Lee, Muh Hwa Yang, Hsing Jien Kung, Pei Ching Chang
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep41623

TLR-exosomes exhibit distinct kinetics and effector function
Cited by: 18
Author(s): Savitha Srinivasan, Michelle Su, Shashidhar Ravishankar, James R. Moore, PamelaSara E. Head, J. Brandon Dixon, Fredrik Vannberg
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep44729

Simulated herbivory in chickpea causes rapid changes in defense pathways and hormonal transcription networks of JA/ethylene/GA/auxin within minutes of wounding
Cited by: 40
Author(s): Saurabh Pandey, Shruti Srivastava, Ridhi Goel, Deepika Lakhwani, Priya Singh, Mehar Hasan Asif, Aniruddha P. Sane
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep44270

Self-renewal and phenotypic conversion are the main physiological responses of macrophages to the endogenous estrogen surge
Cited by: 58
Author(s): Giovanna Pepe, Daniele Braga, Tiziana Ada Renzi, Alessandro Villa, Chiara Bolego, Francesca D’Avila, Cristina Barlassina, Adriana Maggi, Massimo Locati, Elisabetta Vegeto
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep45038

PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4
Cited by: 14
Author(s): Jayme Salsman, Alex Stathakis, Ellen Parker, Dudley Chung, Livia E. Anthes, Kara L. Koskowich, Sara Lahsaee, Daniel Gaston, Kimberly R. Kukurba, Kevin S. Smith, Ian C. Chute, D. Léger, Laura D. Frost, Stephen B. Montgomery, Stephen M. Lewis, Christopher H. Eskiw, Graham Dellaire
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep46271

Genome-wide RNA-seq of iPSC-derived motor neurons indicates selective cytoskeletal perturbation in Brown–Vialetto disease that is partially rescued by riboflavin
Cited by: 21
Author(s): Federica Rizzo, Agnese Ramirez, Claudia Compagnucci, Sabrina Salani, Valentina Melzi, Andreina Bordoni, Francesco Fortunato, Alessia Niceforo, Nereo Bresolin, Giacomo Pietro Comi, Enrico Bertini, Monica Nizzardo, Stefania Corti
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-5478-7

PmiRDiscVali: an integrated pipeline for plant microRNA discovery and validation
Cited by: 9
Author(s): Dongliang Yu, Ying Wan, Hidetaka Ito, Xiaoxia Ma, Tian Xie, Tingzhang Wang, Chaogang Shao, Yijun Meng
Software Mentions: 1
Published: about 6 years ago

10.1038/srep46276

Loss of Polycomb Group Protein Pcgf1 Severely Compromises Proper Differentiation of Embryonic Stem Cells
Cited by: 23
Author(s): Yun Yan, Wukui Zhao, Yikai Huang, Hanxing Tong, Yin Xia, Qing Jiang, Jinzhong Qin
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-06970-8

Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses
Cited by: 20
Author(s): Faiza Ali, Ghulam Qanmber, Zhenzhen Wei, Daoqian Yu, Yong Hui Li, Lei Gan, Fuguang Li, Zhi Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-14-401

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex
Cited by: 41
Author(s): Hua-Ling Wang, Jiaojiao Yang, Laura M. Boykin, Qiongyi Zhao, Qian Li, Xiaowei Wang, Shu‐Sheng Liu
Software Mentions: 1
Published: about 12 years ago

10.18632/oncotarget.23946

Competitive endogenous RNA networks: integrated analysis of non-coding RNA and mRNA expression profiles in infantile hemangioma
Cited by: 10
Author(s): Jun Li, Qian Li, Ling Chen, Yanli Gao, Bei Zhou, Jingyun Li
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-015-1283-0

Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet
Cited by: 22
Author(s): Zhaowei Cai, Xiaoling Jiang, Yongming Pan, Liang Chen, Lifan Zhang, Kun Zhu, Yan Cai, Yun Ling, Fang‐Ming Chen, Xiaoping Xu, Minli Chen
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-019-5902-z

Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense
Cited by: 13
Author(s): Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li, Ming Peng
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-325

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads
Cited by: 93
Author(s): Yu Bai, Min Ni, Blerta Cooper, Yi Wei, Wen Fury
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-017-00069-z

Transcriptome analysis of bagging-treated red Chinese sand pear peels reveals light-responsive pathway functions in anthocyanin accumulation
Cited by: 65
Author(s): Songling Bai, Yongwang Sun, Minjie Qian, Fengxia Yang, Junbei Ni, Ruiyan Tao, Lin Li, Qinmeng Shu, Dong Zhang, Yuanwen Teng
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12915-020-00909-x

Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat
Cited by: 24
Author(s): Jingya Yuan, Jiao Wu, Yanfeng Liu, Wenxue Ye, Xiue Wang, Liu B, Qingxin Song, Z Jeffrey Chen
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-016-2730-2

Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses
Cited by: 30
Author(s): Xiaolong Fang, Lei Wang, Xiao‐Juan Deng, Peng Wang, Qibin Ma, Hai Nian, Yingxiang Wang, Chunrong Yang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-00821-5

RNA sequence analysis of rat acute experimental pancreatitis with and without fatty liver: a gene expression profiling comparative study
Cited by: 12
Author(s): Qian Wang, Hongkai Yan, Gang Wang, Zhaoyan Qiu, Bin Bai, Shiqi Wang, Pengfei Yu, Quanxin Feng, Qingchuan Zhao, Xianli He, Chaoxu Liu
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-12-290

Bias detection and correction in RNA-Sequencing data
Cited by: 137
Author(s): Wei Zheng, Lisa Chung, Hongyu Zhao
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-017-00804-6

Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells
Cited by: 26
Author(s): Yingbo Han, Jianke Ren, Eunice Lee, Xiaoping Xu, Weishi Yu, Kathrin Muegge
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-4022-x

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data
Cited by: 28
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, David C. Samuels, Yu Shyr
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-01624-4

DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer
Cited by: 62
Author(s): Riikka Lund, Kaisa Huhtinen, Jussi Salmi, Juha Rantala, Elizabeth V. Nguyen, Robert Moulder, David R. Goodlett, Riitta Lahesmaa, Olli Carpén
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-01982-z

Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa
Cited by: 8
Author(s): Luis Pastenes, Camilo Valdivieso, Alex Di Génova, Dante Travisany, Andrew Hart, Martín Montecino, Ariel Orellana, Maurício González, Rodrigo A. Gutiérrez, Miguel L. Allende, Alejandro Maass, Marco A. Méndez
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-02549-8

The role of retinol dehydrogenase 10 in the cone visual cycle
Cited by: 11
Author(s): Y. Y. Xue, Shin Sato, David Razafsky, Bhubanananda Sahu, Susan Q. Shen, Chloe Potter, Lisa L. Sandell, Joseph C. Corbo, Krzysztof Palczewski, Akiko Maeda, Didier Hodzic, Vladimir J. Kefalov
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-02487-5

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
Cited by: 37
Author(s): Fanny-Dhelia Pajuste, Lauris Kaplinski, Märt Möls, Tarmo Puurand, Maarja Lepamets, Maido Remm
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-02975-8

Transcriptome responses of Lactobacillus acetotolerans F28 to a short and long term ethanol stress
Cited by: 27
Author(s): Xiaopan Yang, Kunling Teng, Jie Zhang, Fangfang Wang, Tong Zhang, Guomin Ai, Pei‐Jie Han, Feng‐Yan Bai, Jin Zhong
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-021-07780-2

Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection
Cited by: 13
Author(s): Xianhui Ning, Li Sun
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.24147

ERK inhibition represses gefitinib resistance in non-small cell lung cancer cells
Cited by: 19
Author(s): Mengfan Qi, Ye Tian, Wang Li, Dan Li, Tian Zhao, Yuxin Yang, Qiwen Li, Sujun Chen, Yan Yang, Zhixiong Zhang, Liang Tang, Liu Z, Bo Su, Fĕi Li, Yonghong Feng, Fei Ke, Peng Zhang, Fan Zhang, Lei Zhang
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-14-335

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)
Cited by: 83
Author(s): Peng Zhou, Kevin A.T. Silverstein, Liangliang Gao, Jonathan D. Walton, Sumitha Nallu, Joseph Guhlin, Nevin D. Young
Software Mentions: 1
Published: about 11 years ago