bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-016-2540-6

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions
Cited by: 72
Author(s): Yuta Yoshida, Takuya Tomiyama, Takanori Maruta, Masaru Tomita, Takahiro Ishikawa, Kazuharu Arakawa
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4095-6

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses
Cited by: 19
Author(s): Totta Ehret, Simone Spork, Christoph Dieterich, Richard Lucius, Emanuel Heitlinger
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-020-07024-9

Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages
Cited by: 20
Author(s): Jing Yang, Ling Su, Dandan Li, Lixin Luo, Kai Sun, Meng Yang, Fengwei Gu, Aoyun Xia, Yongzhu Liu, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 1
Published: almost 6 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/s12864-018-4723-9

Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential
Cited by: 19
Author(s): Nicky‐Lee Willson, R. E. A. Forder, Rick Tearle, J. L. Williams, Robert J. Hughes, G. S. Nattrass, P. I. Hynd
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-016-2546-0

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
Cited by: 20
Author(s): María Fernanda Torres, Noushin Ghaffari, Ester Alvarenga Santos Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson, Lisa J. Vaillancourt
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4177-5

Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types
Cited by: 29
Author(s): Guillem Ylla, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-2454-3

Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors
Cited by: 75
Author(s): Troy J. Huth, Sean P. Place
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-6149-4

Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis
Cited by: 7
Author(s): Humaira Rasheed, Chenxu Ye, Yufeng Meng, Yuehua Ran, Jing Li, Xiaoqing Su
Software Mentions: 1
Published: almost 7 years ago

10.3390/ani9100753

Transferrin Identification in Sterlet (Acipenser ruthenus) Reproductive System
Cited by: 7
Author(s): Miaomiao Xin, Pavlína Věchtová, Anna Shaliutina‐Kolešová, Zoltán Füssy, Dmitry S. Loginov, Borys Dzyuba, Otomar Linhart, Serhii Boryshpolets, Marek Rodina, Ping Li, Yana F. Loginova, Ján Štěrba
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-018-5310-9

Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis
Cited by: 5
Author(s): Ken Kraaijeveld, Vicencio Oostra, Maartje Liefting, Bregje Wertheim, Emile de Meijer, Jacintha Ellers
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-4144-1

Deciphering the olfactory repertoire of the tiger mosquito Aedes albopictus
Cited by: 29
Author(s): Fabrizio Lombardo, Marco Salvemini, Carmine Fiorillo, Tony Nolan, Laurence J. Zwiebel, José M. C. Ribeiro, Bruno Arcà
Software Mentions: 1
Published: almost 9 years ago

10.3390/ani10040624

Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness
Cited by: 10
Author(s): Kai Xing, Xitong Zhao, Yibing Liu, Fengxia Zhang, Zhen Tan, Xiaolong Qi, Xiangguo Wang, Hemin Ni, Yong Guo, Xihui Sheng, Chuduan Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-2470-3

Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear
Cited by: 30
Author(s): Mao-Song Pei, Jianxin Niu, Chenjing Li, Fuliang Cao, Shaowen Quan
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-6037-y

Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites
Cited by: 15
Author(s): Chenxu Ye, Humaira Rasheed, Yuehua Ran, Yang Xiao, Lianxi Xing, Xiaoqing Su
Software Mentions: 1
Published: almost 7 years ago

10.3390/ani9070399

Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp (Oratosquilla oratoria) under Thermal Stress
Cited by: 8
Author(s): Fangrui Lou, Zhiqiang Han, Tianxiang Gao
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-020-06968-2

Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach
Cited by: 5
Author(s): José Ricardo Parreira, Lorenzo E. Hernández-Castellano, A. Argüello, J. Capote, N. Castro, Susana de Sousa Araújo, André M. Almeida
Software Mentions: 1
Published: almost 6 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

10.3390/ijms22137025

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development
Cited by: 7
Author(s): Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragón-Palomino, Serena Aceto
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3689-3

An evolutionarily conserved transcriptional response to viral infection in Caenorhabditis nematodes
Cited by: 53
Author(s): Kevin Chen, Carl Franz, Hongbing Jiang, Yanfang Jiang, David Wang
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-017-4250-0

Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla)
Cited by: 50
Author(s): Wenjia Wang, Lianfeng Gu, Shanwen Ye, Hangxiao Zhang, Changyang Cai, Mengqi Xiang, Yanfeng Gao, Qin Wang, Chentao Lin, Qiang Zhu
Software Mentions: 1
Published: almost 9 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/s12864-020-6755-1

Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells
Cited by: 9
Author(s): Hanna Helgeland, Ingvild Gabrielsen, Helle Akselsen, Arvind Sundaram, Siri Tennebø Flåm, Benedicte A. Lie
Software Mentions: 1
Published: over 6 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: almost 5 years ago

10.1186/s12864-015-2052-9

Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum
Cited by: 27
Author(s): Erica Lasek‐Nesselquist, Jennifer H. Wisecaver, Jeremiah D. Hackett, Matthew D. Johnson
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-021-08017-y

Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm
Cited by: 2
Author(s): Jianliang Liu, Yefeng Bao, Yuming Zhong, Qin Wang, Huifan Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-018-4669-y

Transcriptomic insights into citrus segment membrane’s cell wall components relating to fruit sensory texture
Cited by: 12
Author(s): Xun Wang, Lijin Lin, Yi Tang, Hui Xia, Xiancong Zhang, Maolan Yue, Qi‐Dong Xia, Ke Xu, Zhihui Wang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-2271-0

Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel
Cited by: 26
Author(s): Keng Po Lai, Jing Woei Li, Je Gu, Ting‐Fung Chan, William Ka Fai Tse, Chris K C Wong
Software Mentions: 1
Published: over 10 years ago

10.3390/ani11051430

Expression Analysis of Circular RNAs in Young and Sexually Mature Boar Testes
Cited by: 5
Author(s): Fei Zhang, Xiaodong Zhang, Ning Wei, Xiangdong Zhang, Zhenyuan Ru, Shiqi Wang, Meiping Sheng, Junrui Zhang, Xueying Zhang, Haiqin Luo, Xin Wang, Zubing Cao, Yunhai Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-98323-y

Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress
Cited by: 2
Author(s): А. Г. Степченко, Т. Н. Порцева, И. А. Глухов, А. П. Котнова, B. M. Lyanova, С. Г. Георгиева, Е. В. Панкратова
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-019-5436-4

Isolation of blue-green eggshell pigmentation-related genes from Putian duck through RNA-seq
Cited by: 7
Author(s): Ding-Ping Bai, Xinyu Lin, Yan Wu, Shi-Ye Zhou, Zhong-bin Huang, Yifan Huang, Ang Li, Xiaohong Huang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-6217-9

Transcriptome responses to different herbivores reveal differences in defense strategies between populations of Eruca sativa
Cited by: 5
Author(s): Ariel Ogran, Adi Faigenboim, Oz Barazani
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-14-878

Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data
Cited by: 47
Author(s): Mauricio González-Agüero, Miguel García-Rojas, Alex Di Génova, Juan Correa, Alejandro Maass, Ariel Orellana, Patricio Hinrichsen
Software Mentions: 1
Published: over 12 years ago

10.1155/2021/2143362

Determination of Genetic and Epigenetic Modifications-Related Prognostic Biomarkers of Breast Cancer: Genome High-Throughput Data Analysis
Cited by: 3
Author(s): Chundi Gao, Huayao Li, Cun Liu, Jibiao Wu, Chao Zhou, Lijuan Liu, Jing Zhuang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-6528-x

Compacta: a fast contig clustering tool for de novo assembled transcriptomes
Cited by: 2
Author(s): Fernando G. Razo-Mendivil, Octavio Martínez, Corina Hayano-Kanashiro
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/6646459

Identification and Analysis of Three Hub Prognostic Genes Related to Osteosarcoma Metastasis
Cited by: 8
Author(s): Jianye Tan, Huiying Liang, Bo Yang, Shuang Zhu, Guofeng Wu, Lutao Li, Zhengwei Liu, Lin Li, Weizhong Qi, Sijing Li, Lin Li
Software Mentions: 1
Published: over 5 years ago

10.3390/ani10030468

MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens
Cited by: 19
Author(s): Xiangfei Ma, Junwei Sun, Shuaipeng Zhu, Zhenwei Du, Donghua Li, Wenting Li, Zhuanjian Li, Yadong Tian, Xiangtao Kang, Guirong Sun
Software Mentions: 1
Published: over 6 years ago

10.1002/advs.202100681

Diclofenac Resensitizes Methicillin‐Resistant Staphylococcus aureus to β‐Lactams and Prevents Implant Infections
Cited by: 23
Author(s): Shutao Zhang, Xinhua Qu, Haozheng Tang, You Wang, Hongtao Yang, Weien Yuan, Bing Yue
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5515-6

Alterations in tissue microRNA after heat stress in the conscious rat: potential biomarkers of organ-specific injury
Cited by: 12
Author(s): Matthew G. Permenter, Bonna C. McDyre, Danielle L. Ippolito, Jonathan D. Stallings
Software Mentions: 1
Published: over 7 years ago

10.3390/s21061938

Gated Graph Attention Network for Cancer Prediction
Cited by: 2
Author(s): Linling Qiu, Li Han, Meihong Wang, Xiaoli Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41392-020-0170-6

p190A inactivating mutations cause aberrant RhoA activation and promote malignant transformation via the Hippo-YAP pathway in endometrial cancer
Cited by: 12
Author(s): Wen Xu, Jing Wan, Qizhi He, Mengfei Wang, Shuangdi Li, Mei Jiang, Zhen Qian, Binya Liu, Wen Lu, Kai Wang, Kun Gao, Xiaoping Wan
Software Mentions: 1
Published: about 6 years ago

10.1080/19768354.2018.1487335

Time-series transcriptomic analysis of the kelp grouper Epinephelus moara in response to low salinity stress
Cited by: 5
Author(s): Qiang Gao, Yanfeng Yue, Minghua Min, Shi-Qing Peng, Zhaohong Shi, Jinbo Wang, Tao Zhang
Software Mentions: 1
Published: about 8 years ago

10.5713/ab.20.0751

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle
Cited by: 1
Author(s): Xin Yan, Jia Wang, Hongbo Li, Liang Gao, Juan Geng, Zhen Ma, Jianming Liu, Jinshan Zhang, Peng-Gui Xie, Lei Chen
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-017-4382-2

The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna
Cited by: 10
Author(s): Ina Maria Schedina, Detlef Groth, Ingo Schlupp, Ralph Tiedemann
Software Mentions: 1
Published: over 8 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: about 11 years ago

10.1186/s12864-019-5626-0

The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation
Cited by: 10
Author(s): Shanice K Krombeen, Vijay Shankar, Rooksana E. Noorai, Christopher Saski, Julia L. Sharp, Matthew E. Wilson, Tiffany A Wilmoth
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-07080-1

Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine
Cited by: 6
Author(s): Mitsuo Nyuji, Yuki Hongo, Michio Yoneda, Masahiro Nakamura
Software Mentions: 1
Published: almost 6 years ago

10.1155/2021/6656337

Discovery and Validation of Circulating EVL mRNA as a Prognostic Biomarker in Pancreatic Cancer
Cited by: 2
Author(s): Yuchen Du, Kai Yao, Qingbo Feng, Feiyu Mao, Zechang Xin, Peng Xu, Jie Yao
Software Mentions: 1
Published: over 5 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

10.1186/s12864-015-2359-6

IL-10 and integrin signaling pathways are associated with head and neck cancer progression
Cited by: 36
Author(s): Sophia Bornstein, Mark Schmidt, Gabrielle Choonoo, Trevor G. Levin, Joe W. Gray, Charles R. Thomas, Melissa Wong, Shannon K. McWeeney
Software Mentions: 1
Published: over 10 years ago

10.1186/s13287-016-0389-x

Adipose-derived mesenchymal stem cells from patients with atherosclerotic renovascular disease have increased DNA damage and reduced angiogenesis that can be modified by hypoxia
Cited by: 24
Author(s): Ahmed Saad, Xiang Yang Zhu, Joerg Herrmann, La Tonya J. Hickson, Hui Tang, Allan B. Dietz, André J. van Wijnen, Lilach O. Lerman, Stephen C. Textor
Software Mentions: 1
Published: almost 10 years ago

10.1002/advs.201901341

Selective Killing of Cancer Cells by Nonplanar Aromatic Hydrocarbon‐Induced DNA Damage
Cited by: 14
Author(s): Yan Zhou, Fuwei Gan, Yuanliang Zhang, Xiaozhen He, Chengshuo Shen, Huibin Qiu, Peifeng Liu
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-14-634

Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki
Cited by: 43
Author(s): Kevin T. Bilyk, C.‐H. Christina Cheng
Software Mentions: 1
Published: over 13 years ago

10.1186/s13287-018-1120-x

OCT4 maintains self-renewal and reverses senescence in human hair follicle mesenchymal stem cells through the downregulation of p21 by DNA methyltransferases
Cited by: 32
Author(s): Yan Lü, Huinan Qu, Da Qi, Wenhong Xu, Shutong Liu, Xiangshu Jin, Peiye Song, Yantong Guo, Yiyang Jia, Xinqi Wang, Hairi Li, Yulin Li, Chengshi Quan
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-4638-5

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine
Cited by: 24
Author(s): Darren Chern Jan Wong, Li Zhang, Isabelle Merlin, Simone D. Castellarin, Grégory A. Gambetta
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.6638

Sorafenib treatment during partial hepatectomy reduces tumorgenesis in an inflammation-associated liver cancer model
Cited by: 16
Author(s): Tamar Zahavi, Tali Lanton, Mali Salmon‐Divon, Asher Salmon, Tamar Peretz, Eithan Galun, Jonathan H. Axelrod, Amir Sonnenblick
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-2219-4

Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei)
Cited by: 59
Author(s): J. Peng, Pinyuan Wei, Bin Zhang, Yang Zhao, Dingyuan Zeng, Xiuli Chen, Ming Li, Xiaohan Chen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-5554-z

Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana
Cited by: 37
Author(s): Mingqi Zhou, Natasha Sng, Collin LeFrois, Anna‐Lisa Paul, Robert J. Ferl
Software Mentions: 1
Published: over 7 years ago

10.1186/s13568-020-01076-6

Comprehensive transcriptomic and proteomic analyses of antroquinonol biosynthetic genes and enzymes in Antrodia camphorata
Cited by: 4
Author(s): Xiaofeng Liu, Yongjun Xia, Yao Zhang, Caiyun Yang, Zhiqiang Xiong, Xin Song, Lianzhong Ai
Software Mentions: 1
Published: about 6 years ago

10.1002/advs.202001334

Human Mesenchymal Stem Cell Derived Exosomes Enhance Cell‐Free Bone Regeneration by Altering Their miRNAs Profiles
Cited by: 120
Author(s): Mengmeng Zhai, Ye Zhu, Mingying Yang, Chuanbin Mao
Software Mentions: 1
Published: about 6 years ago

10.1016/j.isci.2021.102217

Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle
Cited by: 16
Author(s): Riku Egami, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Masatoshi Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Saori Uematsu, Akira Terakawa, Yongping Bai, Yun-long Pan, Toshikazu Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Konishi, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4151-2

Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization
Cited by: 39
Author(s): Audrey M. V. Ah‐Fong, Jolly Shrivastava, Howard S. Judelson
Software Mentions: 1
Published: almost 9 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: almost 5 years ago

10.1186/s12864-015-1707-x

Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition
Cited by: 74
Author(s): Bing Tian, Xueling Li, Mridul Kalita, Steven G. Widen, Jun Yang, Suresh K. Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanlei Kong, Thomas G. Wood, Bruce A. Luxon, Allan R. Brasier
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-15-183

Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilissymbionts
Cited by: 57
Author(s): Yuuki Kodama, Haruo Suzuki, Hideo Dohra, Manabu Sugii, Tatsuya Kitazume, Katsushi Yamaguchi, Shuji Shigenobu, Masahiro Fujishima
Software Mentions: 1
Published: over 12 years ago

10.1111/acel.13115

A lncRNA survey finds increases in neuroprotective LINC‐PINT in Parkinson’s disease substantia nigra
Cited by: 37
Author(s): Alon Simchovitz, Mor Hanan, Nadav Yayon, Songhua Lee, Estelle R. Bennett, David Greenberg, Sebastián Kadener, Hermona Soreq
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-4770-2

Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics
Cited by: 21
Author(s): Xiujun Sun, Zhihong Liu, Biao Wu, Liqing Zhou, Qi Wang, Wei Wu, Aiguo Yang
Software Mentions: 1
Published: about 8 years ago

10.1155/2020/3296192

TRAF6 Promotes Gastric Cancer Cell Self-Renewal, Proliferation, and Migration
Cited by: 12
Author(s): Mengting Yang, Meng Jin, Kailong Li, Haifeng Liu, Xiaonan Yang, Xiaobei Zhang, Bin Zhang, Aihua Gong, Qingli Bie
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-4253-x

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data
Cited by: 20
Author(s): J. B. Griffiths, Antonio Scialdone, John C. Marioni
Software Mentions: 1
Published: over 8 years ago

10.5966/sctm.2015-0429

Direct Isolation and Characterization of Human Nephron Progenitors
Cited by: 22
Author(s): Stefano Da Sacco, Matthew E. Thornton, Astgik Petrosyan, Maria Lavarreda-Pearce, Sargis Sedrakyan, Brendan H. Grubbs, Roger E. De Filippo, Laura Perin
Software Mentions: 1
Published: almost 10 years ago

10.1111/acel.12743

<scp>NHR</scp>‐49/<scp>HNF</scp>4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting
Cited by: 61
Author(s): Grace Ying Shyen Goh, Johnathan J Winter, Forum Bhanshali, Kelsie R. S. Doering, Regina Lai, Kayoung Lee, Elizabeth A. Veal, Stefan Taubert
Software Mentions: 1
Published: over 8 years ago

10.1002/sctm.19-0231

SOX9+/PTF1A+ Cells Define the Tip Progenitor Cells of the Human Fetal Pancreas of the Second Trimester
Cited by: 16
Author(s): Valentina Villani, Matthew E. Thornton, Heather N. Zook, Christiana Crook, Brendan H. Grubbs, Giuseppe Orlando, Roger E. De Filippo, Hsun Teresa Ku, Laura Perin
Software Mentions: 1
Published: almost 7 years ago

10.1111/acel.13106

Transplanting cells from old but not young donors causes physical dysfunction in older recipients
Cited by: 43
Author(s): Binsheng Wang, Zukai Liu, Vicky P. Chen, Lichao Wang, Christina L. Inman, Yueying Zhou, Chun Guo, Tamar Tchkonia, David W. Rowe, George A. Kuchel, Paul Robson, James L. Kirkland, Ming Xu
Software Mentions: 1
Published: over 6 years ago

10.18632/aging.102797

Obg-like ATPase 1 (OLA1) overexpression predicts poor prognosis and promotes tumor progression by regulating P21/CDK2 in hepatocellular carcinoma
Cited by: 16
Author(s): Shanzhou Huang, Chuanzhao Zhang, Chengjun Sun, Ying Hou, Yixi Zhang, Nga Lei Tam, Zekang Wang, Jia Yu, Bowen Huang, Hongkai Zhuang, Zixuan Zhou, Zuyi Ma, Zhonghai Sun, Xiaoshun He, Qi Zhou, Baohua Hou, Linwei Wu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-5180-1

Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq
Cited by: 10
Author(s): Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang, Yushan Jia
Software Mentions: 1
Published: almost 8 years ago

10.1007/s00122-018-3070-1

Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines
Cited by: 16
Author(s): Paola Barba, Jacquelyn Lillis, R. Stephen Luce, Renaud Travadon, Michael V. Osier, Kendra Baumgartner, Wayne F. Wilcox, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 1
Published: over 8 years ago

10.1007/s00122-020-03561-9

Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank
Cited by: 15
Author(s): Anna Gordon, Curt A. McCartney, Ron Knox, Nelzo C. Ereful, Colin W. Hiebert, David Konkin, Ya-Chih Hsueh, Vijai Bhadauria, Mara Sgroi, Donal M. O’Sullivan, Caroline Hadley, Lesley A. Boyd, J. I. Menzies
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-3059-6

RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response
Cited by: 6
Author(s): Andrea Prunotto, Brian J. Stevenson, Corinne Berthonneche, Fanny Schüpfer, Jacques S. Beckmann, Fabienne Maurer, Sven Bergmann
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-016-2665-7

Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum
Cited by: 33
Author(s): Shiri Barad, Noa Sela, Dilip Kumar, Amit Kumar-Dubey, Nofar Glam-Matana, Amir Sherman, Dov Prusky
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4774-y

De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in α-linolenic acid metabolism
Cited by: 13
Author(s): Xiaodi Hu, Bang-Zhen Pan, Qi Fu, Longjian Niu, Maosheng Chen, Zeng-Fu Xu
Software Mentions: 1
Published: about 8 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

10.1186/s12864-020-07028-5

Metabolome and transcriptome analyses of the molecular mechanisms of flower color mutation in tobacco
Cited by: 36
Author(s): Jiao Fangchan, Lu Zhao, Wu Xingfu, Zhiwei Song, Yongping Li
Software Mentions: 1
Published: almost 6 years ago

10.7150/thno.42423

Circular RNA circFBXW4 suppresses hepatic fibrosis via targeting the miR-18b-3p/FBXW7 axis
Cited by: 46
Author(s): Xin Chen, Hai-Di Li, Fang-tian Bu, Xiaofeng Li, Yu Chen, Sai Zhu, Jianan Wang, Siyu Chen, Ying‐Yin Sun, Xue‐Yin Pan, Na-Na Yin, Jiejie Xu, Cheng Huang, Jun Li
Software Mentions: 1
Published: over 6 years ago

10.7150/thno.42010

Skipping of exon 10 in Axl pre-mRNA regulated by PTBP1 mediates invasion and metastasis process of liver cancer cells
Cited by: 27
Author(s): Lianghua Shen, Sijia Lei, Bin Zhang, Shuaiguang Li, Luyuan Huang, Alexander Czachor, Mason Breitzig, Yuman Gao, Meiyan Huang, Xuemei Mo, Qi Zheng, Han Sun, Feng Wang
Software Mentions: 1
Published: over 6 years ago

10.7150/thno.45971

KRAS Mutation-Responsive miR-139-5p inhibits Colorectal Cancer Progression and is repressed by Wnt Signaling
Cited by: 35
Author(s): Feng Du, Tianyu Cao, Hui Xie, Ting Li, Lina Sun, Hao Líu, Hao Guo, Xin Wang, Qi Liu, Taewan Kim, Jeffrey L. Franklin, Ramona Graves‐Deal, Wei Han, Zuhong Tian, Minghui Ge, Yongzhan Nie, Daiming Fan, Robert J. Coffey, Yuanyuan Lu, Xiaodi Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-2197-6

Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA
Cited by: 68
Author(s): Dmitriy Ignatov, Elena G. Salina, Mikhail V. Fursov, Timofey Skvortsov, Tatyana Azhikina, Arseny S. Kaprelyants
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-5881-0

Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum
Cited by: 21
Author(s): Juan Pablo Amelio Ortiz, Olivier Leblanc, Cristian Oscar Rohr, Mauricio Grisolia, Lorena Adelina Siena, Maricel Podio, Carolina Colono, Celeste Azzaro, Silvina Claudia Pessino
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-019-5799-6

MicroRNA-guided regulation of heat stress response in wheat
Cited by: 74
Author(s): Sridhar Ravichandran, Raja Ragupathy, T. Edwards, Michael Domaratzki, Sylvie Cloutier
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-015-1940-3

Gene expression underlying enhanced, steroid-dependent auditory sensitivity of hair cell epithelium in a vocal fish
Cited by: 5
Author(s): Daniel J. Fergus, Ni Feng, Andrew H. Bass
Software Mentions: 1
Published: almost 11 years ago

10.3389/fmicb.2018.01643

Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils
Cited by: 54
Author(s): Liu Jin, Barbara J. Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W. Liu, Julien Tremblay, Kerry LaForge, Michael P. Schellenberg, Chantal Hamel, Luke D. Bainard
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2019.00150

Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Cited by: 35
Author(s): Murugesan Sivaranjani, Katarzyna Leskinen, Chairmandurai Aravindraja, Päivi Saavalainen, Shunmugiah Karutha Pandian, Mikael Skurnik, Arumugam Veera Ravi
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.00859

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8
Cited by: 62
Author(s): Helen L. Hayden, Keith W. Savin, Jenny Wadeson, Vadakattu V. S. R. Gupta, Pauline M. Mele
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2018.01765

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose
Cited by: 18
Author(s): Sabrina Giaretta, Laura Treu, Veronica Vendramin, Vinícius da Silva Duarte, Armin Tarrah, Stefano Campanaro, Viviana Corich
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: over 10 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568