bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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

10.3390/nu12123762

Sasa quelpaertensis Leaf Extract Ameliorates Dyslipidemia, Insulin Resistance, and Hepatic Lipid Accumulation in High-Fructose-Diet-Fed Rats
Cited by: 2
Author(s): Jeong Yong Park, Mi Jang, Jung Min Oh, Hee-Chul Ko, Sung‐Pyo Hur, Jae-Won Kim, Songyee Baek, Se-Jae Kim
Software Mentions: 1
Published: over 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

10.1186/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

10.1186/1755-8794-6-33

An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer
Cited by: 31
Author(s): Jinping Jia, Hemang Parikh, Wenming Xiao, Jason W. Hoskins, Holger Pflicke, Xuelu Liu, Irene Collins, Weiyin Zhou, Zhaoming Wang, John Powell, Snorri S. Thorgeirsson, Udo Rudloff, Gloria M. Petersen, Laufey T. Ámundadóttir
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12920-018-0335-0

Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection
Cited by: 21
Author(s): Na Zhang, Youmei Bao, Amy Hin-Yan Tong, Scott Zuyderduyn, Gary D. Bader, J. S. Malik Peiris, Si Lok, Smy Lee
Software Mentions: 1
Published: over 8 years ago

10.1186/s12920-019-0521-8

Identification of potential biomarkers for diagnosis of pancreatic and biliary tract cancers by sequencing of serum microRNAs
Cited by: 18
Author(s): Kwondo Kim, DongAhn Yoo, Jun Young Lee, Kyong Joo Lee, Soo Been Park, Chanyang Kim, Jung Hyun Jo, Dawoon Jung, Si Young Song
Software Mentions: 1
Published: over 7 years ago

10.1186/s12920-020-00788-9

miRNAs expression signature potentially associated with lymphatic dissemination in locally advanced prostate cancer
Cited by: 17
Author(s): Elena A. Pudova, George S. Krasnov, K. M. Nyushko, Anastasiya A. Kobelyatskaya, М. В. Савватеева, Andrey Poloznikov, Daniyar R. Dolotkazin, Ksenia M. Klimina, Zulfiya G. Guvatova, Sergey A. Simanovsky, Nataliya S. Gladysh, Artemy T. Tokarev, Nataliya V. Melnikova, Alexey A. Dmitriev, B. Ya. Alekseev, А. Д. Каприн, Marina V. Kiseleva, Anastasiya V. Snezhkina, Anna V. Kudryavtseva
Software Mentions: 1
Published: about 6 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

10.1186/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

10.1186/1471-2180-14-47

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

10.1186/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

10.1186/1471-2180-11-45

Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense
Cited by: 160
Author(s): Ann Hess, Abhishek N. Prasad, Andrey A. Ptitsyn, Gregory D. Ebel, Ken E. Olson, Cátálin Bárbácioru, Cinna K. Monighetti, Corey L. Campbell
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2180-14-31

Hyperexpression of α-hemolysin explains enhanced virulence of sequence type 93 community-associated methicillin-resistant Staphylococcus aureus
Cited by: 46
Author(s): Kyra Chua, Ian R. Monk, Ya-Hsun Lin, Torsten Seemann, Kellie L. Tuck, Jessica L. Porter, Justin Stepnell, Geoffrey W. Coombs, John K. Davies, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 1
Published: over 12 years ago

10.1186/s12866-016-0739-y

Identification of the crp gene in avian Pasteurella multocida and evaluation of the effects of crp deletion on its phenotype, virulence and immunogenicity
Cited by: 17
Author(s): Xinxin Zhao, Qing Liu, Kangpeng Xiao, Yunlong Hu, Xueyan Liu, Yanyan Li, Qingke Kong
Software Mentions: 1
Published: about 10 years ago

10.1186/s12866-016-0695-6

In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study
Cited by: 36
Author(s): Yijuan Xu, Raluca Maltesen, Lone Heimann Larsen, Henrik Carl Schønheyder, Vang Quy Le, Jeppe Lund Nielsen, Per Halkjær Nielsen, Trine Rolighed Thomsen, Kåre Lehmann Nielsen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12866-021-02132-2

Interactional mechanisms of Paenibacillus polymyxa SC2 and pepper (Capsicum annuum L.) suggested by transcriptomics
Cited by: 16
Author(s): Hu Liu, Yufei Li, Ke Ge, Binghai Du, Kai Liu, Chengqiang Wang, Yuqiang Ding
Software Mentions: 1
Published: over 5 years ago

10.1186/s12867-017-0080-5

Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae)
Cited by: 21
Author(s): Kangsheng Ma, Fen Li, Ying Liu, Pingzhuo Liang, Xuewei Chen, Xiwu Gao
Software Mentions: 1
Published: over 9 years ago

10.1186/s12868-018-0443-y

Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors
Cited by: 29
Author(s): Hana Hall, Junwei Ma, Sudhanshu Shekhar, Walter D. Leon-Salas, Vikki M. Weake
Software Mentions: 1
Published: about 8 years ago

10.1186/s12886-020-01348-6

Different transcriptome profiles between human retinoblastoma Y79 cells and an etoposide-resistant subline reveal a chemoresistance mechanism
Cited by: 13
Author(s): Wei Song, S. Q. Zheng, Hong Yao, Xiao Zhou, Rui Li, Cheng Yue Zhang, Jun Zhao, Lie Wei Wang, Rong Shao, Liang Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03108-0

Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species
Cited by: 9
Author(s): Mohandas Snigdha, D. Prasath
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-018-1479-y

OsWRKY67 positively regulates blast and bacteria blight resistance by direct activation of PR genes in rice
Cited by: 42
Author(s): Qing Liu, Xia Li, Shijuan Yan, Ting Yu, Yang Jiao, Jingfang Dong, Shaohong Zhang, Junliang Zhao, Ting Yang, Xingxue Mao, Xiaoyuan Zhu, Bin Liu
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-019-2001-x

Comparative analysis of proso millet (Panicum miliaceum L.) leaf transcriptomes for insight into drought tolerance mechanisms
Cited by: 25
Author(s): Yuyu Zhang, Xiaoli Gao, Jing Li, Xiangwei Gong, Pu Yang, Jinfeng Gao, Pengke Wang, Baili Feng
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-019-2037-y

Water-deficit responsive microRNAs in the primary root growth zone of maize
Cited by: 17
Author(s): Candace M. Seeve, Ramanjulu Sunkar, Yun Zheng, Li Liu, Zhijie Liu, Michael D. McMullen, Sven K. Nelson, Robert E. Sharp, Melvin J. Oliver
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-015-0537-y

The effect of red light and far-red light conditions on secondary metabolism in Agarwood
Cited by: 31
Author(s): Tony Kuo, Chuan-Hung Chen, Shu-Hwa Chen, I-Hsuan Lu, Mei-Ju Chu, Li-Chun Huang, Chung‐Yen Lin, Chien‐Yu Chen, Hsiao-Feng Lo, Shih‐Tong Jeng, Long‐Fang O. Chen
Software Mentions: 1
Published: about 11 years ago

10.1186/s12870-019-2134-y

Wheat straw increases the defense response and resistance of watermelon monoculture to Fusarium wilt
Cited by: 14
Author(s): Lili Tang, Shaorui Nie, Wenhui Li, Chao Fan, Siqi Wang, Fengzhi Wu, Kaiwen Pan
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-019-1641-1

Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency
Cited by: 18
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Alexander V. Zyablitsin, Anastasiya V. Snezhkina, Maria S. Fedorova, Elena N. Pushkova, Parfait Kezimana, Roman O. Novakovskiy, Liubov V. Povkhova, М. И. Смирнова, О. В. Муравенко, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-017-1135-y

Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers
Cited by: 13
Author(s): Kaidong Liu, Haili Li, Weijin Li, Jun Zhong, Chen Yan, Chenjia Shen, Changchun Yuan
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12870-019-1940-6

RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes
Cited by: 32
Author(s): Mummadireddy Ramya, Pue Hee Park, Yu Chen Chuang, Oh Keun Kwon, Hye Ryun An, Pil Man Park, Yun Su Baek, Byoung Chorl Kang, Wen Chieh Tsai, Hong Hwa Chen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12870-019-2138-7

Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues
Cited by: 12
Author(s): Yingdan Yuan, Jinchi Zhang, Justin Kallman, Xin Liu, Miaojing Meng, Jie Lin
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-014-0400-6

Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing
Cited by: 45
Author(s): Yue Luo, Xiaona Zhang, Zhitian Luo, Qinglin Zhang, Jihong Liu
Software Mentions: 1
Published: over 11 years ago

10.1186/s12870-020-02486-1

Comparative transcriptome analysis of mulberry reveals anthocyanin biosynthesis mechanisms in black (Morus atropurpurea Roxb.) and white (Morus alba L.) fruit genotypes
Cited by: 27
Author(s): Gaiqun Huang, Yichun Zeng, Wei Ling, Yongquan Yao, Jie Dai, Gang Liu, Zhongzheng Gui
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-020-2265-1

Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress
Cited by: 26
Author(s): Lei Wang, Bo Zheng, Yahong Yuan, Quanxi Xu, Peng Chen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-015-0694-z

Physiological and transcriptional analyses of developmental stages along sugarcane leaf
Cited by: 48
Author(s): Lúcia Mattiello, Diego Mauricio Riaño-Pachón, Marina C. M. Martins, Larissa Prado da Cruz, D. Bassi, Paulo Eduardo Ribeiro Marchiori, Rafael Vasconcelos Ribeiro, Mônica Teresa Veneziano Labate, Carlos Alberto Labate, Marcelo Menossi
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12870-020-02745-1

Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack
Cited by: 11
Author(s): Mary V. Clancy, Georg Haberer, Werner Jud, Bishu Niederbacher, Simon Niederbacher, Matthias Senft, Sharon E. Zytynska, Wolfgang W. Weisser, Jörg‐Peter Schnitzler
Software Mentions: 1
Published: almost 6 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

10.1186/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

10.1186/1471-2229-11-177

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

10.1186/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

10.1186/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/s12870-018-1336-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/s12870-021-02827-8

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

10.1186/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

10.1186/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

10.1186/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/s12870-019-1742-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

10.1186/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/s12870-020-02375-7

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/s12870-020-2244-6

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/s12870-018-1356-8

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

10.1186/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

10.1186/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

10.1186/s12944-020-01222-w

Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet
Cited by: 22
Author(s): Yongming Pan, Yu Chen, Junjie Huang, Yili Rong, Jiaojiao Chen, Minli Chen
Software Mentions: 1
Published: over 6 years ago

10.1007/s00408-019-00257-w

Growth Hormone-Releasing Hormone Receptor Antagonist Modulates Lung Inflammation and Fibrosis due to Bleomycin
Cited by: 29
Author(s): Chongxu Zhang, Renzhi Cai, Aaron Lazerson, Gaëtan J.-R. Delcroix, Medhi Wangpaichitr, Mehdi Mirsaeidi, Anthony J. Griswold, Andrew V. Schally, Robert M. Jackson
Software Mentions: 1
Published: about 7 years ago

10.1155/2020/4623107

Global Transcriptional Profiling Reveals Novel Autocrine Functions of Interleukin 6 in Human Vascular Endothelial Cells
Cited by: 8
Author(s): Liza U. Ljungberg, Mulugeta M. Zegeye, Caroline Kardeby, Knut Fälker, Dirk Repsilber, Allan Sirsjö
Software Mentions: 1
Published: over 6 years ago

10.1016/j.mec.2021.e00184

Transport engineering for improving the production and secretion of valuable alkaloids in Escherichia coli
Cited by: 8
Author(s): Yasuyuki Yamada, Miya Urui, Hidehiro Oki, Kai Inoue, Haruyuki Matsui, Yoshito Ikeda, Akira Nakagawa, Fumihiko Sato, Hiromichi Minami, Nobukazu Shitan
Software Mentions: 1
Published: almost 5 years ago

10.3390/metabo9110268

Study of the Differentially Expressed Genes in the Pomacea canaliculata Transcriptome after Treatment with Pedunsaponin A
Cited by: 2
Author(s): Yang Chun-ping, Tianxing Lv, Yangyang Zhang, Bin Wang, Xuefei Zhao, Min Zhang, Guoshu Gong, Xiaoli Chang, Guizhou Yue, Xiaoyan Qiu, Li Luo, Huabao Chen
Software Mentions: 1
Published: almost 7 years ago

10.1111/1751-7915.13440

Integrated transcriptomic and secretomic approaches reveal critical pathogenicity factors in Pseudofabraea citricarpa inciting citrus target spot
Cited by: 6
Author(s): Yang Yong, Anfei Fang, Yang Yu, Chaowei Bi, Changyong Zhou
Software Mentions: 1
Published: over 7 years ago

10.1186/s12934-021-01603-5

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis
Cited by: 10
Author(s): Jiang Wu, Wei Li, Su Zhao, Qian Senhe, Wang Zhou, Mengjie Zhou, Wenchao Hu, Jian Wang, Liu-xiu Hu, Yan Liu, Zhenglian Xue
Software Mentions: 1
Published: about 5 years ago

10.1186/s12934-020-01503-0

Effect of overexpression of SNF1 on the transcriptional and metabolic landscape of baker’s yeast under freezing stress
Cited by: 10
Author(s): Meng Kai Lü, Yang Xu, Xue Lin, Huan-Yuan Jiang, Xiaoping Hu, Sixin Liu
Software Mentions: 1
Published: over 5 years ago

10.1002/mbo3.836

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

10.1002/mbo3.899

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

10.1099/mic.0.000579

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

10.1186/s40168-020-00888-9

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

10.1186/s40168-020-00812-1

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

10.1186/s40168-021-01051-8

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions
Cited by: 34
Author(s): Emilie Lejal, Julien Chiquet, Julie Aubert, Stéphanie Robin, Agustín Estrada‐Peña, Olivier Rué, Cédric Midoux, Mahendra Mariadassou, Xavier Bailly, Arnaud Cougoul, Patrick Gasqui, Jean-François Cosson, Karine Chalvet‐Monfray, Muriel Vayssier‐Taussat, Thomas V. Pollet
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms8071020

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil
Cited by: 16
Author(s): Nikola Major, Jasper Schierstaedt, Sven Jechalke, Joseph Nesme, Smiljana Goreta Ban, Marko Černe, Søren J. Sørensen, Dean Ban, Adam Schikora
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms5010003

Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae
Cited by: 8
Author(s): Ryan M. Ames
Software Mentions: 1
Published: over 9 years ago

10.3390/microorganisms9081591

Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study
Cited by: 4
Author(s): Susanne Jacksch, Christoph König, Dominik Kaiser, Mirko Weide, Stefan Ratering, Sylvia Schnell, Markus Egert
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms9081560

Transcriptome Analysis of Durusdinium Associated with the Transition from Free-Living to Symbiotic
Cited by: 3
Author(s): Ikuko Yuyama, Naoto Ugawa, Takeji Hashimoto
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms9051065

Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Cited by: 1
Author(s): Liuhong Shen, Lang Gao, Mengjiao Yang, Jian Zhang, Yulu Wang, Yongdong Feng, Liping Wang, Shiwei Wang
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms7120634

Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Cited by: 16
Author(s): Junliang Zhong, Xihong Zhao
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9030652

In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat
Cited by: 11
Author(s): Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Kühl, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada, Vera Thiel
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9081626

Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle
Cited by: 1
Author(s): Anu Yadav, Laurens Maertens, Tim Meese, Filip Van Nieuwerburgh, Mohamed Mysara, Natalie Leys, Ann Cuypers, Paul Janssen
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms8030314

Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates
Cited by: 4
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Kirsten Küsel
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms8020278

Differential Potential of Phytophthora capsici Resistance Mechanisms to the Fungicide Metalaxyl in Peppers
Cited by: 12
Author(s): Weiyan Wang, Xiao Liu, Tao Han, Kunyuan Li, Yang Qu, Zhimou Gao
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms9071408

Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series
Cited by: 8
Author(s): Magali Van den Kerkhof, Philippe Leprohon, Dorien Mabille, Sarah Hendrickx, L.B. Tulloch, Richard J. Wall, Susan Wyllie, Eric Chatelain, Charles E. Mowbray, Stéphanie Braillard, Marc Ouellette, Louis Maes, Guy Caljon
Software Mentions: 1
Published: about 5 years ago

10.1186/s13229-017-0148-6

Effects of a social stimulus on gene expression in a mouse model of fragile X syndrome
Cited by: 6
Author(s): Tiffany D. Rogers, Allison M.J. Anacker, Travis M. Kerr, C. Gunnar Forsberg, Jing Wang, Bing Zhang, Jeremy Veenstra‐VanderWeele
Software Mentions: 1
Published: about 9 years ago

10.1093/molbev/msab099

Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias
Cited by: 13
Author(s): Janaína Lima de Oliveira, Atahualpa Castillo-Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher Thompson, Jason B. Wolf
Software Mentions: 1
Published: over 5 years ago

10.1093/molbev/msab153

A Bivalve Biomineralization Toolbox
Cited by: 21
Author(s): Tejaswi Yarra, Mark Blaxter, Melody S. Clark
Software Mentions: 1
Published: over 5 years ago

10.1093/molbev/msv112

Ecological and Genetic Barriers Differentiate Natural Populations ofSaccharomyces cerevisiae
Cited by: 27
Author(s): Katie J. Clowers, Justin Heilberger, Jeff S. Piotrowski, Jessica L. Will, Audrey P. Gasch
Software Mentions: 1
Published: over 11 years ago

10.1093/molbev/msab123

Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw
Cited by: 16
Author(s): Christine Hirschberger, Victoria A. Sleight, Katharine E. Criswell, Stephen J. Clark, J. Andrew Gillis
Software Mentions: 1
Published: over 5 years ago

10.3390/v13071325

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues
Cited by: 1
Author(s): Yun Tian, Francisco De Jesús Andino, Collins N. Khwatenge, Jiuyi Li, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: about 5 years ago

10.3390/v13071293

Transcriptome and Proteomic Analysis Reveals Up-Regulation of Innate Immunity-Related Genes Expression in Caprine Herpesvirus 1 Infected Madin Darby Bovine Kidney Cells
Cited by: 0
Author(s): Hao Fei, Xing Xie, Maojun Liu, Mao Li, Wenliang Li, Woonsung Na
Software Mentions: 1
Published: about 5 years ago

10.1186/s12957-021-02362-8

Effects of EFNA1 on cell phenotype and prognosis of esophageal carcinoma
Cited by: 2
Author(s): Yongqiang Zhang, Jinning Zhang, Guanlong Pan, Tianhao Guan, Changhao Zhang, A. Hao, Yan Li, Hai Ren
Software Mentions: 1
Published: about 5 years ago

10.1186/s13071-020-04155-6

Glucose transporter GLUT1 influences Plasmodium berghei infection in Anopheles stephensi
Cited by: 4
Author(s): Mengfei Wang, Jingwen Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-016-1856-z

Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages
Cited by: 15
Author(s): Manli He, Jing Xu, Ran He, Nengxing Shen, Xiaobin Gu, Xuerong Peng, Guangyou Yang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13071-021-04624-6

Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage
Cited by: 1
Author(s): Xiaoxiang Hu, Xiaolei Liu, Chen Li, Zhang Yu-lu, Chengyao Li, Yanfeng Li, Yingxi Chen, Hao Guo, Xue Bai, Mingyuan Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s13071-017-2312-4

Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding
Cited by: 20
Author(s): Minique H. de Castro, Daniël de Klerk, Ronel Pienaar, D. J. G. Rees, Ben J. Mans
Software Mentions: 1
Published: about 9 years ago

10.1186/s13071-020-04173-4

Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle
Cited by: 10
Author(s): Pavlína Věchtová, Zoltán Füssy, Radim Čegan, Ján Štěrba, Jan Erhart, Vladimı́r Beneš, Libor Grubhoffer
Software Mentions: 1
Published: about 6 years ago

10.1186/s13071-020-04457-9

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen
Cited by: 9
Author(s): Tianqi Xia, Bikash Ranjan Giri, Jingyi Liu, Pengfei Du, Xue Li, Xuxin Li, Shun Li, Guofeng Cheng
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13071-020-3910-0

Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport
Cited by: 3
Author(s): Marziyeh Anari, Andreas J. Stroehlein, Ross S. Hall, Bill C.H. Chang, Robin B. Gasser, Neil D. Young
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-020-3914-9

Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis
Cited by: 6
Author(s): Lucas Gentil Azevedo, Artur T. L. Queiroz, Aldina Barral, Luciane Amorim Santos, Pablo Ivan Pereira Ramos
Software Mentions: 1
Published: over 6 years ago

10.3390/pathogens6040068

Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection
Cited by: 20
Author(s): Poyin Chen, Taylor Reiter, Bihua C. Huang, Nguyet Kong, Bart C. Weimer
Software Mentions: 1
Published: over 8 years ago

10.1016/j.patter.2021.100246

Quantum processor-inspired machine learning in the biomedical sciences
Cited by: 14
Author(s): Richard Y. Li, Sharvari Gujja, Sweta R. Bajaj, Omar Gamel, Nicholas A. Cilfone, Jeffrey R. Gulcher, Daniel A. Lidar, Thomas Chittenden
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3529

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
Cited by: 11
Author(s): Michael Gerth, Gregory D. D. Hurst
Software Mentions: 1
Published: about 9 years ago

10.7717/peerj.11239

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
Cited by: 9
Author(s): Lanya Shui, Kaisen Huo, Yan Chen, Zilin Zhang, Yanfang Li, Jun Niu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7743

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
Cited by: 3
Author(s): Shuang Fu, Yuhuan Meng, Shudai Lin, Wenlu Zhang, Yuting He, Lizhen Huang, Hongli Du
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8403

Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
Cited by: 12
Author(s): Yue Li, Xiaoyan Zhou, Jiali Liu, Yin Yang, Xin Yuan, Rui Yang, Qi Wang, Jing Ji, Qian He
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8035

Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis
Cited by: 0
Author(s): Jin Li, Juan Perucho, Yuanyuan Liu, Wenwen Xia, Fengfeng Cheng, Wenhui Tian, Lin Zhang, Jianbo Zhu, Aiying Wang
Software Mentions: 1
Published: almost 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568