bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1155/2020/7434737

Nomogram Based on microRNA Signature Contributes to Improve Survival Prediction of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Enfa Zhao, Xiaofang Bai
Software Mentions: 2
Published: over 6 years ago

10.1155/2019/8732023

Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging
Cited by: 8
Author(s): Xiaoyu Xi, Qin Zou, Yingying Wei, Chen Yan, Xue Wang, Daojun Lv, Peilin Li, Anxiang Wen, Li Zhu, Guoqing Tang, Jideng Ma, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Software Mentions: 2
Published: about 7 years ago

10.1155/2018/8518563

Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions
Cited by: 7
Author(s): Li Guo, Liang Zheng, Yang Zhao, Qianyun Wang
Software Mentions: 2
Published: almost 9 years ago

10.1155/2020/1836542

Development and Validation of a Seven-Gene Signature for Predicting the Prognosis of Lung Adenocarcinoma
Cited by: 5
Author(s): Yingqing Zhang, Xiaoping Zhang, Xiaodong Liu, Ming Zhang, Xixi Gao, Jialiang Li, Yufen Xu, Zhixian Fang, Wenyu Chen
Software Mentions: 2
Published: about 6 years ago

10.1155/2015/731938

Similarities in Gene Expression Profiles duringIn VitroAging of Primary Human Embryonic Lung and Foreskin Fibroblasts
Cited by: 33
Author(s): Shiva Marthandan, Stefan Priebe, Mario Baumgart, Marco Groth, Alessandro Cellerino, Reinhard Guthke, Peter Hemmerich, Stephan Diekmann
Software Mentions: 2
Published: almost 12 years ago

10.1155/2020/2094320

The Identification and Verification of Key Long Noncoding RNAs in Ischemic Stroke
Cited by: 7
Author(s): Houxi Xu, Jinzhi Zhang, Yuzhu Ma, Jialin Gu, Xianwen Jing, Lu Shen, Chen Xia, Wenguo Yang, Yaoyao Bian, Shunjun Fu
Software Mentions: 2
Published: almost 6 years ago

10.1155/2017/8032910

RNA Sequencing Analysis Reveals Interactions between Breast Cancer or Melanoma Cells and the Tissue Microenvironment during Brain Metastasis
Cited by: 25
Author(s): Ryo Sato, T. Nakano, Mari Hosonaga, Oltea Sampetrean, Ritsuko Harigai, Takashi Sasaki, Ikuko Koya, Hideyuki Okano, Jun Kudoh, Hideyuki Saya, Yoshimi Arima
Software Mentions: 2
Published: almost 10 years ago

10.1155/2020/4951692

Comprehensive Analysis of lncRNA-Mediated ceRNA Crosstalk and Identification of Prognostic Biomarkers in Wilms’ Tumor
Cited by: 15
Author(s): Hong Zheng, Bai-Hui Li, Chang Liu, Jia Li, Fengting Liu
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/5976127

Novel miRNA Predicts Survival and Prognosis of Cholangiocarcinoma Based on RNA-seq Data and In Vitro Experiments
Cited by: 11
Author(s): Yuan Yao, Dechao Jiao, Zaoqu Liu, Jianjian Chen, Xueliang Zhou, Zhaonan Li, Jing Li, Xinwei Han
Software Mentions: 2
Published: almost 6 years ago

10.1155/2021/1978434

RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker
Cited by: 1
Author(s): Deyong Ge, Yuhan Shao, Mengjie Wang, Huihui Tao, Min Mu, Xinrong Tao
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/9568976

MicroRNA-148b Inhibits the Malignant Biological Behavior of Melanoma by Reducing Sirtuin 7 Expression Levels
Cited by: 2
Author(s): Rui Sun, Meiliang Guo, Xiaojing Fan, Qinqin Meng, Ding Yuan, Xin–Rong Yang, Kexiang Yan, Hui Deng
Software Mentions: 2
Published: almost 6 years ago

10.1155/2017/8682057

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis
Cited by: 11
Author(s): Mafeng Liu, Huang Mi, Dekang Zhu, Mingshu Wang, Renyong Jia, Shun Chen, Kunfeng Sun, Qiao Yang, Ying Wu, Francis Biville, Anchun Cheng
Software Mentions: 2
Published: almost 10 years ago

10.1155/2016/1035945

Modeling Gene Regulation in Liver Hepatocellular Carcinoma with Random Forests
Cited by: 7
Author(s): Hilal Kazan
Software Mentions: 2
Published: almost 11 years ago

10.1155/2018/1235097

Upregulation of Immune Process-Associated Genes in RAW264.7 Macrophage Cells in Response toBurkholderia pseudomalleiInfection
Cited by: 3
Author(s): Dongmei Peng, Feng Pang, Ruiyong Cao, Shu Zhu, Xinggang Yang, Xin Nie, Zhenxing Zhang, Baobao Li, Haifeng Huang, Yaying Li, Guohua Li, Lijun Du, Yafei Wang
Software Mentions: 2
Published: over 8 years ago

10.1155/2019/6581576

Identification of Potential Biomarkers in Glioblastoma through Bioinformatic Analysis and Evaluating Their Prognostic Value
Cited by: 41
Author(s): Yabo Zhou, Yang Li, Xiaoxi Zhang, Rui Chen, Xiuqiong Chen, Wilkin Tang, Mengxian Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/biomedicines9091136

Small Extracellular Vesicle Enrichment of a Retrotransposon-Derived Double-Stranded RNA: A Means to Avoid Autoinflammation?
Cited by: 2
Author(s): Marilou H. Barrios, Alexandra L. Garnham, Andrew D Foers, Lesley Cheng, Seth L. Masters, Ken C Pang
Software Mentions: 2
Published: about 5 years ago

10.3390/biomedicines9081021

Utilizing Patient-Derived Epithelial Ovarian Cancer Tumor Organoids to Predict Carboplatin Resistance
Cited by: 11
Author(s): J Górski, Zhuwei Zhang, Joseph R. McCorkle, Jodi M. DeJohn, Chi Wang, Rachel W. Miller, Holly H. Gallion, Charles S. Dietrich, Frederick R. Ueland
Software Mentions: 2
Published: about 5 years ago

10.3390/biom10050698

Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations
Cited by: 3
Author(s): Carolina Cortes-Urrea, Fernando Bueno-Gutiérrez, Melissa Solarte, Miguel Guevara-Burbano, Fabián Tobar-Tosse, Patricia E. Vélez-Varela, Juan Carlos Leiva, Guillermo Barreto, Jaime Velasco-Medina, Pedro Moreno, Javier De Las Rivas
Software Mentions: 2
Published: over 6 years ago

10.3390/biom11081223

Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae
Cited by: 1
Author(s): Randi Yeager, G. Guy Bushkin, Emily Singer, Rui Fu, Benjamin Cooperman, Michael A. McMurray
Software Mentions: 2
Published: about 5 years ago

10.3390/biom10070974

Transcriptome Based Profiling of the Immune Cell Gene Signature in Rat Experimental Colitis and Human IBD Tissue Samples
Cited by: 3
Author(s): Éva Boros, Bence Prontvai, Zoltán Kellermayer, Péter Balogh, Silvia Patrícia, Áron Vincze, Csaba Varga, Zoltán Maróti, Balázs Balint, István Nagy
Software Mentions: 2
Published: over 6 years ago

10.3390/biom11020274

Low Expression of miR-375 and miR-190b Differentiates Grade 3 Patients with Endometrial Cancer
Cited by: 2
Author(s): Miłosz Pietrus, Michał Seweryn, Przemysław Kapusta, Paweł Wołkow, Kazimierz Pityński, Gracjan Wątor
Software Mentions: 2
Published: over 5 years ago

10.1042/BSR20200487

The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1
Cited by: 21
Author(s): Juntong Wang, Jingshun Gu, Aiwu You, Jun Li, Yuyan Zhang, Guomin Rao, Xuehua Ge, Kun Zhang, Jianfeng Li, Xiaohui Lu, Qianchao Wang, Tzu Chen Lin, Ling Cheng, Meiying Zhu, Xiaotang Wu, Dongchun Wang
Software Mentions: 2
Published: over 6 years ago

10.1042/BSR20190996

Integrated analysis of a competing endogenous RNA network in renal cell carcinoma using bioinformatics tools
Cited by: 14
Author(s): Weidong Jiang, Zhihua Ye
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20191554

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models
Cited by: 14
Author(s): Yan Yao, Tingting Zhang, Ling‐Yu Qi, Ruijuan Liu, Gongxi Liu, Wei Hua Jia, Qi Song, Changgang Sun
Software Mentions: 2
Published: almost 7 years ago

10.1042/BSR20181514

Differential expression and bioinformatics analysis of circRNA in osteosarcoma
Cited by: 36
Author(s): Yizhe Xi, Mitra Fowdur, Yun Liu, Hao Wu, Miao He, Jinmin Zhao
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20203200

Identifying breast cancer subtypes associated modules and biomarkers by integrated bioinformatics analysis
Cited by: 8
Author(s): Yanwei Wang, Li Yu, Baohong Liu, Ailin Song
Software Mentions: 2
Published: almost 6 years ago

10.1042/BSR20191251

The lncRNAs RP1-261G23.7, RP11-69E11.4 and SATB2-AS1 are a novel clinical signature for predicting recurrent osteosarcoma
Cited by: 9
Author(s): Ying Tang, Jia-Yi Dong, Cheng Yuan, Peng Li, Guo Qing-shan
Software Mentions: 2
Published: almost 7 years ago

10.1042/BSR20202203

Developing a risk scoring system based on immune-related lncRNAs for patients with gastric cancer
Cited by: 5
Author(s): Yuzhi Wang, Yu Zhong, Yi Zhang, Chengwen Li
Software Mentions: 2
Published: almost 6 years ago

10.1042/BSR20210021

Construction and analysis of the abnormal lncRNA–miRNA–mRNA network in hypoxic pulmonary hypertension
Cited by: 5
Author(s): Jie Liu, Yuhua Deng, Zeqin Fan, Shuanglan Xu, Wei Li, Xiaoxian Huang, Xin Xing, Jiao Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-016-0471-8

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq
Cited by: 31
Author(s): Yuan Fu, Michele Poli, Gaurav Sablok, Bo Wang, Yanchun Liang, Nicola La Porta, Violeta Velikova, Francesco Loreto, Mingai Li, Claudio Varotto
Software Mentions: 2
Published: over 10 years ago

10.1186/s13068-015-0227-x

Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
Cited by: 131
Author(s): Noppon Lertwattanasakul, Tomoyuki Kosaka, Akira Hosoyama, Yutaka Suzuki, Nadchanok Rodrussamee, Minenosuke Matsutani, Masayuki Murata, Naoko Fujimoto, Suprayogi Suprayogi, Keiko Tsuchikane, Savitree Limtong, Nobuyuki Fujita, Mamoru Yamada
Software Mentions: 2
Published: over 11 years ago

10.1186/s13068-020-01825-6

Evolutionary engineering of E. coli MG1655 for tolerance against isoprenol
Cited by: 12
Author(s): Heiko Babel, Jens O. Krömer
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13068-018-1331-5

Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment
Cited by: 9
Author(s): Pengfei Cheng, Chengxu Zhou, Yan Wu, Zhihui Xu, Jilin Xu, Dongqing Zhou, Yinghui Zhang, Haizhen Wu, Xuezhi Zhang, Tianzhong Liu, Ming Tang, Yang Qiyong, Xiaojun Yan, Jianhua Fan
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13068-015-0357-1

A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa
Cited by: 87
Author(s): Jyoti Dalal, Harry O. Lopez, Naresh Vasani, Zhaohui Hu, Jennifer Swift, Roopa Yalamanchili, Mia Dvora, Xiuli Lin, De‐Yu Xie, Rongda Qu, Heike Sederoff
Software Mentions: 2
Published: about 11 years ago

10.1186/s13068-019-1393-z

Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways
Cited by: 59
Author(s): Wenjuan Mo, Mengzhu Wang, Rongrong Zhan, Yao Yu, Yungang He, Hong Lü
Software Mentions: 2
Published: over 7 years ago

10.1038/s41408-019-0173-0

Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4
Cited by: 57
Author(s): Yuan Xiao Zhu, Chao Shi, Laura A. Bruins, Xuewei Wang, Daniel L. Riggs, Brooke Porter, Jonathan M. Ahmann, Cecília Bonolo de Campos, Esteban Braggio, P. Leif Bergsagel, A. Keith Stewart
Software Mentions: 2
Published: over 7 years ago

10.1038/s41408-020-00404-0

Gene expression profiling-based risk prediction and profiles of immune infiltration in diffuse large B-cell lymphoma
Cited by: 22
Author(s): Selin Merdan, Kritika Subramanian, Turgay Ayer, Johan Van Weyenbergh, Andrés Chang, Jean L. Koff, Christopher R. Flowers
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41413-020-00120-2

MEF2C regulates osteoclastogenesis and pathologic bone resorption via c-FOS
Cited by: 25
Author(s): Takayuki Fujii, Koichi Murata, Se-Hwan Mun, Seyeon Bae, Ye Ji Lee, Tannia Pannellini, Ki‐Woon Kang, David J. Oliver, Kyung‐Hyun Park‐Min, Lionel B. Ivashkiv
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40529-017-0185-7

Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata
Cited by: 20
Author(s): Zhiai Xu, Yuanyuan Li, Hong Ling, Sisi Liu, Mengmeng Liu, Juan Chen, Shun‐Xing Guo
Software Mentions: 2
Published: over 9 years ago

10.1038/s41416-020-0923-6

ASCL1-regulated DARPP-32 and t-DARPP stimulate small cell lung cancer growth and neuroendocrine tumour cell proliferation
Cited by: 15
Author(s): Sk Kayum Alam, Li Wang, Yanan Ren, Christina E. Hernandez, Farhad Kosari, Anja C. Roden, Rendong Yang, Luke H. Hoeppner
Software Mentions: 2
Published: over 6 years ago

10.1038/s41416-018-0196-5

MiR-532-5p suppresses renal cancer cell proliferation by disrupting the ETS1-mediated positive feedback loop with the KRAS-NAP1L1/P-ERK axis
Cited by: 58
Author(s): Wei Zhai, Junjie Ma, Ronggang Zhu, Chun‐Fang Xu, Jin Zhang, Yonghui Chen, Zhiguo Chen, Dongkui Gong, Jiayi Zheng, Chen Chen, Saiyang Li, Butang Li, Yiran Huang, Wei Xue, Junhua Zheng
Software Mentions: 2
Published: over 8 years ago

10.1111/bph.15142

Regulation of gene expression by MF63, a selective inhibitor of microsomal PGE synthase 1 (mPGES1) in human osteoarthritic chondrocytes
Cited by: 5
Author(s): Lauri Tuure, Antti Pemmari, Mari Hämäläinen, Teemu Moilanen, Eeva Moilanen
Software Mentions: 2
Published: about 6 years ago

10.1186/s12944-017-0424-7

The effects of short-term high-fat feeding on exercise capacity: multi-tissue transcriptome changes by RNA sequencing analysis
Cited by: 6
Author(s): Xiao Ye, Wanshan Wang, Liguo Chen, Jieyu Chen, Pingping Jiang, Xiu‐Qiong Fu, Xin Nie, Hiu Yee Kwan, Yanyan Liu, Xiaoshan Zhao
Software Mentions: 2
Published: over 9 years ago

10.3390/md11030830

The CHROMEVALOA Database: A Resource for the Evaluation of Okadaic Acid Contamination in the Marine Environment Based on the Chromatin-Associated Transcriptome of the Mussel Mytilus galloprovincialis
Cited by: 22
Author(s): Victoria Suárez-Ulloa, Juan Fernández‐Tajes, Vanessa Aguiar‐Pulido, Ciro Rivera-Casas, Rodrigo González-Romero, Juan Ausió, Josefina Méndez, Julián Dorado, José M. Eirín‐López
Software Mentions: 2
Published: over 13 years ago

10.1155/2018/6808934

RIG-I Signaling via MAVS Is Dispensable for Survival in Lethal Influenza Infection In Vivo
Cited by: 10
Author(s): Wenxin Wu, Xiaoqiu Wang, Wei Zhang, Lili Tian, J. Leland Booth, Elizabeth S. Duggan, Sunil S. More, Lin Liu, Mikhail G. Dozmorov, Jordan P. Metcalf
Software Mentions: 2
Published: almost 8 years ago

10.3390/medicina57060515

TBX2, a Novel Regulator of Labour
Cited by: 1
Author(s): Febilla Fernando, G. J. M. Veenboer, Martijn A. Oudijk, M. A. M. Kampman, Karst Y. Heida, Louise J M Lagendijk, Joris A. M. van der Post, Aldo Jongejan, Gijs B. Afink, Carrie Ris‐Stalpers
Software Mentions: 2
Published: over 5 years ago

10.1097/MD.0000000000027248

Construction and comprehensive analysis of a competitive endogenous RNA network to reveal potential biomarkers for the malignant differentiation of glioma
Cited by: 0
Author(s): Xin Li, Jingwen Zhang, Min Zhang, Xianghua Qi, Shiyuan Wang, Jing Teng
Software Mentions: 2
Published: about 5 years ago

10.1097/MD.0000000000016437

Analysis of the long non-coding RNA LINC01614 in non-small cell lung cancer
Cited by: 13
Author(s): Yan Sun, Chunhua Ling
Software Mentions: 2
Published: over 7 years ago

10.1590/0074-02760180053

Follow up of a robust meta-signature to identify Zika virus infection in Aedes aegypti: another brick in the wall
Cited by: 2
Author(s): Eduardo R. Fukutani, Moreno S. Rodrigues, José Irahe Kasprzykowski, Cintia Figueiredo de Araújo, Alexandre Rossi Paschoal, Pablo Ivan Pereira Ramos, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 2
Published: over 8 years ago

10.1111/1751-7915.12713

Transcriptional response ofEscherichia colito ammonia and glucose fluctuations
Cited by: 39
Author(s): Joana Danica Simen, Michael Löffler, Günter Jäger, Karin Schäferhoff, Andreas Freund, Jakob Matthes, Jan Müller, Ralf Takors, RecogNice-Team
Software Mentions: 2
Published: over 9 years ago

10.15698/mic2018.05.630

Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK
Cited by: 11
Author(s): Nazif Maqani, Ryan D. Fine, Mehreen Shahid, Mingguang Li, Elisa Enriquez-Hesles, Jeffrey S. Smith
Software Mentions: 2
Published: over 8 years ago

10.1186/s12934-021-01626-y

Alternative oxidase gene induced by nitric oxide is involved in the regulation of ROS and enhances the resistance of Pleurotus ostreatus to heat stress
Cited by: 14
Author(s): Ludan Hou, Ming Zhao, Chenyang Huang, Qi He, Lijiao Zhang, Jinxia Zhang
Software Mentions: 2
Published: over 5 years ago

10.1099/mgen.0.000246

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii
Cited by: 27
Author(s): Christine J. Boinett, Amy K. Cain, Jane Hawkey, Nhu Tran Do Hoang, Nhu Nguyen Thi Khanh, Duy Pham Thanh, Janina Dordel, James I. Campbell, Nguyen Phu Huong Lan, Matthew Mayho, Gemma Langridge, James Hadfield, Nguyễn Văn Vĩnh Châu, Guy Thwaites, Julian Parkhill, Nicholas R. Thomson, Kathryn E. Holt, Stephen Baker
Software Mentions: 2
Published: almost 8 years ago

10.1099/mgen.0.000194

Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Cited by: 28
Author(s): Erin P. Price, Linda T. Viberg, Timothy J. Kidd, Scott C. Bell, Bart J. Currie, Derek S. Sarovich
Software Mentions: 2
Published: over 8 years ago

10.1099/mgen.0.000374

Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex
Cited by: 13
Author(s): Osiel Silva Gonçalves, Kiara França Campos, Jéssica Catarine Silva de Assis, Alexia Suellen Fernandes, Thamires Santos Souza, Luiz Guilherme do Carmo Rodrigues, Marisa Vieira de Queiroz, Mateus Ferreira Santana
Software Mentions: 2
Published: over 6 years ago

10.1099/mgen.0.000148

Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli
Cited by: 6
Author(s): Hélène Gingras, Bédis Dridi, Philippe Leprohon, Marc Ouellette
Software Mentions: 2
Published: almost 9 years ago

10.1002/mbo3.768

Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments
Cited by: 17
Author(s): Luis J Perez Calderon, Evangelia Gontikaki, Lloyd D. Potts, Sophie Shaw, Alejandro Gallego, James A. Anderson, Ursula Witte
Software Mentions: 2
Published: almost 8 years ago

10.1002/mbo3.1153

Microbiota succession during aerobic stability of maize silage inoculated with Lentilactobacillus buchneri NCIMB 40788 and Lentilactobacillus hilgardii CNCM‐I‐4785
Cited by: 22
Author(s): Pascal Drouin, Julien Tremblay, Justin B. Renaud, Emmanuelle Apper
Software Mentions: 2
Published: almost 6 years ago

10.1002/mbo3.608

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free‐living bacteria in the water column
Cited by: 6
Author(s): Limei Shi, Huang Yin-hui, Min Zhang, Xiaoli Shi, Yuanfeng Cai, Shengling Gao, Xiangming Tang, Feizhou Chen, Yaping Lü, Fanxiang Kong
Software Mentions: 2
Published: over 8 years ago

10.1002/mbo3.510

A1S_2811, a CheA/Y-like hybrid two-component regulator fromAcinetobacter baumanniiATCC17978, is involved in surface motility and biofilm formation in this bacterium
Cited by: 27
Author(s): Rong Chen, Ruichen Lv, Xiao Jun Lin, Min Wang, Zongmin Du, Yafang Tan, Yu‐Jun Cui, Yanfeng Yan, Yanping Luo, Ruifu Yang, Yajun Song
Software Mentions: 2
Published: over 9 years ago

10.1186/s40168-019-0780-9

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem
Cited by: 76
Author(s): Xinyu Zhu, Stefano Campanaro, Laura Treu, Rekha Seshadri, Natalia Ivanova, Panagiotis Kougias, Nikos C. Kyrpides, Irini Angelidaki
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-018-0583-4

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics
Cited by: 31
Author(s): Alessandra Fontana, Panagiotis Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, L. Morelli, Irini Angelidaki, Stefano Campanaro
Software Mentions: 2
Published: about 8 years ago

10.1186/s40168-018-0606-1

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages
Cited by: 25
Author(s): Samuel Jacquiod, Inês Nunes, Asker Brejnrod, Mette Sif Hansen, Peter E. Holm, Anders Johansen, Kristian K. Brandt, Anders Priemé, Søren J. Sørensen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-017-0311-5

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism
Cited by: 48
Author(s): Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-018-0589-y

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential
Cited by: 16
Author(s): Celso Martins, Adélia Varela, Céline C. Leclercq, Óscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrián, Cristina Silva Pereira
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-020-00833-w

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions
Cited by: 55
Author(s): Stien Beirinckx, Tom Viaene, Annelies Haegeman, Jane Debode, Fien Amery, Sophie Vandenabeele, Hilde Nelissen, Dirk Inzé, Raúl Y. Tito, Jeroen Raes, Caroline De Tender, Sofie Goormachtig
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8020271

Regulatory Patterns of Crp on Monensin Biosynthesis in Streptomyces cinnamonensis
Cited by: 7
Author(s): Cai‐Xia Lin, Yue Zhang, Jun Wu, Rong-hui Xie, Jianjun Qiao, Guang‐Rong Zhao
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9050991

Global Changes in Asexual Epichloë Transcriptomes during the Early Stages, from Seed to Seedling, of Symbiotum Establishment
Cited by: 6
Author(s): Inoka K Hettiarachchige, Christy J. Vander Jagt, Ross Mann, Tim Sawbridge, Germán Spangenberg, Kathryn M. Guthridge
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9081680

A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites
Cited by: 7
Author(s): Domenico Davolos, Fabiana Russo, Loredana Canfora, Eligio Malusà, Małgorzata Tartanus, Ewa M. Furmanczyk, Andrea Ceci, Oriana Maggi, Anna Maria Persiani
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms7090358

A Discovery of Relevant Hepatoprotective Effects and Underlying Mechanisms of Dietary Clostridium butyricum Against Corticosterone-Induced Liver Injury in Pekin Ducks
Cited by: 8
Author(s): Yanhan Liu, Cun Liu, Liqing Huang, Zhaofei Xia
Software Mentions: 2
Published: about 7 years ago

10.3390/microorganisms8091443

Transcriptome Profiling of Potato (Solanum tuberosum L.) Responses to Root-Knot Nematode (Meloidogyne javanica) Infestation during A Compatible Interaction
Cited by: 8
Author(s): Teresia Nyambura Macharia, Daniel Bellieny-Rabelo, Lucy N. Moleleki
Software Mentions: 2
Published: about 6 years ago

10.3390/microorganisms9071445

Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Cited by: 1
Author(s): Dung Minh Ha-Tran, Trinh Thi My Nguyen, Shou-Chen Lo, Chieh-Chen Huang
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9071417

Acinetobacter tandoii ZM06 Assists Glutamicibacter nicotianae ZM05 in Resisting Cadmium Pressure to Preserve Dipropyl Phthalate Biodegradation
Cited by: 10
Author(s): Xuejun Wang, Si Shen, Hao Wu, Haixia Wang, Lvjing Wang, Zhenmei Lü
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9020391

Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
Cited by: 18
Author(s): Souvik Paul, R. N. Chatterjee, M.V.L.N. Raju, B. Prakash, S.V. Rama Rao, Sandeep Yadav, A. Kannan
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms8111759

Response of Coral Reef Dinoflagellates to Nanoplastics under Experimental Conditions Suggests Downregulation of Cellular Metabolism
Cited by: 24
Author(s): Christina Ripken, Konstantin Khalturin, Eiichi Shoguchi
Software Mentions: 2
Published: almost 6 years ago

10.17912/micropub.biology.000397

Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans.
Cited by: 3
Author(s): Sarah M Cohen, Jessica J. Sun, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 2
Published: over 5 years ago

10.1093/molbev/msaa071

Rampant Misexpression in a Mimulus (Monkeyflower) Introgression Line Caused by Hybrid Sterility, Not Regulatory Divergence
Cited by: 7
Author(s): Rachel E. Kerwin, Andrea L. Sweigart
Software Mentions: 2
Published: over 6 years ago

10.1093/molbev/msx123

Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers
Cited by: 47
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 2
Published: over 9 years ago

10.1093/molbev/msw119

Sex, Scavengers, and Chaperones: Transcriptome Secrets of DivergentSymbiodiniumThermal Tolerances
Cited by: 110
Author(s): Rachel A. Levin, Victor H. Beltran, Ross Hill, Staffan Kjelleberg, Diane McDougald, Peter D. Steinberg, Madeleine J. H. van Oppen
Software Mentions: 2
Published: over 10 years ago

10.1186/s13041-020-00715-0

The novel multiple sclerosis susceptibility gene ATXN1 regulates B cell receptor signaling in B-1a cells
Cited by: 5
Author(s): Qin Ma, Alessandro Didonna
Software Mentions: 2
Published: almost 6 years ago

10.12688/wellcomeopenres.14645.4

Probing Plasmodium falciparum sexual commitment at the single-cell level
Cited by: 44
Author(s): Nicolas M. B. Brancucci, Mariana De Niz, Timothy J. Straub, Deepali Ravel, Lauriane Sollelis, Bruce W. Birren, Till S. Voss, Daniel E. Neafsey, Matthias Marti
Software Mentions: 2
Published: about 8 years ago

10.12688/wellcomeopenres.14797.2

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern
Cited by: 10
Author(s): Jing-wen Lin, Adam J. Reid, Deirdre Cunningham, Ulrike Böhme, Irene Tumwine, Sara Keller-Mclaughlin, Mandy Sanders, Matthew Berriman, Jean Langhorne
Software Mentions: 2
Published: almost 8 years ago

10.12688/wellcomeopenres.15059.1

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313
Cited by: 8
Author(s): Edna Ondari, Elizabeth J. Klemm, Chisomo Msefula, Moataz Abd El Ghany, Jennifer N. Heath, Derek Pickard, Lars Barquist, Gordon Dougan, Robert A. Kingsley, Calman A. MacLennan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12957-020-01909-5

Combining texture features of whole slide images improves prognostic prediction of recurrence-free survival for cutaneous melanoma patients
Cited by: 7
Author(s): Yanbin Peng, Yunfeng Chu, Zhong Chen, Wen Zhou, Shengxiang Wan, Yingfeng Xiao, Youlong Zhang, Jialu Li
Software Mentions: 2
Published: over 6 years ago

10.1186/s13071-019-3506-8

Anopheles aquasalis transcriptome reveals autophagic responses to Plasmodium vivax midgut invasion
Cited by: 7
Author(s): Rosa Amélia Gonçalves Santana, Maurício Oliveira, Iria Cabral, Rubens Celso Andrade Silva, Débora Raysa Teixeira de Sousa, L. S. Ferreira, Marcus Vinícius Guimarães Lacerda, Wuelton Marcelo Monteiro, Patrícia Abrantes, Maria das Graças Vale Barbosa Guerra, Henrique Silveira
Software Mentions: 2
Published: over 7 years ago

10.1186/s13071-014-0622-3

Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery
Cited by: 11
Author(s): Nicholas J. Wheeler, Prince N Agbedanu, Michael J. Kimber, Paula Ribeiro, Tim A. Day, Mostafa Zamanian
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13071-016-1642-y

CAP protein superfamily members in Toxocara canis
Cited by: 6
Author(s): Andreas J. Stroehlein, Neil D. Young, Ross S. Hall, Pasi K. Korhonen, Andreas Hofmann, Paul W. Sternberg, Abdul Jabbar, Robin B. Gasser
Software Mentions: 2
Published: over 10 years ago

10.1186/s13071-018-3086-z

Transcriptomic analysis of male and female Schistosoma mekongi adult worms
Cited by: 25
Author(s): Orawan Phuphisut, Pravech Ajawatanawong, Yanin Limpanont, Onrapak Reamtong, Supaporn Nuamtanong, Sumate Ampawong, Salisa Chaimon, Paron Dekumyoy, Dorn Watthanakulpanich, Brett E. Swierczewski, Poom Adisakwattana
Software Mentions: 2
Published: about 8 years ago

10.3390/pathogens9020145

Comparative Transcriptome Analysis of Two Cucumber Cultivars with Different Sensitivity to Cucumber Mosaic Virus Infection
Cited by: 10
Author(s): Z Šubr, Lukáš Predajňa, Katarína Šoltýs, Boris Bokor, Jaroslav Budiš, Miroslav Glasa
Software Mentions: 2
Published: over 6 years ago

10.3390/pathogens3040875

Comparison of Potato and Asian Citrus Psyllid Adult and Nymph Transcriptomes Identified Vector Transcripts with Potential Involvement in Circulative, Propagative Liberibacter Transmission
Cited by: 35
Author(s): Tonja W. Fisher, Meenal Vyas, Rong He, William M. Nelson, Joseph M. Cicero, Mark R. Willer, Ryan Kim, Robin Kramer, Greg A. May, John A. Crow, Carol Soderlund, David R. Gang, Judith K. Brown
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12969-019-0347-0

Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells
Cited by: 10
Author(s): Kaiyu Jiang, Rie Karasawa, Zihua Hu, Yanmin Chen, Lucy C Holmes, Kathleen M. O’Neil, James N. Jarvis
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.6949

Comprehensive transcriptional profiling of aging porcine liver
Cited by: 6
Author(s): Jianning Chen, Qin Zou, Daojun Lv, Muhammad Ali Raza, Xue Wang, Chen Yan, Xiaoyu Xi, Peilin Li, Anxiang Wen, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.11714

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
Cited by: 1
Author(s): Alex E. Mohr, Rebecca A. Reiss, Monique Beaudet, Johnny A. Sena, Jay S. Naik, Benjimen R. Walker, Karen L. Sweazea
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.3696

RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
Cited by: 4
Author(s): V. Katelyn Chandler, John P. Wares
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.8684

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity inC. elegans
Cited by: 10
Author(s): Charles Viau, Orçun Haçarız, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10204

Transcriptome analysis of diploid and triploid Populus tomentosa
Cited by: 3
Author(s): Bin Wen, Xiaozhen Liu, Zhiming Zhang, Hanyao Zhang
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.6991

Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
Cited by: 18
Author(s): Yidan Song, Yihua Pan, Jun Li
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.7360

A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
Cited by: 22
Author(s): Ruoyan Cao, Qiqi Wu, Qiulan Li, Meiling Yao, Hongbo Zhou
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.7946

High expression of HSP90 is associated with poor prognosis in patients with colorectal cancer
Cited by: 22
Author(s): Shuming Zhang, Shichao Guo, Zhangfu Li, Dan Li, Qimin Zhan
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.11875

Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing
Cited by: 1
Author(s): Tomoko Matsuda
Software Mentions: 2
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568